diff --git a/.gitignore b/.gitignore index 583ed67ce2..1412192e2c 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,60 @@ bin classes/ .metadata/ .DS_Store +.settings/ +abstract-rrf-loader/.settings/ +cts2-model/.settings/ +cts2Impl/.settings/ +graph-loader/.settings/ +lbAdmin/.settings/ +lbExamples/.settings/ +lbGUI/.settings/ +lbImpl/.settings/ +lbIndex/.settings/ +lbInterfaces/.settings/ +lbModel/.settings/ +lbPackager/.settings/ +lbTest/.settings/ +lexevs-dao/.settings/ +lexevs-graph-dao/.settings/ +lexrdf/.settings/ +lgConverter/.settings/ +lgModel/.settings/ +lgResourceReader/.settings/ +lgSharedLibraries/.settings/ +lgUtil/.settings/ +lgValueSets/.settings/ +loader-framework/.settings/ +loader-framework-core/.settings/ +meta-loader/.settings/ +ndfrt-loader/.settings/ +rxnorm-loader/.settings/ +umls-loader/.settings/ + +*.prefs + +graph-loader/.settings/org.eclipse.jdt.core.prefs + +Indexer/.settings/org.eclipse.jdt.core.prefs + +lbAdmin/.settings/org.eclipse.jdt.core.prefs + +lbExamples/.settings/org.eclipse.jdt.core.prefs + +lbGUI/.settings/org.eclipse.jdt.core.prefs + +lbImpl/.settings/org.eclipse.jdt.core.prefs + +lbInterfaces/.settings/org.eclipse.jdt.core.prefs + +lbModel/.settings/org.eclipse.jdt.core.prefs + +lbPackager/.settings/org.eclipse.jdt.core.prefs + +lexrdf/.settings/org.eclipse.jdt.core.prefs + +lgConverter/.settings/org.eclipse.jdt.core.prefs + +lgResourceReader/.settings/org.eclipse.jdt.core.prefs + +lgUtil/.settings/org.eclipse.jdt.core.prefs diff --git a/README.md b/README.md index 9ad706b70c..2922e66f08 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Please see the NOTICE and LICENSE files for details. You will find more details about LexEVS in the following links: * [LexEVS Home](https://wiki.nci.nih.gov/x/OJG4Aw) -* [Public Forum](https://cabig-kc.nci.nih.gov/Vocab/forums/viewforum.php?f=13) +* [Public Forum](https://github.com/lexevs/lexevs/issues) * [Issues Tracker](https://tracker.nci.nih.gov/browse/LEXEVS) * [Documentation](https://wiki.nci.nih.gov/x/OJG4Aw) * [Source code](https://github.com/NCIP/LexEVS) diff --git a/cts2-model/.classpath b/cts2-model/.classpath deleted file mode 100644 index bfaf51ea79..0000000000 --- a/cts2-model/.classpath +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - - - diff --git a/cts2-model/.gitignore b/cts2-model/.gitignore deleted file mode 100644 index 690dcea017..0000000000 --- a/cts2-model/.gitignore +++ /dev/null @@ -1 +0,0 @@ -/Castor diff --git a/cts2-model/.project b/cts2-model/.project deleted file mode 100644 index b1bc33dd02..0000000000 --- a/cts2-model/.project +++ /dev/null @@ -1,18 +0,0 @@ - - - cts2-model - - - - - - org.eclipse.jdt.core.javabuilder - - - - - - org.eclipse.jdt.core.javanature - org.apache.ivyde.eclipse.ivynature - - diff --git a/cts2-model/binding.xml b/cts2-model/binding.xml deleted file mode 100644 index d5b7153698..0000000000 --- a/cts2-model/binding.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/cts2-model/build.properties b/cts2-model/build.properties deleted file mode 100755 index 09ba3dfd6b..0000000000 --- a/cts2-model/build.properties +++ /dev/null @@ -1,4 +0,0 @@ -#Generated by Maven Ant Plugin - DO NOT EDIT THIS FILE! -#Mon Aug 31 13:56:58 CDT 2009 -lbPackager.dir=../lbPackager - diff --git a/cts2-model/build.xml b/cts2-model/build.xml deleted file mode 100755 index bb61b620ac..0000000000 --- a/cts2-model/build.xml +++ /dev/null @@ -1,277 +0,0 @@ - - - Buildfile for the Castor Rendering of the LexBIG data model - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Generate Castor Java - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Generating Castor Java from Schema ${xsdFile} from ${xsd.url}/${type}/${xsdFile}.xsd - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/cts2-model/castorbuilder.properties b/cts2-model/castorbuilder.properties deleted file mode 100755 index c0a7fd0561..0000000000 --- a/cts2-model/castorbuilder.properties +++ /dev/null @@ -1,42 +0,0 @@ -org.exolab.castor.builder.javaclassmapping=type -#Forces the code generator to create 'old' Java 1.4 enumeration classes even in Java 5 mode. -org.exolab.castor.builder.forceJava4Enums=false -org.exolab.castor.builder.enumTypeAccessInterface=false -# Use the primitive wrappers -org.exolab.castor.builder.primitivetowrapper=true -# This property specifies whether the sources generated -# should comply with java 1.4 or 5.0; defaults to 1.4 -org.exolab.castor.builder.javaVersion=5.0 -# XML namespace mapping to Java packages -# -org.exolab.castor.builder.jclassPrinterFactories=\ - org.exolab.castor.builder.printing.TemplateJClassPrinterFactory,\ - org.exolab.castor.builder.printing.StandardJClassPrinterFactory,\ - org.cts2.castor.printer.JClassModifyingWriterJClassPrinterFactory -# -org.exolab.castor.builder.nspackages=\ - http://cts2.org/schema/2010/01/Association=org.cts2.association,\ - http://cts2.org/schema/2010/01/CodeSystem=org.cts2.codesystem,\ - http://cts2.org/schema/2010/01/CodeSystemVersion=org.cts2.codesystemversion,\ - http://cts2.org/schema/2010/01/ConceptDomain=org.cts2.conceptdomain,\ - http://cts2.org/schema/2010/01/Core=org.cts2.core,\ - http://cts2.org/schema/2010/01/Entity=org.cts2.entity,\ - http://cts2.org/schema/2010/01/Map=org.cts2.map,\ - http://cts2.org/schema/2010/01/ValueSet=org.cts2.valueset,\ - http://cts2.org/schema/2010/01/ValueSetResolution=org.cts2.valuesetresolution,\ - http://cts2.org/schema/2010/01/Updates=org.cts2.updates,\ - \ - http://cts2.org/schema/2010/01/AssociationServices=org.cts2.service.association,\ - http://cts2.org/schema/2010/01/CodeSystemServices=org.cts2.service.codesystem,\ - http://cts2.org/schema/2010/01/CodeSystemVersionServices=org.cts2.service.codesystemversion,\ - http://cts2.org/schema/2010/01/ConceptDomainServices=org.cts2.service.conceptdomain,\ - http://cts2.org/schema/2010/01/CoreService=org.cts2.service.core,\ - http://cts2.org/schema/2010/01/EntityDescriptionServices=org.cts2.service.entitydescription,\ - http://cts2.org/schema/2010/01/MapServices=org.cts2.service.map,\ - http://cts2.org/schema/2010/01/MapVersionServices=org.cts2.service.mapversion,\ - http://cts2.org/schema/2010/01/StatementServices=org.cts2.service.statement,\ - http://cts2.org/schema/2010/01/ValueSetDefinitionServices=org.cts2.service.valuesetdefinition,\ - http://cts2.org/schema/2010/01/ValueSetRuleResolutionServices=org.cts2.service.valuesetruleresolution,\ - http://cts2.org/schema/2010/01/ValueSetServices=org.cts2.service.valueset - - \ No newline at end of file diff --git a/cts2-model/ivy.xml b/cts2-model/ivy.xml deleted file mode 100755 index 3d60bd6be5..0000000000 --- a/cts2-model/ivy.xml +++ /dev/null @@ -1,31 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/cts2-model/src/castor/java/org/cts2/castor/fieldhandler/DirectoryURIFieldHandler.java b/cts2-model/src/castor/java/org/cts2/castor/fieldhandler/DirectoryURIFieldHandler.java deleted file mode 100644 index 5cabfe584c..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/fieldhandler/DirectoryURIFieldHandler.java +++ /dev/null @@ -1,61 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.fieldhandler; -import org.cts2.uri.DirectoryURI; -import org.exolab.castor.mapping.GeneralizedFieldHandler; - - -/** - * The Class DirectoryURIFieldHandler. - * - * @author Kevin Peterson - */ -public class DirectoryURIFieldHandler extends GeneralizedFieldHandler { - - /* (non-Javadoc) - * @see org.exolab.castor.mapping.GeneralizedFieldHandler#convertUponGet(java.lang.Object) - */ - @Override - public Object convertUponGet(Object directoryURI) { - if(directoryURI == null){ - return null; - } - - DirectoryURI uri = (DirectoryURI)directoryURI; - - return uri.marshall(); - } - - /* (non-Javadoc) - * @see org.exolab.castor.mapping.GeneralizedFieldHandler#convertUponSet(java.lang.Object) - */ - @Override - public Object convertUponSet(Object arg0) { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.exolab.castor.mapping.GeneralizedFieldHandler#getFieldType() - */ - @Override - public Class getFieldType() { - return DirectoryURI.class; - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifier.java b/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifier.java deleted file mode 100644 index 60344b72f4..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifier.java +++ /dev/null @@ -1,57 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer; - -import org.exolab.javasource.JClass; - -/** - * The Interface JClassModifier. - * - * @author Kevin Peterson - */ -public interface JClassModifier { - - /** - * Modify j class. - * - * @param jClass the j class - * @param outputDir the output dir - * @param lineSeparator the line separator - * @param header the header - */ - public void prePrintModifyJClass(JClass jClass, String outputDir, String lineSeparator, String header); - - /** - * Post print modify j class. - * - * @param jClass the j class - * @param outputDir the output dir - * @param lineSeparator the line separator - * @param header the header - */ - public void postPrintModifyJClass(JClass jClass, String outputDir, String lineSeparator, String header); - - /** - * Checks if is match. - * - * @param jClass the j class - * @return true, if is match - */ - public boolean isMatch(JClass jClass); -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifyingWriterJClassPrinter.java b/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifyingWriterJClassPrinter.java deleted file mode 100644 index 82dbe6a131..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifyingWriterJClassPrinter.java +++ /dev/null @@ -1,73 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer; - -import java.util.HashSet; -import java.util.Set; - -import org.cts2.castor.printer.modifiers.AssociationModifier; -import org.cts2.castor.printer.modifiers.ChangeableResourceInterfaceAdder; -import org.cts2.castor.printer.modifiers.DirectorySubclassesModifier; -import org.cts2.castor.printer.modifiers.DirectoryURIMethodAddingModifier; -import org.cts2.castor.printer.modifiers.ResourceDescriptionModifier; -import org.cts2.castor.printer.modifiers.ValueSetResolutionRuleModifier; -import org.exolab.castor.builder.printing.WriterJClassPrinter; -import org.exolab.javasource.JClass; - -/** - * The Class JClassModifyingWriterJClassPrinter. - * - * @author Kevin Peterson - */ -public class JClassModifyingWriterJClassPrinter extends WriterJClassPrinter { - - /** The modifier map. */ - private Set modifierMap = new HashSet(); - { - modifierMap.add(new DirectoryURIMethodAddingModifier()); - modifierMap.add(new DirectorySubclassesModifier()); - modifierMap.add(new ChangeableResourceInterfaceAdder()); - modifierMap.add(new ResourceDescriptionModifier()); - modifierMap.add(new ValueSetResolutionRuleModifier()); - modifierMap.add(new AssociationModifier()); - } - - /* (non-Javadoc) - * @see org.exolab.castor.builder.printing.WriterJClassPrinter#printClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - public void printClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - - for(JClassModifier modifier : this.modifierMap){ - if(modifier.isMatch(jClass)){ - modifier.prePrintModifyJClass(jClass, outputDir, - lineSeparator, header); - } - } - - super.printClass(jClass, outputDir, lineSeparator, header); - - for(JClassModifier modifier : this.modifierMap){ - if(modifier.isMatch(jClass)){ - modifier.postPrintModifyJClass(jClass, outputDir, - lineSeparator, header); - } - } - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifyingWriterJClassPrinterFactory.java b/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifyingWriterJClassPrinterFactory.java deleted file mode 100644 index 2d7a0c3d84..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/JClassModifyingWriterJClassPrinterFactory.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * Copyright 2005-2008 Werner Guttmann - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.cts2.castor.printer; - -import org.exolab.castor.builder.printing.JClassPrinter; -import org.exolab.castor.builder.printing.JClassPrinterFactory; - -/** - * A factory for creating JClassModifyingWriterJClassPrinter objects. - */ -public class JClassModifyingWriterJClassPrinterFactory implements JClassPrinterFactory { - - /** - * The name of the factory. - */ - private static final String NAME = "modifying-writer"; - - /** - * Gets the j class printer. - * - * @return the j class printer - * {@inheritDoc} - * @see org.exolab.castor.builder.printing.JClassPrinterFactory#getJClassPrinter() - */ - public JClassPrinter getJClassPrinter() { - return new JClassModifyingWriterJClassPrinter(); - } - - /** - * Gets the name. - * - * @return the name - * {@inheritDoc} - * @see org.exolab.castor.builder.printing.JClassPrinterFactory#getName() - */ - public String getName() { - return NAME; - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/AssociationModifier.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/AssociationModifier.java deleted file mode 100644 index 074df730c1..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/AssociationModifier.java +++ /dev/null @@ -1,65 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import org.cts2.castor.printer.JClassModifier; -import org.exolab.javasource.JClass; -import org.exolab.javasource.JMethod; -import org.exolab.javasource.JType; - -/** - * The Class AssociationModifier. - * - * @author Kevin Peterson - */ -public class AssociationModifier implements JClassModifier { - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#prePrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void prePrintModifyJClass( - JClass jClass, - String outputDir, - String lineSeparator, - String header) { - JType jtype = new SimpleJType("java.lang.String"); - JMethod method = new JMethod("getEntryID", jtype, null); - method.setSourceCode("return this.getExternalStatementId();"); - - jClass.addMethod(method); - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#postPrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void postPrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - // - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#isMatch(org.exolab.javasource.JClass) - */ - @Override - public boolean isMatch(JClass jClass) { - return jClass.getName().equals("org.cts2.association.Association"); - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ChangeableResourceInterfaceAdder.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ChangeableResourceInterfaceAdder.java deleted file mode 100644 index 6d2eab0841..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ChangeableResourceInterfaceAdder.java +++ /dev/null @@ -1,60 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import org.cts2.castor.printer.JClassModifier; -import org.exolab.javasource.JClass; - -/** - * The Class ChangeableResourceInterfaceAdder. - * - * @author Kevin Peterson - */ -public class ChangeableResourceInterfaceAdder implements JClassModifier { - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#prePrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void prePrintModifyJClass( - JClass jClass, - String outputDir, - String lineSeparator, - String header) { - jClass.addInterface("org.cts2.core.ChangeableResource"); - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#postPrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void postPrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - // - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#isMatch(org.exolab.javasource.JClass) - */ - @Override - public boolean isMatch(JClass jClass) { - return jClass.getName().equals("org.cts2.core.Changeable"); - } - -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/DirectorySubclassesModifier.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/DirectorySubclassesModifier.java deleted file mode 100644 index 74974870c7..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/DirectorySubclassesModifier.java +++ /dev/null @@ -1,93 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import org.apache.commons.lang.StringUtils; -import org.cts2.castor.printer.JClassModifier; -import org.exolab.javasource.JClass; -import org.exolab.javasource.JField; -import org.exolab.javasource.JType; - -/** - * The Class DirectoryURIMethodAddingModifier. - * - * @author Kevin Peterson - */ -public class DirectorySubclassesModifier implements JClassModifier{ - - /** The Constant DIRECTORY_QUALIFIED_NAME. */ - private static final String DIRECTORY_QUALIFIED_NAME = "org.cts2.core.Directory"; - - /** The Constant DIRECTORYURI_PACKAGE. */ - private static final String DIRECTORYURI_PACKAGE = "org.cts2.uri"; - - /** The Constant DIRECTORYURI_SUFFIX. */ - private static final String DIRECTORYURI_SUFFIX = "URI"; - - /** The Constant GENERIC_REGEX. */ - private static final String GENERIC_REGEX = "<.*>$"; - - /** The Constant LIST_REGEX. */ - private static final String LIST_REGEX = "List$"; - - /** The Constant DIRECTORY_SUFFIX. */ - private static final String DIRECTORY_SUFFIX = "Directory"; - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#prePrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void prePrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - jClass.setSuperClass(jClass.getSuperClassQualifiedName() + "<" + DIRECTORYURI_PACKAGE + "." + jClass.getLocalName().replaceAll(LIST_REGEX, DIRECTORY_SUFFIX) + DIRECTORYURI_SUFFIX + ">"); - } - - /** - * Adjust field. - * - * @param jClass the j class - * @param name the name - * @param type the type - */ - protected void adjustField(JClass jClass, String name, JType type){ - jClass.removeField(jClass.getField(name)); - jClass.addField(new JField(type, name)); - } - - /* (non-Javadoc) - * @see org.cts2.castor.JClassModifier#isMatch(org.exolab.javasource.JClass) - */ - @Override - public boolean isMatch(JClass jClass) { - return StringUtils.isNotBlank(jClass.getSuperClassQualifiedName()) && - ( - jClass.getSuperClassQualifiedName().matches(DIRECTORY_QUALIFIED_NAME) || - jClass.getSuperClassQualifiedName().matches(DIRECTORY_QUALIFIED_NAME + GENERIC_REGEX) - ); - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#postPrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void postPrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - jClass.setSuperClass(jClass.getSuperClassQualifiedName().replaceAll(GENERIC_REGEX, "")); - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/DirectoryURIMethodAddingModifier.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/DirectoryURIMethodAddingModifier.java deleted file mode 100644 index 9ba1b04428..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/DirectoryURIMethodAddingModifier.java +++ /dev/null @@ -1,186 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import java.io.File; -import java.io.IOException; - -import org.apache.commons.io.FileUtils; -import org.cts2.castor.printer.JClassModifier; -import org.exolab.javasource.JClass; -import org.exolab.javasource.JField; -import org.exolab.javasource.JMethod; -import org.exolab.javasource.JParameter; -import org.exolab.javasource.JType; - -/** - * The Class DirectoryURIMethodAddingModifier. - * - * @author Kevin Peterson - */ -public class DirectoryURIMethodAddingModifier implements JClassModifier{ - - /** The Constant DIRECTORY_QUALIFIED_NAME. */ - private static final String DIRECTORY_QUALIFIED_NAME = "org.cts2.core.Directory"; - - /** The Constant URI_SUFFIX. */ - private static final String PREV_FIELD = "_prev"; - - /** The Constant NEXT_FIELD. */ - private static final String NEXT_FIELD = "_next"; - - /** The Constant PREV. */ - private static final String GET_PREV = "getPrev"; - - /** The Constant NEXT. */ - private static final String SET_NEXT = "setNext"; - - /** The Constant PREV. */ - private static final String GET_NEXT = "getNext"; - - /** The Constant NEXT. */ - private static final String SET_PREV = "setPrev"; - - /** The GENERICS. */ - private static String GENERICS = ""; - - private static String DIRECTORY_CLASS_DECLARATION = "public abstract class Directory"; - - /** The GENERI c_ simpl e_ type. */ - private static SimpleJType GENERIC_SIMPLE_TYPE = new SimpleJType("T"); - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#prePrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void prePrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - jClass.removeConstructor(jClass.getConstructors()[0]); - - this.adjustField(jClass, PREV_FIELD, GENERIC_SIMPLE_TYPE); - this.adjustField(jClass, NEXT_FIELD, GENERIC_SIMPLE_TYPE); - - this.adjustJMethod(jClass, GET_PREV, GENERIC_SIMPLE_TYPE, MethodType.GET); - this.adjustJMethod(jClass, SET_PREV, GENERIC_SIMPLE_TYPE, MethodType.SET); - this.adjustJMethod(jClass, GET_NEXT, GENERIC_SIMPLE_TYPE, MethodType.GET); - this.adjustJMethod(jClass, SET_NEXT, GENERIC_SIMPLE_TYPE, MethodType.SET); - } - - /** - * Adjust field. - * - * @param jClass the j class - * @param name the name - * @param type the type - */ - protected void adjustField(JClass jClass, String name, JType type){ - jClass.removeField(jClass.getField(name)); - jClass.addField(new JField(type, name)); - } - - /** - * The Enum MethodType. - * - * @author Kevin Peterson - */ - private enum MethodType { - GET, - SET} - - /** - * Adjust j method. - * - * @param jClass the j class - * @param name the name - * @param jType the j type - * @param methodType the method type - */ - protected void adjustJMethod(JClass jClass, String name, JType jType, MethodType methodType){ - JMethod oldMethod = jClass.getMethod(name, 0); - - JMethod newMethod; - if(methodType.equals(MethodType.GET)){ - newMethod = new JMethod(name, jType, null); - } else { - newMethod = new JMethod(name); - for(JParameter oldParam : oldMethod.getParameters()){ - if(oldParam != null){ - JParameter newParam = new JParameter(jType, oldParam.getName()); - newMethod.getSignature().addParameter(newParam); - break; - } - } - } - - newMethod.setSourceCode(oldMethod.getSourceCode()); - - jClass.removeMethod(oldMethod); - jClass.addMethod(newMethod); - } - - /** - * Adds the generics. - * - * @param name the name - * @return the string - */ - protected String addGenerics(String name){ - return name + GENERICS; - } - - /** - * Removes the generics. - * - * @param name the name - * @return the string - */ - protected String removeGenerics(String name){ - return name.replaceAll(GENERICS, ""); - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#postPrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void postPrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - - try { - File file = new File(jClass.getFilename(outputDir)); - - String originalFile = FileUtils.readFileToString(file); - - String modifiedFile = - originalFile.replaceFirst(DIRECTORY_CLASS_DECLARATION, addGenerics(DIRECTORY_CLASS_DECLARATION)); - - FileUtils.writeStringToFile(file, modifiedFile); - } catch (IOException e) { - throw new RuntimeException(e); - } - } - - /* (non-Javadoc) - * @see org.cts2.castor.JClassModifier#isMatch(org.exolab.javasource.JClass) - */ - @Override - public boolean isMatch(JClass jClass) { - return jClass.getName().equals(DIRECTORY_QUALIFIED_NAME) || - jClass.getName().equals(DIRECTORY_QUALIFIED_NAME + GENERICS); - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ResourceDescriptionModifier.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ResourceDescriptionModifier.java deleted file mode 100644 index 0b935509d8..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ResourceDescriptionModifier.java +++ /dev/null @@ -1,65 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import org.cts2.castor.printer.JClassModifier; -import org.exolab.javasource.JClass; -import org.exolab.javasource.JMethod; -import org.exolab.javasource.JType; - -/** - * The Class ResourceDescriptionModifier. - * - * @author Kevin Peterson - */ -public class ResourceDescriptionModifier implements JClassModifier { - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#prePrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void prePrintModifyJClass( - JClass jClass, - String outputDir, - String lineSeparator, - String header) { - JType jtype = new SimpleJType("java.lang.String"); - JMethod method = new JMethod("getEntryID", jtype, null); - method.setSourceCode("return this.getAbout();"); - - jClass.addMethod(method); - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#postPrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void postPrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - // - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#isMatch(org.exolab.javasource.JClass) - */ - @Override - public boolean isMatch(JClass jClass) { - return jClass.getName().equals("org.cts2.core.ResourceDescription"); - } -} diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/SimpleJType.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/SimpleJType.java deleted file mode 100644 index 51f5043525..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/SimpleJType.java +++ /dev/null @@ -1,46 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import org.exolab.javasource.JType; - -/** - * The Class SimpleJType. - * - * @author Kevin Peterson - */ -public class SimpleJType extends JType{ - - /** - * Instantiates a new simple j type. - * - * @param name the name - */ - public SimpleJType(String name) { - super(name); - } - - /* (non-Javadoc) - * @see java.lang.Object#toString() - */ - public String toString(){ - return this.getName(); - } - -} \ No newline at end of file diff --git a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ValueSetResolutionRuleModifier.java b/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ValueSetResolutionRuleModifier.java deleted file mode 100644 index 74dd2f3e55..0000000000 --- a/cts2-model/src/castor/java/org/cts2/castor/printer/modifiers/ValueSetResolutionRuleModifier.java +++ /dev/null @@ -1,65 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.castor.printer.modifiers; - -import org.cts2.castor.printer.JClassModifier; -import org.exolab.javasource.JClass; -import org.exolab.javasource.JMethod; -import org.exolab.javasource.JType; - -/** - * The Class ValueSetResolutionRuleModifier. - * - * @author Kevin Peterson - */ -public class ValueSetResolutionRuleModifier implements JClassModifier { - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#prePrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void prePrintModifyJClass( - JClass jClass, - String outputDir, - String lineSeparator, - String header) { - JType jtype = new SimpleJType("java.lang.String"); - JMethod method = new JMethod("getEntryID", jtype, null); - method.setSourceCode("return this.getResolutionRuleURI();"); - - jClass.addMethod(method); - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#postPrintModifyJClass(org.exolab.javasource.JClass, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public void postPrintModifyJClass(JClass jClass, String outputDir, - String lineSeparator, String header) { - // - } - - /* (non-Javadoc) - * @see org.cts2.castor.printer.JClassModifier#isMatch(org.exolab.javasource.JClass) - */ - @Override - public boolean isMatch(JClass jClass) { - return jClass.getName().equals("org.cts2.valuesetresolution.ValueSetResolutionRule"); - } -} diff --git a/cts2-model/src/main/java/org/cts2/core/ChangeableResource.java b/cts2-model/src/main/java/org/cts2/core/ChangeableResource.java deleted file mode 100644 index 4521701e8d..0000000000 --- a/cts2-model/src/main/java/org/cts2/core/ChangeableResource.java +++ /dev/null @@ -1,57 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.core; - -import org.cts2.core.types.EntryState; - -/** - * The Interface ChangeableResource. - * - * @author Kevin Peterson - */ -public interface ChangeableResource { - - /** - * Gets the entry id. - * - * @return the entry id - */ - public String getEntryID(); - - /** - * Gets the entry state. - * - * @return the entry state - */ - public EntryState getEntryState(); - - /** - * Gets the status. - * - * @return the status - */ - public StatusReference getStatus(); - - /** - * Gets the change description. - * - * @return the change description - */ - public ChangeDescription getChangeDescription(); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/AssociationDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/AssociationDirectoryURI.java deleted file mode 100644 index 28dbec8992..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/AssociationDirectoryURI.java +++ /dev/null @@ -1,120 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -import org.cts2.core.TargetExpression; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState; - -/** - * The Interface AssociationDirectoryURI. - * - * @author Kevin Peterson - */ -public interface AssociationDirectoryURI - extends DirectoryURI, SetOperable { - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getAllSourceAndTargetEntities( - EntityDirectoryURI directory, QueryControl queryControl, - ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getPredicates(QueryControl queryControl, ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getSourceEntities(QueryControl queryControl, ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getTargetEntities(QueryControl queryControl, ReadContext context); - - /** - * - * @param directory - * @param codeSystemVersion - */ - public AssociationDirectoryURI restrictToCodeSystemVersion(NameOrURI codeSystemVersion); - - /** - * - * @param directory - * @param predicate - */ - public AssociationDirectoryURI restrictToPredicate(EntityNameOrURI predicate); - - /** - * - * @param directory - * @param sourceEntity - */ - public AssociationDirectoryURI restrictToSourceEntity(EntityNameOrURI sourceEntity); - - /** - * - * @param directory - * @param entity - */ - public AssociationDirectoryURI restrictToSourceOrTargetEntity(EntityNameOrURI entity); - - /** - * - * @param directory - * @param target - */ - public AssociationDirectoryURI restrictToTargetEntity(EntityNameOrURI target); - - /** - * - * @param directory - * @param target - */ - public AssociationDirectoryURI restrictToTargetExpression(TargetExpression target); - - /** - * - * @param directory - * @param target - */ - public AssociationDirectoryURI restrictToTargetLiteral(String target); - - public AssociationDirectoryRestrictionState getRestrictionState(); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/AssociationGraphURI.java b/cts2-model/src/main/java/org/cts2/uri/AssociationGraphURI.java deleted file mode 100644 index 004f7763d0..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/AssociationGraphURI.java +++ /dev/null @@ -1,31 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - - -/** - * The Interface AssociationDirectoryURI. - * - * @author Kevin Peterson - */ -public interface AssociationGraphURI - extends DirectoryURI, SetOperable { -} - diff --git a/cts2-model/src/main/java/org/cts2/uri/ChangeSetDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/ChangeSetDirectoryURI.java deleted file mode 100644 index 026b0dd9ab..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/ChangeSetDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface ChangeSetDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/CodeSystemDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/CodeSystemDirectoryURI.java deleted file mode 100644 index 0b2f0f3ccc..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/CodeSystemDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemDirectoryURI. - * - * @author Kevin Peterson - */ -public interface CodeSystemDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/CodeSystemVersionDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/CodeSystemVersionDirectoryURI.java deleted file mode 100644 index 40073664a8..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/CodeSystemVersionDirectoryURI.java +++ /dev/null @@ -1,40 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -import java.util.List; - -import org.cts2.core.EntityReference; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.uri.restriction.CodeSystemVersionRestrictionState; - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface CodeSystemVersionDirectoryURI extends DirectoryURI, SetOperable { - - public CodeSystemVersionRestrictionState getRestrictionState(); - - public CodeSystemVersionDirectoryURI restrictToEntities( - List entities, RestrictionType allOrSome, - ActiveOrAll active); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/ConceptDomainBindingDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/ConceptDomainBindingDirectoryURI.java deleted file mode 100644 index 67f401b49b..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/ConceptDomainBindingDirectoryURI.java +++ /dev/null @@ -1,30 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface ConceptDomainBindingDirectoryURI - extends DirectoryURI, SetOperable { -} - diff --git a/cts2-model/src/main/java/org/cts2/uri/ConceptDomainDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/ConceptDomainDirectoryURI.java deleted file mode 100644 index 976914abaf..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/ConceptDomainDirectoryURI.java +++ /dev/null @@ -1,30 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface ConceptDomainDirectoryURI - extends DirectoryURI, SetOperable { -} - diff --git a/cts2-model/src/main/java/org/cts2/uri/DirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/DirectoryURI.java deleted file mode 100644 index 7cb7e6eeae..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/DirectoryURI.java +++ /dev/null @@ -1,75 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -import org.cts2.core.Directory; -import org.cts2.core.Filter; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.restriction.RestrictionState; - -/** - * The Interface DirectoryURI. - * - * @author Kevin Peterson - */ -public interface DirectoryURI { - - /** - * Gets the restriction state. - * - * @return the restriction state - */ - public RestrictionState getRestrictionState(); - - /** - * Gets the. - * - * @param the - * @param queryControl the query control - * @param readContext the read context - * @param content the content - * @return the t - */ - public > T get(QueryControl queryControl, ReadContext readContext, Class content); - - /** - * Count. - * - * @param readContext the read context - * @return the int - */ - public int count(ReadContext readContext); - - /** - * Restrict. - * - * @param filter the filter - * @return the directory uri - */ - public DirectoryURI restrict(Filter filter); - - /** - * Marshall. - * - * @return the string - */ - public String marshall(); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/EntityDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/EntityDirectoryURI.java deleted file mode 100644 index 1f51ba5384..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/EntityDirectoryURI.java +++ /dev/null @@ -1,56 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -import org.cts2.core.VersionTagReference; -import org.cts2.service.core.NameOrURI; -import org.cts2.uri.restriction.EntityDirectoryRestrictionState; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface EntityDirectoryURI - extends DirectoryURI, SetOperable { - - /** - * Restrict to code systems. - * - * @param codeSystems the code systems - * @param tag the tag - * @return the entity directory uri - */ - public EntityDirectoryURI restrictToCodeSystems(NameOrURI codeSystems, VersionTagReference tag); - - /** - * Restrict to code system versions. - * - * @param codeSystemVersions the code system versions - * @return the entity directory uri - */ - public EntityDirectoryURI restrictToCodeSystemVersions(NameOrURI codeSystemVersions); - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#getRestrictionState() - */ - public EntityDirectoryRestrictionState getRestrictionState(); -} - diff --git a/cts2-model/src/main/java/org/cts2/uri/MapDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/MapDirectoryURI.java deleted file mode 100644 index d78f6d5650..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/MapDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface MapDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/MapEntryDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/MapEntryDirectoryURI.java deleted file mode 100644 index c1e7023b0c..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/MapEntryDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface MapEntryDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/MapVersionDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/MapVersionDirectoryURI.java deleted file mode 100644 index 0d35ecf3c1..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/MapVersionDirectoryURI.java +++ /dev/null @@ -1,38 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -import org.cts2.service.core.NameOrURIList; -import org.cts2.uri.restriction.MapVersionDirectoryRestrictionState; - - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface MapVersionDirectoryURI - extends DirectoryURI, SetOperable { - - public MapVersionDirectoryRestrictionState getRestrictionState(); - - public MapVersionDirectoryURI restrictToCodeSystems(MapVersionDirectoryURI directory, - NameOrURIList codeSystems); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/ResolutionRuleDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/ResolutionRuleDirectoryURI.java deleted file mode 100644 index 410ad61b8b..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/ResolutionRuleDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface ResolutionRuleDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/SetOperable.java b/cts2-model/src/main/java/org/cts2/uri/SetOperable.java deleted file mode 100644 index f9fb4a9d1c..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/SetOperable.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -/** - * The Interface SetOperable. - * - * @param the - * @author Kevin Peterson - */ -public interface SetOperable { - - /** - * Union. - * - * @param set the set - * @return the t - */ - public T union(T set); - - /** - * Intersect. - * - * @param set the set - * @return the t - */ - public T intersect(T set); - - /** - * Difference. - * - * @param set the set - * @return the t - */ - public T difference(T set); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/StatementDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/StatementDirectoryURI.java deleted file mode 100644 index 0ab7871d99..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/StatementDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface StatementDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/UrlBasedDirectoryUriFactory.java b/cts2-model/src/main/java/org/cts2/uri/UrlBasedDirectoryUriFactory.java deleted file mode 100644 index cf5fa69b3c..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/UrlBasedDirectoryUriFactory.java +++ /dev/null @@ -1,110 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -import net.sf.cglib.proxy.Enhancer; -import net.sf.cglib.proxy.NoOp; - -import org.cts2.core.Directory; -import org.cts2.core.Filter; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.restriction.RestrictionState; - -/** - * The Class UrlBasedDirectoryUriFactory. - * - * @author Kevin Peterson - */ -public class UrlBasedDirectoryUriFactory { - - /** - * Creates the url based directory uri. - * - * @param targetClass the target class - * @param uri the uri - * @return the DirectoryURI - */ - @SuppressWarnings("unchecked") - public static T createUrlBasedDirectoryUri(String url, Class targetClass) { - Enhancer enhancer = new Enhancer(); - enhancer.setSuperclass(UrlStringBasedDirectoryURI.class); - enhancer.setInterfaces(new Class[]{targetClass}); - enhancer.setCallback(NoOp.INSTANCE); - return (T)enhancer.create(new Class[]{String.class}, new Object[]{url}); - } - - /** - * The Class UrlStringBasedDirectoryURI. - * - * @author Kevin Peterson - */ - public static class UrlStringBasedDirectoryURI implements DirectoryURI { - - /** The url. */ - private String url; - - /** - * Instantiates a new url string based directory uri. - * - * @param url the url - */ - public UrlStringBasedDirectoryURI(String url){ - this.url = url; - } - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#get(org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext, java.lang.Class) - */ - @Override - public > T get(QueryControl queryControl, - ReadContext readContext, Class content) { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#count(org.cts2.service.core.ReadContext) - */ - @Override - public int count(ReadContext readContext) { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#restrict(org.cts2.core.Filter) - */ - @Override - public DirectoryURI restrict(Filter filter) { - throw new UnsupportedOperationException(); - } - - @Override - public RestrictionState getRestrictionState() { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#marshall() - */ - @Override - public String marshall() { - return this.url; - } - } -} diff --git a/cts2-model/src/main/java/org/cts2/uri/ValueSetDefinitionDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/ValueSetDefinitionDirectoryURI.java deleted file mode 100644 index 3aeb2b2066..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/ValueSetDefinitionDirectoryURI.java +++ /dev/null @@ -1,46 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - -import java.util.List; - -import org.cts2.core.EntityReference; -import org.cts2.uri.restriction.ValueSetDefinitionRestrictionState; - -/** - * The Interface ValueSetDefinitionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface ValueSetDefinitionDirectoryURI - extends DirectoryURI, SetOperable { - - /** - * Restrict to entities. - * - * @param entityList the entity list - * @return the value set definition directory uri - */ - public ValueSetDefinitionDirectoryURI restrictToEntities(List entityList); - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#getRestrictionState() - */ - public ValueSetDefinitionRestrictionState getRestrictionState(); -} diff --git a/cts2-model/src/main/java/org/cts2/uri/ValueSetDirectoryURI.java b/cts2-model/src/main/java/org/cts2/uri/ValueSetDirectoryURI.java deleted file mode 100644 index 660dee2ce4..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/ValueSetDirectoryURI.java +++ /dev/null @@ -1,29 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri; - - -/** - * The Interface CodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public interface ValueSetDirectoryURI - extends DirectoryURI, SetOperable { -} diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/AssociationDirectoryRestrictionState.java b/cts2-model/src/main/java/org/cts2/uri/restriction/AssociationDirectoryRestrictionState.java deleted file mode 100644 index 46801d6d69..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/AssociationDirectoryRestrictionState.java +++ /dev/null @@ -1,393 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri.restriction; - -import java.util.HashSet; -import java.util.Set; - -import org.cts2.core.TargetExpression; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.uri.AssociationDirectoryURI; - -/** - * The Class AssociationDirectoryRestrictionState. - * - * @author Kevin Peterson - */ -public class AssociationDirectoryRestrictionState extends - RestrictionState { - - /** The restrict to code system version restrictions. */ - private Set restrictToCodeSystemVersionRestrictions = new HashSet(); - - /** The restrict to predicate restrictions. */ - private Set restrictToPredicateRestrictions = new HashSet(); - - /** The restrict to source entity restrictions. */ - private Set restrictToSourceEntityRestrictions = new HashSet(); - - /** The restrict to source or target entity restrictions. */ - private Set restrictToSourceOrTargetEntityRestrictions = new HashSet(); - - /** The restrict to target entity restrictions. */ - private Set restrictToTargetEntityRestrictions = new HashSet(); - - /** The restrict to target expression restrictions. */ - private Set restrictToTargetExpressionRestrictions = new HashSet(); - - /** The restrict to target literal restriction. */ - private Set restrictToTargetLiteralRestriction = new HashSet(); - - /** - * The Class RestrictToCodeSystemVersionRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToCodeSystemVersionRestriction { - - /** The code system version. */ - private NameOrURI codeSystemVersion; - - /** - * Sets the code system version. - * - * @param codeSystemVersion the new code system version - */ - public void setCodeSystemVersion(NameOrURI codeSystemVersion) { - this.codeSystemVersion = codeSystemVersion; - } - - /** - * Gets the code system version. - * - * @return the code system version - */ - public NameOrURI getCodeSystemVersion() { - return codeSystemVersion; - } - } - - /** - * The Class RestrictToPredicateRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToPredicateRestriction { - - /** The predicate. */ - private EntityNameOrURI predicate; - - /** - * Sets the predicate. - * - * @param predicate the new predicate - */ - public void setPredicate(EntityNameOrURI predicate) { - this.predicate = predicate; - } - - /** - * Gets the predicate. - * - * @return the predicate - */ - public EntityNameOrURI getPredicate() { - return predicate; - } - } - - /** - * The Class RestrictToSourceEntityRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToSourceEntityRestriction { - - /** The source entity. */ - private EntityNameOrURI sourceEntity; - - /** - * Sets the source entity. - * - * @param sourceEntity the new source entity - */ - public void setSourceEntity(EntityNameOrURI sourceEntity) { - this.sourceEntity = sourceEntity; - } - - /** - * Gets the source entity. - * - * @return the source entity - */ - public EntityNameOrURI getSourceEntity() { - return sourceEntity; - } - } - - /** - * The Class RestrictToSourceOrTargetEntityRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToSourceOrTargetEntityRestriction { - - /** The entity. */ - private EntityNameOrURI entity; - - /** - * Sets the entity. - * - * @param entity the new entity - */ - public void setEntity(EntityNameOrURI entity) { - this.entity = entity; - } - - /** - * Gets the entity. - * - * @return the entity - */ - public EntityNameOrURI getEntity() { - return entity; - } - } - - /** - * The Class RestrictToTargetEntityRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToTargetEntityRestriction { - - /** The target. */ - private EntityNameOrURI target; - - /** - * Sets the target. - * - * @param target the new target - */ - public void setTarget(EntityNameOrURI target) { - this.target = target; - } - - /** - * Gets the target. - * - * @return the target - */ - public EntityNameOrURI getTarget() { - return target; - } - } - - /** - * The Class RestrictToTargetExpressionRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToTargetExpressionRestriction { - - /** The target. */ - private TargetExpression target; - - /** - * Sets the target. - * - * @param target the new target - */ - public void setTarget(TargetExpression target) { - this.target = target; - } - - /** - * Gets the target. - * - * @return the target - */ - public TargetExpression getTarget() { - return target; - } - } - - /** - * The Class RestrictToTargetLiteralRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToTargetLiteralRestriction { - - /** The target. */ - private String target; - - /** - * Sets the target. - * - * @param target the new target - */ - public void setTarget(String target) { - this.target = target; - } - - /** - * Gets the target. - * - * @return the target - */ - public String getTarget() { - return target; - } - } - - /** - * Gets the restrict to code system version restrictions. - * - * @return the restrict to code system version restrictions - */ - public Set getRestrictToCodeSystemVersionRestrictions() { - return restrictToCodeSystemVersionRestrictions; - } - - /** - * Sets the restrict to code system version restrictions. - * - * @param restrictToCodeSystemVersionRestrictions the new restrict to code system version restrictions - */ - public void setRestrictToCodeSystemVersionRestrictions( - Set restrictToCodeSystemVersionRestrictions) { - this.restrictToCodeSystemVersionRestrictions = restrictToCodeSystemVersionRestrictions; - } - - /** - * Gets the restrict to predicate restrictions. - * - * @return the restrict to predicate restrictions - */ - public Set getRestrictToPredicateRestrictions() { - return restrictToPredicateRestrictions; - } - - /** - * Sets the restrict to predicate restrictions. - * - * @param restrictToPredicateRestrictions the new restrict to predicate restrictions - */ - public void setRestrictToPredicateRestrictions( - Set restrictToPredicateRestrictions) { - this.restrictToPredicateRestrictions = restrictToPredicateRestrictions; - } - - /** - * Gets the restrict to source entity restrictions. - * - * @return the restrict to source entity restrictions - */ - public Set getRestrictToSourceEntityRestrictions() { - return restrictToSourceEntityRestrictions; - } - - /** - * Sets the restrict to source entity restrictions. - * - * @param restrictToSourceEntityRestrictions the new restrict to source entity restrictions - */ - public void setRestrictToSourceEntityRestrictions( - Set restrictToSourceEntityRestrictions) { - this.restrictToSourceEntityRestrictions = restrictToSourceEntityRestrictions; - } - - /** - * Gets the restrict to source or target entity restrictions. - * - * @return the restrict to source or target entity restrictions - */ - public Set getRestrictToSourceOrTargetEntityRestrictions() { - return restrictToSourceOrTargetEntityRestrictions; - } - - /** - * Sets the restrict to source or target entity restrictions. - * - * @param restrictToSourceOrTargetEntityRestrictions the new restrict to source or target entity restrictions - */ - public void setRestrictToSourceOrTargetEntityRestrictions( - Set restrictToSourceOrTargetEntityRestrictions) { - this.restrictToSourceOrTargetEntityRestrictions = restrictToSourceOrTargetEntityRestrictions; - } - - /** - * Gets the restrict to target entity restrictions. - * - * @return the restrict to target entity restrictions - */ - public Set getRestrictToTargetEntityRestrictions() { - return restrictToTargetEntityRestrictions; - } - - /** - * Sets the restrict to target entity restrictions. - * - * @param restrictToTargetEntityRestrictions the new restrict to target entity restrictions - */ - public void setRestrictToTargetEntityRestrictions( - Set restrictToTargetEntityRestrictions) { - this.restrictToTargetEntityRestrictions = restrictToTargetEntityRestrictions; - } - - /** - * Gets the restrict to target expression restrictions. - * - * @return the restrict to target expression restrictions - */ - public Set getRestrictToTargetExpressionRestrictions() { - return restrictToTargetExpressionRestrictions; - } - - /** - * Sets the restrict to target expression restrictions. - * - * @param restrictToTargetExpressionRestrictions the new restrict to target expression restrictions - */ - public void setRestrictToTargetExpressionRestrictions( - Set restrictToTargetExpressionRestrictions) { - this.restrictToTargetExpressionRestrictions = restrictToTargetExpressionRestrictions; - } - - /** - * Gets the restrict to target literal restriction. - * - * @return the restrict to target literal restriction - */ - public Set getRestrictToTargetLiteralRestriction() { - return restrictToTargetLiteralRestriction; - } - - /** - * Sets the restrict to target literal restriction. - * - * @param restrictToTargetLiteralRestriction the new restrict to target literal restriction - */ - public void setRestrictToTargetLiteralRestriction( - Set restrictToTargetLiteralRestriction) { - this.restrictToTargetLiteralRestriction = restrictToTargetLiteralRestriction; - } -} \ No newline at end of file diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/CodeSystemVersionRestrictionState.java b/cts2-model/src/main/java/org/cts2/uri/restriction/CodeSystemVersionRestrictionState.java deleted file mode 100644 index 74e7e821b6..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/CodeSystemVersionRestrictionState.java +++ /dev/null @@ -1,131 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri.restriction; - -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.cts2.core.EntityReference; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.uri.CodeSystemVersionDirectoryURI; - -/** - * The Class CodeSystemVersionRestrictionState. - * - * @author Kevin Peterson - */ -public class CodeSystemVersionRestrictionState extends - RestrictionState { - - /** The restrict to entities restrictions. */ - private Set restrictToEntitiesRestrictions = new HashSet(); - - /** - * Sets the restrict to entities restriction. - * - * @param restrictToEntitiesRestrictions the new restrict to entities restriction - */ - public void setRestrictToEntitiesRestriction( - Set restrictToEntitiesRestrictions) { - this.restrictToEntitiesRestrictions = restrictToEntitiesRestrictions; - } - - /** - * Gets the restrict to entities restrictions. - * - * @return the restrict to entities restrictions - */ - public Set getRestrictToEntitiesRestrictions() { - return restrictToEntitiesRestrictions; - } - - /** - * The Class RestrictToEntitiesRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToEntitiesRestriction { - - /** The entities. */ - private List entities; - - /** The all or some. */ - private RestrictionType allOrSome; - - /** The active. */ - private ActiveOrAll active; - - /** - * Gets the entities. - * - * @return the entities - */ - public List getEntities() { - return entities; - } - - /** - * Sets the entities. - * - * @param entities the new entities - */ - public void setEntities(List entities) { - this.entities = entities; - } - - /** - * Gets the all or some. - * - * @return the all or some - */ - public RestrictionType getAllOrSome() { - return allOrSome; - } - - /** - * Sets the all or some. - * - * @param allOrSome the new all or some - */ - public void setAllOrSome(RestrictionType allOrSome) { - this.allOrSome = allOrSome; - } - - /** - * Gets the active. - * - * @return the active - */ - public ActiveOrAll getActive() { - return active; - } - - /** - * Sets the active. - * - * @param active the new active - */ - public void setActive(ActiveOrAll active) { - this.active = active; - } - - } -} \ No newline at end of file diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/EntityDirectoryRestrictionState.java b/cts2-model/src/main/java/org/cts2/uri/restriction/EntityDirectoryRestrictionState.java deleted file mode 100644 index c05ccc725c..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/EntityDirectoryRestrictionState.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri.restriction; - -import java.util.HashSet; -import java.util.Set; - -import org.cts2.service.core.NameOrURIList; -import org.cts2.uri.EntityDirectoryURI; - -/** - * The Class CodeSystemVersionRestrictionState. - * - * @author Kevin Peterson - */ -public class EntityDirectoryRestrictionState extends - RestrictionState { - - /** The restrict to code system versions restrictions. */ - private Set restrictToCodeSystemVersionsRestrictions = new HashSet(); - - /** - * Sets the restrict to code system versions restrictions. - * - * @param restrictToCodeSystemVersionsRestrictions the new restrict to code system versions restrictions - */ - public void setRestrictToCodeSystemVersionsRestrictions( - Set restrictToCodeSystemVersionsRestrictions) { - this.restrictToCodeSystemVersionsRestrictions = restrictToCodeSystemVersionsRestrictions; - } - - /** - * Gets the restrict to code system versions restrictions. - * - * @return the restrict to code system versions restrictions - */ - public Set getRestrictToCodeSystemVersionsRestrictions() { - return restrictToCodeSystemVersionsRestrictions; - } - - /** - * The Class RestrictToCodeSystemVersionsRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToCodeSystemVersionsRestriction { - - /** The code system versions. */ - private NameOrURIList codeSystemVersions; - - /** - * Sets the code system versions. - * - * @param codeSystemVersions the new code system versions - */ - public void setCodeSystemVersions(NameOrURIList codeSystemVersions) { - this.codeSystemVersions = codeSystemVersions; - } - - /** - * Gets the code system versions. - * - * @return the code system versions - */ - public NameOrURIList getCodeSystemVersions() { - return codeSystemVersions; - } - } - -} \ No newline at end of file diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/MapVersionDirectoryRestrictionState.java b/cts2-model/src/main/java/org/cts2/uri/restriction/MapVersionDirectoryRestrictionState.java deleted file mode 100644 index e711b91e65..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/MapVersionDirectoryRestrictionState.java +++ /dev/null @@ -1,17 +0,0 @@ -package org.cts2.uri.restriction; - - -import org.cts2.uri.MapVersionDirectoryURI; - -/** - * The Class MapVersionDirectoryRestrictionState - * - * @author Zonghui Lian - * - */ -public class MapVersionDirectoryRestrictionState extends - RestrictionState { - -// private Set restrictToCodeSystemVersionsRestrictions = new HashSet(); - -} diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/RestrictionState.java b/cts2-model/src/main/java/org/cts2/uri/restriction/RestrictionState.java deleted file mode 100644 index b8b7506812..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/RestrictionState.java +++ /dev/null @@ -1,76 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri.restriction; - -import java.util.HashSet; -import java.util.Set; - -import org.cts2.core.Filter; -import org.cts2.uri.DirectoryURI; - -/** - * The Class RestrictionState. - * - * @param the - * @author Kevin Peterson - */ -public class RestrictionState { - - /** The set composite. */ - private SetComposite setComposite; - - /** The filters. */ - private Set filters = new HashSet(); - - /** - * Gets the sets the composite. - * - * @return the sets the composite - */ - public SetComposite getSetComposite() { - return setComposite; - } - - /** - * Sets the sets the composite. - * - * @param setComposite the new sets the composite - */ - public void setSetComposite(SetComposite setComposite) { - this.setComposite = setComposite; - } - - /** - * Gets the filters. - * - * @return the filters - */ - public Set getFilters() { - return filters; - } - - /** - * Sets the filters. - * - * @param filters the new filters - */ - public void setFilters(Set filters) { - this.filters = filters; - } -} \ No newline at end of file diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/SetComposite.java b/cts2-model/src/main/java/org/cts2/uri/restriction/SetComposite.java deleted file mode 100644 index 9e6ce9e430..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/SetComposite.java +++ /dev/null @@ -1,94 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri.restriction; - -import org.cts2.core.types.SetOperator; -import org.cts2.uri.DirectoryURI; - -/** - * The Class SetComposite. - * - * @param the - * @author Kevin Peterson - */ -public class SetComposite { - - /** The set operator. */ - private SetOperator setOperator; - - /** The directory uri1. */ - private T directoryUri1; - - /** The directory uri2. */ - private T directoryUri2; - - /** - * Gets the sets the operator. - * - * @return the sets the operator - */ - public SetOperator getSetOperator() { - return setOperator; - } - - /** - * Sets the sets the operator. - * - * @param setOperator the new sets the operator - */ - public void setSetOperator(SetOperator setOperator) { - this.setOperator = setOperator; - } - - /** - * Gets the directory uri1. - * - * @return the directory uri1 - */ - public T getDirectoryUri1() { - return directoryUri1; - } - - /** - * Sets the directory uri1. - * - * @param directoryUri1 the new directory uri1 - */ - public void setDirectoryUri1(T directoryUri1) { - this.directoryUri1 = directoryUri1; - } - - /** - * Gets the directory uri2. - * - * @return the directory uri2 - */ - public T getDirectoryUri2() { - return directoryUri2; - } - - /** - * Sets the directory uri2. - * - * @param directoryUri2 the new directory uri2 - */ - public void setDirectoryUri2(T directoryUri2) { - this.directoryUri2 = directoryUri2; - } -} \ No newline at end of file diff --git a/cts2-model/src/main/java/org/cts2/uri/restriction/ValueSetDefinitionRestrictionState.java b/cts2-model/src/main/java/org/cts2/uri/restriction/ValueSetDefinitionRestrictionState.java deleted file mode 100644 index f6ea4dd966..0000000000 --- a/cts2-model/src/main/java/org/cts2/uri/restriction/ValueSetDefinitionRestrictionState.java +++ /dev/null @@ -1,88 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.uri.restriction; - -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.cts2.core.EntityReference; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; - -/** - * The Class ValueSetDefinitionRestrictionState. - * - * @author Kevin Peterson - */ -public class ValueSetDefinitionRestrictionState extends - RestrictionState { - - private Set restrictToEntitiesRestriction = new HashSet(); - - /** - * The Class RestrictToEntitiesRestriction. - * - * @author Kevin Peterson - */ - public static class RestrictToEntitiesRestriction { - - /** The code system versions. */ - private List entityReferences; - - /** - * Sets the entity references. - * - * @param entityReferences the new entity references - */ - public void setEntityReferences(List entityReferences) { - this.entityReferences = entityReferences; - } - - /** - * Gets the entity references. - * - * @return the entity references - */ - public List getEntityReferences() { - return entityReferences; - } - - - } - - /** - * Sets the restrict to entities restriction. - * - * @param restrictToEntitiesRestriction the new restrict to entities restriction - */ - public void setRestrictToEntitiesRestriction( - Set restrictToEntitiesRestriction) { - this.restrictToEntitiesRestriction = restrictToEntitiesRestriction; - } - - /** - * Gets the restrict to entities restriction. - * - * @return the restrict to entities restriction - */ - public Set getRestrictToEntitiesRestriction() { - return restrictToEntitiesRestriction; - } - -} \ No newline at end of file diff --git a/cts2Impl/.classpath b/cts2Impl/.classpath deleted file mode 100644 index 3875862ae5..0000000000 --- a/cts2Impl/.classpath +++ /dev/null @@ -1,16 +0,0 @@ - - - - - - - - - - - - - - - - diff --git a/cts2Impl/.project b/cts2Impl/.project deleted file mode 100644 index 39f4a3e33c..0000000000 --- a/cts2Impl/.project +++ /dev/null @@ -1,18 +0,0 @@ - - - cts2Impl - - - - - - org.eclipse.jdt.core.javabuilder - - - - - - org.eclipse.jdt.core.javanature - org.apache.ivyde.eclipse.ivynature - - diff --git a/cts2Impl/.settings/org.eclipse.jdt.core.prefs b/cts2Impl/.settings/org.eclipse.jdt.core.prefs deleted file mode 100644 index dd53e5cf0b..0000000000 --- a/cts2Impl/.settings/org.eclipse.jdt.core.prefs +++ /dev/null @@ -1,12 +0,0 @@ -#Tue Jun 01 08:26:38 CDT 2010 -eclipse.preferences.version=1 -org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 -org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve -org.eclipse.jdt.core.compiler.compliance=1.6 -org.eclipse.jdt.core.compiler.debug.lineNumber=generate -org.eclipse.jdt.core.compiler.debug.localVariable=generate -org.eclipse.jdt.core.compiler.debug.sourceFile=generate -org.eclipse.jdt.core.compiler.problem.assertIdentifier=error -org.eclipse.jdt.core.compiler.problem.enumIdentifier=error -org.eclipse.jdt.core.compiler.source=1.6 diff --git a/cts2Impl/build.properties b/cts2Impl/build.properties deleted file mode 100755 index 9f2817787d..0000000000 --- a/cts2Impl/build.properties +++ /dev/null @@ -1,17 +0,0 @@ -#Generated by Maven Ant Plugin - DO NOT EDIT THIS FILE! -#Mon Aug 31 13:56:58 CDT 2009 -lbPackager.dir=../lbPackager -ivy.organisation=lexevs -test.reports=${build.dir}/test-reports -reporting.outputDirectory=${build.dir}/site -build.outputDir=${build.dir}/classes -build.resourceDir=src/main/resources -build.testOutputDir=${build.dir}/test-classes -settings.offline=false -build.dir=target -settings.interactiveMode=true -build.srcDir=src/main/java -build.testDir=NA -build.testResourceDir=NA -test.skip=true -no.tests=true diff --git a/cts2Impl/build.xml b/cts2Impl/build.xml deleted file mode 100755 index bd5917e2d0..0000000000 --- a/cts2Impl/build.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/cts2Impl/ivy.xml b/cts2Impl/ivy.xml deleted file mode 100755 index 3d9a6a1258..0000000000 --- a/cts2Impl/ivy.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/constant/ExternalCts2Constants.java b/cts2Impl/src/main/java/org/cts2/constant/ExternalCts2Constants.java deleted file mode 100644 index 8ee8ff443c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/constant/ExternalCts2Constants.java +++ /dev/null @@ -1,53 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.constant; - -/** - * The Class ExternalCts2Constants. - * - * @author Kevin Peterson - */ -public class ExternalCts2Constants { - - public static final String CONCAT_STRING = ":"; - - public static final String SLASH = "/"; - - public static final String CTS2_URI = "http://cts2.org"; - - public static final String MODEL = "model"; - - public static final String ATTRIBUTE = "attribute"; - - public static final String MA_ENTITY_DESCRIPTION_DESIGNATION_NAME = "entityDescriptionDesignation"; - - public static final String MA_ABOUT_NAME = "about"; - - public static final String MA_MAPVERSION_NAME_MEANING = "MODEL_ATTRIBUTE_ROOT#mapVersion"; - - public static final String MA_MAPVERSION_NAME_CONTENT = "MapVersion"; - - private static final String MODEL_ATTRIBUTE_ROOT = CTS2_URI + SLASH + MODEL + SLASH + ATTRIBUTE; - - public static final String MA_ABOUT_URI = MODEL_ATTRIBUTE_ROOT + CONCAT_STRING + MA_ABOUT_NAME; - - public static final String MA_ENTITY_DESCRIPTION_DESIGNATION_URI = MODEL_ATTRIBUTE_ROOT + CONCAT_STRING + MA_ENTITY_DESCRIPTION_DESIGNATION_NAME; - -} - diff --git a/cts2Impl/src/main/java/org/cts2/internal/lexevs/identity/DefaultLexEvsIdentityConverter.java b/cts2Impl/src/main/java/org/cts2/internal/lexevs/identity/DefaultLexEvsIdentityConverter.java deleted file mode 100644 index fd89dd50d9..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/lexevs/identity/DefaultLexEvsIdentityConverter.java +++ /dev/null @@ -1,373 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.lexevs.identity; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.Core.ConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.ServiceUtility; -import org.LexGrid.codingSchemes.CodingScheme; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.types.DesignationRole; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexevs.system.service.CodingSchemeAliasHolder; -import org.lexevs.system.service.SystemResourceService.CodingSchemeMatcher; - -/** - * The Class LexEvsIdentityConverter. - * - * @author Kevin Peterson - */ -public class DefaultLexEvsIdentityConverter implements LexEvsIdentityConverter { - - /** The DEFAUL t_ nam e_ conca t_ string. */ - public static String DEFAULT_NAME_CONCAT_STRING = ":"; - - /** The DEFAUL t_ ur i_ conca t_ string. */ - public static String DEFAULT_URI_CONCAT_STRING = ":"; - - /** The name concat string. */ - private String nameConcatString = DEFAULT_NAME_CONCAT_STRING; - - /** The uri concat string. */ - private String uriConcatString = DEFAULT_URI_CONCAT_STRING; - - /** The lex big service. */ - public LexBIGService lexBigService; - - private LexEvsServiceLocator lexEvsServiceLocator; - - /* - * (non-Javadoc) - * - * @see org.cts2.internal.lexevs.identity.LexEvsIdentityConverter# - * nameOrUriToAbsoluteCodingSchemeVersionReference - * (org.cts2.service.core.NameOrURI) - */ - @Override - public AbsoluteCodingSchemeVersionReference nameOrUriToAbsoluteCodingSchemeVersionReference( - NameOrURI nameOrUri) { - if (StringUtils.isNotBlank(nameOrUri.getName())) { - return this.codeSystemVersionNameToCodingSchemeReference(nameOrUri - .getName()); - } else { - return this - .codeSystemVersionDocumentUriToCodingSchemeReference(nameOrUri - .getUri()); - } - } - - @Override - public ConceptReference entityNameOrUriToConceptReference( - EntityNameOrURI nameOrUri) { - // TODO Auto-generated method stub - return null; - } - - /* - * (non-Javadoc) - * - * @see org.cts2.internal.lexevs.identity.LexEvsIdentityConverter# - * codeSystemVersionNameToCodingSchemeReference(java.lang.String) - */ - @Override - public AbsoluteCodingSchemeVersionReference codeSystemVersionNameToCodingSchemeReference( - String codeSystemVersionName) { - - return this.getCodeSystemVersionNameMatch(codeSystemVersionName); - } - - @Override - public String codingSchemeToCodeSystemVersionName(CodingScheme codingScheme) { - return this.constructCodeSystemVersionName( - codingScheme.getCodingSchemeName(), - codingScheme.getRepresentsVersion()); - } - - @Override - public String codingSchemeSummaryToCodeSystemVersionName( - CodingSchemeSummary codingSchemeSummary) { - return this.constructCodeSystemVersionName( - codingSchemeSummary.getLocalName(), - codingSchemeSummary.getRepresentsVersion()); - } - - /* - * (non-Javadoc) - * - * @see org.cts2.internal.lexevs.identity.LexEvsIdentityConverter# - * codingSchemeReferenceToCodeSystemVersionName - * (org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference) - */ - @Override - public String codingSchemeReferenceToCodeSystemVersionName( - AbsoluteCodingSchemeVersionReference ref) { - String codingSchemeName; - try { - codingSchemeName = ServiceUtility.getCodingSchemeName( - ref.getCodingSchemeURN(), ref.getCodingSchemeVersion()); - } catch (LBParameterException e) { - throw new RuntimeException(e); - } - return this.constructCodeSystemVersionName(codingSchemeName, - ref.getCodingSchemeVersion()); - } - - /* - * (non-Javadoc) - * - * @see org.cts2.internal.lexevs.identity.LexEvsIdentityConverter# - * codeSystemVersionDocumentUriToCodingSchemeReference(java.lang.String) - */ - @Override - public AbsoluteCodingSchemeVersionReference codeSystemVersionDocumentUriToCodingSchemeReference( - String codeSystemVersionDocumentUri) { - - return this - .getCodeSystemVersionDocumentUriMatch(codeSystemVersionDocumentUri); - } - - @Override - public String codingSchemeToCodeSystemVersionDocumentUri( - CodingScheme codingScheme) { - return this.constructCodeSystemVersionDocumentUri( - codingScheme.getCodingSchemeURI(), - codingScheme.getRepresentsVersion()); - } - - @Override - public String codingSchemeReferenceToCodeSystemVersionDocumentUri( - AbsoluteCodingSchemeVersionReference ref) { - - return this.constructCodeSystemVersionDocumentUri( - ref.getCodingSchemeURN(), ref.getCodingSchemeVersion()); - } - - /** - * Gets the code system version name match. - * - * @param codeSystemVersionLocalName - * the code system version local name - * @return the code system version name match - */ - protected AbsoluteCodingSchemeVersionReference getCodeSystemVersionNameMatch( - final String codeSystemVersionLocalName) { - List result = lexEvsServiceLocator - .getSystemResourceService().getMatchingCodingSchemeResources( - new CodingSchemeMatcher() { - - @Override - public boolean isMatch( - CodingSchemeAliasHolder aliasHolder) { - return StringUtils - .equals(codeSystemVersionLocalName, - constructCodeSystemVersionName( - aliasHolder - .getCodingSchemeName(), - aliasHolder - .getRepresentsVersion())); - } - }); - - if (result.size() != 1) { - throw new RuntimeException( - "Error -- waiting for real CTS2 exceptions..."); - } - - return result.get(0); - } - - /** - * Gets the code system version document uri match. - * - * @param documentUri - * the document uri - * @return the code system version document uri match - */ - protected AbsoluteCodingSchemeVersionReference getCodeSystemVersionDocumentUriMatch( - final String documentUri) { - List result = lexEvsServiceLocator - .getSystemResourceService().getMatchingCodingSchemeResources( - new CodingSchemeMatcher() { - - @Override - public boolean isMatch( - CodingSchemeAliasHolder aliasHolder) { - return StringUtils - .equals(documentUri, - constructCodeSystemVersionDocumentUri( - aliasHolder - .getCodingSchemeName(), - aliasHolder - .getRepresentsVersion())); - } - }); - - if (result.size() != 1) { - throw new RuntimeException( - "Error -- waiting for real CTS2 exceptions..."); - } - - return result.get(0); - } - - /** - * Construct code system version name. - * - * @param codingSchemeName - * the coding scheme name - * @param version - * the version - * @return the string - */ - protected String constructCodeSystemVersionName(String codingSchemeName, - String version) { - return codingSchemeName + nameConcatString + version; - } - - /** - * Construct map version name. - * - * @param codingSchemeName - * the coding scheme name - * @param version - * the version - * @return the string - */ - protected String constructMapVersionName(String codingSchemeName, - String version) { - return codingSchemeName + nameConcatString + version; - } - - /** - * Construct code system version document uri. - * - * @param uri - * the uri - * @param version - * the version - * @return the string - */ - protected String constructCodeSystemVersionDocumentUri(String uri, - String version) { - return uri + uriConcatString + version; - } - - /** - * Gets the name concat string. - * - * @return the name concat string - */ - public String getNameConcatString() { - return nameConcatString; - } - - /** - * Sets the name concat string. - * - * @param nameConcatString - * the new name concat string - */ - public void setNameConcatString(String nameConcatString) { - this.nameConcatString = nameConcatString; - } - - /** - * Gets the uri concat string. - * - * @return the uri concat string - */ - public String getUriConcatString() { - return uriConcatString; - } - - /** - * Sets the uri concat string. - * - * @param uriConcatString - * the new uri concat string - */ - public void setUriConcatString(String uriConcatString) { - this.uriConcatString = uriConcatString; - } - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - public LexBIGService getLexBigService() { - return lexBigService; - } - - /** - * Sets the lex big service. - * - * @param lexBigService - * the new lex big service - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } - - @Override - public String nsUriAndCodeToUri(String nsUri, String code) { - return nsUri + this.uriConcatString + code; - } - - @Override - public DesignationRole preferredtoDestinationRole(boolean b) { - if (b == true) - return DesignationRole.PREFERRED; - else - return DesignationRole.ALTERNATIVE; - } - - @Override - public DefinitionRole preferredtoDefinitionRole(boolean b) { - if (b == true) - return DefinitionRole.NORMATIVE; - else - return DefinitionRole.INFORMATIVE; - } - - public void setLexEvsServiceLocator( - LexEvsServiceLocator lexEvsServiceLocator) { - this.lexEvsServiceLocator = lexEvsServiceLocator; - } - - public LexEvsServiceLocator getLexEvsServiceLocator() { - return lexEvsServiceLocator; - } - - @Override - public String codingSchemeSummaryToMapVersionName( - CodingSchemeSummary codingSchemeSummary) { - return this.constructMapVersionName( - codingSchemeSummary.getLocalName(), - codingSchemeSummary.getRepresentsVersion()); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/lexevs/identity/LexEvsIdentityConverter.java b/cts2Impl/src/main/java/org/cts2/internal/lexevs/identity/LexEvsIdentityConverter.java deleted file mode 100644 index 863b53c4a6..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/lexevs/identity/LexEvsIdentityConverter.java +++ /dev/null @@ -1,76 +0,0 @@ -package org.cts2.internal.lexevs.identity; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.Core.ConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.types.DesignationRole; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; - -public interface LexEvsIdentityConverter { - - /** - * Name or uri to absolute coding scheme version reference. - * - * @param nameOrUri - * the name or uri - * @return the absolute coding scheme version reference - */ - public AbsoluteCodingSchemeVersionReference nameOrUriToAbsoluteCodingSchemeVersionReference( - NameOrURI nameOrUri); - - public ConceptReference entityNameOrUriToConceptReference( - EntityNameOrURI nameOrUri); - - /** - * Code system version name to coding scheme reference. - * - * @param codeSystemVersionName - * the code system version name - * @return the absolute coding scheme version reference - */ - public AbsoluteCodingSchemeVersionReference codeSystemVersionNameToCodingSchemeReference( - String codeSystemVersionName); - - /** - * Coding scheme reference to code system version name. - * - * @param ref - * the ref - * @return the string - */ - public String codingSchemeReferenceToCodeSystemVersionName( - AbsoluteCodingSchemeVersionReference ref); - - public String codingSchemeToCodeSystemVersionName(CodingScheme codingScheme); - - public String codingSchemeSummaryToCodeSystemVersionName( - CodingSchemeSummary codingSchemeSummary); - - public String codingSchemeSummaryToMapVersionName( - CodingSchemeSummary codingSchemeSummary); - - public String codingSchemeReferenceToCodeSystemVersionDocumentUri( - AbsoluteCodingSchemeVersionReference ref); - - /** - * Code system version document uri to coding scheme reference. - * - * @param codeSystemVersionDocumentUri - * the code system version document uri - * @return the absolute coding scheme version reference - */ - public AbsoluteCodingSchemeVersionReference codeSystemVersionDocumentUriToCodingSchemeReference( - String codeSystemVersionDocumentUri); - - public String codingSchemeToCodeSystemVersionDocumentUri( - CodingScheme codingScheme); - - public String nsUriAndCodeToUri(String nsUri, String code); - - public DesignationRole preferredtoDestinationRole(boolean b); - - public DefinitionRole preferredtoDefinitionRole(boolean b); -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/internal/logging/LoggingAspect.java b/cts2Impl/src/main/java/org/cts2/internal/logging/LoggingAspect.java deleted file mode 100644 index a6a5e9e2c5..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/logging/LoggingAspect.java +++ /dev/null @@ -1,74 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.logging; - -import org.LexGrid.LexBIG.Utility.logging.LgLoggerIF; -import org.aspectj.lang.ProceedingJoinPoint; -import org.aspectj.lang.annotation.Around; -import org.aspectj.lang.annotation.Aspect; -import org.aspectj.lang.reflect.MethodSignature; -import org.lexevs.logging.LoggerFactory; - -/** - * The Class LoggingAspect. - * - * @author Kevin Peterson - */ -@Aspect -public class LoggingAspect { - - private LgLoggerIF logger; - - /** - * Log method. - * - * @param pjp the pjp - * @return the object - * @throws Throwable the throwable - */ - @Around("@within(org.cts2.internal.logging.annotation.Loggable) && " + - "( @annotation(org.cts2.internal.logging.annotation.Loggable) )") - public Object logMethod(ProceedingJoinPoint pjp) throws Throwable { - MethodSignature sig = (MethodSignature)pjp.getSignature(); - - String msg = this.logMethod(sig); - - this.logger.info(msg); - - return pjp.proceed(); - } - - /** - * Log method. - * - * @param signature the signature - * @return the string - */ - protected String logMethod(MethodSignature signature){ - return signature.toLongString(); - } - - public void setLogger(LgLoggerIF logger) { - this.logger = logger; - } - - public LgLoggerIF getLogger() { - return logger; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/logging/annotation/Loggable.java b/cts2Impl/src/main/java/org/cts2/internal/logging/annotation/Loggable.java deleted file mode 100644 index cf5bde879f..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/logging/annotation/Loggable.java +++ /dev/null @@ -1,12 +0,0 @@ -package org.cts2.internal.logging.annotation; - -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; - -@Retention(RetentionPolicy.RUNTIME) -@Target({ElementType.METHOD,ElementType.TYPE}) -public @interface Loggable { - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/BaseDozerBeanMapper.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/BaseDozerBeanMapper.java deleted file mode 100644 index 09b1b3587a..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/BaseDozerBeanMapper.java +++ /dev/null @@ -1,58 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper; - -import org.dozer.DozerBeanMapper; - -/** - * The Class BaseDozerBeanMapper. - * - * @author Kevin Peterson - */ -public class BaseDozerBeanMapper implements BeanMapper{ - - /** The dozer bean mapper. */ - private DozerBeanMapper dozerBeanMapper; - - /* (non-Javadoc) - * @see org.cts2.internal.mapper.BeanMapper#map(java.lang.Object, java.lang.Class) - */ - public T map(Object source, Class targetClass){ - return this.dozerBeanMapper.map(source, targetClass); - } - - /** - * Gets the dozer bean mapper. - * - * @return the dozer bean mapper - */ - public DozerBeanMapper getDozerBeanMapper() { - return this.dozerBeanMapper; - } - - /** - * Sets the dozer bean mapper. - * - * @param dozerBeanMapper the new dozer bean mapper - */ - public void setDozerBeanMapper(DozerBeanMapper dozerBeanMapper) { - this.dozerBeanMapper = dozerBeanMapper; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/BeanMapper.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/BeanMapper.java deleted file mode 100644 index 3587069cfb..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/BeanMapper.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper; - -/** - * The Interface BeanMapper. - * - * @author Kevin Peterson - */ -public interface BeanMapper { - - /** - * Map. - * - * @param the - * @param source the source - * @param targetClass the target class - * @return the t - */ - public T map(Object source, Class targetClass); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionAboutConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionAboutConverter.java deleted file mode 100644 index c310848a4c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionAboutConverter.java +++ /dev/null @@ -1,76 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedNamespace; - -import org.apache.commons.lang.StringUtils; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class AnonymousEntityDescriptionAboutConverter extends - DozerConverter { - private CodingSchemeService codingSchemeService; - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public AnonymousEntityDescriptionAboutConverter() { - super(ResolvedConceptReference.class, AnonymousEntityDescription.class); - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - @Override - public ResolvedConceptReference convertFrom(AnonymousEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public AnonymousEntityDescription convertTo(ResolvedConceptReference source, - AnonymousEntityDescription target) { - - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - if (cs != null) { - try { - SupportedNamespace sns = DaoUtility.getURIMap(cs, - SupportedNamespace.class, source.getCodeNamespace()); - String uri; - if (sns != null && !StringUtils.isBlank(sns.getUri())) { - uri = lexEvsIdentityConverter.nsUriAndCodeToUri(sns.getUri(), source.getCode()); - } - else { - uri = lexEvsIdentityConverter.nsUriAndCodeToUri(cs.getCodingSchemeURI(), source.getCode()); - } - target.setAbout(uri); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - return target; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionDefinitionListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionDefinitionListConverter.java deleted file mode 100644 index 029811ae0f..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionDefinitionListConverter.java +++ /dev/null @@ -1,102 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.ContextReference; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class AnonymousEntityDescriptionDefinitionListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public AnonymousEntityDescriptionDefinitionListConverter() { - super(ResolvedConceptReference.class, AnonymousEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(AnonymousEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public AnonymousEntityDescription convertTo(ResolvedConceptReference source, - AnonymousEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.concepts.Definition d : source.getEntity() - .getDefinition()) { - org.cts2.core.Definition definition = this.baseDozerBeanMapper.map( - d, org.cts2.core.Definition.class); - - // process supported mappings - if (cs != null) { - if (definition.getFormat() != null - && !StringUtils.isEmpty(definition.getFormat() - .getContent())) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, definition.getFormat() - .getContent()); - if (supportedDataType != null) - definition.getFormat().setMeaning( - supportedDataType.getUri()); - } - - if (definition.getLanguage() != null - && !StringUtils.isEmpty(definition.getLanguage() - .getContent())) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, definition - .getLanguage().getContent()); - if (supportedLanguage != null) - definition.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - - ContextReference context = definition.getUsageContext(); - if (context != null - && !StringUtils.isEmpty(context.getContent())) { - SupportedContext supportedContext = DaoUtility.getURIMap( - cs, SupportedContext.class, context.getContent()); - if (supportedContext != null) { - context.setMeaning(supportedContext.getUri()); - } - } - } - target.addDefinition(definition); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionDesignationListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionDesignationListConverter.java deleted file mode 100644 index 951bb0098c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionDesignationListConverter.java +++ /dev/null @@ -1,126 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedDegreeOfFidelity; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.SupportedProperty; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.ContextReference; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.hsqldb.lib.StringUtil; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class AnonymousEntityDescriptionDesignationListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public AnonymousEntityDescriptionDesignationListConverter() { - super(ResolvedConceptReference.class, AnonymousEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(AnonymousEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public AnonymousEntityDescription convertTo(ResolvedConceptReference source, - AnonymousEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.concepts.Presentation p : source.getEntity() - .getPresentation()) { - org.cts2.entity.Designation designation = this.baseDozerBeanMapper - .map(p, org.cts2.entity.Designation.class); - - // process supported mappings - if (cs != null) { - if (designation.getDegreeOfFidelity() != null - && !StringUtils.isEmpty(designation - .getDegreeOfFidelity().getContent())) { - SupportedDegreeOfFidelity supportedDegreeOfFidelity = DaoUtility - .getURIMap(cs, SupportedDegreeOfFidelity.class, - designation.getDegreeOfFidelity() - .getContent()); - if (supportedDegreeOfFidelity != null) - designation.getDegreeOfFidelity().setMeaning( - supportedDegreeOfFidelity.getUri()); - } - if (designation.getDesignationType() != null - && !StringUtil.isEmpty(designation.getDesignationType() - .getContent())) { - SupportedProperty supportedProperty = DaoUtility.getURIMap( - cs, SupportedProperty.class, designation - .getDesignationType().getContent()); - if (supportedProperty != null) - designation.getDesignationType().setMeaning( - supportedProperty.getUri()); - } - - if (designation.getFormat() != null - && !StringUtils.isEmpty(designation.getFormat() - .getContent())) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, designation - .getFormat().getContent()); - if (supportedDataType != null) - designation.getFormat().setMeaning( - supportedDataType.getUri()); - } - - if (designation.getLanguage() != null - && !StringUtils.isEmpty(designation.getLanguage() - .getContent())) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, designation - .getLanguage().getContent()); - if (supportedLanguage != null) - designation.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - - for (ContextReference context : designation.getUsageContext()) { - if (!StringUtils.isEmpty(context.getContent())){ - SupportedContext supportedContext = DaoUtility.getURIMap(cs, SupportedContext.class, context.getContent()); - if (supportedContext != null) { - context.setMeaning(supportedContext.getUri()); - } - } - } - } - target.addDesignation(designation); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionNoteListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionNoteListConverter.java deleted file mode 100644 index d5cf6b6e25..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionNoteListConverter.java +++ /dev/null @@ -1,91 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.apache.commons.lang.StringUtils; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class AnonymousEntityDescriptionNoteListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public AnonymousEntityDescriptionNoteListConverter() { - super(ResolvedConceptReference.class, AnonymousEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(AnonymousEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public AnonymousEntityDescription convertTo(ResolvedConceptReference source, - AnonymousEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.concepts.Comment c : source.getEntity() - .getComment()) { - org.cts2.core.Comment comment = this.baseDozerBeanMapper.map( - c, org.cts2.core.Comment.class); - - // process supported mappings - if (cs != null) { - if (comment.getFormat() != null - && !StringUtils.isEmpty(comment.getFormat() - .getContent())) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, comment.getFormat() - .getContent()); - if (supportedDataType != null) - comment.getFormat().setMeaning( - supportedDataType.getUri()); - } - - if (comment.getLanguage() != null - && !StringUtils.isEmpty(comment.getLanguage() - .getContent())) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, comment - .getLanguage().getContent()); - if (supportedLanguage != null) - comment.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - - } - target.addNote(comment); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionPropertyListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionPropertyListConverter.java deleted file mode 100644 index 95b176bd14..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/AnonymousEntityDescriptionPropertyListConverter.java +++ /dev/null @@ -1,90 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.EntryDescription; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class AnonymousEntityDescriptionPropertyListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public AnonymousEntityDescriptionPropertyListConverter() { - super(ResolvedConceptReference.class, AnonymousEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(AnonymousEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public AnonymousEntityDescription convertTo(ResolvedConceptReference source, - AnonymousEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.commonTypes.Property p : source.getEntity() - .getProperty()) { - org.cts2.core.Property ctsProp = this.baseDozerBeanMapper.map(p, - org.cts2.core.Property.class); - - EntryDescription enDesc = ctsProp.getValue(); - // process supported mappings - if (cs != null && enDesc != null) { - if (enDesc.getFormat() != null - && StringUtils.isEmpty(enDesc.getFormat().getContent()) == false) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, enDesc.getFormat() - .getContent()); - if (supportedDataType != null) - enDesc.getFormat().setMeaning( - supportedDataType.getUri()); - } - if (enDesc.getLanguage() != null - && StringUtils.isEmpty(enDesc.getLanguage() - .getContent()) == false) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, enDesc.getLanguage() - .getContent()); - if (supportedLanguage != null) - enDesc.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - } - target.addProperty(ctsProp); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/ChangeTypeConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/ChangeTypeConverter.java deleted file mode 100644 index 738d583765..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/ChangeTypeConverter.java +++ /dev/null @@ -1,90 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.versions.types.ChangeType; -import org.dozer.DozerConverter; - -/** - * The Class ChangeTypeConverter. LexGrid ChangeType <--> CTS2 ChangeType - * - * @author Sridhar Dwarkanath - */ -public class ChangeTypeConverter extends DozerConverter { - - public ChangeTypeConverter() { - super(ChangeType.class, org.cts2.core.types.ChangeType.class); - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertFrom(java.lang.Object, java.lang.Object) - */ - @Override - public ChangeType convertFrom( - org.cts2.core.types.ChangeType cts2ChangeType, - ChangeType lgChangeType) { - if(lgChangeType == null){ - return null; - } - switch (cts2ChangeType) { - case CREATE : { - return ChangeType.NEW; - } - case UPDATE : { - return ChangeType.MODIFY; - } - case DELETE : { - return ChangeType.REMOVE; - } - case METADATA : { - return ChangeType.VERSIONABLE; - } - default : { - throw new RuntimeException(cts2ChangeType + " cannot be mapped."); - } - } - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertTo(java.lang.Object, java.lang.Object) - */ - @Override - public org.cts2.core.types.ChangeType convertTo(ChangeType lgChangeType, org.cts2.core.types.ChangeType cts2ChangeType) { - if(lgChangeType == null){ - return null; - } - switch (lgChangeType) { - case NEW : { - return org.cts2.core.types.ChangeType.CREATE; - } - case MODIFY : { - return org.cts2.core.types.ChangeType.UPDATE; - } - case REMOVE : { - return org.cts2.core.types.ChangeType.DELETE; - } - case VERSIONABLE : { - return org.cts2.core.types.ChangeType.METADATA; - } - default : { - throw new RuntimeException(lgChangeType + " cannot be mapped."); - } - } - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CodeSystemVersionDirectoryEntryIdentityConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CodeSystemVersionDirectoryEntryIdentityConverter.java deleted file mode 100644 index 15f6a8fee5..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CodeSystemVersionDirectoryEntryIdentityConverter.java +++ /dev/null @@ -1,74 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.cts2.codesystemversion.CodeSystemVersionDirectoryEntry; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; - -/** - * The Class DefinitionOperatorToSetOperatorConverter. - * - * @author Kevin Peterson - */ -public class CodeSystemVersionDirectoryEntryIdentityConverter extends DozerConverter { - - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public CodeSystemVersionDirectoryEntryIdentityConverter() { - super(CodingSchemeRendering.class, CodeSystemVersionDirectoryEntry.class); - } - - @Override - public CodingSchemeRendering convertFrom(CodeSystemVersionDirectoryEntry codeSystemVersionDirectoryEntry, - CodingSchemeRendering codingSchemeRendering) { - return null; - } - - @Override - public CodeSystemVersionDirectoryEntry convertTo(CodingSchemeRendering codingSchemeRendering, - CodeSystemVersionDirectoryEntry codeSystemVersionDirectoryEntry) { - - String codeSystemVersionDirectoryEntryName = this.lexEvsIdentityConverter. - codingSchemeReferenceToCodeSystemVersionName( - Constructors.createAbsoluteCodingSchemeVersionReference(codingSchemeRendering.getCodingSchemeSummary())); - - String codeSystemVersionDocumentUri = this.lexEvsIdentityConverter. - codingSchemeReferenceToCodeSystemVersionDocumentUri( - Constructors.createAbsoluteCodingSchemeVersionReference(codingSchemeRendering.getCodingSchemeSummary())); - - codeSystemVersionDirectoryEntry.setCodeSystemVersionName(codeSystemVersionDirectoryEntryName); - codeSystemVersionDirectoryEntry.setResourceName(codeSystemVersionDirectoryEntryName); - codeSystemVersionDirectoryEntry.setDocumentURI(codeSystemVersionDocumentUri); - codeSystemVersionDirectoryEntry.setResourceID(codeSystemVersionDocumentUri); - - return codeSystemVersionDirectoryEntry; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CodeSystemVersionIdentityConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CodeSystemVersionIdentityConverter.java deleted file mode 100644 index 3c15dcf6ad..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CodeSystemVersionIdentityConverter.java +++ /dev/null @@ -1,68 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.codingSchemes.CodingScheme; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; - -/** - * The Class DefinitionOperatorToSetOperatorConverter. - * - * @author Kevin Peterson - */ -public class CodeSystemVersionIdentityConverter extends DozerConverter { - - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public CodeSystemVersionIdentityConverter() { - super(CodingScheme.class, CodeSystemVersion.class); - } - - @Override - public CodingScheme convertFrom(CodeSystemVersion csv, CodingScheme cs) { - //this.lexEvsIdentityConverter.codingSchemeToCodeSystemVersionName(cs); - return null; - } - - @Override - public CodeSystemVersion convertTo(CodingScheme cs, CodeSystemVersion csv) { - String codeSystemVersionName = - this.lexEvsIdentityConverter.codingSchemeToCodeSystemVersionName(cs); - - String codeSystemVersionDocumentUri = - this.lexEvsIdentityConverter.codingSchemeToCodeSystemVersionDocumentUri(cs); - - csv.setCodeSystemVersionName(codeSystemVersionName); - csv.setDocumentURI(codeSystemVersionDocumentUri); - - return csv; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CopyrightConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CopyrightConverter.java deleted file mode 100644 index f2049a4cff..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/CopyrightConverter.java +++ /dev/null @@ -1,87 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.URIMap; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.core.DataTypeReference; -import org.cts2.core.OpaqueData; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.utility.DaoUtility; - -/** - * The Class DefinitionOperatorToSetOperatorConverter. - * - * @author Kevin Peterson - */ -public class CopyrightConverter extends DozerConverter { - - public CopyrightConverter() { - super(CodingScheme.class, CodeSystemVersion.class); - } - - @Override - public CodingScheme convertFrom(CodeSystemVersion csv, CodingScheme cs) { - // TODO Auto-generated method stub - return null; - } - - @Override - public CodeSystemVersion convertTo(CodingScheme cs, CodeSystemVersion csv) { - Text copyright = cs.getCopyright(); - - if(copyright == null){ - return csv; - } - - if(csv == null){ - csv = new CodeSystemVersion(); - } - - OpaqueData od = new OpaqueData(); - od.setValue(copyright.getContent()); - csv.setRights(od); - - String datatype = cs.getCopyright().getDataType(); - - if(datatype != null){ - - try { - URIMap uriMap = - DaoUtility.getURIMap(cs, SupportedDataType.class, datatype); - - DataTypeReference dataTypeRef = new DataTypeReference(); - dataTypeRef.setContent(uriMap.getLocalId()); - dataTypeRef.setHref(uriMap.getUri()); - - csv.getRights().setFormat(dataTypeRef); - - } catch (Exception e) { - throw new RuntimeException(e); - } - } - - csv.setRights(od); - - return csv; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefaultLanguageConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefaultLanguageConverter.java deleted file mode 100644 index 40d1df138c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefaultLanguageConverter.java +++ /dev/null @@ -1,80 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.URIMap; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.core.LanguageReference; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.utility.DaoUtility; - -/** - * The Class DefinitionOperatorToSetOperatorConverter. - * - * @author Kevin Peterson - */ -public class DefaultLanguageConverter extends DozerConverter { - - public DefaultLanguageConverter() { - super(CodingScheme.class, CodeSystemVersion.class); - } - - @Override - public CodingScheme convertFrom(CodeSystemVersion csv, CodingScheme cs) { - // TODO Auto-generated method stub - return null; - } - - @Override - public CodeSystemVersion convertTo(CodingScheme cs, CodeSystemVersion csv) { - String language = cs.getDefaultLanguage(); - - if(language == null){ - return csv; - } - - if(csv == null){ - csv = new CodeSystemVersion(); - } - - try { - URIMap uriMap = - DaoUtility.getURIMap(cs, SupportedLanguage.class, language); - - if(uriMap == null){ - return csv; - } - - LanguageReference languageRef = new LanguageReference(); - languageRef.setContent(uriMap.getLocalId()); - languageRef.setHref(uriMap.getUri()); - - languageRef.setContent(language); - - csv.setDefaultLanguage(languageRef); - - } catch (Exception e) { - throw new RuntimeException(e); - } - - return csv; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionEntryToValueSetDefinitionEntryConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionEntryToValueSetDefinitionEntryConverter.java deleted file mode 100644 index c53957dabe..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionEntryToValueSetDefinitionEntryConverter.java +++ /dev/null @@ -1,215 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.valueSets.DefinitionEntry; -import org.LexGrid.valueSets.EntityReference; -import org.LexGrid.valueSets.PropertyReference; -import org.cts2.core.CodeSystemReference; -import org.cts2.core.FilterComponent; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.NameOrURI; -import org.cts2.core.PredicateReference; -import org.cts2.core.ScopedEntityName; -import org.cts2.core.ValueSetReference; -import org.cts2.core.types.SetOperator; -import org.cts2.core.types.TargetReferenceType; -import org.cts2.valueset.AssociatedEntitiesReference; -import org.cts2.valueset.CompleteCodeSystemReference; -import org.cts2.valueset.CompleteValueSetReference; -import org.cts2.valueset.PropertyQueryReference; -import org.cts2.valueset.ValueSetDefinitionEntry; -import org.cts2.valueset.types.AssociationDirection; -import org.cts2.valueset.types.LeafOrAll; -import org.cts2.valueset.types.TransitiveClosure; -import org.cts2.valueset.types.ValueSetDefinitionEntryType; -import org.dozer.DozerConverter; - -/** - * The Class DefinitionEntryToValueSetDefinitionEntryConverter. - * - * @author Sridhar Dwarkanath - */ -public class DefinitionEntryToValueSetDefinitionEntryConverter extends DozerConverter { - - private DefinitionOperatorToSetOperatorConverter definitionOperatorToSetOperatorConverter; - - public DefinitionEntryToValueSetDefinitionEntryConverter() { - super(DefinitionEntry.class, ValueSetDefinitionEntry.class); - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertTo(java.lang.Object, java.lang.Object) - */ - @Override - public ValueSetDefinitionEntry convertTo(DefinitionEntry definitionEntry, - ValueSetDefinitionEntry valueSetDefinitionEntry) { - if (definitionOperatorToSetOperatorConverter == null) - definitionOperatorToSetOperatorConverter = new DefinitionOperatorToSetOperatorConverter(); - - ValueSetDefinitionEntry vde = null; - if (definitionEntry.getCodingSchemeReference() != null) - { - CompleteCodeSystemReference csRef = new CompleteCodeSystemReference(); - CodeSystemReference cs = new CodeSystemReference(); - cs.setContent(definitionEntry.getCodingSchemeReference().getCodingScheme()); - csRef.setCodeSystem(cs); - - csRef.setEntryType(ValueSetDefinitionEntryType.COMPLETE_CODE_SYSTEM); - - csRef.setOperator(this.definitionOperatorToSetOperatorConverter.convertTo(definitionEntry.getOperator())); - - return csRef; - } else if (definitionEntry.getValueSetDefinitionReference() != null) - { - CompleteValueSetReference vsRef = new CompleteValueSetReference(); - - ValueSetReference vs = new ValueSetReference(); - vs.setContent(definitionEntry.getValueSetDefinitionReference().getValueSetDefinitionURI()); - vsRef.setValueSet(vs); - vsRef.setValueSetDefinition(vs); - - vsRef.setEntryType(ValueSetDefinitionEntryType.COMPLETE_VALUE_SET); - - vsRef.setOperator(this.definitionOperatorToSetOperatorConverter.convertTo(definitionEntry.getOperator())); - - return vsRef; - } else if (definitionEntry.getEntityReference() != null) - { - EntityReference lgER = definitionEntry.getEntityReference(); - AssociatedEntitiesReference aeRef = new AssociatedEntitiesReference(); - - CodeSystemReference cs = new CodeSystemReference(); - cs.setContent(lgER.getEntityCodeNamespace()); - aeRef.setCodeSystem(cs); - - // set directional - if (lgER.getTargetToSource() != null) - { - if (lgER.isTargetToSource()) - aeRef.setDirection(AssociationDirection.TARGET_TO_SOURCE); - else - aeRef.setDirection(AssociationDirection.SOURCE_TO_TARGET); - } - - - // set leafOnly - if (lgER.getLeafOnly() != null) - { - if (lgER.isLeafOnly()) - aeRef.setLeafOnly(LeafOrAll.LEAF_ONLY); - else - aeRef.setLeafOnly(LeafOrAll.ALL_INTERMEDIATE_NODES); - } - - // set predicate - PredicateReference pr = new PredicateReference(); - pr.setContent(lgER.getReferenceAssociation()); - aeRef.setPredicate(pr); - - // set referenceEntity - org.cts2.core.EntityReference er = new org.cts2.core.EntityReference(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName(lgER.getEntityCode()); - entityName.setNamespace(lgER.getEntityCodeNamespace()); - er.setLocalEntityName(entityName); - aeRef.setReferencedEntity(er); - - // set transitivity - if (lgER.getTransitiveClosure() != null) - { - if (lgER.isTransitiveClosure()) - aeRef.setTransitivity(TransitiveClosure.TRANSITIVE_CLOSURE); - else - aeRef.setTransitivity(TransitiveClosure.DIRECTLY_ASSOCIATED); - } - - aeRef.setEntryType(ValueSetDefinitionEntryType.ASSOCIATED_ENTITIES); - - aeRef.setOperator(this.definitionOperatorToSetOperatorConverter.convertTo(definitionEntry.getOperator())); - - return aeRef; - } else if (definitionEntry.getPropertyReference() != null) - { - PropertyReference lgPropRef = definitionEntry.getPropertyReference(); - PropertyQueryReference propQueryRef = new PropertyQueryReference(); - - CodeSystemReference cs = new CodeSystemReference(); - cs.setContent(lgPropRef.getCodingScheme()); - - propQueryRef.setCodeSystem(cs); - - FilterComponent fc = new FilterComponent(); - - if (lgPropRef.getPropertyName() != null) - { - org.cts2.core.PropertyReference propRef = new org.cts2.core.PropertyReference(); - NameOrURI nameOrURI = new NameOrURI(); - nameOrURI.setName(lgPropRef.getPropertyName()); - propRef.setReferenceType(TargetReferenceType.PROPERTY); - - fc.setFilterComponent(propRef); - } - - if (lgPropRef.getPropertyMatchValue() != null) - { - MatchAlgorithmReference matchRef = new MatchAlgorithmReference(); - matchRef.setContent(lgPropRef.getPropertyMatchValue().getMatchAlgorithm()); - - fc.setMatchAlgorithm(matchRef); - fc.setMatchValue(lgPropRef.getPropertyMatchValue().getContent()); - } - - propQueryRef.setFilter(fc); - - propQueryRef.setEntryType(ValueSetDefinitionEntryType.PROPERTY_QUERY); - - propQueryRef.setOperator(this.definitionOperatorToSetOperatorConverter.convertTo(definitionEntry.getOperator())); - - return propQueryRef; - } - return vde; - } - - /* - * (non-Javadoc) - * @see org.dozer.DozerConverter#convertFrom(java.lang.Object, java.lang.Object) - */ - @Override - public DefinitionEntry convertFrom(ValueSetDefinitionEntry valueSetDefinitionEntry, - DefinitionEntry definitionEntry) { - // TODO Auto-generated method stub - return null; - } - - /** - * @return the definitionOperatorToSetOperatorConverter - */ - public DefinitionOperatorToSetOperatorConverter getDefinitionOperatorToSetOperatorConverter() { - return definitionOperatorToSetOperatorConverter; - } - - /** - * @param definitionOperatorToSetOperatorConverter the definitionOperatorToSetOperatorConverter to set - */ - public void setDefinitionOperatorToSetOperatorConverter( - DefinitionOperatorToSetOperatorConverter definitionOperatorToSetOperatorConverter) { - this.definitionOperatorToSetOperatorConverter = definitionOperatorToSetOperatorConverter; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionOperatorToSetOperatorConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionOperatorToSetOperatorConverter.java deleted file mode 100644 index 345bd98c6c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionOperatorToSetOperatorConverter.java +++ /dev/null @@ -1,79 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.valueSets.types.DefinitionOperator; -import org.cts2.core.types.SetOperator; -import org.dozer.DozerConverter; - -/** - * The Class DefinitionOperatorToSetOperatorConverter. - * - * @author Kevin Peterson - */ -public class DefinitionOperatorToSetOperatorConverter extends DozerConverter { - - public DefinitionOperatorToSetOperatorConverter() { - super(DefinitionOperator.class, SetOperator.class); - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertFrom(java.lang.Object, java.lang.Object) - */ - @Override - public DefinitionOperator convertFrom( - SetOperator setOperator, - DefinitionOperator definitionOperator) { - switch (setOperator) { - case UNION : { - return DefinitionOperator.OR; - } - case INTERSECT : { - return DefinitionOperator.AND; - } - case SUBTRACT : { - return DefinitionOperator.SUBTRACT; - } - default : { - throw new RuntimeException(setOperator + " cannot be mapped."); - } - } - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertTo(java.lang.Object, java.lang.Object) - */ - @Override - public SetOperator convertTo(DefinitionOperator definitionOperator, SetOperator convertFrom) { - switch (definitionOperator) { - case OR : { - return SetOperator.UNION; - } - case AND : { - return SetOperator.INTERSECT; - } - case SUBTRACT : { - return SetOperator.SUBTRACT; - } - default : { - throw new RuntimeException(definitionOperator + " cannot be mapped."); - } - } - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionPreferredToDefinitionRoleConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionPreferredToDefinitionRoleConverter.java deleted file mode 100644 index 2378084c39..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionPreferredToDefinitionRoleConverter.java +++ /dev/null @@ -1,41 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.concepts.Definition; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; - -public class DefinitionPreferredToDefinitionRoleConverter extends - DozerConverter { - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public DefinitionPreferredToDefinitionRoleConverter() { - super(org.LexGrid.concepts.Definition.class, org.cts2.core.Definition.class); - } - - @Override - public org.cts2.core.Definition convertTo(org.LexGrid.concepts.Definition source, org.cts2.core.Definition destination) { - boolean b; - if (source.getIsPreferred() == null) - b= false; - else - b = source.getIsPreferred(); - destination.setDefinitionRole(this.lexEvsIdentityConverter - .preferredtoDefinitionRole(b)); - return destination; - } - - @Override - public Definition convertFrom(org.cts2.core.Definition arg0, org.LexGrid.concepts.Definition arg1) { - return null; - } - - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionUsageContextListToContextReferenceListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionUsageContextListToContextReferenceListConverter.java deleted file mode 100644 index 10ef4a0188..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/DefinitionUsageContextListToContextReferenceListConverter.java +++ /dev/null @@ -1,30 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.cts2.core.ContextReference; -import org.dozer.DozerConverter; - -public class DefinitionUsageContextListToContextReferenceListConverter extends DozerConverter{ - - public DefinitionUsageContextListToContextReferenceListConverter() { - super(org.LexGrid.concepts.Definition.class, org.cts2.core.Definition.class); - } - - @Override - public org.cts2.core.Definition convertTo(org.LexGrid.concepts.Definition source, org.cts2.core.Definition destination) { - for (String content: source.getUsageContext()) { - ContextReference context = new ContextReference(); - context.setContent(content); - //TODO not an array??? - destination.setUsageContext(context); - break; - } - return destination; - } - - @Override - public org.LexGrid.concepts.Definition convertFrom(org.cts2.core.Definition source, org.LexGrid.concepts.Definition destination) { - return null; - } - - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/EntityDirectoryEntryAboutConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/EntityDirectoryEntryAboutConverter.java deleted file mode 100644 index ae94a23414..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/EntityDirectoryEntryAboutConverter.java +++ /dev/null @@ -1,84 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedNamespace; -import org.apache.commons.lang.StringUtils; -import org.cts2.entity.EntityDirectoryEntry; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -/** - * - * @author Zonghui Lian - * - */ -public class EntityDirectoryEntryAboutConverter extends - DozerConverter { - - private CodingSchemeService codingSchemeService; - private LexEvsIdentityConverter lexEvsIdentityConverter; - - - public EntityDirectoryEntryAboutConverter() { - super(ResolvedConceptReference.class, EntityDirectoryEntry.class); - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - @Override - public ResolvedConceptReference convertFrom(EntityDirectoryEntry arg0, - ResolvedConceptReference arg1) { - return null; - } - - @Override - public EntityDirectoryEntry convertTo(ResolvedConceptReference conRef, - EntityDirectoryEntry dirEntry) { - - if (StringUtils.isBlank(conRef.getCode()) - || StringUtils.isBlank(conRef.getCodeNamespace())) { - return dirEntry; - } - - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - conRef.getCodingSchemeURI(), conRef.getCodingSchemeVersion()); - - if (cs != null) { - try { - SupportedNamespace sns = DaoUtility.getURIMap(cs, - SupportedNamespace.class, conRef.getCodeNamespace()); - String uri; - if (sns != null && !StringUtils.isBlank(sns.getUri())) { - uri = lexEvsIdentityConverter.nsUriAndCodeToUri(sns.getUri(), conRef.getCode()); - } - else { - uri = lexEvsIdentityConverter.nsUriAndCodeToUri(cs.getCodingSchemeURI(), conRef.getCode()); - } - dirEntry.setAbout(uri); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - - return dirEntry; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/IsActiveToEntryStateConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/IsActiveToEntryStateConverter.java deleted file mode 100644 index a05f6dfaae..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/IsActiveToEntryStateConverter.java +++ /dev/null @@ -1,70 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.mapper.converter; - -import org.cts2.core.types.EntryState; -import org.dozer.DozerConverter; - -/** - * The Class IsActiveToEntryStateConverter. - * - * @author Kevin Peterson - */ -public class IsActiveToEntryStateConverter extends DozerConverter{ - - /** - * Instantiates a new checks if is active to entry state converter. - */ - public IsActiveToEntryStateConverter() { - super(Boolean.class, EntryState.class); - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertFrom(java.lang.Object, java.lang.Object) - */ - @Override - public Boolean convertFrom(EntryState es, Boolean bl) { - if(es == null){ - return null; - } - - switch (es){ - case ACTIVE :{ return true ; } - case INACTIVE :{ return true ; } - default : { throw new IllegalArgumentException("Could not map EntryState"); } - } - } - - /* (non-Javadoc) - * @see org.dozer.DozerConverter#convertTo(java.lang.Object, java.lang.Object) - */ - @Override - public EntryState convertTo(Boolean bl, EntryState es) { - if(bl == null){ - return null; - } - - if(bl){ - return EntryState.ACTIVE; - } else { - return EntryState.INACTIVE; - } - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionAboutConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionAboutConverter.java deleted file mode 100644 index e6b982f936..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionAboutConverter.java +++ /dev/null @@ -1,76 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedNamespace; - -import org.apache.commons.lang.StringUtils; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class NamedEntityDescriptionAboutConverter extends - DozerConverter { - private CodingSchemeService codingSchemeService; - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public NamedEntityDescriptionAboutConverter() { - super(ResolvedConceptReference.class, NamedEntityDescription.class); - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - @Override - public ResolvedConceptReference convertFrom(NamedEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public NamedEntityDescription convertTo(ResolvedConceptReference source, - NamedEntityDescription target) { - - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - if (cs != null) { - try { - SupportedNamespace sns = DaoUtility.getURIMap(cs, - SupportedNamespace.class, source.getCodeNamespace()); - String uri; - if (sns != null && !StringUtils.isBlank(sns.getUri())) { - uri = lexEvsIdentityConverter.nsUriAndCodeToUri(sns.getUri(), source.getCode()); - } - else { - uri = lexEvsIdentityConverter.nsUriAndCodeToUri(cs.getCodingSchemeURI(), source.getCode()); - } - target.setAbout(uri); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - return target; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionDefinitionListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionDefinitionListConverter.java deleted file mode 100644 index daec1cb159..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionDefinitionListConverter.java +++ /dev/null @@ -1,102 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.ContextReference; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class NamedEntityDescriptionDefinitionListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public NamedEntityDescriptionDefinitionListConverter() { - super(ResolvedConceptReference.class, NamedEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(NamedEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public NamedEntityDescription convertTo(ResolvedConceptReference source, - NamedEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.concepts.Definition d : source.getEntity() - .getDefinition()) { - org.cts2.core.Definition definition = this.baseDozerBeanMapper.map( - d, org.cts2.core.Definition.class); - - // process supported mappings - if (cs != null) { - if (definition.getFormat() != null - && !StringUtils.isEmpty(definition.getFormat() - .getContent())) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, definition.getFormat() - .getContent()); - if (supportedDataType != null) - definition.getFormat().setMeaning( - supportedDataType.getUri()); - } - - if (definition.getLanguage() != null - && !StringUtils.isEmpty(definition.getLanguage() - .getContent())) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, definition - .getLanguage().getContent()); - if (supportedLanguage != null) - definition.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - - ContextReference context = definition.getUsageContext(); - if (context != null - && !StringUtils.isEmpty(context.getContent())) { - SupportedContext supportedContext = DaoUtility.getURIMap( - cs, SupportedContext.class, context.getContent()); - if (supportedContext != null) { - context.setMeaning(supportedContext.getUri()); - } - } - } - target.addDefinition(definition); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionDesignationListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionDesignationListConverter.java deleted file mode 100644 index 04d6a03e6b..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionDesignationListConverter.java +++ /dev/null @@ -1,126 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedDegreeOfFidelity; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.SupportedProperty; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.ContextReference; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.hsqldb.lib.StringUtil; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class NamedEntityDescriptionDesignationListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public NamedEntityDescriptionDesignationListConverter() { - super(ResolvedConceptReference.class, NamedEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(NamedEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public NamedEntityDescription convertTo(ResolvedConceptReference source, - NamedEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.concepts.Presentation p : source.getEntity() - .getPresentation()) { - org.cts2.entity.Designation designation = this.baseDozerBeanMapper - .map(p, org.cts2.entity.Designation.class); - - // process supported mappings - if (cs != null) { - if (designation.getDegreeOfFidelity() != null - && !StringUtils.isEmpty(designation - .getDegreeOfFidelity().getContent())) { - SupportedDegreeOfFidelity supportedDegreeOfFidelity = DaoUtility - .getURIMap(cs, SupportedDegreeOfFidelity.class, - designation.getDegreeOfFidelity() - .getContent()); - if (supportedDegreeOfFidelity != null) - designation.getDegreeOfFidelity().setMeaning( - supportedDegreeOfFidelity.getUri()); - } - if (designation.getDesignationType() != null - && !StringUtil.isEmpty(designation.getDesignationType() - .getContent())) { - SupportedProperty supportedProperty = DaoUtility.getURIMap( - cs, SupportedProperty.class, designation - .getDesignationType().getContent()); - if (supportedProperty != null) - designation.getDesignationType().setMeaning( - supportedProperty.getUri()); - } - - if (designation.getFormat() != null - && !StringUtils.isEmpty(designation.getFormat() - .getContent())) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, designation - .getFormat().getContent()); - if (supportedDataType != null) - designation.getFormat().setMeaning( - supportedDataType.getUri()); - } - - if (designation.getLanguage() != null - && !StringUtils.isEmpty(designation.getLanguage() - .getContent())) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, designation - .getLanguage().getContent()); - if (supportedLanguage != null) - designation.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - - for (ContextReference context : designation.getUsageContext()) { - if (!StringUtils.isEmpty(context.getContent())){ - SupportedContext supportedContext = DaoUtility.getURIMap(cs, SupportedContext.class, context.getContent()); - if (supportedContext != null) { - context.setMeaning(supportedContext.getUri()); - } - } - } - } - target.addDesignation(designation); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionNoteListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionNoteListConverter.java deleted file mode 100644 index 65be720f72..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionNoteListConverter.java +++ /dev/null @@ -1,91 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.apache.commons.lang.StringUtils; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class NamedEntityDescriptionNoteListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public NamedEntityDescriptionNoteListConverter() { - super(ResolvedConceptReference.class, NamedEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(NamedEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public NamedEntityDescription convertTo(ResolvedConceptReference source, - NamedEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.concepts.Comment c : source.getEntity() - .getComment()) { - org.cts2.core.Comment comment = this.baseDozerBeanMapper.map( - c, org.cts2.core.Comment.class); - - // process supported mappings - if (cs != null) { - if (comment.getFormat() != null - && !StringUtils.isEmpty(comment.getFormat() - .getContent())) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, comment.getFormat() - .getContent()); - if (supportedDataType != null) - comment.getFormat().setMeaning( - supportedDataType.getUri()); - } - - if (comment.getLanguage() != null - && !StringUtils.isEmpty(comment.getLanguage() - .getContent())) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, comment - .getLanguage().getContent()); - if (supportedLanguage != null) - comment.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - - } - target.addNote(comment); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionPropertyListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionPropertyListConverter.java deleted file mode 100644 index 7b4773ecef..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/NamedEntityDescriptionPropertyListConverter.java +++ /dev/null @@ -1,90 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.EntryDescription; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.dozer.DozerConverter; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; -import org.lexevs.dao.database.utility.DaoUtility; - -public class NamedEntityDescriptionPropertyListConverter extends - DozerConverter { - - private BaseDozerBeanMapper baseDozerBeanMapper; - private CodingSchemeService codingSchemeService; - - public NamedEntityDescriptionPropertyListConverter() { - super(ResolvedConceptReference.class, NamedEntityDescription.class); - } - - public BaseDozerBeanMapper getBaseDozerBeanMapper() { - return baseDozerBeanMapper; - } - - public void setBaseDozerBeanMapper(BaseDozerBeanMapper baseDozerBeanMapper) { - this.baseDozerBeanMapper = baseDozerBeanMapper; - } - - @Override - public ResolvedConceptReference convertFrom(NamedEntityDescription source, - ResolvedConceptReference target) { - return null; - } - - @Override - public NamedEntityDescription convertTo(ResolvedConceptReference source, - NamedEntityDescription target) { - if (StringUtils.isBlank(source.getCode()) - || StringUtils.isBlank(source.getCodeNamespace())) { - return target; - } - CodingScheme cs = codingSchemeService.getCodingSchemeByUriAndVersion( - source.getCodingSchemeURI(), source.getCodingSchemeVersion()); - - for (org.LexGrid.commonTypes.Property p : source.getEntity() - .getProperty()) { - org.cts2.core.Property ctsProp = this.baseDozerBeanMapper.map(p, - org.cts2.core.Property.class); - - EntryDescription enDesc = ctsProp.getValue(); - // process supported mappings - if (cs != null && enDesc != null) { - if (enDesc.getFormat() != null - && StringUtils.isEmpty(enDesc.getFormat().getContent()) == false) { - SupportedDataType supportedDataType = DaoUtility.getURIMap( - cs, SupportedDataType.class, enDesc.getFormat() - .getContent()); - if (supportedDataType != null) - enDesc.getFormat().setMeaning( - supportedDataType.getUri()); - } - if (enDesc.getLanguage() != null - && StringUtils.isEmpty(enDesc.getLanguage() - .getContent()) == false) { - SupportedLanguage supportedLanguage = DaoUtility.getURIMap( - cs, SupportedLanguage.class, enDesc.getLanguage() - .getContent()); - if (supportedLanguage != null) - enDesc.getLanguage().setMeaning( - supportedLanguage.getUri()); - } - } - target.addProperty(ctsProp); - } - return target; - } - - public void setCodingSchemeService(CodingSchemeService codingSchemeService) { - this.codingSchemeService = codingSchemeService; - } - - public CodingSchemeService getCodingSchemeService() { - return codingSchemeService; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/PresentationPreferredToDesignationRoleConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/PresentationPreferredToDesignationRoleConverter.java deleted file mode 100644 index 9e4b6bf03a..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/PresentationPreferredToDesignationRoleConverter.java +++ /dev/null @@ -1,42 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.concepts.Presentation; -import org.cts2.entity.Designation; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.dozer.DozerConverter; - -public class PresentationPreferredToDesignationRoleConverter extends - DozerConverter { - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public PresentationPreferredToDesignationRoleConverter() { - super(Presentation.class, Designation.class); - } - - @Override - public Designation convertTo(Presentation source, Designation destination) { - boolean b; - if (source.getIsPreferred() == null) - b= false; - else - b = source.getIsPreferred(); - destination.setDesignationRole(this.lexEvsIdentityConverter - .preferredtoDestinationRole(b)); - return destination; - } - - @Override - public Presentation convertFrom(Designation source, Presentation destination) { - return null; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/PresentationUsageContextListToContextReferenceListConverter.java b/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/PresentationUsageContextListToContextReferenceListConverter.java deleted file mode 100644 index e214804328..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/mapper/converter/PresentationUsageContextListToContextReferenceListConverter.java +++ /dev/null @@ -1,30 +0,0 @@ -package org.cts2.internal.mapper.converter; - -import org.LexGrid.concepts.Presentation; -import org.cts2.core.ContextReference; -import org.cts2.entity.Designation; -import org.dozer.DozerConverter; - -public class PresentationUsageContextListToContextReferenceListConverter extends DozerConverter{ - - public PresentationUsageContextListToContextReferenceListConverter() { - super(Presentation.class, Designation.class); - } - - @Override - public Designation convertTo(Presentation source, Designation destination) { - for (String content: source.getUsageContext()) { - ContextReference context = new ContextReference(); - context.setContent(content); - destination.addUsageContext(context); - } - return destination; - } - - @Override - public Presentation convertFrom(Designation source, Presentation destination) { - return null; - } - - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/AbstractMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/AbstractMatcher.java deleted file mode 100644 index a5b992cc2b..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/AbstractMatcher.java +++ /dev/null @@ -1,81 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import org.cts2.internal.match.BaseCompositeMatchAlgorithm.Matcher; - -/** - * The Class AbstractMatcher. - * - * @author Kevin Peterson - */ -public abstract class AbstractMatcher implements Matcher { - - /** The case sensitive. */ - private boolean caseSensitive = false; - - /** The N o_ match. */ - protected static float NO_MATCH = 0f; - - /** The EXAC t_ match. */ - protected static float EXACT_MATCH = 1f; - - /* (non-Javadoc) - * @see org.cts2.internal.match.BaseMatchAlgorithm.Matcher#isMatch(java.lang.String, java.lang.String) - */ - @Override - public float matchScore(String matchText, String candidate) { - //TODO: null check, validation, etc.. - matchText = matchText.trim(); - candidate = candidate.trim(); - - if(this.caseSensitive){ - return this.doMatchScore(matchText, candidate); - } else { - return this.doMatchScore(matchText.toLowerCase(), candidate.toLowerCase()); - } - } - - /** - * Do is match. - * - * @param matchText the match text - * @param cadidate the cadidate - * @return true, if successful - */ - protected abstract float doMatchScore(String matchText, String cadidate); - - /** - * Sets the case sensitive. - * - * @param caseSensitive the new case sensitive - */ - public void setCaseSensitive(boolean caseSensitive) { - this.caseSensitive = caseSensitive; - } - - /** - * Checks if is case sensitive. - * - * @return true, if is case sensitive - */ - public boolean isCaseSensitive() { - return caseSensitive; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/AbstractNonScoringMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/AbstractNonScoringMatcher.java deleted file mode 100644 index e111025d14..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/AbstractNonScoringMatcher.java +++ /dev/null @@ -1,68 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -/** - * The Class AbstractMatcher. - * - * @author Kevin Peterson - */ -public abstract class AbstractNonScoringMatcher extends AbstractMatcher { - - /** The N o_ match. */ - protected static float NO_MATCH = 0f; - - /** The EXAC t_ match. */ - protected static float EXACT_MATCH = 1f; - - /** - * Boolean to score. - * - * @param isMatch the is match - * @return the float - */ - private float booleanToScore(boolean isMatch){ - if(isMatch){ - return EXACT_MATCH; - } else { - return NO_MATCH; - } - } - - /** - * Do is match. - * - * @param matchText the match text - * @param cadidate the cadidate - * @return true, if successful - */ - protected float doMatchScore(String matchText, String cadidate){ - return this.booleanToScore( - this.isMatch(matchText, cadidate)); - } - - /** - * Checks if is match. - * - * @param matchText the match text - * @param cadidate the cadidate - * @return true, if is match - */ - protected abstract boolean isMatch(String matchText, String cadidate); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/AttributeResolver.java b/cts2Impl/src/main/java/org/cts2/internal/match/AttributeResolver.java deleted file mode 100644 index cafcf32949..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/AttributeResolver.java +++ /dev/null @@ -1,40 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import java.io.Serializable; - - -/** - * The Interface AttributeResolver. - * - * @param the - * @author Kevin Peterson - */ -public interface AttributeResolver extends Serializable { - - /** - * Resolve attribute. - * - * @param modelObject the model object - * @return the string - */ - public String resolveAttribute(T modelObject); - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/BaseCompositeMatchAlgorithm.java b/cts2Impl/src/main/java/org/cts2/internal/match/BaseCompositeMatchAlgorithm.java deleted file mode 100644 index e03732852a..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/BaseCompositeMatchAlgorithm.java +++ /dev/null @@ -1,76 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -/** - * The Class AbstractMatchAlgorithm. - * - * @author Kevin Peterson - */ -public class BaseCompositeMatchAlgorithm implements MatchAlgorithm { - - /** The name. */ - private String name; - - /** The algorithm. */ - private Matcher algorithm; - - /** - * Instantiates a new abstract match algorithm. - * - * @param name the name - * @param algorithm the algorithm - */ - public BaseCompositeMatchAlgorithm(String name, Matcher algorithm){ - this.name = name; - this.algorithm = algorithm; - } - - /* (non-Javadoc) - * @see org.cts2.internal.match.MatchAlgorithm#isMatch(java.lang.String, java.lang.Object) - */ - @Override - public float matchScore(String matchText, String compareString) { - return this.algorithm.matchScore(matchText, compareString); - } - - /* (non-Javadoc) - * @see org.cts2.internal.match.MatchAlgorithm#getName() - */ - public String getName(){ - return this.name; - } - - /** - * The Interface Matcher. - * - * @author Kevin Peterson - */ - public static interface Matcher { - - /** - * Checks if is match. - * - * @param matchText the match text - * @param cadidate the cadidate - * @return true, if is match - */ - public float matchScore(String matchText, String cadidate); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/ContainsMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/ContainsMatcher.java deleted file mode 100644 index 3b48d9ba9d..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/ContainsMatcher.java +++ /dev/null @@ -1,36 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - - -/** - * The Class ContainsMatcher. - * - * @author Kevin Peterson - */ -public class ContainsMatcher extends AbstractNonScoringMatcher { - - /* (non-Javadoc) - * @see org.cts2.internal.match.AbstractMatcher#doIsMatch(java.lang.String, java.lang.String) - */ - @Override - protected boolean isMatch(String matchText, String cadidate) { - return cadidate.contains(matchText); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/ExactMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/ExactMatcher.java deleted file mode 100644 index e44bb10418..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/ExactMatcher.java +++ /dev/null @@ -1,35 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -/** - * The Class ExactMatcher. - * - * @author Kevin Peterson - */ -public class ExactMatcher extends AbstractNonScoringMatcher { - - /* (non-Javadoc) - * @see org.cts2.internal.match.AbstractMatcher#doIsMatch(java.lang.String, java.lang.String) - */ - @Override - protected boolean isMatch(String matchText, String cadidate) { - return cadidate.equals(matchText); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/LevenshteinDistanceMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/LevenshteinDistanceMatcher.java deleted file mode 100644 index 66a2af4871..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/LevenshteinDistanceMatcher.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import org.apache.commons.lang.StringUtils; - -/** - * The Class LevenshteinDistanceMatcher. - * - * @author Kevin Peterson - */ -public class LevenshteinDistanceMatcher extends AbstractMatcher { - - /* (non-Javadoc) - * @see org.cts2.internal.match.AbstractMatcher#doIsMatch(java.lang.String, java.lang.String) - */ - @Override - protected float doMatchScore(String matchText, String cadidate) { - int longestString = - Math.max(matchText.length(), cadidate.length()); - - int score = StringUtils.getLevenshteinDistance(matchText, cadidate); - return this.normalize(score, longestString); - } - - /** - * Normalize. - * - * @param score the score - * @param longestString the longest string - * @return the float - */ - protected float normalize(float score, int longestString){ - return 1f - (score / longestString); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/MatchAlgorithm.java b/cts2Impl/src/main/java/org/cts2/internal/match/MatchAlgorithm.java deleted file mode 100644 index 8f3e5604cc..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/MatchAlgorithm.java +++ /dev/null @@ -1,43 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -/** - * The Interface MatchAlgorithm. - * - * @author Kevin Peterson - */ -public interface MatchAlgorithm { - - /** - * Checks if is match. - * - * @param matchText the match text - * @param compareString the compare string - * @return true, if is match - */ - public float matchScore(String matchText, String compareString); - - /** - * Gets the name. - * - * @return the name - */ - public String getName(); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/OperationExecutingModelAttributeReference.java b/cts2Impl/src/main/java/org/cts2/internal/match/OperationExecutingModelAttributeReference.java deleted file mode 100644 index 393db72e8a..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/OperationExecutingModelAttributeReference.java +++ /dev/null @@ -1,80 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import java.io.Serializable; - -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.ModelAttributeReference; - -/** - * The Class OperationExecutingModelAttributeReference. - * - * @author Kevin Peterson - */ -public class OperationExecutingModelAttributeReference extends ModelAttributeReference { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = 5500382462242484409L; - - /** The operation. */ - private RestrictionOperation operation; - - /** - * Instantiates a new operation executing model attribute reference. - * - * @param operation the operation - */ - public OperationExecutingModelAttributeReference(RestrictionOperation operation){ - super(); - this.operation = operation; - } - - /** - * Gets the model attribute value. - * - * @param stateObject the state object - * @param setOperator the set operator - * @param matchText the match text - * @param algorithm the algorithm - * @return the model attribute value - */ - public T executeOperation(T stateObject, String matchText, MatchAlgorithmReference algorithm){ - return this.operation.restrict(stateObject, matchText, algorithm); - } - - /** - * The Interface Operation. - * - * @param the - * @author Kevin Peterson - */ - public static interface RestrictionOperation extends Serializable { - - /** - * Restrict. - * - * @param stateObject the state object - * @param matchText the match text - * @param algorithm the algorithm - * @return the t - */ - public T restrict(T stateObject, String matchText, MatchAlgorithmReference algorithm); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/PropertyResolver.java b/cts2Impl/src/main/java/org/cts2/internal/match/PropertyResolver.java deleted file mode 100644 index 5059cd2994..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/PropertyResolver.java +++ /dev/null @@ -1,40 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import java.util.List; - -import org.cts2.service.core.NameOrURI; - -/** - * The Interface PropertyResolver. - * - * @author Kevin Peterson - */ -public interface PropertyResolver { - - /** - * Resolve property. - * - * @param reference the reference - * @return the list - */ - public List resolveProperty(NameOrURI reference); - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/RegexMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/RegexMatcher.java deleted file mode 100644 index 850b6c4603..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/RegexMatcher.java +++ /dev/null @@ -1,51 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import java.util.regex.Pattern; - -/** - * The Class RegexMatcher. - * - * @author Kevin Peterson - */ -public class RegexMatcher extends AbstractNonScoringMatcher { - - /* (non-Javadoc) - * @see org.cts2.internal.match.AbstractNonScoringMatcher#isMatch(java.lang.String, java.lang.String) - */ - @Override - protected boolean isMatch(String matchText, String cadidate) { - return this.regexMatch(matchText, cadidate); - } - - /** - * Regex match. - * - * @param matchText the match text - * @param cadidate the cadidate - * @return true, if successful - */ - protected boolean regexMatch(String matchText, String cadidate){ - Pattern pattern = Pattern.compile(matchText); - java.util.regex.Matcher matcher = pattern.matcher(cadidate); - - return matcher.matches(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/ResolvableModelAttributeReference.java b/cts2Impl/src/main/java/org/cts2/internal/match/ResolvableModelAttributeReference.java deleted file mode 100644 index adda14e430..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/ResolvableModelAttributeReference.java +++ /dev/null @@ -1,56 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import org.cts2.core.ModelAttributeReference; - -/** - * The Class ResolvableModelAttributeReference. - * - * @param the - * @author Kevin Peterson - */ -public class ResolvableModelAttributeReference extends ModelAttributeReference { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = 5500382462242484409L; - - /** The attribute resolver. */ - private AttributeResolver attributeResolver; - - /** - * Instantiates a new resolvable model attribute reference. - * - * @param attributeResolver the attribute resolver - */ - public ResolvableModelAttributeReference(AttributeResolver attributeResolver){ - this.attributeResolver = attributeResolver; - } - - /** - * Gets the model attribute value. - * - * @param modelObject the model object - * @return the model attribute value - */ - public String getModelAttributeValue(T modelObject){ - return this.attributeResolver.resolveAttribute(modelObject); - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/SoundexMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/SoundexMatcher.java deleted file mode 100644 index 14121ea88a..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/SoundexMatcher.java +++ /dev/null @@ -1,72 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -import org.apache.commons.codec.EncoderException; -import org.apache.commons.codec.language.RefinedSoundex; - -/** - * The Class SoundexMatcher. - * - * @author Kevin Peterson - */ -public class SoundexMatcher extends AbstractMatcher { - - /** The refined soundex. */ - private RefinedSoundex refinedSoundex = new RefinedSoundex(); - - /* (non-Javadoc) - * @see org.cts2.internal.match.AbstractMatcher#doIsMatch(java.lang.String, java.lang.String) - */ - @Override - protected float doMatchScore(String matchText, String cadidate) { - float score; - try { - score = this.refinedSoundex.difference(matchText, cadidate); - } catch (EncoderException e) { - throw new IllegalStateException(e); - } - - int matchTextEncodedLength = this.getEncodedStringLength(matchText); - int candidateEncodedLength = this.getEncodedStringLength(cadidate); - - return this.normalizeScore(score, Math.min(matchTextEncodedLength, candidateEncodedLength)); - } - - /** - * Gets the encoded string length. - * - * @param text the text - * @return the encoded string length - */ - private int getEncodedStringLength(String text){ - return this.refinedSoundex.encode(text).length(); - } - - /** - * Normalize score. - * - * @param score the score - * @param shortestEncodedLength the shortest encoded length - * @return the float - */ - protected float normalizeScore(float score, int shortestEncodedLength){ - return score / shortestEncodedLength; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/StartsWithMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/StartsWithMatcher.java deleted file mode 100644 index dc56aa75ea..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/StartsWithMatcher.java +++ /dev/null @@ -1,35 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -/** - * The Class StartsWithMatcher. - * - * @author Kevin Peterson - */ -public class StartsWithMatcher extends AbstractNonScoringMatcher { - - /* (non-Javadoc) - * @see org.cts2.internal.match.AbstractMatcher#doIsMatch(java.lang.String, java.lang.String) - */ - @Override - protected boolean isMatch(String matchText, String cadidate) { - return cadidate.startsWith(matchText); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/match/WildcardMatcher.java b/cts2Impl/src/main/java/org/cts2/internal/match/WildcardMatcher.java deleted file mode 100644 index f0f3098a03..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/match/WildcardMatcher.java +++ /dev/null @@ -1,43 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.match; - -/** - * The Class WildcardMatcher. - * - * @author Kevin Peterson - */ -public class WildcardMatcher extends RegexMatcher { - - /** The WILDCARD. */ - public static String WILDCARD = "*"; - - /** The MATC h_ al l_ regex. */ - public static String MATCH_ALL_REGEX = ".*"; - - /* (non-Javadoc) - * @see org.cts2.internal.match.RegexMatcher#regexMatch(java.lang.String, java.lang.String) - */ - @Override - protected boolean regexMatch(String matchText, String cadidate) { - matchText = matchText.replace(WILDCARD, MATCH_ALL_REGEX); - - return super.regexMatch(matchText, cadidate); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ListBackedValueSetDirectory.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ListBackedValueSetDirectory.java deleted file mode 100644 index 981703d1e3..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ListBackedValueSetDirectory.java +++ /dev/null @@ -1,100 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.directory; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.valueset.ValueSetDirectory; -import org.cts2.valueset.ValueSetDirectoryEntry; -import org.lexgrid.valuesets.dto.ResolvedValueSetDefinition; - -/** - * The Class ListBackedValueSetDirectory. - * - * @author Kevin Peterson - */ -public class ListBackedValueSetDirectory extends ValueSetDirectory { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -235309050016482174L; - - /** The cache. */ - private List list; - - /** - * Instantiates a new resolved concept references iterator backed entity directory. - * - * @param codedNodeSet the coded node set - * @param beanMapper the bean mapper - * @throws LBException the LB exception - */ - public ListBackedValueSetDirectory( - List resolvedValueSetDefinitions, - BeanMapper beanMapper) throws LBException { - this.list = this.createValueSetDirectoryEntryList(resolvedValueSetDefinitions, beanMapper); - } - - protected List createValueSetDirectoryEntryList( - List resolvedValueSetDefinitions, - BeanMapper beanMapper) { - List returnList = new ArrayList(); - for(ResolvedValueSetDefinition resolvedValueSetDefinition : resolvedValueSetDefinitions) { - returnList.add(beanMapper.map(resolvedValueSetDefinition, ValueSetDirectoryEntry.class)); - } - - return returnList; - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry(int) - */ - @Override - public ValueSetDirectoryEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.list.get(index); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry() - */ - @Override - public ValueSetDirectoryEntry[] getEntry() { - return this.list.toArray(new ValueSetDirectoryEntry[this.list.size()]); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#iterateEntry() - */ - @Override - public Iterator iterateEntry() { - return this.list.iterator(); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntryCount() - */ - @Override - public int getEntryCount() { - return this.list.size(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedAssociationDirectory.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedAssociationDirectory.java deleted file mode 100644 index 9687b93a39..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedAssociationDirectory.java +++ /dev/null @@ -1,92 +0,0 @@ -package org.cts2.internal.model.directory; - -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.cts2.association.AssociationDirectory; -import org.cts2.association.AssociationDirectoryEntry; -import org.cts2.internal.model.directory.iterator.DirectoryEntryIterator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.util.PagingList; - -public class ResolvedConceptReferencesIteratorBackedAssociationDirectory extends - AssociationDirectory { - /** - * - */ - private static final long serialVersionUID = 1L; - /** The cache. */ - private List cache; - - public ResolvedConceptReferencesIteratorBackedAssociationDirectory( - CodedNodeGraph codedNodeGraph, - BeanMapper beanMapper) throws LBException { - this(codedNodeGraph.resolveAsList(null, true, false, 1000, -1, null, null, null, null, -1), beanMapper); - } - - public ResolvedConceptReferencesIteratorBackedAssociationDirectory( - ResolvedConceptReferenceList list, - BeanMapper beanMapper){ - try { - this.cache = this.buildCacheList(list, beanMapper); - } catch (LBException e) { - throw new RuntimeException(e); - } - } - - private List buildCacheList( - ResolvedConceptReferenceList list, BeanMapper beanMapper) throws LBResourceUnavailableException { - @SuppressWarnings("unchecked") - Iterator iterator = (Iterator) list.iterateResolvedConceptReference(); - return new PagingList( - this.buildDirectoryEntryIterator(iterator, beanMapper), - list.getResolvedConceptReferenceCount()); - } - - private Iterator buildDirectoryEntryIterator( - Iterator iterator, BeanMapper beanMapper) { - return new - DirectoryEntryIterator( - iterator, AssociationDirectoryEntry.class, beanMapper); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry(int) - */ - @Override - public AssociationDirectoryEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.cache.get(index); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry() - */ - @Override - public AssociationDirectoryEntry[] getEntry() { - return this.cache.toArray(new AssociationDirectoryEntry[this.cache.size()]); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#iterateEntry() - */ - @Override - public Iterator iterateEntry() { - return this.cache.iterator(); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntryCount() - */ - @Override - public int getEntryCount() { - return this.cache.size(); - } - - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedAssociationList.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedAssociationList.java deleted file mode 100644 index f85828d5d6..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedAssociationList.java +++ /dev/null @@ -1,152 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.directory; - -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.cts2.association.AssociationList; -import org.cts2.association.AssociationListEntry; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.iterator.DirectoryEntryIterator; -import org.cts2.internal.util.PagingList; -/** - * @author Scott Bauer - * - */ -public class ResolvedConceptReferencesIteratorBackedAssociationList extends - AssociationList { - - /** - * - */ - private static final long serialVersionUID = 1L; - - /** The cache. */ - private List cache; - - /** - * Instantiates a new resolved concept references iterator backed - * Association directory. - * - * @param codedNodeSet - * the coded node set - * @param beanMapper - * the bean mapper - * @throws LBException - * the LB exception - */ - public ResolvedConceptReferencesIteratorBackedAssociationList( - CodedNodeGraph codedNodeGraph, BeanMapper beanMapper) - throws LBException { - this(codedNodeGraph.resolveAsList(null, true, false, 1000, -1, null, - null, null, null, -1), beanMapper); - } - - /** - * Instantiates a new resolved concept references list backed - * Association directory. - * - * @param list - * the iterator - * @param beanMapper - * the bean mapper - */ - public ResolvedConceptReferencesIteratorBackedAssociationList( - ResolvedConceptReferenceList list, BeanMapper beanMapper) { - try { - this.cache = this.buildCacheList(list, beanMapper); - } catch (LBException e) { - throw new RuntimeException(e); - } - } - - protected List buildCacheList( - ResolvedConceptReferenceList list, BeanMapper beanMapper) - throws LBException { - @SuppressWarnings("unchecked") - Iterator iterator = (Iterator) list - .iterateResolvedConceptReference(); - return new PagingList( - this.buildDirectoryEntryIterator(iterator, beanMapper), - list.getResolvedConceptReferenceCount()); - - } - - /** - * Builds the List entry iterator. - * - * @param iterator - * the iterator - * @param beanMapper - * the bean mapper - * @return the iterator - */ - private Iterator buildDirectoryEntryIterator( - Iterator iterator, BeanMapper beanMapper) { - return new - DirectoryEntryIterator( - iterator, AssociationListEntry.class, beanMapper); - } - - /* - * (non-Javadoc) - * - * @see org.cts2.association.AssociationList#getEntry(int) - */ - @Override - public AssociationListEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.cache.get(index); - } - - /* - * (non-Javadoc) - * - * @see org.cts2.association.AssociationList#getEntry() - */ - @Override - public AssociationListEntry[] getEntry() { - return this.cache.toArray(new AssociationListEntry[this.cache.size()]); - } - - /* - * (non-Javadoc) - * - * @see org.cts2.association.AssociationList#iterateEntry() - */ - @Override - public Iterator iterateEntry() { - return this.cache.iterator(); - } - - /* - * (non-Javadoc) - * - * @see org.cts2.association.AssociationList#getEntryCount() - */ - @Override - public int getEntryCount() { - return this.cache.size(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedEntityDirectory.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedEntityDirectory.java deleted file mode 100644 index 8d0b7c482b..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedEntityDirectory.java +++ /dev/null @@ -1,139 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.directory; - -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.helpers.ResolvedConceptReferencesIteratorAdapter; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.cts2.entity.EntityDirectory; -import org.cts2.entity.EntityDirectoryEntry; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.iterator.DirectoryEntryIterator; -import org.cts2.internal.util.PagingList; - -/** - * The Class ResolvedConceptReferencesIteratorBackedEntityDirectory. - * - * @author Kevin Peterson - */ -public class ResolvedConceptReferencesIteratorBackedEntityDirectory extends EntityDirectory { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -235309050016482174L; - - /** The cache. */ - private List cache; - - /** - * Instantiates a new resolved concept references iterator backed entity directory. - * - * @param codedNodeSet the coded node set - * @param beanMapper the bean mapper - * @throws LBException the LB exception - */ - public ResolvedConceptReferencesIteratorBackedEntityDirectory( - CodedNodeSet codedNodeSet, - BeanMapper beanMapper) throws LBException { - this(codedNodeSet.resolve(null, null, null, null, false), beanMapper); - } - - /** - * Instantiates a new resolved concept references iterator backed entity directory. - * - * @param iterator the iterator - * @param beanMapper the bean mapper - */ - public ResolvedConceptReferencesIteratorBackedEntityDirectory( - ResolvedConceptReferencesIterator iterator, - BeanMapper beanMapper){ - try { - this.cache = this.buildCacheList(iterator, beanMapper); - } catch (LBException e) { - throw new RuntimeException(e); - } - } - - /** - * Builds the cache list. - * - * @param iterator the iterator - * @param beanMapper the bean mapper - * @return the list - * @throws LBException the LB exception - */ - protected List buildCacheList(ResolvedConceptReferencesIterator iterator, BeanMapper beanMapper) - throws LBException{ - return new PagingList( - this.buildDirectoryEntryIterator(iterator, beanMapper), - iterator.numberRemaining()); - } - - /** - * Builds the directory entry iterator. - * - * @param iterator the iterator - * @param beanMapper the bean mapper - * @return the iterator - */ - protected Iterator - buildDirectoryEntryIterator(ResolvedConceptReferencesIterator iterator, BeanMapper beanMapper){ - return new - DirectoryEntryIterator( - new ResolvedConceptReferencesIteratorAdapter(iterator), EntityDirectoryEntry.class, beanMapper); - } - - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry(int) - */ - @Override - public EntityDirectoryEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.cache.get(index); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry() - */ - @Override - public EntityDirectoryEntry[] getEntry() { - return this.cache.toArray(new EntityDirectoryEntry[this.cache.size()]); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#iterateEntry() - */ - @Override - public Iterator iterateEntry() { - return this.cache.iterator(); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntryCount() - */ - @Override - public int getEntryCount() { - return this.cache.size(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedEntityList.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedEntityList.java deleted file mode 100644 index 7305573642..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedEntityList.java +++ /dev/null @@ -1,139 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.directory; - -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.helpers.ResolvedConceptReferencesIteratorAdapter; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.cts2.entity.EntityList; -import org.cts2.entity.EntityListEntry; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.iterator.DirectoryEntryIterator; -import org.cts2.internal.util.PagingList; - -/** - * The Class ResolvedConceptReferencesIteratorBackedEntityList. - * - * @author Kevin Peterson - */ -public class ResolvedConceptReferencesIteratorBackedEntityList extends EntityList { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -235309050016482174L; - - /** The cache. */ - private List cache; - - /** - * Instantiates a new resolved concept references iterator backed entity directory. - * - * @param codedNodeSet the coded node set - * @param beanMapper the bean mapper - * @throws LBException the LB exception - */ - public ResolvedConceptReferencesIteratorBackedEntityList( - CodedNodeSet codedNodeSet, - BeanMapper beanMapper) throws LBException { - this(codedNodeSet.resolve(null, null, null, null, false), beanMapper); - } - - /** - * Instantiates a new resolved concept references iterator backed entity directory. - * - * @param iterator the iterator - * @param beanMapper the bean mapper - */ - public ResolvedConceptReferencesIteratorBackedEntityList( - ResolvedConceptReferencesIterator iterator, - BeanMapper beanMapper){ - try { - this.cache = this.buildCacheList(iterator, beanMapper); - } catch (LBException e) { - throw new RuntimeException(e); - } - } - - /** - * Builds the cache list. - * - * @param iterator the iterator - * @param beanMapper the bean mapper - * @return the list - * @throws LBException the LB exception - */ - protected List buildCacheList(ResolvedConceptReferencesIterator iterator, BeanMapper beanMapper) - throws LBException{ - return new PagingList( - this.buildDirectoryEntryIterator(iterator, beanMapper), - iterator.numberRemaining()); - } - - /** - * Builds the directory entry iterator. - * - * @param iterator the iterator - * @param beanMapper the bean mapper - * @return the iterator - */ - protected Iterator - buildDirectoryEntryIterator(ResolvedConceptReferencesIterator iterator, BeanMapper beanMapper){ - return new - DirectoryEntryIterator( - new ResolvedConceptReferencesIteratorAdapter(iterator), EntityListEntry.class, beanMapper); - } - - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry(int) - */ - @Override - public EntityListEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.cache.get(index); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntry() - */ - @Override - public EntityListEntry[] getEntry() { - return this.cache.toArray(new EntityListEntry[this.cache.size()]); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#iterateEntry() - */ - @Override - public Iterator iterateEntry() { - return this.cache.iterator(); - } - - /* (non-Javadoc) - * @see org.cts2.entity.EntityDirectory#getEntryCount() - */ - @Override - public int getEntryCount() { - return this.cache.size(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedMapVersionDirectory.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedMapVersionDirectory.java deleted file mode 100644 index e9a7a56eb2..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedMapVersionDirectory.java +++ /dev/null @@ -1,80 +0,0 @@ -package org.cts2.internal.model.directory; - -import java.util.ArrayList; -import java.util.Collection; -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; -import org.LexGrid.LexBIG.Extensions.Generic.MappingExtension.Mapping; -import org.LexGrid.LexBIG.Impl.helpers.ResolvedConceptReferencesIteratorAdapter; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.iterator.DirectoryEntryIterator; -import org.cts2.internal.util.PagingList; -import org.cts2.map.MapVersionDirectory; -import org.cts2.map.MapVersionDirectoryEntry; - -import com.google.common.collect.Iterators; - -/** - * The class ResolvedConceptReferencesIteratorBackedMapVersionDirectory - * - * @author Zonghui Lian - * - */ -public class ResolvedConceptReferencesIteratorBackedMapVersionDirectory extends - MapVersionDirectory { - - private static final long serialVersionUID = -7474745464435213892L; - private List cache; - - public ResolvedConceptReferencesIteratorBackedMapVersionDirectory( - Iterable csrIterator, BeanMapper beanMapper) - throws LBException { - - this.cache = this.buildCacheList(csrIterator, beanMapper); - } - - private List buildCacheList( - Iterable csrIterator, BeanMapper beanMapper) - throws LBResourceUnavailableException { - - return new PagingList( - this.buildMapVersionDirectoryEntryIterator(csrIterator, - beanMapper), Iterators.size(csrIterator.iterator())); - } - - private Iterator buildMapVersionDirectoryEntryIterator( - Iterable csrIterator, BeanMapper beanMapper) { - return new DirectoryEntryIterator( - csrIterator.iterator(), MapVersionDirectoryEntry.class, - beanMapper); - } - - @Override - public MapVersionDirectoryEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.cache.get(index); - } - - @Override - public MapVersionDirectoryEntry[] getEntry() { - return this.cache.toArray(new MapVersionDirectoryEntry[this.cache - .size()]); - } - - @Override - public Iterator iterateEntry() { - return this.cache.iterator(); - } - - @Override - public int getEntryCount() { - return this.cache.size(); - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedMapVersionListDirectory.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedMapVersionListDirectory.java deleted file mode 100644 index 895843f35e..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/ResolvedConceptReferencesIteratorBackedMapVersionListDirectory.java +++ /dev/null @@ -1,75 +0,0 @@ -package org.cts2.internal.model.directory; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; -import org.LexGrid.LexBIG.Extensions.Generic.MappingExtension.Mapping; -import org.LexGrid.LexBIG.Impl.helpers.ResolvedConceptReferencesIteratorAdapter; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.iterator.DirectoryEntryIterator; -import org.cts2.internal.util.PagingList; -import org.cts2.map.MapVersionList; -import org.cts2.map.MapVersionListEntry; - -import com.google.common.collect.Iterators; - -/** - * The class ResolvedConceptReferencesIteratorBackedMapVersionListDirectory - * - * @author Zonghui Lian - * - */ -public class ResolvedConceptReferencesIteratorBackedMapVersionListDirectory - extends MapVersionList { - private static final long serialVersionUID = -68126108480534728L; - - /* The cache */ - private List cache; - - public ResolvedConceptReferencesIteratorBackedMapVersionListDirectory( - Iterable csrIterator, BeanMapper beanMapper) - throws LBException { - this.cache = this.buildCacheList(csrIterator, beanMapper); - } - - private List buildCacheList( - Iterable csrIterator, BeanMapper beanMapper) - throws LBResourceUnavailableException { - return new PagingList( - this.buildMapVersionListEntryIterator(csrIterator, beanMapper), - Iterators.size(csrIterator.iterator())); - } - - private Iterator buildMapVersionListEntryIterator( - Iterable csrIterator, BeanMapper beanMapper) { - return new DirectoryEntryIterator( - csrIterator.iterator(), MapVersionListEntry.class, beanMapper); - } - - @Override - public MapVersionListEntry getEntry(int index) - throws IndexOutOfBoundsException { - return this.cache.get(index); - } - - @Override - public MapVersionListEntry[] getEntry() { - return this.cache.toArray(new MapVersionListEntry[this.cache.size()]); - } - - @Override - public Iterator iterateEntry() { - return this.cache.iterator(); - } - - @Override - public int getEntryCount() { - return this.cache.size(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/directory/iterator/DirectoryEntryIterator.java b/cts2Impl/src/main/java/org/cts2/internal/model/directory/iterator/DirectoryEntryIterator.java deleted file mode 100644 index 5bcb67ddee..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/directory/iterator/DirectoryEntryIterator.java +++ /dev/null @@ -1,81 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.directory.iterator; - -import java.util.Iterator; - -import org.cts2.internal.mapper.BeanMapper; - -/** - * The Class DirectoryEntryIterator. - * - * @author Kevin Peterson - */ -public class DirectoryEntryIterator implements Iterator{ - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -2616653453721025571L; - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /** The iterator. */ - private Iterator iterator; - - /** The output class. */ - private Class outputClass; - - /** - * Instantiates a new directory entry iterator. - * - * @param iterator the iterator - * @param outputClass the output class - * @param beanMapper the bean mapper - */ - public DirectoryEntryIterator(Iterator iterator, Class outputClass, BeanMapper beanMapper) { - super(); - this.iterator = iterator; - this.outputClass = outputClass; - this.beanMapper = beanMapper; - } - - /* (non-Javadoc) - * @see java.util.Iterator#next() - */ - @Override - public O next() { - return this.beanMapper.map(this.iterator.next(), this.outputClass); - } - - /* (non-Javadoc) - * @see java.util.Iterator#hasNext() - */ - @Override - public boolean hasNext() { - return this.iterator.hasNext(); - } - - /* (non-Javadoc) - * @see java.util.Iterator#remove() - */ - @Override - public void remove() { - throw new UnsupportedOperationException(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/AbstractResourceFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/AbstractResourceFactory.java deleted file mode 100644 index 7f50812fc2..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/AbstractResourceFactory.java +++ /dev/null @@ -1,72 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.resource.factory; - -import java.sql.Timestamp; -import java.util.Date; - -import org.lexevs.dao.database.access.DaoManager; -import org.lexevs.dao.database.service.daocallback.DaoCallbackService.DaoCallback; -import org.lexevs.locator.LexEvsServiceLocator; - -/** - * A factory for creating AbstractResource objects. - */ -public abstract class AbstractResourceFactory { - - /** The lex evs service locator. */ - private LexEvsServiceLocator lexEvsServiceLocator; - - /** - * Gets the revision id by date. - * - * @param date the date - * @return the revision id by date - */ - protected String getRevisionIdByDate(final Date date){ - return this.lexEvsServiceLocator. - getDatabaseServiceManager(). - getDaoCallbackService(). - executeInDaoLayer(new DaoCallback(){ - - @Override - public String execute(DaoManager daoManager) { - return daoManager.getRevisionDao().getRevisionIdForDate(new Timestamp(date.getTime())); - } - }); - } - - /** - * Sets the lex evs service locator. - * - * @param lexEvsServiceLocator the new lex evs service locator - */ - public void setLexEvsServiceLocator(LexEvsServiceLocator lexEvsServiceLocator) { - this.lexEvsServiceLocator = lexEvsServiceLocator; - } - - /** - * Gets the lex evs service locator. - * - * @return the lex evs service locator - */ - public LexEvsServiceLocator getLexEvsServiceLocator() { - return lexEvsServiceLocator; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/AssociationFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/AssociationFactory.java deleted file mode 100644 index c4f201c8e1..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/AssociationFactory.java +++ /dev/null @@ -1,121 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.resource.factory; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.codingSchemes.CodingScheme; -import org.cts2.association.Association; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.uri.factory.DirectoryURIFactory; -import org.cts2.profile.query.EntityDescriptionQueryService; -import org.cts2.service.core.NameOrURI; -import org.cts2.uri.EntityDirectoryURI; - -/** - * A factory for creating Association objects. - */ -public class AssociationFactory { - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /** The lex big service. */ - private LexBIGService lexBigService; - - /** The lex evs identity converter. */ - private LexEvsIdentityConverter lexEvsIdentityConverter; - - /** The entity description query service. */ - private EntityDescriptionQueryService entityDescriptionQueryService; - - /** The entity directory uri factory. */ - private DirectoryURIFactory entityDirectoryUriFactory; - - /** - * Gets the Association. - * - * @param nameOrUri the name or uri - * @return the code system version - */ - public Association getAssociation(NameOrURI nameOrUri ){ - AbsoluteCodingSchemeVersionReference ref = this.lexEvsIdentityConverter.nameOrUriToAbsoluteCodingSchemeVersionReference(nameOrUri); - - return new Association(); - } - - /** - * Gets the bean mapper. - * - * @return the bean mapper - */ - public BeanMapper getBeanMapper() { - return beanMapper; - } - - /** - * Sets the bean mapper. - * - * @param beanMapper the new bean mapper - */ - public void setBeanMapper(BeanMapper beanMapper) { - this.beanMapper = beanMapper; - } - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - public LexBIGService getLexBigService() { - return lexBigService; - } - - /** - * Sets the lex big service. - * - * @param lexBigService the new lex big service - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } - - /** - * Gets the lex evs identity converter. - * - * @return the lex evs identity converter - */ - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - /** - * Sets the lex evs identity converter. - * - * @param lexEvsIdentityConverter the new lex evs identity converter - */ - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/CodeSystemVersionFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/CodeSystemVersionFactory.java deleted file mode 100644 index 13eed38cce..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/CodeSystemVersionFactory.java +++ /dev/null @@ -1,214 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.resource.factory; - -import java.util.Date; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.codingSchemes.CodingScheme; -import org.apache.commons.lang.StringUtils; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.uri.factory.DirectoryURIFactory; -import org.cts2.profile.query.EntityDescriptionQueryService; -import org.cts2.service.core.NameOrURI; -import org.cts2.uri.EntityDirectoryURI; - -/** - * A factory for creating CodeSystemVersion objects. - */ -public class CodeSystemVersionFactory extends AbstractResourceFactory { - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /** The lex big service. */ - private LexBIGService lexBigService; - - /** The lex evs identity converter. */ - private LexEvsIdentityConverter lexEvsIdentityConverter; - - /** The entity description query service. */ - private EntityDescriptionQueryService entityDescriptionQueryService; - - /** The entity directory uri factory. */ - private DirectoryURIFactory entityDirectoryUriFactory; - - public CodeSystemVersion getCurrentCodeSystemVersion(NameOrURI nameOrUri){ - return this.getCodeSystemVersionByRevisionId(nameOrUri, null); - } - - public CodeSystemVersion getCodeSystemVersionByDate(NameOrURI nameOrUri, Date date){ - String revisionId; - - if(date == null){ - return this.getCurrentCodeSystemVersion(nameOrUri); - } else { - revisionId = this.getRevisionIdByDate(date); - return this.getCodeSystemVersionByRevisionId(nameOrUri, revisionId); - } - } - - /** - * Gets the code system version. - * - * @param nameOrUri the name or uri - * @return the code system version - */ - public CodeSystemVersion getCodeSystemVersionByRevisionId(NameOrURI nameOrUri, String revisionId){ - AbsoluteCodingSchemeVersionReference ref = this.lexEvsIdentityConverter.nameOrUriToAbsoluteCodingSchemeVersionReference(nameOrUri); - - CodingScheme codingScheme; - try { - if(StringUtils.isBlank(revisionId)){ - codingScheme = getCodingScheme(ref); - } else { - codingScheme = getCodingScheme(ref, revisionId); - } - } catch (LBException e) { - throw new RuntimeException(e); - } - - CodeSystemVersion codeSystemVersion = this.beanMapper.map(codingScheme, CodeSystemVersion.class); - - EntityDirectoryURI entityDirectoryURI = this.entityDirectoryUriFactory.getDirectoryURI(); - - this.entityDescriptionQueryService.restrictToCodeSystemVersions(entityDirectoryURI, nameOrUri); - - codeSystemVersion.setEntityDescriptions(this.entityDirectoryUriFactory.getDirectoryURI()); - - return codeSystemVersion; - } - - private CodingScheme getCodingScheme( - AbsoluteCodingSchemeVersionReference ref) throws LBException { - CodingScheme codingScheme = this.lexBigService.resolveCodingScheme( - ref.getCodingSchemeURN(), - Constructors.createCodingSchemeVersionOrTagFromVersion(ref.getCodingSchemeVersion())); - return codingScheme; - } - - private CodingScheme getCodingScheme( - AbsoluteCodingSchemeVersionReference ref, String revisionId) throws LBException { - - return this.getLexEvsServiceLocator(). - getDatabaseServiceManager(). - getCodingSchemeService(). - resolveCodingSchemeByRevision( - ref.getCodingSchemeURN(), - ref.getCodingSchemeVersion(), revisionId); - } - - /** - * Gets the bean mapper. - * - * @return the bean mapper - */ - public BeanMapper getBeanMapper() { - return beanMapper; - } - - /** - * Sets the bean mapper. - * - * @param beanMapper the new bean mapper - */ - public void setBeanMapper(BeanMapper beanMapper) { - this.beanMapper = beanMapper; - } - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - public LexBIGService getLexBigService() { - return lexBigService; - } - - /** - * Sets the lex big service. - * - * @param lexBigService the new lex big service - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } - - /** - * Gets the lex evs identity converter. - * - * @return the lex evs identity converter - */ - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - /** - * Sets the lex evs identity converter. - * - * @param lexEvsIdentityConverter the new lex evs identity converter - */ - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - /** - * Gets the entity description query service. - * - * @return the entity description query service - */ - public EntityDescriptionQueryService getEntityDescriptionQueryService() { - return entityDescriptionQueryService; - } - - /** - * Sets the entity description query service. - * - * @param entityDescriptionQueryService the new entity description query service - */ - public void setEntityDescriptionQueryService( - EntityDescriptionQueryService entityDescriptionQueryService) { - this.entityDescriptionQueryService = entityDescriptionQueryService; - } - - /** - * Gets the entity directory uri factory. - * - * @return the entity directory uri factory - */ - public DirectoryURIFactory getEntityDirectoryUriFactory() { - return entityDirectoryUriFactory; - } - - /** - * Sets the entity directory uri factory. - * - * @param entityDirectoryUriFactory the new entity directory uri factory - */ - public void setEntityDirectoryUriFactory( - DirectoryURIFactory entityDirectoryUriFactory) { - this.entityDirectoryUriFactory = entityDirectoryUriFactory; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/EntityDescriptionFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/EntityDescriptionFactory.java deleted file mode 100644 index f4fa652523..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/EntityDescriptionFactory.java +++ /dev/null @@ -1,293 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.resource.factory; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Collections.ConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.LexBIG.Utility.ConvenienceMethods; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.types.EntityTypes; -import org.apache.commons.lang.BooleanUtils; -import org.cts2.core.CodeSystemVersionReference; -import org.cts2.core.EntityReference; -import org.cts2.core.ScopedEntityName; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.entity.AnonymousIndividualDescription; -import org.cts2.entity.EntityDescription; -import org.cts2.entity.EntityDescriptionChoice; -import org.cts2.entity.EntityList; -import org.cts2.entity.EntityListEntry; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.entity.NamedIndividualDescription; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.lexevs.locator.LexEvsServiceLocator; - -/** - * A factory for creating EntityDescription objects. - * * @author Kevin Peterson - * * @author Zonghui Lian - */ -public class EntityDescriptionFactory { - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /** The lex big service. */ - private LexBIGService lexBigService; - - /** The lexevs identify converter*/ - private LexEvsIdentityConverter lexEvsIdentityConverter; - - public EntityDescription getEntityDescription( - EntityNameOrURI entityDescriptionNameOrUri, - NameOrURI codeSystemVersionNameOrUri) { - AbsoluteCodingSchemeVersionReference ref = this.lexEvsIdentityConverter - .nameOrUriToAbsoluteCodingSchemeVersionReference(codeSystemVersionNameOrUri); - - try { - CodedNodeSet cns = this.lexBigService.getNodeSet(ref - .getCodingSchemeURN(), Constructors - .createCodingSchemeVersionOrTagFromVersion(ref - .getCodingSchemeVersion()), null); - ConceptReferenceList conceptRefList = ConvenienceMethods - .createConceptReferenceList(entityDescriptionNameOrUri - .getEntityName().getName()); - CodedNodeSet restCns = cns.restrictToCodes(conceptRefList); - ResolvedConceptReferencesIterator iterator = restCns.resolve(null, - null, null, null, true); - if (iterator.hasNext()) { - ResolvedConceptReference conRef = iterator.next(); - return this.ResolvedConceptReferenceToEntityDescription(conRef); - } - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - return null; - - } - - public EntityList getEntityDescriptionList(EntityNameOrURI entityNameOrUri) { - EntityList list = new EntityList(); - CodingSchemeRenderingList schemeList; - try { - schemeList = this.lexBigService.getSupportedCodingSchemes(); - for (CodingSchemeRendering csr : schemeList - .getCodingSchemeRendering()) { - CodingSchemeSummary css = csr.getCodingSchemeSummary(); - CodedNodeSet cns = this.lexBigService.getNodeSet(css - .getCodingSchemeURI(), Constructors - .createCodingSchemeVersionOrTagFromVersion(css - .getRepresentsVersion()), null); - ConceptReferenceList conceptRefList = ConvenienceMethods - .createConceptReferenceList(entityNameOrUri - .getEntityName().getName()); - CodedNodeSet restCns = cns.restrictToCodes(conceptRefList); - ResolvedConceptReferencesIterator iterator = restCns.resolve( - null, null, null, null, true); - if (iterator.hasNext()) { - EntityListEntry entry = new EntityListEntry(); - ResolvedConceptReference conRef = iterator.next(); - entry.setItem(this - .ResolvedConceptReferenceToEntityDescriptionChoice(conRef)); - list.addEntry(entry); - } - } - } catch (LBInvocationException e1) { - // TODO Auto-generated catch block - e1.printStackTrace(); - } catch (LBException e) { - e.printStackTrace(); - } - return list; - } - - public EntityReference availableDescriptions(EntityNameOrURI entityNameOrURI) { - EntityReference entityReference = new EntityReference(); - entityReference.setAbout(entityNameOrURI.getUri()); - ScopedEntityName scopedEntityName = entityNameOrURI.getEntityName(); - entityReference.setLocalEntityName(scopedEntityName); - - try { - CodingSchemeRenderingList schemeList = this.lexBigService - .getSupportedCodingSchemes(); - for (CodingSchemeRendering csr : schemeList - .getCodingSchemeRendering()) { - CodeSystemVersionReference codeSystemVersionReference = new CodeSystemVersionReference(); - - CodingSchemeSummary css = csr.getCodingSchemeSummary(); - CodingScheme cs = LexEvsServiceLocator - .getInstance() - .getDatabaseServiceManager() - .getCodingSchemeService() - .getCodingSchemeByUriAndVersion( - css.getCodingSchemeURI(), - css.getRepresentsVersion()); - CodedNodeSet cns = this.lexBigService.getNodeSet(css - .getCodingSchemeURI(), Constructors - .createCodingSchemeVersionOrTagFromVersion(css - .getRepresentsVersion()), null); - ConceptReferenceList conceptRefList = ConvenienceMethods - .createConceptReferenceList(entityNameOrURI - .getEntityName().getName()); - CodedNodeSet restCns = cns.restrictToCodes(conceptRefList); - ResolvedConceptReferencesIterator iterator = restCns.resolve( - null, null, null, null, true); - if (iterator.hasNext()) { - codeSystemVersionReference - .setContent(this.lexEvsIdentityConverter - .codingSchemeSummaryToCodeSystemVersionName(css)); - codeSystemVersionReference - .setMeaning(this.lexEvsIdentityConverter - .codingSchemeToCodeSystemVersionDocumentUri(cs)); - // codeSystemVersionReference.setCodeSystem(codeSystem) TODO - entityReference - .addDescribingCodeSystemVersion(codeSystemVersionReference); - } - } - } catch (LBInvocationException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - return entityReference; - } - - /** - * Gets the bean mapper. - * - * @return the bean mapper - */ - public BeanMapper getBeanMapper() { - return beanMapper; - } - - /** - * Sets the bean mapper. - * - * @param beanMapper - * the new bean mapper - */ - public void setBeanMapper(BeanMapper beanMapper) { - this.beanMapper = beanMapper; - } - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - public LexBIGService getLexBigService() { - return lexBigService; - } - - /** - * Sets the lex big service. - * - * @param lexBigService - * the new lex big service - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } - - /** - * Gets the lex evs identity converter. - * - * @return the lex evs identity converter - */ - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - /** - * Sets the lex evs identity converter. - * - * @param lexEvsIdentityConverter - * the new lex evs identity converter - */ - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - private EntityDescription ResolvedConceptReferenceToEntityDescription( - ResolvedConceptReference conRef) { - if (conRef.getEntityType(0).equalsIgnoreCase( - EntityTypes.CONCEPT.toString())) { - if (!BooleanUtils.toBoolean(conRef.getEntity().isIsAnonymous())) { - return this.beanMapper - .map(conRef, NamedEntityDescription.class); - } else { - return this.beanMapper.map(conRef, - AnonymousEntityDescription.class); - } - } else if (conRef.getEntityType(0).equalsIgnoreCase( - EntityTypes.INSTANCE.toString())) { - if (!BooleanUtils.toBoolean(conRef.getEntity().isIsAnonymous())) { - return this.beanMapper.map(conRef, - NamedIndividualDescription.class); - } else { - return this.beanMapper.map(conRef, - AnonymousIndividualDescription.class); - } - } else { - // TODO entity type is ASSOCIATION, map to? - return null; - } - } - - private EntityDescriptionChoice ResolvedConceptReferenceToEntityDescriptionChoice( - ResolvedConceptReference conRef) { - EntityDescriptionChoice entityDescriptionChoice = new EntityDescriptionChoice(); - EntityDescription ed = this - .ResolvedConceptReferenceToEntityDescription(conRef); - if (ed instanceof NamedIndividualDescription) - entityDescriptionChoice - .setNamedIndividual((NamedIndividualDescription) ed); - else if (ed instanceof AnonymousIndividualDescription) - entityDescriptionChoice - .setAnonymousIndividual((AnonymousIndividualDescription) ed); - else if (ed instanceof NamedEntityDescription) - entityDescriptionChoice.setNamedEntity((NamedEntityDescription) ed); - else if (ed instanceof AnonymousEntityDescription) - entityDescriptionChoice - .setAnonymousEntity((AnonymousEntityDescription) ed); - else { - // TODO ClassDescription and PredicateDescription - } - - return entityDescriptionChoice; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/ValueSetDefinitionFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/ValueSetDefinitionFactory.java deleted file mode 100644 index 8233e9218d..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/resource/factory/ValueSetDefinitionFactory.java +++ /dev/null @@ -1,160 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.resource.factory; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.cts2.core.NameOrURI; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.valueset.ValueSetDefinition; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; - -/** - * A factory for creating ValueSetDefinition objects. - */ -public class ValueSetDefinitionFactory { - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /** The lexEVSValueSetDefinition service. */ - private LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService; - - /** - * Gets the value set definition for a URI. - * - * @param valueSetDefinitionURI the URI of value set definition - * @return the value set definition - */ - public ValueSetDefinition getValueSetDefinition(URI valueSetDefinitionURI){ - - org.LexGrid.valueSets.ValueSetDefinition vsd = null; - try { - vsd = this.lexEVSValueSetDefinitionService.getValueSetDefinition(valueSetDefinitionURI, null); - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - if (vsd != null) - { - return this.beanMapper.map(vsd, ValueSetDefinition.class); - } - - return null; - } - - /** - * Gets the value set definition for a name. - * - * @param valueSetDefinitionName the name of Value Set Definition - * @return the value set definition - * @throws LBParameterException - * @throws LBException - */ - public ValueSetDefinition getValueSetDefinition(String valueSetDefinitionName) throws LBParameterException { - - org.LexGrid.valueSets.ValueSetDefinition vsd = null; - List vsds = null; - try { - vsds = this.lexEVSValueSetDefinitionService.listValueSetDefinitions(valueSetDefinitionName); - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - if (vsds.isEmpty()) - return null; - - if (vsds.size() > 1) - throw new LBParameterException("More than 1 Value Set Definition found for name : " + valueSetDefinitionName); - - try { - vsd = this.getLexEVSValueSetDefinitionService().getValueSetDefinition(new URI(vsds.get(0)), null); - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (URISyntaxException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - if (vsd != null) - { - return this.beanMapper.map(vsd, ValueSetDefinition.class); - } - - return null; - } - - /** - * Gets the value set definition for a name or URI. - * - * @param valueSetDefinitionNameOrURI the name or URI of Value Set Definition - * @return the value set definition - * @throws LBParameterException - * @throws LBException - */ - public ValueSetDefinition getValueSetDefinition(NameOrURI valueSetDefinitionNameOrURI) throws LBParameterException { - - if (valueSetDefinitionNameOrURI.getUri() != null) - return this.getValueSetDefinition(valueSetDefinitionNameOrURI.getUri()); - else - return this.getValueSetDefinition(valueSetDefinitionNameOrURI.getName()); - } - - /** - * Gets the bean mapper. - * - * @return the bean mapper - */ - public BeanMapper getBeanMapper() { - return beanMapper; - } - - /** - * Sets the bean mapper. - * - * @param beanMapper the new bean mapper - */ - public void setBeanMapper(BeanMapper beanMapper) { - this.beanMapper = beanMapper; - } - - /** - * @return the lexEVSValueSetDefinitionService - */ - public LexEVSValueSetDefinitionServices getLexEVSValueSetDefinitionService() { - return lexEVSValueSetDefinitionService; - } - - /** - * @param lexEVSValueSetDefinitionService the lexEVSValueSetDefinitionService to set - */ - public void setLexEVSValueSetDefinitionService( - LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService) { - this.lexEVSValueSetDefinitionService = lexEVSValueSetDefinitionService; - } - - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractDirectoryURI.java deleted file mode 100644 index a27f219f08..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractDirectoryURI.java +++ /dev/null @@ -1,68 +0,0 @@ -package org.cts2.internal.model.uri; - -import org.cts2.core.Filter; -import org.cts2.core.types.SetOperator; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.DirectoryURI; -import org.cts2.uri.SetOperable; - -public abstract class AbstractDirectoryURI implements DirectoryURI, SetOperable { - - protected abstract int doCount(ReadContext readContext); - - @Override - public int count(ReadContext readContext) { - return this.doCount(readContext); - } - - //TODO: throw some sort of validation exception - /** - * Validate query control. - * - * @param queryControl the query control - * @return the query control - */ - protected QueryControl validateQueryControl(QueryControl queryControl){ - if(queryControl == null){ - return new QueryControl(); - } else { - return queryControl; - } - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractDirectoryURI#restrict(org.cts2.core.Filter) - */ - @Override - public T restrict(Filter filter) { - this.getRestrictionState().getFilters().add(filter); - - return clone(); - } - - protected abstract T createSetOperatedDirectoryURI(SetOperator setOperator, T directoryUri1, T directoryUri2); - - public T union(T directoryUri) { - return this.createSetOperatedDirectoryURI(SetOperator.UNION, this.clone() , directoryUri); - } - - public T intersect(T directoryUri) { - return this.createSetOperatedDirectoryURI(SetOperator.INTERSECT, this.clone() , directoryUri); - } - - public T difference(T directoryUri) { - return this.createSetOperatedDirectoryURI(SetOperator.SUBTRACT, this.clone(), directoryUri); - } - - @Override - public String marshall() { - //TODO: Context based marshalling - return this.toString(); - } - - /* (non-Javadoc) - * @see java.lang.Object#clone() - */ - protected abstract T clone(); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractIterableLexEvsBackedResolvingDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractIterableLexEvsBackedResolvingDirectoryURI.java deleted file mode 100644 index 758770c7c7..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractIterableLexEvsBackedResolvingDirectoryURI.java +++ /dev/null @@ -1,96 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import org.cts2.core.Directory; -import org.cts2.internal.model.uri.restrict.IterableBasedResolvingRestrictionHandler; -import org.cts2.internal.model.uri.restrict.IterableRestriction; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.DirectoryURI; - -import com.google.common.collect.Iterables; -import com.google.common.collect.Iterators; - -/** - * The Class AbstractIterableLexEvsBackedResolvingDirectoryURI. - * - * @author Kevin Peterson - */ -public abstract class AbstractIterableLexEvsBackedResolvingDirectoryURI extends AbstractResolvingDirectoryURI { - - /** The restriction handler. */ - private IterableBasedResolvingRestrictionHandler restrictionHandler; - - /** - * Instantiates a new abstract iterable lex evs backed resolving directory uri. - * - * @param restrictionHandler the restriction handler - * @param restrictionState - */ - protected AbstractIterableLexEvsBackedResolvingDirectoryURI(IterableBasedResolvingRestrictionHandler restrictionHandler){ - this.restrictionHandler = restrictionHandler; - } - - /** - * Gets the original state. - * - * @return the original state - */ - protected abstract Iterable getOriginalState(); - - /** - * Transform. - * - * @param the - * @param lexevsObject the lexevs object - * @param clazz the clazz - * @return the o - */ - protected abstract O transform(Iterable lexevsObject, Class clazz); - - @Override - protected int doCount(ReadContext readContext) { - IterableRestriction restriction = this.restrictionHandler.compile( this.clone() ); - - return Iterators.size(this.restrictionHandler.apply(restriction, this.getOriginalState()).iterator()); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractResolvingDirectoryURI#doGet(org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext, java.lang.Class) - */ - @Override - protected > D doGet( - QueryControl queryControl, - final ReadContext readContext, - final Class resolveClass) { - - Iterable originalState = Iterables.unmodifiableIterable(this.getOriginalState()); - - IterableRestriction restriction = this.restrictionHandler.compile( this.clone() ); - - Iterable restrictedState = this.restrictionHandler.apply(restriction, originalState); - - return this.transform(restrictedState, resolveClass); - } - - protected IterableBasedResolvingRestrictionHandler getRestrictionHandler() { - return restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractNonIterableLexEvsBackedResolvingDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractNonIterableLexEvsBackedResolvingDirectoryURI.java deleted file mode 100644 index a6e3056b44..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractNonIterableLexEvsBackedResolvingDirectoryURI.java +++ /dev/null @@ -1,122 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import org.cts2.core.Directory; -import org.cts2.internal.model.uri.restrict.NonIterableBasedResolvingRestrictionHandler; -import org.cts2.internal.model.uri.restrict.OriginalStateProvider; -import org.cts2.internal.model.uri.restrict.Restriction; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.DirectoryURI; - -/** - * The Class AbstractResolvingDirectoryURI. - * - * @author Kevin Peterson - */ -public abstract class AbstractNonIterableLexEvsBackedResolvingDirectoryURI extends AbstractResolvingDirectoryURI { - - /** The restriction handler. */ - private NonIterableBasedResolvingRestrictionHandler restrictionHandler; - - /** - * Instantiates a new abstract non iterable lex evs backed resolving directory uri. - * - * @param restrictionHandler the restriction handler - */ - protected AbstractNonIterableLexEvsBackedResolvingDirectoryURI(NonIterableBasedResolvingRestrictionHandler restrictionHandler){ - this.restrictionHandler = restrictionHandler; - } - - /** - * Gets the original state. - * - * @return the original state - */ - protected abstract T getOriginalState(); - - protected OriginalStateProvider getOriginalStateProvider(){ - return new OriginalStateProvider(){ - - @Override - public T getOriginalState() { - return AbstractNonIterableLexEvsBackedResolvingDirectoryURI.this.getOriginalState(); - } - }; - } - - /** - * Transform. - * - * @param the - * @param lexevsObject the lexevs object - * @param clazz the clazz - * @return the o - */ - protected abstract O transform(T lexevsObject, Class clazz); - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractResolvingDirectoryURI#doGet(org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext, java.lang.Class) - */ - @Override - protected > D doGet( - QueryControl queryControl, - final ReadContext readContext, - final Class resolveClass) { - - T originalState = makeOriginalStateUnmodifiable(this.getOriginalState()); - - Restriction restriction = this.restrictionHandler.compile(this.getThis(), new OriginalStateProvider(){ - - @Override - public T getOriginalState() { - return AbstractNonIterableLexEvsBackedResolvingDirectoryURI.this.getOriginalState(); - } - }); - - T restrictedState = this.restrictionHandler.apply(restriction, originalState); - - return this.transform(restrictedState, resolveClass); - } - - /* (non-Javadoc) - * @see java.lang.Object#clone() - */ - protected abstract L clone(); - - /** - * Make original state unmodifiable. - * - * @param originalState the original state - * @return the l - */ - protected T makeOriginalStateUnmodifiable(T originalState){ - return originalState; - } - - /** - * Gets the restriction handler. - * - * @return the restriction handler - */ - protected NonIterableBasedResolvingRestrictionHandler getRestrictionHandler(){ - return this.restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractResolvingDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractResolvingDirectoryURI.java deleted file mode 100644 index 9c43bb5d9f..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/AbstractResolvingDirectoryURI.java +++ /dev/null @@ -1,71 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import java.util.concurrent.Callable; - -import org.cts2.core.Directory; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.DirectoryURI; -import org.cts2.utility.ExecutionUtils; - -/** - * The Class AbstractResolvingDirectoryURI. - * - * @param the - * @author Kevin Peterson - */ -public abstract class AbstractResolvingDirectoryURI extends AbstractDirectoryURI { - - /* (non-Javadoc) - * @see org.cts2.uri.DirectoryURI#get(org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext, java.lang.Class) - */ - public > D get(final QueryControl queryControl, final ReadContext readContext, final Class content){ - final QueryControl validatedQueryControl = validateQueryControl(queryControl); - return ExecutionUtils.callWithTimeout(new Callable(){ - - @Override - public D call() { - return doGet(validatedQueryControl, readContext, content); - } - - }, queryControl); - } - - @SuppressWarnings("unchecked") - protected T getThis(){ - return (T) this; - } - - /** - * Do resolve. - * - * @param the - * @param format the format - * @param queryControl the query control - * @param readContext the read context - * @param resolveClass the resolve class - * @return the d - */ - protected abstract > D doGet( - QueryControl queryControl, - ReadContext readContext, - Class resolveClass); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultAssociationDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultAssociationDirectoryURI.java deleted file mode 100644 index 9c04e83c60..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultAssociationDirectoryURI.java +++ /dev/null @@ -1,230 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.association.AssociationDirectory; -import org.cts2.association.AssociationList; -import org.cts2.core.TargetExpression; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.ResolvedConceptReferencesIteratorBackedAssociationDirectory; -import org.cts2.internal.model.directory.ResolvedConceptReferencesIteratorBackedAssociationList; -import org.cts2.internal.model.uri.restrict.NonIterableBasedResolvingRestrictionHandler; -import org.cts2.internal.profile.ProfileUtils; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.AssociationDirectoryURI; -import org.cts2.uri.EntityDirectoryURI; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState; -import org.cts2.uri.restriction.SetComposite; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToCodeSystemVersionRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToPredicateRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToSourceEntityRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToSourceOrTargetEntityRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToTargetEntityRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToTargetExpressionRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToTargetLiteralRestriction; -/** - * @author Scott Bauer - * - */ -public class DefaultAssociationDirectoryURI - extends AbstractNonIterableLexEvsBackedResolvingDirectoryURI implements AssociationDirectoryURI { - - /** - * The common LexBIGService. - */ - private LexBIGService lexBigService; - /** - * The beanmapper for this class. - */ - private BeanMapper beanMapper; - /** - * a restriction state for the associations - */ - private AssociationDirectoryRestrictionState restrictionState = new AssociationDirectoryRestrictionState(); - - public DefaultAssociationDirectoryURI( - LexBIGService lexBigService, - NonIterableBasedResolvingRestrictionHandler restrictionHandler, - BeanMapper beanMapper){ - super(restrictionHandler); - this.beanMapper = beanMapper; - this.lexBigService = lexBigService; - } - - @SuppressWarnings("unchecked") - @Override - protected O transform( - CodedNodeGraph lexevsObject, Class clazz) { - try { - if(clazz.equals(AssociationDirectory.class)){ - return (O) new ResolvedConceptReferencesIteratorBackedAssociationDirectory(lexevsObject, this.beanMapper); - } - if(clazz.equals(AssociationList.class)){ - return (O) new ResolvedConceptReferencesIteratorBackedAssociationList(lexevsObject, this.beanMapper); - } - } catch (LBException e) { - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - @Override - protected int doCount(ReadContext readContext) { - return 0; - } - - public EntityDirectoryURI getAllSourceAndTargetEntities( - EntityDirectoryURI directory, QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - - public EntityDirectoryURI getPredicates(QueryControl queryControl, ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - - public EntityDirectoryURI getSourceEntities(QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - - public EntityDirectoryURI getTargetEntities( - AssociationDirectoryURI directory, QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - @Override - public EntityDirectoryURI getTargetEntities(QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - public AssociationDirectoryURI restrictToCodeSystemVersion( - NameOrURI codeSystemVersions) { - RestrictToCodeSystemVersionRestriction restriction = new RestrictToCodeSystemVersionRestriction(); - restriction.setCodeSystemVersion(codeSystemVersions); - this.getRestrictionState().getRestrictToCodeSystemVersionRestrictions() - .add(restriction); - - return this.clone(); - } - - public AssociationDirectoryURI restrictToPredicate(EntityNameOrURI predicate) { - RestrictToPredicateRestriction restriction = new RestrictToPredicateRestriction(); - restriction.setPredicate(predicate); - this.getRestrictionState().getRestrictToPredicateRestrictions(); - return this.clone(); - } - - - public AssociationDirectoryURI restrictToSourceEntity(EntityNameOrURI sourceEntity) { - RestrictToSourceEntityRestriction restriction = new RestrictToSourceEntityRestriction(); - restriction.setSourceEntity(sourceEntity); - this.getRestrictionState().getRestrictToPredicateRestrictions(); - return this.clone(); - } - - - public AssociationDirectoryURI restrictToSourceOrTargetEntity(EntityNameOrURI entity) { - RestrictToSourceOrTargetEntityRestriction restriction = new RestrictToSourceOrTargetEntityRestriction(); - restriction.setEntity(entity); - this.getRestrictionState().getRestrictToSourceEntityRestrictions(); - return this.clone(); - } - - - public AssociationDirectoryURI restrictToTargetEntity(EntityNameOrURI target) { - RestrictToTargetEntityRestriction restriction = new RestrictToTargetEntityRestriction(); - restriction.setTarget(target); - this.getRestrictionState().getRestrictToTargetEntityRestrictions(); - return this.clone(); - } - - - public AssociationDirectoryURI restrictToTargetExpression(TargetExpression target) { - RestrictToTargetExpressionRestriction restriction = new RestrictToTargetExpressionRestriction(); - restriction.setTarget(target); - this.getRestrictionState().getRestrictToTargetExpressionRestrictions(); - return this.clone(); - } - - - public AssociationDirectoryURI restrictToTargetLiteral(String target) { - RestrictToTargetLiteralRestriction restriction = new RestrictToTargetLiteralRestriction(); - restriction.setTarget(target); - this.getRestrictionState().getRestrictToTargetLiteralRestriction(); - return this.clone(); - } - - @Override - protected CodedNodeGraph getOriginalState() { - try { - return ProfileUtils.unionAllGraphs(this.lexBigService); - } catch (LBException e) { - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - } - - @Override - protected AssociationDirectoryURI clone() { - return this; - } - - @Override - public AssociationDirectoryRestrictionState getRestrictionState() { - return this.restrictionState; - } - - @Override - protected AssociationDirectoryURI createSetOperatedDirectoryURI( - SetOperator setOperator, AssociationDirectoryURI directoryUri1, - AssociationDirectoryURI directoryUri2) { - DefaultAssociationDirectoryURI uri = new DefaultAssociationDirectoryURI( - this.lexBigService, - this.getRestrictionHandler(), - this.beanMapper); - - uri.getRestrictionState().setSetComposite(new SetComposite()); - uri.getRestrictionState().getSetComposite().setSetOperator(setOperator); - uri.getRestrictionState().getSetComposite().setDirectoryUri1(directoryUri1); - uri.getRestrictionState().getSetComposite().setDirectoryUri2(directoryUri2); - - return uri; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultCodeSystemVersionDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultCodeSystemVersionDirectoryURI.java deleted file mode 100644 index c4fd6e3c95..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultCodeSystemVersionDirectoryURI.java +++ /dev/null @@ -1,189 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Core.types.CodingSchemeVersionStatus; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.core.EntityReference; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.uri.restrict.IterableBasedResolvingRestrictionHandler; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.uri.CodeSystemVersionDirectoryURI; -import org.cts2.uri.restriction.CodeSystemVersionRestrictionState; -import org.cts2.uri.restriction.CodeSystemVersionRestrictionState.RestrictToEntitiesRestriction; -import org.cts2.uri.restriction.SetComposite; - -import scala.actors.threadpool.Arrays; - -import com.google.common.collect.Iterables; - -/** - * The Class DefaultCodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public class DefaultCodeSystemVersionDirectoryURI extends - AbstractIterableLexEvsBackedResolvingDirectoryURI - implements CodeSystemVersionDirectoryURI{ - - /** The coding scheme rendering list. */ - private CodingSchemeRenderingList codingSchemeRenderingList; - - /** The bean mapper. */ - private BeanMapper beanMapper; - - private LexBIGService lexBigService; - - private CodeSystemVersionRestrictionState restrictionState = new CodeSystemVersionRestrictionState(); - - /** - * Instantiates a new default code system version directory uri. - * - * @param codingSchemeRenderingList the coding scheme rendering list - * @param restrictionHandler the restriction handler - * @param beanMapper the bean mapper - */ - public DefaultCodeSystemVersionDirectoryURI( - LexBIGService lexBigService, - CodingSchemeRenderingList codingSchemeRenderingList, - IterableBasedResolvingRestrictionHandler restrictionHandler, - BeanMapper beanMapper) { - super(restrictionHandler); - this.lexBigService = lexBigService; - this.codingSchemeRenderingList = codingSchemeRenderingList; - this.beanMapper = beanMapper; - } - - /* (non-Javadoc) - * @see org.cts2.uri.CodeSystemVersionDirectoryURI#restrictToEntities(java.util.List, org.cts2.service.core.types.RestrictionType, org.cts2.service.core.types.ActiveOrAll) - */ - @Override - public CodeSystemVersionRestrictionState getRestrictionState() { - return this.restrictionState; - } - - @Override - public CodeSystemVersionDirectoryURI restrictToEntities( - final List entities, - final RestrictionType allOrSome, - final ActiveOrAll active) { - - RestrictToEntitiesRestriction restrictToEntities = new RestrictToEntitiesRestriction(); - - restrictToEntities.setActive(active); - restrictToEntities.setAllOrSome(allOrSome); - restrictToEntities.setEntities(entities); - - this.getRestrictionState().getRestrictToEntitiesRestrictions().add(restrictToEntities); - - return clone(); - } - - /** - * Restrict to active or all. - * - * @param csrl the csrl - * @param activeOrAll the active or all - * @return the coding scheme rendering list - */ - protected CodingSchemeRenderingList restrictToActiveOrAll(CodingSchemeRenderingList csrl, ActiveOrAll activeOrAll){ - if(activeOrAll == null){ - return csrl; - } - - CodingSchemeRenderingList returnList = new CodingSchemeRenderingList(); - - for (CodingSchemeRendering csr : csrl.getCodingSchemeRendering()) { - boolean active = - csr.getRenderingDetail().getVersionStatus().equals(CodingSchemeVersionStatus.ACTIVE); - - switch (activeOrAll) { - case ACTIVE_ONLY : { - if(!active){ - break; - } - } - default : { - returnList.addCodingSchemeRendering(csr); - } - } - } - - return returnList; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractIterableLexEvsBackedResolvingDirectoryURI#getOriginalState() - */ - @SuppressWarnings("unchecked") - @Override - protected Iterable getOriginalState() { - return Arrays.asList(this.codingSchemeRenderingList.getCodingSchemeRendering()); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractIterableLexEvsBackedResolvingDirectoryURI#transform(java.lang.Iterable, java.lang.Class) - */ - @Override - protected O transform( - Iterable lexevsObject, - Class clazz) { - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - csrl.setCodingSchemeRendering(Iterables.toArray(lexevsObject,CodingSchemeRendering.class)); - - return this.beanMapper.map(csrl, clazz); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractIterableLexEvsBackedResolvingDirectoryURI#clone() - */ - @Override - protected CodeSystemVersionDirectoryURI clone() { - //TODO: implement no-destructive clone - return this; - } - - - @Override - protected CodeSystemVersionDirectoryURI createSetOperatedDirectoryURI( - SetOperator setOperator, - CodeSystemVersionDirectoryURI directoryUri1, - CodeSystemVersionDirectoryURI directoryUri2) { - DefaultCodeSystemVersionDirectoryURI newUri = - new DefaultCodeSystemVersionDirectoryURI( - this.lexBigService, - this.codingSchemeRenderingList, - this.getRestrictionHandler(), - this.beanMapper); - - newUri.getRestrictionState().setSetComposite(new SetComposite()); - newUri.getRestrictionState().getSetComposite().setDirectoryUri1(directoryUri1); - newUri.getRestrictionState().getSetComposite().setDirectoryUri2(directoryUri2); - - newUri.getRestrictionState().getSetComposite().setSetOperator(setOperator); - - return newUri; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultEntityDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultEntityDirectoryURI.java deleted file mode 100644 index 2ad342097e..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultEntityDirectoryURI.java +++ /dev/null @@ -1,187 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.core.VersionTagReference; -import org.cts2.core.types.SetOperator; -import org.cts2.entity.EntityDirectory; -import org.cts2.entity.EntityList; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.ResolvedConceptReferencesIteratorBackedEntityDirectory; -import org.cts2.internal.model.directory.ResolvedConceptReferencesIteratorBackedEntityList; -import org.cts2.internal.model.uri.restrict.NonIterableBasedResolvingRestrictionHandler; -import org.cts2.internal.model.uri.restrict.Restriction; -import org.cts2.internal.profile.ProfileUtils; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.NameOrURIList; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.EntityDirectoryURI; -import org.cts2.uri.restriction.EntityDirectoryRestrictionState; -import org.cts2.uri.restriction.EntityDirectoryRestrictionState.RestrictToCodeSystemVersionsRestriction; -import org.cts2.uri.restriction.SetComposite; - -/** - * The Class DefaultEntityDirectoryURI. - * - * @author Kevin Peterson - */ -public class DefaultEntityDirectoryURI extends AbstractNonIterableLexEvsBackedResolvingDirectoryURI implements EntityDirectoryURI { - - /** The coded node set. */ - //private CodedNodeSet codedNodeSet; - - /** The bean mapper. */ - private BeanMapper beanMapper; - - private LexBIGService lexBigService; - - private EntityDirectoryRestrictionState entityDirectoryRestrictionState = new EntityDirectoryRestrictionState(); - - /** - * Instantiates a new default code system version directory uri. - * - * @param codedNodeSet the coded node set - * @param restrictionHandler the restriction handler - * @param beanMapper the bean mapper - */ - public DefaultEntityDirectoryURI( - LexBIGService lexBigService, - NonIterableBasedResolvingRestrictionHandler restrictionHandler, - BeanMapper beanMapper) { - super(restrictionHandler); - this.lexBigService = lexBigService; - this.beanMapper = beanMapper; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractDirectoryURI#doCount(org.cts2.service.core.ReadContext) - */ - @Override - protected int doCount(ReadContext readContext) { - try { - Restriction restriction = - this.getRestrictionHandler().compile(this.getThis(), this.getOriginalStateProvider()); - - return this.getRestrictionHandler().apply( restriction, getOriginalState()).resolve(null, null, null, null).numberRemaining(); - } catch (LBException e) { - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractNonIterableLexEvsBackedResolvingDirectoryURI#getOriginalState() - */ - @Override - protected CodedNodeSet getOriginalState() { - try { - return ProfileUtils.unionAll(this.lexBigService); - } catch (LBException e) { - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractNonIterableLexEvsBackedResolvingDirectoryURI#transform(java.lang.Object, java.lang.Class) - */ - @SuppressWarnings("unchecked") - @Override - protected O transform( - CodedNodeSet lexevsObject, Class clazz) { - try { - if(clazz.equals(EntityDirectory.class)){ - return (O) new ResolvedConceptReferencesIteratorBackedEntityDirectory(lexevsObject, this.beanMapper); - } - if(clazz.equals(EntityList.class)){ - return (O) new ResolvedConceptReferencesIteratorBackedEntityList(lexevsObject, this.beanMapper); - } - } catch (LBException e) { - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - - //TODO: real cts2 exception here - throw new IllegalStateException(); - } - - - - /* (non-Javadoc) - * @see org.cts2.uri.EntityDirectoryURI#restrictToCodeSystems(org.cts2.service.core.NameOrURI, org.cts2.core.VersionTagReference) - */ - @Override - public EntityDirectoryURI restrictToCodeSystems( - NameOrURI codeSystems, - VersionTagReference tag) { - //this.entityDirectoryRestrictionState.add... - return clone(); - } - - /* (non-Javadoc) - * @see org.cts2.uri.EntityDirectoryURI#restrictToCodeSystemVersions(org.cts2.service.core.NameOrURI) - */ - @Override - public EntityDirectoryURI restrictToCodeSystemVersions( - NameOrURI codeSystemVersions) { - RestrictToCodeSystemVersionsRestriction restriction = new RestrictToCodeSystemVersionsRestriction(); - NameOrURIList list = new NameOrURIList(); - list.addEntry(codeSystemVersions); - - restriction.setCodeSystemVersions(list); - - this.getThis().getRestrictionState().getRestrictToCodeSystemVersionsRestrictions().add(restriction); - - return clone(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.AbstractNonIterableLexEvsBackedResolvingDirectoryURI#clone() - */ - @Override - protected EntityDirectoryURI clone() { - return this; - } - - @Override - public EntityDirectoryRestrictionState getRestrictionState() { - return this.entityDirectoryRestrictionState; - } - - @Override - protected EntityDirectoryURI createSetOperatedDirectoryURI( - SetOperator setOperator, - EntityDirectoryURI directoryUri1, - EntityDirectoryURI directoryUri2) { - DefaultEntityDirectoryURI uri = new DefaultEntityDirectoryURI( - this.lexBigService, - this.getRestrictionHandler(), - this.beanMapper); - - uri.getRestrictionState().setSetComposite(new SetComposite()); - uri.getRestrictionState().getSetComposite().setSetOperator(setOperator); - uri.getRestrictionState().getSetComposite().setDirectoryUri1(directoryUri1); - uri.getRestrictionState().getSetComposite().setDirectoryUri2(directoryUri2); - - return uri; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultMapVersionDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultMapVersionDirectoryURI.java deleted file mode 100644 index d6df7d8361..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultMapVersionDirectoryURI.java +++ /dev/null @@ -1,133 +0,0 @@ -package org.cts2.internal.model.uri; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.directory.ResolvedConceptReferencesIteratorBackedMapVersionDirectory; -import org.cts2.internal.model.directory.ResolvedConceptReferencesIteratorBackedMapVersionListDirectory; -import org.cts2.internal.model.uri.restrict.IterableBasedResolvingRestrictionHandler; -import org.cts2.map.MapVersionDirectory; -import org.cts2.map.MapVersionList; -import org.cts2.service.core.NameOrURIList; -import org.cts2.uri.MapVersionDirectoryURI; -import org.cts2.uri.restriction.MapVersionDirectoryRestrictionState; -import org.cts2.uri.restriction.SetComposite; - - -import scala.actors.threadpool.Arrays; - -/** - * - * @author Zonghui Lian - * - */ -public class DefaultMapVersionDirectoryURI - extends - AbstractIterableLexEvsBackedResolvingDirectoryURI - implements MapVersionDirectoryURI { - - private BeanMapper beanMapper; - private LexBIGService lexBigService; - private CodingSchemeRenderingList codingSchemeRenderingList; - private MapVersionDirectoryRestrictionState restrictionState = new MapVersionDirectoryRestrictionState(); // TODO - // double - // check - // MapVersionDirectoryRestrictionState - - /** - * Instantiates a new default map version directory uri. - * - * @param lexBigService - * @param codingSchemeRenderingList - * @param restrictionHandler - * @param beanMapper - */ - public DefaultMapVersionDirectoryURI( - LexBIGService lexBigService, - CodingSchemeRenderingList codingSchemeRenderingList, - IterableBasedResolvingRestrictionHandler restrictionHandler, - BeanMapper beanMapper) { - super(restrictionHandler); - this.lexBigService = lexBigService; - this.beanMapper = beanMapper; - this.codingSchemeRenderingList = codingSchemeRenderingList; - } - - @Override - public MapVersionDirectoryRestrictionState getRestrictionState() { - return this.restrictionState; - } - - @Override - public MapVersionDirectoryURI restrictToCodeSystems( - MapVersionDirectoryURI directory, NameOrURIList codeSystems) { - // TODO Auto-generated method stub - return null; - } - - @SuppressWarnings("unchecked") - @Override - protected Iterable getOriginalState() { - return Arrays.asList(this.codingSchemeRenderingList - .getCodingSchemeRendering()); - } - - @SuppressWarnings("unchecked") - @Override - protected O transform(Iterable lexevsObject, - Class clazz) { - if (clazz.equals(MapVersionDirectory.class)) { - try { - return (O) new ResolvedConceptReferencesIteratorBackedMapVersionDirectory( - lexevsObject, this.beanMapper); - } catch (LBException e) { - throw new RuntimeException(e); - } - } - if (clazz.equals(MapVersionList.class)) { - try { - return (O) new ResolvedConceptReferencesIteratorBackedMapVersionListDirectory( - lexevsObject, this.beanMapper); - } catch (LBException e) { - throw new RuntimeException(e); - } - } - return null; -// CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); -// csrl.setCodingSchemeRendering(Iterables.toArray(lexevsObject, -// CodingSchemeRendering.class)); -// -// return this.beanMapper.map(csrl, clazz); - } - - @Override - protected MapVersionDirectoryURI createSetOperatedDirectoryURI( - SetOperator setOperator, MapVersionDirectoryURI directoryUri1, - MapVersionDirectoryURI directoryUri2) { - DefaultMapVersionDirectoryURI newUri = new DefaultMapVersionDirectoryURI( - this.lexBigService, this.codingSchemeRenderingList, - this.getRestrictionHandler(), this.beanMapper); - - newUri.getRestrictionState().setSetComposite( - new SetComposite()); - newUri.getRestrictionState().getSetComposite() - .setDirectoryUri1(directoryUri1); - newUri.getRestrictionState().getSetComposite() - .setDirectoryUri2(directoryUri2); - - newUri.getRestrictionState().getSetComposite() - .setSetOperator(setOperator); - - return newUri; - } - - @Override - protected MapVersionDirectoryURI clone() { - // TODO - return this; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultValueSetDefinitionDirectoryURI.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultValueSetDefinitionDirectoryURI.java deleted file mode 100644 index 1d79ed9879..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/DefaultValueSetDefinitionDirectoryURI.java +++ /dev/null @@ -1,122 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.LexGrid.valueSets.ValueSetDefinitions; -import org.cts2.core.EntityReference; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.model.uri.restrict.IterableBasedResolvingRestrictionHandler; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; -import org.cts2.uri.restriction.SetComposite; -import org.cts2.uri.restriction.ValueSetDefinitionRestrictionState; -import org.cts2.uri.restriction.ValueSetDefinitionRestrictionState.RestrictToEntitiesRestriction; - -import com.google.common.collect.Iterables; - -import scala.actors.threadpool.Arrays; - -/** - * The Class DefaultCodeSystemVersionDirectoryURI. - * - * @author Kevin Peterson - */ -public class DefaultValueSetDefinitionDirectoryURI extends AbstractIterableLexEvsBackedResolvingDirectoryURI - implements ValueSetDefinitionDirectoryURI{ - - private BeanMapper beanMapper; - - private ValueSetDefinitions valueSetDefinitions; - - private ValueSetDefinitionRestrictionState valueSetDefinitionRestrictionState = new ValueSetDefinitionRestrictionState(); - - /** - * Instantiates a new default value set definition directory uri. - * - * @param valueSetDefinitionList the list value set definition - * @param beanMapper the bean mapper - */ - public DefaultValueSetDefinitionDirectoryURI( - ValueSetDefinitions valueSetDefinitions, - IterableBasedResolvingRestrictionHandler restrictionHandler, - BeanMapper beanMapper) { - super(restrictionHandler); - this.valueSetDefinitions = valueSetDefinitions; - this.beanMapper = beanMapper; - } - - @SuppressWarnings("unchecked") - @Override - protected Iterable getOriginalState() { - return Arrays.asList(this.valueSetDefinitions.getValueSetDefinition()); - } - - @Override - protected ValueSetDefinitionDirectoryURI clone() { - return this; - } - - @Override - public ValueSetDefinitionRestrictionState getRestrictionState() { - return this.valueSetDefinitionRestrictionState; - } - - @Override - protected O transform(Iterable lexevsObject, - Class clazz) { - ValueSetDefinitions vsds = new ValueSetDefinitions(); - vsds.setValueSetDefinition(Iterables.toArray(lexevsObject,ValueSetDefinition.class)); - return this.beanMapper.map(vsds, clazz); - } - - @Override - public ValueSetDefinitionDirectoryURI restrictToEntities( - List entityList) { - RestrictToEntitiesRestriction restriction = new RestrictToEntitiesRestriction(); - restriction.setEntityReferences(entityList); - - this.getRestrictionState().getRestrictToEntitiesRestriction().add(restriction); - - return this.clone(); - } - - @Override - protected ValueSetDefinitionDirectoryURI createSetOperatedDirectoryURI( - SetOperator setOperator, - ValueSetDefinitionDirectoryURI directoryUri1, - ValueSetDefinitionDirectoryURI directoryUri2) { - DefaultValueSetDefinitionDirectoryURI newUri = - new DefaultValueSetDefinitionDirectoryURI( - this.valueSetDefinitions, - this.getRestrictionHandler(), - this.beanMapper); - - newUri.getRestrictionState().setSetComposite(new SetComposite()); - newUri.getRestrictionState().getSetComposite().setDirectoryUri1(directoryUri1); - newUri.getRestrictionState().getSetComposite().setDirectoryUri2(directoryUri2); - - newUri.getRestrictionState().getSetComposite().setSetOperator(setOperator); - - return newUri; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/AbstractCompositeDirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/AbstractCompositeDirectoryURIFactory.java deleted file mode 100644 index 39dc087c46..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/AbstractCompositeDirectoryURIFactory.java +++ /dev/null @@ -1,119 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.uri.DirectoryURI; -import org.lexgrid.valuesets.LexEVSPickListDefinitionServices; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; - -/** - * A factory for creating AbstractDirectoryURI objects. - * - * @author Kevin Peterson - */ -public abstract class AbstractCompositeDirectoryURIFactory implements DirectoryURIFactory{ - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /** The lex big service. */ - private LexBIGService lexBigService; - - /** The LexEVS Value Set Definition Service. */ - private LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService; - - /** The LexEVS Pick List Definition Service. */ - private LexEVSPickListDefinitionServices lexEVSPickListDefinitionService; - - @Override - public T getDirectoryURI() { - return - this.doBuildDirectoryURI(); - } - - protected abstract T doBuildDirectoryURI(); - - /** - * Gets the bean mapper. - * - * @return the bean mapper - */ - public BeanMapper getBeanMapper() { - return this.beanMapper; - } - - /** - * Sets the bean mapper. - * - * @param beanMapper the new bean mapper - */ - public void setBeanMapper(BeanMapper beanMapper) { - this.beanMapper = beanMapper; - } - - /** - * Sets the lex big service. - * - * @param lexBigService the new lex big service - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - public LexBIGService getLexBigService() { - return this.lexBigService; - } - - /** - * @return the lexEVSValueSetDefinitionService - */ - public LexEVSValueSetDefinitionServices getLexEVSValueSetDefinitionService() { - return lexEVSValueSetDefinitionService; - } - - /** - * @param lexEVSValueSetDefinitionService the lexEVSValueSetDefinitionService to set - */ - public void setLexEVSValueSetDefinitionService( - LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService) { - this.lexEVSValueSetDefinitionService = lexEVSValueSetDefinitionService; - } - - /** - * @return the lexEVSPickListDefinitionService - */ - public LexEVSPickListDefinitionServices getLexEVSPickListDefinitionService() { - return lexEVSPickListDefinitionService; - } - - /** - * @param lexEVSPickListDefinitionService the lexEVSPickListDefinitionService to set - */ - public void setLexEVSPickListDefinitionService( - LexEVSPickListDefinitionServices lexEVSPickListDefinitionService) { - this.lexEVSPickListDefinitionService = lexEVSPickListDefinitionService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/AssociationDirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/AssociationDirectoryURIFactory.java deleted file mode 100644 index 92924d3122..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/AssociationDirectoryURIFactory.java +++ /dev/null @@ -1,56 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.internal.model.uri.DefaultAssociationDirectoryURI; -import org.cts2.internal.model.uri.restrict.NonIterableBasedResolvingRestrictionHandler; -import org.cts2.internal.profile.ProfileUtils; -import org.cts2.uri.AssociationDirectoryURI; -import org.springframework.util.Assert; - -/** - * An Association Directory URI Factory - * - * @author Scott Bauer - * - */ -public class AssociationDirectoryURIFactory extends - AbstractCompositeDirectoryURIFactory { - - //TODO Check for correct implementation recent changes - private NonIterableBasedResolvingRestrictionHandler restrictionHandler; - - @Override - protected AssociationDirectoryURI doBuildDirectoryURI() { - Assert.notNull(this.restrictionHandler); - return new DefaultAssociationDirectoryURI(this.getLexBigService(), this.restrictionHandler, this.getBeanMapper()); - } - - public NonIterableBasedResolvingRestrictionHandler getRestrictionHandler() { - return restrictionHandler; - } - - public void setRestrictionHandler( - NonIterableBasedResolvingRestrictionHandler restrictionHandler) { - this.restrictionHandler = restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/CodeSystemDirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/CodeSystemDirectoryURIFactory.java deleted file mode 100644 index 0099a7d834..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/CodeSystemDirectoryURIFactory.java +++ /dev/null @@ -1,35 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import org.cts2.uri.CodeSystemDirectoryURI; - -/** - * A factory for creating CodeSystemDirectoryURI objects. - * - * @author Kevin Peterson - */ -public class CodeSystemDirectoryURIFactory extends AbstractCompositeDirectoryURIFactory { - - @Override - protected CodeSystemDirectoryURI doBuildDirectoryURI() { - // TODO Auto-generated method stub - return null; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/CodeSystemVersionDirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/CodeSystemVersionDirectoryURIFactory.java deleted file mode 100644 index e39d027cbb..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/CodeSystemVersionDirectoryURIFactory.java +++ /dev/null @@ -1,65 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import junit.framework.Assert; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.cts2.internal.model.uri.DefaultCodeSystemVersionDirectoryURI; -import org.cts2.internal.model.uri.restrict.IterableBasedResolvingRestrictionHandler; -import org.cts2.uri.CodeSystemVersionDirectoryURI; - -/** - * A factory for creating CodeSystemVersionDirectoryURIFactory objects. - * - * @author Kevin Peterson - */ -public class CodeSystemVersionDirectoryURIFactory extends AbstractCompositeDirectoryURIFactory { - - private IterableBasedResolvingRestrictionHandler restrictionHandler; - - /* (non-Javadoc) - * @see org.cts2.internal.uri.factory.AbstractDirectoryURIFactory#doGetDirectoryURI() - */ - @Override - protected CodeSystemVersionDirectoryURI doBuildDirectoryURI() { - Assert.assertNotNull(this.restrictionHandler); - - CodingSchemeRenderingList codingSchemeRenderingList; - - try { - codingSchemeRenderingList = this.getLexBigService().getSupportedCodingSchemes(); - } catch (LBInvocationException e) { - throw new RuntimeException(e); - } - - return new DefaultCodeSystemVersionDirectoryURI(this.getLexBigService(), codingSchemeRenderingList, this.restrictionHandler, this.getBeanMapper()); - } - - public IterableBasedResolvingRestrictionHandler getRestrictionHandler() { - return restrictionHandler; - } - - public void setRestrictionHandler( - IterableBasedResolvingRestrictionHandler restrictionHandler) { - this.restrictionHandler = restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/DirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/DirectoryURIFactory.java deleted file mode 100644 index 923fd1b31d..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/DirectoryURIFactory.java +++ /dev/null @@ -1,36 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import org.cts2.uri.DirectoryURI; - -/** - * A factory for creating DirectoryURI objects. - * - * @author Kevin Peterson - */ -public interface DirectoryURIFactory { - - /** - * Gets the directory uri. - * - * @return the directory uri - */ - public T getDirectoryURI(); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/EntityDirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/EntityDirectoryURIFactory.java deleted file mode 100644 index 88d7bbb65e..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/EntityDirectoryURIFactory.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import junit.framework.Assert; - -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.cts2.internal.model.uri.DefaultEntityDirectoryURI; -import org.cts2.internal.model.uri.restrict.NonIterableBasedResolvingRestrictionHandler; -import org.cts2.uri.EntityDirectoryURI; - - -/** - * A factory for creating CodeSystemVersionDirectoryURIFactory objects. - * - * @author Kevin Peterson - */ -public class EntityDirectoryURIFactory extends AbstractCompositeDirectoryURIFactory { - - private NonIterableBasedResolvingRestrictionHandler restrictionHandler; - - @Override - protected EntityDirectoryURI doBuildDirectoryURI() { - Assert.assertNotNull(this.restrictionHandler); - - return new DefaultEntityDirectoryURI(this.getLexBigService(), this.restrictionHandler, this.getBeanMapper()); - } - - public void setRestrictionHandler(NonIterableBasedResolvingRestrictionHandler restrictionHandler) { - this.restrictionHandler = restrictionHandler; - } - - public NonIterableBasedResolvingRestrictionHandler getRestrictionHandler() { - return restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/ValueSetDefinitionDirectoryURIFactory.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/ValueSetDefinitionDirectoryURIFactory.java deleted file mode 100644 index 7c4ac02038..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/factory/ValueSetDefinitionDirectoryURIFactory.java +++ /dev/null @@ -1,82 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.factory; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.ArrayList; -import java.util.List; - -import junit.framework.Assert; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.LexGrid.valueSets.ValueSetDefinitions; -import org.cts2.internal.model.uri.DefaultValueSetDefinitionDirectoryURI; -import org.cts2.internal.model.uri.restrict.IterableBasedResolvingRestrictionHandler; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; - -/** - * A factory for creating ValueSetDefinitionDirectoryURIFactory objects. - * - * @author Sridhar Dwarkanath - */ -public class ValueSetDefinitionDirectoryURIFactory extends AbstractCompositeDirectoryURIFactory { - - private IterableBasedResolvingRestrictionHandler restrictionHandler; - - /* (non-Javadoc) - * @see org.cts2.internal.uri.factory.AbstractDirectoryURIFactory#doGetDirectoryURI() - */ - @Override - protected ValueSetDefinitionDirectoryURI doBuildDirectoryURI() { - Assert.assertNotNull(this.restrictionHandler); - - ValueSetDefinitions valueSetDefinitions = new ValueSetDefinitions(); - - try { - List valueSetURIs = this.getLexEVSValueSetDefinitionService().listValueSetDefinitionURIs(); - - for (String vsdURI : valueSetURIs) - { - valueSetDefinitions.addValueSetDefinition(this.getLexEVSValueSetDefinitionService().getValueSetDefinition(new URI(vsdURI), null)); - } - } catch (LBInvocationException e) { - throw new RuntimeException(e); - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (URISyntaxException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - return new DefaultValueSetDefinitionDirectoryURI(valueSetDefinitions, this.restrictionHandler, this.getBeanMapper()); - } - - public IterableBasedResolvingRestrictionHandler getRestrictionHandler() { - return restrictionHandler; - } - - public void setRestrictionHandler( - IterableBasedResolvingRestrictionHandler restrictionHandler) { - this.restrictionHandler = restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractIterableLexEvsBackedRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractIterableLexEvsBackedRestrictionHandler.java deleted file mode 100644 index ad5ea9c35b..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractIterableLexEvsBackedRestrictionHandler.java +++ /dev/null @@ -1,297 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.apache.commons.collections.CollectionUtils; -import org.cts2.core.Filter; -import org.cts2.core.FilterComponent; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.NameOrURI; -import org.cts2.core.PredicateReference; -import org.cts2.core.types.SetOperator; -import org.cts2.core.types.TargetReferenceType; -import org.cts2.internal.match.MatchAlgorithm; -import org.cts2.internal.match.ResolvableModelAttributeReference; -import org.cts2.uri.DirectoryURI; -import org.cts2.uri.restriction.RestrictionState; - -import com.google.common.collect.Iterables; - -/** - * The Class AbstractIterableLexEvsBackedRestrictionHandler. - * - * @author Kevin Peterson - */ -public abstract class AbstractIterableLexEvsBackedRestrictionHandler extends AbstractRestrictionHandler - implements IterableBasedResolvingRestrictionHandler { - - private static float DEFAULT_SCORE_THRESHOLD = 0.5f; - - /** The resolvable model attribute references. */ - private List> resolvableModelAttributeReferences; - - /** The match algorithms. */ - private List matchAlgorithms; - - /** - * Instantiates a new abstract iterable lex evs backed restriction handler. - */ - public AbstractIterableLexEvsBackedRestrictionHandler(){ - super(); - this.resolvableModelAttributeReferences = this.registerSupportedModelAttributeReferences(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.RestrictionHandler#getSupportedPredicateReferences() - */ - @Override - public List getSupportedPredicateReferences() { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.ResolvingRestrictionHandler#getSupportedModelAttributes() - */ - @Override - public List> getSupportedModelAttributeReferences() { - return this.resolvableModelAttributeReferences; - } - - /** - * Register supported model attributes. - * - * @return the list - */ - public abstract List> registerSupportedModelAttributeReferences(); - - public abstract List> processOtherRestictions(D directoryUri); - - public Iterable apply(IterableRestriction restriction, Iterable state){ - return restriction.processRestriction(state); - } - - public IterableRestriction processSetOperation(final D i1, final D i2, final SetOperator setOperator) { - return new IterableRestriction(){ - - @Override - public Iterable processRestriction(Iterable state) { - Set set1 = new HashSet(); - Set set2 = new HashSet(); - - IterableRestriction restrictions1 = compile(i1); - IterableRestriction restrictions2 = compile(i2); - - Iterables.addAll(set1, restrictions1.processRestriction(state)); - - Iterables.addAll(set2, restrictions2.processRestriction(state)); - - switch (setOperator){ - case UNION : { - set1.addAll(set2); - return set1; - } - case INTERSECT : { - set1.retainAll(set2); - return set1; - } - case SUBTRACT : { - set1.removeAll(set2); - return set1; - } - } - - throw new IllegalStateException(); - } - }; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.ListBasedResolvingRestrictionHandler#restrict(java.util.List, org.cts2.core.Filter) - */ - @SuppressWarnings("unchecked") - public IterableRestriction compile(D directoryURI) { - RestrictionState restriction = directoryURI.getRestrictionState(); - - final List> returnList = new ArrayList>(); - - for(final Filter filter : restriction.getFilters()){ - - returnList.add(new IterableRestriction(){ - - @Override - public Iterable processRestriction(Iterable originalState) { - - originalState = Iterables.unmodifiableIterable(originalState); - - List filterComponents = Arrays.asList(filter.getComponent()); - - Collection restrictedState = new ArrayList(); - - for (FilterComponent filterComponent : filterComponents) { - restrictedState.addAll(doRestrict(originalState, filterComponent, DEFAULT_SCORE_THRESHOLD)); - } - - return restrictedState; - }; - }); - } - - List> otherRestrictions = this.processOtherRestictions(directoryURI); - if(CollectionUtils.isNotEmpty(otherRestrictions)){ - returnList.addAll(otherRestrictions); - } - - if(restriction.getSetComposite() != null){ - returnList.add(this.processSetOperation( - (D)restriction.getSetComposite().getDirectoryUri1(), - (D)restriction.getSetComposite().getDirectoryUri2(), - restriction.getSetComposite().getSetOperator())); - } - - return RestrictionUtils.combineIterableRestrictions(returnList); - } - - - - /** - * Do restrict. - * - * @param originalState the original state - * @param filterComponent the filter component - * @param minScore the min score - * @return the list - */ - protected Collection doRestrict(Iterable originalState, FilterComponent filterComponent, float minScore){ - MatchAlgorithm algorithm = this.getMatchAlgorithm(filterComponent.getMatchAlgorithm()); - - TargetReferenceType referenceType = filterComponent.getFilterComponent().getReferenceType(); - - List returnList = new ArrayList(); - - String matchText = filterComponent.getMatchValue(); - - for(T candidate : originalState){ - String candidateText = - this.getCandidateText(filterComponent, referenceType, candidate); - float score = algorithm.matchScore(matchText, candidateText); - - if(score != 0 && score >= minScore){ - returnList.add(candidate); - } - } - - return returnList; - } - - /** - * Gets the candidate text. - * - * @param filterComponent the filter component - * @param referenceType the reference type - * @param candidate the candidate - * @return the candidate text - */ - private String getCandidateText( - FilterComponent filterComponent, - TargetReferenceType referenceType, - T candidate) { - String candidateText; - - switch (referenceType) { - case PROPERTY : { - throw new UnsupportedOperationException(); - } - case ATTRIBUTE : { - ResolvableModelAttributeReference modelAttributeReference = - this.getResolvableModelAttributeReferences(filterComponent.getFilterComponent().getReferenceTarget()); - - candidateText = modelAttributeReference.getModelAttributeValue(candidate); - break; - } - case SPECIAL : { - throw new UnsupportedOperationException(); - } - - default : { - throw new IllegalStateException(); - } - } - - return candidateText; - } - - /** - * Gets the resolvable model attribute references. - * - * @param nameOrUri the name or uri - * @return the resolvable model attribute references - */ - private ResolvableModelAttributeReference getResolvableModelAttributeReferences(NameOrURI nameOrUri){ - for(ResolvableModelAttributeReference modelAttribute : this.resolvableModelAttributeReferences){ - if(modelAttribute.getContent().equals(nameOrUri.getName())){ - return modelAttribute; - } - } - - //TODO: validate this instead of returning null - return null; - } - - /** - * Gets the match algorithm. - * - * @param reference the reference - * @return the match algorithm - */ - protected MatchAlgorithm getMatchAlgorithm(MatchAlgorithmReference reference){ - for(MatchAlgorithm matchAlgorithm : this.matchAlgorithms){ - if(matchAlgorithm.getName().equals(reference.getContent())){ - return matchAlgorithm; - } - } - - //TODO: validate this instead of returning null - return null; - } - - /** - * Gets the match algorithms. - * - * @return the match algorithms - */ - public List getMatchAlgorithms() { - return matchAlgorithms; - } - - /** - * Sets the match algorithms. - * - * @param matchAlgorithms the new match algorithms - */ - public void setMatchAlgorithms(List matchAlgorithms) { - this.matchAlgorithms = matchAlgorithms; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractNonIterableLexEvsBackedRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractNonIterableLexEvsBackedRestrictionHandler.java deleted file mode 100644 index 412289bc2b..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractNonIterableLexEvsBackedRestrictionHandler.java +++ /dev/null @@ -1,182 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.collections.CollectionUtils; -import org.cts2.core.Filter; -import org.cts2.core.FilterComponent; -import org.cts2.core.NameOrURI; -import org.cts2.core.PredicateReference; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.match.OperationExecutingModelAttributeReference; -import org.cts2.uri.DirectoryURI; -import org.cts2.uri.restriction.RestrictionState; - -/** - * The Class AbstractNonIterableLexEvsBackedRestrictionHandler. - * - * @param the - * @author Kevin Peterson - */ -public abstract class AbstractNonIterableLexEvsBackedRestrictionHandler - extends AbstractRestrictionHandler implements NonIterableBasedResolvingRestrictionHandler { - - /** The operation executing model attribute reference. */ - private List> operationExecutingModelAttributeReferences; - - public AbstractNonIterableLexEvsBackedRestrictionHandler() { - super(); - this.operationExecutingModelAttributeReferences = this.registerSupportedModelAttributeReferences(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.NonIterableBasedResolvingRestrictionHandler#restrict(java.lang.Object, org.cts2.core.Filter) - */ - @SuppressWarnings("unchecked") - @Override - public Restriction compile(D directoryURI, OriginalStateProvider originalStateProvider) { - - RestrictionState restriction = directoryURI.getRestrictionState(); - - final List> returnList = new ArrayList>(); - - for(final Filter filter : restriction.getFilters()){ - - returnList.add(new Restriction(){ - - @Override - public T processRestriction(T state) { - List filterComponents = Arrays.asList(filter.getComponent()); - - for (FilterComponent filterComponent : filterComponents) { - OperationExecutingModelAttributeReference operation = - getOperationExecutingModelAttributeReference(filterComponent.getFilterComponent().getReferenceTarget()); - - state = operation.executeOperation( - state, - filterComponent.getMatchValue(), - filterComponent.getMatchAlgorithm()); - } - - return state; - } - }); - } - - List> otherRestrictions = this.processOtherRestictions(directoryURI); - if(CollectionUtils.isNotEmpty(otherRestrictions)){ - returnList.addAll(otherRestrictions); - } - - if(restriction.getSetComposite() != null){ - returnList.add(this.processSetOperation( - (D)restriction.getSetComposite().getDirectoryUri1(), - (D)restriction.getSetComposite().getDirectoryUri2(), - restriction.getSetComposite().getSetOperator(), - originalStateProvider)); - } - - return RestrictionUtils.combineRestrictions(returnList); - } - - public T apply(Restriction restriction, T state){ - return restriction.processRestriction(state); - } - - protected abstract List> processOtherRestictions(D directoryURI); - - public Restriction processSetOperation(final D directoryUri1, final D directoryUri2, final SetOperator setOperator, final OriginalStateProvider originalStateProvider) { - return new Restriction(){ - - @Override - public T processRestriction(T state) { - - switch (setOperator){ - case UNION : { - return doUnion(directoryUri1, directoryUri2, originalStateProvider); - } - case INTERSECT : { - return doIntersect(directoryUri1, directoryUri2, originalStateProvider); - } - case SUBTRACT : { - return doDifference(directoryUri1, directoryUri2, originalStateProvider); - } - } - - throw new IllegalStateException(); - } - }; - } - - protected abstract T doUnion(final D directoryUri1, final D directoryUri2, OriginalStateProvider originalStateProvider); - - protected abstract T doIntersect(final D directoryUri1, final D directoryUri2, OriginalStateProvider originalStateProvider); - - protected abstract T doDifference(final D directoryUri1, final D directoryUri2, OriginalStateProvider originalStateProvider); - - /** - * Register supported model attribute references. - * - * @return the list - */ - public abstract List> registerSupportedModelAttributeReferences(); - - /** - * Gets the operation executing model attribute reference. - * - * @param nameOrUri the name or uri - * @return the operation executing model attribute reference - */ - private OperationExecutingModelAttributeReference getOperationExecutingModelAttributeReference(NameOrURI nameOrUri){ - for(OperationExecutingModelAttributeReference modelAttribute : this.operationExecutingModelAttributeReferences){ - if(modelAttribute.getContent().equals(nameOrUri.getName())){ - return modelAttribute; - } - - if(modelAttribute.getMeaning().equals(nameOrUri.getUri())){ - return modelAttribute; - } - } - - //TODO: validate this instead of returning null - return null; - } - - - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.RestrictionHandler#getSupportedPredicateReferences() - */ - @Override - public List getSupportedPredicateReferences() { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.ResolvingRestrictionHandler#getSupportedModelAttributes() - */ - @Override - public List> getSupportedModelAttributeReferences() { - return this.operationExecutingModelAttributeReferences; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractRestrictionHandler.java deleted file mode 100644 index c70661363c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/AbstractRestrictionHandler.java +++ /dev/null @@ -1,49 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.List; - -import org.cts2.core.MatchAlgorithmReference; - -/** - * The Class AbstractRestrictionHandler. - * - * @author Kevin Peterson - */ -public abstract class AbstractRestrictionHandler implements RestrictionHandler { - - /** The match algorithm references. */ - private List matchAlgorithmReferences; - - /** - * Register supported match algorithm references. - * - * @return the list - */ - public abstract List registerSupportedMatchAlgorithmReferences(); - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.RestrictionHandler#getSupportedMatchAlgorithmReferences() - */ - @Override - public List getSupportedMatchAlgorithmReferences() { - return this.matchAlgorithmReferences; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultAssociationRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultAssociationRestrictionHandler.java deleted file mode 100644 index ad18a057e7..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultAssociationRestrictionHandler.java +++ /dev/null @@ -1,372 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.ArrayList; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.ConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Collections.NameAndValueList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.cts2.constant.ExternalCts2Constants; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.VersionTagReference; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.match.OperationExecutingModelAttributeReference; -import org.cts2.internal.match.OperationExecutingModelAttributeReference.RestrictionOperation; -import org.cts2.internal.profile.ProfileUtils; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.uri.AssociationDirectoryURI; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToCodeSystemVersionRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToPredicateRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToSourceEntityRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToSourceOrTargetEntityRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToTargetEntityRestriction; -import org.cts2.uri.restriction.AssociationDirectoryRestrictionState.RestrictToTargetLiteralRestriction; - -/** - * The Class DefaultEntityDescriptionRestrictionHandler. - * - * @author Kevin Peterson - * @author Scott Bauer - * - */ -public class DefaultAssociationRestrictionHandler - extends AbstractNonIterableLexEvsBackedRestrictionHandler { - - /** The lex evs identity converter. */ - //TODO provide new identity converter or supporting methods for this restriction handler - private LexEvsIdentityConverter lexEvsIdentityConverter; - - /** The lex big service. */ - private LexBIGService lexBigService; - - protected Restriction restrictToCodeSystems( - NameOrURI codeSystems, - VersionTagReference tag) { - //TODO: decide strategy for implementing CodeSystem profile. - throw new UnsupportedOperationException(); - } - - /** - * @param codeSystemVersions - * @return - */ - protected Restriction restrictToCodeSystemVersions( - final NameOrURI codeSystemVersions) { - - return new Restriction(){ - - @Override - public CodedNodeGraph processRestriction(CodedNodeGraph state) { - AbsoluteCodingSchemeVersionReference ref = - lexEvsIdentityConverter.nameOrUriToAbsoluteCodingSchemeVersionReference(codeSystemVersions); - - try { - CodedNodeGraph versionToRestrictTo = - lexBigService.getNodeGraph(ref.getCodingSchemeURN(), - Constructors.createCodingSchemeVersionOrTagFromVersion(ref.getCodingSchemeVersion()), null); - - return state.intersect(versionToRestrictTo); - } catch (LBException e) { - //TODO: throw real CTS2 exception - throw new RuntimeException(e); - } - } - }; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractNonIterableLexEvsBackedRestrictionHandler#registerSupportedModelAttributeReferences() - */ - @Override - public List> registerSupportedModelAttributeReferences() { - //Not doing filtered restrictions on the Associations so we return an empty list. - List> returnList = - new ArrayList>(); - return returnList; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractRestrictionHandler#registerSupportedMatchAlgorithmReferences() - */ - @Override - public List registerSupportedMatchAlgorithmReferences() { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractNonIterableLexEvsBackedRestrictionHandler#processOtherRestictions(org.cts2.uri.DirectoryURI) - */ - @Override - protected List> processOtherRestictions( - AssociationDirectoryURI directoryURI) { - List> returnList = new ArrayList>(); - - AssociationDirectoryRestrictionState state = directoryURI.getRestrictionState(); - - for(RestrictToCodeSystemVersionRestriction restriction : state.getRestrictToCodeSystemVersionRestrictions()){ - returnList.add(this.restrictToCodeSystemVersions(restriction.getCodeSystemVersion())); - } - for(RestrictToPredicateRestriction restriction : state.getRestrictToPredicateRestrictions()){ - returnList.add(this.restrictToPredicate(restriction.getPredicate())); - } - for(RestrictToPredicateRestriction restriction : state.getRestrictToPredicateRestrictions()){ - returnList.add(this.restrictToPredicate(restriction.getPredicate())); - } - for(RestrictToSourceEntityRestriction restriction : state.getRestrictToSourceEntityRestrictions()){ - returnList.add(this.restrictToSourceEntityRestrictions(restriction.getSourceEntity())); - } - for(RestrictToSourceOrTargetEntityRestriction restriction : state.getRestrictToSourceOrTargetEntityRestrictions()){ - returnList.add(this.restrictToSourceOrTargetEntityRestriction(restriction.getEntity())); - } - for(RestrictToTargetEntityRestriction restriction : state.getRestrictToTargetEntityRestrictions()){ - returnList.add(this.restrictToTargetEntityRestriction(restriction.getTarget())); - } - for(RestrictToTargetLiteralRestriction restriction : state.getRestrictToTargetLiteralRestriction()){ - returnList.add(this.restrictToTargetLiteralRestriction(restriction.getTarget())); - } - return returnList; - } - - /** - * - * Restrict to the predicate (Association Name) for this association - * @param predicate - a wrapper class containing the name - * @return this restriction to the coded node graph. - */ - protected Restriction restrictToPredicate(final EntityNameOrURI predicate) { - - return new Restriction(){ - - @Override - public CodedNodeGraph processRestriction(CodedNodeGraph state) { - NameAndValueList association = - Constructors.createNameAndValueList(predicate.getEntityName().getName(), null); - try { - state = state.restrictToAssociations(association, null); - } catch (Exception e) { - // TODO throw CTS2 Exception - throw new RuntimeException(e); - } - return state; - } - }; - } - - /** - * Restrict to the source entity unique identifier - * @param sourceEntity - wrapper class for the unique identifier - * @return this restriction to the coded node graph. - */ - protected Restriction restrictToSourceEntityRestrictions(final EntityNameOrURI sourceEntity) { - - return new Restriction(){ - @Override - public CodedNodeGraph processRestriction(CodedNodeGraph state) { - - try { - //TODO find a method of restricting codes to the current restricted state of this node graph. - CodedNodeSet codes = ProfileUtils.unionAll(lexBigService); - ConceptReferenceList codeList = Constructors.createConceptReferenceList(sourceEntity.getEntityName().getName()); - codes.restrictToCodes(codeList); - return state.restrictToSourceCodes(codes); - } catch (LBException e) { - // TODO Auto-generated catch block - throw new RuntimeException(); - } - } - }; - } - - - /** - * Restrict to the source or target entity unique identifier of the coded node graph - * @param entity - wrapper class for the unique identifier for this class - * @return this restriction to the coded node graph. - */ - protected Restriction restrictToSourceOrTargetEntityRestriction( - final EntityNameOrURI entity) { - - return new Restriction() { - @Override - public CodedNodeGraph processRestriction(CodedNodeGraph state) { - try { - CodedNodeSet codes = ProfileUtils.unionAll(lexBigService); - ConceptReferenceList codeList = Constructors.createConceptReferenceList(entity.getEntityName().getName()); - codes.restrictToCodes(codeList); - return state.restrictToCodes(codes); - } catch (LBException e) { - // TODO Auto-generated catch block - throw new RuntimeException(); - } - } - }; - } - - - /** - * Restrict to the unique identifier of the target entity of this association - * @param target - wrapper class for the target unique identifier - * @return this restriction to the coded node graph. - */ - protected Restriction restrictToTargetEntityRestriction(final EntityNameOrURI target){ - - return new Restriction(){ - @Override - public CodedNodeGraph processRestriction(CodedNodeGraph state) { - - try { - //TODO find a method of restricting codes to the current restricted state of this node graph. - CodedNodeSet codes = ProfileUtils.unionAll(lexBigService); - ConceptReferenceList codeList = Constructors.createConceptReferenceList(target.getEntityName().getName()); - codes.restrictToCodes(codeList); - return state.restrictToTargetCodes(codes); - } catch (LBException e) { - // TODO Auto-generated catch block - throw new RuntimeException(); - } - } - }; - } - - /** - * Restrict to the target literal of this association - * @param target - the target literal - * @return this restriction to the coded node graph. - */ - protected Restriction restrictToTargetLiteralRestriction(final String target){ - return new Restriction(){ - @Override - public CodedNodeGraph processRestriction(CodedNodeGraph state) { - - //TODO: decide strategy for implementing Supporting LexEVS code (Association to Data). - throw new UnsupportedOperationException(); - } - }; - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractNonIterableLexEvsBackedRestrictionHandler#doUnion(org.cts2.uri.DirectoryURI, org.cts2.uri.DirectoryURI, org.cts2.internal.model.uri.restrict.OriginalStateProvider) - */ - @Override - protected CodedNodeGraph doUnion( - AssociationDirectoryURI directoryUri1, - AssociationDirectoryURI directoryUri2, - OriginalStateProvider originalStateProvider) { - return this.doSetOperation(directoryUri1, directoryUri2, originalStateProvider, SetOperator.UNION); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractNonIterableLexEvsBackedRestrictionHandler#doIntersect(org.cts2.uri.DirectoryURI, org.cts2.uri.DirectoryURI, org.cts2.internal.model.uri.restrict.OriginalStateProvider) - */ - @Override - protected CodedNodeGraph doIntersect( - AssociationDirectoryURI directoryUri1, - AssociationDirectoryURI directoryUri2, - OriginalStateProvider originalStateProvider) { - return this.doSetOperation(directoryUri1, directoryUri2, originalStateProvider, SetOperator.INTERSECT); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractNonIterableLexEvsBackedRestrictionHandler#doDifference(org.cts2.uri.DirectoryURI, org.cts2.uri.DirectoryURI, org.cts2.internal.model.uri.restrict.OriginalStateProvider) - */ - @Override - protected CodedNodeGraph doDifference( - AssociationDirectoryURI directoryUri1, - AssociationDirectoryURI directoryUri2, - OriginalStateProvider originalStateProvider) { - return this.doSetOperation(directoryUri1, directoryUri2, originalStateProvider, SetOperator.SUBTRACT); - } - - /** - * @param directoryUri1 - * @param directoryUri2 - * @param originalState - * @param setOperator - * @return - */ - protected CodedNodeGraph doSetOperation(AssociationDirectoryURI directoryUri1, AssociationDirectoryURI directoryUri2, OriginalStateProvider originalState, SetOperator setOperator){ - Restriction restriction1 = this.compile(directoryUri1, originalState); - Restriction restriction2 = this.compile(directoryUri2, originalState); - - CodedNodeGraph cng1 = this.apply(restriction1, originalState.getOriginalState()); - CodedNodeGraph cng2 = this.apply(restriction2, originalState.getOriginalState()); - - switch (setOperator){ - case UNION : { - try { - return cng1.union(cng2); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - case INTERSECT : { - try { - return cng1.intersect(cng2); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - case SUBTRACT : { - throw new UnsupportedOperationException("Difference not implemented on CodedNodeGraph"); - } - } - - throw new IllegalStateException(); - } - - /** - * @return - */ - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - /** - * @param lexEvsIdentityConverter - */ - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - /** - * @return - */ - public LexBIGService getLexBigService() { - return lexBigService; - } - - /** - * @param lexBigService - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultCodeSystemVersionRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultCodeSystemVersionRestrictionHandler.java deleted file mode 100644 index 5355ee7646..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultCodeSystemVersionRestrictionHandler.java +++ /dev/null @@ -1,184 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.ArrayList; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.ActiveOption; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.cts2.core.EntityReference; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.match.AttributeResolver; -import org.cts2.internal.match.ResolvableModelAttributeReference; -import org.cts2.internal.profile.ProfileUtils; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.uri.CodeSystemVersionDirectoryURI; -import org.cts2.uri.restriction.CodeSystemVersionRestrictionState.RestrictToEntitiesRestriction; - -/** - * The Class CodeSystemVersionRestrictionHandler. - * - * @author Kevin Peterson - */ -public class DefaultCodeSystemVersionRestrictionHandler - extends AbstractIterableLexEvsBackedRestrictionHandler { - - /** The lex evs identity converter. */ - private LexEvsIdentityConverter lexEvsIdentityConverter; - - private LexBIGService lexBigService; - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractIterableLexEvsBackedRestrictionHandler#registerSupportedModelAttributes() - */ - @Override - public List> registerSupportedModelAttributeReferences() { - List> returnList = - new ArrayList>(); - - ResolvableModelAttributeReference codeSystmeVersionName = - new ResolvableModelAttributeReference(new CodeSystemVersionNameAttributeResolver()); - - returnList.add(codeSystmeVersionName); - - return returnList; - } - - @Override - public List> processOtherRestictions(CodeSystemVersionDirectoryURI directoryUri) { - List> returnList = new ArrayList>(); - - for(RestrictToEntitiesRestriction restriction : directoryUri.getRestrictionState().getRestrictToEntitiesRestrictions()){ - returnList.add(this.restrictToEntities(restriction)); - } - - return returnList; - } - - protected IterableRestriction restrictToEntities(final RestrictToEntitiesRestriction restriction) { - return new IterableRestriction(){ - - @Override - public Iterable processRestriction( - Iterable state) { - - ActiveOrAll activeOrAll = restriction.getActive(); - RestrictionType allOrSome = restriction.getAllOrSome(); - List entities = restriction.getEntities(); - - List returnList = new ArrayList(); - - for(CodingSchemeRendering rendering : state){ - String uri = rendering.getCodingSchemeSummary().getCodingSchemeURI(); - String version = rendering.getCodingSchemeSummary().getRepresentsVersion(); - - try { - CodedNodeSet cns = lexBigService.getNodeSet(uri, Constructors.createCodingSchemeVersionOrTagFromVersion(version), null); - - cns = cns.restrictToCodes(ProfileUtils.entityReferenceToConceptReferenceList(entities)); - - switch (activeOrAll) { - case ACTIVE_ONLY : { - cns = cns.restrictToStatus(ActiveOption.ACTIVE_ONLY, null); - break; - } - - case ACTIVE_AND_INACTIVE : { - cns = cns.restrictToStatus(ActiveOption.ALL, null); - break; - } - } - - int number = cns.resolve(null, null, null, null, false).numberRemaining(); - - switch (allOrSome) { - case ALL : { - if(number == entities.size()){ - returnList.add(rendering); - } - break; - } - - case AT_LEAST_ONE : { - if(number > 0){ - returnList.add(rendering); - } - break; - } - } - - } catch (LBException e) { - //TODO: Throw CTS2 Exception here. - throw new RuntimeException(e); - } - } - - return returnList; - } - }; - } - - /** - * The Class CodeSystemVersionNameAttributeResolver. - * - * @author Kevin Peterson - */ - private class CodeSystemVersionNameAttributeResolver implements AttributeResolver { - - /* (non-Javadoc) - * @see org.cts2.internal.match.AttributeResolver#resolveAttribute(java.lang.Object) - */ - @Override - public String resolveAttribute( - CodingSchemeRendering modelObject) { - - return lexEvsIdentityConverter.codingSchemeSummaryToCodeSystemVersionName(modelObject.getCodingSchemeSummary()); - } - } - - @Override - public List registerSupportedMatchAlgorithmReferences() { - // TODO Auto-generated method stub - return null; - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - public LexBIGService getLexBigService() { - return lexBigService; - } - - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultEntityDescriptionRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultEntityDescriptionRestrictionHandler.java deleted file mode 100644 index b0d1da4789..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultEntityDescriptionRestrictionHandler.java +++ /dev/null @@ -1,286 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Map.Entry; - -import org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.ModuleDescription; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.apache.commons.lang.StringUtils; -import org.cts2.constant.ExternalCts2Constants; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.VersionTagReference; -import org.cts2.core.types.SetOperator; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.match.OperationExecutingModelAttributeReference; -import org.cts2.internal.match.OperationExecutingModelAttributeReference.RestrictionOperation; -import org.cts2.service.core.NameOrURI; -import org.cts2.uri.EntityDirectoryURI; -import org.cts2.uri.restriction.EntityDirectoryRestrictionState; -import org.cts2.uri.restriction.EntityDirectoryRestrictionState.RestrictToCodeSystemVersionsRestriction; -import org.springframework.beans.factory.InitializingBean; - -/** - * The Class DefaultEntityDescriptionRestrictionHandler. - * - * @author Kevin Peterson - */ -public class DefaultEntityDescriptionRestrictionHandler - extends AbstractNonIterableLexEvsBackedRestrictionHandler implements InitializingBean { - - /** The lex evs identity converter. */ - private LexEvsIdentityConverter lexEvsIdentityConverter; - - /** The lex big service. */ - private LexBIGService lexBigService; - - /** The match algorithm reference to search name. */ - private Map matchAlgorithmReferenceToSearchName = - new HashMap(); - - @Override - public void afterPropertiesSet() throws Exception { - this.registerSupportedMatchAlgorithmReferences(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractNonIterableLexEvsBackedRestrictionHandler#registerSupportedModelAttributeReferences() - */ - @Override - public List> registerSupportedModelAttributeReferences() { - List> returnList = - new ArrayList>(); - - OperationExecutingModelAttributeReference restrictToDesignations = - new OperationExecutingModelAttributeReference( - new RestrictToMatchingDesignationsOperation()); - - restrictToDesignations.setContent(ExternalCts2Constants.MA_ENTITY_DESCRIPTION_DESIGNATION_NAME); - restrictToDesignations.setMeaning(ExternalCts2Constants.MA_ENTITY_DESCRIPTION_DESIGNATION_URI); - - returnList.add(restrictToDesignations); - - return returnList; - } - - - protected Restriction restrictToCodeSystems( - NameOrURI codeSystems, - VersionTagReference tag) { - //TODO: decide strategy for implementing CodeSystem profile. - throw new UnsupportedOperationException(); - } - - protected Restriction restrictToCodeSystemVersions( - final NameOrURI codeSystemVersions) { - - return new Restriction(){ - - @Override - public CodedNodeSet processRestriction(CodedNodeSet state) { - AbsoluteCodingSchemeVersionReference ref = - lexEvsIdentityConverter.nameOrUriToAbsoluteCodingSchemeVersionReference(codeSystemVersions); - - try { - CodedNodeSet versionToRestrictTo = - lexBigService.getNodeSet(ref.getCodingSchemeURN(), - Constructors.createCodingSchemeVersionOrTagFromVersion(ref.getCodingSchemeVersion()), null); - - return state.intersect(versionToRestrictTo); - } catch (LBException e) { - //TODO: throw real CTS2 exception - throw new RuntimeException(e); - } - } - }; - } - - @Override - protected List> processOtherRestictions( - EntityDirectoryURI directoryURI) { - List> returnList = new ArrayList>(); - - EntityDirectoryRestrictionState state = directoryURI.getRestrictionState(); - - for(RestrictToCodeSystemVersionsRestriction restriction : state.getRestrictToCodeSystemVersionsRestrictions()){ - //TODO: - } - - return returnList; - } - - @Override - protected CodedNodeSet doUnion(EntityDirectoryURI i1, EntityDirectoryURI i2, OriginalStateProvider originalState){ - return this.doSetOperation(i1, i2, originalState, SetOperator.UNION); - } - - @Override - protected CodedNodeSet doIntersect(EntityDirectoryURI i1, - EntityDirectoryURI i2, OriginalStateProvider originalState){ - return this.doSetOperation(i1, i2, originalState, SetOperator.INTERSECT); - } - - @Override - protected CodedNodeSet doDifference(EntityDirectoryURI i1, - EntityDirectoryURI i2, OriginalStateProvider originalState){ - return this.doSetOperation(i1, i2, originalState, SetOperator.SUBTRACT); - } - - protected CodedNodeSet doSetOperation(EntityDirectoryURI i1, EntityDirectoryURI i2, OriginalStateProvider originalState, SetOperator setOperator){ - Restriction restriction1 = this.compile(i1, originalState); - Restriction restriction2 = this.compile(i2, originalState); - - CodedNodeSet cns1 = this.apply(restriction1, originalState.getOriginalState()); - CodedNodeSet cns2 = this.apply(restriction2, originalState.getOriginalState()); - - switch (setOperator){ - case UNION : { - try { - return cns1.union(cns2); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - case INTERSECT : { - try { - return cns1.intersect(cns2); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - case SUBTRACT : { - try { - return cns1.difference(cns2); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - } - - throw new IllegalStateException(); - } - - /** - * The Class RestrictToMatchingDesignationsOperation. - * - * @author Kevin Peterson - */ - private class RestrictToMatchingDesignationsOperation implements RestrictionOperation{ - - /* (non-Javadoc) - * @see org.cts2.internal.match.OperationExecutingModelAttributeReference.Operation#union(java.lang.Object, java.lang.String, org.cts2.core.MatchAlgorithmReference) - */ - @Override - public CodedNodeSet restrict(CodedNodeSet stateObject, String matchText, MatchAlgorithmReference algorithm) { - try { - //CodedNodeSet restriction = ProfileUtils.unionAll(lexBigService); - return stateObject.restrictToMatchingDesignations(matchText, SearchDesignationOption.ALL, getSearchName(algorithm), null); - //return stateObject.intersect(restriction); - } catch (LBException e) { - //TODO: throw real CTS2 exception - throw new RuntimeException(e); - } - } - } - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractRestrictionHandler#registerSupportedMatchAlgorithmReferences() - */ - @Override - public List registerSupportedMatchAlgorithmReferences() { - List returnList = new ArrayList(); - - ModuleDescriptionList matchAlgorithms = this.lexBigService.getMatchAlgorithms(); - - if(matchAlgorithms == null || matchAlgorithms.getModuleDescriptionCount() == 0){ - return returnList; - } - - for(ModuleDescription moduleDescription : this.lexBigService.getMatchAlgorithms().getModuleDescription()){ - returnList.add(this.buildMatchAlgorithmReference(moduleDescription)); - } - - return returnList; - } - - /** - * Builds the match algorithm reference. - * - * @param moduleDescription the module description - * @return the match algorithm reference - */ - protected MatchAlgorithmReference buildMatchAlgorithmReference(ModuleDescription moduleDescription){ - MatchAlgorithmReference ref = new MatchAlgorithmReference(); - - String searchName = moduleDescription.getName(); - - ref.setContent(searchName); - ref.setMeaning(ExternalCts2Constants.CTS2_URI + ExternalCts2Constants.CONCAT_STRING + searchName); - - this.matchAlgorithmReferenceToSearchName.put(ref, searchName); - - return ref; - } - - /** - * Gets the search name. - * - * @param reference the reference - * @return the search name - */ - private String getSearchName(MatchAlgorithmReference reference){ - for(Entry entry : this.matchAlgorithmReferenceToSearchName.entrySet()){ - if(StringUtils.equals(reference.getContent(), entry.getKey().getContent()) - || - (StringUtils.equals(reference.getHref(), entry.getKey().getMeaning()))){ - return entry.getValue(); - } - } - - //TODO: throw real CTS2 exception - throw new IllegalStateException(); - } - - public LexEvsIdentityConverter getLexEvsIdentityConverter() { - return lexEvsIdentityConverter; - } - - public void setLexEvsIdentityConverter( - LexEvsIdentityConverter lexEvsIdentityConverter) { - this.lexEvsIdentityConverter = lexEvsIdentityConverter; - } - - public LexBIGService getLexBigService() { - return lexBigService; - } - - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultMapVersionVersionRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultMapVersionVersionRestrictionHandler.java deleted file mode 100644 index af61c561c4..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/DefaultMapVersionVersionRestrictionHandler.java +++ /dev/null @@ -1,75 +0,0 @@ -package org.cts2.internal.model.uri.restrict; - -import java.util.ArrayList; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.cts2.constant.ExternalCts2Constants; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.match.AttributeResolver; -import org.cts2.internal.match.ResolvableModelAttributeReference; -import org.cts2.uri.MapVersionDirectoryURI; - -public class DefaultMapVersionVersionRestrictionHandler - extends - AbstractIterableLexEvsBackedRestrictionHandler { - - private LexEvsIdentityConverter lexEvsIdentityConverter; - - @Override - public List> registerSupportedModelAttributeReferences() { - List> returnList = new ArrayList>(); - - ResolvableModelAttributeReference mapVersionName = new ResolvableModelAttributeReference( - new MapVersionNameAttributeResolver()); - - mapVersionName.setContent(ExternalCts2Constants.MA_MAPVERSION_NAME_CONTENT); - mapVersionName.setMeaning(ExternalCts2Constants.MA_MAPVERSION_NAME_MEANING); - returnList.add(mapVersionName); - - return returnList; - } - - @Override - public List> processOtherRestictions( - MapVersionDirectoryURI directoryUri) { - List> returnList = new ArrayList>(); - - // TODO: Wait for the feedback of MapVersion restrictions from Harold - - return returnList; - } - - @Override - public List registerSupportedMatchAlgorithmReferences() { - // TODO Auto-generated method stub - return null; - } - - /** - * The Class MapVersionNameAttributeResolver. - * - * @author Zonghui Lian - */ - private class MapVersionNameAttributeResolver implements - AttributeResolver { - private static final long serialVersionUID = -6257292429464806843L; - - /* - * (non-Javadoc) - * - * @see - * org.cts2.internal.match.AttributeResolver#resolveAttribute(java.lang - * .Object) - */ - @Override - public String resolveAttribute(CodingSchemeRendering modelObject) { - - return lexEvsIdentityConverter - .codingSchemeSummaryToMapVersionName(modelObject - .getCodingSchemeSummary()); - } - } - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/IterableBasedResolvingRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/IterableBasedResolvingRestrictionHandler.java deleted file mode 100644 index 0fe0a79d37..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/IterableBasedResolvingRestrictionHandler.java +++ /dev/null @@ -1,48 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import org.cts2.uri.DirectoryURI; - -/** - * The Interface ListBasedResolvingRestrictionHandler. - * - * @author Kevin Peterson - */ -public interface IterableBasedResolvingRestrictionHandler extends ResolvingRestrictionHandler { - - /** - * Restrict. - * - * @param originalState the original state - * @param filter the filter - * @return the list - */ - public IterableRestriction compile(D directoryUri); - - /** - * Apply. - * - * @param restriction the restriction - * @param state the state - * @return the iterable - */ - public Iterable apply(IterableRestriction restriction, Iterable state); - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/IterableRestriction.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/IterableRestriction.java deleted file mode 100644 index 44d364bcd0..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/IterableRestriction.java +++ /dev/null @@ -1,36 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -/** - * The Interface IterableRestriction. - * - * @param the - * @author Kevin Peterson - */ -public interface IterableRestriction { - - /** - * Process restriction. - * - * @param state the state - * @return the iterable - */ - public Iterable processRestriction(Iterable state); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/NonIterableBasedResolvingRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/NonIterableBasedResolvingRestrictionHandler.java deleted file mode 100644 index 367a4c9405..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/NonIterableBasedResolvingRestrictionHandler.java +++ /dev/null @@ -1,34 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import org.cts2.uri.DirectoryURI; - -/** - * The Interface ListBasedResolvingRestrictionHandler. - * - * @author Kevin Peterson - */ -public interface NonIterableBasedResolvingRestrictionHandler extends OperationRestrictionHandler { - - public Restriction compile(D directoryURI, OriginalStateProvider originalState); - - public T apply(Restriction restriction, T state); - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/OperationRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/OperationRestrictionHandler.java deleted file mode 100644 index 386fd4ad99..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/OperationRestrictionHandler.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.List; - -import org.cts2.internal.match.OperationExecutingModelAttributeReference; - -/** - * The Interface ResolvingRestrictionHandler. - * - * @author Kevin Peterson - */ -public interface OperationRestrictionHandler extends RestrictionHandler { - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.RestrictionHandler#getSupportedModelAttributes() - */ - public List> getSupportedModelAttributeReferences(); - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/OriginalStateProvider.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/OriginalStateProvider.java deleted file mode 100644 index ea6991bf05..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/OriginalStateProvider.java +++ /dev/null @@ -1,35 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -/** - * The Interface OriginalStateProvider. - * - * @param the - * @author Kevin Peterson - */ -public interface OriginalStateProvider { - - /** - * Gets the original state. - * - * @return the original state - */ - public T getOriginalState(); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/ResolvingRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/ResolvingRestrictionHandler.java deleted file mode 100644 index a4554cef99..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/ResolvingRestrictionHandler.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.List; - -import org.cts2.internal.match.ResolvableModelAttributeReference; - -/** - * The Interface ResolvingRestrictionHandler. - * - * @author Kevin Peterson - */ -public interface ResolvingRestrictionHandler extends RestrictionHandler { - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.RestrictionHandler#getSupportedModelAttributes() - */ - public List> getSupportedModelAttributeReferences(); - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/Restriction.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/Restriction.java deleted file mode 100644 index cafedc9885..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/Restriction.java +++ /dev/null @@ -1,35 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -/** - * The Interface Restriction. - * - * @author Kevin Peterson - */ -public interface Restriction { - - /** - * Process restriction. - * - * @param state the state - * @return the t - */ - public T processRestriction(T state); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/RestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/RestrictionHandler.java deleted file mode 100644 index a3904ac7b1..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/RestrictionHandler.java +++ /dev/null @@ -1,54 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.util.List; - -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.ModelAttributeReference; -import org.cts2.core.PredicateReference; - -/** - * The Interface RestrictionHandler. - * - * @author Kevin Peterson - */ -public interface RestrictionHandler { - - /** - * Gets the supported predicate references. - * - * @return the supported predicate references - */ - public List getSupportedPredicateReferences(); - - /** - * Gets the supported model attributes. - * - * @return the supported model attributes - */ - public List getSupportedModelAttributeReferences(); - - /** - * Gets the supported match algorithm references. - * - * @return the supported match algorithm references - */ - public List getSupportedMatchAlgorithmReferences(); -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/RestrictionUtils.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/RestrictionUtils.java deleted file mode 100644 index 099685ed8c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/RestrictionUtils.java +++ /dev/null @@ -1,44 +0,0 @@ -package org.cts2.internal.model.uri.restrict; - -import com.google.common.collect.Iterables; - -public class RestrictionUtils { - - @SuppressWarnings("unchecked") - public static > T combineIterableRestrictions(Iterable restrictions){ - return (T) combineRestrictions(Iterables.toArray(restrictions, IterableRestriction.class)); - } - - @SuppressWarnings("unchecked") - public static > T combineRestrictions(Iterable restrictions){ - return (T) combineRestrictions(Iterables.toArray(restrictions, Restriction.class)); - } - - public static IterableRestriction combineRestrictions(final IterableRestriction... restrictions){ - return new IterableRestriction(){ - - @Override - public Iterable processRestriction(Iterable state) { - for(IterableRestriction restriction : restrictions){ - state = restriction.processRestriction(state); - } - - return state; - } - }; - } - - public static Restriction combineRestrictions(final Restriction... restrictions){ - return new Restriction(){ - - @Override - public T processRestriction(T state) { - for(Restriction restriction : restrictions){ - state = restriction.processRestriction(state); - } - - return state; - } - }; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/ValueSetDefinitionRestrictionHandler.java b/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/ValueSetDefinitionRestrictionHandler.java deleted file mode 100644 index e71a86b234..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/model/uri/restrict/ValueSetDefinitionRestrictionHandler.java +++ /dev/null @@ -1,163 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.model.uri.restrict; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.cts2.core.CodeSystemVersionReference; -import org.cts2.core.EntityReference; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.internal.match.AttributeResolver; -import org.cts2.internal.match.ResolvableModelAttributeReference; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; -import org.cts2.uri.restriction.ValueSetDefinitionRestrictionState.RestrictToEntitiesRestriction; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; - -/** - * The Class ValueSetDefinitionRestrictionHandler. - * - * @author Kevin Peterson - */ -public class ValueSetDefinitionRestrictionHandler extends AbstractIterableLexEvsBackedRestrictionHandler{ - - /** The lexEVSValueSetDefinition service. */ - private LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService; - - /* (non-Javadoc) - * @see org.cts2.internal.model.uri.restrict.AbstractIterableLexEvsBackedRestrictionHandler#registerSupportedModelAttributes() - */ - @Override - public List> registerSupportedModelAttributeReferences() { - List> returnList = - new ArrayList>(); - - - - AttributeResolver valueSetDefinitionNameResolver = new AttributeResolver(){ - - @Override - public String resolveAttribute(ValueSetDefinition modelObject) { - return modelObject.getValueSetDefinitionName(); - } - }; - - //TODO: Example only - ResolvableModelAttributeReference valueSetDefinitionName = new ResolvableModelAttributeReference(valueSetDefinitionNameResolver); - valueSetDefinitionName.setContent("valueSetDefinitionName"); - - returnList.add(valueSetDefinitionName); - - - - return returnList; - } - - @Override - public List> processOtherRestictions( - ValueSetDefinitionDirectoryURI directoryUri) { - - List> returnList = new ArrayList>(); - - Iterator restrictions = directoryUri.getRestrictionState().getRestrictToEntitiesRestriction().iterator(); - - while (restrictions.hasNext()) - { - RestrictToEntitiesRestriction restriction = restrictions.next(); - returnList.add(this.restrictToEntities(restriction)); - } - - return returnList; - } - - protected IterableRestriction restrictToEntities(final RestrictToEntitiesRestriction restriction) { - return new IterableRestriction(){ - - @Override - public Iterable processRestriction( - Iterable state) { - - List entities = restriction.getEntityReferences(); - - List returnList = new ArrayList(); - - for(ValueSetDefinition vsd : state){ - for (EntityReference entity : entities) - { - String entityCode = entity.getLocalEntityName().getName(); - String entityCodeNamespace = entity.getLocalEntityName().getNamespace(); - - AbsoluteCodingSchemeVersionReferenceList csVersionList = new AbsoluteCodingSchemeVersionReferenceList(); - - //TODO . . get code system version list -// for (CodeSystemVersionReference csvr : entity.getDescribingCodeSystemVersion()) -// { -// csVersionList.addAbsoluteCodingSchemeVersionReference(Constructors.createAbsoluteCodingSchemeVersionReference(csvr.getCodeSystem().g, version)) -// } - - try { - if (lexEVSValueSetDefinitionService.isEntityInValueSet(entityCode, new URI(entityCodeNamespace), new URI(vsd.getValueSetDefinitionURI()), null, csVersionList, null) != null) - { - returnList.add(vsd); - System.out.println("vsd.uri : " + vsd.getValueSetDefinitionURI()); - break; - } - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (URISyntaxException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - } - } - - return returnList; - } - }; - } - - @Override - public List registerSupportedMatchAlgorithmReferences() { - // TODO Auto-generated method stub - return null; - } - - /** - * @return the lexEVSValueSetDefinitionService - */ - public LexEVSValueSetDefinitionServices getLexEVSValueSetDefinitionService() { - return lexEVSValueSetDefinitionService; - } - - /** - * @param lexEVSValueSetDefinitionService the lexEVSValueSetDefinitionService to set - */ - public void setLexEVSValueSetDefinitionService( - LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService) { - this.lexEVSValueSetDefinitionService = lexEVSValueSetDefinitionService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/AbstractBaseService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/AbstractBaseService.java deleted file mode 100644 index 6feec1744d..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/AbstractBaseService.java +++ /dev/null @@ -1,88 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile; - -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.lexgrid.valuesets.LexEVSPickListDefinitionServices; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; - -/** - * The Class AbstractBaseService. - * - * @author Kevin Peterson - */ -public abstract class AbstractBaseService { - - /** The lex big service. */ - private LexBIGService lexBigService; - - /** The LexEVS Value Set Definition Service. */ - private LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService; - - /** The LexEVS Pick List Definition Service. */ - private LexEVSPickListDefinitionServices lexEVSPickListDefinitionService; - - /** - * Sets the lex big service. - * - * @param lexBigService the new lex big service - */ - public void setLexBigService(LexBIGService lexBigService) { - this.lexBigService = lexBigService; - } - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - public LexBIGService getLexBigService() { - return this.lexBigService; - } - - /** - * @return the lexEVSValueSetDefinitionService - */ - public LexEVSValueSetDefinitionServices getLexEVSValueSetDefinitionService() { - return lexEVSValueSetDefinitionService; - } - - /** - * @param lexEVSValueSetDefinitionService the lexEVSValueSetDefinitionService to set - */ - public void setLexEVSValueSetDefinitionService( - LexEVSValueSetDefinitionServices lexEVSValueSetDefinitionService) { - this.lexEVSValueSetDefinitionService = lexEVSValueSetDefinitionService; - } - - /** - * @return the lexEVSPickListDefinitionService - */ - public LexEVSPickListDefinitionServices getLexEVSPickListDefinitionService() { - return lexEVSPickListDefinitionService; - } - - /** - * @param lexEVSPickListDefinitionService the lexEVSPickListDefinitionService to set - */ - public void setLexEVSPickListDefinitionService( - LexEVSPickListDefinitionServices lexEVSPickListDefinitionService) { - this.lexEVSPickListDefinitionService = lexEVSPickListDefinitionService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/DefaultBaseService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/DefaultBaseService.java deleted file mode 100644 index 66b1738ad4..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/DefaultBaseService.java +++ /dev/null @@ -1,49 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile; - -import org.cts2.profile.BaseService; -import org.cts2.profile.query.QueryService; - -/** - * The Class DefaultBaseService. - * - * @author Kevin Peterson - */ -public class DefaultBaseService implements BaseService { - - /** The query service. */ - private QueryService queryService; - - /** - * Sets the query service. - * - * @param queryService the new query service - */ - public void setQueryService(QueryService queryService) { - this.queryService = queryService; - } - - /* (non-Javadoc) - * @see org.cts2.profile.BaseService#getQueryService() - */ - public QueryService getQueryService() { - return this.queryService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/ProfileUtils.java b/cts2Impl/src/main/java/org/cts2/internal/profile/ProfileUtils.java deleted file mode 100644 index 07f7ddde7d..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/ProfileUtils.java +++ /dev/null @@ -1,139 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile; - -import java.util.ArrayList; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.ConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.ConceptReference; -import org.LexGrid.LexBIG.DataModel.Core.types.CodingSchemeVersionStatus; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Extensions.Generic.MappingExtension.Mapping; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.EntityReference; -import org.cts2.service.core.ReadContext; - -/** - * The Class ProfileUtils. - * - * @author Kevin Peterson - */ -public class ProfileUtils { - - //TODO: Validate with real CTS2 Exceptions - public static void validateReadContext(ReadContext readContext){ - if(readContext != null){ - if(StringUtils.isNotBlank(readContext.getChangeSetContext()) - && - readContext.getReferenceTime() != null){ - throw new RuntimeException("ChangeSetURI and ReferenceTime cannot both be set."); - } - } - } - - /** - * Union all. - * - * @param lexBigService the lex big service - * @return the coded node set - * @throws LBException the LB exception - */ - public static CodedNodeSet unionAll(LexBIGService lexBigService) throws LBException { - CodedNodeSet cns = null; - for(CodingSchemeRendering csr : lexBigService.getSupportedCodingSchemes().getCodingSchemeRendering()){ - CodedNodeSet newCns = lexBigService.getNodeSet( - csr.getCodingSchemeSummary().getCodingSchemeURI(), - Constructors.createCodingSchemeVersionOrTagFromVersion(csr.getCodingSchemeSummary().getRepresentsVersion()), - null); - - if(cns == null){ - cns = newCns; - } else { - cns = cns.union(newCns); - } - } - - return cns; - } - - public static Mapping getMapping(LexBIGService lexBigService) { - Mapping mapping = null; - //TODO - return mapping; - } - - /** - * Gets the all active coding schemes. - * - * @param lexBigService the lex big service - * @return the all active coding schemes - * @throws LBException the LB exception - */ - public static List getAllActiveCodingSchemes(LexBIGService lexBigService) throws LBException { - List returnList = new ArrayList(); - - for(CodingSchemeRendering csr : lexBigService.getSupportedCodingSchemes().getCodingSchemeRendering()){ - if(csr.getRenderingDetail().getVersionStatus().equals(CodingSchemeVersionStatus.ACTIVE)){ - returnList.add(Constructors.createAbsoluteCodingSchemeVersionReference(csr.getCodingSchemeSummary())); - } - } - - return returnList; - } - - - public static ConceptReferenceList entityReferenceToConceptReferenceList(List entities){ - ConceptReferenceList returnList = new ConceptReferenceList(); - - for(EntityReference entityReference : entities) { - ConceptReference ref = new ConceptReference(); - ref.setCode(entityReference.getLocalEntityName().getName()); - ref.setCodeNamespace(entityReference.getLocalEntityName().getNamespace()); - - returnList.addConceptReference(ref); - } - - return returnList; - } - - public static CodedNodeGraph unionAllGraphs(LexBIGService lexBigService) throws LBException { - CodedNodeGraph cng = null; - for(CodingSchemeRendering csr : lexBigService.getSupportedCodingSchemes().getCodingSchemeRendering()){ - CodedNodeGraph newCns = lexBigService.getNodeGraph( - csr.getCodingSchemeSummary().getCodingSchemeURI(), - Constructors.createCodingSchemeVersionOrTagFromVersion(csr.getCodingSchemeSummary().getRepresentsVersion()), - null); - - if(cng == null){ - cng = newCns; - } else { - cng = cng.union(newCns); - } - } - - return cng; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/author/LexEvsCodeSystemVersionAuthoringService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/author/LexEvsCodeSystemVersionAuthoringService.java deleted file mode 100644 index de4bc6007e..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/author/LexEvsCodeSystemVersionAuthoringService.java +++ /dev/null @@ -1,103 +0,0 @@ -package org.cts2.internal.profile.author; - -import java.util.Date; - -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.core.ChangeSetBase; -import org.cts2.core.ChangeableResource; -import org.cts2.core.OpaqueData; -import org.cts2.core.SourceAndNotation; -import org.cts2.core.SourceReference; -import org.cts2.core.types.EntryState; -import org.cts2.internal.profile.AbstractBaseService; -import org.cts2.profile.author.CodeSystemVersionAuthoringService; -import org.cts2.service.codesystemversion.UpdateCodeSystemVersionRequest; -import org.cts2.service.core.ChangeSetEntryList; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.SuccessIndicator; -import org.cts2.service.core.ValidationResponse; -import org.cts2.updates.ChangeSet; - -public class LexEvsCodeSystemVersionAuthoringService extends AbstractBaseService - implements CodeSystemVersionAuthoringService { - - @Override - public ChangeSetBase readChangeSet(String changeSetUri) { - // TODO Auto-generated method stub - return null; - } - - @Override - public void commitChangeSet(String changeSetUri) { - // TODO Auto-generated method stub - - } - - @Override - public ChangeSet createChangeSet() { - // TODO Auto-generated method stub - return null; - } - - @Override - public ChangeSet deleteChangeable(String changeSetUri, - ChangeableResource target) { - // TODO Auto-generated method stub - return null; - } - - @Override - public void rollbackChangeSet(String changeSetUri) { - // TODO Auto-generated method stub - - } - - @Override - public void updateChangeSetMetadata(String changeSetUri, - ChangeableResource target, NameOrURI owner, NameOrURI status, - EntryState entryState) { - // TODO Auto-generated method stub - - } - - @Override - public void updateChangeSetMetadata(String changeSetUri, - SourceReference creator, OpaqueData changeInstructions) { - // TODO Auto-generated method stub - - } - - @Override - public SuccessIndicator putChangeSet(ChangeSet changeSet) { - // TODO Auto-generated method stub - return null; - } - - @Override - public ValidationResponse validateChangeSet(ChangeSet changeSet) { - // TODO Auto-generated method stub - return null; - } - - @Override - public ChangeSetEntryList listChanges(Date fromDate, Date toDate) { - // TODO Auto-generated method stub - return null; - } - - @Override - public void createCodeSystemVersion(String changeSetUri, - String documentUri, String name, - SourceAndNotation sourceAndNotation, NameOrURI versionOf) { - // TODO Auto-generated method stub - - } - - @Override - public CodeSystemVersion updateCodeSystemVersion( - NameOrURI codeSystemVersion, UpdateCodeSystemVersionRequest request) { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/history/DefaultHistoryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/history/DefaultHistoryService.java deleted file mode 100644 index 602df4da95..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/history/DefaultHistoryService.java +++ /dev/null @@ -1,60 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.history; - -import java.util.Date; - -import org.cts2.profile.history.HistoryService; -import org.cts2.uri.ChangeSetDirectoryURI; - -/** - * The Class DefaultHistoryService. - * - * @author Kevin Peterson - */ -public class DefaultHistoryService implements HistoryService { - - /* (non-Javadoc) - * @see org.cts2.profile.history.HistoryService#getChangeHistory() - */ - @Override - public ChangeSetDirectoryURI getChangeHistory() { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.cts2.profile.history.HistoryService#getEarliestChange() - */ - @Override - public Date getEarliestChange() { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.cts2.profile.history.HistoryService#getLatestChange() - */ - @Override - public Date getLatestChange() { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/AbstractBaseQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/AbstractBaseQueryService.java deleted file mode 100644 index e7a7ea5fc5..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/AbstractBaseQueryService.java +++ /dev/null @@ -1,131 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.query; - -import java.util.List; - -import org.cts2.core.Filter; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.ModelAttributeReference; -import org.cts2.internal.model.uri.factory.DirectoryURIFactory; -import org.cts2.internal.model.uri.restrict.RestrictionHandler; -import org.cts2.internal.profile.AbstractBaseService; -import org.cts2.profile.query.BaseQueryService; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.DirectoryURI; -import org.cts2.uri.SetOperable; - -/** - * The Class AbstractBaseQueryService. - * - * @param the - * @author Kevin Peterson - */ -public abstract class AbstractBaseQueryService> extends AbstractBaseService implements BaseQueryService { - - /** The directory uri factory. */ - private DirectoryURIFactory directoryURIFactory; - - /** The restriction handler. */ - private RestrictionHandler restrictionHandler; - - /* (non-Javadoc) - * @see org.cts2.profile.query.BaseQueryService#count(org.cts2.uri.DirectoryURI, org.cts2.service.core.ReadContext) - */ - @Override - public int count(U directoryUri, ReadContext readContext) { - return directoryUri.count(readContext); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.BaseQueryService#restrict(org.cts2.uri.DirectoryURI, org.cts2.core.Filter) - */ - @SuppressWarnings("unchecked") - @Override - public U restrict(U directoryUri, Filter filter) { - return (U) directoryUri.restrict(filter); - } - - @Override - public U union(U directoryUri1, U directoryUri2) { - return directoryUri1.union(directoryUri2); - } - - @Override - public U intersect(U directoryUri1, U directoryUri2) { - return directoryUri1.intersect(directoryUri2); - } - - @Override - public U difference(U directoryUri1, U directoryUri2) { - return directoryUri1.difference(directoryUri2); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.BaseQueryService#getSupportedModelAttributeReferences() - */ - @Override - public List getSupportedModelAttributeReferences() { - return this.restrictionHandler.getSupportedModelAttributeReferences(); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.BaseQueryService#getSupportedMatchAlgorithmReferences() - */ - @Override - public List getSupportedMatchAlgorithmReferences() { - return this.restrictionHandler.getSupportedMatchAlgorithmReferences(); - } - - /** - * Sets the directory uri factory. - * - * @param directoryURIFactory the new directory uri factory - */ - public void setDirectoryURIFactory(DirectoryURIFactory directoryURIFactory) { - this.directoryURIFactory = directoryURIFactory; - } - - /** - * Gets the directory uri factory. - * - * @return the directory uri factory - */ - public DirectoryURIFactory getDirectoryURIFactory() { - return this.directoryURIFactory; - } - - /** - * Gets the restriction handler. - * - * @return the restriction handler - */ - public RestrictionHandler getRestrictionHandler() { - return restrictionHandler; - } - - /** - * Sets the restriction handler. - * - * @param restrictionHandler the new restriction handler - */ - public void setRestrictionHandler(RestrictionHandler restrictionHandler) { - this.restrictionHandler = restrictionHandler; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/DefaultQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/DefaultQueryService.java deleted file mode 100644 index 19a5b23eca..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/DefaultQueryService.java +++ /dev/null @@ -1,68 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.query; - -import org.cts2.profile.query.AssociationQueryService; -import org.cts2.profile.query.CodeSystemQueryService; -import org.cts2.profile.query.QueryService; -import org.cts2.profile.query.ValueSetDefinitionQueryService; - -/** - * The Class DefaultQueryService. - * - * @author Kevin Peterson - */ -public class DefaultQueryService implements QueryService{ - - /** The code system query. */ - private CodeSystemQueryService codeSystemQueryService; - - /** The association query. */ - private AssociationQueryService associationQueryService; - - /** The value set definition query. */ - private ValueSetDefinitionQueryService valueSetDefinitionQueryService; - - public CodeSystemQueryService getCodeSystemQueryService() { - return codeSystemQueryService; - } - - public void setCodeSystemQueryService( - CodeSystemQueryService codeSystemQueryService) { - this.codeSystemQueryService = codeSystemQueryService; - } - - public AssociationQueryService getAssociationQueryService() { - return associationQueryService; - } - - public void setAssociationQueryService( - AssociationQueryService associationQueryService) { - this.associationQueryService = associationQueryService; - } - - public ValueSetDefinitionQueryService getValueSetDefinitionQueryService() { - return valueSetDefinitionQueryService; - } - - public void setValueSetDefinitionQueryService( - ValueSetDefinitionQueryService valueSetDefinitionQueryService) { - this.valueSetDefinitionQueryService = valueSetDefinitionQueryService; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsAssociationQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsAssociationQueryService.java deleted file mode 100644 index 6559f483ac..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsAssociationQueryService.java +++ /dev/null @@ -1,137 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.query; - -import org.cts2.association.AssociationDirectory; -import org.cts2.association.AssociationList; -import org.cts2.core.TargetExpression; -import org.cts2.profile.query.AssociationQueryService; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.AssociationDirectoryURI; -import org.cts2.uri.EntityDirectoryURI; - -/** - * The class LexEVSAssociationQuery - * - * @author Scott Bauer - * - */ -public class LexEvsAssociationQueryService extends - AbstractBaseQueryService - implements AssociationQueryService { - - - public AssociationDirectoryURI getAssociations(){ - return this.getDirectoryURIFactory().getDirectoryURI(); - } - - @Override - public AssociationDirectory resolve( - AssociationDirectoryURI associationQueryURI, - QueryControl queryControl, ReadContext readContext) { - return associationQueryURI.get(queryControl, readContext, AssociationDirectory.class); - } - - @Override - public AssociationList resolveAsList( - AssociationDirectoryURI associationQueryURI, - QueryControl queryControl, ReadContext readContext) { - return associationQueryURI.get(queryControl, readContext, AssociationList.class); - } - - @Override - public EntityDirectoryURI getAllSourceAndTargetEntities( - EntityDirectoryURI directory, QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - @Override - public EntityDirectoryURI getPredicates(AssociationDirectoryURI directory, - QueryControl queryControl, ReadContext context) { - - return directory.getPredicates(queryControl, context); - } - - @Override - public EntityDirectoryURI getSourceEntities( - AssociationDirectoryURI directory, QueryControl queryControl, - ReadContext context) { - return directory.getSourceEntities(queryControl, context); - } - - @Override - public EntityDirectoryURI getTargetEntities( - AssociationDirectoryURI directory, QueryControl queryControl, - ReadContext context) { - return directory.getTargetEntities(queryControl, context); - } - - @Override - public AssociationDirectoryURI restrictToCodeSystemVersion( - AssociationDirectoryURI directory, NameOrURI codeSystemVersion) { - return directory.restrictToCodeSystemVersion(codeSystemVersion); - } - - @Override - public AssociationDirectoryURI restrictToPredicate( - AssociationDirectoryURI directory, EntityNameOrURI predicate) { - return directory.restrictToPredicate(predicate); - } - - @Override - public AssociationDirectoryURI restrictToSourceEntity( - AssociationDirectoryURI directory, EntityNameOrURI sourceEntity) { - return directory.restrictToSourceEntity(sourceEntity); - } - - @Override - public AssociationDirectoryURI restrictToSourceOrTargetEntity( - AssociationDirectoryURI directory, EntityNameOrURI entity) { - return directory.restrictToSourceOrTargetEntity(entity); - } - - @Override - public AssociationDirectoryURI restrictToTargetEntity( - AssociationDirectoryURI directory, EntityNameOrURI target) { - return directory.restrictToTargetEntity(target); - } - - @Override - public AssociationDirectoryURI restrictToTargetExpression( - AssociationDirectoryURI directory, TargetExpression target) { - return directory.restrictToTargetExpression(target); - } - - @Override - public AssociationDirectoryURI restrictToTargetLiteral( - AssociationDirectoryURI directory, String target) { - return directory.restrictToTargetLiteral(target); - } - - - - - - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryService.java deleted file mode 100644 index d3dce21340..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryService.java +++ /dev/null @@ -1,58 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.query; - -import org.cts2.codesystem.CodeSystemDirectory; -import org.cts2.codesystem.CodeSystemList; -import org.cts2.profile.query.CodeSystemQueryService; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.CodeSystemDirectoryURI; - -/** - * The Class LexEvsCodeSystemQuery. - * - * @author Kevin Peterson - */ -public class LexEvsCodeSystemQueryService - extends AbstractBaseQueryService - implements CodeSystemQueryService { - - @Override - public CodeSystemDirectoryURI getAllCodeSystems() { - // TODO Auto-generated method stub - return null; - } - - @Override - public CodeSystemDirectory resolve( - CodeSystemDirectoryURI codeSystemQueryURI, - QueryControl queryControl, ReadContext readContext) { - // TODO Auto-generated method stub - return null; - } - - @Override - public CodeSystemList resolveAsList( - CodeSystemDirectoryURI codeSystemQueryURI, - QueryControl queryControl, ReadContext readContext) { - // TODO Auto-generated method stub - return null; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryService.java deleted file mode 100644 index 0f5d749ee3..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryService.java +++ /dev/null @@ -1,82 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.query; - -import java.util.List; - -import org.cts2.codesystemversion.CodeSystemVersionDirectory; -import org.cts2.codesystemversion.CodeSystemVersionList; -import org.cts2.core.EntityReference; -import org.cts2.profile.query.CodeSystemVersionQueryService; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.uri.CodeSystemVersionDirectoryURI; - -/** - * The Class LexEvsCodeSystemVersionQuery. - * - * @author Kevin Peterson - */ -public class LexEvsCodeSystemVersionQueryService extends AbstractBaseQueryService - implements CodeSystemVersionQueryService { - - /* (non-Javadoc) - * @see org.cts2.profile.query.CodeSystemVersionQueryService#restrictToEntities(org.cts2.uri.CodeSystemVersionDirectoryURI, java.util.List, org.cts2.service.core.types.RestrictionType, org.cts2.service.core.types.ActiveOrAll) - */ - @Override - public CodeSystemVersionDirectoryURI restrictToEntities( - CodeSystemVersionDirectoryURI codeSystemVersionDirectoryURI, - List entities, - RestrictionType allOrSome, - ActiveOrAll active) { - return codeSystemVersionDirectoryURI.restrictToEntities(entities, allOrSome, active); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.CodeSystemVersionQueryService#resolve(org.cts2.uri.CodeSystemVersionDirectoryURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public CodeSystemVersionDirectory resolve( - CodeSystemVersionDirectoryURI codeSystemVersionDirectoryURI, - QueryControl queryControl, - ReadContext readContext) { - return codeSystemVersionDirectoryURI.get(queryControl, readContext, CodeSystemVersionDirectory.class); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.CodeSystemVersionQueryService#resolveAsList(org.cts2.uri.CodeSystemVersionDirectoryURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public CodeSystemVersionList resolveAsList( - CodeSystemVersionDirectoryURI codeSystemVersionDirectoryURI, - QueryControl queryControl, - ReadContext readContext) { - return codeSystemVersionDirectoryURI.get(queryControl, readContext, CodeSystemVersionList.class); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.CodeSystemVersionQueryService#getCodeSystemVersions() - */ - @Override - public CodeSystemVersionDirectoryURI getCodeSystemVersions() { - return this.getDirectoryURIFactory().getDirectoryURI(); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsEntityDescriptionQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsEntityDescriptionQueryService.java deleted file mode 100644 index 49973a30fb..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsEntityDescriptionQueryService.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.query; - -import org.cts2.core.VersionTagReference; -import org.cts2.entity.EntityDirectory; -import org.cts2.entity.EntityList; -import org.cts2.profile.query.EntityDescriptionQueryService; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.EntityDirectoryURI; - -/** - * The Class LexEvsEntityDescriptionQueryService. - * - * @author Kevin Peterson Zonghui Lian - */ -public class LexEvsEntityDescriptionQueryService extends - AbstractBaseQueryService implements - EntityDescriptionQueryService { - - /* (non-Javadoc) - * @see org.cts2.profile.query.EntityDescriptionQueryService#getEntities() - */ - @Override - public EntityDirectoryURI getEntities() { - return this.getDirectoryURIFactory().getDirectoryURI(); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.EntityDescriptionQueryService#resolve(org.cts2.uri.EntityDirectoryURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public EntityDirectory resolve(EntityDirectoryURI entityQueryURI, - QueryControl queryControl, ReadContext readContext) { - return entityQueryURI.get(queryControl, readContext, - EntityDirectory.class); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.EntityDescriptionQueryService#resolveAsList(org.cts2.uri.EntityDirectoryURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public EntityList resolveAsList(EntityDirectoryURI codeSystemQueryURI, - QueryControl queryControl, ReadContext readContext) { - return codeSystemQueryURI.get(queryControl, readContext, - EntityList.class); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.EntityDescriptionQueryService#restrictToCodeSystems(org.cts2.uri.EntityDirectoryURI, org.cts2.service.core.NameOrURI, org.cts2.core.VersionTagReference) - */ - @Override - public EntityDirectoryURI restrictToCodeSystems( - EntityDirectoryURI entityDirectoryUri, NameOrURI codeSystems, - VersionTagReference tag) { - return entityDirectoryUri.restrictToCodeSystems(codeSystems, tag); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.EntityDescriptionQueryService#restrictToCodeSystemVersions(org.cts2.uri.EntityDirectoryURI, org.cts2.service.core.NameOrURI) - */ - @Override - public EntityDirectoryURI restrictToCodeSystemVersions( - EntityDirectoryURI entityDirectoryUri, NameOrURI codeSystemVersions) { - return entityDirectoryUri.restrictToCodeSystemVersions(codeSystemVersions); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsMapVersionQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsMapVersionQueryService.java deleted file mode 100644 index 45fd655bfd..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsMapVersionQueryService.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.cts2.internal.profile.query; - -import org.cts2.map.MapVersionDirectory; -import org.cts2.map.MapVersionList; -import org.cts2.profile.query.MapVersionQueryService; -import org.cts2.service.core.NameOrURIList; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.MapVersionDirectoryURI; - -public class LexEvsMapVersionQueryService extends - AbstractBaseQueryService implements - MapVersionQueryService { - - @Override - public MapVersionDirectory resolve(MapVersionDirectoryURI directory, - QueryControl queryControl, ReadContext readContext) { - return directory.get(queryControl, readContext, - MapVersionDirectory.class); - } - - @Override - public MapVersionList resolveAsList(MapVersionDirectoryURI directory, - QueryControl queryControl, ReadContext readContext) { - return directory.get(queryControl, readContext, MapVersionList.class); - } - - @Override - public MapVersionDirectoryURI restrictToCodeSystems(MapVersionDirectoryURI directory, - NameOrURIList codeSystems) { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryService.java deleted file mode 100644 index 14dac0f252..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryService.java +++ /dev/null @@ -1,54 +0,0 @@ -package org.cts2.internal.profile.query; - -import java.util.List; - -import org.cts2.core.EntityReference; -import org.cts2.profile.query.ValueSetDefinitionQueryService; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; -import org.cts2.valueset.ValueSetDefinitionDirectory; -import org.cts2.valueset.ValueSetDefinitionList; - -/** - * Implementation of CTS2 ValueSetDefinitionQueryService. - * - * @author Sridhar Dwarkanath - */ -public class LexEvsValueSetDefinitionQueryService extends AbstractBaseQueryService - implements ValueSetDefinitionQueryService { - - /* - * (non-Javadoc) - * @see org.cts2.profile.query.ValueSetDefinitionQueryService#resolve(org.cts2.uri.ValueSetDefinitionDirectoryURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public ValueSetDefinitionDirectory resolve( - ValueSetDefinitionDirectoryURI valueSetDefinitionDirectoryURI, - QueryControl queryControl, - ReadContext readContext) { - return valueSetDefinitionDirectoryURI.get(queryControl, readContext, ValueSetDefinitionDirectory.class); - } - - /* - * (non-Javadoc) - * @see org.cts2.profile.query.ValueSetDefinitionQueryService#resolveAsList(org.cts2.uri.ValueSetDefinitionDirectoryURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public ValueSetDefinitionList resolveAsList( - ValueSetDefinitionDirectoryURI valueSetDefinitionDirectoryURI, - QueryControl queryControl, - ReadContext context) { - return valueSetDefinitionDirectoryURI.get(queryControl, context, ValueSetDefinitionList.class); - } - - /* (non-Javadoc) - * @see org.cts2.profile.query.ValueSetDefinitionQueryService#restrictToEntities(org.cts2.uri.ValueSetDefinitionDirectoryURI, java.util.List) - */ - @Override - public ValueSetDefinitionDirectoryURI restrictToEntities( - ValueSetDefinitionDirectoryURI valueSetDefinitionDirectoryURI, - List entityList) { - return valueSetDefinitionDirectoryURI.restrictToEntities(entityList); - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/read/AbstractBaseReadService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/read/AbstractBaseReadService.java deleted file mode 100644 index 5a2f627d02..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/read/AbstractBaseReadService.java +++ /dev/null @@ -1,57 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.read; - -import org.cts2.internal.mapper.BeanMapper; -import org.cts2.internal.profile.AbstractBaseService; -import org.cts2.profile.read.BaseReadService; - -/** - * The Class AbstractBaseReadService. - * - * @param the - * @author Kevin Peterson - */ -public abstract class AbstractBaseReadService extends AbstractBaseService implements BaseReadService { - - /** The bean mapper. */ - private BeanMapper beanMapper; - - /* (non-Javadoc) - * @see org.cts2.profile.read.BaseReadService#read(org.cts2.service.core.NameOrURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - - /** - * Gets the bean mapper. - * - * @return the bean mapper - */ - public BeanMapper getBeanMapper() { - return beanMapper; - } - - /** - * Sets the bean mapper. - * - * @param beanMapper the new bean mapper - */ - public void setBeanMapper(BeanMapper beanMapper) { - this.beanMapper = beanMapper; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsAssociationReadService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsAssociationReadService.java deleted file mode 100644 index 88171f1f06..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsAssociationReadService.java +++ /dev/null @@ -1,42 +0,0 @@ -package org.cts2.internal.profile.read; - -import org.cts2.association.Association; -import org.cts2.profile.read.AssociationReadService; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; - -public class LexEvsAssociationReadService extends AbstractBaseReadService implements AssociationReadService { - - //private AssociationFactory associationFactory; - - @Override - public boolean exists(NameOrURI entryID, ReadContext context) { - // TODO Auto-generated method stub - return false; - } - - @Override - public boolean existsByExternalStatementId( - NameOrURI assertingCodeSystemVersion, String externalStatementId, - ReadContext context) { - // TODO Auto-generated method stub - return false; - } - - @Override - public Association readByExternalStatementId( - NameOrURI assertingCodeSystemVersion, String externalStatementId, - QueryControl queryControl, ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - @Override - public Association read(NameOrURI entryID, QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadService.java deleted file mode 100644 index 67a6ee6d92..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadService.java +++ /dev/null @@ -1,168 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.read; - -import java.util.Date; -import java.util.concurrent.Callable; -import java.util.concurrent.TimeUnit; - -import org.apache.commons.lang.StringUtils; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.internal.model.resource.factory.CodeSystemVersionFactory; -import org.cts2.internal.profile.ProfileUtils; -import org.cts2.profile.read.CodeSystemVersionReadService; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.utility.ExecutionUtils; - -/** - * The Class LexEvsCodeSystemVersionReadService. - * - * @author Kevin Peterson - */ -public class LexEvsCodeSystemVersionReadService extends AbstractBaseReadService implements CodeSystemVersionReadService { - - - /** The code system version factory. */ - private CodeSystemVersionFactory codeSystemVersionFactory; - - /* (non-Javadoc) - * @see org.cts2.profile.read.CodeSystemVersionReadService#existsCodeSystemVersionForCodeSystem(org.cts2.service.core.NameOrURI, org.cts2.service.core.NameOrURI, org.cts2.service.core.ReadContext) - */ - @Override - public boolean existsCodeSystemVersionForCodeSystem( - NameOrURI codeSystem, - NameOrURI tag, - ReadContext context) { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.profile.read.CodeSystemVersionReadService#existsExternalId(org.cts2.service.core.NameOrURI, java.lang.String, org.cts2.service.core.ReadContext) - */ - @Override - public boolean existsVersionId( - NameOrURI codeSystem, - String officialResourceVersionId, - ReadContext context) { - throw new UnsupportedOperationException(); - } - - @Override - public CodeSystemVersion read( - NameOrURI id, - QueryControl queryControl, - ReadContext readContext) { - - return this.doRead(id, queryControl, readContext); - } - - /* (non-Javadoc) - * @see org.cts2.profile.read.BaseReadService#exists(org.cts2.service.core.NameOrURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public boolean exists( - NameOrURI id, - QueryControl queryControl, - ReadContext readContext) { - return this.doRead( - id, - queryControl, - readContext) != null; - } - - /* (non-Javadoc) - * @see org.cts2.profile.read.CodeSystemVersionReadService#getCodeSystemVersionByExternalId(org.cts2.service.core.NameOrURI, java.lang.String, org.cts2.service.core.QueryControl) - */ - @Override - public boolean getCodeSystemVersionByVersionId( - NameOrURI codeSystem, - String officialResourceVersionId, - QueryControl queryControl) { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.profile.read.CodeSystemVersionReadService#getCodeSystemVersionForCodeSystem(org.cts2.service.core.NameOrURI, org.cts2.service.core.NameOrURI, org.cts2.service.core.QueryControl) - */ - @Override - public boolean getCodeSystemVersionForCodeSystem( - NameOrURI codeSystem, - NameOrURI tag, - QueryControl queryControl) { - throw new UnsupportedOperationException(); - } - - /* (non-Javadoc) - * @see org.cts2.internal.profile.read.AbstractBaseReadService#doRead(org.cts2.service.core.NameOrURI) - */ - protected CodeSystemVersion doRead( - final NameOrURI nameOrUri, - QueryControl queryControl, - final ReadContext readContext) { - - ProfileUtils.validateReadContext(readContext); - - return ExecutionUtils.callWithTimeout(new Callable(){ - - @Override - public CodeSystemVersion call() throws Exception { - String revisionId = null; - Date revisionDate = null; - - if(readContext != null){ - revisionId = readContext.getChangeSetContext(); - revisionDate = readContext.getReferenceTime(); - } - - if(StringUtils.isNotBlank(revisionId)){ - return codeSystemVersionFactory.getCodeSystemVersionByRevisionId(nameOrUri, revisionId); - } - - if(revisionDate != null){ - return codeSystemVersionFactory.getCodeSystemVersionByDate(nameOrUri, revisionDate); - } - - return codeSystemVersionFactory.getCurrentCodeSystemVersion(nameOrUri); - } - - }, queryControl, TimeUnit.MILLISECONDS); - } - - - /** - * Gets the code system version factory. - * - * @return the code system version factory - */ - public CodeSystemVersionFactory getCodeSystemVersionFactory() { - return codeSystemVersionFactory; - } - - /** - * Sets the code system version factory. - * - * @param codeSystemVersionFactory the new code system version factory - */ - public void setCodeSystemVersionFactory( - CodeSystemVersionFactory codeSystemVersionFactory) { - this.codeSystemVersionFactory = codeSystemVersionFactory; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsEntityDescriptionReadService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsEntityDescriptionReadService.java deleted file mode 100644 index 1550c55595..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsEntityDescriptionReadService.java +++ /dev/null @@ -1,116 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.read; - -import java.util.concurrent.Callable; -import java.util.concurrent.TimeUnit; - -import org.cts2.core.EntityReference; -import org.cts2.entity.EntityDescription; -import org.cts2.entity.EntityList; -import org.cts2.internal.model.resource.factory.EntityDescriptionFactory; -import org.cts2.profile.read.EntityDescriptionReadService; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.utility.ExecutionUtils; - -/** - * The Class LexEvsCodeSystemVersionReadService. - * - * @author Kevin Peterson - */ -public class LexEvsEntityDescriptionReadService extends - AbstractBaseReadService implements - EntityDescriptionReadService { - - /** The code system version factory. */ - private EntityDescriptionFactory entityDescriptionFactory; - - private EntityDescription doRead(final EntityNameOrURI id, - final NameOrURI codeSystemVersion, QueryControl queryControl, - ReadContext readContext) { - - return ExecutionUtils.callWithTimeout( - new Callable() { - - @Override - public EntityDescription call() throws Exception { - return entityDescriptionFactory.getEntityDescription( - id, codeSystemVersion); - } - }, queryControl, TimeUnit.MILLISECONDS); - } - - @Override - public EntityDescription read(EntityNameOrURI id, - NameOrURI codeSystemVersion, QueryControl queryControl, - ReadContext readContext) { - return this.doRead(id, codeSystemVersion, queryControl, readContext); - } - - @Override - public boolean exists(EntityNameOrURI id, NameOrURI codeSystemVersion, - QueryControl queryControl, ReadContext readContext) { - return this.doRead(id, codeSystemVersion, queryControl, readContext) != null; - } - - public void setEntityDescriptionFactory( - EntityDescriptionFactory entityDescriptionFactory) { - this.entityDescriptionFactory = entityDescriptionFactory; - } - - public EntityDescriptionFactory getEntityDescriptionFactory() { - return entityDescriptionFactory; - } - - @Override - public EntityList readEntityDescriptions(final EntityNameOrURI id, - QueryControl queryControl, ReadContext context) { - - return ExecutionUtils.callWithTimeout(new Callable() { - @Override - public EntityList call() throws Exception { - return entityDescriptionFactory.getEntityDescriptionList(id); - } - }, queryControl, TimeUnit.MILLISECONDS ); - } - - @Override - public EntityReference availableDescriptions(EntityNameOrURI id, - ReadContext context) { - return this.entityDescriptionFactory.availableDescriptions(id); - } - - @Override - public EntityDescription readByCodeSystem(EntityNameOrURI id, - NameOrURI codeSystem, NameOrURI tag, QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - @Override - public boolean existsInCodeSystem(EntityNameOrURI id, NameOrURI codeSystem, - NameOrURI tag, ReadContext context) { - // TODO Auto-generated method stub - return false; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsMapVersionReadService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsMapVersionReadService.java deleted file mode 100644 index f904b44cff..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsMapVersionReadService.java +++ /dev/null @@ -1,54 +0,0 @@ -package org.cts2.internal.profile.read; - -import org.cts2.map.MapVersion; -import org.cts2.profile.read.MapVersionReadService; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; - -public class LexEvsMapVersionReadService extends - AbstractBaseReadService implements MapVersionReadService { - - @Override - public MapVersion read(NameOrURI mapVersion, QueryControl queryContro, - ReadContext readContext) { - // TODO Auto-generated method stub - return null; - } - - @Override - public boolean exists(NameOrURI mapVersion, ReadContext context) { - // TODO Auto-generated method stub - return false; - } - - @Override - public MapVersion readMapVersionForMap(NameOrURI map, NameOrURI tag, - QueryControl queryControl, ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - @Override - public MapVersion existsMapVersionForMap(NameOrURI map, NameOrURI tag, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - - @Override - public boolean existsExternalId(NameOrURI map, String externalIdentifer, - ReadContext context) { - // TODO Auto-generated method stub - return false; - } - - @Override - public MapVersion getMapVersionByExternalId(NameOrURI map, - String externalIdentifier, QueryControl queryControl, - ReadContext context) { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsValueSetDefinitionReadService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsValueSetDefinitionReadService.java deleted file mode 100644 index dce7d4ce47..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/read/LexEvsValueSetDefinitionReadService.java +++ /dev/null @@ -1,144 +0,0 @@ -package org.cts2.internal.profile.read; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.List; -import java.util.concurrent.Callable; -import java.util.concurrent.TimeUnit; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.apache.commons.lang.StringUtils; -import org.cts2.core.NameOrURI; -import org.cts2.internal.model.resource.factory.ValueSetDefinitionFactory; -import org.cts2.profile.read.ValueSetDefinitionReadService; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.utility.ExecutionUtils; -import org.cts2.valueset.ValueSetDefinition; - -public class LexEvsValueSetDefinitionReadService extends AbstractBaseReadService - implements ValueSetDefinitionReadService { - - /** The code system version factory. */ - private ValueSetDefinitionFactory valueSetDefinitionFactory; - - @Override - public Boolean exists(URI valueSetDefinitionURI, ReadContext context) { - org.LexGrid.valueSets.ValueSetDefinition vsd = null; - try { - vsd = this.getLexEVSValueSetDefinitionService().getValueSetDefinition(valueSetDefinitionURI, null); - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - return this.inContext(vsd, context); - } - - private Boolean inContext(org.LexGrid.valueSets.ValueSetDefinition vsd, ReadContext context){ - if (vsd == null) - return null; - - if (context == null) - return true; - - // check for active or not active - - // check for changeSetURI - String changeSetContext = context.getChangeSetContext(); - if (StringUtils.isNotEmpty(changeSetContext)) - { - if (vsd.getEntryState() == null) - return false; - else if (StringUtils.isEmpty(vsd.getEntryState().getContainingRevision()) - || !vsd.getEntryState().getContainingRevision().equalsIgnoreCase(changeSetContext)) - return false; - } - // check for referenceLanguage - - // check for referenceTime - - return true; - } - - @Override - public Boolean existsDefinitionForValueSet(NameOrURI valueSet, - NameOrURI tag, ReadContext context) { - org.LexGrid.valueSets.ValueSetDefinition vsd = null; - - if (valueSet == null) - return null; - - try { - if (valueSet.getUri() != null) - { - vsd = this.getLexEVSValueSetDefinitionService().getValueSetDefinition(new URI(valueSet.getUri()), null); - if (vsd != null) - return true; - } - else - { - List vsds = this.getLexEVSValueSetDefinitionService().listValueSetDefinitions(valueSet.getName()); - if (!vsds.isEmpty()) - return true; - } - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (URISyntaxException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - return null; - } - - @Override - public ValueSetDefinition getDefinitionForValueSet(final NameOrURI valueSet, - NameOrURI tag, QueryControl queryControl, ReadContext context) { - if (valueSet == null) - return null; - - return ExecutionUtils.callWithTimeout(new Callable(){ - - @Override - public ValueSetDefinition call() throws Exception { - return valueSetDefinitionFactory.getValueSetDefinition(valueSet); - } - - }, queryControl, TimeUnit.MILLISECONDS); - } - - /* - * (non-Javadoc) - * @see org.cts2.profile.read.ValueSetDefinitionReadService#read(java.net.URI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext) - */ - @Override - public ValueSetDefinition read(final URI valueSetDefinitionURI, - QueryControl queryControl, ReadContext context) { - - return ExecutionUtils.callWithTimeout(new Callable(){ - - @Override - public ValueSetDefinition call() throws Exception { - return valueSetDefinitionFactory.getValueSetDefinition(valueSetDefinitionURI); - } - - }, queryControl, TimeUnit.MILLISECONDS); - } - - /** - * @return the valueSetDefinitionFactory - */ - public ValueSetDefinitionFactory getValueSetDefinitionFactory() { - return valueSetDefinitionFactory; - } - - /** - * @param valueSetDefinitionFactory the valueSetDefinitionFactory to set - */ - public void setValueSetDefinitionFactory( - ValueSetDefinitionFactory valueSetDefinitionFactory) { - this.valueSetDefinitionFactory = valueSetDefinitionFactory; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/profile/update/DefaultUpdateService.java b/cts2Impl/src/main/java/org/cts2/internal/profile/update/DefaultUpdateService.java deleted file mode 100644 index 205f8d1f04..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/profile/update/DefaultUpdateService.java +++ /dev/null @@ -1,65 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.profile.update; - -import java.util.Date; - -import org.cts2.internal.profile.AbstractBaseService; -import org.cts2.profile.update.UpdateService; -import org.cts2.service.core.ChangeSetEntryList; -import org.cts2.service.core.SuccessIndicator; -import org.cts2.service.core.ValidationResponse; -import org.cts2.updates.ChangeSet; - -/** - * The Class DefaultUpdateService. - * - * @author Kevin Peterson - */ -public class DefaultUpdateService extends AbstractBaseService implements UpdateService{ - - /* (non-Javadoc) - * @see org.cts2.profile.update.UpdateService#putChangeSet(org.cts2.updates.ChangeSet) - */ - @Override - public SuccessIndicator putChangeSet(ChangeSet changeSet) { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.cts2.profile.update.UpdateService#validateChangeSet(org.cts2.updates.ChangeSet) - */ - @Override - public ValidationResponse validateChangeSet(ChangeSet changeSet) { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.cts2.profile.update.UpdateService#listChanges(java.util.Date, java.util.Date) - */ - @Override - public ChangeSetEntryList listChanges(Date fromDate, Date toDate) { - // TODO Auto-generated method stub - return null; - } - - -} diff --git a/cts2Impl/src/main/java/org/cts2/internal/util/PagingList.java b/cts2Impl/src/main/java/org/cts2/internal/util/PagingList.java deleted file mode 100644 index 4270b09148..0000000000 --- a/cts2Impl/src/main/java/org/cts2/internal/util/PagingList.java +++ /dev/null @@ -1,88 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.util; - -import java.util.AbstractList; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -/** - * An Iterator backed List designed to lazily populate a List by resolving the Iterator - * on demand. Useful for Iterator->List conversions where a full traverse of the Iterator - * is expensive. - * - * @author Kevin Peterson - */ -public class PagingList extends AbstractList { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -5575701992345467751L; - - /** The iterator. */ - private Iterator iterator; - - /** The size. */ - private int size; - - /** The cache. */ - private List cache = new ArrayList(); - - /** - * Instantiates a new paging list. - * - * @param iterator the iterator - * @param size the size - */ - public PagingList(Iterator iterator, int size){ - this.iterator = iterator; - this.size = size; - } - - /* (non-Javadoc) - * @see java.util.AbstractList#get(int) - */ - @Override - public T get(int index) { - return doGet(index); - } - - /** - * Do get. - * - * @param index the index - * @return the t - */ - protected T doGet(int index){ - while(this.cache.size() < (index + 1) - && this.iterator.hasNext()){ - this.cache.add(this.iterator.next()); - } - - return this.cache.get(index); - } - - /* (non-Javadoc) - * @see java.util.AbstractCollection#size() - */ - @Override - public int size() { - return this.size; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/BaseService.java b/cts2Impl/src/main/java/org/cts2/profile/BaseService.java deleted file mode 100644 index 57b1a8a056..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/BaseService.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile; - -import org.cts2.profile.query.QueryService; - -/** - * The Interface BaseService. - * - * @author Kevin Peterson - */ -public interface BaseService { - - /** - * Gets the query service. - * - * @return the query service - */ - public QueryService getQueryService(); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/BaseServiceFactory.java b/cts2Impl/src/main/java/org/cts2/profile/BaseServiceFactory.java deleted file mode 100644 index 77e5c47952..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/BaseServiceFactory.java +++ /dev/null @@ -1,116 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile; - -import org.apache.commons.lang.StringUtils; -import org.lexevs.system.constants.SystemVariables; -import org.springframework.beans.factory.FactoryBean; -import org.springframework.context.ApplicationContext; -import org.springframework.context.support.ClassPathXmlApplicationContext; - -/** - * A factory for creating BaseService objects. - */ -public class BaseServiceFactory implements FactoryBean { - - private static String APPLICATION_CONFIG_CONTEXT = "cts2-application-config.xml"; - - /** The base service factory. */ - private static BaseServiceFactory baseServiceFactory; - - /** The base service. */ - private BaseService baseService; - - /** The lg config file. */ - private String lgConfigFile; - - /** - * Instance. - * - * @return the base service factory - */ - public static synchronized BaseServiceFactory instance(){ - if(baseServiceFactory == null){ - baseServiceFactory = new BaseServiceFactory(); - } - return baseServiceFactory; - } - - /** - * Gets the base service. - * - * @return the base service - */ - public synchronized BaseService getBaseService(){ - - if(this.baseService == null){ - - if(StringUtils.isNotBlank(this.lgConfigFile)){ - System.setProperty(SystemVariables.LG_CONFIG_FILE_SYSTEM_VARIABLE, this.lgConfigFile); - } - - ApplicationContext appContext = new ClassPathXmlApplicationContext(APPLICATION_CONFIG_CONTEXT); - this.baseService = appContext.getBean(BaseService.class); - } - - return this.baseService; - } - - /* (non-Javadoc) - * @see org.springframework.beans.factory.FactoryBean#getObject() - */ - @Override - public BaseService getObject() throws Exception { - return getBaseService(); - } - - /* (non-Javadoc) - * @see org.springframework.beans.factory.FactoryBean#getObjectType() - */ - @Override - public Class getObjectType() { - return BaseService.class; - } - - /* (non-Javadoc) - * @see org.springframework.beans.factory.FactoryBean#isSingleton() - */ - @Override - public boolean isSingleton() { - return true; - } - - /** - * Sets the lg config file. - * - * @param lgConfigFile the new lg config file - */ - public void setLgConfigFile(String lgConfigFile) { - this.lgConfigFile = lgConfigFile; - } - - /** - * Gets the lg config file. - * - * @return the lg config file - */ - public String getLgConfigFile() { - return this.lgConfigFile; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/author/BaseAuthoringService.java b/cts2Impl/src/main/java/org/cts2/profile/author/BaseAuthoringService.java deleted file mode 100644 index 20b0379f44..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/author/BaseAuthoringService.java +++ /dev/null @@ -1,94 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.author; - -import org.cts2.core.ChangeSetBase; -import org.cts2.core.ChangeableResource; -import org.cts2.core.OpaqueData; -import org.cts2.core.SourceReference; -import org.cts2.core.types.EntryState; -import org.cts2.profile.update.UpdateService; -import org.cts2.service.core.NameOrURI; -import org.cts2.updates.ChangeSet; - -/** - * The Interface BaseAuthoringService. - * - * @author Kevin Peterson - */ -public interface BaseAuthoringService extends UpdateService { - - /** - * Read change set. - * - * @param changeSetUri the change set uri - * @return the change set base - */ - public ChangeSetBase readChangeSet(String changeSetUri); - - /** - * Commit change set. - * - * @param changeSetUri the change set uri - */ - public void commitChangeSet(String changeSetUri); - - /** - * Creates the change set. - * - * @return the change set - */ - public ChangeSet createChangeSet(); - - /** - * Delete changeable. - * - * @param changeSetUri the change set uri - * @param target the target - * @return the change set - */ - public ChangeSet deleteChangeable(String changeSetUri, ChangeableResource target); - - /** - * Rollback change set. - * - * @param changeSetUri the change set uri - */ - public void rollbackChangeSet(String changeSetUri); - - /** - * Update change set metadata. - * - * @param changeSetUri the change set uri - * @param target the target - * @param owner the owner - * @param status the status - * @param entryState the entry state - */ - public void updateChangeSetMetadata(String changeSetUri, ChangeableResource target, NameOrURI owner, NameOrURI status, EntryState entryState); - - /** - * Update change set metadata. - * - * @param changeSetUri the change set uri - * @param creator the creator - * @param changeInstructions the change instructions - */ - public void updateChangeSetMetadata(String changeSetUri, SourceReference creator, OpaqueData changeInstructions); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/author/CodeSystemVersionAuthoringService.java b/cts2Impl/src/main/java/org/cts2/profile/author/CodeSystemVersionAuthoringService.java deleted file mode 100644 index 0ab3bd0f68..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/author/CodeSystemVersionAuthoringService.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.author; - -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.core.SourceAndNotation; -import org.cts2.service.codesystemversion.UpdateCodeSystemVersionRequest; -import org.cts2.service.core.NameOrURI; - -/** - * The Interface CodeSystemVersionAuthoringService. - * - * @author Kevin Peterson - */ -public interface CodeSystemVersionAuthoringService extends BaseAuthoringService { - - /** - * Creates the code system version. - * - * @param changeSetUri the change set uri - * @param documentUri the document uri - * @param name the name - * @param sourceAndNotation the source and notation - * @param versionOf the version of - */ - public void createCodeSystemVersion(String changeSetUri, String documentUri, String name, SourceAndNotation sourceAndNotation, NameOrURI versionOf); - - /** - * Update code system version. - * - * @param codeSystemVersion the code system version - * @param request the request - * @return the code system version - */ - public CodeSystemVersion updateCodeSystemVersion(NameOrURI codeSystemVersion, UpdateCodeSystemVersionRequest request); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/history/HistoryService.java b/cts2Impl/src/main/java/org/cts2/profile/history/HistoryService.java deleted file mode 100644 index b363d44d22..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/history/HistoryService.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.history; - -import java.util.Date; - -import org.cts2.uri.ChangeSetDirectoryURI; - -/** - * The Interface HistoryService. - * - * @author Kevin Peterson - */ -public interface HistoryService { - - /** - * Gets the change history. - * - * @return the change history - */ - public ChangeSetDirectoryURI getChangeHistory(); - - /** - * Gets the earliest change. - * - * @return the earliest change - */ - public Date getEarliestChange(); - - /** - * Gets the latest change. - * - * @return the latest change - */ - public Date getLatestChange(); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/AssociationQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/AssociationQueryService.java deleted file mode 100644 index 56c26bf645..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/AssociationQueryService.java +++ /dev/null @@ -1,151 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - -import org.cts2.association.AssociationDirectory; -import org.cts2.association.AssociationList; -import org.cts2.core.TargetExpression; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.AssociationDirectoryURI; -import org.cts2.uri.EntityDirectoryURI; - -/** - * @author Scott Bauer - * - */ -public interface AssociationQueryService extends - BaseQueryService { - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getAllSourceAndTargetEntities( - EntityDirectoryURI directory, QueryControl queryControl, - ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getPredicates(AssociationDirectoryURI directory, - QueryControl queryControl, ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getSourceEntities( - AssociationDirectoryURI directory, QueryControl queryControl, - ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public EntityDirectoryURI getTargetEntities( - AssociationDirectoryURI directory, QueryControl queryControl, - ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public AssociationDirectory resolve(AssociationDirectoryURI directory, - QueryControl queryControl, ReadContext context); - - /** - * - * @param directory - * @param queryControl - * @param context - */ - public AssociationList resolveAsList(AssociationDirectoryURI directory, - QueryControl queryControl, ReadContext context); - - /** - * - * @param directory - * @param codeSystemVersion - */ - public AssociationDirectoryURI restrictToCodeSystemVersion( - AssociationDirectoryURI directory, NameOrURI codeSystemVersion); - - /** - * - * @param directory - * @param predicate - */ - public AssociationDirectoryURI restrictToPredicate( - AssociationDirectoryURI directory, EntityNameOrURI predicate); - - /** - * - * @param directory - * @param sourceEntity - */ - public AssociationDirectoryURI restrictToSourceEntity( - AssociationDirectoryURI directory, EntityNameOrURI sourceEntity); - - /** - * - * @param directory - * @param entity - */ - public AssociationDirectoryURI restrictToSourceOrTargetEntity( - AssociationDirectoryURI directory, EntityNameOrURI entity); - - /** - * - * @param directory - * @param target - */ - public AssociationDirectoryURI restrictToTargetEntity( - AssociationDirectoryURI directory, EntityNameOrURI target); - - /** - * - * @param directory - * @param target - */ - public AssociationDirectoryURI restrictToTargetExpression( - AssociationDirectoryURI directory, TargetExpression target); - - /** - * - * @param directory - * @param target - */ - public AssociationDirectoryURI restrictToTargetLiteral( - AssociationDirectoryURI directory, String target); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/BaseQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/BaseQueryService.java deleted file mode 100644 index d8a28a93d0..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/BaseQueryService.java +++ /dev/null @@ -1,74 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - -import java.util.List; - -import org.cts2.core.Filter; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.ModelAttributeReference; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.DirectoryURI; - -/** - * The Interface BaseQueryService. - * - * @param the - * @author Kevin Peterson - */ -public interface BaseQueryService { - - /** - * Count. - * - * @param directoryUri the directory uri - * @param readContext the read context - * @return the int - */ - public int count(U directoryUri, ReadContext readContext); - - /** - * Restrict. - * - * @param restrictable the restrictable - * @param filter the filter - * @return the t - */ - public U restrict(U restrictable, Filter filter); - - public U union(U directoryUri1, U directoryUri2); - - public U intersect(U directoryUri1, U directoryUri2); - - public U difference(U directoryUri1, U directoryUri2); - - /** - * Gets the supported model attribute references. - * - * @return the supported model attribute references - */ - public List getSupportedModelAttributeReferences(); - - /** - * Gets the supported match algorithm references. - * - * @return the supported match algorithm references - */ - public List getSupportedMatchAlgorithmReferences(); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/CodeSystemQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/CodeSystemQueryService.java deleted file mode 100644 index 1ca67e8689..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/CodeSystemQueryService.java +++ /dev/null @@ -1,46 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - -import org.cts2.codesystem.CodeSystemDirectory; -import org.cts2.codesystem.CodeSystemList; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.CodeSystemDirectoryURI; - - -/** - * The Interface CodeSystemQuery. - * - * @author Kevin Peterson - */ -public interface CodeSystemQueryService extends BaseQueryService{ - - /** - * Gets the all code systems. - * - * @return the all code systems - */ - public CodeSystemDirectoryURI getAllCodeSystems(); - - public CodeSystemDirectory resolve(CodeSystemDirectoryURI codeSystemQueryURI, QueryControl queryControl, ReadContext readContext); - - public CodeSystemList resolveAsList(CodeSystemDirectoryURI codeSystemQueryURI, QueryControl queryControl, ReadContext readContext); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/CodeSystemVersionQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/CodeSystemVersionQueryService.java deleted file mode 100644 index f7256357b0..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/CodeSystemVersionQueryService.java +++ /dev/null @@ -1,77 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - -import java.util.List; - -import org.cts2.codesystemversion.CodeSystemVersionDirectory; -import org.cts2.codesystemversion.CodeSystemVersionList; -import org.cts2.core.EntityReference; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.uri.CodeSystemVersionDirectoryURI; - -/** - * The Interface CodeSystemVersionQuery. - * - * @author Kevin Peterson - */ -public interface CodeSystemVersionQueryService extends BaseQueryService{ - - //TODO: 'entities aren't supposed to be a List, I'm pretty sure -- but there is on 'EntityReferenceList' in the model... ask Harold. - /** - * Restrict to entities. - * - * @param codeSystemQueryURI the code system query uri - * @param entities the entities - * @param allOrSome the all or some - * @param active the active - * @return the code system version directory uri - */ - public CodeSystemVersionDirectoryURI restrictToEntities(CodeSystemVersionDirectoryURI codeSystemQueryURI, List entities, RestrictionType allOrSome, ActiveOrAll active); - - /** - * Resolve. - * - * @param codeSystemQueryURI the code system query uri - * @param queryControl the query control - * @param readContext the read context - * @return the code system version directory - */ - public CodeSystemVersionDirectory resolve(CodeSystemVersionDirectoryURI codeSystemQueryURI, QueryControl queryControl, ReadContext readContext); - - /** - * Resolve as list. - * - * @param codeSystemQueryURI the code system query uri - * @param queryControl the query control - * @param readContext the read context - * @return the code system version list - */ - public CodeSystemVersionList resolveAsList(CodeSystemVersionDirectoryURI codeSystemQueryURI, QueryControl queryControl, ReadContext readContext); - - /** - * Gets the code system versions. - * - * @return the code system versions - */ - public CodeSystemVersionDirectoryURI getCodeSystemVersions(); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/EntityDescriptionQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/EntityDescriptionQueryService.java deleted file mode 100644 index 8db73e2cc4..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/EntityDescriptionQueryService.java +++ /dev/null @@ -1,46 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - -import org.cts2.core.VersionTagReference; -import org.cts2.entity.EntityDirectory; -import org.cts2.entity.EntityList; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.EntityDirectoryURI; - -/** - * The Interface CodeSystemVersionQuery. - * - * @author Kevin Peterson - */ -public interface EntityDescriptionQueryService extends BaseQueryService{ - - public EntityDirectoryURI getEntities(); - - public EntityDirectory resolve(EntityDirectoryURI entityQueryURI, QueryControl queryControl, ReadContext readContext); - - public EntityList resolveAsList(EntityDirectoryURI codeSystemQueryURI, QueryControl queryControl, ReadContext readContext); - - public EntityDirectoryURI restrictToCodeSystems(EntityDirectoryURI codeSystemQueryURI, NameOrURI codeSystems, VersionTagReference tag); - - public EntityDirectoryURI restrictToCodeSystemVersions(EntityDirectoryURI codeSystemQueryURI, NameOrURI codeSystemVersions); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/MapVersionQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/MapVersionQueryService.java deleted file mode 100644 index 65d097e804..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/MapVersionQueryService.java +++ /dev/null @@ -1,27 +0,0 @@ -package org.cts2.profile.query; - -import org.cts2.map.MapVersionDirectory; -import org.cts2.map.MapVersionList; -import org.cts2.service.core.NameOrURIList; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.MapVersionDirectoryURI; - -/** - * The Interface CodeSystemVersionQuery. - * - * @author Zonghui Lian - */ -public interface MapVersionQueryService extends - BaseQueryService { - public MapVersionDirectory resolve(MapVersionDirectoryURI directory, - QueryControl queryControl, ReadContext readContext); - - public MapVersionList resolveAsList(MapVersionDirectoryURI directory, - QueryControl queryControl, ReadContext readContext); - - public MapVersionDirectoryURI restrictToCodeSystems(MapVersionDirectoryURI directory, - NameOrURIList codeSystems); - - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/QueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/QueryService.java deleted file mode 100644 index c71b5c1eb9..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/QueryService.java +++ /dev/null @@ -1,49 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - - -/** - * The Interface QueryService. - * - * @author Kevin Peterson - */ -public interface QueryService { - - /** - * Gets the code system query. - * - * @return the code system query - */ - public CodeSystemQueryService getCodeSystemQueryService(); - - /** - * Gets the association query - * - * @return the association query - */ - public AssociationQueryService getAssociationQueryService(); - - /** - * Gets the value set definition query - * - * @return the value set definition query - */ - public ValueSetDefinitionQueryService getValueSetDefinitionQueryService(); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/ValueSetDefinitionQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/ValueSetDefinitionQueryService.java deleted file mode 100644 index d6d7d93c7f..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/ValueSetDefinitionQueryService.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.cts2.profile.query; - -import java.util.List; - -import org.cts2.core.EntityReference; -import org.cts2.service.core.QueryControl; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; -import org.cts2.valueset.ValueSetDefinitionDirectory; -import org.cts2.valueset.ValueSetDefinitionList; -import org.cts2.service.core.ReadContext; - -/** - * Interface for CTS2 ValueSetDefinitionQuery Service. - * - * @author Sridhar Dwarkanath - */ -public interface ValueSetDefinitionQueryService extends BaseQueryService { - - /** - * Retrieve the value set definitions available at the specified location on the service. - * - * @param directory - * @param queryControl - * @param context - */ - public ValueSetDefinitionDirectory resolve(ValueSetDefinitionDirectoryURI valueSetDefinitionDirectoryURI, QueryControl queryControl, ReadContext context); - - /** - * Retrieve a listing of value set definitions available at the specified location - * on the service. - * - * @param directory - * @param queryControl - * @param context - */ - public ValueSetDefinitionList resolveAsList(ValueSetDefinitionDirectoryURI valueSetDefinitionDirectoryURI, QueryControl queryControl, ReadContext context); - - /** - * Determine which value set definitions on the service contain the specified entities - * (concepts). - * - * @param valueSetDirectory - * @param entityList - */ - public ValueSetDefinitionDirectoryURI restrictToEntities(ValueSetDefinitionDirectoryURI valueSetDefinitionDirectoryURI, List entityList); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/query/ValueSetQueryService.java b/cts2Impl/src/main/java/org/cts2/profile/query/ValueSetQueryService.java deleted file mode 100644 index 26708c080c..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/query/ValueSetQueryService.java +++ /dev/null @@ -1,38 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.query; - -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.uri.ValueSetDirectoryURI; -import org.cts2.valueset.ValueSetDirectory; -import org.cts2.valueset.ValueSetList; - -/** - * The Interface ValueSetQueryService. - * - * @author Kevin Peterson - */ -public interface ValueSetQueryService extends BaseQueryService{ - - public ValueSetDirectory resolve(ValueSetDirectoryURI valueSetDirectoryURI, QueryControl queryControl, ReadContext readContext); - - public ValueSetList resolveAsList(ValueSetDirectoryURI valueSetDirectoryURI, QueryControl queryControl, ReadContext readContext); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/read/AssociationReadService.java b/cts2Impl/src/main/java/org/cts2/profile/read/AssociationReadService.java deleted file mode 100644 index 7b11641602..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/read/AssociationReadService.java +++ /dev/null @@ -1,78 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.read; - -import org.cts2.association.Association; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; - -/** - * Interface AssociationReadService - * - * @author Scott Bauer - * - */ -public interface AssociationReadService extends BaseReadService { - - /** - * Determine if the specified association exists on the service. - * - * @param entryID - * @param context - * @return boolean - */ - public boolean exists(NameOrURI entryID, ReadContext context); - - /** - * Determine if the association specified by external statement identifier - * exists on the service. - * - * @param assertingCodeSystemVersion - * @param externalStatementId - * @param context - * @return boolean - */ - public boolean existsByExternalStatementId( - NameOrURI assertingCodeSystemVersion, String externalStatementId, - ReadContext context); - - /** - * Retrieve the specified association from the service. - * - * @param entryID - * @param queryControl - * @param context - */ - public Association read(NameOrURI entryID, QueryControl queryControl, - ReadContext context); - - /** - * Retrieve the specified association by the external statement identifier. - * - * @param assertingCodeSystemVersion - * @param externalStatementId - * @param queryControl - * @param context - * @return Association - */ - public Association readByExternalStatementId( - NameOrURI assertingCodeSystemVersion, String externalStatementId, - QueryControl queryControl, ReadContext context); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/read/BaseReadService.java b/cts2Impl/src/main/java/org/cts2/profile/read/BaseReadService.java deleted file mode 100644 index 3f8a56f3d1..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/read/BaseReadService.java +++ /dev/null @@ -1,8 +0,0 @@ -package org.cts2.profile.read; - - -public interface BaseReadService { - - -} - \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/cts2/profile/read/CodeSystemVersionReadService.java b/cts2Impl/src/main/java/org/cts2/profile/read/CodeSystemVersionReadService.java deleted file mode 100644 index 9441ac55c2..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/read/CodeSystemVersionReadService.java +++ /dev/null @@ -1,27 +0,0 @@ -package org.cts2.profile.read; - -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; - -public interface CodeSystemVersionReadService extends BaseReadService { - - public boolean existsCodeSystemVersionForCodeSystem(NameOrURI codeSystem, NameOrURI tag, ReadContext context); - - public boolean existsVersionId(NameOrURI codeSystem, String officialResourceVersionId, ReadContext context); - - public boolean getCodeSystemVersionByVersionId(NameOrURI codeSystem, String officialResourceVersionId, QueryControl queryControl); - - public boolean getCodeSystemVersionForCodeSystem(NameOrURI codeSystem, NameOrURI tag, QueryControl queryControl); - - public CodeSystemVersion read( - NameOrURI id, - QueryControl queryControl, - ReadContext readContext); - - public boolean exists( - NameOrURI id, - QueryControl queryControl, - ReadContext readContext); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/read/EntityDescriptionReadService.java b/cts2Impl/src/main/java/org/cts2/profile/read/EntityDescriptionReadService.java deleted file mode 100644 index 3350078da9..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/read/EntityDescriptionReadService.java +++ /dev/null @@ -1,47 +0,0 @@ -package org.cts2.profile.read; - -import org.cts2.core.EntityReference; -import org.cts2.entity.EntityDescription; -import org.cts2.entity.EntityList; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; - -public interface EntityDescriptionReadService extends BaseReadService { - - public EntityDescription read( - EntityNameOrURI id, - NameOrURI codeSystemVersion, - QueryControl queryControl, - ReadContext readContext); - - public boolean exists( - EntityNameOrURI id, - NameOrURI codeSystemVersion, - QueryControl queryControl, - ReadContext readContext); - - public EntityList readEntityDescriptions( - EntityNameOrURI id, - QueryControl queryControl, - ReadContext context - ); - - public EntityReference availableDescriptions( - EntityNameOrURI id, - ReadContext context); - - public EntityDescription readByCodeSystem( - EntityNameOrURI id, - NameOrURI codeSystem, - NameOrURI tag, - QueryControl queryControl, - ReadContext context); - - public boolean existsInCodeSystem( - EntityNameOrURI id, - NameOrURI codeSystem, - NameOrURI tag, - ReadContext context); -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/read/MapVersionReadService.java b/cts2Impl/src/main/java/org/cts2/profile/read/MapVersionReadService.java deleted file mode 100644 index 60cca23594..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/read/MapVersionReadService.java +++ /dev/null @@ -1,27 +0,0 @@ -package org.cts2.profile.read; - -import org.cts2.map.MapVersion; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; - -public interface MapVersionReadService extends BaseReadService { - public MapVersion read(NameOrURI mapVersion, QueryControl queryContro, - ReadContext readContext); - - public boolean exists(NameOrURI mapVersion, ReadContext context); - - public MapVersion readMapVersionForMap(NameOrURI map, NameOrURI tag, - QueryControl queryControl, ReadContext context); - - public MapVersion existsMapVersionForMap(NameOrURI map, NameOrURI tag, - ReadContext context); - - public boolean existsExternalId(NameOrURI map, String externalIdentifer, - ReadContext context); - - public MapVersion getMapVersionByExternalId(NameOrURI map, - String externalIdentifier, QueryControl queryControl, - ReadContext context); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/read/ValueSetDefinitionReadService.java b/cts2Impl/src/main/java/org/cts2/profile/read/ValueSetDefinitionReadService.java deleted file mode 100644 index ae693d3f3b..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/read/ValueSetDefinitionReadService.java +++ /dev/null @@ -1,55 +0,0 @@ -package org.cts2.profile.read; - -import java.net.URI; - -import org.cts2.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.valueset.ValueSetDefinition; - -/** - * Interface for CTS2 ValueSetDefinitionRead Service. - * - * @author Sridhar Dwarkanath - */ -public interface ValueSetDefinitionReadService extends BaseReadService{ - - /** - * Determine if the specified value set definition exists on the service. - * - * @param valueSetDefinitionURI - * @param context - */ - public Boolean exists(URI valueSetDefinitionURI, ReadContext context); - - /** - * Determine if the value set definition for the specified value set exists on the - * service. - * - * @param valueSet - * @param tag - * @param context - */ - public Boolean existsDefinitionForValueSet(NameOrURI valueSet, NameOrURI tag, ReadContext context); - - /** - * Retrieve the value set definition for the specified value set. - * - * @param valueSet - * @param tag - * @param queryControl - * @param context - */ - public ValueSetDefinition getDefinitionForValueSet(NameOrURI valueSet, NameOrURI tag, - QueryControl queryControl, ReadContext context); - - /** - * Retrieve the specified value set definition. - * - * @param valueSetDefinitionURI - * @param queryControl - * @param context - */ - public ValueSetDefinition read(URI valueSetDefinitionURI, QueryControl queryControl, ReadContext context); - -} diff --git a/cts2Impl/src/main/java/org/cts2/profile/update/UpdateService.java b/cts2Impl/src/main/java/org/cts2/profile/update/UpdateService.java deleted file mode 100644 index bc4d709398..0000000000 --- a/cts2Impl/src/main/java/org/cts2/profile/update/UpdateService.java +++ /dev/null @@ -1,59 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.profile.update; - -import java.util.Date; - -import org.cts2.service.core.ChangeSetEntryList; -import org.cts2.service.core.SuccessIndicator; -import org.cts2.service.core.ValidationResponse; -import org.cts2.updates.ChangeSet; - -/** - * The Interface UpdateService. - * - * @author Kevin Peterson - */ -public interface UpdateService { - - /** - * Put change set. - * - * @param changeSet the change set - * @return the success indicator - */ - public SuccessIndicator putChangeSet(ChangeSet changeSet); - - /** - * Validate change set. - * - * @param changeSet the change set - * @return the validation response - */ - public ValidationResponse validateChangeSet(ChangeSet changeSet); - - /** - * List changes. - * - * @param fromDate the from date - * @param toDate the to date - * @return the change set entry list - */ - public ChangeSetEntryList listChanges(Date fromDate, Date toDate); -} diff --git a/cts2Impl/src/main/java/org/cts2/utility/ConstructorUtils.java b/cts2Impl/src/main/java/org/cts2/utility/ConstructorUtils.java deleted file mode 100644 index 1a2f3c3cb2..0000000000 --- a/cts2Impl/src/main/java/org/cts2/utility/ConstructorUtils.java +++ /dev/null @@ -1,55 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.utility; - -import org.cts2.service.core.NameOrURI; - -/** - * The Class ConstructorUtils. - * - * @author Kevin Peterson - */ -public class ConstructorUtils { - - /** - * Uri to name or uri. - * - * @param uri the uri - * @return the name or uri - */ - public static NameOrURI uriToNameOrURI(String uri){ - NameOrURI nameOrUri = new NameOrURI(); - nameOrUri.setUri(uri); - - return nameOrUri; - } - - /** - * Name to name or uri. - * - * @param name the name - * @return the name or uri - */ - public static NameOrURI nameToNameOrURI(String name){ - NameOrURI nameOrUri = new NameOrURI(); - nameOrUri.setName(name); - - return nameOrUri; - } -} diff --git a/cts2Impl/src/main/java/org/cts2/utility/ExecutionUtils.java b/cts2Impl/src/main/java/org/cts2/utility/ExecutionUtils.java deleted file mode 100644 index 9092cafdfa..0000000000 --- a/cts2Impl/src/main/java/org/cts2/utility/ExecutionUtils.java +++ /dev/null @@ -1,84 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.utility; - -import java.util.concurrent.Callable; -import java.util.concurrent.TimeUnit; - -import org.cts2.service.core.QueryControl; - -import com.google.common.util.concurrent.SimpleTimeLimiter; - -/** - * The Class ExecutionUtils. - * - * @author Kevin Peterson - */ -public class ExecutionUtils { - - private static SimpleTimeLimiter TIME_LIMITER = new SimpleTimeLimiter(); - - /** - * Call with timeout. - * - * @param callable the callable - * @param timeoutDuration the timeout duration - * @param timeoutUnit the timeout unit - * @return T - */ - public static T callWithTimeout(Callable callable, long timeoutDuration, TimeUnit timeoutUnit){ - - try { - return TIME_LIMITER.callWithTimeout(callable, timeoutDuration, timeoutUnit, false); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - - /** - * Call with timeout. - * - * @param callable the callable - * @param queryControl the query control - * @return T - */ - public static T callWithTimeout(Callable callable, QueryControl queryControl){ - return callWithTimeout(callable, queryControl, TimeUnit.MILLISECONDS); - } - - /** - * Call with timeout. - * - * @param callable the callable - * @param queryControl the query control - * @param timeoutUnit the timeout unit - * @return T - */ - public static T callWithTimeout(Callable callable, QueryControl queryControl, TimeUnit timeoutUnit){ - if(queryControl == null || queryControl.getTimeLimit() == null){ - try { - return callable.call(); - } catch (Exception e) { - throw new RuntimeException(e); - } - } else { - return callWithTimeout(callable, queryControl.getTimeLimit(), timeoutUnit); - } - } -} diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/BaseService.java b/cts2Impl/src/main/java/org/lexevs/cts2/BaseService.java deleted file mode 100644 index 01957ff4ee..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/BaseService.java +++ /dev/null @@ -1,63 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2; - -import org.lexevs.dao.database.key.Java5UUIDKeyGenerator; - -/** - * The Class BaseService. - * - * @author Sridhar Dwarkanath - */ -public abstract class BaseService extends LexEvsBasedService { - - private transient LexEvsCTS2 lexEvsCTS2; - private ServiceInfo serviceInfo_ = null; - - public static enum SortableProperties { - matchToQuery, code, codeSystem, entityDescription, conceptStatus, isActive - }; - - public static enum KnownTags { - PRODUCTION - }; - - public ServiceInfo getServiceInfo(){ - if (serviceInfo_ == null) - serviceInfo_ = new ServiceInfo(); - - return serviceInfo_; - } - - protected LexEvsCTS2 getLexEvsCTS2() { - if(this.lexEvsCTS2 == null) { - this.lexEvsCTS2 = LexEvsCTS2Impl.defaultInstance(); - } - return this.lexEvsCTS2; - } - - /** - * Creates the unique id. - * - * @return the string - */ - protected String createUniqueId(){ - return Java5UUIDKeyGenerator.getRandomUUID().toString(); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsBasedService.java b/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsBasedService.java deleted file mode 100644 index 4e9a8b5758..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsBasedService.java +++ /dev/null @@ -1,108 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; -import org.lexevs.dao.database.service.DatabaseServiceManager; -import org.lexevs.dao.index.service.IndexServiceManager; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexevs.system.service.SystemResourceService; - -/** - * The Class LexEvsBasedService. - * - * @author Kevin Peterson - */ -public abstract class LexEvsBasedService { - - /** The lbs_. */ - private transient LexBIGService lbs_ = null; - - /** - * Gets the lex big service. - * - * @return the lex big service - */ - protected LexBIGService getLexBIGService(){ - if (lbs_ == null) { - lbs_ = LexBIGServiceImpl.defaultInstance(); - } - - return lbs_; - } - - /** - * Gets the lex big service manager. - * - * @return the lex big service manager - * - * @throws LBException the LB exception - */ - protected LexBIGServiceManager getLexBIGServiceManager() throws LBException{ - return this.getLexBIGService().getServiceManager(this.getLexBIGServiceManagerCredentials()); - } - - /** - * Gets the system resource service. - * - * @return the system resource service - */ - protected SystemResourceService getSystemResourceService() { - return this.getLexEvsServiceLocator().getSystemResourceService(); - } - - /** - * Gets the database service manager. - * - * @return the database service manager - */ - protected DatabaseServiceManager getDatabaseServiceManager() { - return this.getLexEvsServiceLocator().getDatabaseServiceManager(); - } - - /** - * Gets the index service manager. - * - * @return the index service manager - */ - protected IndexServiceManager getIndexServiceManager() { - return this.getLexEvsServiceLocator().getIndexServiceManager(); - } - - /** - * Gets the lex evs service locator. - * - * @return the lex evs service locator - */ - private LexEvsServiceLocator getLexEvsServiceLocator() { - return LexEvsServiceLocator.getInstance(); - } - - /** - * Gets the lex big service manager credentials. - * - * @return the lex big service manager credentials - */ - protected Object getLexBIGServiceManagerCredentials() { - return null; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsCTS2.java b/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsCTS2.java deleted file mode 100644 index 79eb2b043e..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsCTS2.java +++ /dev/null @@ -1,111 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Extensions.Generic.GenericExtension; -import org.lexevs.cts2.admin.AdminOperation; -import org.lexevs.cts2.author.AuthoringOperation; -import org.lexevs.cts2.query.QueryOperation; - -/** - * Main interface for LexEVS CTS2 implementation. - * - * @author Sridhar Dwarkanath - */ -public interface LexEvsCTS2 extends GenericExtension{ - /** - * Returns LexEVS implementation of CTS2 Administration Operations. - * - * @return AdminOperation - */ - public AdminOperation getAdminOperation(); - - /** - * Returns LexEVS implementation of CTS Authoring Operations. - * - * @return AuthoringOperations - */ - public AuthoringOperation getAuthoringOperation(); - - /** - * Returns LexEVS implementation of CTS Query Operations. - * - * @return QueryOperation - */ - public QueryOperation getQueryOperation(); - - /** - * Returns service provider information. - * - * @return serviceInfo - */ - public ServiceInfo getServiceInfo(); - - /** - * Returns list of Search Algorithms supported by this LexEVS instance. - * - * @return List of Supported Search Algorithms - * @throws LBException - */ - public ExtensionDescriptionList getSupportedSearchAlgorithms() throws LBException; - - /** - * Returns list of Loaders supported by this LexEVS instance. - * - * @return List of supported Loaders - * @throws LBException - */ - public ExtensionDescriptionList getSupportedLoaders() throws LBException; - - /** - * Returns list of Exporters supported by this LexEVS instance. - * - * @return List of supported Exporters - * @throws LBException - */ - public ExtensionDescriptionList getSupportedExporters() throws LBException; - - /** - * Returns list of Search Algorithm names supported by this LexEVS instance. - * - * @return List of Supported Search Algorithm names - * @throws LBException - */ - public List getSupportedSearchAlgorithmNames() throws LBException; - - /** - * Returns list of Loader names supported by this LexEVS instance. - * - * @return List of supported Loader names - * @throws LBException - */ - public List getSupportedLoaderNames() throws LBException; - - /** - * Returns list of Exporter names supported by this LexEVS instance. - * - * @return List of supported Exporter names - * @throws LBException - */ - public List getSupportedExporterNames() throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsCTS2Impl.java b/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsCTS2Impl.java deleted file mode 100644 index 9392c628d0..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/LexEvsCTS2Impl.java +++ /dev/null @@ -1,321 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2; - -import java.util.ArrayList; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.ExtensionDescription; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.LexGrid.LexBIG.Extensions.ExtensionRegistry; -import org.LexGrid.LexBIG.Impl.Extensions.ExtensionRegistryImpl; -import org.lexevs.cts2.admin.AdminOperation; -import org.lexevs.cts2.admin.AdminOperationImpl; -import org.lexevs.cts2.author.AuthoringOperation; -import org.lexevs.cts2.author.AuthoringOperationImpl; -import org.lexevs.cts2.query.QueryOperation; -import org.lexevs.cts2.query.QueryOperationImpl; - -/** - * Implementation of LexEVS CTS2 - * - * @author Sridhar Dwarkanath - */ -public class LexEvsCTS2Impl extends LexEvsBasedService implements LexEvsCTS2 { - /** - * - */ - private static final long serialVersionUID = 1L; - private static transient LexEvsCTS2 lexevsCTS2_; - private transient AdminOperation adminOp_; - private transient AuthoringOperation authOp_; - private transient QueryOperation queryOp_; - - public static LexEvsCTS2 defaultInstance(){ - if (lexevsCTS2_ == null) - { - lexevsCTS2_ = new LexEvsCTS2Impl(); - try { - LexEvsCTS2Impl.register(); - } catch (Exception e) { - throw new RuntimeException(e); - } - } - - return lexevsCTS2_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getAdminOperation() - */ - @Override - public AdminOperation getAdminOperation() { - if (adminOp_ == null) - adminOp_ = new AdminOperationImpl(); - return adminOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getAuthoringOperation() - */ - @Override - public AuthoringOperation getAuthoringOperation() { - if (authOp_ == null) - authOp_ = new AuthoringOperationImpl(); - return authOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getQueryOperation() - */ - @Override - public QueryOperation getQueryOperation() { - if (queryOp_ == null) - queryOp_ = new QueryOperationImpl(); - return queryOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getSupportedSearchAlgorithms() - */ - public ExtensionDescriptionList getSupportedSearchAlgorithms() throws LBException{ - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null) - return extensionRegistry.getGenericExtensions(); - - return null; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getSupportedSearchAlgorithmNames() - */ - public List getSupportedSearchAlgorithmNames() throws LBException{ - List searchAlgNames = new ArrayList(); - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null && extensionRegistry.getSearchExtensions() != null) - { - for (ExtensionDescription ed : extensionRegistry.getSearchExtensions().getExtensionDescription()) - searchAlgNames.add(ed.getName()); - } - return searchAlgNames; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getSupportedLoaders() - */ - public ExtensionDescriptionList getSupportedLoaders() throws LBException{ - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null) - return extensionRegistry.getLoadExtensions(); - - return null; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getSupportedLoaderNames() - */ - public List getSupportedLoaderNames() throws LBException{ - List loaderNames = new ArrayList(); - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null && extensionRegistry.getLoadExtensions() != null) - { - for (ExtensionDescription ed : extensionRegistry.getLoadExtensions().getExtensionDescription()) - loaderNames.add(ed.getName()); - } - return loaderNames; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getSupportedExporters() - */ - public ExtensionDescriptionList getSupportedExporters() throws LBException{ - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null) - return extensionRegistry.getExportExtensions(); - - return null; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getSupportedExporterNames() - */ - public List getSupportedExporterNames() throws LBException{ - List exporterNames = new ArrayList(); - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null && extensionRegistry.getExportExtensions() != null) - { - for (ExtensionDescription ed : extensionRegistry.getExportExtensions().getExtensionDescription()) - exporterNames.add(ed.getName()); - } - return exporterNames; - } - - /* - * - */ - public ExtensionDescriptionList getSupportedFilters() throws LBException{ - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null) - return extensionRegistry.getFilterExtensions(); - - return null; - } - - public List getSupportedFilterNames() throws LBException{ - List filterNames = new ArrayList(); - ExtensionRegistry extensionRegistry = getLexBIGServiceManager().getExtensionRegistry(); - if (extensionRegistry != null && extensionRegistry.getFilterExtensions() != null) - { - for (ExtensionDescription ed : extensionRegistry.getFilterExtensions().getExtensionDescription()) - filterNames.add(ed.getName()); - } - return filterNames; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.LexEvsCTS2#getServiceInfo() - */ - @Override - public ServiceInfo getServiceInfo() { - return new ServiceInfo(); - } - - /* - * (non-Javadoc) - * @see org.LexGrid.LexBIG.Extensions.Extendable#getDescription() - */ - @Override - public String getDescription() { - return getServiceInfo().getServiceDescription(); - } - - /* - * (non-Javadoc) - * @see org.LexGrid.LexBIG.Extensions.Extendable#getName() - */ - @Override - public String getName() { - return getServiceInfo().getServiceName(); - } - - /* - * (non-Javadoc) - * @see org.LexGrid.LexBIG.Extensions.Extendable#getProvider() - */ - @Override - public String getProvider() { - return getServiceInfo().getServiceProvider(); - } - - /* - * (non-Javadoc) - * @see org.LexGrid.LexBIG.Extensions.Extendable#getVersion() - */ - @Override - public String getVersion() { - return getServiceInfo().getServiceVersion(); - } - - /* - * - */ - public static void register() throws LBParameterException, LBException { - ExtensionDescription temp = new ExtensionDescription(); - temp.setExtensionBaseClass(LexEvsCTS2Impl.class.getInterfaces()[0].getName()); - temp.setExtensionClass(LexEvsCTS2Impl.class.getName()); - ServiceInfo serviceInfo = new ServiceInfo(); - temp.setDescription(serviceInfo.getServiceDescription()); - temp.setName(serviceInfo.getServiceName()); - temp.setVersion(serviceInfo.getServiceVersion()); - - // Registered here as part of the impl to avoid the LexBig service - // manager API. If writing an add-on extension, registration should be - // performed through the proper interface. - ExtensionRegistryImpl.instance().registerGenericExtension(temp); - } - - public static void main(String[] args){ - LexEvsCTS2Impl cts2 = new LexEvsCTS2Impl(); - System.out.println(cts2.getServiceInfo().getServiceName()); - System.out.println(cts2.getServiceInfo().getServiceProvider()); - System.out.println(cts2.getServiceInfo().getServiceDescription()); - System.out.println(cts2.getServiceInfo().getServiceVersion()); - - try { - ExtensionDescriptionList loaders = cts2.getSupportedLoaders(); - if (loaders != null) - { - for (ExtensionDescription loader : loaders.getExtensionDescription()) - { - System.out.println("loader getExtensionBaseClass : " + loader.getExtensionBaseClass()); - System.out.println("loader getExtensionClass : " + loader.getExtensionClass()); - System.out.println("loader getName : " + loader.getName()); - System.out.println("--------------------------"); - } - } - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - try { - ExtensionDescriptionList exporters = cts2.getSupportedExporters(); - if (exporters != null) - { - for (ExtensionDescription exporter : exporters.getExtensionDescription()) - { - System.out.println("exporter getExtensionBaseClass : " + exporter.getExtensionBaseClass()); - System.out.println("exporter getExtensionClass : " + exporter.getExtensionClass()); - System.out.println("exporter getName : " + exporter.getName()); - System.out.println("--------------------------"); - } - } - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - try { - ExtensionDescriptionList exporters = cts2.getLexBIGServiceManager().getExtensionRegistry().getGenericExtensions(); - if (exporters != null) - { - for (ExtensionDescription exporter : exporters.getExtensionDescription()) - { - System.out.println("generic getExtensionBaseClass : " + exporter.getExtensionBaseClass()); - System.out.println("generic getExtensionClass : " + exporter.getExtensionClass()); - System.out.println("generic getName : " + exporter.getName()); - System.out.println("--------------------------"); - } - } - } catch (LBException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/ServiceInfo.java b/cts2Impl/src/main/java/org/lexevs/cts2/ServiceInfo.java deleted file mode 100644 index fb74bd655f..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/ServiceInfo.java +++ /dev/null @@ -1,66 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2; - -/** - * Class ServiceInfo provides information about the service provider. - * - * @author Sridhar Dwarkanath - */ -public class ServiceInfo { - - private String serviceName = "LexEVSCTS2Impl"; - private String serviceDescription = "LexEVS CTS2 Implementation";; - private String serviceProvider = "Mayo Clinic"; - private String serviceVersion = "1.0"; - - public ServiceInfo(){ - } - - public void finalize() throws Throwable { - } - - /** - * @return the serviceName - */ - public String getServiceName() { - return serviceName; - } - - /** - * @return the serviceDescription - */ - public String getServiceDescription() { - return serviceDescription; - } - - /** - * @return the serviceProvider - */ - public String getServiceProvider() { - return serviceProvider; - } - - /** - * @return the serviceVersion - */ - public String getServiceVersion() { - return serviceVersion; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/AdminOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/AdminOperation.java deleted file mode 100644 index fc4585460a..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/AdminOperation.java +++ /dev/null @@ -1,83 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin; - -import org.lexevs.cts2.admin.export.AssociationExportOperation; -import org.lexevs.cts2.admin.export.CodeSystemExportOperation; -import org.lexevs.cts2.admin.export.ValueSetExportOperation; -import org.lexevs.cts2.admin.load.AssociationLoadOperation; -import org.lexevs.cts2.admin.load.CodeSystemLoadOperation; -import org.lexevs.cts2.admin.load.ValueSetLoadOperation; - -/** - * LexEVS implementation of CTS2 Administration Operations. - * - * @author Sridhar Dwarkanath - */ -public interface AdminOperation { - - /** - * Returns Association Export Operation interface. - * - * @return AssociationExportOperation - */ - public AssociationExportOperation getAssociationExportOperation(); - - /** - * Returns Association Load Operation interface. - * - * @return AssociationLoadOperation - */ - public AssociationLoadOperation getAssociationLoadOperation(); - - /** - * Returns Code System Load Operation interface. - * - * @return CodeSystemLoadOperation - */ - public CodeSystemLoadOperation getCodeSystemLoadOperation(); - - /** - * Returns Code System Export Operation interface. - * - * @return CodeSystemExportOperation - */ - public CodeSystemExportOperation getCodeSystemExportOperation(); - - /** - * Returns Notification Administration Operation interface. - * - * @return NotificationAdminOperation - */ - public NotificationAdminOperation getNotificationAdminOperation(); - - /** - * Returns Value Set Load Operation interface. - * - * @return ValueSetAdminOperation - */ - public ValueSetLoadOperation getValueSetLoadOperation(); - - /** - * Returns Value Set Export Operation interface. - * - * @return ValueSetExportOperation - */ - public ValueSetExportOperation getValueSetExportOperation(); -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/AdminOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/AdminOperationImpl.java deleted file mode 100644 index 6fffc553ba..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/AdminOperationImpl.java +++ /dev/null @@ -1,132 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin; - -import org.lexevs.cts2.BaseService; -import org.lexevs.cts2.admin.export.AssociationExportOperation; -import org.lexevs.cts2.admin.export.AssociationExportOperationImpl; -import org.lexevs.cts2.admin.export.CodeSystemExportOperation; -import org.lexevs.cts2.admin.export.CodeSystemExportOperationImpl; -import org.lexevs.cts2.admin.export.ValueSetExportOperation; -import org.lexevs.cts2.admin.export.ValueSetExportOperationImpl; -import org.lexevs.cts2.admin.load.AssociationLoadOperation; -import org.lexevs.cts2.admin.load.AssociationLoadOperationImpl; -import org.lexevs.cts2.admin.load.CodeSystemLoadOperation; -import org.lexevs.cts2.admin.load.CodeSystemLoadOperationImpl; -import org.lexevs.cts2.admin.load.ValueSetLoadOperation; -import org.lexevs.cts2.admin.load.ValueSetLoadOperationImpl; - -/** - * Class returns individual CTS 2 Administration Operation interfaces. - * - * @author Sridhar Dwarkanath - * - */ -public class AdminOperationImpl extends BaseService implements AdminOperation { - private CodeSystemLoadOperation csLoadOp_; - private CodeSystemExportOperation csExportOp_; - private ValueSetLoadOperation vsLoadOp_; - private ValueSetExportOperation vsExportOp_; - private NotificationAdminOperation notificationAdminOp_; - private AssociationExportOperation assnExportOp_; - private AssociationLoadOperation assnLoadOp_; - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getAssociationExportOperation() - */ - @Override - public AssociationExportOperation getAssociationExportOperation() { - if (assnExportOp_ == null) - assnExportOp_ = new AssociationExportOperationImpl(); - return assnExportOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getAssociationLoadOperation() - */ - @Override - public AssociationLoadOperation getAssociationLoadOperation() { - if (assnLoadOp_ == null) - assnLoadOp_ = new AssociationLoadOperationImpl(); - return assnLoadOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getCodeSystemExportOperation() - */ - @Override - public CodeSystemExportOperation getCodeSystemExportOperation() { - if (csExportOp_ == null) - csExportOp_ = new CodeSystemExportOperationImpl(); - - return csExportOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getCodeSystemLoadOperation() - */ - @Override - public CodeSystemLoadOperation getCodeSystemLoadOperation() { - if (csLoadOp_ == null) - csLoadOp_ = new CodeSystemLoadOperationImpl(); - - return csLoadOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getNotificationAdminOperation() - */ - @Override - public NotificationAdminOperation getNotificationAdminOperation() { - if(this.notificationAdminOp_ == null) { - notificationAdminOp_ = new NotificationAdminOperationImpl(); - } - return this.notificationAdminOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getValueSetExportOperation() - */ - @Override - public ValueSetExportOperation getValueSetExportOperation() { - if (vsExportOp_ == null) - vsExportOp_ = new ValueSetExportOperationImpl(); - - return vsExportOp_; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.AdminOperation#getValueSetLoadOperation() - */ - @Override - public ValueSetLoadOperation getValueSetLoadOperation() { - if (vsLoadOp_ == null) - vsLoadOp_ = new ValueSetLoadOperationImpl(); - - return vsLoadOp_; - } - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/NotificationAdminOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/NotificationAdminOperation.java deleted file mode 100644 index 9e3e0a70fe..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/NotificationAdminOperation.java +++ /dev/null @@ -1,74 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin; - -import org.lexevs.cts2.exception.admin.NotificationNotRegisteredException; -import org.lexevs.dao.database.service.event.DatabaseServiceEventListener; - -/** - * The Interface NotificationAdminOperation controls the registration and maintenence of Content - * Notification Listeners. - */ -public interface NotificationAdminOperation { - - /** - * The Enum NotificationStatus. - * - * SUSPEND: Notifications will cease being processed until further notice. - * REINSTATE: Notifications will resume processing. - * REMOVE: The Notification will be removed, and cannot be REINSTATE'd. - */ - public enum NotificationStatus { - SUSPEND, - REINSTATE, - REMOVE} - - /** - * Register the given Notification Listener in the system. - * - * @param listener - * The Notification Listener - * - * @return - * The Notification Identifier: The unique identifier of the particular Notification - * in the system. - */ - public String registerForNotification(DatabaseServiceEventListener listener); - - /** - * Replaces a Notification Listener with an Updated Notification Listener - * - * @param notificationId - * The Notification Identifier of the Notification to be updated. - * @param listener the listener - */ - public void updateNotificationRegistration(String notificationId, DatabaseServiceEventListener listener) - throws NotificationNotRegisteredException; - - /** - * Update the Notification Registration Status of a Notification Listener. - * - * @param status - * The new Notification Registration Status - * @param notificationId - * The Notification Identifier of the Notification to be updated. - */ - public void updateNotificationRegistrationStatus(String notificationId, NotificationStatus status) - throws NotificationNotRegisteredException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/NotificationAdminOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/NotificationAdminOperationImpl.java deleted file mode 100644 index 8a0a03dc3a..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/NotificationAdminOperationImpl.java +++ /dev/null @@ -1,92 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin; - -import org.lexevs.cts2.exception.admin.NotificationNotRegisteredException; -import org.lexevs.dao.database.service.event.DatabaseServiceEventListener; -import org.lexevs.dao.database.service.event.registry.ListenerRegistry; -import org.lexevs.locator.LexEvsServiceLocator; - -/** - * The Class NotificationAdminOperationImpl. - * - * @author Kevin Peterson - */ -public class NotificationAdminOperationImpl implements NotificationAdminOperation { - - /* (non-Javadoc) - * @see org.lexevs.cts2.admin.NotificationAdminOperation#registerForNotification(org.lexevs.dao.database.service.event.DatabaseServiceEventListener) - */ - @Override - public String registerForNotification(DatabaseServiceEventListener listener) { - return this.getListenerRegistry().registerListener(listener); - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.admin.NotificationAdminOperation#updateNotificationRegistration(java.lang.String, org.lexevs.dao.database.service.event.DatabaseServiceEventListener) - */ - @Override - public void updateNotificationRegistration(String listenerId, - DatabaseServiceEventListener listener) throws NotificationNotRegisteredException { - verifyListener(listenerId); - this.getListenerRegistry().registerListener(listenerId, listener); - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.admin.NotificationAdminOperation#updateNotificationRegistrationStatus(java.lang.String, org.lexevs.cts2.admin.NotificationAdminOperation.NotificationStatus) - */ - @Override - public void updateNotificationRegistrationStatus( - String listenerId, NotificationStatus status) throws NotificationNotRegisteredException { - verifyListener(listenerId); - - switch (status) { - case REMOVE: { - this.getListenerRegistry().unregisterListener(listenerId); - break; - } - case REINSTATE: { - this.getListenerRegistry().getRegisteredListener(listenerId).setActive(true); - break; - } - case SUSPEND: { - this.getListenerRegistry().getRegisteredListener(listenerId).setActive(false); - break; - } - } - } - - /** - * Gets the listener registry. - * - * @return the listener registry - */ - protected ListenerRegistry getListenerRegistry() { - return LexEvsServiceLocator.getInstance(). - getDatabaseServiceManager().getListenerRegistry(); - } - - private void verifyListener(String listenerId) - throws NotificationNotRegisteredException { - if(this.getListenerRegistry().getRegisteredListener(listenerId) == null) { - throw new NotificationNotRegisteredException(listenerId); - } - } - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/AssociationExportOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/AssociationExportOperation.java deleted file mode 100644 index 1657e6fefd..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/AssociationExportOperation.java +++ /dev/null @@ -1,36 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.export; - -import java.net.URI; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; - -public interface AssociationExportOperation { - - public void exportAssociation( - String codeSystemNameOrURI, - String codeSystemVersion, - CodedNodeGraph cng, - URI exportDestination, - boolean overwrite, - boolean stopOnErrors, - boolean async) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/AssociationExportOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/AssociationExportOperationImpl.java deleted file mode 100644 index 036c177037..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/AssociationExportOperationImpl.java +++ /dev/null @@ -1,65 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.export; - -import java.net.URI; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.exporters.LexGridExport; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.lexevs.cts2.BaseService; - -/** - * The Class AssociationExportOperationImpl. - * - * @author Kevin Peterson - */ -public class AssociationExportOperationImpl extends BaseService implements AssociationExportOperation { - - /* (non-Javadoc) - * @see org.lexevs.cts2.admin.export.AssociationExportOperation#exportAssociation(java.lang.String, java.lang.String, org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph, java.net.URI, boolean, boolean, boolean) - */ - @Override - public void exportAssociation( - String codeSystemNameOrURI, - String codeSystemVersion, - CodedNodeGraph cng, - URI exportDestination, - boolean overwrite, - boolean stopOnErrors, - boolean async) throws LBException { - - LexGridExport exporter; - try { - exporter = (LexGridExport)getLexBIGService().getServiceManager(null).getExporter(LexGridExport.name); - } catch (LBException e) { - throw new RuntimeException(e); - } - - exporter.setCng(cng); - - exporter.export( - Constructors.createAbsoluteCodingSchemeVersionReference(codeSystemNameOrURI, codeSystemVersion), - exportDestination, - overwrite, - stopOnErrors, - async); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/CodeSystemExportOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/CodeSystemExportOperation.java deleted file mode 100644 index 1ca3c5f9e3..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/CodeSystemExportOperation.java +++ /dev/null @@ -1,123 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.export; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Extensions.Export.Exporter; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; - -/** - * LexEVS CTS 2 Code System Export Operation. - * - * @author Sridhar Dwarkanath - */ -public interface CodeSystemExportOperation { - /** - * Exports contents of the code system using the exporter specified. - * @param codeSystemNameOrURI URI of the Code System to be exported - * @param codeSystemVersion Version of the Code System to be exported - * @param exportDestination Destination path information for the exported file. - * @param exporter to use. Use getSupportedExporterNames to get all the exporters supported by this instance of CTS2. - * @return URI of destination if successfully exported. - * @throws LBException - */ - public URI exportCodeSystemContent(String codeSystemNameOrURI, String codeSystemVersion, - URI exportDestination, Exporter exporter) throws LBException; - - /** - * Returns CodedNodeSet(CNS) for a Code System Version. This CNS can be used to apply further restrictions before exporting. - * - * @param codeSystemNameOrURI URI of the Code System to be exported - * @param codeSystemVersion Version of the Code System to be exported - * @return CodedNodeSet of the Code System Version - * @throws LBException - */ - public CodedNodeSet getCodeSystemCodedNodeSet(String codeSystemNameOrURI, String codeSystemVersion) - throws LBException; - - /** - * Returns CodedNodeGraph(CNG) for a Code System Version. This CNG can be used to apply further restrictions before exporting. - * - * @param codeSystemNameOrURI URI of the Code System to be exported - * @param codeSystemVersion Version of the Code System to be exported - * @return CodedNodeGraph of the Code System Version - * @throws LBException - */ - public CodedNodeGraph getCodeSystemCodedNodeGraph(String codeSystemNameOrURI, String codeSystemVersion) - throws LBException; - - /** - * Resolves the given CodedNodeSet(CNS) and exports the contents. - * - * @param codeSystemNameOrURI URI of the Code System to be used for resolving the CNS - * @param codeSystemVersion Version of the Code System to be used for resolving the CNS - * @param cns Coded Node Set - * @param exportDestination Destination for the exported file - * @param overwrite True means, any existing file will be overwritten - * @param stopOnErrors True means stop if any export error is detected. False means - * attempt to export what can be exported if recoverable errors are - * encountered. - * @param async Flag controlling whether export occurs in the calling thread. - * If true, the export will occur in a separate asynchronous process. - * If false, this method blocks until the export operation - * completes or fails. Regardless of setting, the getStatus and - * getLog calls are used to fetch results. - * @return URI of destination if successfully exported. - * @throws LBException - */ - public URI exportCodedNodeSet(String codeSystemNameOrURI, - String codeSystemVersion, CodedNodeSet cns, URI exportDestination, boolean overwrite, - boolean stopOnErrors, boolean async) throws LBException; - - /** - * Resolves the given CodedNodeGraph(CNG) and exports the contents. - * - * @param codeSystemNameOrURI URI of the Code System to be used for resolving the CNG - * @param codeSystemVersion Version of the Code System to be used for resolving the CNG - * @param cng Coded Node Graph - * @param exportDestination Destination for the exported file - * @param overwrite True means, any existing file will be overwritten - * @param stopOnErrors True means stop if any export error is detected. False means - * attempt to export what can be exported if recoverable errors are - * encountered. - * @param async Flag controlling whether export occurs in the calling thread. - * If true, the export will occur in a separate asynchronous process. - * If false, this method blocks until the export operation - * completes or fails. Regardless of setting, the getStatus and - * getLog calls are used to fetch results. - * @return URI of destination if successfully exported. - * @throws LBException - */ - public URI exportCodedNodeGraph(String codeSystemNameOrURI, - String codeSystemVersion, CodedNodeGraph cng, URI exportDestination, boolean overwrite, - boolean stopOnErrors, boolean async) throws LBException; - - /** - * Returns list of Exporter names supported by this LexEVS instance. - * - * @return List of supported Exporter names - * @throws LBException - */ - public List getSupportedExporterNames() throws LBException; - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/CodeSystemExportOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/CodeSystemExportOperationImpl.java deleted file mode 100644 index 2708cb16ae..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/CodeSystemExportOperationImpl.java +++ /dev/null @@ -1,168 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.export; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Extensions.Export.Exporter; -import org.LexGrid.LexBIG.Impl.exporters.LexGridExport; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.BaseService; - -/** - * Implementation CTS 2 Code System Export Operation. - * - * @author Sridhar Dwarkanath - */ -public class CodeSystemExportOperationImpl extends BaseService implements CodeSystemExportOperation { - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.CodeSystemExportOperation#exportCodeSystemContent(java.lang.String, java.lang.String, java.net.URI, org.LexGrid.LexBIG.Extensions.Export.Exporter) - */ - @Override - public URI exportCodeSystemContent(String codeSystemNameOrURI, - String codeSystemVersion, URI exportDestination, Exporter exporter) throws LBException { - if (exporter == null) - throw new LBException("Code system exporter can not be null. Call getSupportedExporterNames() to get supported exporters."); - - if (!getSupportedExporterNames().contains(exporter.getName())) - throw new LBException("Exporter not supported. Call getSupportedExporterNames() to get supported exporters."); - - exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(codeSystemNameOrURI, codeSystemVersion), exportDestination); - - while (exporter.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - - if (exporter.getReferences() != null) - { - URI[] uris = exporter.getReferences(); - return uris[0]; - } - - return null; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.CodeSystemExportOperation#exportCodedNodeGraph(java.lang.String, java.lang.String, org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph, java.net.URI, boolean, boolean, boolean) - */ - @Override - public URI exportCodedNodeGraph(String codeSystemNameOrURI, - String codeSystemVersion, CodedNodeGraph cng, - URI exportDestination, boolean overwrite, boolean stopOnErrors, boolean async) throws LBException { - - if (cng == null) - throw new LBException("Coded Node Graph can not be null"); - if (StringUtils.isEmpty(codeSystemNameOrURI)) - throw new LBException("Code System Name or URI can not be null"); - - LexGridExport exporter; - try { - exporter = (LexGridExport)getLexBIGService().getServiceManager(null).getExporter(LexGridExport.name); - } catch (LBException e) { - throw new RuntimeException(e); - } - - exporter.setCng(cng); - exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(codeSystemNameOrURI, codeSystemVersion), exportDestination, overwrite, stopOnErrors, async); - - while (exporter.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - - return exporter.getResourceUri(); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.CodeSystemExportOperation#exportCodedNodeSet(java.lang.String, java.lang.String, org.LexGrid.LexBIG.LexBIGService.CodedNodeSet, java.net.URI, boolean, boolean, boolean) - */ - @Override - public URI exportCodedNodeSet(String codeSystemNameOrURI, - String codeSystemVersion, CodedNodeSet cns, URI exportDestination, - boolean overwrite, boolean stopOnErrors, boolean async) throws LBException { - if (cns == null) - throw new LBException("Coded Node Set can not be null"); - if (StringUtils.isEmpty(codeSystemNameOrURI)) - throw new LBException("Code System Name or URI can not be null"); - - LexGridExport exporter; - try { - exporter = (LexGridExport)getLexBIGService().getServiceManager(null).getExporter(LexGridExport.name); - } catch (LBException e) { - throw new RuntimeException(e); - } - - exporter.setCns(cns); - exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(codeSystemNameOrURI, codeSystemVersion), exportDestination, overwrite, stopOnErrors, async); - - while (exporter.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - - return exporter.getResourceUri(); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.CodeSystemExportOperation#getCodeSystemCodedNodeGraph(java.lang.String, java.lang.String) - */ - @Override - public CodedNodeGraph getCodeSystemCodedNodeGraph( - String codeSystemNameOrURI, String codeSystemVersion) - throws LBException { - return getLexBIGService().getNodeGraph(codeSystemNameOrURI, - Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion), null); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.CodeSystemExportOperation#getCodeSystemCodedNodeSet(java.lang.String, java.lang.String) - */ - @Override - public CodedNodeSet getCodeSystemCodedNodeSet(String codeSystemNameOrURI, - String codeSystemVersion) throws LBException { - return getLexBIGService().getNodeSet(codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion), null); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.CodeSystemExportOperation#getSupportedExporterNames() - */ - @Override - public List getSupportedExporterNames() throws LBException { - return this.getLexEvsCTS2().getSupportedExporterNames(); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/ValueSetExportOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/ValueSetExportOperation.java deleted file mode 100644 index 954bf0ebe0..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/ValueSetExportOperation.java +++ /dev/null @@ -1,94 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.export; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.Exceptions.LBException; - -public interface ValueSetExportOperation { - -/** - * Export Value Set Definition to LexGrid canonical XML format. - * - * @param valueSetDefinitionURI - * value set definition URI - * @param valueSetDefinitionVersion - * value set definition version - * @param xmlFullPathName - * File location (including file name *.xml) to save the definition - * @param overwrite - * True: to override the existing file. - * @param failOnAllErrors - * True: stops exporting if any error. - * @throws LBException - */ -public void exportValueSetDefinition(URI valueSetDefinitionURI, String valueSetDefinitionVersion, String xmlFullPathName, boolean overwrite, boolean failOnAllErrors) throws LBException; - - /** - * Exports contents of the Value Set Definition using the exporter specified. - * - * @param valueSetDefinitionURI - * URI of the Value Set Definition to be exported - * @param valueSetDefinitionVersion - * version of the Value Set Definition to be exported - * @param exportDestination - * Destination path information for the exported file. - * @param exporter - * Name of the exporter to use. Use getSupportedExporterNames to get all the exporters supported by this instance of CTS2. - * @return URI of destination if successfully exported. - * @throws LBException - */ - public URI exportValueSetContents(URI valueSetDefinitionURI, String valueSetDefinitionVersion, URI exportDestination, String exporter) throws LBException; - - /** - * Exports contents of Value Set Definition as Code System in LexGrid canonical XML format. - * - * @param valueSetDefinitionURI - * value set definition URI - * @param valueSetDefinitionVersion - * value set definition version - * @param exportDestination - * Location (path to the folder withOUT the file name) to save the definition - * @param csVersionList - * A list of coding scheme URI's and versions to be used. These will be used only if they are present in - * the service. If absent, the most recent version will be used instead. - * @param csVersionTag - * the tag (e.g "devel", "production", ...) to be used to reconcile coding schemes when more than one is present. - * @param overwrite - * True: to override the existing file. - * @param failOnAllErrors - * True: stops exporting if any error. - * @return URI of destination if successfully exported. - * @throws LBException - */ - public URI exportValueSetContents(URI valueSetDefinitionURI, String valueSetDefinitionVersion, - URI exportDestination, AbsoluteCodingSchemeVersionReferenceList csVersionList, - String csVersionTag, boolean overwrite, boolean failOnAllErrors) throws LBException; - - /** - * Returns list of Exporter names supported by this LexEVS instance. - * - * @return List of supported Exporter names - * @throws LBException - */ - public List getSupportedExporterNames() throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/ValueSetExportOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/ValueSetExportOperationImpl.java deleted file mode 100644 index b4a2c3345b..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/export/ValueSetExportOperationImpl.java +++ /dev/null @@ -1,104 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.export; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Extensions.Export.Exporter; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.BaseService; -import org.lexevs.cts2.LexEvsCTS2Impl; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; -import org.lexgrid.valuesets.impl.LexEVSValueSetDefinitionServicesImpl; - -/** - * Implementation of CTS 2 Value Set Export Operation. - * - * @author Sridhar Dwarkanath - */ -public class ValueSetExportOperationImpl extends BaseService implements ValueSetExportOperation{ - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.ValueSetExportOperation#exportValueSetDefinition(java.net.URI, java.lang.String, java.lang.String, boolean, boolean) - */ - @Override - public void exportValueSetDefinition(URI valueSetDefinitionURI, String valueSetDefinitionVersion, String xmlFullPathName, boolean overwrite, boolean failOnAllErrors) throws LBException { - LexEVSValueSetDefinitionServices vsdServ = LexEVSValueSetDefinitionServicesImpl.defaultInstance(); - vsdServ.exportValueSetDefinition(valueSetDefinitionURI, valueSetDefinitionVersion, xmlFullPathName, overwrite, failOnAllErrors); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.ValueSetExportOperation#exportValueSetContents(java.net.URI, java.lang.String, java.net.URI, java.lang.String) - */ - @Override - public URI exportValueSetContents(URI valueSetDefinitionURI, String valueSetDefinitionVersion, URI exportDestination, String exporterName) - throws LBException { - if (StringUtils.isEmpty(exporterName)) - throw new LBException("Value Set exporterName is not specified. Call getExporterNames() to get supported exporters."); - - if (!getSupportedExporterNames().contains(exporterName)) - throw new LBException("Exporter name specified is not supported. Call getSystemExporterNames() to get supported exporters."); - - Exporter exporter = getLexBIGServiceManager().getExporter(exporterName); - exporter.exportValueSetDefinition(valueSetDefinitionURI, valueSetDefinitionVersion, exportDestination); - - while (exporter.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - - if (exporter.getReferences() != null) - { - URI[] uris = exporter.getReferences(); - return uris[0]; - } - - return null; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.ValueSetExportOperation#exportValueSetContents(java.net.URI, java.lang.String, java.net.URI, org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList, java.lang.String, boolean, boolean) - */ - @Override - public URI exportValueSetContents(URI valueSetDefinitionURI, String valueSetDefinitionVersion, - URI exportDestination, AbsoluteCodingSchemeVersionReferenceList csVersionList, - String csVersionTag, boolean overwrite, boolean failOnAllErrors) throws LBException { - LexEVSValueSetDefinitionServices vsdServ = LexEVSValueSetDefinitionServicesImpl.defaultInstance(); - return vsdServ.exportValueSetResolution(valueSetDefinitionURI, valueSetDefinitionVersion, exportDestination, csVersionList, csVersionTag, overwrite, failOnAllErrors); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.export.ValueSetExportOperation#getSupportedExporterNames() - */ - @Override - public List getSupportedExporterNames() throws LBException { - return this.getLexEvsCTS2().getSupportedExporterNames(); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/AssociationLoadOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/AssociationLoadOperation.java deleted file mode 100644 index caeb58b458..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/AssociationLoadOperation.java +++ /dev/null @@ -1,47 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.load; - -import java.net.URI; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; - -public interface AssociationLoadOperation { - - public void importAssociationVersion( - URI source, - URI metadata, - URI manifest, - String loaderName, - Boolean stopOnErrors, - Boolean async, - Boolean overwriteMetadata, - String versionTag, - Boolean activate) throws LBException; - - public void importAssociationVersion( - CodingScheme codeSystem, - URI metadata, - Boolean stopOnErrors, - Boolean async, - Boolean overwriteMetadata, - String versionTag, - Boolean activate) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/AssociationLoadOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/AssociationLoadOperationImpl.java deleted file mode 100644 index 6de787f020..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/AssociationLoadOperationImpl.java +++ /dev/null @@ -1,74 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.load; - -import java.net.URI; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.lexevs.cts2.BaseService; - -public class AssociationLoadOperationImpl extends BaseService implements AssociationLoadOperation { - - @Override - public void importAssociationVersion( - CodingScheme codeSystem, - URI metadata, - Boolean stopOnErrors, - Boolean async, - Boolean overwriteMetadata, - String versionTag, - Boolean activate) throws LBException { - this.getCodeSystemLoadOperation().load( - codeSystem, - metadata, - stopOnErrors, - async, - overwriteMetadata, - versionTag, - activate); - } - - @Override - public void importAssociationVersion( - URI source, - URI metadata, - URI manifest, - String loaderName, - Boolean stopOnErrors, - Boolean async, - Boolean overwriteMetadata, - String versionTag, - Boolean activate) throws LBException { - this.getCodeSystemLoadOperation().load( - source, - metadata, - manifest, - loaderName, - stopOnErrors, - async, - overwriteMetadata, - versionTag, - activate); - } - - protected CodeSystemLoadOperation getCodeSystemLoadOperation() { - return this.getLexEvsCTS2().getAdminOperation().getCodeSystemLoadOperation(); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/CodeSystemLoadOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/CodeSystemLoadOperation.java deleted file mode 100644 index b2f559b7c4..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/CodeSystemLoadOperation.java +++ /dev/null @@ -1,208 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.load; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.lexevs.cts2.core.update.RevisionInfo; - -import edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair; - -/** - * LexEVS CTS 2 Code System Load Operation. - * - * @author Sridhar Dwarkanath - */ -public interface CodeSystemLoadOperation { - - /** - * Installs a code system (aka terminology) into the terminology service - * for subsequent access by other service functions. This operation is used - * for the initial install of the overall terminology structure itself. - * This may include the full set of concepts, relationships and so on, or - * some of these elements may be loaded using the Import Code System Revision - * operation. - * - * @param source - * URI corresponding to the code system file. - * @param metadata - * (Optional) URI of the XML file containing custom code system meta data. - * loads additional data to be maintained and queried as - * terminology meta-information within the system. - * All tags and values are interpreted as simple text-based key/value - * pairs. - * @param manifest - * (Optional) URI corresponding to the manifest file. - * The LexGrid Manifest accommodates the need to supplement or - * override default information provided by the source. More specifically, - * the manifest provides a means to customize the same code system metadata - * defined by the LexGrid model, since each element of the manifest extends - * directly from an element used to define the LexGrid coding scheme(aka code system) object. - * Each extended element allows for the administrator to specify whether - * the manifest definition replaces or supplements original values provided - * in the terminology source. Like the LexGrid Terminology model, the manifest - * is defined by a formal model mastered as XML Schema. - * @param loaderName - * Loader to use for loading the code system. - * LexEvsCTS2.getSupportedLoaders method returns all the loaders supported - * by the service. - * For example, 'OBOLoader' could be used to load code system source that is in OBO format, - * 'OWLLoader' for code system source in OWL format, etc. - * @param stopOnErrors - * True means stop if any load error is detected. False means - * attempt to load what can be loaded if recoverable errors are - * encountered. - * @param async - * Flag controlling whether load occurs in the calling thread. - * If true, the load will occur in a separate asynchronous process. - * If false, this method blocks until the load operation - * completes or fails. Regardless of setting, the getStatus and - * getLog calls are used to fetch results. - * @param overwriteMetadata - * If true, existing meta data for the code system will be erased. - * If false, new meta data will be appended to existing meta data. - * @param versionTag - - * The tag (e.g "devel", "production", ...) to be set for the this code system - * @param activate - * True: activates the code system after the load. - * @return URN and Version of the loaded code system - * @throws LBException - */ - public abstract URNVersionPair[] load(URI source, URI metadata, URI manifest, String loaderName, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate) throws LBException; - - /** - * Installs a code system (aka terminology) into the terminology service - * for subsequent access by other service functions. This operation is used - * for the initial install of the overall terminology structure itself. - * This may include the full set of concepts, relationships and so on, or - * some of these elements may be loaded using the Import Code System Revision - * operation. - * - * @param codeSystem - * code system object to be loaded into the terminology service. - * @param metadata - * (Optional) URI of the XML file containing custom code system meta data. - * loads additional data to be maintained and queried as - * terminology meta-information within the system. - * All tags and values are interpreted as simple text-based key/value - * pairs. - * @param stopOnErrors - * True means stop if any load error is detected. False means - * attempt to load what can be loaded if recoverable errors are - * encountered. - * @param async - * Flag controlling whether load occurs in the calling thread. - * If true, the load will occur in a separate asynchronous process. - * If false, this method blocks until the load operation - * completes or fails. Regardless of setting, the getStatus and - * getLog calls are used to fetch results. - * @param overwriteMetadata - * If true, existing meta data for the code system will be erased. - * If false, new meta data will be appended to existing meta data. - * @param versionTag - * The tag (e.g "devel", "production", ...) to be set for the this code system - * @param activate - * True: activates the code system after the load. - * @return URN and Version of the loaded code system - * @throws LBException - */ - public abstract URNVersionPair[] load(CodingScheme codeSystem, URI metadata, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate) throws LBException; - - /** - * Loads custom code system meta data. This is to load additional data to be maintained and queried as - * terminology meta-information within the system. - * - * @param codeSystemNameOrURI - * Code system name or URI. - * @param codeSystemVersionOrTag - * Code system version or tag. - * @param metadata - * URI of the XML file containing custom code system meta data. - * loads additional data to be maintained and queried as - * terminology meta-information within the system. - * All tags and values are interpreted as simple text-based key/value - * pairs. - * @param stopOnErrors - * True means stop if any load error is detected. False means - * attempt to load what can be loaded if recoverable errors are - * encountered. - * @param async - * Flag controlling whether load occurs in the calling thread. - * If true, the load will occur in a separate asynchronous process. - * If false, this method blocks until the load operation - * completes or fails. Regardless of setting, the getStatus and - * getLog calls are used to fetch results. - * @param overwriteMetadata - * If true, existing meta data for the code system will be erased. - * If false, new meta data will be appended to existing meta data. - * @return URN and Version of the code system - * @throws LBException - */ - public URNVersionPair applyMetadataToCodeSystem(String codeSystemNameOrURI, CodingSchemeVersionOrTag codeSystemVersionOrTag, URI metadata, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata) throws LBException; - - /** - * Installs either an entire new version or the necessary revision updates - * for an already loaded code system (terminology) into the terminology server - * repository (content included by value or by reference to a location). - * Includes indicator as to whether intent is to replace whole code system or - * just replace some elements (codes, associations etc). - * - * @return - * @throws LBException - */ - public void loadCodeSystemRevsion(CodingScheme codingScheme, RevisionInfo revisionInfo) throws LBException; - - /** - * Activates the loaded code system version. Only activated code system version will be available - * for access by other other terminology service functions. - * - * @param codeSystemURI - * URI corresponding to the code system. - * @param codeSyatemVersion - * version of the code system. - * @return true if activated - * @throws LBException - */ - public boolean activateCodeSystem(String codeSystemURI, String codeSyatemVersion) throws LBException; - - /** - * Deactivates the loaded code system version. Deactivated code system version will not be available - * for access by other other terminology service functions. - * - * @param codeSystemURI - * URI corresponding to the code system. - * @param codeSyatemVersion - * version of the code system. - * @return true if deactivated - * @throws LBException - */ - public boolean deactivateCodeSystem(String codeSystemURI, String codeSyatemVersion) throws LBException; - - /** - * Returns list of Loader names supported by this LexEVS instance. - * - * @return List of supported Loader names - * @throws LBException - */ - public List getSupportedLoaderNames() throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/CodeSystemLoadOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/CodeSystemLoadOperationImpl.java deleted file mode 100644 index eacc3d5cdc..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/CodeSystemLoadOperationImpl.java +++ /dev/null @@ -1,333 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.load; - -import java.net.URI; -import java.util.Date; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.ExtensionDescription; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Extensions.Load.Loader; -import org.LexGrid.LexBIG.Extensions.Load.MetaData_Loader; -import org.LexGrid.LexBIG.Extensions.Load.options.OptionHolder; -import org.LexGrid.LexBIG.Impl.loaders.BaseLoader; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.Revision; -import org.apache.commons.lang.BooleanUtils; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.author.AuthoringCore; -import org.lexevs.cts2.core.update.RevisionInfo; - -import edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair; - -/** - * Implementation of LexEVS CTS 2 Code System Load Operation. - * - * @author Sridhar Dwarkanath - */ -public class CodeSystemLoadOperationImpl extends AuthoringCore implements CodeSystemLoadOperation { - - private static final long serialVersionUID = 1L; - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#loadCodeSystemRevsion() - */ - @Override - public void loadCodeSystemRevsion( - CodingScheme codingScheme, - RevisionInfo revisionInfo) - throws LBException { - Revision revision = this.getLexGridRevisionObject(revisionInfo); - - ChangedEntry entry = new ChangedEntry(); - entry.setChangedCodingSchemeEntry(codingScheme); - - revision.addChangedEntry(entry); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision( - revision, - revisionInfo.getSystemReleaseURI(), null); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#load(org.LexGrid.codingSchemes.CodingScheme, java.net.URI, java.lang.Boolean, java.lang.Boolean, java.lang.Boolean, java.lang.String, java.lang.Boolean) - */ - @Override - public URNVersionPair[] load( - CodingScheme codeSystem, - URI metadata, - Boolean stopOnErrors, - Boolean async, - Boolean overwriteMetadata, - String versionTag, - Boolean activate) throws LBException { - if (codeSystem == null) - throw new LBException("Code System can not be empty"); - - CodingSchemeLoader codingSchemeLoader = new CodingSchemeLoader(codeSystem); - codingSchemeLoader.load(stopOnErrors, async); - - while (codingSchemeLoader.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - - // load code system meta data if provided - if (metadata != null) - { - loadCSMetaData(codeSystem.getCodingSchemeURI(), codeSystem.getRepresentsVersion(), metadata, overwriteMetadata, stopOnErrors, async); - } - - // apply version tag if provided - if (StringUtils.isNotEmpty(versionTag)) - { - applyCSTag(codeSystem.getCodingSchemeURI(), codeSystem.getRepresentsVersion(), versionTag); - } - - // activate loaded code system if specified - if (activate) - { - activateCodeSystem(codeSystem.getCodingSchemeURI(), codeSystem.getRepresentsVersion()); - } - - URNVersionPair urnVersionPair = new URNVersionPair(codeSystem.getCodingSchemeURI(), codeSystem.getRepresentsVersion()); - return new URNVersionPair[] {urnVersionPair}; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#applyMetadataToCodeSystem(java.lang.String, org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag, java.net.URI, java.lang.Boolean, java.lang.Boolean, java.lang.Boolean) - */ - @Override - public URNVersionPair applyMetadataToCodeSystem(String codeSystemNameOrURI, CodingSchemeVersionOrTag codeSystemVersionOrTag, URI metadata, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata) throws LBException - { - CodingScheme codeSystem = getLexBIGService().resolveCodingScheme(codeSystemNameOrURI, codeSystemVersionOrTag); - - URNVersionPair urnVersionPair = null; - if (codeSystem != null) - { - loadCSMetaData(codeSystem.getCodingSchemeURI(), codeSystem.getRepresentsVersion(), metadata, overwriteMetadata, stopOnErrors, async); - - urnVersionPair = new URNVersionPair(codeSystem.getCodingSchemeURI(), codeSystem.getRepresentsVersion()); - } - - return urnVersionPair; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#load(java.net.URI, java.net.URI, java.net.URI, java.lang.String, java.lang.Boolean, java.lang.Boolean, java.lang.Boolean, java.lang.String, java.lang.Boolean) - */ - @Override - public URNVersionPair[] load(URI source, URI metadata, URI manifest, String loaderName, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate) throws LBException{ - if (loaderName == null) - throw new LBException("Code System loader must be specified. Use LexEVSCTS2.getSupportedCodeSystemLoaders for supported list of loaders in the service."); - - if (!this.getLexEvsCTS2().getSupportedLoaderNames().contains(loaderName)) - { - throw new LBException("Provided Code System loader not supported. Use LexEVSCTS2.getSupportedCodeSystemLoaders/LoaderNames for supported list of loaders in the service."); - } - - return loadSource(source, loaderName, metadata, manifest, stopOnErrors, async, overwriteMetadata, versionTag, activate); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#activateCodeSystem(java.lang.String, java.lang.String) - */ - public boolean activateCodeSystem(String codeSystemURI, String codeSyatemVersion) throws LBException{ - AbsoluteCodingSchemeVersionReference acsvr = new AbsoluteCodingSchemeVersionReference(); - acsvr.setCodingSchemeURN(codeSystemURI); - acsvr.setCodingSchemeVersion(codeSyatemVersion); - getLexBIGServiceManager().activateCodingSchemeVersion(acsvr); - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#deactivateCodeSystem(java.lang.String, java.lang.String) - */ - public boolean deactivateCodeSystem(String codeSystemURI, String codeSyatemVersion) throws LBException{ - AbsoluteCodingSchemeVersionReference acsvr = new AbsoluteCodingSchemeVersionReference(); - acsvr.setCodingSchemeURN(codeSystemURI); - acsvr.setCodingSchemeVersion(codeSyatemVersion); - getLexBIGServiceManager().deactivateCodingSchemeVersion(acsvr, new Date()); - return true; - } - - - private URNVersionPair[] loadSource(URI source, String loaderName, URI metadata, URI manifest, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate) throws LBException{ - Loader loader = getLexBIGServiceManager().getLoader(loaderName); - loader.getOptions().getBooleanOption(BaseLoader.FAIL_ON_ERROR_OPTION).setOptionValue(stopOnErrors); - loader.getOptions().getBooleanOption(BaseLoader.ASYNC_OPTION).setOptionValue(async); - loader.setCodingSchemeManifestURI(manifest); - loader.load(source); - - while (loader.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - - if (metadata != null) - { - loadCSMetaData(loader, metadata, overwriteMetadata, stopOnErrors, async); - } - - if (BooleanUtils.isTrue(activate)) - { - activateCS(loader); - } - - if (StringUtils.isNotEmpty(versionTag)) - { - applyCSTag(loader, versionTag); - } - - URNVersionPair urnVersion = null; - URNVersionPair[] urnVersionArray = null; - - AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); - if (refs != null) - { - urnVersionArray = new URNVersionPair[refs.length]; - for (int i = 0; i < refs.length; i++) { - AbsoluteCodingSchemeVersionReference ref = refs[i]; - urnVersion = new URNVersionPair(ref.getCodingSchemeURN(), ref.getCodingSchemeVersion()); - urnVersionArray[i] = urnVersion; - } - } - return urnVersionArray; - } - - private void loadCSMetaData(String csURI, String csVersion, URI metadata, boolean overwriteMetadata, boolean stopOnErrors, boolean async) throws LBException{ - AbsoluteCodingSchemeVersionReference acsvr = new AbsoluteCodingSchemeVersionReference(); - acsvr.setCodingSchemeURN(csURI); - acsvr.setCodingSchemeVersion(csVersion); - MetaData_Loader loader = (MetaData_Loader) getLexBIGServiceManager().getLoader("MetaDataLoader"); - loader.loadAuxiliaryData(metadata, acsvr, overwriteMetadata, stopOnErrors, async); - - while (loader.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - } - - private void loadCSMetaData(Loader loader, URI metadata, boolean overwriteMetadata, boolean stopOnErrors, boolean async) throws LBException{ - AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); - for (int i = 0; i < refs.length; i++) { - AbsoluteCodingSchemeVersionReference ref = refs[i]; - MetaData_Loader metaLoader = (MetaData_Loader) getLexBIGServiceManager().getLoader("MetaDataLoader"); - metaLoader.loadAuxiliaryData(metadata, ref, overwriteMetadata, stopOnErrors, async); - while (metaLoader.getStatus().getEndTime() == null) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - } - } - } - } - - private void applyCSTag(String csURI, String csVersion, String versionTag) throws LBException{ - AbsoluteCodingSchemeVersionReference acsvr = new AbsoluteCodingSchemeVersionReference(); - acsvr.setCodingSchemeURN(csURI); - acsvr.setCodingSchemeVersion(csVersion); - getLexBIGServiceManager().setVersionTag(acsvr, versionTag); - } - - private void activateCS(Loader loader) throws LBException{ - AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); - for (int i = 0; i < refs.length; i++) { - AbsoluteCodingSchemeVersionReference ref = refs[i]; - getLexBIGServiceManager().activateCodingSchemeVersion(ref); - } - } - - private void applyCSTag(Loader loader, String versionTag) throws LBException{ - AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); - for (int i = 0; i < refs.length; i++) { - AbsoluteCodingSchemeVersionReference ref = refs[i]; - getLexBIGServiceManager().setVersionTag(ref, versionTag); - } - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.CodeSystemLoadOperation#getSupportedLoaderNames() - */ - @Override - public List getSupportedLoaderNames() throws LBException { - return this.getLexEvsCTS2().getSupportedLoaderNames(); - } - - private class CodingSchemeLoader extends BaseLoader { - - private static final long serialVersionUID = 2623487391846644470L; - - private CodingScheme codingScheme; - - private CodingSchemeLoader(CodingScheme codingScheme){ - this.codingScheme = codingScheme; - this.setDoApplyPostLoadManifest(false); - } - - public void load(boolean stopOnErrors, boolean async) { - this.getOptions().getBooleanOption(FAIL_ON_ERROR_OPTION).setOptionValue(stopOnErrors); - this.getOptions().getBooleanOption(ASYNC_OPTION).setOptionValue(async); - this.load(null); - } - - @Override - protected OptionHolder declareAllowedOptions(OptionHolder holder) { - return holder; - } - - @Override - protected URNVersionPair[] doLoad() throws Exception { - this.persistCodingSchemeToDatabase(this.codingScheme); - - return this.constructVersionPairsFromCodingSchemes(codingScheme); - } - - @Override - protected ExtensionDescription buildExtensionDescription() { - ExtensionDescription ed = new ExtensionDescription(); - ed.setName("CTS 2 Code System Loader"); - return ed; -// return null; - } - } - - public static void main(String[] args){ -// LexEvsCTS2 lexevsCTS2 = LexEvsCTS2Impl.defaultInstance(); -// CodeSystemLoadOperation csLoad = lexevsCTS2.getAdminOperation().getCodeSystemLoadOperation(); - - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/ValueSetLoadOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/ValueSetLoadOperation.java deleted file mode 100644 index 5a378951ef..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/ValueSetLoadOperation.java +++ /dev/null @@ -1,67 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.load; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.valueSets.ValueSetDefinition; - -import edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair; - -/** - * LexEVS CTS 2 Value Set Load Operation. - * - * @author Sridhar Dwarkanath - */ -public interface ValueSetLoadOperation { - - /** - * Load the value set definition. - * - * @param source location of the source file - * @param releaseURI Release URI the loaded contents belong to - * @param loaderName Name of the loader to be used. Call getSupportedLoaderNames() - * to get list of loaders supported by this instance of LexEVS. - * @param stopOnErrors True means stop if any load error is detected. False means - * attempt to load what can be loaded if recoverable errors are - * encountered. - */ - public abstract URNVersionPair[] load(URI source, URI releaseURI, String loaderName, Boolean stopOnErrors) throws LBException; - - /** - * Load value set definition. - * - * @param valueSetDefinition Value Set Definition object to be loaded - * @param releaseURI Release URI the loaded contents belong to - * @param stopOnErrors True means stop if any load error is detected. False means - * attempt to load what can be loaded if recoverable errors are - * encountered. - */ - public abstract String load(ValueSetDefinition valueSetDefinition, URI releaseURI, Boolean stopOnErrors) throws LBException; - - /** - * Returns list of Loader names supported by this LexEVS instance. - * - * @return List of supported Loader names - * @throws LBException - */ - public List getSupportedLoaderNames() throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/ValueSetLoadOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/ValueSetLoadOperationImpl.java deleted file mode 100644 index 959a631860..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/admin/load/ValueSetLoadOperationImpl.java +++ /dev/null @@ -1,76 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.admin.load; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.BaseService; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; -import org.lexgrid.valuesets.impl.LexEVSValueSetDefinitionServicesImpl; - -import edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair; - -/** - * Implementation of LexEVS CTS 2 Value Set Load Operation. - * - * @author Sridhar Dwarkanath - */ -public class ValueSetLoadOperationImpl extends BaseService implements ValueSetLoadOperation { - - private LexEVSValueSetDefinitionServices vsdService_; - - /* (non-Javadoc) - * @see org.lexevs.cts2.admin.load.ValueSetLoadOperation#load(java.net.URI, java.net.URI, java.lang.String, java.lang.Boolean) - */ - @Override - public URNVersionPair[] load(URI source, URI releaseURI, String loaderName, - Boolean stopOnErrors) throws LBException { - return this.getLexEvsCTS2().getAdminOperation().getCodeSystemLoadOperation().load(source, null, null, loaderName, stopOnErrors, true, false, null, null); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.ValueSetLoadOperation#load(org.LexGrid.valueSets.ValueSetDefinition, java.net.URI, java.lang.Boolean) - */ - @Override - public String load(ValueSetDefinition valueSetDefinition, URI releaseURI, Boolean stopOnErrors) throws LBException { - if (valueSetDefinition == null) - throw new LBException("Value Set Definition object can not be empty"); - - if (StringUtils.isEmpty(valueSetDefinition.getValueSetDefinitionURI())) - throw new LBException("Value Set Definition URI can not be empty"); - - vsdService_ = LexEVSValueSetDefinitionServicesImpl.defaultInstance(); - vsdService_.loadValueSetDefinition(valueSetDefinition, releaseURI == null ? null : releaseURI.toString(), null); - return valueSetDefinition.getValueSetDefinitionURI(); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.admin.load.ValueSetLoadOperation#getSupportedLoaderNames() - */ - @Override - public List getSupportedLoaderNames() throws LBException { - return this.getLexEvsCTS2().getSupportedLoaderNames(); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/AssociationAuthoringOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/AssociationAuthoringOperation.java deleted file mode 100644 index 8b64bcffee..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/AssociationAuthoringOperation.java +++ /dev/null @@ -1,109 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.relations.AssociationQualification; -import org.LexGrid.relations.AssociationSource; -import org.LexGrid.versions.EntryState; -import org.LexGrid.versions.Revision; - -/** - * The Interface AssociationAuthoringOperation. - */ -public interface AssociationAuthoringOperation { - - /** - * Creates the association. - * - * @param createMappingScheme - create a mapping coding scheme if one does not exist - * @param revision - revision data - * @param entryState - revision data container granular to the versionable class. - * @param mappingScheme - existing mapping scheme, required if adding mapped association - * @param sourceCodeSystemIdentifier - minimum code system identification - * @param targetCodeSystemIdentifier - minimum code system identification - * @param sourceConceptCodeIdentifier - source concept code - * @param targetConceptCodeIdentifier - target concept code - * @param relationsContainerName - relations container identifier - * @param associationType - association type identifier - * @param associationQualifiers - qualifications to add to this association - * - * @return - returns a representation of this association as a LexGrid object. - * - * @throws LBException the LB exception - */ - public AssociationSource createAssociation( - boolean createMappingScheme, - Revision revision, - EntryState entryState, - AbsoluteCodingSchemeVersionReference mappingScheme, - AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier, - AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier, - String sourceConceptCodeIdentifier, - String targetConceptCodeIdentifier, - String relationsContainerName, - String associationType, - AssociationQualification[] associationQualifiers) - throws LBException; - - /** - * Update association status. - * - * @param revision the revision - * @param entryState the entry state - * @param scheme the scheme - * @param relationsContainer the relations container - * @param associationName the association name - * @param sourcCode the sourc code - * @param sourceNamespace the source namespace - * @param targetCode the target code - * @param targetNamespace the target namespace - * @param instanceId the instance id - * @param status the status - * @param isActive the is active - * - * @return true, if update association status - * - * @throws LBException the LB exception - */ - public boolean updateAssociationStatus( - Revision revision, - EntryState entryState, - AbsoluteCodingSchemeVersionReference scheme, - String relationsContainer, - String associationName, - String sourcCode, - String sourceNamespace, - String targetCode, - String targetNamespace, - String instanceId, - String status, - boolean isActive) throws LBException; - - /** - * Creates the lexical association. - */ - public void createLexicalAssociation(); - - /** - * Creates the rule based association. - */ - public void createRuleBasedAssociation(); -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/AssociationAuthoringOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/AssociationAuthoringOperationImpl.java deleted file mode 100644 index 3196c8ce0f..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/AssociationAuthoringOperationImpl.java +++ /dev/null @@ -1,167 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.util.Arrays; -import java.util.Date; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.LexEVSAuthoringServiceImpl; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.relations.AssociationQualification; -import org.LexGrid.relations.AssociationSource; -import org.LexGrid.relations.AssociationTarget; -import org.LexGrid.versions.EntryState; -import org.LexGrid.versions.Revision; - -/** - * @author Scott Bauer - * - */ -public class AssociationAuthoringOperationImpl implements - AssociationAuthoringOperation { - - LexEVSAuthoringServiceImpl authoring; - public AssociationAuthoringOperationImpl(){ - - authoring = new LexEVSAuthoringServiceImpl(); - } - - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AssociationAuthoringOperation#createAssociation(boolean, org.LexGrid.versions.Revision, org.LexGrid.versions.EntryState, org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference, org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference, org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference, java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.LexGrid.relations.AssociationQualification[]) - */ - @Override - public AssociationSource createAssociation( - boolean createMappingScheme, - Revision revision, - EntryState entryState, - AbsoluteCodingSchemeVersionReference mappingScheme, - AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier, - AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier, - String sourceConceptCodeIdentifier, - String targetConceptCodeIdentifier, String relationsContainerName, - String associationType, - AssociationQualification[] associationQualifiers) - throws LBException { - AssociationSource source = null; - if (createMappingScheme == true) - { - CodingScheme scheme = authoring.getCodingSchemeMetaData(sourceCodeSystemIdentifier); - AssociationTarget target = authoring.createAssociationTarget( - entryState, - null, - null, - false, - false, - null, - null, - targetCodeSystemIdentifier, - targetConceptCodeIdentifier); - String namespace = authoring.getCodingSchemeNamespace(scheme, - sourceCodeSystemIdentifier.getCodingSchemeURN()); - source = new AssociationSource(); - source.setSourceEntityCode(sourceConceptCodeIdentifier); - source.setSourceEntityCodeNamespace(namespace); - source.setTarget(Arrays.asList(target)); - AssociationSource[] sources = new AssociationSource[] { source }; - String sourceCodingSchemeName = authoring.getCodingSchemeNameForMininumReference(sourceCodeSystemIdentifier); - String targetCodingSchemeName = authoring.getCodingSchemeNameForMininumReference(targetCodeSystemIdentifier); - authoring.createMappingWithDefaultValues(sources, - sourceCodingSchemeName, - sourceCodeSystemIdentifier.getCodingSchemeVersion(), - targetCodingSchemeName, - targetCodeSystemIdentifier.getCodingSchemeVersion(), - associationType, false); - } - if (createMappingScheme == false && mappingScheme != null){ - CodingScheme sourceScheme = authoring.getCodingSchemeMetaData(sourceCodeSystemIdentifier); - AssociationTarget target = authoring.createAssociationTarget( - entryState, - null, - null, - false, - false, - null, - null, - targetCodeSystemIdentifier, - targetConceptCodeIdentifier); - String namespace = authoring.getCodingSchemeNamespace(sourceScheme, - sourceScheme.getCodingSchemeURI()); - source = new AssociationSource(); - source.setSourceEntityCode(sourceConceptCodeIdentifier); - source.setSourceEntityCodeNamespace(namespace); - source.setTarget(Arrays.asList(target)); - AssociationSource[] sources = new AssociationSource[] { source }; - Date effectiveDate = new Date(); - authoring.createAssociationMapping(entryState, mappingScheme, - sourceCodeSystemIdentifier, targetCodeSystemIdentifier, - sources, associationType, relationsContainerName, - effectiveDate, associationQualifiers, revision, true); - } - if (createMappingScheme == false && mappingScheme == null){ - AssociationTarget target = authoring.createAssociationTarget( - entryState, - null, - null, - false, - false, - null, - null, - targetCodeSystemIdentifier, - targetConceptCodeIdentifier); - AssociationTarget[] targets = new AssociationTarget[] { target }; - source = authoring.createAssociationSource(revision, entryState, - sourceCodeSystemIdentifier, sourceConceptCodeIdentifier, - relationsContainerName, associationType, targets); - } - return source; - } - - @Override - public void createLexicalAssociation() { - // TODO Auto-generated method stub - - } - - @Override - public void createRuleBasedAssociation() { - // TODO Auto-generated method stub - - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AssociationAuthoringOperation#updateAssociationStatus(org.LexGrid.versions.Revision, org.LexGrid.versions.EntryState, org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean) - */ - @Override - public boolean updateAssociationStatus(Revision revision, - EntryState entryState, AbsoluteCodingSchemeVersionReference scheme, - String relationsContainer, String associationName, - String sourceCode, String sourceNamespace, String targetCode, - String targetNamespace, String instanceId, String status, - boolean isActive) throws LBException { - - return authoring.setAssociationStatus(revision, entryState, scheme, - relationsContainer, associationName, sourceCode, - sourceNamespace, targetCode, targetNamespace, instanceId, - status, isActive); - } - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringCore.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringCore.java deleted file mode 100644 index c41311c203..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringCore.java +++ /dev/null @@ -1,266 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.net.URI; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.EntityDescription; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.concepts.Entities; -import org.LexGrid.concepts.Entity; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.EntryState; -import org.LexGrid.versions.Revision; -import org.LexGrid.versions.SystemRelease; -import org.LexGrid.versions.types.ChangeType; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.BaseService; -import org.lexevs.cts2.core.update.RevisionInfo; -import org.lexevs.cts2.core.update.SystemReleaseInfo; -import org.lexevs.dao.database.service.version.AuthoringService; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexevs.system.service.SystemResourceService; - -public class AuthoringCore extends BaseService{ - private AuthoringService authServ_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService(); - public String createSystemRelease(SystemReleaseInfo systemReleaseInfo) throws LBException{ - if (systemReleaseInfo == null) - throw new LBException("Problem : System release information is empty"); - if (StringUtils.isEmpty(systemReleaseInfo.getReleaseURI())) - throw new LBException("Problem : System release URI is empty"); - return authServ_.insertSystemReleaseMetadata(getLexGridSystemRelease(systemReleaseInfo)); - } - - public SystemReleaseInfo getSystemReleaseInfoByReleaseId(String releaseId) throws LBException{ - SystemRelease sr = authServ_.getSystemReleaseMetadataById(releaseId); - if (sr == null) - throw new LBException("Problem : No System Release found for releaseId : " + releaseId); - - return getSystemReleaseInfo(sr); - } - - public SystemReleaseInfo getSystemReleaseInfoByReleaseURI(URI releaseURI) throws LBException{ - if (releaseURI == null) - throw new LBException("Problem : Release URI is empty"); - - SystemRelease sr = authServ_.getSystemReleaseMetadataByUri(releaseURI.toString()); - if (sr == null) - throw new LBException("Problem : No System Release found for releaseURI : " + releaseURI); - - return getSystemReleaseInfo(sr); - } - - private SystemReleaseInfo getSystemReleaseInfo(SystemRelease lgSystemRelease){ - SystemReleaseInfo srInfo = new SystemReleaseInfo(); - srInfo.setBasedOnRelease(lgSystemRelease.getBasedOnRelease()); - srInfo.setReleaseAgency(lgSystemRelease.getReleaseAgency()); - srInfo.setReleaseDate(lgSystemRelease.getReleaseDate()); - srInfo.setReleaseId(lgSystemRelease.getReleaseId()); - srInfo.setReleaseURI(lgSystemRelease.getReleaseURI()); - if (lgSystemRelease.getEntityDescription() != null) - srInfo.setDescription(lgSystemRelease.getEntityDescription().getContent()); - return srInfo; - } - - private SystemRelease getLexGridSystemRelease(SystemReleaseInfo systemReleaseInfo){ - SystemRelease sr = new SystemRelease(); - sr.setBasedOnRelease(systemReleaseInfo.getBasedOnRelease()); - sr.setReleaseAgency(systemReleaseInfo.getReleaseAgency()); - sr.setReleaseDate(systemReleaseInfo.getReleaseDate()); - sr.setReleaseId(systemReleaseInfo.getReleaseId()); - sr.setReleaseURI(systemReleaseInfo.getReleaseURI()); - if (StringUtils.isNotEmpty(systemReleaseInfo.getDescription())) - { - EntityDescription ed = new EntityDescription(); - ed.setContent(systemReleaseInfo.getDescription()); - sr.setEntityDescription(ed); - } - return sr; - } - - public boolean validateRevisionInfo(RevisionInfo revisionInfo) throws LBException{ - if (revisionInfo == null) - throw new LBException("Revision information can not be empty"); - - if (revisionInfo.getRevisionId() == null) - throw new LBException("Revision ID can not be empty"); - - return true; - } - - public Revision getLexGridRevisionObject(RevisionInfo revisionInfo) - { - Revision lgRevision = new Revision(); - lgRevision.setChangeAgent(revisionInfo.getChangeAgent()); - lgRevision.setEditOrder(revisionInfo.getEditOrder()); - if (revisionInfo.getDescription() != null) - { - EntityDescription ed= new EntityDescription(); - ed.setContent(revisionInfo.getDescription()); - lgRevision.setEntityDescription(ed); - } - if (StringUtils.isNotEmpty(revisionInfo.getChangeInstruction())) - { - Text text = new Text(); - text.setContent(revisionInfo.getChangeInstruction()); - lgRevision.setChangeInstructions(text); - } - lgRevision.setRevisionDate(revisionInfo.getRevisionDate()); - lgRevision.setRevisionId(revisionInfo.getRevisionId()); - - return lgRevision; - } - - protected T addEntryState( - T versionable, - ChangeType changeType, - String revisionId, String prevRevisionId, - Long relativeOrder){ - EntryState entryState = this.populateEntryState( - changeType, - revisionId, - prevRevisionId, - relativeOrder); - - versionable.setEntryState(entryState); - - return versionable; - } - - protected Revision populateRevisionShell( - String codingSchemeUri, - String codingSchemeVersion, - String entityCode, - String entityCodeNamespace, - Property property, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) { - Property revisableProperty = - this.addEntryState(property, changeType, revisionInfo.getRevisionId(), prevRevisionId, relativeOrder); - - Entity entity = new Entity(); - entity.setEntityCode(entityCode); - entity.setEntityCodeNamespace(entityCodeNamespace); - entity.addAnyProperty(revisableProperty); - - return this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entity, - ChangeType.DEPENDENT, - null, - 0l, - revisionInfo); - } - - protected Revision populateRevisionShell( - String codingSchemeUri, - String codingSchemeVersion, - Entity entity, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) { - Entity revisableEntity = - this.addEntryState(entity, changeType, revisionInfo.getRevisionId(), prevRevisionId, relativeOrder); - - CodingScheme codingScheme = new CodingScheme(); - codingScheme.setCodingSchemeURI(codingSchemeUri); - codingScheme.setRepresentsVersion(codingSchemeVersion); - - codingScheme.setEntities(new Entities()); - codingScheme.getEntities().addEntity(revisableEntity); - - return this.populateRevisionShell( - codingScheme, - ChangeType.DEPENDENT, - null, - 0l, - revisionInfo); - } - - protected Revision populateRevisionShell( - CodingScheme codingScheme, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) { - CodingScheme revisableCodingScheme = - this.addEntryState(codingScheme, changeType, revisionInfo.getRevisionId(), prevRevisionId, relativeOrder); - - ChangedEntry changeEntry = new ChangedEntry(); - changeEntry.setChangedCodingSchemeEntry(revisableCodingScheme); - - Revision revision = this.getLexGridRevisionObject(revisionInfo); - revision.addChangedEntry(changeEntry); - - return revision; - } - - public EntryState populateEntryState(ChangeType changeType, String revisionId, String prevRevisionId, Long relativeOrder){ - EntryState entryState = new EntryState(); - entryState.setChangeType(changeType); - entryState.setContainingRevision(revisionId); - entryState.setPrevRevision(prevRevisionId); - entryState.setRelativeOrder(0L); - return entryState; - } - - protected void validatedCodingScheme(String codingSchemeUri, String codingSchemeVersion) throws LBException { - if(! this.getSystemResourceService().containsCodingSchemeResource(codingSchemeUri, codingSchemeVersion)) { - throw new LBException("The Coding Scheme URI: " + codingSchemeUri + - " Version: " + codingSchemeVersion + " does not exist. Before creating a Concept, " - + " the Coding Scheme must exist."); - } - } - - protected CodingScheme getCodeSystemShell(String codeSystemURI, String codeSystemVersion, String revisionId, ChangeType changeType) throws LBException{ - CodingScheme conceptDomainCS = new CodingScheme(); - conceptDomainCS.setCodingSchemeURI(codeSystemURI); - conceptDomainCS.setRepresentsVersion(codeSystemVersion); - - conceptDomainCS.setEntryState(populateEntryState(changeType, revisionId, null, 0L)); - - return conceptDomainCS; - } - - protected Entity getEntityShell(String entityId, String namespace, String codeSystemNameOrURI, String codeSystemVersion, String revisionId, ChangeType changeType) throws LBException{ - - Entity conceptDomain = new Entity(); - conceptDomain.setEntityCode(entityId); - conceptDomain.setEntityCodeNamespace(namespace); - - conceptDomain.setEntryState(populateEntryState(changeType, revisionId, null, 0L)); - - return conceptDomain; - } - - protected String getCodeSystemURI(String codeSystemNameOrUri, String version) throws LBParameterException{ - SystemResourceService systemResourceService = LexEvsServiceLocator.getInstance().getSystemResourceService(); - - return systemResourceService.getUriForUserCodingSchemeName(codeSystemNameOrUri, version); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringOperation.java deleted file mode 100644 index 37db3fcdfa..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringOperation.java +++ /dev/null @@ -1,62 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -/** - * LexEVS implementation of CTS2 Authoring Operations. - * - * @author Sridhar Dwarkanath - */ -public interface AuthoringOperation { - - /** - * Returns Association Authoring Operation interface. - * - * @return AssociationAuthoringOperation - */ - public AssociationAuthoringOperation getAssociationAuthoringOperation(); - - /** - * Returns Code System Authoring Operation interface. - * - * @return CodeSystemAuthoringOperation - */ - public CodeSystemAuthoringOperation getCodeSystemAuthoringOperation(); - - /** - * Returns Concept Domain Authoring Operation interface. - * - * @return ConceptDomainAuthoringOperation - */ - public ConceptDomainAuthoringOperation getConceptDomainAuthoringOperation(); - - /** - * Returns Usage Context Authoring Operation interface. - * - * @return UsageContextAuthoringOperation - */ - public UsageContextAuthoringOperation getUsageContextAuthoringOperation(); - - /** - * Returns Value Set Authoring Operation interface. - * - * @return ValueSetAuthoringOperation - */ - public ValueSetAuthoringOperation getValueSetAuthoringOperation(); -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringOperationImpl.java deleted file mode 100644 index 0a3f55dfd5..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/AuthoringOperationImpl.java +++ /dev/null @@ -1,87 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import org.lexevs.cts2.BaseService; - -/** - * Class returns individual CTS 2 Authoring Operation interfaces. - * - * @author Sridhar Dwarkanath - */ -public class AuthoringOperationImpl extends BaseService implements AuthoringOperation { - - private transient ValueSetAuthoringOperation valueSetAuthop_; - private transient CodeSystemAuthoringOperation codeSystemAuthop_; - private transient ConceptDomainAuthoringOperation conceptDomainAuthOp_; - private transient UsageContextAuthoringOperation usageContextAuthOp_; - private transient AssociationAuthoringOperation assnAuthOp_; - - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AuthoringOperation#getAssociationAuthoringOperation() - */ - @Override - public AssociationAuthoringOperation getAssociationAuthoringOperation() { - if (assnAuthOp_ == null) - assnAuthOp_ = new AssociationAuthoringOperationImpl(); - return assnAuthOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AuthoringOperation#getCodeSystemAuthoringOperation() - */ - @Override - public CodeSystemAuthoringOperation getCodeSystemAuthoringOperation() { - if (codeSystemAuthop_ == null) - codeSystemAuthop_ = new CodeSystemAuthoringOperationImpl(); - return codeSystemAuthop_ ; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AuthoringOperation#getConceptDomainAuthoringOperation() - */ - @Override - public ConceptDomainAuthoringOperation getConceptDomainAuthoringOperation() { - if (conceptDomainAuthOp_ == null) - conceptDomainAuthOp_ = new ConceptDomainAuthoringOperationImpl(); - return conceptDomainAuthOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AuthoringOperation#getUsageContextAuthoringOperation() - */ - @Override - public UsageContextAuthoringOperation getUsageContextAuthoringOperation() { - if (usageContextAuthOp_ == null) - usageContextAuthOp_ = new UsageContextAuthoringOperationImpl(); - return usageContextAuthOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.AuthoringOperation#getValueSetAuthoringOperation() - */ - @Override - public ValueSetAuthoringOperation getValueSetAuthoringOperation() { - if (valueSetAuthop_ == null) - valueSetAuthop_ = new ValueSetAuthoringOperationImpl(); - return valueSetAuthop_; - } - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/CodeSystemAuthoringOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/CodeSystemAuthoringOperation.java deleted file mode 100644 index 182b55acdc..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/CodeSystemAuthoringOperation.java +++ /dev/null @@ -1,368 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.Mappings; -import org.LexGrid.relations.AssociationEntity; -import org.LexGrid.versions.Revision; -import org.lexevs.cts2.core.update.RevisionInfo; -import org.lexevs.cts2.exception.author.InvalidCodeSystemSupplementException; - -/** - * The Interface CodeSystemAuthoringOperation. - */ -public interface CodeSystemAuthoringOperation { - -/** - * Creates the code system. - * - * @param revision the revision - * @param codingSchemeName the coding scheme name - * @param codingSchemeURI the coding scheme uri - * @param formalName the formal name - * @param defaultLanguage the default language - * @param approxNumConcepts the approx num concepts - * @param representsVersion the represents version - * @param localNameList the local name list - * @param sourceList the source list - * @param copyright the copyright - * @param mappings the mappings - * - * @return the coding scheme - * - * @throws LBException the LB exception - */ -public CodingScheme createCodeSystem(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException; - - /** - * Removes the code system. - * - * @param revision the revision - * @param codingSchemeURI the coding scheme uri - * @param representsVersion the represents version - * - * @return true, if successful - * - * @throws LBException the LB exception - */ - public boolean removeCodeSystem(RevisionInfo revision, String codingSchemeURI, String representsVersion) throws LBException; - - /** - * Update code system. - * - * @param revision the revision - * @param codingSchemeName the coding scheme name - * @param codingSchemeURI the coding scheme uri - * @param formalName the formal name - * @param defaultLanguage the default language - * @param approxNumConcepts the approx num concepts - * @param representsVersion the represents version - * @param localNameList the local name list - * @param sourceList the source list - * @param copyright the copyright - * @param mappings the mappings - * - * @return the coding scheme - * - * @throws LBException the LB exception - */ - public CodingScheme updateCodeSystem(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException; - - /** - * Adds the code system properties. - * - * @param revision the revision - * @param codingSchemeName the coding scheme name - * @param codingSchemeURI the coding scheme uri - * @param representsVersion the represents version - * @param properties the properties - * - * @return the coding scheme - * - * @throws LBException the LB exception - */ - public CodingScheme addCodeSystemProperties(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String representsVersion, - Properties properties) throws LBException; - - /** - * Update code system properties. - * - * @param revision the revision - * @param codingSchemeName the coding scheme name - * @param codingSchemeURI the coding scheme uri - * @param representsVersion the represents version - * @param properties the properties - * - * @return the coding scheme - * - * @throws LBException the LB exception - */ - public CodingScheme updateCodeSystemProperties(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String representsVersion, - Properties properties) throws LBException; - - /** - * Removes the code system property. - * - * @param revision the revision - * @param codingSchemeURI the coding scheme uri - * @param representsVersion the represents version - * @param propertyId the property id - * - * @return the coding scheme - * - * @throws LBException the LB exception - */ - public CodingScheme removeCodeSystemProperty(RevisionInfo revision, String codingSchemeURI, String representsVersion, - String propertyId) throws LBException; - - /** - * Creates the code system change set. - * - * @param agent the agent - * @param changeInstruction the change instruction - * - * @return the revision - */ - public Revision createCodeSystemChangeSet(String agent, String changeInstruction); - - /** - * Commit change set. - * - * @param changeSet the change set - * - * @return the int - */ - public int commitChangeSet(Revision changeSet); - - /** - * Update code system version status. - * - * @param codingSchemeURI the coding scheme uri - * @param codeSystemVersion the code system version - * @param status the status - * @param isActive the is active - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void updateCodeSystemVersionStatus(String codingSchemeURI, String codeSystemVersion, String status, Boolean isActive, - RevisionInfo revision) throws LBException; - - /** - * Creates the code system suppliment. - * - * @param parent the parent - * @param supplement the supplement - * - * @throws InvalidCodeSystemSupplementException the invalid code system supplement exception - */ - public void createCodeSystemSuppliment( - AbsoluteCodingSchemeVersionReference parent, - AbsoluteCodingSchemeVersionReference supplement) throws InvalidCodeSystemSupplementException; - - /** - * Creates the concept. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param conceptCode the concept code - * @param namespace the namespace - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void createConcept( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - RevisionInfo revision) throws LBException; - - /** - * Update concept. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param entity the entity - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void updateConcept( - String codingSchemeUri, - String codeSystemVersion, - Entity entity, - RevisionInfo revision) throws LBException; - - /** - * Delete concept. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param conceptCode the concept code - * @param namespace the namespace - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void deleteConcept( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - RevisionInfo revision) throws LBException; - - /** - * Adds the new concept property. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param conceptCode the concept code - * @param namespace the namespace - * @param property the property - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void addNewConceptProperty( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - Property property, - RevisionInfo revision) throws LBException; - - /** - * Update concept property. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param conceptCode the concept code - * @param namespace the namespace - * @param property the property - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void updateConceptProperty( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - Property property, - RevisionInfo revision) throws LBException; - - /** - * Delete concept property. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param conceptCode the concept code - * @param namespace the namespace - * @param property the property - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void deleteConceptProperty( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - Property property, - RevisionInfo revision) throws LBException; - - /** - * Update concept status. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param conceptCode the concept code - * @param namespace the namespace - * @param status the status - * @param isActive the is active - * @param revisionInfo the revision info - * - * @throws LBException the LB exception - */ - public void updateConceptStatus( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - String status, - Boolean isActive, - RevisionInfo revisionInfo) throws LBException; - - /** - * Creates the association type. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param relationsContainerName the relations container name - * @param associationName the association name - * @param forwardName the forward name - * @param reverseName the reverse name - * @param isNavigable the is navigable - * @param isTransitive the is transitive - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void createAssociationType( - String codingSchemeUri, - String codeSystemVersion, - String relationsContainerName, - String associationName, - String forwardName, - String reverseName, - Boolean isNavigable, - Boolean isTransitive, - RevisionInfo revision) throws LBException; - - /** - * Update association type. - * - * @param codingSchemeUri the coding scheme uri - * @param codeSystemVersion the code system version - * @param associationEntity the association entity - * @param revision the revision - * - * @throws LBException the LB exception - */ - public void updateAssociationType( - String codingSchemeUri, - String codeSystemVersion, - AssociationEntity associationEntity, - RevisionInfo revision) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/CodeSystemAuthoringOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/CodeSystemAuthoringOperationImpl.java deleted file mode 100644 index eb7dc8e29f..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/CodeSystemAuthoringOperationImpl.java +++ /dev/null @@ -1,719 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; -import org.LexGrid.LexBIG.Impl.LexEVSAuthoringServiceImpl; -import org.LexGrid.LexBIG.LexBIGService.LexEVSAuthoringService; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.LexBIG.Utility.ServiceUtility; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Entities; -import org.LexGrid.concepts.Entity; -import org.LexGrid.custom.concepts.EntityFactory; -import org.LexGrid.naming.Mappings; -import org.LexGrid.relations.AssociationEntity; -import org.LexGrid.relations.Relations; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.Revision; -import org.LexGrid.versions.types.ChangeType; -import org.apache.commons.lang.SerializationUtils; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.core.update.RevisionInfo; -import org.lexevs.cts2.exception.author.InvalidCodeSystemSupplementException; - -public class CodeSystemAuthoringOperationImpl extends AuthoringCore implements - CodeSystemAuthoringOperation { - - @Override - public int commitChangeSet(Revision changeSet) { - // TODO Auto-generated method stub - return 0; - } - - protected void commitCodeSystemChangeSet(CodingScheme codeSystem, RevisionInfo revision, String previousRevisionID, ChangeType changeType, Boolean indexCodeSystem) throws LBException { - - // Create the changed entry for code system - ChangedEntry changedEntry = new ChangedEntry(); - changedEntry.setChangedCodingSchemeEntry(codeSystem); - - // Create revision object - Revision lgRevision = getLexGridRevisionObject(revision); - - // Add code system changed entry to revision - lgRevision.addChangedEntry(changedEntry); - - // Assign the entry state - codeSystem.setEntryState(populateEntryState(changeType, lgRevision.getRevisionId(), previousRevisionID, 0L)); - - //load as revision - this.getDatabaseServiceManager().getAuthoringService().loadRevision(lgRevision, null, indexCodeSystem); - - } - - @Override - public CodingScheme createCodeSystem(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException { - - if(codingSchemeName == null){ - throw new LBException("Coding scheme name cannot be null"); - } - if(codingSchemeURI == null){ - throw new LBException("Coding scheme URI cannot be null"); - } - if(representsVersion == null){ - throw new LBException("Coding scheme version cannot be null"); - } - if(mappings == null){ - throw new LBException("Coding scheme mappings cannot be null"); - } - - - CodingScheme scheme = new CodingScheme(); - - scheme.setCodingSchemeName(codingSchemeName); - - scheme.setCodingSchemeURI(codingSchemeURI); - - if (formalName != null) - scheme.setFormalName(formalName); - - if (defaultLanguage != null) - scheme.setDefaultLanguage(defaultLanguage); - - scheme.setApproxNumConcepts(approxNumConcepts); - - scheme.setRepresentsVersion(representsVersion); - - if (localNameList != null) - scheme.setLocalName(localNameList); - - if (sourceList != null) - scheme.setSource(sourceList); - - if (copyright != null) - scheme.setCopyright(copyright); - - scheme.setMappings(mappings); - - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - commitCodeSystemChangeSet(scheme, revision, null, ChangeType.NEW, true); - - CodingScheme updatedCodingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - - return updatedCodingScheme; - } - - @Override - public boolean removeCodeSystem(RevisionInfo revision, String codingSchemeURI, String representsVersion) throws LBException { - - if(codingSchemeURI == null){ - throw new LBException("Coding scheme URI cannot be null"); - } - - CodingScheme codingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - if (codingScheme == null) - throw new LBException("No Coding Scheme found with URI : " + codingSchemeURI.toString()); - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - commitCodeSystemChangeSet(codingScheme, revision, null, ChangeType.REMOVE, null); - - return true; -} - - - @Override - public CodingScheme updateCodeSystem(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException { - - if(codingSchemeURI == null){ - throw new LBException("Coding scheme URI cannot be null"); - } - - CodingScheme codingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService().getCodingSchemeByUriAndVersion( - codingSchemeURI, representsVersion); - codingScheme = (CodingScheme) SerializationUtils.clone(codingScheme); - codingScheme.setProperties(new Properties()); - codingScheme.setEntities(new Entities()); - codingScheme.setRelations(new Relations[0]); - - String prevRevisionId = codingScheme.getEntryState() != null?codingScheme.getEntryState().getContainingRevision():null; - - if (codingScheme == null) - throw new LBException("No Coding Scheme found with URI : " + codingSchemeURI.toString()); - - - if (StringUtils.isNotEmpty(codingSchemeName)) - codingScheme.setCodingSchemeName(codingSchemeName); - - if (StringUtils.isNotEmpty(codingSchemeURI)) - codingScheme.setCodingSchemeURI(codingSchemeURI); - - if (StringUtils.isNotEmpty(formalName)) - codingScheme.setFormalName(formalName); - - if (StringUtils.isNotEmpty(defaultLanguage)) - codingScheme.setDefaultLanguage(defaultLanguage); - - if (approxNumConcepts !=0L) - codingScheme.setApproxNumConcepts(approxNumConcepts); - - if (representsVersion !=null) - codingScheme.setRepresentsVersion(representsVersion); - - if (localNameList != null) - codingScheme.setLocalName(localNameList); - - if (sourceList != null) - codingScheme.setSource(sourceList); - - if (copyright !=null) - codingScheme.setCopyright(copyright); - - if (mappings !=null) - codingScheme.setMappings(mappings); - - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - commitCodeSystemChangeSet(codingScheme, revision, prevRevisionId, ChangeType.MODIFY, null); - - CodingScheme updatedCodingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - return updatedCodingScheme; - } - - @Override - public CodingScheme addCodeSystemProperties(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String representsVersion, - Properties properties) throws LBException { - - if(codingSchemeURI == null){ - throw new LBException("Coding scheme URI cannot be null"); - } - - CodingScheme codingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - String prevRevisionId = codingScheme.getEntryState() != null?codingScheme.getEntryState().getContainingRevision():null; - - if (codingScheme == null) - throw new LBException("No Coding Scheme found with URI : " + codingSchemeURI.toString()); - - if (properties !=null) - - codingScheme.setProperties(processAddProperties(revision, properties)); - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - commitCodeSystemChangeSet(codingScheme, revision, prevRevisionId, ChangeType.MODIFY, null); - - CodingScheme updatedCodingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - return updatedCodingScheme; - } - - @Override - public CodingScheme updateCodeSystemProperties(RevisionInfo revision, String codingSchemeName, String codingSchemeURI, String representsVersion, - Properties properties) throws LBException { - - if(codingSchemeURI == null){ - throw new LBException("Coding scheme URI cannot be null"); - } - - CodingScheme codingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - String prevRevisionId = codingScheme.getEntryState() != null?codingScheme.getEntryState().getContainingRevision():null; - - if (codingScheme == null) - throw new LBException("No Coding Scheme found with URI : " + codingSchemeURI.toString()); - - if (properties !=null) - - codingScheme.setProperties(processUpdateProperties(revision, properties)); - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - - commitCodeSystemChangeSet(codingScheme, revision, prevRevisionId, ChangeType.MODIFY, null); - - CodingScheme updatedCodingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - return updatedCodingScheme; - } - - @Override - public CodingScheme removeCodeSystemProperty(RevisionInfo revision, String codingSchemeURI, String representsVersion, - String propertyId) throws LBException { - - if(codingSchemeURI == null){ - throw new LBException("Coding scheme URI cannot be null"); - } - - CodingScheme codingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - String prevRevisionId = codingScheme.getEntryState() != null?codingScheme.getEntryState().getContainingRevision():null; - - if (codingScheme == null) - throw new LBException("No Coding Scheme found with URI : " + codingSchemeURI.toString()); - - - Property currentProperty = null; - - for (Property prop : codingScheme.getProperties().getPropertyAsReference()) - { - if (prop.getPropertyId().equalsIgnoreCase(propertyId)) - currentProperty = prop; - } - - if (currentProperty == null) - throw new LBException("No property found with id : " + propertyId); - - // remove all other properties but the one that needs to be removed - codingScheme.setProperties(null); - Properties props = new Properties(); - props.addProperty(currentProperty); - codingScheme.setProperties(props); - - // setup entry state for coding scheme - codingScheme.setEntryState(populateEntryState(ChangeType.DEPENDENT, - revision.getRevisionId(), prevRevisionId, 0L)); - - // setup entry state for property to be removed - String propPrevRevId = currentProperty.getEntryState() != null?currentProperty.getEntryState().getContainingRevision():null; - currentProperty.setEntryState(populateEntryState(ChangeType.REMOVE, - revision.getRevisionId(), propPrevRevId, 0L)); - - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - commitCodeSystemChangeSet(codingScheme, revision, prevRevisionId, ChangeType.DEPENDENT, null); - - CodingScheme updatedCodingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCompleteCodingScheme(codingSchemeURI, representsVersion); - - - return updatedCodingScheme; - } - - - protected Properties processAddProperties(RevisionInfo revision, Properties properties) { - - Property currentProperty = null; - Properties updatedProps = new Properties(); - - for (Property prop : properties.getPropertyAsReference()) - { - currentProperty = prop; - - // setup entry state for property to be changed - String propPrevRevId = currentProperty.getEntryState() != null?currentProperty.getEntryState().getContainingRevision():null; - currentProperty.setEntryState(populateEntryState(ChangeType.NEW, - revision.getRevisionId(), propPrevRevId, 0L)); - updatedProps.addProperty(currentProperty); - } - - return updatedProps; - - } - - protected Properties processUpdateProperties(RevisionInfo revision, Properties properties) { - - Property currentProperty = null; - Properties updatedProps = new Properties(); - - - for (Property prop : properties.getPropertyAsReference()) - { - currentProperty = prop; - - // setup entry state for property to be changed - String propPrevRevId = currentProperty.getEntryState() != null?currentProperty.getEntryState().getContainingRevision():null; - currentProperty.setEntryState(populateEntryState(ChangeType.MODIFY, - revision.getRevisionId(), propPrevRevId, 0L)); - updatedProps.addProperty(currentProperty); - } - - return updatedProps; - - } - - - - @Override - public Revision createCodeSystemChangeSet(String agent, - String changeInstruction) { - // TODO Auto-generated method stub - return null; - } - - @Override - public void createCodeSystemSuppliment( - AbsoluteCodingSchemeVersionReference parent, - AbsoluteCodingSchemeVersionReference supplement) throws InvalidCodeSystemSupplementException { - try { - LexBIGServiceImpl.defaultInstance().getServiceManager(null). - registerCodingSchemeAsSupplement(parent, supplement); - } catch (LBException e) { - throw new InvalidCodeSystemSupplementException( - parent, - supplement, - e); - } - } - - @Override - public void createConcept( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - RevisionInfo revisionInfo) throws LBException { - - Entity entity = new Entity(); - entity.setEntityCode(conceptCode); - entity.setEntityCodeNamespace(namespace); - - this.doReviseConcept( - codingSchemeUri, - codeSystemVersion, - entity, - ChangeType.NEW, - null, - 0l, - revisionInfo); - } - - @Override - public void updateCodeSystemVersionStatus( - String codingSchemeURI, - String codeSystemVersion, - String status, - Boolean isActive, - RevisionInfo revision) throws LBException { - - this.validatedCodingScheme(codingSchemeURI, codeSystemVersion); - - - CodingScheme codingScheme = - this.getDatabaseServiceManager(). - getCodingSchemeService(). - getCodingSchemeByUriAndVersion(codingSchemeURI, codeSystemVersion); - - if( codingScheme != null ) { - - codingScheme.removeAllRelations(); - codingScheme.setEntities(null); - codingScheme.setProperties(null); - } - - String prevRevisionId = codingScheme.getEntryState() != null?codingScheme.getEntryState().getContainingRevision():null; - - if(StringUtils.isNotBlank(status)) { - codingScheme.setStatus(status); - } - - if(isActive != null) { - codingScheme.setIsActive(isActive); - } - - - // Ensure RevisionInfo is provided - validateRevisionInfo(revision); - - commitCodeSystemChangeSet(codingScheme, revision, prevRevisionId, ChangeType.VERSIONABLE, null); - } - - - public void updateConcept( - String codingSchemeUri, - String codeSystemVersion, - Entity entity, - RevisionInfo revisionInfo) throws LBException { - this.doReviseConcept( - codingSchemeUri, - codeSystemVersion, - entity, - ChangeType.MODIFY, - null, - 0l, - revisionInfo); - } - - @Override - public void addNewConceptProperty( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - Property property, - RevisionInfo revisionInfo) throws LBException { - this.doReviseEntityProperty( - codingSchemeUri, - codeSystemVersion, - conceptCode, - namespace, - property, - ChangeType.NEW, - null, - 0l, - revisionInfo); - } - - @Override - public void deleteConcept( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - RevisionInfo revisionInfo) - throws LBException { - Entity entity = new Entity(); - entity.setEntityCode(conceptCode); - entity.setEntityCodeNamespace(namespace); - - this.doReviseConcept( - codingSchemeUri, - codeSystemVersion, - entity, - ChangeType.REMOVE, - null, - 0l, - revisionInfo); - } - - @Override - public void deleteConceptProperty(String codingSchemeUri, - String codeSystemVersion, String conceptCode, String namespace, - Property property, RevisionInfo revisionInfo) throws LBException { - this.doReviseEntityProperty( - codingSchemeUri, - codeSystemVersion, - conceptCode, - namespace, - property, - ChangeType.REMOVE, - null, - 0l, - revisionInfo); - } - - @Override - public void updateConceptProperty( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - Property property, - RevisionInfo revisionInfo) throws LBException { - this.doReviseEntityProperty( - codingSchemeUri, - codeSystemVersion, - conceptCode, - namespace, - property, - ChangeType.MODIFY, - null, - 0l, - revisionInfo); - } - - protected void doReviseConcept( - String codingSchemeUri, - String codingSchemeVersion, - Entity entity, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) throws LBException { - - this.validatedCodingScheme(codingSchemeUri, codingSchemeVersion); - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entity, - changeType, - prevRevisionId, - relativeOrder, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } - - protected void doReviseEntityProperty( - String codingSchemeUri, - String codingSchemeVersion, - String entityCode, - String entityCodeNamespace, - Property property, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) throws LBException { - - this.validatedCodingScheme(codingSchemeUri, codingSchemeVersion); - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entityCode, - entityCodeNamespace, - property, - changeType, - prevRevisionId, - relativeOrder, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } - - @Override - public void updateConceptStatus( - String codingSchemeUri, - String codeSystemVersion, - String conceptCode, - String namespace, - String status, - Boolean isActive, - RevisionInfo revisionInfo) throws LBException { - this.validatedCodingScheme(codingSchemeUri, codeSystemVersion); - - Entity entity = new Entity(); - entity.setEntityCode(conceptCode); - entity.setEntityCodeNamespace(namespace); - - if(StringUtils.isNotBlank(status)) { - entity.setStatus(status); - } - - if(isActive != null) { - entity.setIsActive(isActive); - } - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codeSystemVersion, - entity, - ChangeType.VERSIONABLE, - null, - 0l, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } - - @Override - public void createAssociationType( - String codingSchemeUri, - String codeSystemVersion, - String relationsContainerName, - String associationName, - String forwardName, - String reverseName, - Boolean isNavigable, - Boolean isTransitive, - RevisionInfo revisionInfo) throws LBException { - LexEVSAuthoringService authoring = new LexEVSAuthoringServiceImpl(); - - AssociationEntity associationEntity = EntityFactory.createAssociation(); - associationEntity.setEntityCode(associationName); - associationEntity.setEntityCodeNamespace(ServiceUtility.getCodingSchemeName(codingSchemeUri, codeSystemVersion)); - associationEntity.setForwardName(forwardName); - associationEntity.setReverseName(reverseName); - associationEntity.setIsNavigable(isNavigable); - associationEntity.setIsTransitive(isTransitive); - - authoring.createAssociationPredicate( - this.getLexGridRevisionObject(revisionInfo), - this.populateEntryState(ChangeType.NEW, revisionInfo.getRevisionId(), null, 0l), - Constructors.createAbsoluteCodingSchemeVersionReference(codingSchemeUri, codeSystemVersion), - relationsContainerName, - associationName); - - this.doReviseConcept( - codingSchemeUri, - codeSystemVersion, - associationEntity, - ChangeType.NEW, - null, - 0l, - revisionInfo); - } - - @Override - public void updateAssociationType( - String codingSchemeUri, - String codeSystemVersion, - AssociationEntity associationEntity, - RevisionInfo revisionInfo) throws LBException { - this.updateConcept( - codingSchemeUri, - codeSystemVersion, - associationEntity, - revisionInfo); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/ConceptDomainAuthoringOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/ConceptDomainAuthoringOperation.java deleted file mode 100644 index 0ae73f0aab..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/ConceptDomainAuthoringOperation.java +++ /dev/null @@ -1,236 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.naming.Mappings; -import org.lexevs.cts2.core.update.RevisionInfo; - -/** - * LexEVS CTS 2 Concept Domain Authoring Operations. - * - * @author Sridhar Dwarkanath - */ -public interface ConceptDomainAuthoringOperation { - - /** - * Create a code system to hold concept domain entities. - * - * @param revision - revision information - * @param codeSystemName - concept domain code system name - * @param codeSystemURI - concept domain code system URI - * @param formalName - concept domain code system formal name - * @param defaultLanguage - default language - * @param representsVersion - concept domain code system version - * @param localNameList - (Optional) list of alternate names used for this code system - * @param sourceList - source list - * @param copyright - copy right information - * @param mappings - list of attributes supported by this code system - * @return concept domain code system - * @throws LBException - */ - public CodingScheme createConceptDomainCodeSystem(RevisionInfo revision, String codeSystemName, String codeSystemURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException; - - /** - * Create new concept domain. - * - * @param conceptDomainId - concept domain id - * @param conceptDomainName - concept domain name - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param revisionInfo - revision information - * @param description - description of concept domain - * @param status - status of concept domain - * @param isActive - is concept domain active - * @param properties - concept domain properties - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @return concept domain id if created successfully - * @throws LBException - */ - public String createConceptDomain( - String conceptDomainId, - String conceptDomainName, - String namespace, - RevisionInfo revisionInfo, - String description, - String status, - boolean isActive, - Properties properties, - String codeSystemNameOrURI, - String codeSystemVersion) throws LBException; - - /** - * Update concept domain status. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param newStatus - new status for concept domain - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - concept domain code system version - * @return true; if update was success - * @throws LBException - */ - public boolean updateConceptDomainStatus(String conceptDomainId, String namespace, String newStatus, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Activate concept domain. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if activation was success - * @throws LBException - */ - public boolean activateConceptDomain(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * DeActivate concept domain. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if deactivation was success - * @throws LBException - */ - public boolean deactivateConceptDomain(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Update concept domain versionable attributes like effective date, expiration date, owner, status etc. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param changedVersionable - versionable (like:owner, effectiveDate, expirationDate, status etc) changes - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if update was success - * @throws LBException - */ - public boolean updateConceptDomainVersionable(String conceptDomainId, String namespace, - Versionable changedVersionable, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Add new property for a concept domain. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param newProperty - new concept domain property - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if addition of new property was success - * @throws LBException - */ - public boolean addConceptDomainProperty(String conceptDomainId, String namespace, Property newProperty, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Update existing property of a concept domain. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param changedProperty - modified concept domain property - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if update was success - * @throws LBException - */ - public boolean updateConceptDomainProperty(String conceptDomainId, String namespace, Property changedProperty, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Remove existing property of a concept domain. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param property - property to be removed - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if remove was success - * @throws LBException - */ - public boolean removeConceptDomainProperty(String conceptDomainId, String namespace, Property property, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Add concept domain to value set binding. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param valueSetURI - value set definition uri - * @param revisionInfo - revision information - * @return true; if binding update was success - * @throws LBException - */ - public boolean addConceptDomainToValueSetBinding(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, URI valueSetURI, RevisionInfo revisionInfo) throws LBException; - - /** - * Remove concept domain to value set binding. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param valueSetURI - value set definition uri - * @param revisionInfo - revision information - * @return true; if binding update was success - * @throws LBException - */ - public boolean removeConceptDomainToValueSetBinding(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, URI valueSetURI, RevisionInfo revisionInfo) throws LBException; - - /** - * Remove concept domain. - * - * @param conceptDomainId - concept domain id - * @param namespace - concept domain name space (If not provided, formal name of the code system will be used) - * @param @param codeSystemNameOrURI - concept domain code system name or uri - * @param codeSystemVersion - concept domain code system version - * @param revisionInfo - revision information - * @return true; if remove was success - * @throws LBException - */ - public boolean removeConceptDomain(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/ConceptDomainAuthoringOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/ConceptDomainAuthoringOperationImpl.java deleted file mode 100644 index e8116c6abe..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/ConceptDomainAuthoringOperationImpl.java +++ /dev/null @@ -1,443 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.EntityDescription; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.concepts.Definition; -import org.LexGrid.concepts.Entities; -import org.LexGrid.concepts.Entity; -import org.LexGrid.concepts.Presentation; -import org.LexGrid.naming.Mappings; -import org.LexGrid.util.sql.lgTables.SQLTableConstants; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.Revision; -import org.LexGrid.versions.types.ChangeType; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.LexEvsCTS2Impl; -import org.lexevs.cts2.core.update.RevisionInfo; -import org.lexevs.cts2.query.ConceptDomainQueryOperation; -import org.lexevs.cts2.query.ValueSetQueryOperation; -import org.lexevs.dao.database.service.version.AuthoringService; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexgrid.conceptdomain.util.ConceptDomainConstants; - -/** - * Implementation of LexEVS CTS2 Concept Domain Authoring Operation. - * - * @author Kevin Peterson - * @author Sridhar Dwarkanath - */ -public class ConceptDomainAuthoringOperationImpl extends AuthoringCore implements ConceptDomainAuthoringOperation { - private AuthoringService authServ_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService(); - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#createConceptDomainCodeSystem(org.lexevs.cts2.core.update.RevisionInfo, java.lang.String, java.lang.String, java.lang.String, java.lang.String, long, java.lang.String, java.util.List, java.util.List, org.LexGrid.commonTypes.Text, org.LexGrid.naming.Mappings, org.LexGrid.commonTypes.Properties) - */ - public CodingScheme createConceptDomainCodeSystem(RevisionInfo revision, String codeSystemName, String codeSystemURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException{ - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - - return csAuthOp.createCodeSystem(revision, codeSystemName, codeSystemURI, formalName, defaultLanguage, 0, - representsVersion, localNameList, sourceList, copyright, mappings); - } - - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#createConceptDomain(java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo, java.lang.String, java.lang.String, boolean, org.LexGrid.commonTypes.Properties, java.lang.String, java.lang.String) - */ - @Override - public String createConceptDomain( - String conceptDomainId, - String conceptDomainName, - String namespace, - RevisionInfo revisionInfo, - String description, - String status, - boolean isActive, - Properties properties, - String codeSystemNameOrURI, - String codeSystemVersion) throws LBException{ - - if (StringUtils.isEmpty(conceptDomainId)) - conceptDomainId = createUniqueId(); - - if (StringUtils.isEmpty(conceptDomainName)) - throw new LBException("concept domain name can not be empty"); - - // create an entity object for concept domain - Entity entity = new Entity(); - entity.setEntityCode(conceptDomainId); - entity.setEntityCodeNamespace(namespace); - EntityDescription ed = new EntityDescription(); - ed.setContent(conceptDomainName); - entity.setEntityDescription(ed); - entity.setStatus(status); - entity.setIsActive(isActive); - entity.addEntityType(ConceptDomainConstants.CONCEPT_DOMAIN_ENTITY_TYPE); - - Presentation pres = new Presentation(); - pres.setPropertyName(SQLTableConstants.TBLCOLVAL_TEXTUALPRESENTATION); - Text text = new Text(); - text.setContent(conceptDomainName); - pres.setValue(text); - pres.setIsPreferred(true); - - entity.addPresentation(pres); - - if (StringUtils.isNotEmpty(description)) - { - Definition def = new Definition(); - def.setPropertyName("Description"); - text = new Text(); - text.setContent(description); - def.setValue(text); - entity.addDefinition(def); - } - - if (properties != null) - entity.addAnyProperties(properties.getPropertyAsReference()); - - //insert - this.doReviseEntity(getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion), codeSystemVersion, entity, ChangeType.NEW, null, 0L, revisionInfo); - - return conceptDomainId; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#updateConceptDomainStatus(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateConceptDomainStatus(String conceptDomainId, String namespace, - String newStatus, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException - { - if (StringUtils.isEmpty(conceptDomainId)) - throw new LBException("Concept Domain Id can not be empty"); - - Versionable ver = new Versionable(); - ver.setStatus(newStatus); - - return updateConceptDomainVersionable(conceptDomainId, namespace, ver, getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion), codeSystemVersion, revisionInfo); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#activateConceptDomain(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean activateConceptDomain(String conceptDomainId, String namespace, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revisionInfo) throws LBException - { - if (StringUtils.isEmpty(conceptDomainId)) - throw new LBException("Concept Domain Id can not be empty"); - - Versionable ver = new Versionable(); - ver.setIsActive(true); - - return updateConceptDomainVersionable(conceptDomainId, namespace, ver, getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion), codeSystemVersion, revisionInfo); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#deactivateConceptDomain(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean deactivateConceptDomain(String conceptDomainId, String namespace, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revisionInfo) throws LBException - { - if (StringUtils.isEmpty(conceptDomainId)) - throw new LBException("Concept Domain Id can not be empty"); - - Versionable ver = new Versionable(); - ver.setIsActive(false); - - return updateConceptDomainVersionable(conceptDomainId, namespace, ver, getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion), codeSystemVersion, revisionInfo); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#updateConceptDomainVersionable(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Versionable, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateConceptDomainVersionable(String conceptDomainId, String namespace, - Versionable changedVersionable, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revision) throws LBException { - if (conceptDomainId == null) - throw new LBException("conceptDomainId can not be empty"); - - if (changedVersionable == null) - throw new LBException("Changed Versionable information can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - Entity conceptDomain = this.getEntityShell(conceptDomainId, namespace, csURI, codeSystemVersion, revision.getRevisionId(), ChangeType.VERSIONABLE); - - if (StringUtils.isNotEmpty(changedVersionable.getOwner())) - { - conceptDomain.setOwner(changedVersionable.getOwner()); - } - - if (StringUtils.isNotEmpty(changedVersionable.getStatus())) - { - conceptDomain.setStatus(changedVersionable.getStatus()); - } - - if (changedVersionable.getEffectiveDate() != null) - { - conceptDomain.setEffectiveDate(changedVersionable.getEffectiveDate()); - } - - if (changedVersionable.getExpirationDate() != null) - { - conceptDomain.setExpirationDate(changedVersionable.getExpirationDate()); - } - - if (changedVersionable.getIsActive() != null) - { - conceptDomain.setIsActive(changedVersionable.getIsActive()); - } - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - CodingScheme conceptDomainCS = this.getCodeSystemShell(csURI, codeSystemVersion, lgRevision.getRevisionId(), ChangeType.DEPENDENT); - - Entities entities = new Entities(); - entities.addEntity(conceptDomain); - - conceptDomainCS.setEntities(entities); - - ce.setChangedCodingSchemeEntry(conceptDomainCS); - - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#addConceptDomainProperty(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Property, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean addConceptDomainProperty(String conceptDomainId, String namespace, Property newProperty, String codeSystemNameOrURI, - String codeSystemVersion, - RevisionInfo revision) - throws LBException { - if (conceptDomainId == null) - throw new LBException("Concept Domain Id can not be empty"); - if (newProperty == null) - throw new LBException("New property can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.addNewConceptProperty(csURI, codeSystemVersion, conceptDomainId, namespace, newProperty, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#updateConceptDomainProperty(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Property, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateConceptDomainProperty(String conceptDomainId, String namespace, Property changedProperty, String codeSystemNameOrURI, - String codeSystemVersion, - RevisionInfo revision) - throws LBException { - if (conceptDomainId == null) - throw new LBException("Concept Domain Id can not be empty"); - if (changedProperty == null) - throw new LBException("Changed property can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.updateConceptProperty(csURI, codeSystemVersion, conceptDomainId, namespace, changedProperty, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#removeConceptDomainProperty(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Property, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeConceptDomainProperty(String conceptDomainId, String namespace, Property property, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revision) throws LBException { - if (conceptDomainId == null) - throw new LBException("Concept Domain Id can not be empty"); - if (property == null) - throw new LBException("property can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.deleteConceptProperty(csURI, codeSystemVersion, conceptDomainId, namespace, property, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#addConceptDomainToValueSetBinding(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.net.URI, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean addConceptDomainToValueSetBinding(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, URI valueSetURI, RevisionInfo revisionInfo) throws LBException { - if (StringUtils.isEmpty(conceptDomainId)) - throw new LBException("Concept Domain Id can not be empty"); - if (valueSetURI == null) - throw new LBException("Value Set URI can not be empty"); - - ValueSetAuthoringOperation vsAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getValueSetAuthoringOperation(); - - vsAuthOp.updateValueSetMetaData(valueSetURI, null, null, conceptDomainId, null, null, revisionInfo); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#removeConceptDomain(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeConceptDomain(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revision) throws LBException { - if (conceptDomainId == null) - throw new LBException("Concept Domain Id can not be empty"); - - validateRevisionInfo(revision); - - // check if concept domain being removed is binded to any value set, if it is, we can not remove this concept domain - ConceptDomainQueryOperation cdQueryOp = LexEvsCTS2Impl.defaultInstance().getQueryOperation().getConceptDomainQueryOperation(); - List vsds = cdQueryOp.getConceptDomainBindings(conceptDomainId, codeSystemNameOrURI); - if (vsds != null && vsds.size() > 0) - { - throw new LBException("Concept Domain '" + conceptDomainId + "' can not be removed as it is binded to existing value sets."); - } - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.deleteConcept(csURI, codeSystemVersion, conceptDomainId, namespace, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ConceptDomainAuthoringOperation#removeConceptDomainToValueSetBinding(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.net.URI, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeConceptDomainToValueSetBinding(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, URI valueSetURI, RevisionInfo revisionInfo) throws LBException { - if (StringUtils.isEmpty(conceptDomainId)) - throw new LBException("Concept Domain Id can not be empty"); - if (valueSetURI == null) - throw new LBException("Value Set URI can not be empty"); - - ValueSetAuthoringOperation vsAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getValueSetAuthoringOperation(); - ValueSetQueryOperation vsQueryOp = LexEvsCTS2Impl.defaultInstance().getQueryOperation().getValueSetQueryOperation(); - - ValueSetDefinition vsd = vsQueryOp.getValueSetDetails(valueSetURI.toString(), null); - if (vsd != null) - { - if (!StringUtils.isEmpty(vsd.getConceptDomain()) && vsd.getConceptDomain().equalsIgnoreCase(conceptDomainId)) - vsAuthOp.updateValueSetMetaData(valueSetURI, null, null, " ", null, null, revisionInfo); - } - - return true; - } - - protected void doReviseEntity( - String codingSchemeUri, - String codingSchemeVersion, - Entity entity, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) throws LBException { - - this.validatedCodingScheme(codingSchemeUri, codingSchemeVersion); - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entity, - changeType, - prevRevisionId, - relativeOrder, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } - - protected void doReviseEntityProperty( - String codingSchemeUri, - String codingSchemeVersion, - String entityCode, - String entityCodeNamespace, - Property property, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) throws LBException { - - this.validatedCodingScheme(codingSchemeUri, codingSchemeVersion); - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entityCode, - entityCodeNamespace, - property, - changeType, - prevRevisionId, - relativeOrder, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/UsageContextAuthoringOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/UsageContextAuthoringOperation.java deleted file mode 100644 index e4daca2dfd..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/UsageContextAuthoringOperation.java +++ /dev/null @@ -1,204 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.naming.Mappings; -import org.lexevs.cts2.core.update.RevisionInfo; - -/** - * LexEVS CTS 2 Usage Context Authoring Operations. - * - * @author Sridhar Dwarkanath - */ -public interface UsageContextAuthoringOperation { - - /** - * Create a code system to hold usage context entities. - * - * @param revision - revision information - * @param codeSystemName - usage context code system name - * @param codeSystemURI - usage context code system URI - * @param formalName - usage context code system formal name - * @param defaultLanguage - default language - * @param representsVersion - usage context code system version - * @param localNameList - (Optional) list of alternate names used for this code system - * @param sourceList - source list - * @param copyright - copy right information - * @param mappings - list of attributes supported by this code system - * @return usage context code system - * @throws LBException - */ - public CodingScheme createUsageContextCodeSystem(RevisionInfo revision, String codeSystemName, String codeSystemURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException; - - /** - * Create new usage context. - * - * @param usageContextId - usage context id - * @param usageContextName - usage context name - * @param namespace - usage context name space (If not provided, formal name of the code system will be used) - * @param revisionInfo - revision information - * @param description - description of usage context - * @param status - status of usage context - * @param isActive - is usage context active - * @param properties - usage context properties - * @param codeSystemNameOrURI - usage context code system name or uri - * @param codeSystemVersion - usage context code system version - * @return usage context id if created successfully - * @throws LBException - */ - public String createUsageContext( - String usageContextId, - String usageContextName, - String namespace, - RevisionInfo revisionInfo, - String description, - String status, - boolean isActive, - Properties properties, - String codeSystemNameOrURI, - String codeSystemVersion) throws LBException; - - /** - * Update usage context status. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param newStatus - new status for concept domain - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean updateUsageContextStatus(String usageContextId, String namespace, String newStatus, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Activate usage context. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean activateUsageContext(String usageContextId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * DeActivate usage context. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean deactivateUsageContext(String usageContextId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException; - - /** - * Update usage context versionable attributes like effective date, expiration date, owner, status etc. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param changedVersionable - modified usage context versionable attributes - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean updateUsageContextVersionable(String usageContextId, String namespace, Versionable changedVersionable, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException; - - /** - * Add new property for a usage context. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param newProperty - new usage context property - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean addUsageContextProperty(String usageContextId, String namespace, Property newProperty, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException; - - /** - * Update existing property of a usage context. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param changedProperty - modified usage context property - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean updateUsageContextProperty(String usageContextId, String namespace, Property changedProperty, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException; - - /** - * Remove existing property of a usage context. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param property - usage context property to be removed - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean removeUsageContextProperty(String usageContextId, String namespace, Property property, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException; - - /** - * Remove existing usage context. - * - * @param usageContextId - usage context id - * @param namespace - usage context name space - * @param codeSystemNameOrURI - usage context code system name or URI - * @param codeSystemVersion - usage context code system version - * @param revisionInfo - revision information - * @return true, if update was success - * @throws LBException - */ - public boolean removeUsageContext(String usageContextId, String namespace, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/UsageContextAuthoringOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/UsageContextAuthoringOperationImpl.java deleted file mode 100644 index 44d2b28645..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/UsageContextAuthoringOperationImpl.java +++ /dev/null @@ -1,373 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.EntityDescription; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.concepts.Definition; -import org.LexGrid.concepts.Entities; -import org.LexGrid.concepts.Entity; -import org.LexGrid.concepts.Presentation; -import org.LexGrid.naming.Mappings; -import org.LexGrid.util.sql.lgTables.SQLTableConstants; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.Revision; -import org.LexGrid.versions.types.ChangeType; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.LexEvsCTS2Impl; -import org.lexevs.cts2.core.update.RevisionInfo; -import org.lexevs.dao.database.service.version.AuthoringService; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexgrid.usagecontext.util.UsageContextConstants; - -/** - * Implementation of LexEVS CTS2 Usage Context Authoring Operation. - * - * @author Sridhar Dwarkanath - */ -public class UsageContextAuthoringOperationImpl extends AuthoringCore implements - UsageContextAuthoringOperation { - - private AuthoringService authServ_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService(); - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#activateUsageContext(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean activateUsageContext(String usageContextId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException - { - if (StringUtils.isEmpty(usageContextId)) - throw new LBException("Usage Context Id can not be empty"); - - Versionable ver = new Versionable(); - ver.setIsActive(true); - - return updateUsageContextVersionable(usageContextId, namespace, ver, codeSystemNameOrURI, codeSystemVersion, revisionInfo); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#addUsageContextProperty(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Property, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean addUsageContextProperty(String usageContextId, String namespace, Property newProperty, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException { - if (usageContextId == null) - throw new LBException("Concept Domain Id can not be empty"); - if (newProperty == null) - throw new LBException("New property can not be empty"); - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.addNewConceptProperty(csURI, codeSystemVersion, usageContextId, namespace, newProperty, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#createUsageContext(java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo, java.lang.String, java.lang.String, boolean, org.LexGrid.commonTypes.Properties, java.lang.String, java.lang.String) - */ - @Override - public String createUsageContext(String usageContextId, String usageContextName, String namespace, - RevisionInfo revisionInfo, String description, String status, boolean isActive, - Properties properties, String codeSystemNameOrURI, String codeSystemVersion) throws LBException { - - if (StringUtils.isEmpty(usageContextId)) - usageContextId = createUniqueId(); - - if (StringUtils.isEmpty(usageContextName)) - throw new LBException("usage context name can not be empty"); - - // create an entity object for usageContext - Entity entity = new Entity(); - entity.setEntityCode(usageContextId); - entity.setEntityCodeNamespace(namespace); - EntityDescription ed = new EntityDescription(); - ed.setContent(usageContextId); - entity.setEntityDescription(ed); - entity.setStatus(status); - entity.setIsActive(isActive); - entity.addEntityType(UsageContextConstants.USAGE_CONTEXT_ENTITY_TYPE); - - Presentation pres = new Presentation(); - pres.setPropertyName(SQLTableConstants.TBLCOLVAL_TEXTUALPRESENTATION); - Text text = new Text(); - text.setContent(usageContextName); - pres.setValue(text); - pres.setIsPreferred(true); - - entity.addPresentation(pres); - - if (StringUtils.isNotEmpty(description)) - { - Definition def = new Definition(); - def.setPropertyName("Description"); - text = new Text(); - text.setContent(description); - def.setValue(text); - entity.addDefinition(def); - } - - if (properties != null) - entity.addAnyProperties(properties.getPropertyAsReference()); - - //insert - this.doReviseEntity(getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion), codeSystemVersion, entity, ChangeType.NEW, null, 0L, revisionInfo); - - return usageContextId; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#createUsageContextCodeSystem(org.lexevs.cts2.core.update.RevisionInfo, java.lang.String, java.lang.String, java.lang.String, java.lang.String, long, java.lang.String, java.util.List, java.util.List, org.LexGrid.commonTypes.Text, org.LexGrid.naming.Mappings) - */ - @Override - public CodingScheme createUsageContextCodeSystem(RevisionInfo revision, String codeSystemName, String codeSystemURI, String formalName, - String defaultLanguage, long approxNumConcepts, String representsVersion, List localNameList, - List sourceList, Text copyright, Mappings mappings) throws LBException{ - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - - return csAuthOp.createCodeSystem(revision, codeSystemName, codeSystemURI, formalName, defaultLanguage, 0, - representsVersion, localNameList, sourceList, copyright, mappings); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#deactivateUsageContext(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean deactivateUsageContext(String usageContextId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revisionInfo) throws LBException { - if (StringUtils.isEmpty(usageContextId)) - throw new LBException("Usage Context Id can not be empty"); - - Versionable ver = new Versionable(); - ver.setIsActive(false); - - return updateUsageContextVersionable(usageContextId, namespace, ver, codeSystemNameOrURI, codeSystemVersion, revisionInfo); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#removeUsageContext(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeUsageContext(String usageContextId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion, RevisionInfo revision) throws LBException { - if (usageContextId == null) - throw new LBException("Usage Context Id can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.deleteConcept(csURI, codeSystemVersion, usageContextId, namespace, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#removeUsageContextProperty(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Property, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeUsageContextProperty(String usageContextId, String namespace, Property property, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException { - if (usageContextId == null) - throw new LBException("Usage Context Id can not be empty"); - if (property == null) - throw new LBException("property can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.deleteConceptProperty(csURI, codeSystemVersion, usageContextId, namespace, property, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#updateUsageContextProperty(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Property, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateUsageContextProperty(String usageContextId, String namespace, Property changedProperty, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException { - if (usageContextId == null) - throw new LBException("Usage Context Id can not be empty"); - if (changedProperty == null) - throw new LBException("Changed property can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - CodeSystemAuthoringOperation csAuthOp = LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); - csAuthOp.updateConceptProperty(csURI, codeSystemVersion, usageContextId, namespace, changedProperty, revision); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#updateUsageContextStatus(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateUsageContextStatus(String usageContextId, String namespace, String newStatus, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revisionInfo) throws LBException { - if (StringUtils.isEmpty(usageContextId)) - throw new LBException("Usage Context Id can not be empty"); - - Versionable ver = new Versionable(); - ver.setStatus(newStatus); - - return updateUsageContextVersionable(usageContextId, namespace, ver, codeSystemNameOrURI, codeSystemVersion, revisionInfo); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.UsageContextAuthoringOperation#updateUsageContextVersionable(java.lang.String, java.lang.String, org.LexGrid.commonTypes.Versionable, java.lang.String, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateUsageContextVersionable(String usageContextId, String namespace, Versionable changedVersionable, - String codeSystemNameOrURI, String codeSystemVersion, RevisionInfo revision) throws LBException { - if (usageContextId == null) - throw new LBException("usageContextId can not be empty"); - - if (changedVersionable == null) - throw new LBException("Changed Versionable information can not be empty"); - - validateRevisionInfo(revision); - - String csURI = getCodeSystemURI(codeSystemNameOrURI, codeSystemVersion); - - Entity conceptDomain = this.getEntityShell(usageContextId, namespace, csURI, codeSystemVersion, revision.getRevisionId(), ChangeType.VERSIONABLE); - - if (StringUtils.isNotEmpty(changedVersionable.getOwner())) - { - conceptDomain.setOwner(changedVersionable.getOwner()); - } - - if (StringUtils.isNotEmpty(changedVersionable.getStatus())) - { - conceptDomain.setStatus(changedVersionable.getStatus()); - } - - if (changedVersionable.getEffectiveDate() != null) - { - conceptDomain.setEffectiveDate(changedVersionable.getEffectiveDate()); - } - - if (changedVersionable.getExpirationDate() != null) - { - conceptDomain.setExpirationDate(changedVersionable.getExpirationDate()); - } - - if (changedVersionable.getIsActive() != null) - { - conceptDomain.setIsActive(changedVersionable.getIsActive()); - } - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - CodingScheme conceptDomainCS = this.getCodeSystemShell(csURI, codeSystemVersion, lgRevision.getRevisionId(), ChangeType.DEPENDENT); - - Entities entities = new Entities(); - entities.addEntity(conceptDomain); - - conceptDomainCS.setEntities(entities); - - ce.setChangedCodingSchemeEntry(conceptDomainCS); - - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - - return true; - } - - protected void doReviseEntity( - String codingSchemeUri, - String codingSchemeVersion, - Entity entity, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) throws LBException { - - this.validatedCodingScheme(codingSchemeUri, codingSchemeVersion); - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entity, - changeType, - prevRevisionId, - relativeOrder, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } - - protected void doReviseEntityProperty( - String codingSchemeUri, - String codingSchemeVersion, - String entityCode, - String entityCodeNamespace, - Property property, - ChangeType changeType, - String prevRevisionId, - Long relativeOrder, - RevisionInfo revisionInfo) throws LBException { - - this.validatedCodingScheme(codingSchemeUri, codingSchemeVersion); - - Revision revision = this.populateRevisionShell( - codingSchemeUri, - codingSchemeVersion, - entityCode, - entityCodeNamespace, - property, - changeType, - prevRevisionId, - relativeOrder, - revisionInfo); - - this.getDatabaseServiceManager().getAuthoringService().loadRevision(revision, revisionInfo.getSystemReleaseURI(), null); - } - - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/ValueSetAuthoringOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/ValueSetAuthoringOperation.java deleted file mode 100644 index 3c6f13f40a..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/ValueSetAuthoringOperation.java +++ /dev/null @@ -1,184 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.valueSets.DefinitionEntry; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.lexevs.cts2.core.update.RevisionInfo; - -/** - * LexEVS CTS 2 Value Set Authoring Operation. - * - * @author Sridhar Dwarkanath - */ -public interface ValueSetAuthoringOperation { - - /** - * Creates a new value set definition and loads into repository. - * - * @param valueSetURI URI of value set definition - * @param valueSetName Name of value set definition - * @param defaultCodeSystem local name of default code system - * @param conceptDomainId (Optional)local name of concept domain - * @param sourceList (Optional)list of source - * @param usageContextList (Optional)list of usage context - * @param properties (Optional)collection of properties - * @param ruleSetList list of definition entries (rule sets) - * @param versionable versionable entries (status, isActive, effective date etc) - * @param revision revision information - * @return value set definition URI - * @throws LBException - */ - public URI createValueSet(URI valueSetURI, String valueSetName, String defaultCodeSystem, String conceptDomainId, - List sourceList, List usageContextList, Properties properties, List ruleSetList, - Versionable versionable, RevisionInfo revision) throws LBException; - - /** - * Creates new value set definition and loads into repository. - * - * @param valueSetDefininition Value Set Definition object to be loaded into repository - * @param revision revision information - * @return value set definition URI - * @throws LBException - */ - public URI createValueSet(ValueSetDefinition valueSetDefininition, RevisionInfo revision) throws LBException; - - /** - * Updates value set definition meta data. - * - * @param valueSetURI URI of value set definition that will be modified - * @param valueSetName modified value set definition name - * @param defaultCodeSystem modified default code system name - * @param conceptDomainId modified concept domain id - * @param sourceList modified complete list of source - * @param usageContext modified complete list of context - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean updateValueSetMetaData(URI valueSetURI, String valueSetName, String defaultCodeSystem, - String conceptDomainId, List sourceList, List usageContext, RevisionInfo revision) throws LBException; - - /** - * Updates versionable attributes of value set definition. - * Versionable attributes are : Status, isActive, Effective Date, Expiration Date, and owner. - * @param valueSetURI URI of value set definition that will be modified - * @param changedVersionable modified versionable object - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean updateValueSetVersionable(URI valueSetURI, Versionable changedVersionable, - RevisionInfo revision) throws LBException; - - /** - * Add new Property to existing value set definition. - * - * @param valueSetURI URI of value set definition this new property will be added - * @param newProperty new Property object - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean addValueSetProperty(URI valueSetURI, Property newProperty, RevisionInfo revision) throws LBException; - - /** - * Updates existing property of a value set definition. - * - * @param valueSetURI URI of value set definition - * @param changedProperty modified property object - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean updateValueSetProperty(URI valueSetURI, Property changedProperty, RevisionInfo revision) throws LBException; - - /** - * Add new definition entry (rule set) to a value set definition. - * - * @param valueSetURI URI of value set definition - * @param newDefinitionEntry Definition Entry object to be added - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean addDefinitionEntry(URI valueSetURI, DefinitionEntry newDefinitionEntry, RevisionInfo revision) throws LBException; - - /** - * Update existing definition entry (rule set) of a value set definition. - * - * @param valueSetURI URI of value set definition - * @param changedDefinitionEntry modified definition entry object - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean updateDefinitionEntry(URI valueSetURI, DefinitionEntry changedDefinitionEntry, RevisionInfo revision) throws LBException; - - /** - * Updates value set definition status. - * - * @param valueSetURI URI of value set definition - * @param status modified status - * @param revision revision information - * @return True if update was successful - * @throws LBException - */ - public boolean updateValueSetStatus(URI valueSetURI, String status, RevisionInfo revision) throws LBException; - - /** - * Removes value set definition from the system. This operation is permanent removal of value set definition. - * - * @param valueSetURI URI of value set definition to be removed - * @param revision revision information - * @return True if removal was successful - * @throws LBException - */ - public boolean removeValueSet(URI valueSetURI, RevisionInfo revision) throws LBException; - - /** - * Removes definition entry (rule set) of a value set definition. - * - * @param valueSetURI URI of a value set definition - * @param ruleOrder rule set order id to be removed - * @param revision revision information - * @return True if removal was successful - * @throws LBException - */ - public boolean removeDefinitionEntry(URI valueSetURI, Long ruleOrder, RevisionInfo revision) throws LBException; - - /** - * Removes property of a value set definition. - * - * @param valueSetURI URI of a value set definition - * @param propertyId id of a property that needs to be removed - * @param revision revision information - * @return True if removal was successful - * @throws LBException - */ - public boolean removeValueSetProperty(URI valueSetURI, String propertyId, RevisionInfo revision) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/author/ValueSetAuthoringOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/author/ValueSetAuthoringOperationImpl.java deleted file mode 100644 index 1fa0a005c6..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/author/ValueSetAuthoringOperationImpl.java +++ /dev/null @@ -1,684 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.author; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.commonTypes.Properties; -import org.LexGrid.commonTypes.Property; -import org.LexGrid.commonTypes.Source; -import org.LexGrid.commonTypes.Versionable; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedCodingScheme; -import org.LexGrid.naming.SupportedConceptDomain; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedSource; -import org.LexGrid.valueSets.DefinitionEntry; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.Revision; -import org.LexGrid.versions.types.ChangeType; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.core.update.RevisionInfo; -import org.lexevs.dao.database.service.valuesets.ValueSetDefinitionService; -import org.lexevs.dao.database.service.version.AuthoringService; -import org.lexevs.locator.LexEvsServiceLocator; - -/** - * Implementation LexEVS CTS 2 Value Set Authoring Operation. - * - * @author Sridhar Dwarkanath - */ -public class ValueSetAuthoringOperationImpl extends AuthoringCore implements - ValueSetAuthoringOperation { - - private ValueSetDefinitionService vsdServ_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getValueSetDefinitionService(); - private AuthoringService authServ_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService(); - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#addDefinitionEntry(java.net.URI, org.LexGrid.valueSets.DefinitionEntry, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean addDefinitionEntry(URI valueSetURI, - DefinitionEntry newDefinitionEntry, RevisionInfo revision) throws LBException { - validateRevisionInfo(revision); - - if (newDefinitionEntry == null) - throw new LBException("New Definition Entry can not be empty"); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - - if (vsd == null) - { - throw new LBException("No Value set definition found with uri : " + valueSetURI); - } - // remove any existing definition entry from the vsd object - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - vsd.setProperties(null); - - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - - Revision lgRevision = getLexGridRevisionObject(revision); - - // setup entrystate for vsd - vsd.setEntryState(populateEntryState(ChangeType.DEPENDENT, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - // setup entrystate for new definition entry - newDefinitionEntry.setEntryState(populateEntryState(ChangeType.NEW, - lgRevision.getRevisionId(), null, 0L)); - - // add new definition entry to vsd - vsd.addDefinitionEntry(newDefinitionEntry); - - ChangedEntry ce = new ChangedEntry(); - ce.setChangedValueSetDefinitionEntry(vsd); - - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#addValueSetProperty(java.net.URI, org.LexGrid.commonTypes.Property, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean addValueSetProperty(URI valueSetURI, Property newProperty, - RevisionInfo revision) - throws LBException { - if (valueSetURI == null) - throw new LBException("Value Set Definition URI can not be empty"); - if (newProperty == null) - throw new LBException("New property can not be empty"); - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - if (vsd == null) - { - throw new LBException("No Value set definition found with uri : " + valueSetURI); - } - - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - - // setup entry state for vsd - vsd.setEntryState(populateEntryState(ChangeType.DEPENDENT, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - // setup entry state for new property - newProperty.setEntryState(populateEntryState(ChangeType.NEW, - lgRevision.getRevisionId(), null, 0L)); - - Properties props = new Properties(); - props.addProperty(newProperty); - vsd.setProperties(props); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#createValueSet(java.net.URI, java.lang.String, java.lang.String, java.lang.String, java.util.List, java.util.List, org.LexGrid.commonTypes.Properties, java.util.List, org.LexGrid.commonTypes.Versionable, org.lexevs.cts2.core.update.RevisionInfo, org.LexGrid.versions.EntryState) - */ - @Override - public URI createValueSet(URI valueSetURI, String valueSetName, - String defaultCodeSystem, String conceptDomainId, - List sourceList, List usageContext, - Properties properties, List ruleSetList, - Versionable versionable, RevisionInfo revision) throws LBException { - if (valueSetURI == null) - throw new LBException("Value Set Definition URI can not be empty"); - validateRevisionInfo(revision); - - ValueSetDefinition vsd = new ValueSetDefinition(); - vsd.setValueSetDefinitionURI(valueSetURI.toString()); - vsd.setValueSetDefinitionName(valueSetName); - vsd.setDefaultCodingScheme(defaultCodeSystem); - vsd.setConceptDomain(conceptDomainId); - if (sourceList != null) - vsd.setSource(sourceList); - if (usageContext != null) - vsd.setRepresentsRealmOrContext(usageContext); - if (properties != null) - vsd.setProperties(properties); - if (ruleSetList != null) - vsd.setDefinitionEntry(ruleSetList); - if (versionable != null) - { - vsd.setEffectiveDate(versionable.getEffectiveDate()); - vsd.setExpirationDate(versionable.getExpirationDate()); - vsd.setIsActive(versionable.getIsActive()); - vsd.setOwner(versionable.getOwner()); - vsd.setStatus(versionable.getStatus()); - } - - return createValueSet(vsd, revision); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#createValueSet(org.LexGrid.valueSets.ValueSetDefinition, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public URI createValueSet(ValueSetDefinition valueSetDefininition, - RevisionInfo revision) throws LBException { - if (valueSetDefininition == null) - throw new LBException("ValueSetDefinition object can not be empty"); - - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - // setup entry state for new vsd - valueSetDefininition.setEntryState(populateEntryState(ChangeType.NEW, - lgRevision.getRevisionId(), null, 0L)); - - ChangedEntry ce = new ChangedEntry(); - ce.setChangedValueSetDefinitionEntry(valueSetDefininition); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - URI vsdURI = null; - try { - vsdURI = new URI(valueSetDefininition.getValueSetDefinitionURI()); - } catch (URISyntaxException e) { - throw new LBException("Problem resolving value set definition URI",e); - } - return vsdURI; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#updateDefinitionEntry(java.net.URI, org.LexGrid.valueSets.DefinitionEntry, org.lexevs.cts2.core.update.RevisionInfo, org.LexGrid.versions.EntryState) - */ - @Override - public boolean updateDefinitionEntry(URI valueSetURI, - DefinitionEntry changedDefinitionEntry, RevisionInfo revision) throws LBException { - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - if (changedDefinitionEntry == null) - throw new LBException("changedDefinitionEntry can not be empty"); - - if (changedDefinitionEntry.getRuleOrder() == null) - throw new LBException("changedDefinitionEntry RuleOrder can not be empty. It is unique id to identify definition entry."); - - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - DefinitionEntry currentDefEntry = null; - - for (DefinitionEntry de : vsd.getDefinitionEntryAsReference()) - { - if (de.getRuleOrder().equals(changedDefinitionEntry.getRuleOrder())) - currentDefEntry = de; - } - - if (currentDefEntry == null) - throw new LBException("No Definition Entry found with Rule Order : " + changedDefinitionEntry.getRuleOrder()); - - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - vsd.setProperties(null); - - // setup entry state for vsd - vsd.setEntryState(populateEntryState(ChangeType.DEPENDENT, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - // setup entry state for update definition entry - String defEntryPrecRevId = currentDefEntry.getEntryState() != null?currentDefEntry.getEntryState().getContainingRevision():null; - changedDefinitionEntry.setEntryState(populateEntryState(ChangeType.MODIFY, - lgRevision.getRevisionId(), defEntryPrecRevId, 0L)); - - vsd.addDefinitionEntry(changedDefinitionEntry); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#updateValueSetMetaData(java.net.URI, java.lang.String, java.lang.String, java.lang.String, java.util.List, java.util.List, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateValueSetMetaData(URI valueSetURI, String valueSetName, - String defaultCodeSystem, String conceptDomainId, - List sourceList, List usageContext, - RevisionInfo revision) throws LBException { - - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - validateRevisionInfo(revision); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - vsd.setProperties(null); - - Mappings maps = new Mappings(); - - if (StringUtils.isNotEmpty(valueSetName)) - vsd.setValueSetDefinitionName(valueSetName); - - if (StringUtils.isNotEmpty(defaultCodeSystem)) - { - vsd.setDefaultCodingScheme(defaultCodeSystem); - SupportedCodingScheme scs = new SupportedCodingScheme(); - scs.setContent(defaultCodeSystem); - scs.setLocalId(defaultCodeSystem); - - maps.addSupportedCodingScheme(scs); - } - - if (conceptDomainId != null) - { - vsd.setConceptDomain(conceptDomainId); - - SupportedConceptDomain scd = new SupportedConceptDomain(); - scd.setContent(conceptDomainId); - scd.setLocalId(conceptDomainId); - - maps.addSupportedConceptDomain(scd); - } - - if (sourceList != null) - { - vsd.setSource(sourceList); - - for (Source src : sourceList) - { - SupportedSource ss = new SupportedSource(); - ss.setAssemblyRule(src.getRole()); - ss.setContent(src.getContent()); - ss.setLocalId(src.getContent()); - - maps.addSupportedSource(ss); - } - } - - if (usageContext != null) - { - vsd.setRepresentsRealmOrContext(usageContext); - - for (String uc : usageContext) - { - SupportedContext sc = new SupportedContext(); - sc.setContent(uc); - sc.setLocalId(uc); - - maps.addSupportedContext(sc); - } - } - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - vsd.setEntryState(populateEntryState(ChangeType.MODIFY, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - vsd.setMappings(maps); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#updateValueSetProperty(java.net.URI, org.LexGrid.commonTypes.Property, org.lexevs.cts2.core.update.RevisionInfo, org.LexGrid.versions.EntryState) - */ - @Override - public boolean updateValueSetProperty(URI valueSetURI, - Property changedProperty, RevisionInfo revision) throws LBException { - - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - if (changedProperty == null) - throw new LBException("property can not be empty"); - - if (StringUtils.isEmpty(changedProperty.getPropertyId())) - throw new LBException("property ID can not be empty"); - - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - if (vsd.getProperties() == null) - throw new LBException("No properties found in value set definition : " + valueSetURI); - - Property currentProperty = null; - - for (Property prop : vsd.getProperties().getPropertyAsReference()) - { - if (prop.getPropertyId().equalsIgnoreCase(changedProperty.getPropertyId())) - currentProperty = prop; - } - - if (currentProperty == null) - throw new LBException("No property found with id : " + changedProperty.getPropertyId()); - - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - - // remove all other properties but the one that needs to be changed - vsd.setProperties(null); - Properties props = new Properties(); - props.addProperty(changedProperty); - vsd.setProperties(props); - - // setup entry state for vsd - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.setEntryState(populateEntryState(ChangeType.DEPENDENT, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - // setup entry state for property to be changed - String propPrevRevId = currentProperty.getEntryState() != null?currentProperty.getEntryState().getContainingRevision():null; - changedProperty.setEntryState(populateEntryState(ChangeType.MODIFY, - lgRevision.getRevisionId(), propPrevRevId, 0L)); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#updateValueSetStatus(java.net.URI, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateValueSetStatus(URI valueSetURI, String status, RevisionInfo revision) - throws LBException { - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - if (status == null) - throw new LBException("Status can not be empty"); - - validateRevisionInfo(revision); - - Versionable ver = new Versionable(); - ver.setStatus(status); - - return this.updateValueSetVersionable(valueSetURI, ver, revision); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#updateValueSetVersionable(java.net.URI, org.LexGrid.commonTypes.Versionable, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean updateValueSetVersionable(URI valueSetURI, - Versionable changedVersionable, RevisionInfo revision) throws LBException { - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - if (changedVersionable == null) - throw new LBException("Changed Versionable information can not be empty"); - - validateRevisionInfo(revision); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - vsd.setProperties(null); - - if (StringUtils.isNotEmpty(changedVersionable.getOwner())) - { - vsd.setOwner(changedVersionable.getOwner()); - } - - if (StringUtils.isNotEmpty(changedVersionable.getStatus())) - { - vsd.setStatus(changedVersionable.getStatus()); - } - - if (changedVersionable.getEffectiveDate() != null) - { - vsd.setEffectiveDate(changedVersionable.getEffectiveDate()); - } - - if (changedVersionable.getExpirationDate() != null) - { - vsd.setExpirationDate(changedVersionable.getExpirationDate()); - } - - if (changedVersionable.getIsActive() != null) - { - vsd.setIsActive(changedVersionable.getIsActive()); - } - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - - vsd.setEntryState(populateEntryState(ChangeType.VERSIONABLE, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#removeDefinitionEntry(java.net.URI, java.lang.Long, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeDefinitionEntry(URI valueSetURI, Long ruleOrder, - RevisionInfo revision) throws LBException { - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - if (ruleOrder == null) - throw new LBException("ruleOrder can not be empty"); - - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - DefinitionEntry currentDefEntry = null; - - for (DefinitionEntry de : vsd.getDefinitionEntryAsReference()) - { - if (de.getRuleOrder().equals(ruleOrder)) - currentDefEntry = de; - } - - if (currentDefEntry == null) - throw new LBException("No Definition Entry found with Rule Order : " + ruleOrder); - - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - vsd.setProperties(null); - - // setup entry state for vsd - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.setEntryState(populateEntryState(ChangeType.DEPENDENT, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - // setup entry state for update definition entry - String defEntryPrevRevId = currentDefEntry.getEntryState() != null?currentDefEntry.getEntryState().getContainingRevision():null; - currentDefEntry.setEntryState(populateEntryState(ChangeType.REMOVE, - lgRevision.getRevisionId(), defEntryPrevRevId, 0L)); - - vsd.addDefinitionEntry(currentDefEntry); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#removeValueSet(java.net.URI, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeValueSet(URI valueSetURI, RevisionInfo revision) - throws LBException { - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - - // setup entry state for vsd - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.setEntryState(populateEntryState(ChangeType.REMOVE, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.author.ValueSetAuthoringOperation#removeValueSetProperty(java.net.URI, java.lang.String, org.lexevs.cts2.core.update.RevisionInfo) - */ - @Override - public boolean removeValueSetProperty(URI valueSetURI, String propertyId, - RevisionInfo revision) throws LBException { - if (valueSetURI == null) - throw new LBException("ValueSetDefinitionURI can not be empty"); - - if (StringUtils.isEmpty(propertyId)) - throw new LBException("propertyId can not be empty"); - - validateRevisionInfo(revision); - - Revision lgRevision = getLexGridRevisionObject(revision); - ChangedEntry ce = new ChangedEntry(); - - ValueSetDefinition vsd = vsdServ_.getValueSetDefinitionByUri(valueSetURI); - - if (vsd == null) - throw new LBException("No Value Set Definition found with URI : " + valueSetURI.toString()); - - if (vsd.getProperties() == null) - throw new LBException("No property found with id : " + propertyId); - - Property currentProperty = null; - - for (Property prop : vsd.getProperties().getPropertyAsReference()) - { - if (prop.getPropertyId().equalsIgnoreCase(propertyId)) - currentProperty = prop; - } - - if (currentProperty == null) - throw new LBException("No property found with id : " + propertyId); - - vsd.removeAllDefinitionEntry(); - vsd.removeAllRepresentsRealmOrContext(); - vsd.removeAllSource(); - - // remove all other properties but the one that needs to be removed - vsd.setProperties(null); - Properties props = new Properties(); - props.addProperty(currentProperty); - vsd.setProperties(props); - - // setup entry state for vsd - String prevRevisionId = vsd.getEntryState() != null?vsd.getEntryState().getContainingRevision():null; - vsd.setEntryState(populateEntryState(ChangeType.DEPENDENT, - lgRevision.getRevisionId(), prevRevisionId, 0L)); - - // setup entry state for property to be removed - String propPrevRevId = currentProperty.getEntryState() != null?currentProperty.getEntryState().getContainingRevision():null; - currentProperty.setEntryState(populateEntryState(ChangeType.REMOVE, - lgRevision.getRevisionId(), propPrevRevId, 0L)); - - ce.setChangedValueSetDefinitionEntry(vsd); - lgRevision.addChangedEntry(ce); - - authServ_.loadRevision(lgRevision, revision.getSystemReleaseURI(), null); - return true; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/core/update/RevisionInfo.java b/cts2Impl/src/main/java/org/lexevs/cts2/core/update/RevisionInfo.java deleted file mode 100644 index e57830415c..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/core/update/RevisionInfo.java +++ /dev/null @@ -1,121 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.core.update; - -import java.util.Date; - -/** - * Version information of a resource. - * - * @author Sridhar Dwarkanath - */ -public class RevisionInfo { - private String changeAgent; - private String changeInstruction; - private String revisionId; - private Long editOrder; - private Date revisionDate; - private String description; - private String systemReleaseURI; - - /** - * @return the revisionId - */ - public String getRevisionId() { - return revisionId; - } - /** - * @param revisionId the revisionId to set - */ - public void setRevisionId(String revisionId) { - this.revisionId = revisionId; - } - /** - * @return the changeAgent - */ - public String getChangeAgent() { - return changeAgent; - } - /** - * @param changeAgent the changeAgent to set - */ - public void setChangeAgent(String changeAgent) { - this.changeAgent = changeAgent; - } - /** - * @return the changeInstruction - */ - public String getChangeInstruction() { - return changeInstruction; - } - /** - * @param changeInstruction the changeInstruction to set - */ - public void setChangeInstruction(String changeInstruction) { - this.changeInstruction = changeInstruction; - } - /** - * @return the editOrder - */ - public Long getEditOrder() { - return editOrder; - } - /** - * @param editOrder the editOrder to set - */ - public void setEditOrder(Long editOrder) { - this.editOrder = editOrder; - } - /** - * @return the revisionDate - */ - public Date getRevisionDate() { - return revisionDate; - } - /** - * @param revisionDate the revisionDate to set - */ - public void setRevisionDate(Date revisionDate) { - this.revisionDate = revisionDate; - } - /** - * @return the description - */ - public String getDescription() { - return description; - } - /** - * @param description the description to set - */ - public void setDescription(String description) { - this.description = description; - } - /** - * @return the systemReleaseURI - */ - public String getSystemReleaseURI() { - return systemReleaseURI; - } - /** - * @param systemReleaseURI the systemReleaseURI to set - */ - public void setSystemReleaseURI(String systemReleaseURI) { - this.systemReleaseURI = systemReleaseURI; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/core/update/SystemReleaseInfo.java b/cts2Impl/src/main/java/org/lexevs/cts2/core/update/SystemReleaseInfo.java deleted file mode 100644 index d2193735bd..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/core/update/SystemReleaseInfo.java +++ /dev/null @@ -1,72 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.core.update; - -import java.util.Date; - -/** - * System Release information of a resource. - * - * @author Sridhar Dwarkanath - */ -public class SystemReleaseInfo { - private String basedOnRelease; - private String releaseAgency; - private Date releaseDate; - private String releaseId; - private String releaseURI; - private String description; - - public String getBasedOnRelease() { - return basedOnRelease; - } - public void setBasedOnRelease(String basedOnRelease) { - this.basedOnRelease = basedOnRelease; - } - public String getReleaseAgency() { - return releaseAgency; - } - public void setReleaseAgency(String releaseAgency) { - this.releaseAgency = releaseAgency; - } - public Date getReleaseDate() { - return releaseDate; - } - public void setReleaseDate(Date releaseDate) { - this.releaseDate = releaseDate; - } - public String getReleaseId() { - return releaseId; - } - public void setReleaseId(String releaseId) { - this.releaseId = releaseId; - } - public String getReleaseURI() { - return releaseURI; - } - public void setReleaseURI(String releaseURI) { - this.releaseURI = releaseURI; - } - public String getDescription() { - return description; - } - public void setDescription(String description) { - this.description = description; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/exception/AbstractCTS2CheckedException.java b/cts2Impl/src/main/java/org/lexevs/cts2/exception/AbstractCTS2CheckedException.java deleted file mode 100644 index 0afa9f3251..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/exception/AbstractCTS2CheckedException.java +++ /dev/null @@ -1,95 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.exception; - -import java.util.Date; -import java.util.UUID; - -import org.LexGrid.LexBIG.Exceptions.LBException; - -/** - * The Class AbstractCTS2CheckedException. - * - * @author Kevin Peterson - */ -public abstract class AbstractCTS2CheckedException extends Exception { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -8963284974393488275L; - - /** The exception identifier. */ - private String exceptionIdentifier; - - /** The exception date. */ - private Date exceptionDate; - - /** - * Instantiates a new abstract ct s2 checked exception. - * - * @param message the message - */ - protected AbstractCTS2CheckedException(String message) { - super(message); - this.exceptionIdentifier = UUID.randomUUID().toString(); - this.exceptionDate = new Date(); - } - - protected AbstractCTS2CheckedException(String message, LBException exception) { - super(message + "\n\n" + - " -- LexEVS Exception: " + exception.getMessage()); - this.exceptionIdentifier = UUID.randomUUID().toString(); - this.exceptionDate = new Date(); - } - - /** - * Gets the exception identifier. - * - * @return the exception identifier - */ - public String getExceptionIdentifier() { - return exceptionIdentifier; - } - - /** - * Sets the exception identifier. - * - * @param exceptionIdentifier the new exception identifier - */ - public void setExceptionIdentifier(String exceptionIdentifier) { - this.exceptionIdentifier = exceptionIdentifier; - } - - /** - * Gets the exception date. - * - * @return the exception date - */ - public Date getExceptionDate() { - return exceptionDate; - } - - /** - * Sets the exception date. - * - * @param exceptionDate the new exception date - */ - public void setExceptionDate(Date exceptionDate) { - this.exceptionDate = exceptionDate; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/exception/admin/NotificationNotRegisteredException.java b/cts2Impl/src/main/java/org/lexevs/cts2/exception/admin/NotificationNotRegisteredException.java deleted file mode 100644 index 72f8d90e3b..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/exception/admin/NotificationNotRegisteredException.java +++ /dev/null @@ -1,42 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.exception.admin; - -import org.lexevs.cts2.exception.AbstractCTS2CheckedException; - -/** - * The Class NotificationNotRegisteredException. - * - * @author Kevin Peterson - */ -public class NotificationNotRegisteredException extends AbstractCTS2CheckedException { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = 474720380649284821L; - - /** - * Instantiates a new notification not registered exception. - * - * @param notificationId the notification id - */ - public NotificationNotRegisteredException(String notificationId) { - super("A Notification with identifier: " + notificationId + - " has not been registered."); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/exception/author/InvalidCodeSystemSupplementException.java b/cts2Impl/src/main/java/org/lexevs/cts2/exception/author/InvalidCodeSystemSupplementException.java deleted file mode 100644 index 4577526048..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/exception/author/InvalidCodeSystemSupplementException.java +++ /dev/null @@ -1,42 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.exception.author; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Utility.ObjectToString; -import org.lexevs.cts2.exception.AbstractCTS2CheckedException; - -/** - * The Class NotificationNotRegisteredException. - * - * @author Kevin Peterson - */ -public class InvalidCodeSystemSupplementException extends AbstractCTS2CheckedException { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = 474720380649284821L; - - public InvalidCodeSystemSupplementException( - AbsoluteCodingSchemeVersionReference parent, - AbsoluteCodingSchemeVersionReference supplement, - LBException exception) { - super("There was an error registring: " + ObjectToString.toString(parent) + " and: " + ObjectToString.toString(parent)); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/AssociationQueryOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/AssociationQueryOperation.java deleted file mode 100644 index dd518b7bb5..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/AssociationQueryOperation.java +++ /dev/null @@ -1,87 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.DataModel.Core.ConceptReference; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.lexevs.dao.database.service.association.AssociationService.AssociationTriple; - -public interface AssociationQueryOperation { - -/** - * Returns the resolved concept reference (which contains the associations) according to given node. - * @param codingSystemName - * @param versionOrTag - * @param namespace - * @param code - * @param associationName - * @param isBackward - * @param depth - * @param maxToReturn - * @return ResolvedConceptReferenceList - */ -public ResolvedConceptReferenceList listAssociations( - String codingSystemName, CodingSchemeVersionOrTag versionOrTag, - String namespace, String code, String associationName, - boolean isBackward, int depth, int maxToReturn); - - /** - * Returns the path according to given two nodes. - * @param codingSystemUri - * @param versionOrTag - * @param relationContainerName - * @param associationName - * @param sourceCode - * @param sourceNS - * @param targetCode - * @param targetNS - * @return ResolvedConceptReference - */ - public ResolvedConceptReference determineTransitiveConceptRelationship( - String codingSystemUri, CodingSchemeVersionOrTag versionOrTag, - String relationContainerName, String associationName, - String sourceCode, String sourceNS, String targetCode, - String targetNS); - - /** - * Return whether the two nodes has a transitive closure path - * @param codingSystemName - * @param versionOrTag - * @param associationtype - * @param parentCode - * @param childCode - * @return boolean - */ - public boolean computeSubsumptionRelationship(String codingSystemName, - CodingSchemeVersionOrTag versionOrTag, String associationtype, - ConceptReference sourceCode, ConceptReference targetCode); - - /** - * Return association triple according to association instance id - * @param codingSchemeUri - * @param versionOrTag - * @param associationInstanceId - * @return AssociationTriple - */ - public AssociationTriple getAssociationDetails(String codingSchemeUri, - CodingSchemeVersionOrTag versionOrTag, - String associationInstanceId); -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/AssociationQueryOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/AssociationQueryOperationImpl.java deleted file mode 100644 index 629ce5e3ee..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/AssociationQueryOperationImpl.java +++ /dev/null @@ -1,137 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.DataModel.Core.ConceptReference; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; -import org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods; -import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.LexBIG.Utility.ServiceUtility; -import org.apache.commons.lang.StringUtils; -import org.lexevs.cts2.BaseService; -import org.lexevs.dao.database.service.association.AssociationService.AssociationTriple; - -public class AssociationQueryOperationImpl extends BaseService implements AssociationQueryOperation { - - @Override - public boolean computeSubsumptionRelationship(String codingSystemName, - CodingSchemeVersionOrTag versionOrTag, String associationtype, - ConceptReference sourceCode, ConceptReference targetCode) { - try { - if (StringUtils.equals(sourceCode.getCodeNamespace(), targetCode - .getCodeNamespace()) == false - || StringUtils.equals(sourceCode.getCodingSchemeName(), - targetCode.getCodingSchemeName()) == false) { - throw new LBParameterException( - "Does not support different coding systems subsumes"); - } else { - CodedNodeGraph cng = LexBIGServiceImpl.defaultInstance() - .getNodeGraph(codingSystemName, versionOrTag, null); - return cng.areCodesRelated(Constructors.createNameAndValue( - associationtype, null), sourceCode, targetCode, false); - } - } catch (LBParameterException e) { - e.printStackTrace(); - } catch (LBInvocationException e) { - e.printStackTrace(); - } catch (LBResourceUnavailableException e) { - e.printStackTrace(); - } - return false; - } - - @Override - public ResolvedConceptReference determineTransitiveConceptRelationship( - String codingSystemUri, CodingSchemeVersionOrTag versionOrTag, - String relationContainerName, String associationName, - String sourceCode, String sourceNS, String targetCode, - String targetNS) { - - LexBIGServiceConvenienceMethods lbscm; - try { - lbscm = (LexBIGServiceConvenienceMethods) LexBIGServiceImpl - .defaultInstance().getGenericExtension( - "LexBIGServiceConvenienceMethods"); - return lbscm.getNodesPath(codingSystemUri, versionOrTag, - relationContainerName, associationName, sourceCode, - sourceNS, targetCode, targetNS); - } catch (LBParameterException e) { - e.printStackTrace(); - } catch (LBInvocationException e) { - e.printStackTrace(); - } - - return null; - } - - @Override - public ResolvedConceptReferenceList listAssociations( - String codingSystemName, CodingSchemeVersionOrTag versionOrTag, - String namespace, String code, String associationName, - boolean isBackward, int depth, int maxToReturn) { - ResolvedConceptReferenceList list = new ResolvedConceptReferenceList(); - - try { - CodedNodeGraph cng = LexBIGServiceImpl.defaultInstance() - .getNodeGraph(codingSystemName, versionOrTag, null); - ConceptReference conRef = new ConceptReference(); - conRef.setCode(code); - conRef.setCodeNamespace(namespace); - conRef.setCodingSchemeName(codingSystemName); - conRef.setConceptCode(code); - - if (StringUtils.isEmpty(associationName) == false) { - cng = cng.restrictToAssociations(Constructors - .createNameAndValueList(associationName), null); - } - return cng.resolveAsList(conRef, !(isBackward), isBackward, -1, - depth, null, null, null, null, maxToReturn); - } catch (LBParameterException e) { - e.printStackTrace(); - } catch (LBInvocationException e) { - e.printStackTrace(); - } catch (LBResourceUnavailableException e) { - e.printStackTrace(); - } - return list; - } - - @Override - public AssociationTriple getAssociationDetails(String codingSchemeUri, - CodingSchemeVersionOrTag versionOrTag, - String associationInstanceId) { - - String version; - try { - version = ServiceUtility.getVersion(codingSchemeUri, versionOrTag); - return this.getDatabaseServiceManager().getAssociationService().getAssociationTripleByAssociationInstanceId(codingSchemeUri, version, associationInstanceId); - - } catch (LBParameterException e) { - e.printStackTrace(); - } - return null; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/CodeSystemQueryOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/CodeSystemQueryOperation.java deleted file mode 100644 index e2a34c6126..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/CodeSystemQueryOperation.java +++ /dev/null @@ -1,109 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Collections.LocalNameList; -import org.LexGrid.LexBIG.DataModel.Collections.SortOptionList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.SupportedAssociation; -import org.LexGrid.relations.AssociationEntity; - -public interface CodeSystemQueryOperation { - -/** - * List the coding systems that are available in cts 2 system - * - * @param queryByExample - * . Query by example. - * @return a list of codingSystems - * @throws LBInvocationException - */ -public CodingSchemeRenderingList listCodeSystems( - CodingSchemeSummary queryByExample); - - /** - * Return a detailed codingScheme according to provided codingName and - * versionOrTag - * - * @param codingSchemeName - * @param versionOrTag - * @return codingSystem - * @throws LBInvocationException - * @throws LBParameterException - */ - public CodingScheme getCodeSystemDetails(String codingSchemeName, - CodingSchemeVersionOrTag versionOrTag); - - /** - * List the concepts in a specific codingSystem - * - * @param codingSchemeName - * @param versionOrTag - * @param entityTypes (Optional) - * @param sortOptionList (Optional) - * @return Iterator of codingSystemEntities - * @throws LBException - */ - public ResolvedConceptReferencesIterator listCodeSystemConcepts( - String codingSchemeName, CodingSchemeVersionOrTag versionOrTag, - LocalNameList entityTypes, SortOptionList sortOptionList); - - /** - * Return an instance of Entity according the requests - * - * @param codingSchemeName - * @param versionOrTag - * @param code - * @param namespace - * @return coding system entity - * @throws LBException - */ - public Entity getConceptDetails(String codingSchemeName, - CodingSchemeVersionOrTag versionOrTag, String code, String namespace); - - /** - * List all the associationTypes in a specific codingSystem - * - * @param codingSchemeName - * @param versionOrTag - * @return a list of association types - */ - public List listAssociationTypes( - String codingSchemeName, CodingSchemeVersionOrTag versionOrTag); - - /** - * Return detailed information for a certain associationType - * - * @param codingSchemeName - * @param versionOrTag - * @param associationName - * @return association type detail - * @throws LBException - */ - public AssociationEntity getAssociationTypeDetails(String codingSchemeName, - CodingSchemeVersionOrTag versionOrTag, String associationName); - -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/CodeSystemQueryOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/CodeSystemQueryOperationImpl.java deleted file mode 100644 index 86f008de8e..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/CodeSystemQueryOperationImpl.java +++ /dev/null @@ -1,177 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Collections.LocalNameList; -import org.LexGrid.LexBIG.DataModel.Collections.SortOptionList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.types.EntityTypes; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.SupportedAssociation; -import org.LexGrid.relations.AssociationEntity; -import org.apache.commons.lang.StringUtils; - -public class CodeSystemQueryOperationImpl implements CodeSystemQueryOperation { - public CodeSystemQueryOperationImpl() { - - } - - @Override - public AssociationEntity getAssociationTypeDetails(String codingSchemeName, - CodingSchemeVersionOrTag versionOrTag, String associationName) { - try { - String sacodingSchemeName = null; - String code = null; - String namespace = null; - for(SupportedAssociation assoc : this.listAssociationTypes(codingSchemeName, versionOrTag)) { - if(assoc.getContent().equals(associationName)) { - if (assoc.getCodingScheme() == null) - sacodingSchemeName = codingSchemeName; - else - sacodingSchemeName = assoc.getCodingScheme(); - if (assoc.getEntityCode() == null) - code = associationName; - else - code = assoc.getEntityCode(); - if (assoc.getEntityCodeNamespace() == null) - namespace = codingSchemeName; - else - namespace = assoc.getEntityCodeNamespace(); - } - } - - CodedNodeSet cns = LexBIGServiceImpl.defaultInstance().getNodeSet(sacodingSchemeName, versionOrTag, Constructors.createLocalNameList("association")); - - cns = cns.restrictToCodes(Constructors.createConceptReferenceList(code, namespace, sacodingSchemeName)); - ResolvedConceptReferencesIterator resolvedConList = cns.resolve(null, null, null); - if (resolvedConList.hasNext()) { - Object entity = cns.resolve(null, null, null).next().getEntity(); - if (entity instanceof AssociationEntity) - return (AssociationEntity)entity; - else - throw new LBException("Now valid Association Entity found"); - } - } catch (LBException e) { - e.printStackTrace(); - } - return null; - } - - @Override - public CodingScheme getCodeSystemDetails(String codingSchemeName, - CodingSchemeVersionOrTag versionOrTag) { - try { - return LexBIGServiceImpl.defaultInstance().resolveCodingScheme(codingSchemeName, versionOrTag); - } catch (LBInvocationException e) { - e.printStackTrace(); - } catch (LBParameterException e) { - e.printStackTrace(); - } - return null; - } - - @Override - public Entity getConceptDetails(String codingSchemeName, - CodingSchemeVersionOrTag versionOrTag, String code, String namespace) { - try { - LocalNameList lnl = new LocalNameList(); - lnl.addEntry(EntityTypes.CONCEPT.toString()); - CodedNodeSet cns = LexBIGServiceImpl.defaultInstance().getNodeSet(codingSchemeName, versionOrTag, lnl); - ResolvedConceptReferencesIterator conceptIterator = cns.resolve(null, null, null, null, true); - while (conceptIterator.hasNext()) { - ResolvedConceptReference conceptRef = conceptIterator.next(); - if (StringUtils.equals(code, conceptRef.getCode()) && StringUtils.equals(namespace, conceptRef.getCodeNamespace())) - return conceptRef.getEntity(); - } - } catch (LBException e) { - e.printStackTrace(); - } - return null; - } - - @Override - public List listAssociationTypes(String codingSchemeName, CodingSchemeVersionOrTag versionOrTag) { - CodingScheme cs = this.getCodeSystemDetails(codingSchemeName, versionOrTag); - return cs.getMappings().getSupportedAssociationAsReference(); - } - - @Override - public ResolvedConceptReferencesIterator listCodeSystemConcepts( - String codingSchemeName, CodingSchemeVersionOrTag versionOrTag, LocalNameList entityTypes, SortOptionList sortOptionList) { - try { - CodedNodeSet cns = LexBIGServiceImpl.defaultInstance().getNodeSet(codingSchemeName, versionOrTag, entityTypes); - return cns.resolve(sortOptionList, null, null, null); - } catch (LBException e) { - e.printStackTrace(); - } - return null; - } - - @Override - public CodingSchemeRenderingList listCodeSystems( - CodingSchemeSummary queryByExample) { - CodingSchemeRenderingList csList = new CodingSchemeRenderingList(); - try { - for (CodingSchemeRendering csr : LexBIGServiceImpl - .defaultInstance().getSupportedCodingSchemes() - .getCodingSchemeRendering()) { - CodingSchemeSummary css = csr.getCodingSchemeSummary(); - if (queryByExample.getCodingSchemeURI() != null - && StringUtils.equals(css.getCodingSchemeURI(), - queryByExample.getCodingSchemeURI()) == false) - continue; - - if (queryByExample.getRepresentsVersion() != null - && StringUtils.equals(css.getRepresentsVersion(), - queryByExample.getRepresentsVersion()) == false) - continue; - - if (queryByExample.getFormalName() != null - && StringUtils.equals(css.getFormalName(), - queryByExample.getFormalName()) == false) - continue; - - if (queryByExample.getLocalName() != null - && StringUtils.equals(css.getLocalName(), - queryByExample.getLocalName()) == false) - continue; - - csList.addCodingSchemeRendering(csr); - } - - } catch (LBInvocationException e) { - e.printStackTrace(); - } - return csList; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/ConceptDomainQueryOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/ConceptDomainQueryOperation.java deleted file mode 100644 index 71cff47cb3..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/ConceptDomainQueryOperation.java +++ /dev/null @@ -1,142 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.concepts.Entity; - -/** - * LexEVS CTS 2 Concept Domain Query Operations. - * - * @author Sridhar Dwarkanath - */ -public interface ConceptDomainQueryOperation { - - /** - * Gets the concept domain coding scheme. - * @param codeSystemNameOrURI concept domain coding scheme name or URI - * @param codeSystemVersion concept domain coding scheme version - * @return the concept domain coding scheme - * @throws LBException - */ - public CodingScheme getConceptDomainCodingScheme(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns concept domain entity object of the concept domain id. - * - * @param conceptDomainId id of concept domain - * @param namespace concept domain name space - * @param codeSystemNameOrURI concept domain coding scheme name or URI - * @param codeSystemVersion concept domain coding scheme version - * @return concept domain entity object - * @throws LBException - */ - public Entity getConceptDomainEntity(String conceptDomainId, String namespace, String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns list of concept domain entities matching the name provided. - * @param conceptDomainName - * match name of concept domain - * @param codeSystemNameOrURI - * concept domain coding scheme name or URI - * @param codeSystemVersion - * concept domain coding scheme version - * @param option - * Indicates the designations to search (one of the enumerated - * type SearchDesignationOption). - * @param matchAlgorithm - * Local name of the match algorithm - possible algorithms are - * returned in LexBigService.getMatchAlgorithms(). - * @param language - * Language of search string. If missing, use the default - * language specified in the context. - * @return list of entities containing matching concept domain name - * @throws LBException - */ - public List getConceptDomainEntitisWithName(String conceptDomainName, String codeSystemNameOrURI, String codeSystemVersion, SearchDesignationOption option, String matchAlgorithm, String language) throws LBException; - - /** - * Returns coded node set for concept domain entities. - * - * @param codeSystemNameOrURI concept domain coding scheme name or URI - * @param codeSystemVersion concept domain coding scheme version - * @return codedNodeSet of concept domain entities - * @throws LBException - */ - public CodedNodeSet getConceptDomainCodedNodeSet(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Gets all the concept domain found in the system as entities. - * - * @param codeSystemNameOrURI concept domain coding scheme name or URI - * @param codeSystemVersion concept domain coding scheme version - * @return List of concept domain entities - * @throws LBException - */ - public List listAllConceptDomainEntities(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns all the concept domain identifiers found in the system. - * - * @param codeSystemNameOrURI concept domain coding scheme name or URI - * @param codeSystemVersion concept domain coding scheme version - * @return List of concept domain identifiers - * @throws LBException - */ - public List listAllConceptDomainIds(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns list of value set definition URIs that are bound to given concept domain. - * - * @param conceptDomainId - - * Identifier of the concept domain - * @param codeSystemNameOrURI - - * coding scheme name or URI to which the concept domain belongs to - * @return list of value set definition URIs - * @throws LBException - */ - public List getConceptDomainBindings(String conceptDomainId, String codeSystemNameOrURI) throws LBException; - - /** - * Determines whether the supplied coded concept exists in a code system in use for the specified concept domain, - * optionally within specific usage contexts. - * - * Returns true if a coded concept is an element of a value set expansion bound to the provided concept domain, - * or bound to both concept domain and usage context. - * - * @param conceptDomainId - id of concept domain - * @param namespace - code system namespace - * @param codeSystemNameOrURI - concept domain code system name or URI - * @param entityCode - entity code to check if it participates in concept domain - * @param codingSchemeVersionList - list of coding scheme URI and version that contains the entity code - * and to be used to resolve. - * @param usageContext - (Optional) list of usage context - * @return list of value set definition URIs that are bound to concept domain (and usageContext) - * and that contains given entity code. - * @throws LBException - */ - public List isEntityInConceptDomain(String conceptDomainId, String namespace, String codeSystemNameOrURI, String entityCode, AbsoluteCodingSchemeVersionReferenceList codingSchemeVersionList, List usageContext) - throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/ConceptDomainQueryOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/ConceptDomainQueryOperationImpl.java deleted file mode 100644 index 2ff9ef8c94..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/ConceptDomainQueryOperationImpl.java +++ /dev/null @@ -1,154 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBParameterException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.concepts.Entity; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexevs.system.service.SystemResourceService; -import org.lexgrid.conceptdomain.LexEVSConceptDomainServices; -import org.lexgrid.conceptdomain.impl.LexEVSConceptDomainServicesImpl; - -/** - * LexEVS Implementation of CTS2 Concept Domain Query Operation. - * - * @author Sridhar Dwarkanath - */ -public class ConceptDomainQueryOperationImpl implements - ConceptDomainQueryOperation { - - private transient LexEVSConceptDomainServices cdServ_; - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#getConceptDomainBindings(java.lang.String, java.lang.String) - */ - @Override - public List getConceptDomainBindings(String conceptDomainId, - String codeSystemNameOrURI) throws LBException { - return getLexEVSConceptDomainServices().getConceptDomainBindings(conceptDomainId, codeSystemNameOrURI); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#getConceptDomainCodedNodeSet(java.lang.String, java.lang.String) - */ - @Override - public CodedNodeSet getConceptDomainCodedNodeSet( - String codeSystemNameOrURI, String codeSystemVersion) throws LBException { - return getLexEVSConceptDomainServices().getConceptDomainCodedNodeSet( - codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#getConceptDomainCodingScheme(java.lang.String, java.lang.String) - */ - @Override - public CodingScheme getConceptDomainCodingScheme( - String codeSystemNameOrURI, String codeSystemVersion) throws LBException { - return getLexEVSConceptDomainServices().getConceptDomainCodingScheme( - codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#getConceptDomainEntitisWithName(java.lang.String, java.lang.String, java.lang.String, org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption, java.lang.String, java.lang.String) - */ - @Override - public List getConceptDomainEntitisWithName( - String conceptDomainName, String codeSystemNameOrURI, String codeSystemVersion, - SearchDesignationOption option, String matchAlgorithm, - String language) throws LBException { - return getLexEVSConceptDomainServices().getConceptDomainEntitisWithName(conceptDomainName, - codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion), - option, matchAlgorithm, language); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#getConceptDomainEntity(java.lang.String, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public Entity getConceptDomainEntity(String conceptDomainId, String namespace, - String codeSystemNameOrURI, String codeSystemVersion) throws LBException { - return getLexEVSConceptDomainServices().getConceptDomainEntity(conceptDomainId, namespace, - codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#isEntityInConceptDomain(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList, java.util.List) - */ - @Override - public List isEntityInConceptDomain(String conceptDomainId, String namespace, String codeSystemNameOrURI, - String entityCode, AbsoluteCodingSchemeVersionReferenceList codingSchemeVersionList, - List usageContext) throws LBException { - return getLexEVSConceptDomainServices().isEntityInConceptDomain(conceptDomainId, namespace, getCodeSystemURI(codeSystemNameOrURI), - entityCode, codingSchemeVersionList, usageContext); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#listAllConceptDomainEntities(java.lang.String, java.lang.String) - */ - @Override - public List listAllConceptDomainEntities( - String codeSystemNameOrURI, String codeSystemVersion) throws LBException { - return getLexEVSConceptDomainServices().listAllConceptDomainEntities( - codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ConceptDomainQueryOperation#listAllConceptDomainIds(java.lang.String, java.lang.String) - */ - @Override - public List listAllConceptDomainIds( - String codeSystemNameOrURI, String codeSystemVersion) throws LBException { - return getLexEVSConceptDomainServices().listAllConceptDomainIds( - codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /** - * Gets the LexEVS concept domain services. - * - * @return the LexEVS concept domain services - */ - private LexEVSConceptDomainServices getLexEVSConceptDomainServices() { - if (cdServ_ == null) - cdServ_ = LexEVSConceptDomainServicesImpl.defaultInstance(); - - return cdServ_; - } - - private String getCodeSystemURI(String codeSystemNameOrUri) throws LBParameterException{ - SystemResourceService systemResourceService = LexEvsServiceLocator.getInstance().getSystemResourceService(); - - return systemResourceService.getUriForUserCodingSchemeName(codeSystemNameOrUri, null); - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/QueryOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/QueryOperation.java deleted file mode 100644 index 1485f7629e..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/QueryOperation.java +++ /dev/null @@ -1,61 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -/** - * LexEVS implementation of CTS2 Query Operations. - * - * @author Sridhar Dwarkanath - */ -public interface QueryOperation { - /** - * Returns Association Query Operation interface. - * - * @return AssociationQueryOperation - */ - public AssociationQueryOperation getAssociationQueryOperation(); - - /** - * Returns Code System Query Operation interface. - * - * @return CodeSystemQueryOperation - */ - public CodeSystemQueryOperation getCodeSystemQueryOperation(); - - /** - * Returns Concept Domain Query Operation interface. - * - * @return ConceptDomainQueryOperation - */ - public ConceptDomainQueryOperation getConceptDomainQueryOperation(); - - /** - * Returns Usage Context Query Operation interface. - * - * @return UsageContextQueryOperation - */ - public UsageContextQueryOperation getUsageContextQueryOperation(); - - /** - * Returns Value Set Query Operation interface. - * - * @return ValueSetQueryOperation - */ - public ValueSetQueryOperation getValueSetQueryOperation(); -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/QueryOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/QueryOperationImpl.java deleted file mode 100644 index bc937f3b87..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/QueryOperationImpl.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import org.lexevs.cts2.BaseService; - -/** - * Class returns individual CTS 2 Query Operation interfaces. - * - * @author Sridhar Dwarkanath - */ -public class QueryOperationImpl extends BaseService implements QueryOperation { - private transient ValueSetQueryOperation valueSetQueryOp_; - private transient ConceptDomainQueryOperation conceptDomainQueryOp_; - private transient UsageContextQueryOperation usageContextQueryOp_; - private transient AssociationQueryOperation assnQueryOp_; - private transient CodeSystemQueryOperation codeSystemQueryOp_; - - /* (non-Javadoc) - * @see org.lexevs.cts2.query.QueryOperation#getAssociationQueryOperation() - */ - @Override - public AssociationQueryOperation getAssociationQueryOperation() { - if (assnQueryOp_ == null) - assnQueryOp_ = new AssociationQueryOperationImpl(); - return assnQueryOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.query.QueryOperation#getCodeSystemQueryOperation() - */ - @Override - public CodeSystemQueryOperation getCodeSystemQueryOperation() { - if (codeSystemQueryOp_ == null) - codeSystemQueryOp_ = new CodeSystemQueryOperationImpl(); - return codeSystemQueryOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.query.QueryOperation#getConceptDomainQueryOperation() - */ - @Override - public ConceptDomainQueryOperation getConceptDomainQueryOperation() { - if (conceptDomainQueryOp_ == null) - conceptDomainQueryOp_ = new ConceptDomainQueryOperationImpl(); - - return conceptDomainQueryOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.query.QueryOperation#getUsageContextQueryOperation() - */ - @Override - public UsageContextQueryOperation getUsageContextQueryOperation() { - if (usageContextQueryOp_ == null) - usageContextQueryOp_ = new UsageContextQueryOperationImpl(); - - return usageContextQueryOp_; - } - - /* (non-Javadoc) - * @see org.lexevs.cts2.query.QueryOperation#getValueSetQueryOperation() - */ - @Override - public ValueSetQueryOperation getValueSetQueryOperation() { - if (valueSetQueryOp_ == null) - valueSetQueryOp_ = new ValueSetQueryOperationImpl(); - return valueSetQueryOp_; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/UsageContextQueryOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/UsageContextQueryOperation.java deleted file mode 100644 index b420f9f869..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/UsageContextQueryOperation.java +++ /dev/null @@ -1,113 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.concepts.Entity; - -/** - * LexEVS Implementation of CTS2 Usage Context Query Operation. - * - * @author Sridhar Dwarkanath - */ -public interface UsageContextQueryOperation { - /** - * Gets the Usage Context coding scheme. - * @param codeSystemNameOrURI usageContext code system name or URI - * @param codeSystemVersion usageContext coding scheme version - * @return the usage context coding scheme - * @throws LBException - */ - public CodingScheme getUsageContextCodingScheme(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns UsageContext entity object with usageContextId. - * - * @param usageContextId id of usage context - * @param namespace of usage context - * @param codeSystemNameOrURI usageContext code system name or URI - * @param codeSystemVersion usageContext coding scheme version - * @return usage context entity object - * @throws LBException - */ - public Entity getUsageContextEntity(String usageContextId, String namespace, String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns list of usage context entities matching the name provided. - * @param usageContextName - * match name of usage context - * @param codeSystemNameOrURI - * usageContext code system name or URI - * @param codeSystemVersion - * usageContext code system version - * @param option - * Indicates the designations to search (one of the enumerated - * type SearchDesignationOption). - * @param matchAlgorithm - * Local name of the match algorithm - possible algorithms are - * returned in LexBigService.getMatchAlgorithms(). - * @param language - * Language of search string. If missing, use the default - * language specified in the context. - * @return list of entities containing matching concept domain name - * @throws LBException - */ - public List getUsageContextEntitisWithName(String usageContextName, String codeSystemNameOrURI, String codeSystemVersion, SearchDesignationOption option, String matchAlgorithm, String language) throws LBException; - - /** - * Returns coded node set for usage context entities. - * - * @param codeSystemNameOrURI - * usageContext code system name or URI - * @param codeSystemVersion - * usageContext coding scheme version - * @return codedNodeSet of usageContext entities - * @throws LBException - */ - public CodedNodeSet getUsageContextCodedNodeSet(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Gets all the usage context found in the system as entities. - * - * @param codeSystemNameOrURI - * usageContext code system name or URI - * @param codeSystemVersion - * usageContext coding scheme version - * @return List of usage context entities - * @throws LBException - */ - public List listAllUsageContextEntities(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; - - /** - * Returns all the usage context identifiers found in the system. - * - * @param codeSystemNameOrURI - * usageContext code system name or URI - * @param codeSystemVersion - * usageContext coding scheme version - * @return List of usage context identifiers - * @throws LBException - */ - public List listAllUsageContextIds(String codeSystemNameOrURI, String codeSystemVersion) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/UsageContextQueryOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/UsageContextQueryOperationImpl.java deleted file mode 100644 index 12d3bef2f9..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/UsageContextQueryOperationImpl.java +++ /dev/null @@ -1,117 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.util.List; - -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.concepts.Entity; -import org.lexgrid.usagecontext.LexEVSUsageContextServices; -import org.lexgrid.usagecontext.impl.LexEVSUsageContextServicesImpl; - -/** - * Implementation of LexEVS CTS2 Usage Context Query Operation. - * - * @author Sridhar Dwarkanath - */ -public class UsageContextQueryOperationImpl implements - UsageContextQueryOperation { - private transient LexEVSUsageContextServices ucServ_; - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.UsageContextQueryOperation#getUsageContextCodedNodeSet(java.lang.String, java.lang.String) - */ - @Override - public CodedNodeSet getUsageContextCodedNodeSet(String codeSystemNameOrURI, - String codeSystemVersion) throws LBException { - return getLexEVSUsageContextServices().getUsageContextCodedNodeSet(codeSystemNameOrURI, Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.UsageContextQueryOperation#getUsageContextCodingScheme(java.lang.String, java.lang.String) - */ - @Override - public CodingScheme getUsageContextCodingScheme(String codeSystemNameOrURI, - String codeSystemVersion) throws LBException { - return getLexEVSUsageContextServices().getUsageContextCodingScheme(codeSystemNameOrURI, - Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.UsageContextQueryOperation#getUsageContextEntitisWithName(java.lang.String, java.lang.String, java.lang.String, org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption, java.lang.String, java.lang.String) - */ - @Override - public List getUsageContextEntitisWithName(String usageContextName, String codeSystemNameOrURI, String codeSystemVersion, - SearchDesignationOption option, String matchAlgorithm, String language) throws LBException { - return getLexEVSUsageContextServices().getUsageContextEntitisWithName(usageContextName, codeSystemNameOrURI, - Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion), option, matchAlgorithm, language); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.UsageContextQueryOperation#getUsageContextEntity(java.lang.String, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public Entity getUsageContextEntity(String usageContextId, String namespace, String codeSystemNameOrURI, - String codeSystemVersion) throws LBException { - return getLexEVSUsageContextServices().getUsageContextEntity(usageContextId, namespace, codeSystemNameOrURI, - Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.UsageContextQueryOperation#listAllUsageContextEntities(java.lang.String, java.lang.String) - */ - @Override - public List listAllUsageContextEntities(String codeSystemNameOrURI, - String codeSystemVersion) throws LBException { - return getLexEVSUsageContextServices().listAllUsageContextEntities(codeSystemNameOrURI, - Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.UsageContextQueryOperation#listAllUsageContextIds(java.lang.String, java.lang.String) - */ - @Override - public List listAllUsageContextIds(String codeSystemNameOrURI, - String codeSystemVersion) throws LBException { - return getLexEVSUsageContextServices().listAllUsageContextIds(codeSystemNameOrURI, - Constructors.createCodingSchemeVersionOrTag(null, codeSystemVersion)); - } - - /** - * Gets the LexEVS usage context services. - * - * @return the LexEVS usage context services - */ - private LexEVSUsageContextServices getLexEVSUsageContextServices() { - if (ucServ_ == null) - ucServ_ = LexEVSUsageContextServicesImpl.defaultInstance(); - - return ucServ_; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/ValueSetQueryOperation.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/ValueSetQueryOperation.java deleted file mode 100644 index c7700d830c..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/ValueSetQueryOperation.java +++ /dev/null @@ -1,129 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.net.URI; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.SortOption; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.lexgrid.valuesets.dto.ResolvedValueSetDefinition; - -/** - * LexEVS Implementation of CTS2 Value Set Query Operation. - * - * @author Sridhar Dwarkanath - */ -public interface ValueSetQueryOperation { - - /** - * Lists the value sets that are available to the CTS 2 service. - * @param codeSystemId (Optional) code system id the value set should reference - * @param conceptDomainId (Optional) conceptDomain the value set should be bound to - * @param usageContextId (Optional) usage context, the value set can be used - * @param codeSystemURI URI of code system the codeSystemId or conceptDomainId or usageContextId belongs to - * @param sortOption Ascending or Descending the return list of value set identifiers - * @return List of value set identifiers - * @throws LBException - */ - public List listValueSets(String codeSystemId, String conceptDomainId, String usageContextId, String codeSystemURI, SortOption sortOption) throws LBException; - - /** - * Lists all the value sets that are available to the CTS 2 service. - * @param sortOption Ascending or Descending the return list of value set identifiers - * @return List of value set identifiers - * @throws LBException - */ - public List listAllValueSets(SortOption sortOption) throws LBException; - - /** - * Returns detailed information (meta data) for a given value set. - * @param valueSetId id of the value set - * @param valueSetVersion (Optional) version of the value set - * @return object ValueSetDefinition - * @throws LBException - */ - public ValueSetDefinition getValueSetDetails(String valueSetId, String valueSetVersion) throws LBException; - - /** - * Lists out the contents (entries) of a given value set, filtering based - * on input criteria. This function is to be used to create the value set expansion. - * - * @param valueSetId id of value set - * @param valueSetVersion (Optional) version of value set - * @param csVersionList code system version reference list to be used to resolve value set - * @param versionTag the tag (e.g. "devel", "production", ...) to be used to determine which code system to be used - * @param sortOption (Optional) sort option to apply on resolved concepts - * @return A resolved Value Set definition containing the code system version reference list - * that was used to resolve the value set and an iterator for resolved concepts. - * @throws LBException - */ - public ResolvedValueSetDefinition listValueSetContents(String valueSetId, String valueSetVersion, AbsoluteCodingSchemeVersionReferenceList csVersionList, - String versionTag, SortOption sortOption) throws LBException; - - - /** - * Determine whether one of the two supplied value sets subsumes the other. - * - * @param childValueSetId child value set id - * @param childValueSetVersion (Optional) child value set version - * @param parentValueSetId parent value set id - * @param parentValueSetVersion (Optional) parent value set version - * @param csVersionList list of code system versions to use in resolution. - * @param versionTag the tag (e.g. "devel", "production", ...) to be used to determine which code system to be used - * @return True; if childValueSet subsumes parentValueSet. False; otherwise. - * @throws LBException - */ - public boolean checkValueSetSubsumption(String childValueSetId, String childValueSetVersion, - String parentValueSetId, String parentValueSetVersion, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; - - /** - * Determine whether the supplied coded concept exists in the supplied value set . - * @param conceptCode coded concept id - * @param entityCodeNamespace the URI of the entity code namespace. If omitted, the default coding scheme namespace for the value domain - * will be used, if it is present. Otherwise the first matching entity code, if any, will pass - * @param codeSystemAndVersion code system and version reference to be used - * @param valueSetId value set id - * @param valueSetVersion (Optional) value set version - * @param versionTag the tag (e.g "devel", "production", ...) to be used to reconcile coding schemes when more than one is present. - * Note that non-tagged versions will be used if the tagged version is missing. - * @return True; if coded concept exists in value set. False; otherwise. - * @throws LBException - */ - public boolean checkConceptValueSetMembership(String conceptCode, URI entityCodeNamespace, AbsoluteCodingSchemeVersionReference codeSystemAndVersion, String valueSetId, String valueSetVersion, String versionTag) throws LBException; - - /** - * Returns all the value set definition uris that contains supplied concept code. - * - * @param conceptCode - coded concept id - * @param entityCodeNamespace - the URI of the entity code namespace. If omitted, the default coding scheme namespace for the value domain - * will be used, if it is present. Otherwise the first matching entity code, if any, will pass - * @param csVersionList - a list of coding scheme URI's and versions to be used. These will be used only if they are present in - * the service. If absent, the most recent version will be used instead. - * @param versionTag - the tag (e.g "devel", "production", ...) to be used to reconcile coding schemes when more than one is present. - * Note that non-tagged versions will be used if the tagged version is missing. - * @return The value set definition URIs - * @throws LBException - */ - public List listValueSetsWithConceptCode(String conceptCode, URI entityCodeNamespace, - AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; -} \ No newline at end of file diff --git a/cts2Impl/src/main/java/org/lexevs/cts2/query/ValueSetQueryOperationImpl.java b/cts2Impl/src/main/java/org/lexevs/cts2/query/ValueSetQueryOperationImpl.java deleted file mode 100644 index 6bd315358b..0000000000 --- a/cts2Impl/src/main/java/org/lexevs/cts2/query/ValueSetQueryOperationImpl.java +++ /dev/null @@ -1,259 +0,0 @@ -/* - * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.lexevs.cts2.query; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.Collections; -import java.util.List; - -import org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList; -import org.LexGrid.LexBIG.DataModel.Collections.SortOptionList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.SortOption; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBRevisionException; -import org.LexGrid.valueSets.ValueSetDefinition; -import org.apache.commons.lang.StringUtils; -import org.lexevs.dao.database.service.DatabaseServiceManager; -import org.lexevs.dao.database.service.valuesets.ValueSetDefinitionService; -import org.lexevs.locator.LexEvsServiceLocator; -import org.lexgrid.valuesets.LexEVSValueSetDefinitionServices; -import org.lexgrid.valuesets.dto.ResolvedValueSetDefinition; -import org.lexgrid.valuesets.impl.LexEVSValueSetDefinitionServicesImpl; - -/** - * LexEVS Implementation of CTS2 Value Set Query Operation. - * - * @author Sridhar Dwarkanath - */ -public class ValueSetQueryOperationImpl implements ValueSetQueryOperation { - private LexEVSValueSetDefinitionServices lexEVSValueSetService_; - private ValueSetDefinitionService vsdDBService_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getValueSetDefinitionService(); - private DatabaseServiceManager databaseServiceManager_ = LexEvsServiceLocator.getInstance().getDatabaseServiceManager(); - - /* (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#checkConceptValueSetMembership(java.lang.String, java.net.URI, org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference, java.lang.String, java.lang.String, java.lang.String) - */ - @Override - public boolean checkConceptValueSetMembership(String conceptCode, URI entityCodeNamespace, - AbsoluteCodingSchemeVersionReference codeSystemAndVersion, - String valueSetId, String valueSetVersion, String versionTag) throws LBException { - if (StringUtils.isEmpty(conceptCode) || StringUtils.isEmpty(valueSetId) || codeSystemAndVersion == null) - { - throw new LBException("Invalid parametes. ConceptCode, codeSystemAndVersion or ValueSetId can not be empty"); - } - - if (!validateCodeSystem(codeSystemAndVersion.getCodingSchemeURN(), codeSystemAndVersion.getCodingSchemeVersion())) - { - throw new LBException("No code system found with id : '" + codeSystemAndVersion.getCodingSchemeURN() + - "' and version : '" + codeSystemAndVersion.getCodingSchemeVersion() + "'"); - } - - if (!validateValueSet(valueSetId, valueSetVersion)) - { - throw new LBException("No Value Set found with id : '" + valueSetId + - "' and version : '" + valueSetVersion + "'"); - } - - AbsoluteCodingSchemeVersionReferenceList csVersionList = new AbsoluteCodingSchemeVersionReferenceList(); - csVersionList.addAbsoluteCodingSchemeVersionReference(codeSystemAndVersion); - - try { - AbsoluteCodingSchemeVersionReference csVersion = getValueSetService().isEntityInValueSet(conceptCode, entityCodeNamespace, new URI(valueSetId), valueSetVersion, csVersionList, versionTag); - if (csVersion != null && csVersion.getCodingSchemeURN() != null) - return true; - } catch (URISyntaxException e) { - throw new LBException("Problem processing Value Set Query Operation : ", e); - } - return false; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#listValueSetsWithConceptCode(java.lang.String, java.net.URI, org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList, java.lang.String) - */ - public List listValueSetsWithConceptCode(String conceptCode, URI entityCodeNamespace, - AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException { - if (StringUtils.isEmpty(conceptCode)) - { - throw new LBException("Invalid parametes. ConceptCode can not be empty"); - } - - return getValueSetService().listValueSetsWithEntityCode(conceptCode, entityCodeNamespace, csVersionList, versionTag); - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#checkValueSetSubsumption(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList, java.lang.String) - */ - @Override - public boolean checkValueSetSubsumption(String childValueSetId, - String childValueSetVersion, String parentValueSetId, - String parentValueSetVersion, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException { - - if (StringUtils.isEmpty(childValueSetId)) - throw new LBException("Invalid parameters. ChildValueSetId can not be empty"); - - if (StringUtils.isEmpty(parentValueSetId)) - throw new LBException("Invalid parameters. ParentValueSetId can not be empty"); - - boolean isSubset = false; - try { - isSubset = getValueSetService().isSubSet(new URI(childValueSetId), new URI(parentValueSetId), csVersionList, versionTag); - } catch (URISyntaxException e) { - throw new LBException("Problem processing Value Set Query Operation : ", e); - } - return isSubset; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#getValueSetDetails(java.lang.String, java.lang.String) - */ - @Override - public ValueSetDefinition getValueSetDetails(String valueSetId, - String valueSetVersion) throws LBException { - if (StringUtils.isEmpty(valueSetId)) - throw new LBException("Invalid parameters. valueSetId can not be empty"); - ValueSetDefinition vsd = null; - try { - vsd = getValueSetService().getValueSetDefinition(new URI(valueSetId), valueSetVersion); - } catch (URISyntaxException e) { - throw new LBException("Problem processing Value Set Query Operation : ", e); - } - return vsd; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#listValueSetContents(java.lang.String, java.lang.String, org.LexGrid.LexBIG.DataModel.Collections.AbsoluteCodingSchemeVersionReferenceList, java.lang.String, org.LexGrid.LexBIG.DataModel.InterfaceElements.SortOption) - */ - @Override - public ResolvedValueSetDefinition listValueSetContents(String valueSetId, - String valueSetVersion,AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag, - SortOption sortOption) throws LBException { - if (StringUtils.isEmpty(valueSetId)) - throw new LBException("Invalid parameters. valueSetId can not be empty"); - - ResolvedValueSetDefinition vsContents = null; - SortOptionList sortOptionList = null; - - if (sortOption != null) - { - sortOptionList = new SortOptionList(); - sortOptionList.addEntry(sortOption); - } - try { - vsContents = getValueSetService().resolveValueSetDefinition(new URI(valueSetId), valueSetVersion, csVersionList, versionTag, sortOptionList); - } catch (URISyntaxException e) { - throw new LBException("Problem processing Value Set Query Operation : ", e); - } - return vsContents; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#listValueSets(java.lang.String, java.lang.String, java.lang.String, java.lang.String, org.LexGrid.LexBIG.DataModel.InterfaceElements.SortOption) - */ - @Override - public List listValueSets(String codeSystemId, - String conceptDomainId, String usageContextId, String codeSystemURI, SortOption sortOption) - throws LBException { - List finalList = getValueSetService().listValueSetDefinitionURIs(); - - if (StringUtils.isNotEmpty(codeSystemId)) - { - finalList.retainAll(getValueSetService().getValueSetDefinitionURIsWithCodingScheme(codeSystemId, codeSystemURI)); - } - - if (StringUtils.isNotEmpty(conceptDomainId)) - { - finalList.retainAll(getValueSetService().getValueSetDefinitionURIsWithConceptDomain(conceptDomainId, codeSystemURI)); - } - - if (StringUtils.isNotEmpty(usageContextId)) - { - finalList.retainAll(getValueSetService().getValueSetDefinitionURIsWithConceptDomain(usageContextId, codeSystemURI)); - } - - if (sortOption != null && finalList != null) - { - if (sortOption.isAscending()) - Collections.sort(finalList, String.CASE_INSENSITIVE_ORDER); - else - Collections.sort(finalList, Collections.reverseOrder()); - } - return finalList; - } - - /* - * (non-Javadoc) - * @see org.lexevs.cts2.query.ValueSetQueryOperation#listAllValueSets(org.LexGrid.LexBIG.DataModel.InterfaceElements.SortOption) - */ - @Override - public List listAllValueSets(SortOption sortOption) - throws LBException { - List vsdURIs = getValueSetService().listValueSetDefinitionURIs(); - - if (sortOption != null) - { - if (sortOption.isAscending()) - Collections.sort(vsdURIs, String.CASE_INSENSITIVE_ORDER); - else - Collections.sort(vsdURIs, Collections.reverseOrder()); - } - return vsdURIs; - } - - private boolean validateCodeSystem(String csURI, String csVersion){ - CodingSchemeSummary csSummary = databaseServiceManager_.getCodingSchemeService(). - getCodingSchemeSummaryByUriAndVersion(csURI, csVersion); - - if (csSummary == null) - return false; - - return true; - } - - private boolean validateValueSet(String vsID, String vsVersion) throws LBRevisionException{ - ValueSetDefinition vsd = null; - try { - if (StringUtils.isNotEmpty(vsVersion)) - vsd = vsdDBService_.getValueSetDefinitionByRevision(vsID, vsVersion); - else - vsd = vsdDBService_.getValueSetDefinitionByUri(new URI(vsID)); - } catch (URISyntaxException e) { - e.printStackTrace(); - } - - if (vsd == null) - return false; - - return true; - } - - private LexEVSValueSetDefinitionServices getValueSetService(){ - if (lexEVSValueSetService_ == null) - lexEVSValueSetService_ = LexEVSValueSetDefinitionServicesImpl.defaultInstance(); - - return lexEVSValueSetService_; - } -} \ No newline at end of file diff --git a/cts2Impl/src/main/resources/cts2-application-config.xml b/cts2Impl/src/main/resources/cts2-application-config.xml deleted file mode 100755 index 501d27543e..0000000000 --- a/cts2Impl/src/main/resources/cts2-application-config.xml +++ /dev/null @@ -1,326 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/cts2Impl/src/main/resources/mapper/dozer/associationMapper.xml b/cts2Impl/src/main/resources/mapper/dozer/associationMapper.xml deleted file mode 100644 index 80d15fd568..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/associationMapper.xml +++ /dev/null @@ -1,181 +0,0 @@ - - - - - org.LexGrid.LexBIG.DataModel.Core.Association - org.cts2.association.Association - - associationName - predicate.content - - - - org.LexGrid.naming.SupportedCodingScheme - org.cts2.association.Association - - uri - predicate.meaning - - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - - org.cts2.association.Association - - entity.entityCode - subject.localEntityName.name - - - entity.entityCodeNamespace - subject.localEntityName.namespace - - - - org.LexGrid.codingSchemes.CodingScheme - org.cts2.association.Association - - codingSchemeURI - assertedBy.meaning - - - codingSchemeName - assertedBy.content - - - codingSchemeURI - assertedIn.meaning - - - codingSchemeName - assertedIn.content - - - - org.LexGrid.LexBIG.DataModel.Core.AssociatedConcept - org.cts2.association.Association - - referencedEntry.entityCode - target.entity.localEntityName.name - - - referencedEntry.entityCodeNamespace - target.entity.localEntityName.namespace - - - - - org.LexGrid.LexBIG.DataModel.Core.AssociatedData - org.cts2.association.Association - - id - externalStatementId - - - - - org.LexGrid.LexBIG.DataModel.Core.Association - org.cts2.association.AssociationDirectoryEntry - - associationName - predicate.content - - - - org.LexGrid.naming.SupportedCodingScheme - org.cts2.association.AssociationDirectoryEntry - - uri - predicate.meaning - - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - - org.cts2.association.AssociationDirectoryEntry - - entity.entityCode - subject.localEntityName.name - - - entity.entityCodeNamespace - subject.localEntityName.namespace - - - - org.LexGrid.codingSchemes.CodingScheme - org.cts2.association.AssociationDirectoryEntry - - codingSchemeURI - assertedBy.meaning - - - codingSchemeName - assertedBy.content - - - - org.LexGrid.LexBIG.DataModel.Core.AssociatedConcept - org.cts2.association.AssociationDirectoryEntry - - referencedEntry.entityCode - target.entity.localEntityName.name - - - referencedEntry.entityCodeNamespace - target.entity.localEntityName.namespace - - - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - - org.cts2.association.AssociationGraph - - entity.entityCode - focusEntity.localEntityName.name - - - entity.entityCodeNamespace - focusEntity.localEntityName.namespace - - - - org.LexGrid.LexBIG.DataModel.Core.Association - org.cts2.association.GraphNode - - associationName - predicate.content - - - - org.LexGrid.LexBIG.DataModel.Core.AssociatedConcept - org.cts2.association.GraphNode - - referencedEntry.entityCode - target.entity.localEntityName.name - - - referencedEntry.entityCodeNamespace - target.entity.localEntityName.namespace - - - - org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList - org.cts2.association.AssociationDirectory - - resolvedConceptReference - entry - - - - - org.LexGrid.relations.AssociationEntity - org.cts2.association.Association - - entityCode - externalStatementId - - - \ No newline at end of file diff --git a/cts2Impl/src/main/resources/mapper/dozer/codeSystemMapper.xml b/cts2Impl/src/main/resources/mapper/dozer/codeSystemMapper.xml deleted file mode 100644 index 44f04f8885..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/codeSystemMapper.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - - - org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList - org.cts2.codesystem.CodeSystemDirectory - - - codingSchemeRendering - entry - - - - - org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering - org.cts2.codesystem.CodeSystemDirectoryEntry - - - codingSchemeSummary.codingSchemeURI - about - - - - codingSchemeSummary.codingSchemeDescription - resourceSynopsis - - - - - - org.LexGrid.commonTypes.Property - org.cts2.core.Property - - - propertyName - externalIdentifier - - - - - - - this - sourceCodingSchemeVersion.codeSystem.content - - - value.content - value.value - - - - - org.LexGrid.commonTypes.Source - org.cts2.core.SourceAndRoleReference - - content - content - - - role - role.content - - - - - org.LexGrid.codingSchemes.CodingScheme - org.cts2.core.ChangeDescription - - - entryState.changeType - changeType - - - effectiveDate - effectiveDate - - - diff --git a/cts2Impl/src/main/resources/mapper/dozer/codeSystemVersionMapper.xml b/cts2Impl/src/main/resources/mapper/dozer/codeSystemVersionMapper.xml deleted file mode 100644 index aef15418da..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/codeSystemVersionMapper.xml +++ /dev/null @@ -1,92 +0,0 @@ - - - - - org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList - org.cts2.codesystemversion.CodeSystemVersionDirectory - - - codingSchemeRendering - entry - - - - - org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering - org.cts2.codesystemversion.CodeSystemVersionDirectoryEntry - - - codingSchemeSummary.codingSchemeURI - about - - - - codingSchemeSummary.representsVersion - officialResourceVersionId - - - - this - this - - - - codingSchemeSummary.formalName - formalName - - - - codingSchemeSummary.codingSchemeDescription - resourceSynopsis - - - - _renderingDetail._versionTags._tagList - _codeSystemVersionTagList - - - - - org.LexGrid.codingSchemes.CodingScheme - org.cts2.codesystemversion.CodeSystemVersion - - - codingSchemeURI - about - - - - formalName - formalName - - - - localName - keyword - - - - representsVersion - officialResourceVersionId - - - - this - this - - - - this - this - - - - this - this - - - - - diff --git a/cts2Impl/src/main/resources/mapper/dozer/configuration.xml b/cts2Impl/src/main/resources/mapper/dozer/configuration.xml deleted file mode 100644 index 1164f1177b..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/configuration.xml +++ /dev/null @@ -1,32 +0,0 @@ - - - - true - true - - - - org.LexGrid.valueSets.types.DefinitionOperator - org.cts2.core.types.SetOperator - - - - java.lang.Boolean - org.cts2.core.types.EntryState - - - - org.LexGrid.valueSets.DefinitionEntry - org.cts2.valueset.ValueSetDefinitionEntry - - - org.LexGrid.versions.types.ChangeType - org.cts2.core.types.ChangeType - - - - - - \ No newline at end of file diff --git a/cts2Impl/src/main/resources/mapper/dozer/coreMapper.xml b/cts2Impl/src/main/resources/mapper/dozer/coreMapper.xml deleted file mode 100644 index 969c3096df..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/coreMapper.xml +++ /dev/null @@ -1,101 +0,0 @@ - - - - - org.LexGrid.commonTypes.EntityDescription - org.cts2.core.EntryDescription - - - content - value - - - - - org.LexGrid.commonTypes.VersionableAndDescribable - org.cts2.core.ResourceDescription - - - entityDescription - resourceSynopsis - - - - - org.LexGrid.commonTypes.Describable - org.cts2.core.ResourceDescription - - - entityDescription - resourceSynopsis - - - - - - org.LexGrid.commonTypes.Versionable - org.cts2.core.Changeable - - - isActive - entryState - - - - - org.LexGrid.commonTypes.VersionableAndDescribable - org.cts2.core.Changeable - - - status - status.content - - - owner - owner.content - - - effectiveDate - changeDescription.effectiveDate - - - entryState.changeType - changeDescription.changeType - - - entryState.containingRevision - changeDescription.containingChangeSet - - - entryState.prevRevision - changeDescription.prevChangeSet - - - - - java.lang.String - org.cts2.core.VersionTagReference - - - this - content - - - - - org.LexGrid.commonTypes.Source - org.cts2.core.SourceAndRoleReference - - - content - content - - - role - role.content - - - - diff --git a/cts2Impl/src/main/resources/mapper/dozer/entityDescriptionMapper.xml b/cts2Impl/src/main/resources/mapper/dozer/entityDescriptionMapper.xml deleted file mode 100644 index f97a124af6..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/entityDescriptionMapper.xml +++ /dev/null @@ -1,384 +0,0 @@ - - - - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - org.cts2.entity.NamedIndividualDescription - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - org.cts2.entity.AnonymousIndividualDescription - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - org.cts2.entity.EntityDirectoryEntry - - code - resourceName - - - code - localEntityName.name - - - codeNamespace - localEntityName.namespace - - - this - this - - - - - - - - - - - - - - - - - - - - - - - - - - - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - org.cts2.entity.AnonymousEntityDescription - - code - entityId.name - - - codeNamespace - entityId.namespace - - - codingSchemeURI - describingCodeSystemVersion.meaning - - - codingSchemeName - describingCodeSystemVersion.content - - - this - this - - - this - this - - - this - this - - - this - this - - - this - this - - - - org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference - org.cts2.entity.NamedEntityDescription - - - - - - - code - entityId.name - - - codeNamespace - entityId.namespace - - - codingSchemeURI - describingCodeSystemVersion.meaning - - - codingSchemeName - describingCodeSystemVersion.content - - - this - this - - - this - this - - - this - this - - - this - this - - - this - this - - - - - - - - - - - - - - - - - - - - - - - - - - - - - org.LexGrid.concepts.Presentation - org.cts2.entity.Designation - - degreeOfFidelity - degreeOfFidelity.content - - - language - language.content - - - propertyId - externalIdentifier - - - value.content - value - - - this - this - - - value.dataType - format.content - - - propertyName - designationType.content - - - this - this - - - - - - - - - - - - - - - - - - - - org.LexGrid.concepts.Definition - org.cts2.core.Definition - - - - - - - - - - - propertyId - externalIdentifier - - - language - language.content - - - value.content - value - - - value.dataType - format.content - - - this - this - - - this - this - - - - - - - - - - - - - org.LexGrid.concepts.Comment - org.cts2.core.Comment - - propertyId - externalIdentifier - - - value.content - value - - - language - language.content - - - value.dataType - format.content - - - - - - org.LexGrid.commonTypes.Property - org.cts2.core.Property - - propertyId - externalIdentifier - - - value.content - value.value - - - value.dataType - value.format.content - - - language - value.language.content - - - - \ No newline at end of file diff --git a/cts2Impl/src/main/resources/mapper/dozer/valueSetMapper.xml b/cts2Impl/src/main/resources/mapper/dozer/valueSetMapper.xml deleted file mode 100644 index 55bd8ee3ca..0000000000 --- a/cts2Impl/src/main/resources/mapper/dozer/valueSetMapper.xml +++ /dev/null @@ -1,127 +0,0 @@ - - - - - org.LexGrid.valueSets.ValueSetDefinition - org.cts2.valueset.ValueSetDefinition - - - valueSetDefinitionURI - about - - - valueSetDefinitionURI - formalName - - - definitionEntry - entry - - - valueSetDefinitionURI - definedValueSet.content - - - _properties._propertyList - _propertyList - - - status - status.content - - - owner - owner.content - - - effectiveDate - changeDescription.effectiveDate - - - - - - - - - - - - - - - source - source - - - - - org.LexGrid.valueSets.ValueSetDefinition - org.cts2.core.ValueSetReference - - - valueSetDefinitionURI - content - - - - - - org.LexGrid.valueSets.ValueSetDefinitions - org.cts2.valueset.ValueSetDefinitionDirectory - - - valueSetDefinition - entry - - - - - org.LexGrid.valueSets.ValueSetDefinition - org.cts2.valueset.ValueSetDefinitionDirectoryEntry - - - valueSetDefinitionURI - definedValueSet.content - - - valueSetDefinitionURI - about - - - valueSetDefinitionURI - resourceID - - - valueSetDefinitionName - formalName - - - entityDescription.content - resourceSynopsis.value - - - - - org.LexGrid.valueSets.ValueSetDefinitions - org.cts2.valueset.ValueSetDefinitionList - - - valueSetDefinition - entry - - - - - org.LexGrid.valueSets.ValueSetDefinition - org.cts2.valueset.ValueSetDefinitionListEntry - - - this - item - - - - \ No newline at end of file diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/ProfileUtilsTest.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/ProfileUtilsTest.java deleted file mode 100644 index 1c0a96ad01..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/ProfileUtilsTest.java +++ /dev/null @@ -1,46 +0,0 @@ -package org.cts2.internal.profile; - -import static org.junit.Assert.*; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Collections.AssociatedConceptList; -import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.AssociatedConcept; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.cts2.test.BaseCts2IntegrationTest; -import org.junit.Test; - - -public class ProfileUtilsTest extends BaseCts2IntegrationTest{ - - @Resource - private LexBIGServiceImpl lexBigServiceImpl; - - - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void getAllGraphsFromTheService() throws LBException{ - - - CodedNodeGraph graph = ProfileUtils.unionAllGraphs(lexBigServiceImpl); - ResolvedConceptReferenceList list = graph.resolveAsList(null, true, false, 100, -1, null, null, null, null, -1); - ResolvedConceptReference[] array = list.getResolvedConceptReference(); - int count = 0; - for(ResolvedConceptReference rcr: array){ - AssociatedConceptList concepts = rcr.getSourceOf().getAssociation(0).getAssociatedConcepts(); - AssociatedConcept[] conceptArray = concepts.getAssociatedConcept(); - for(AssociatedConcept concept: conceptArray) - {count++;} - } - assertTrue(count > 0); - - } - - -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/author/LexEvsCodeSystemVersionAuthoringServiceTest.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/author/LexEvsCodeSystemVersionAuthoringServiceTest.java deleted file mode 100644 index 848d3a2ba6..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/author/LexEvsCodeSystemVersionAuthoringServiceTest.java +++ /dev/null @@ -1,49 +0,0 @@ -package org.cts2.internal.profile.author; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.cts2.service.codesystemversion.UpdateCodeSystemVersionRequest; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.utility.ConstructorUtils; -import org.junit.Test; - -public class LexEvsCodeSystemVersionAuthoringServiceTest extends - BaseCts2IntegrationTest { - - @Resource - private LexEvsCodeSystemVersionAuthoringService service; - - @Resource - private LexBIGService lbs; - - @Test - public void testSetUp(){ - assertNotNull(this.service); - } - - @Test - public void testCreateCodeSystemVersionCount() throws Exception { - this.service.createCodeSystemVersion("http://a.change.org", "http://mycsv.org", "testName", null, null); - - assertEquals(1, lbs.getSupportedCodingSchemes().getCodingSchemeRenderingCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testUpdateCodeSystemVersionFormalName() throws Exception { - UpdateCodeSystemVersionRequest request = new UpdateCodeSystemVersionRequest(); - request.setFormalName("updated formal name"); - - this.service.updateCodeSystemVersion( - ConstructorUtils.nameToNameOrURI("Automobiles:1.0"), request); - - assertEquals(1, this.lbs.getSupportedCodingSchemes().getCodingSchemeRenderingCount()); - assertEquals("updated formal name", - this.lbs.getSupportedCodingSchemes().getCodingSchemeRendering(0).getCodingSchemeSummary().getFormalName()); - } -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsAssociationQueryServiceTestIT.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsAssociationQueryServiceTestIT.java deleted file mode 100644 index 97ecb57298..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsAssociationQueryServiceTestIT.java +++ /dev/null @@ -1,239 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.cts2.association.AssociationDirectory; -import org.cts2.association.AssociationList; -import org.cts2.core.ScopedEntityName; -import org.cts2.internal.model.uri.factory.AssociationDirectoryURIFactory; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.service.core.ReadContext; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.uri.AssociationDirectoryURI; -import org.junit.Test; - -public class LexEvsAssociationQueryServiceTestIT extends - BaseCts2IntegrationTest { - - @Resource - private LexEvsAssociationQueryService lexEvsAssociationQueryService; - - @Resource - AssociationDirectoryURIFactory associationDirectoryURIFactory; - - @Test - public void testInit(){ - assertNotNull(lexEvsAssociationQueryService); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testResolve() { - QueryControl queryControl = new QueryControl(); - ReadContext readContext = null; - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - AssociationDirectory associationDirectory = lexEvsAssociationQueryService.resolve(associationQueryURI, queryControl , readContext); - assertTrue(associationDirectory.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testResolveAsList() { - QueryControl queryControl = new QueryControl(); - ReadContext readContext = null; - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - AssociationList associationList = lexEvsAssociationQueryService.resolveAsList(associationQueryURI, queryControl , readContext); - assertTrue(associationList.getEntryCount()>0); - } - - @Test - public void testGetAllSourceAndTargetEntities() { - - } - - @Test - public void testGetPredicates() { - fail("Not yet implemented"); - } - - @Test - public void testGetSourceEntities() { - fail("Not yet implemented"); - } - - @Test - public void testGetTargetEntities() { - fail("Not yet implemented"); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToCodeSystemVersionForAssociationList() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - NameOrURI version = new NameOrURI(); - version.setName("Automobiles:1.0"); - //version.setUri("urn:oid:11.11.0.1"); - lexEvsAssociationQueryService.restrictToCodeSystemVersion(associationQueryURI, version); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationList list = lexEvsAssociationQueryService.resolveAsList(associationQueryURI, queryControl , readContext); - assertTrue(list.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToPredicateForAssociationList() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - //NameOrURI version = new NameOrURI(); - EntityNameOrURI predicate = new EntityNameOrURI(); - //version.setName("Automobiles"); - ScopedEntityName name = new ScopedEntityName(); - name.setName("hasSubtype"); - predicate.setEntityName(name); - //lexEvsAssociationQueryService.restrictToCodeSystemVersion(associationQueryURI, version); - lexEvsAssociationQueryService.restrictToPredicate(associationQueryURI, predicate); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationList associationList = lexEvsAssociationQueryService.resolveAsList(associationQueryURI, queryControl , readContext); - assertTrue(associationList.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToSourceEntityForAssociationList() { - AssociationDirectoryURI directory = lexEvsAssociationQueryService.getAssociations(); - EntityNameOrURI sourceEntity = new EntityNameOrURI(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName("A0001"); - sourceEntity.setEntityName(entityName); - lexEvsAssociationQueryService.restrictToSourceEntity(directory, sourceEntity); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationList associationList = lexEvsAssociationQueryService.resolveAsList(directory, queryControl , readContext); - assertTrue(associationList.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToSourceOrTargetEntityForAssociationList() { - AssociationDirectoryURI directory = lexEvsAssociationQueryService.getAssociations(); - EntityNameOrURI entity = new EntityNameOrURI(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName("A0001"); - entity.setEntityName(entityName); - lexEvsAssociationQueryService.restrictToSourceOrTargetEntity(directory, entity); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationList associationList = lexEvsAssociationQueryService.resolveAsList(directory, queryControl , readContext); - assertTrue(associationList.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToTargetEntityForAssociationList() { - AssociationDirectoryURI directory = lexEvsAssociationQueryService.getAssociations(); - EntityNameOrURI targetEntity = new EntityNameOrURI(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName("C0001"); - targetEntity.setEntityName(entityName); - lexEvsAssociationQueryService.restrictToTargetEntity(directory, targetEntity); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationList associationList = lexEvsAssociationQueryService.resolveAsList(directory, queryControl , readContext); - assertTrue(associationList.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToCodeSystemVersionForAssociationDir() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - NameOrURI version = new NameOrURI(); - version.setName("Automobiles:1.0"); - //version.setUri("urn:oid:11.11.0.1"); - lexEvsAssociationQueryService.restrictToCodeSystemVersion(associationQueryURI, version); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationDirectory directory = lexEvsAssociationQueryService.resolve(associationQueryURI, queryControl , readContext); - assertTrue(directory.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToPredicateForAssociationDir() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - //NameOrURI version = new NameOrURI(); - EntityNameOrURI predicate = new EntityNameOrURI(); - //version.setName("Automobiles"); - ScopedEntityName name = new ScopedEntityName(); - name.setName("hasSubtype"); - predicate.setEntityName(name); - //lexEvsAssociationQueryService.restrictToCodeSystemVersion(associationQueryURI, version); - lexEvsAssociationQueryService.restrictToPredicate(associationQueryURI, predicate); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationDirectory directory = lexEvsAssociationQueryService.resolve(associationQueryURI, queryControl , readContext); - assertTrue(directory.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToSourceEntityForAssociationDir() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - EntityNameOrURI sourceEntity = new EntityNameOrURI(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName("A0001"); - sourceEntity.setEntityName(entityName); - lexEvsAssociationQueryService.restrictToSourceEntity(associationQueryURI, sourceEntity); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationDirectory directory = lexEvsAssociationQueryService.resolve(associationQueryURI, queryControl , readContext); - assertTrue(directory.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToSourceOrTargetEntityForAssociationDir() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - EntityNameOrURI entity = new EntityNameOrURI(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName("A0001"); - entity.setEntityName(entityName); - lexEvsAssociationQueryService.restrictToSourceOrTargetEntity(associationQueryURI, entity); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationDirectory directory = lexEvsAssociationQueryService.resolve(associationQueryURI, queryControl , readContext); - assertTrue(directory.getEntryCount()>0); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToTargetEntityForAssociationDir() { - AssociationDirectoryURI associationQueryURI = lexEvsAssociationQueryService.getAssociations(); - EntityNameOrURI targetEntity = new EntityNameOrURI(); - ScopedEntityName entityName = new ScopedEntityName(); - entityName.setName("C0001"); - targetEntity.setEntityName(entityName); - lexEvsAssociationQueryService.restrictToTargetEntity(associationQueryURI, targetEntity); - ReadContext readContext = null; - QueryControl queryControl = new QueryControl(); - AssociationDirectory directory = lexEvsAssociationQueryService.resolve(associationQueryURI, queryControl , readContext); - assertTrue(directory.getEntryCount()>0); - } - @Test - public void testRestrictToTargetExpression() { - fail("Not yet implemented"); - } - - @Test - public void testRestrictToTargetLiteral() { - fail("Not yet implemented"); - } - -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryServiceTestIT.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryServiceTestIT.java deleted file mode 100644 index e500a4aedc..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryServiceTestIT.java +++ /dev/null @@ -1,49 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.cts2.codesystem.CodeSystemDirectory; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.uri.CodeSystemDirectoryURI; -import org.junit.Test; - -public class LexEvsCodeSystemQueryServiceTestIT extends BaseCts2IntegrationTest { - - @Resource - private LexEvsCodeSystemQueryService lexEvsCodeSystemQuery; - - @Test - public void testInit(){ - assertNotNull(lexEvsCodeSystemQuery); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testGetAllCodeSystemsNotNull(){ - assertNotNull(lexEvsCodeSystemQuery.getAllCodeSystems()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testGetCount(){ - CodeSystemDirectoryURI directoryURI = lexEvsCodeSystemQuery.getAllCodeSystems(); - assertEquals(1,lexEvsCodeSystemQuery.count(directoryURI, null)); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolve(){ - CodeSystemDirectoryURI directoryURI = lexEvsCodeSystemQuery.getAllCodeSystems(); - - CodeSystemDirectory csDir = lexEvsCodeSystemQuery.resolve(directoryURI, null, null); - - assertEquals(1,csDir.getEntryCount()); - - assertEquals("Automobiles",csDir.getEntry()[0].getCodeSystemName()); - } - -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryServiceTestIT.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryServiceTestIT.java deleted file mode 100644 index a3c64f2c96..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryServiceTestIT.java +++ /dev/null @@ -1,98 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import java.util.Arrays; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.cts2.core.EntityReference; -import org.cts2.core.ScopedEntityName; -import org.cts2.service.core.types.ActiveOrAll; -import org.cts2.service.core.types.RestrictionType; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.uri.CodeSystemVersionDirectoryURI; -import org.junit.Test; - -public class LexEvsCodeSystemVersionQueryServiceTestIT extends BaseCts2IntegrationTest { - - @Resource - private LexEvsCodeSystemVersionQueryService lexEvsCodeSystemVersionQuery; - - @Test - public void testInit(){ - assertNotNull(lexEvsCodeSystemVersionQuery); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testGetAllCodeSystemVersionsNotNull(){ - assertNotNull(lexEvsCodeSystemVersionQuery.getCodeSystemVersions()); - } - - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testCount(){ - CodeSystemVersionDirectoryURI uri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - assertEquals(2,lexEvsCodeSystemVersionQuery.count(uri, null)); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToEntities(){ - CodeSystemVersionDirectoryURI uri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - - EntityReference entityReference = new EntityReference(); - ScopedEntityName name = new ScopedEntityName(); - name.setName("C0001"); - entityReference.setLocalEntityName(name); - - uri = lexEvsCodeSystemVersionQuery.restrictToEntities(uri, Arrays.asList(entityReference), RestrictionType.ALL, ActiveOrAll.ACTIVE_ONLY); - - assertEquals(1,lexEvsCodeSystemVersionQuery.resolve(uri, null, null).getEntryCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToEntitiesAllWithWrongEntity(){ - CodeSystemVersionDirectoryURI uri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - - EntityReference entityReference1 = new EntityReference(); - ScopedEntityName name1 = new ScopedEntityName(); - name1.setName("C0001"); - entityReference1.setLocalEntityName(name1); - - EntityReference entityReference2 = new EntityReference(); - ScopedEntityName name2 = new ScopedEntityName(); - name2.setName("___INVALID____"); - entityReference2.setLocalEntityName(name2); - - uri = lexEvsCodeSystemVersionQuery.restrictToEntities(uri, Arrays.asList(entityReference1,entityReference2), RestrictionType.ALL, ActiveOrAll.ACTIVE_ONLY); - - assertEquals(0,lexEvsCodeSystemVersionQuery.resolve(uri, null, null).getEntryCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictToEntitiesAtLeastOneWithWrongEntity(){ - CodeSystemVersionDirectoryURI uri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - - EntityReference entityReference1 = new EntityReference(); - ScopedEntityName name1 = new ScopedEntityName(); - name1.setName("C0001"); - entityReference1.setLocalEntityName(name1); - - EntityReference entityReference2 = new EntityReference(); - ScopedEntityName name2 = new ScopedEntityName(); - name2.setName("___INVALID____"); - entityReference2.setLocalEntityName(name2); - - uri = lexEvsCodeSystemVersionQuery.restrictToEntities(uri, Arrays.asList(entityReference1,entityReference2), RestrictionType.AT_LEAST_ONE, ActiveOrAll.ACTIVE_ONLY); - - assertEquals(1,lexEvsCodeSystemVersionQuery.resolve(uri, null, null).getEntryCount()); - } - -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsEntityDescriptionQueryServiceTestIT.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsEntityDescriptionQueryServiceTestIT.java deleted file mode 100644 index 0f83f5f80a..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsEntityDescriptionQueryServiceTestIT.java +++ /dev/null @@ -1,235 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.cts2.constant.ExternalCts2Constants; -import org.cts2.core.Filter; -import org.cts2.core.FilterComponent; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.NameOrURI; -import org.cts2.core.PropertyReference; -import org.cts2.core.types.TargetReferenceType; -import org.cts2.entity.EntityDirectory; -import org.cts2.entity.EntityList; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.uri.DirectoryURI; -import org.cts2.uri.EntityDirectoryURI; -import org.junit.Test; - -public class LexEvsEntityDescriptionQueryServiceTestIT extends BaseCts2IntegrationTest { - - @Resource - private LexEvsEntityDescriptionQueryService lexEvsEntityDescriptionQueryService; - - @Test - public void testInit(){ - assertNotNull(lexEvsEntityDescriptionQueryService); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testGetEntitiesNotNull(){ - assertNotNull(lexEvsEntityDescriptionQueryService.getEntities()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testGetCount(){ - DirectoryURI uri = - lexEvsEntityDescriptionQueryService.getEntities(); - - assertEquals(19,uri.count(null)); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveEntityNotNull(){ - EntityDirectoryURI uri = - lexEvsEntityDescriptionQueryService.getEntities(); - - EntityDirectory ed = - lexEvsEntityDescriptionQueryService.resolve(uri, null, null); - - assertNotNull(ed); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveEntityCount(){ - EntityDirectoryURI uri = - lexEvsEntityDescriptionQueryService.getEntities(); - - EntityDirectory ed = - lexEvsEntityDescriptionQueryService.resolve(uri, null, null); - - assertEquals(19,ed.getEntryCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveToList(){ - EntityDirectoryURI uri = - lexEvsEntityDescriptionQueryService.getEntities(); - - EntityList list = - lexEvsEntityDescriptionQueryService.resolveAsList(uri, null, null); - - assertEquals(19,list.getEntryCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testRestrictToEntityDescription(){ - EntityDirectoryURI uri = - lexEvsEntityDescriptionQueryService.getEntities(); - Filter filter = new Filter(); - - FilterComponent filterComponent = new FilterComponent(); - filterComponent.setMatchValue("automobile"); - - MatchAlgorithmReference matchRef = new MatchAlgorithmReference(); - matchRef.setContent("LuceneQuery"); - - filterComponent.setMatchAlgorithm(matchRef); - - PropertyReference ref = new PropertyReference(); - ref.setReferenceType(TargetReferenceType.ATTRIBUTE); - - NameOrURI nameOrUri = new NameOrURI(); - nameOrUri.setUri(ExternalCts2Constants.MA_ENTITY_DESCRIPTION_DESIGNATION_URI); - ref.setReferenceTarget(nameOrUri); - - filterComponent.setFilterComponent(ref); - - filter.addComponent(filterComponent); - - uri = lexEvsEntityDescriptionQueryService.restrict(uri, filter); - - EntityDirectory ed = lexEvsEntityDescriptionQueryService.resolve(uri, null, null); - - assertEquals(1,ed.getEntryCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testUnion(){ - NameOrURI nameOrUri = new NameOrURI(); - nameOrUri.setUri(ExternalCts2Constants.MA_ENTITY_DESCRIPTION_DESIGNATION_URI); - - EntityDirectoryURI uri1 = - lexEvsEntityDescriptionQueryService.getEntities(); - Filter filter1 = new Filter(); - - FilterComponent filterComponent1 = new FilterComponent(); - filterComponent1.setMatchValue("automobile"); - - MatchAlgorithmReference matchRef1 = new MatchAlgorithmReference(); - matchRef1.setContent("LuceneQuery"); - - filterComponent1.setMatchAlgorithm(matchRef1); - - PropertyReference ref1 = new PropertyReference(); - ref1.setReferenceType(TargetReferenceType.ATTRIBUTE); - - - ref1.setReferenceTarget(nameOrUri); - - filterComponent1.setFilterComponent(ref1); - - filter1.addComponent(filterComponent1); - - uri1 = lexEvsEntityDescriptionQueryService.restrict(uri1, filter1); - - EntityDirectoryURI uri2 = - lexEvsEntityDescriptionQueryService.getEntities(); - Filter filter2 = new Filter(); - - FilterComponent filterComponent2 = new FilterComponent(); - filterComponent2.setMatchValue("ford"); - - MatchAlgorithmReference matchRef2 = new MatchAlgorithmReference(); - matchRef2.setContent("LuceneQuery"); - - filterComponent2.setMatchAlgorithm(matchRef2); - - PropertyReference ref2 = new PropertyReference(); - ref2.setReferenceType(TargetReferenceType.ATTRIBUTE); - - ref2.setReferenceTarget(nameOrUri); - - filterComponent2.setFilterComponent(ref2); - - filter2.addComponent(filterComponent2); - - uri2 = lexEvsEntityDescriptionQueryService.restrict(uri2, filter2); - - EntityDirectoryURI uri3 = lexEvsEntityDescriptionQueryService.union(uri1, uri2); - - EntityDirectory ed = lexEvsEntityDescriptionQueryService.resolve(uri3, null, null); - - assertEquals(2,ed.getEntryCount()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testIntersect(){ - NameOrURI nameOrUri = new NameOrURI(); - nameOrUri.setUri(ExternalCts2Constants.MA_ENTITY_DESCRIPTION_DESIGNATION_URI); - - EntityDirectoryURI uri1 = - lexEvsEntityDescriptionQueryService.getEntities(); - Filter filter1 = new Filter(); - - FilterComponent filterComponent1 = new FilterComponent(); - filterComponent1.setMatchValue("automobile"); - - MatchAlgorithmReference matchRef1 = new MatchAlgorithmReference(); - matchRef1.setContent("LuceneQuery"); - - filterComponent1.setMatchAlgorithm(matchRef1); - - PropertyReference ref1 = new PropertyReference(); - ref1.setReferenceType(TargetReferenceType.ATTRIBUTE); - - ref1.setReferenceTarget(nameOrUri); - - filterComponent1.setFilterComponent(ref1); - - filter1.addComponent(filterComponent1); - - uri1 = lexEvsEntityDescriptionQueryService.restrict(uri1, filter1); - - EntityDirectoryURI uri2 = - lexEvsEntityDescriptionQueryService.getEntities(); - Filter filter2 = new Filter(); - - FilterComponent filterComponent2 = new FilterComponent(); - filterComponent2.setMatchValue("*a*"); - - MatchAlgorithmReference matchRef2 = new MatchAlgorithmReference(); - matchRef2.setContent("LuceneQuery"); - - filterComponent2.setMatchAlgorithm(matchRef2); - - PropertyReference ref2 = new PropertyReference(); - ref2.setReferenceType(TargetReferenceType.ATTRIBUTE); - - ref2.setReferenceTarget(nameOrUri); - - filterComponent2.setFilterComponent(ref2); - - filter2.addComponent(filterComponent2); - - uri2 = lexEvsEntityDescriptionQueryService.restrict(uri2, filter2); - - EntityDirectoryURI uri3 = lexEvsEntityDescriptionQueryService.intersect(uri1, uri2); - - EntityDirectory ed = lexEvsEntityDescriptionQueryService.resolve(uri3, null, null); - - assertEquals(1,ed.getEntryCount()); - } -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryServiceTestIT.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryServiceTestIT.java deleted file mode 100644 index bd34b5d32a..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryServiceTestIT.java +++ /dev/null @@ -1,143 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertNotNull; - -import java.util.ArrayList; -import java.util.List; - -import javax.annotation.Resource; - -import org.cts2.core.EntityReference; -import org.cts2.core.ScopedEntityName; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.test.BaseCts2UnitTest; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; -import org.cts2.valueset.ValueSetDefinitionDirectory; -import org.cts2.valueset.ValueSetDefinitionList; -import org.junit.Test; - -public class LexEvsValueSetDefinitionQueryServiceTestIT extends BaseCts2UnitTest { - - @Resource - private LexEvsValueSetDefinitionQueryService lexEvsValueSetDefinitionVersionQuery; - - @Test - public void testInit(){ - assertNotNull(lexEvsValueSetDefinitionVersionQuery); - } - -// @Test -// @LoadContent(contentPath="classpath:content/Automobiles.xml") -// public void testGetAllCodeSystemVersionsNotNull(){ -// assertNotNull(lexEvsValueSetDefinitionVersionQuery.getCodeSystemVersions()); -// } - - -// @Test -//// @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") -// public void testCount(){ -// ValueSetDefinitionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getDirectoryURIFactory().getDirectoryURI(); -// System.out.println(uri.count(null)); -// } - -// @Test -//// @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") -// public void testResolve(){ -// ValueSetDefinitionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getDirectoryURIFactory().getDirectoryURI(); -// ValueSetDefinitionDirectory vsdDirectory = lexEvsValueSetDefinitionVersionQuery.resolve(uri, null, null); -// System.out.println(vsdDirectory.getEntryCount()); -// } - -// @Test -//////@LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") -// public void testResolveAsList(){ -// ValueSetDefinitionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getDirectoryURIFactory().getDirectoryURI(); -// ValueSetDefinitionList vsdList = lexEvsValueSetDefinitionVersionQuery.resolveAsList(uri, null, null); -// System.out.println(vsdList.getEntryCount()); -// } - - @Test -////@LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") - public void testRestrictAndResolveAsList(){ - ValueSetDefinitionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getDirectoryURIFactory().getDirectoryURI(); - - List entityList = new ArrayList(); - - EntityReference entity = new EntityReference(); - ScopedEntityName localEntityName = new ScopedEntityName(); - localEntityName.setName("Ford"); - localEntityName.setNamespace("Automobiles"); - entity.setLocalEntityName(localEntityName); - - entityList.add(entity); - - entity = new EntityReference(); - localEntityName = new ScopedEntityName(); - localEntityName.setName("GM"); - localEntityName.setNamespace("Automobiles"); - entity.setLocalEntityName(localEntityName); - - entityList.add(entity); - - lexEvsValueSetDefinitionVersionQuery.restrictToEntities(uri, entityList); - - ValueSetDefinitionList vsdList = lexEvsValueSetDefinitionVersionQuery.resolveAsList(uri, null, null); - System.out.println(vsdList.getEntryCount()); - } - -// @Test -// @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") -// public void testRestrictToEntities(){ -// CodeSystemVersionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getCodeSystemVersions(); -// -// EntityReference entityReference = new EntityReference(); -// ScopedEntityName name = new ScopedEntityName(); -// name.setName("C0001"); -// entityReference.setLocalEntityName(name); -// -// uri = lexEvsValueSetDefinitionVersionQuery.restrictToEntities(uri, Arrays.asList(entityReference), RestrictionType.ALL, ActiveOrAll.ACTIVE_ONLY); -// -// assertEquals(1,lexEvsValueSetDefinitionVersionQuery.resolve(uri, null, null).getEntryCount()); -// } -// -// @Test -// @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") -// public void testRestrictToEntitiesAllWithWrongEntity(){ -// CodeSystemVersionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getCodeSystemVersions(); -// -// EntityReference entityReference1 = new EntityReference(); -// ScopedEntityName name1 = new ScopedEntityName(); -// name1.setName("C0001"); -// entityReference1.setLocalEntityName(name1); -// -// EntityReference entityReference2 = new EntityReference(); -// ScopedEntityName name2 = new ScopedEntityName(); -// name2.setName("___INVALID____"); -// entityReference2.setLocalEntityName(name2); -// -// uri = lexEvsValueSetDefinitionVersionQuery.restrictToEntities(uri, Arrays.asList(entityReference1,entityReference2), RestrictionType.ALL, ActiveOrAll.ACTIVE_ONLY); -// -// assertEquals(0,lexEvsValueSetDefinitionVersionQuery.resolve(uri, null, null).getEntryCount()); -// } -// -// @Test -// @LoadContent(contentPath="classpath:content/Automobiles.xml,classpath:content/German_Made_Parts.xml") -// public void testRestrictToEntitiesAtLeastOneWithWrongEntity(){ -// CodeSystemVersionDirectoryURI uri = lexEvsValueSetDefinitionVersionQuery.getCodeSystemVersions(); -// -// EntityReference entityReference1 = new EntityReference(); -// ScopedEntityName name1 = new ScopedEntityName(); -// name1.setName("C0001"); -// entityReference1.setLocalEntityName(name1); -// -// EntityReference entityReference2 = new EntityReference(); -// ScopedEntityName name2 = new ScopedEntityName(); -// name2.setName("___INVALID____"); -// entityReference2.setLocalEntityName(name2); -// -// uri = lexEvsValueSetDefinitionVersionQuery.restrictToEntities(uri, Arrays.asList(entityReference1,entityReference2), RestrictionType.AT_LEAST_ONE, ActiveOrAll.ACTIVE_ONLY); -// -// assertEquals(1,lexEvsValueSetDefinitionVersionQuery.resolve(uri, null, null).getEntryCount()); -// } -// -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadServiceTestIT.java b/cts2Impl/src/test/integration/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadServiceTestIT.java deleted file mode 100644 index 3e316f7055..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadServiceTestIT.java +++ /dev/null @@ -1,223 +0,0 @@ -package org.cts2.internal.profile.read; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import java.util.Date; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.test.LexEvsTestRunner.LoadContent; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.versions.ChangedEntry; -import org.LexGrid.versions.EntryState; -import org.LexGrid.versions.Revision; -import org.LexGrid.versions.types.ChangeType; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.service.core.ReadContext; -import org.cts2.test.BaseCts2IntegrationTest; -import org.cts2.utility.ConstructorUtils; -import org.junit.Test; -import org.lexevs.locator.LexEvsServiceLocator; - -public class LexEvsCodeSystemVersionReadServiceTestIT extends BaseCts2IntegrationTest { - - @Resource - private LexEvsCodeSystemVersionReadService lexEvsCodeSystemVersionReadService; - - @Test - public void testInit(){ - assertNotNull(lexEvsCodeSystemVersionReadService); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveCodeSystemVersion(){ - CodeSystemVersion codeSystemVersion = - lexEvsCodeSystemVersionReadService.read(ConstructorUtils.nameToNameOrURI("Automobiles:1.0"), null, null); - - assertEquals("urn:oid:11.11.0.1", codeSystemVersion.getAbout()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveCodeSystemVersionDifferentRevisionFirstRevision() throws Exception { - Revision rev1 = new Revision(); - rev1.setRevisionId("r1"); - - CodingScheme cs1 = new CodingScheme(); - cs1.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs1.setRepresentsVersion("1.0"); - cs1.setEntryState(new EntryState()); - cs1.getEntryState().setChangeType(ChangeType.MODIFY); - cs1.getEntryState().setContainingRevision("r1"); - cs1.setFormalName("r1 formal name"); - - rev1.addChangedEntry(new ChangedEntry()); - rev1.getChangedEntry()[0].setChangedCodingSchemeEntry(cs1); - - Revision rev2 = new Revision(); - rev2.setRevisionId("r2"); - - CodingScheme cs2 = new CodingScheme(); - cs2.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs2.setRepresentsVersion("1.0"); - cs2.setEntryState(new EntryState()); - cs2.getEntryState().setChangeType(ChangeType.MODIFY); - cs2.getEntryState().setContainingRevision("r2"); - cs2.setFormalName("r2 formal name"); - - rev2.addChangedEntry(new ChangedEntry()); - rev2.getChangedEntry()[0].setChangedCodingSchemeEntry(cs2); - - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev1, null, false); - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev2, null, false); - - ReadContext readContext = new ReadContext(); - readContext.setChangeSetContext("r1"); - - CodeSystemVersion codeSystemVersion = - lexEvsCodeSystemVersionReadService.read(ConstructorUtils.nameToNameOrURI("Automobiles:1.0"), null, readContext); - - assertEquals("r1 formal name", codeSystemVersion.getFormalName()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveCodeSystemVersionDifferentRevisionAnotherRevision() throws Exception { - Revision rev1 = new Revision(); - rev1.setRevisionId("r1"); - - CodingScheme cs1 = new CodingScheme(); - cs1.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs1.setRepresentsVersion("1.0"); - cs1.setEntryState(new EntryState()); - cs1.getEntryState().setChangeType(ChangeType.MODIFY); - cs1.getEntryState().setContainingRevision("r1"); - cs1.setFormalName("r1 formal name"); - - rev1.addChangedEntry(new ChangedEntry()); - rev1.getChangedEntry()[0].setChangedCodingSchemeEntry(cs1); - - Revision rev2 = new Revision(); - rev2.setRevisionId("r2"); - - CodingScheme cs2 = new CodingScheme(); - cs2.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs2.setRepresentsVersion("1.0"); - cs2.setEntryState(new EntryState()); - cs2.getEntryState().setChangeType(ChangeType.MODIFY); - cs2.getEntryState().setContainingRevision("r2"); - cs2.setFormalName("r2 formal name"); - - rev2.addChangedEntry(new ChangedEntry()); - rev2.getChangedEntry()[0].setChangedCodingSchemeEntry(cs2); - - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev1, null, false); - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev2, null, false); - - ReadContext readContext = new ReadContext(); - readContext.setChangeSetContext("r2"); - - CodeSystemVersion codeSystemVersion = - lexEvsCodeSystemVersionReadService.read(ConstructorUtils.nameToNameOrURI("Automobiles:1.0"), null, readContext); - - assertEquals("r2 formal name", codeSystemVersion.getFormalName()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveCodeSystemVersionByDate() throws Exception { - Revision rev1 = new Revision(); - rev1.setRevisionId("r1"); - - CodingScheme cs1 = new CodingScheme(); - cs1.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs1.setRepresentsVersion("1.0"); - cs1.setEntryState(new EntryState()); - cs1.getEntryState().setChangeType(ChangeType.MODIFY); - cs1.getEntryState().setContainingRevision("r1"); - cs1.setFormalName("r1 formal name"); - - rev1.addChangedEntry(new ChangedEntry()); - rev1.getChangedEntry()[0].setChangedCodingSchemeEntry(cs1); - - Revision rev2 = new Revision(); - rev2.setRevisionId("r2"); - - CodingScheme cs2 = new CodingScheme(); - cs2.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs2.setRepresentsVersion("1.0"); - cs2.setEntryState(new EntryState()); - cs2.getEntryState().setChangeType(ChangeType.MODIFY); - cs2.getEntryState().setContainingRevision("r2"); - cs2.setFormalName("r2 formal name"); - - rev2.addChangedEntry(new ChangedEntry()); - rev2.getChangedEntry()[0].setChangedCodingSchemeEntry(cs2); - - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev1, null, false); - Date date1 = new Date(); - Thread.sleep(100); - - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev2, null, false); - Date date2 = new Date(); - Thread.sleep(100); - - ReadContext readContext = new ReadContext(); - readContext.setReferenceTime(date1); - - CodeSystemVersion codeSystemVersion = - lexEvsCodeSystemVersionReadService.read(ConstructorUtils.nameToNameOrURI("Automobiles:1.0"), null, readContext); - - assertEquals("r1 formal name", codeSystemVersion.getFormalName()); - } - - @Test - @LoadContent(contentPath="classpath:content/Automobiles.xml") - public void testResolveCodeSystemVersionByDifferentDate() throws Exception { - Revision rev1 = new Revision(); - rev1.setRevisionId("r1"); - - CodingScheme cs1 = new CodingScheme(); - cs1.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs1.setRepresentsVersion("1.0"); - cs1.setEntryState(new EntryState()); - cs1.getEntryState().setChangeType(ChangeType.MODIFY); - cs1.getEntryState().setContainingRevision("r1"); - cs1.setFormalName("r1 formal name"); - - rev1.addChangedEntry(new ChangedEntry()); - rev1.getChangedEntry()[0].setChangedCodingSchemeEntry(cs1); - - Revision rev2 = new Revision(); - rev2.setRevisionId("r2"); - - CodingScheme cs2 = new CodingScheme(); - cs2.setCodingSchemeURI("urn:oid:11.11.0.1"); - cs2.setRepresentsVersion("1.0"); - cs2.setEntryState(new EntryState()); - cs2.getEntryState().setChangeType(ChangeType.MODIFY); - cs2.getEntryState().setContainingRevision("r2"); - cs2.setFormalName("r2 formal name"); - - rev2.addChangedEntry(new ChangedEntry()); - rev2.getChangedEntry()[0].setChangedCodingSchemeEntry(cs2); - - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev1, null, false); - Date date1 = new Date(); - Thread.sleep(100); - - LexEvsServiceLocator.getInstance().getDatabaseServiceManager().getAuthoringService().loadRevision(rev2, null, false); - Date date2 = new Date(); - Thread.sleep(100); - - ReadContext readContext = new ReadContext(); - readContext.setReferenceTime(date2); - - CodeSystemVersion codeSystemVersion = - lexEvsCodeSystemVersionReadService.read(ConstructorUtils.nameToNameOrURI("Automobiles:1.0"), null, readContext); - - assertEquals("r2 formal name", codeSystemVersion.getFormalName()); - } -} diff --git a/cts2Impl/src/test/integration/java/org/cts2/test/BaseCts2IntegrationTest.java b/cts2Impl/src/test/integration/java/org/cts2/test/BaseCts2IntegrationTest.java deleted file mode 100644 index 78823e9fb1..0000000000 --- a/cts2Impl/src/test/integration/java/org/cts2/test/BaseCts2IntegrationTest.java +++ /dev/null @@ -1,17 +0,0 @@ -package org.cts2.test; - -import org.LexGrid.LexBIG.test.BaseContentLoadingInMemoryTest; -import org.junit.Test; -import org.springframework.test.context.ContextConfiguration; - -@ContextConfiguration( - value = "/cts2-application-config-integration-test.xml" -) -public class BaseCts2IntegrationTest extends BaseContentLoadingInMemoryTest { - - @Test - public void testInit(){ - //test to check initialization of test context - } - -} diff --git a/cts2Impl/src/test/integration/resources/content/Automobiles.xml b/cts2Impl/src/test/integration/resources/content/Automobiles.xml deleted file mode 100644 index 49d67fb93d..0000000000 --- a/cts2Impl/src/test/integration/resources/content/Automobiles.xml +++ /dev/null @@ -1,356 +0,0 @@ - - - - Automobiles - 11.11.0.1 - Automobiles - SomeOtherValue - lexgrid.org - Copyright by Mayo Clinic. - - - hasSubtype - uses - A1 - hasEngine - since - sold - Automobiles - Expendable Parts - German Made Parts - relations - test/html - text/plain - hasSubtype - en - Automobiles - Expendable Parts - German Made Parts - TestForSameCodeNamespace - definition - textualPresentation - genericProperty - lexgrid.org - 11.11.0.1 - - - - sampleOwner - lexgrid.org - sampleUsageContext - - Property Qualifier Text - - Property Text - - - - - Domestic Auto Makers - concept - - lexgrid.org - lexgrid.org - Domestic Auto Makers - - - American Car Companies - - - - Oldsmobile - concept - - Oldsmobile - - - Olds - - - Oldsmobile Auto Manufacturing - - - - Top level node for relationships - concept - - Top level node for relationships - - - - Automobile - concept - - Automobile - - - An automobile - - - A Generic Property - - - - isAnonymous=true - concept - - A concept for testing whether or not the isAnonymous flag is being heeded. - - - Anonymous-mobile - - - - A concept for testing Graph Building on Concepts with no relations - concept - - A concept for testing Graph Building on Concepts with no relations - - - - Concept containing special characters - concept - - a^s sp*cial co{nce]pt - - - - Car - concept - - Car - - - Car (with special) charaters! - - - - Car With Trailer - concept - - TrailerCar(Yahoo) - - - Car (with special) Trailer! - - - - Kar - concept - - Kar - - - Kar (with special) charaters! - - - - Chevrolet - concept - - Chevy - - - Chevrolet - - - - Ford Motor Company - concept - - Mayo - Ford - - - Ford Motor Company - - - - General Motors - concept - - General Motors - - - GM - - - - Jaguar - concept - - Jaguar - - - - - Concept for testing same code but different Namespace - 1 - concept - - Concept for testing same code but different Namespace - 1 - - - - - Concept for testing same code but different Namespace - 2 - concept - - Concept for testing same code but different Namespace - 2 - - - - - - Truck - concept - - Truck - - - - Domestic Auto Makers VD - valueDomain - - Domestic Auto Makers - - - American Car Companies - - - - First Code in cycle - concept - - First Code in cycle - - - - Second Code in cycle - concept - - Second Code in cycle - - - - Third Code in cycle - concept - - Third Code in cycle - - - - - - - - - - - - - - - - - - - - - - - - - asD - - - - - - - - - - - - - - - true - - - - - - - - true - - - - - - - 1998 - - - 2009 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/cts2Impl/src/test/integration/resources/content/German_Made_Parts.xml b/cts2Impl/src/test/integration/resources/content/German_Made_Parts.xml deleted file mode 100755 index cd9ee7d5cc..0000000000 --- a/cts2Impl/src/test/integration/resources/content/German_Made_Parts.xml +++ /dev/null @@ -1,107 +0,0 @@ - - - - GermanMadeParts - 11.11.0.2 - GermanMadeParts - lexgrid.org - - - hasSubtype - German Made Parts - text/plain - en - ge - German Made Parts Namespace - Some Other Namespace - ns1 - ns2 - textualPresentation - lexgrid.org - - - - Engine - concept - - Engine - - - - Piston - concept - - Piston - - - - Rims - concept - - Rims - - - - Tires - concept - - Tires - - - - - codeWithMultileNs - concept - - codeWithMultileNs - - - - - codeWithMultileNs - concept - - codeWithMultileNs - - - - - - DifferentNamespaceEntity - concept - - DifferentNamespaceEntity - - - - - - asd - - - - - - - - - - diff --git a/cts2Impl/src/test/integration/resources/cts2-application-config-integration-test.xml b/cts2Impl/src/test/integration/resources/cts2-application-config-integration-test.xml deleted file mode 100755 index 5ccf4dcdf3..0000000000 --- a/cts2Impl/src/test/integration/resources/cts2-application-config-integration-test.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/logging/LoggingAspectTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/logging/LoggingAspectTest.java deleted file mode 100644 index cc5de76782..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/logging/LoggingAspectTest.java +++ /dev/null @@ -1,79 +0,0 @@ -/* - * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and - * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the - * triple-shield Mayo logo are trademarks and service marks of MFMER. - * - * Except as contained in the copyright notice above, or as used to identify - * MFMER as the author of this software, the trade names, trademarks, service - * marks, or product names of the copyright holder shall not be used in - * advertising, promotion or otherwise in connection with this software without - * prior written authorization of the copyright holder. - * - * Licensed under the Eclipse Public License, Version 1.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.eclipse.org/legal/epl-v10.html - * - */ -package org.cts2.internal.logging; - -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -import javax.annotation.Resource; - -import org.cts2.test.BaseCts2UnitTest; -import org.cts2.test.NoOpLogger; -import org.cts2.test.TestLoggableClass; -import org.junit.Test; -import org.springframework.test.annotation.DirtiesContext; - -public class LoggingAspectTest extends BaseCts2UnitTest { - - @Resource - private LoggingAspect loggingAspect; - - @Resource - private TestLoggableClass testLoggableClass; - - @Test - public void testNotNull(){ - assertNotNull(this.loggingAspect); - } - - @DirtiesContext - @Test - public void testLoggingIntercepted(){ - TestLogger testLogger = new TestLogger(); - this.loggingAspect.setLogger(testLogger); - - testLoggableClass.loggableMethod(); - - assertTrue(testLogger.called); - } - - @DirtiesContext - @Test - public void testLoggingInterceptedNonLoggable(){ - TestLogger testLogger = new TestLogger(); - this.loggingAspect.setLogger(testLogger); - - testLoggableClass.unLoggableMethod(); - - assertFalse(testLogger.called); - } - - private class TestLogger extends NoOpLogger { - - private boolean called = false; - - @Override - public String info(String message) { - this.called = true; - - return null; - } - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/BaseDozerBeanMapperTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/BaseDozerBeanMapperTest.java deleted file mode 100644 index a3e9eebe64..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/BaseDozerBeanMapperTest.java +++ /dev/null @@ -1,20 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.cts2.internal.mapper.BaseDozerBeanMapper; -import org.cts2.test.BaseCts2UnitTest; -import org.junit.Test; - -public class BaseDozerBeanMapperTest extends BaseCts2UnitTest{ - - @Resource - protected BaseDozerBeanMapper baseDozerBeanMapper; - - @Test - public void testInitDozer(){ - assertNotNull(baseDozerBeanMapper); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CTS2AssociationToLexEVSRelationsElements.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CTS2AssociationToLexEVSRelationsElements.java deleted file mode 100644 index 67b1db3cfc..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CTS2AssociationToLexEVSRelationsElements.java +++ /dev/null @@ -1,228 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; -import org.LexGrid.LexBIG.DataModel.Core.AssociatedConcept; -import org.LexGrid.LexBIG.DataModel.Core.AssociatedData; -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.SupportedCodingScheme; -import org.LexGrid.relations.AssociationEntity; -import org.junit.Test; - -public class CTS2AssociationToLexEVSRelationsElements extends - BaseDozerBeanMapperTest { - String codingSchemeName = "NCI Thesaurus"; - String codingSchemeURI = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"; - String association = "is_a"; - String conceptCode = "C1234"; - String conceptCode1 = "C4321"; - String nameSpace = "NCIt"; - - - @Test - public void AssociationDirectoryEntryToLexBIGAssociationgTest() { - - org.LexGrid.LexBIG.DataModel.Core.Association lbAssoc = new org.LexGrid.LexBIG.DataModel.Core.Association(); - lbAssoc.setAssociationName(association); - org.cts2.association.AssociationDirectoryEntry cts2Assoc = baseDozerBeanMapper.map( - lbAssoc, org.cts2.association.AssociationDirectoryEntry.class); - assertEquals(association, cts2Assoc.getPredicate().getContent()); - } - - @Test - public void AssociationDirectoryEntryToResolvedConceptReferenceTest() { - ResolvedConceptReference rcnr = new ResolvedConceptReference(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode); - entity.setEntityCodeNamespace(nameSpace); - rcnr.setEntity(entity); - org.cts2.association.AssociationDirectoryEntry cts2Assoc = baseDozerBeanMapper.map( - rcnr, org.cts2.association.AssociationDirectoryEntry.class); - assertEquals(conceptCode, cts2Assoc.getSubject().getLocalEntityName() - .getName()); - assertEquals(nameSpace, cts2Assoc.getSubject().getLocalEntityName() - .getNamespace()); - } - @Test - public void AssociationDirectoryEntryToCodingSchemeTest(){ - CodingScheme cs = new CodingScheme(); - cs.setCodingSchemeName(codingSchemeName); - cs.setCodingSchemeURI(codingSchemeURI); - org.cts2.association.AssociationDirectoryEntry cts2Assoc = baseDozerBeanMapper.map( - cs, org.cts2.association.AssociationDirectoryEntry.class); - assertEquals(codingSchemeName, cts2Assoc.getAssertedBy().getContent()); - assertEquals(codingSchemeURI, cts2Assoc.getAssertedBy().getMeaning()); - } - @Test - public void AssociationDirectoryEntryToSupportedCodingScheme(){ - SupportedCodingScheme supCodingScheme = new SupportedCodingScheme(); - supCodingScheme.setUri(codingSchemeURI); - org.cts2.association.AssociationDirectoryEntry cts2Assoc = baseDozerBeanMapper.map( - supCodingScheme, org.cts2.association.AssociationDirectoryEntry.class); - assertEquals(codingSchemeURI,cts2Assoc.getPredicate().getMeaning()); - } - @Test - public void AssociationDirectoryEntryToAssociatedConceptTest() { - AssociatedConcept ac = new AssociatedConcept(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode1); - entity.setEntityCodeNamespace(nameSpace); - ac.setReferencedEntry(entity); - org.cts2.association.AssociationDirectoryEntry cts2Assoc = baseDozerBeanMapper.map( - ac, org.cts2.association.AssociationDirectoryEntry.class); - assertEquals(conceptCode1, cts2Assoc.getTarget().getEntity() - .getLocalEntityName().getName()); - assertEquals(nameSpace, cts2Assoc.getSubject().getLocalEntityName() - .getNamespace()); - } - @Test - public void AssociationDirectoryEntryToCodingSchemeDefinition(){ - CodingScheme cs = new CodingScheme(); - cs.setCodingSchemeName(codingSchemeName); - cs.setCodingSchemeURI(codingSchemeURI); - org.cts2.association.AssociationDirectoryEntry cts2Assoc = baseDozerBeanMapper.map( - cs, org.cts2.association.AssociationDirectoryEntry.class); - assertEquals(codingSchemeName, cts2Assoc.getAssertedBy().getContent()); - assertEquals(codingSchemeURI, cts2Assoc.getAssertedBy().getMeaning()); - } - - @Test - public void AssociationToAssociatedDataTest() { - AssociatedData ad = new AssociatedData(); - ad.setId("id123"); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - ad, org.cts2.association.Association.class); - assertEquals("id123", cts2Assoc.getExternalStatementId()); - } - @Test - public void AssociationToLexBIGAssociationgTest() { - - org.LexGrid.LexBIG.DataModel.Core.Association lbAssoc = new org.LexGrid.LexBIG.DataModel.Core.Association(); - lbAssoc.setAssociationName(association); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - lbAssoc, org.cts2.association.Association.class); - assertEquals(association, cts2Assoc.getPredicate().getContent()); - } - - @Test - public void AssociationToResolvedConcepteferenceTest() { - ResolvedConceptReference rcnr = new ResolvedConceptReference(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode); - entity.setEntityCodeNamespace(nameSpace); - rcnr.setEntity(entity); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - rcnr, org.cts2.association.Association.class); - assertEquals(conceptCode, cts2Assoc.getSubject().getLocalEntityName() - .getName()); - assertEquals(nameSpace, cts2Assoc.getSubject().getLocalEntityName() - .getNamespace()); - } - @Test - public void AssociationToCodingSchemeTest(){ - CodingScheme cs = new CodingScheme(); - cs.setCodingSchemeName(codingSchemeName); - cs.setCodingSchemeURI(codingSchemeURI); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - cs, org.cts2.association.Association.class); - assertEquals(codingSchemeName, cts2Assoc.getAssertedBy().getContent()); - assertEquals(codingSchemeURI, cts2Assoc.getAssertedBy().getMeaning()); - } - @Test - public void AssociationToSupportedCodingScheme(){ - SupportedCodingScheme supCodingScheme = new SupportedCodingScheme(); - supCodingScheme.setUri(codingSchemeURI); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - supCodingScheme, org.cts2.association.Association.class); - assertEquals(codingSchemeURI,cts2Assoc.getPredicate().getMeaning()); - } - @Test - public void AssociationToAssociatedConceptTest() { - AssociatedConcept ac = new AssociatedConcept(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode1); - entity.setEntityCodeNamespace(nameSpace); - ac.setReferencedEntry(entity); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - ac, org.cts2.association.Association.class); - assertEquals(conceptCode1, cts2Assoc.getTarget().getEntity() - .getLocalEntityName().getName()); - assertEquals(nameSpace, cts2Assoc.getSubject().getLocalEntityName() - .getNamespace()); - } - @Test - public void AssociationToCodingSchemeDefinition(){ - CodingScheme cs = new CodingScheme(); - cs.setCodingSchemeName(codingSchemeName); - cs.setCodingSchemeURI(codingSchemeURI); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - cs, org.cts2.association.Association.class); - assertEquals(codingSchemeName, cts2Assoc.getAssertedBy().getContent()); - assertEquals(codingSchemeURI, cts2Assoc.getAssertedBy().getMeaning()); - assertEquals(codingSchemeName, cts2Assoc.getAssertedIn().getContent()); - assertEquals(codingSchemeURI, cts2Assoc.getAssertedIn().getMeaning()); - } - @Test - public void AssociationGraphToResolvedConceptReferenceTest() { - ResolvedConceptReference rcnr = new ResolvedConceptReference(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode); - entity.setEntityCodeNamespace(nameSpace); - rcnr.setEntity(entity); - org.cts2.association.AssociationGraph cts2Assoc = baseDozerBeanMapper.map( - rcnr, org.cts2.association.AssociationGraph.class); - assertEquals(conceptCode, cts2Assoc.getFocusEntity().getLocalEntityName() - .getName()); - assertEquals(nameSpace, cts2Assoc.getFocusEntity().getLocalEntityName() - .getNamespace()); - } - @Test - public void GraphNodeToLexBIGAssociationgTest() { - - org.LexGrid.LexBIG.DataModel.Core.Association lbAssoc = new org.LexGrid.LexBIG.DataModel.Core.Association(); - lbAssoc.setAssociationName(association); - org.cts2.association.GraphNode cts2Assoc = baseDozerBeanMapper.map( - lbAssoc, org.cts2.association.GraphNode.class); - assertEquals(association, cts2Assoc.getPredicate().getContent()); - } - @Test - public void GraphNodeToAssociatedConceptTest() { - AssociatedConcept ac = new AssociatedConcept(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode1); - entity.setEntityCodeNamespace(nameSpace); - ac.setReferencedEntry(entity); - org.cts2.association.GraphNode cts2Assoc = baseDozerBeanMapper.map( - ac, org.cts2.association.GraphNode.class); - assertEquals(conceptCode1, cts2Assoc.getTarget().getEntity() - .getLocalEntityName().getName()); - - } - @Test - public void ResolvedConceptReferenceListToAssociationDiretory(){ - ResolvedConceptReferenceList rcrl = new ResolvedConceptReferenceList(); - ResolvedConceptReference rcr = new ResolvedConceptReference(); - Entity entity = new Entity(); - entity.setEntityCode(conceptCode1); - entity.setEntityCodeNamespace(nameSpace); - rcr.setEntity(entity); - rcrl.addResolvedConceptReference(rcr); - org.cts2.association.AssociationDirectory cts2Assoc = baseDozerBeanMapper.map( - rcrl, org.cts2.association.AssociationDirectory.class); - assertEquals(conceptCode1, cts2Assoc.getEntry(0).getSubject().getLocalEntityName().getName()); - assertEquals(nameSpace, cts2Assoc.getEntry(0).getSubject().getLocalEntityName().getNamespace()); - } - - public void AssociationEntityToAssociation(){ - AssociationEntity entity = new AssociationEntity(); - entity.setEntityCode(conceptCode1); - org.cts2.association.Association cts2Assoc = baseDozerBeanMapper.map( - entity, org.cts2.association.Association.class); - assertEquals(conceptCode1, cts2Assoc.getTarget().getEntity() - .getLocalEntityName().getName()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeRenderingListToCodeSystemDirectoryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeRenderingListToCodeSystemDirectoryTest.java deleted file mode 100644 index ce3d195929..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeRenderingListToCodeSystemDirectoryTest.java +++ /dev/null @@ -1,39 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.cts2.codesystem.CodeSystemDirectory; -import org.junit.Test; - -public class CodingSchemeRenderingListToCodeSystemDirectoryTest extends BaseDozerBeanMapperTest { - - @Test - public void CodingSchemeRenderingList_To_CodeSystemDirectory_Count(){ - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new CodingSchemeRendering(); - csrl.addCodingSchemeRendering(csr); - - CodeSystemDirectory csd = baseDozerBeanMapper.map(csrl, CodeSystemDirectory.class); - - assertEquals(1, csd.getEntryCount()); - } - - @Test - public void CodingSchemeRenderingList_To_CodeSystemDirectoryUri_About(){ - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new CodingSchemeRendering(); - CodingSchemeSummary css = new CodingSchemeSummary(); - css.setCodingSchemeURI("someUri"); - csr.setCodingSchemeSummary(css); - csrl.addCodingSchemeRendering(csr); - - CodeSystemDirectory csd = baseDozerBeanMapper.map(csrl, CodeSystemDirectory.class); - - assertEquals("someUri", csd.getEntry(0).getAbout()); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeRenderingToCodeSystemVersionDirectoryEntryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeRenderingToCodeSystemVersionDirectoryEntryTest.java deleted file mode 100644 index 6452a1b8bb..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeRenderingToCodeSystemVersionDirectoryEntryTest.java +++ /dev/null @@ -1,127 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeTagList; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.RenderingDetail; -import org.LexGrid.LexBIG.Utility.Constructors; -import org.cts2.codesystemversion.CodeSystemVersionDirectoryEntry; -import org.cts2.core.VersionTagReference; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Test; -import org.springframework.test.annotation.DirtiesContext; - -public class CodingSchemeRenderingToCodeSystemVersionDirectoryEntryTest extends BaseDozerBeanMapperTest { - - @Resource - private org.cts2.internal.mapper.converter.CodeSystemVersionDirectoryEntryIdentityConverter converter; - - - @Test - public void testFormalName(){ - CodingSchemeRendering csr = new CodingSchemeRendering(); - CodingSchemeSummary css = new CodingSchemeSummary(); - css.setFormalName("test formal name"); - csr.setCodingSchemeSummary(css); - - CodeSystemVersionDirectoryEntry mapped = - baseDozerBeanMapper.map(csr, CodeSystemVersionDirectoryEntry.class); - - assertEquals("test formal name", mapped.getFormalName()); - - } - - @Test - public void testEntityDescription(){ - CodingSchemeRendering csr = new CodingSchemeRendering(); - CodingSchemeSummary css = new CodingSchemeSummary(); - css.setCodingSchemeDescription(Constructors.createEntityDescription("test desc")); - csr.setCodingSchemeSummary(css); - - CodeSystemVersionDirectoryEntry mapped = - baseDozerBeanMapper.map(csr, CodeSystemVersionDirectoryEntry.class); - - assertEquals("test desc", mapped.getResourceSynopsis().getValue()); - - } - - @Test - @DirtiesContext - public void Map_Everything(){ - LexEvsIdentityConverter converter = EasyMock.createMock(LexEvsIdentityConverter.class); - - AbsoluteCodingSchemeVersionReference ref = (AbsoluteCodingSchemeVersionReference)EasyMock.anyObject(); - - EasyMock.expect(converter.codingSchemeReferenceToCodeSystemVersionName( - ref)).andReturn("test local name:testVersion").anyTimes(); - - ref = (AbsoluteCodingSchemeVersionReference)EasyMock.anyObject(); - - EasyMock.expect(converter.codingSchemeReferenceToCodeSystemVersionDocumentUri( - ref)).andReturn("testURI:testVersion:RRF").anyTimes(); - - EasyMock.replay(converter); - - this.converter.setLexEvsIdentityConverter(converter); - - CodingSchemeRendering csr = new CodingSchemeRendering(); - - csr.setRenderingDetail(new RenderingDetail()); - CodingSchemeTagList tags = new CodingSchemeTagList(); - tags.addTag("TEST"); - tags.addTag("PRODUCTION"); - - csr.getRenderingDetail().setVersionTags(tags); - - CodingSchemeSummary css = new CodingSchemeSummary(); - css.setCodingSchemeURI("testURI"); - css.setRepresentsVersion("testVersion"); - css.setFormalName("Test Formal Name"); - css.setLocalName("test local name"); - - css.setCodingSchemeDescription(Constructors.createEntityDescription("test desc")); - - csr.setCodingSchemeSummary(css); - - CodeSystemVersionDirectoryEntry mapped = - baseDozerBeanMapper.map(csr, CodeSystemVersionDirectoryEntry.class); - - assertEquals("testURI", mapped.getAbout()); - assertEquals("test local name:testVersion", mapped.getCodeSystemVersionName()); - assertEquals("testURI:testVersion:RRF", mapped.getDocumentURI()); - assertEquals("Test Formal Name", mapped.getFormalName()); - - //not tracked in LexEVS - assertEquals(null, mapped.getMatchStrength()); - - //not tracked in LexEVS - assertEquals(null, mapped.getOfficialReleaseDate()); - assertEquals("testVersion", mapped.getOfficialResourceVersionId()); - assertEquals("test local name:testVersion", mapped.getResourceName()); - assertEquals("testURI:testVersion:RRF", mapped.getResourceID()); - assertEquals("test desc", mapped.getResourceSynopsis().getValue()); - - //not supported in LexEVS - assertEquals(null, mapped.getVersionOf()); - - assertEquals(2,mapped.getCodeSystemVersionTagCount()); - - } - - @Test - public void Map_VersionTagReference(){ - String tag = "PRODUCTION"; - - VersionTagReference mapped = - baseDozerBeanMapper.map(tag, VersionTagReference.class); - - assertEquals("PRODUCTION", mapped.getContent()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeToCodeSystemVersionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeToCodeSystemVersionTest.java deleted file mode 100644 index 5f3975f7bd..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CodingSchemeToCodeSystemVersionTest.java +++ /dev/null @@ -1,220 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.*; - -import java.util.Arrays; -import java.util.Date; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedLanguage; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.core.types.EntryState; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Before; -import org.junit.Test; -import org.springframework.test.annotation.DirtiesContext; - -public class CodingSchemeToCodeSystemVersionTest extends BaseDozerBeanMapperTest { - - @Resource - private org.cts2.internal.mapper.converter.CodeSystemVersionIdentityConverter converter; - - private CodingScheme cs; - - @Before - public void buildCodingScheme(){ - cs = new CodingScheme(); - cs.setApproxNumConcepts(1000l); - cs.setCodingSchemeName("test_cs_name"); - cs.setCodingSchemeURI("test_cs_uri"); - cs.setCopyright(Constructors.createText("test copyright")); - cs.setDefaultLanguage("ENG"); - cs.setEffectiveDate(new Date()); - cs.setEntityDescription(Constructors.createEntityDescription("test description")); - cs.setExpirationDate(new Date()); - cs.setFormalName("test_formal_name"); - cs.setIsActive(true); - cs.addLocalName("ln1"); - cs.addLocalName("ln2"); - cs.setOwner("some_owner"); - cs.setRepresentsVersion("v1"); - cs.setStatus("test_status"); - } - - @Test - public void Map_CodingSchemeURI_To_About(){ - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("test_cs_uri", csv.getAbout()); - } - - @Test - @DirtiesContext - public void Map_CodingSchemeName_To_CodeSystemVersionName(){ - LexEvsIdentityConverter converter = EasyMock.createNiceMock(LexEvsIdentityConverter.class); - - CodingScheme mockCs = (CodingScheme)EasyMock.anyObject(); - - EasyMock.expect(converter.codingSchemeToCodeSystemVersionName( - mockCs)).andReturn("test_cs_name:v1").anyTimes(); - - EasyMock.replay(converter); - - this.converter.setLexEvsIdentityConverter(converter); - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("test_cs_name:v1", csv.getCodeSystemVersionName()); - } - - @Test - @DirtiesContext - public void Map_CodingScheme_To_CodeSystemVersionDocumentURI(){ - LexEvsIdentityConverter converter = EasyMock.createNiceMock(LexEvsIdentityConverter.class); - - CodingScheme mockCs = (CodingScheme)EasyMock.anyObject(); - - EasyMock.expect(converter.codingSchemeToCodeSystemVersionDocumentUri( - mockCs)).andReturn("test_cs_uri:v1:RRF").anyTimes(); - - EasyMock.replay(converter); - - this.converter.setLexEvsIdentityConverter(converter); - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("test_cs_uri:v1:RRF", csv.getDocumentURI()); - } - - @Test - @DirtiesContext - public void Map_CodingScheme_Copyright_To_CodeSystemVersionDocumentURI(){ - LexEvsIdentityConverter converter = EasyMock.createNiceMock(LexEvsIdentityConverter.class); - - CodingScheme mockCs = (CodingScheme)EasyMock.anyObject(); - - EasyMock.expect(converter.codingSchemeToCodeSystemVersionDocumentUri( - mockCs)).andReturn("test_cs_uri:v1:RRF").anyTimes(); - - EasyMock.replay(converter); - - this.converter.setLexEvsIdentityConverter(converter); - - cs.getCopyright().setDataType("d"); - - cs.setMappings(new Mappings()); - SupportedDataType datatype = new SupportedDataType(); - datatype.setUri("datatypeUri"); - datatype.setLocalId("d"); - cs.getMappings().addSupportedDataType(datatype); - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("test copyright", csv.getRights().getValue()); - - assertEquals("d", csv.getRights().getFormat().getContent()); - assertEquals("datatypeUri", csv.getRights().getFormat().getHref()); - } - - @Test - @DirtiesContext - public void Map_CodingScheme_DefaultLanguage_To_DefaultLanguage(){ - LexEvsIdentityConverter converter = EasyMock.createNiceMock(LexEvsIdentityConverter.class); - - CodingScheme mockCs = (CodingScheme)EasyMock.anyObject(); - - EasyMock.expect(converter.codingSchemeToCodeSystemVersionDocumentUri( - mockCs)).andReturn("test_cs_uri:v1:RRF").anyTimes(); - - EasyMock.replay(converter); - - this.converter.setLexEvsIdentityConverter(converter); - - cs.setMappings(new Mappings()); - SupportedLanguage language = new SupportedLanguage(); - language.setUri("languageUri"); - language.setLocalId("ENG"); - cs.getMappings().addSupportedLanguage(language); - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("ENG", csv.getDefaultLanguage().getContent()); - assertEquals("languageUri", csv.getDefaultLanguage().getHref()); - } - - @Test - public void Map_CodingScheme_EntityDescription(){ - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("test description", csv.getResourceSynopsis().getValue()); - } - - @Test - public void Map_CodingScheme_FormalName(){ - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("test_formal_name", csv.getFormalName()); - } - - @Test - public void Map_CodingScheme_IsActive(){ - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals(EntryState.ACTIVE,csv.getEntryState()); - - cs.setIsActive(false); - csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals(EntryState.INACTIVE,csv.getEntryState()); - - cs.setIsActive(null); - csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertNull(csv.getEntryState()); - } - - @Test - public void Map_CodingScheme_localNames(){ - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals(2, csv.getKeyword().length); - - String[] result = csv.getKeyword(); - String[] expected = new String[]{"ln1", "ln2"}; - - Arrays.sort(result); - Arrays.sort(expected); - - assertArrayEquals(expected,result); - } - - @Test - public void Map_CodingScheme_RepresentsVersion(){ - - CodeSystemVersion csv = - this.baseDozerBeanMapper.map(cs, CodeSystemVersion.class); - - assertEquals("v1",csv.getOfficialResourceVersionId()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CommentToCommentTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CommentToCommentTest.java deleted file mode 100644 index dbefeaa563..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/CommentToCommentTest.java +++ /dev/null @@ -1,53 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import org.LexGrid.commonTypes.Text; -import org.junit.Before; -import org.junit.Test; - -public class CommentToCommentTest extends BaseDozerBeanMapperTest{ - private org.LexGrid.concepts.Comment lgComm; - private org.cts2.core.Comment ctsComm; - @Before - public void initialize() { - lgComm = new org.LexGrid.concepts.Comment(); - lgComm.setLanguage("testLanguage"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - lgComm.setValue(t); - lgComm.setPropertyId("propertyId"); - - ctsComm = baseDozerBeanMapper.map(lgComm, org.cts2.core.Comment.class); -// ctsComm.setExternalIdentifier(externalIdentifier) done -// ctsComm.setAssertedByCodeSystemVersion(assertedByCodeSystemVersion) TODO -// ctsComm.setAssertedInCodeSystemVersion(assertedInCodeSystemVersion) TODO -// ctsComm.setCorrespondingStatement(correspondingStatement) TODO -// ctsComm.setFormat(format) done -// ctsComm.setLanguage(language) done -// ctsComm.setSchema(schema) TODO -// ctsComm.setValue(value) done - } - - @Test - public void testGetValue() { - assertEquals("content", ctsComm.getValue()); - } - - @Test - public void testGetLanugange() { - assertEquals("testLanguage", ctsComm.getLanguage().getContent()); - } - - @Test - public void testGetDataType() { - assertEquals("string", ctsComm.getFormat().getContent()); - } - - @Test - public void testGetPropertyId(){ - assertEquals("propertyId", ctsComm.getExternalIdentifier()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/DefinitionToDefinitionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/DefinitionToDefinitionTest.java deleted file mode 100644 index 8c9f79e06b..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/DefinitionToDefinitionTest.java +++ /dev/null @@ -1,80 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.commonTypes.Text; -import org.cts2.core.types.DefinitionRole; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.DefinitionPreferredToDefinitionRoleConverter; -import org.junit.Before; -import org.junit.Test; - -public class DefinitionToDefinitionTest extends BaseDozerBeanMapperTest{ - @Resource - private DefinitionPreferredToDefinitionRoleConverter converter; - - private org.LexGrid.concepts.Definition lgDef; - private org.cts2.core.Definition ctsDef; - - @Before - public void initialize() { - lgDef = new org.LexGrid.concepts.Definition(); - lgDef.setPropertyId("test propertyid"); - lgDef.setLanguage("test language"); - Text t = new Text(); - t.setDataType("string"); - t.setContent("content"); - lgDef.setValue(t); - lgDef.addUsageContext("usage context 1"); - lgDef.addUsageContext("usage context 2"); - - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.converter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - - ctsDef = baseDozerBeanMapper.map(lgDef, org.cts2.core.Definition.class); -// ctsDef.setAssertedByCodeSystemVersion(assertedByCodeSystemVersion) n/a -// ctsDef.setAssertedInCodeSystemVersion(assertedInCodeSystemVersion) n/a -// ctsDef.setCorrespondingStatement(correspondingStatement) n/a -// ctsDef.setDefinitionRole(definitionRole) done -// ctsDef.setExternalIdentifier(externalIdentifier) done -// ctsDef.setFormat(format) done -// ctsDef.setLanguage(language) done -// ctsDef.setSchema(schema) n/a -// ctsDef.setUsageContext(usageContext) -// ctsDef.setValue(value) done - } - - @Test - public void testGetPropertyId(){ - assertEquals("test propertyid", ctsDef.getExternalIdentifier()); - } - - @Test - public void testGetLanguage() { - assertEquals("test language", ctsDef.getLanguage().getContent()); - } - - @Test - public void testGetValue() { - assertEquals("content", ctsDef.getValue()); - } - - @Test - public void testGetDataType() { - assertEquals("string", ctsDef.getFormat().getContent()); - } - - @Test - public void testGetIsPrefferred(){ - assertEquals(DefinitionRole.INFORMATIVE, ctsDef.getDefinitionRole()); - } - - @Test - public void testGetUsageContext() { - assertEquals("usage context 1", ctsDef.getUsageContext().getContent()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/PresentationToDesignationTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/PresentationToDesignationTest.java deleted file mode 100644 index eb2a56e540..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/PresentationToDesignationTest.java +++ /dev/null @@ -1,98 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Presentation; -import org.cts2.entity.Designation; -import org.cts2.entity.types.DesignationRole; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.PresentationPreferredToDesignationRoleConverter; -import org.junit.Before; -import org.junit.Test; - -public class PresentationToDesignationTest extends BaseDozerBeanMapperTest{ - - @Resource - private PresentationPreferredToDesignationRoleConverter converter; - private Presentation presentation; - private Designation designation; - - - @Before - public void initialize() { - presentation = new Presentation(); - presentation.setDegreeOfFidelity("testFed"); - presentation.setPropertyId("testPropertyID"); - presentation.setLanguage("en"); - Text value = new Text(); - value.setContent("testValue"); - value.setDataType("string"); - presentation.setValue(value); - presentation.setPropertyName("property name"); - - presentation.addUsageContext("test usage context 1"); - presentation.addUsageContext("test usage context 2"); - presentation.addUsageContext("test usage context 3"); - - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.converter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - - designation = baseDozerBeanMapper.map(presentation, Designation.class); - - // // renderURI -// designation.setCorrespondingStatement(correspondingStatement); n/a -// // enum: PREFERRED, ALTERNATIVE, HIDDEN -// designation.setDesignationRole(designationRole); -// designation.setDesignationType(designationType); - property name -// designation.setFormat(format); value type -// designation.setSchema(schema); n/a - // qualifier, source post to wiki - - } - - @Test - public void testGetDegreeOfFidelity() { - assertEquals("testFed", designation.getDegreeOfFidelity().getContent()); - } - - @Test - public void testGetPropertyId() { - assertEquals("testPropertyID", designation.getExternalIdentifier()); - } - - @Test - public void testGetValue() { - assertEquals("testValue", designation.getValue()); - } - - @Test - public void testGetLanguange() { - assertEquals("en", designation.getLanguage().getContent()); - } - - @Test - public void testGetUsageContext() { - assertEquals("test usage context 1", designation.getUsageContext(0).getContent()); - assertEquals("test usage context 2", designation.getUsageContext(1).getContent()); - assertEquals("test usage context 3", designation.getUsageContext(2).getContent()); - } - - @Test - public void testGetValueDataType() { - assertEquals("string", designation.getFormat().getContent()); - } - - @Test - public void testGetPropertyName(){ - assertEquals("property name", designation.getDesignationType().getContent()); - } - - @Test - public void testGetIsPreferred() { - assertEquals(DesignationRole.ALTERNATIVE, designation.getDesignationRole()); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/PropertyToPropertyTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/PropertyToPropertyTest.java deleted file mode 100644 index ce8374f9fa..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/PropertyToPropertyTest.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import org.LexGrid.commonTypes.Text; -import org.junit.Before; -import org.junit.Test; - -public class PropertyToPropertyTest extends BaseDozerBeanMapperTest { - private org.cts2.core.Property ctsProp; - private org.LexGrid.commonTypes.Property lgProp; - - @Before - public void initialize() { - lgProp = new org.LexGrid.commonTypes.Property(); - lgProp.setPropertyId("propertyId"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - lgProp.setValue(t); - lgProp.setLanguage("test lang"); - - ctsProp = baseDozerBeanMapper.map(lgProp, org.cts2.core.Property.class); -// ctsProp.setCorrespondingStatement(correspondingStatement) -// ctsProp.setExternalIdentifier(externalIdentifier) -// ctsProp.setSourceCodingSchemeVersion(sourceCodingSchemeVersion) -// ctsProp.setTag(tag) -// ctsProp.setValue(value) - - } - - @Test - public void testGetPropertyId() { - assertEquals("propertyId", ctsProp.getExternalIdentifier()); - } - - @Test - public void testGetValue() { - assertEquals("content", ctsProp.getValue().getValue()); - assertEquals("string", ctsProp.getValue().getFormat().getContent()); - } - - @Test - public void testGetLanguange() { - assertEquals("test lang", ctsProp.getValue().getLanguage().getContent()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToAnonymousEntityDescriptionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToAnonymousEntityDescriptionTest.java deleted file mode 100644 index 27bb0d5583..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToAnonymousEntityDescriptionTest.java +++ /dev/null @@ -1,360 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedDegreeOfFidelity; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.SupportedNamespace; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.AnonymousEntityDescription; -import org.cts2.entity.types.DesignationRole; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.AnonymousEntityDescriptionAboutConverter; -import org.cts2.internal.mapper.converter.AnonymousEntityDescriptionDefinitionListConverter; -import org.cts2.internal.mapper.converter.AnonymousEntityDescriptionDesignationListConverter; -import org.cts2.internal.mapper.converter.AnonymousEntityDescriptionNoteListConverter; -import org.cts2.internal.mapper.converter.AnonymousEntityDescriptionPropertyListConverter; -import org.cts2.internal.mapper.converter.DefinitionPreferredToDefinitionRoleConverter; -import org.cts2.internal.mapper.converter.PresentationPreferredToDesignationRoleConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Before; -import org.junit.Test; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; - -public class ResolvedConceptReferenceToAnonymousEntityDescriptionTest extends - BaseDozerBeanMapperTest { - private ResolvedConceptReference ref; - private AnonymousEntityDescription mapped; - - @Resource - private AnonymousEntityDescriptionAboutConverter anonymousEntityDescriptionAboutConverter; - @Resource - private PresentationPreferredToDesignationRoleConverter presentationConverter; - @Resource - private DefinitionPreferredToDefinitionRoleConverter definitionConverter; - @Resource - private AnonymousEntityDescriptionPropertyListConverter anonymousEntityDescriptionPropertyListConverter; - @Resource - private AnonymousEntityDescriptionDesignationListConverter anonymousEntityDescriptionDesignationListConverter; - @Resource - private AnonymousEntityDescriptionDefinitionListConverter anonymousEntityDescriptionDefinitionListConverter; - @Resource - private AnonymousEntityDescriptionNoteListConverter anonymousEntityDescriptionNoteListConverter; - - - @Before - public void initialize() { - ref = new ResolvedConceptReference(); - ref.setCode("testCode"); - ref.setCodeNamespace("testNamespace"); - ref.setCodingSchemeName("codingSchemeName"); - ref.setCodingSchemeURI("testUri"); - ref.setCodingSchemeVersion("testVersion"); - - Entity entity = new Entity(); - entity.setEntityCode("testCode"); - entity.setEntityCodeNamespace("testNamespace"); - - ref.setEntity(entity); - - // presentation - this.initPresentations(); - - // property - this.initProperties(); - - // comment - this.initComments(); - - // definition - this.initDefinitions(); - - CodingSchemeService css = EasyMock - .createMock(CodingSchemeService.class); - - CodingScheme cs = new CodingScheme(); - cs.setMappings(new Mappings()); - cs.getMappings().addSupportedNamespace(new SupportedNamespace()); - cs.getMappings().getSupportedNamespace(0).setLocalId("test-namespace"); - cs.getMappings().getSupportedNamespace(0).setUri("test-namespace-uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(0).setLocalId("test lang"); - cs.getMappings().getSupportedLanguage(0).setUri("test lang uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(1).setLocalId("en"); - cs.getMappings().getSupportedLanguage(1).setUri("en uri"); - cs.getMappings().addSupportedDataType(new SupportedDataType()); - cs.getMappings().getSupportedDataType(0).setLocalId("string"); - cs.getMappings().getSupportedDataType(0).setUri("string uri"); - cs.getMappings().addSupportedDegreeOfFidelity( - new SupportedDegreeOfFidelity()); - cs.getMappings().getSupportedDegreeOfFidelity(0).setLocalId("testFed"); - cs.getMappings().getSupportedDegreeOfFidelity(0).setUri("testFed uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(0) - .setLocalId("test usage context 1"); - cs.getMappings().getSupportedContext(0) - .setUri("test usage context 1 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(1) - .setLocalId("test usage context 2"); - cs.getMappings().getSupportedContext(1) - .setUri("test usage context 2 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(2) - .setLocalId("test usage context 3"); - cs.getMappings().getSupportedContext(2) - .setUri("test usage context 3 uri"); - - cs.setRepresentsVersion("testVersion"); - cs.setCodingSchemeURI("testUri"); - - EasyMock.expect( - css.getCodingSchemeByUriAndVersion("testUri", "testVersion")) - .andReturn(cs).times(5); - - EasyMock.replay(css); - - this.anonymousEntityDescriptionAboutConverter.setCodingSchemeService(css); - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.anonymousEntityDescriptionAboutConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - this.presentationConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - definitionConverter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - anonymousEntityDescriptionPropertyListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - anonymousEntityDescriptionPropertyListConverter.setCodingSchemeService(css); - anonymousEntityDescriptionDesignationListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - anonymousEntityDescriptionDesignationListConverter - .setCodingSchemeService(css); - anonymousEntityDescriptionDefinitionListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - anonymousEntityDescriptionDefinitionListConverter - .setCodingSchemeService(css); - anonymousEntityDescriptionNoteListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - anonymousEntityDescriptionNoteListConverter.setCodingSchemeService(css); - - mapped = baseDozerBeanMapper.map(ref, AnonymousEntityDescription.class); - // mapped.setAbout(about) - // mapped.setDefinition(vDefinitionArray) - // mapped.setDesignation(vDesignationArray) - // mapped.setEntityType(vEntityTypeArray) - // mapped.setNote(vNoteArray) - // mapped.setEntryState(entryState) ? - // mapped.setProperty(vPropertyArray) - // mapped.setEquivalentEntities(vEquivalentEntitiesArray) - // mapped.setDescribingCodeSystemVersion(describingCodeSystemVersion) - // mapped.setInstances(instances) - - } - - @Test - public void testGetCode() { - assertEquals("testCode", mapped.getEntityId().getName()); - } - - @Test - public void testGetNamespace() { - assertEquals("testNamespace", mapped.getEntityId().getNamespace()); - } - - @Test - public void testGetCodingSchemeURI() { - assertEquals("testUri", mapped.getDescribingCodeSystemVersion() - .getMeaning()); - } - - @Test - public void testGetCodingSchemeName() { - assertEquals("codingSchemeName", mapped - .getDescribingCodeSystemVersion().getContent()); - } - - @Test - public void testGetAbout() { - assertEquals("testUri:testCode", mapped.getAbout()); - } - - @Test - public void testGetPresentationCount() { - assertEquals(2, mapped.getDesignationCount()); - } - - @Test - public void testGetPresentation() { - assertEquals("testFed", mapped.getDesignation(0).getDegreeOfFidelity() - .getContent()); - assertEquals("en", mapped.getDesignation(0).getLanguage().getContent()); - assertEquals("testPropertyID", mapped.getDesignation(0) - .getExternalIdentifier()); - assertEquals("testValue", mapped.getDesignation(0).getValue()); - assertEquals("test usage context 1", mapped.getDesignation(0) - .getUsageContext(0).getContent()); - assertEquals("test usage context 2", mapped.getDesignation(0) - .getUsageContext(1).getContent()); - assertEquals("test usage context 3", mapped.getDesignation(0) - .getUsageContext(2).getContent()); - assertEquals(DesignationRole.ALTERNATIVE, mapped.getDesignation(0) - .getDesignationRole()); - assertEquals("en uri", mapped.getDesignation(0).getLanguage() - .getMeaning()); - assertEquals("testFed uri", mapped.getDesignation(0) - .getDegreeOfFidelity().getMeaning()); - assertEquals("string uri", mapped.getDesignation(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDesignation(0) - .getUsageContext(0).getMeaning()); - assertEquals("test usage context 2 uri", mapped.getDesignation(0) - .getUsageContext(1).getMeaning()); - assertEquals("test usage context 3 uri", mapped.getDesignation(0) - .getUsageContext(2).getMeaning()); - } - - @Test - public void testGetPropertyCount() { - assertEquals(2, mapped.getPropertyCount()); - } - - @Test - public void testGetProperty() { - assertEquals("propertyId", mapped.getProperty(0) - .getExternalIdentifier()); - assertEquals("content", mapped.getProperty(0).getValue().getValue()); - assertEquals("string", mapped.getProperty(0).getValue().getFormat() - .getContent()); - assertEquals("string uri", mapped.getProperty(0).getValue().getFormat() - .getMeaning()); - assertEquals("test lang", mapped.getProperty(0).getValue() - .getLanguage().getContent()); - assertEquals("test lang uri", mapped.getProperty(0).getValue() - .getLanguage().getMeaning()); - } - - @Test - public void testGetCommentCount() { - assertEquals(2, mapped.getNoteCount()); - } - - @Test - public void testGetComment() { - assertEquals("content", mapped.getNote(0).getValue()); - assertEquals("test lang", mapped.getNote(0).getLanguage() - .getContent()); - assertEquals("string", mapped.getNote(0).getFormat().getContent()); - assertEquals("propertyId", mapped.getNote(0).getExternalIdentifier()); - assertEquals("string uri", mapped.getNote(0).getFormat().getMeaning()); - assertEquals("test lang uri", mapped.getNote(0).getLanguage().getMeaning()); - } - - @Test - public void testGetDefinitionCount() { - assertEquals(2, mapped.getDefinitionCount()); - } - - @Test - public void testGetDefinition() { - assertEquals("test propertyid", mapped.getDefinition(0) - .getExternalIdentifier()); - assertEquals("test lang", mapped.getDefinition(0).getLanguage() - .getContent()); - assertEquals("content", mapped.getDefinition(0).getValue()); - assertEquals("string", mapped.getDefinition(0).getFormat().getContent()); - assertEquals(DefinitionRole.INFORMATIVE, mapped.getDefinition(0) - .getDefinitionRole()); - assertEquals("test usage context 1", mapped.getDefinition(0) - .getUsageContext().getContent()); - assertEquals("test lang uri", mapped.getDefinition(0).getLanguage() - .getMeaning()); - assertEquals("string uri", mapped.getDefinition(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDefinition(0) - .getUsageContext().getMeaning()); - - } - - private void initProperties() { - org.LexGrid.commonTypes.Property prop1 = new org.LexGrid.commonTypes.Property(); - prop1.setPropertyId("propertyId"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - prop1.setValue(t); - prop1.setLanguage("test lang"); - org.LexGrid.commonTypes.Property prop2 = new org.LexGrid.commonTypes.Property(); - prop2.setPropertyId("prop2"); - - ref.getEntity().addProperty(prop1); - ref.getEntity().addProperty(prop2); - } - - private void initComments() { - org.LexGrid.concepts.Comment com1 = new org.LexGrid.concepts.Comment(); - com1.setLanguage("test lang"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - com1.setValue(t); - com1.setPropertyId("propertyId"); - org.LexGrid.concepts.Comment com2 = new org.LexGrid.concepts.Comment(); - com2.setLanguage("test lang2"); - com2.setPropertyId("propertyId2"); - - ref.getEntity().addComment(com1); - ref.getEntity().addComment(com2); - } - - private void initDefinitions() { - org.LexGrid.concepts.Definition def1 = new org.LexGrid.concepts.Definition(); - def1.setPropertyId("test propertyid"); - def1.setLanguage("test lang"); - Text t = new Text(); - t.setDataType("string"); - t.setContent("content"); - def1.setValue(t); - def1.addUsageContext("test usage context 1"); - def1.addUsageContext("test usage context 2"); - org.LexGrid.concepts.Definition def2 = new org.LexGrid.concepts.Definition(); - def2.setPropertyId("test propertyid 2"); - - ref.getEntity().addDefinition(def1); - ref.getEntity().addDefinition(def2); - } - - private void initPresentations() { - org.LexGrid.concepts.Presentation presentation1 = new org.LexGrid.concepts.Presentation(); - presentation1.setDegreeOfFidelity("testFed"); - presentation1.setPropertyId("testPropertyID"); - presentation1.setLanguage("en"); - Text value = new Text(); - value.setContent("testValue"); - value.setDataType("string"); - presentation1.setValue(value); - presentation1.setPropertyName("property name"); - presentation1.addUsageContext("test usage context 1"); - presentation1.addUsageContext("test usage context 2"); - presentation1.addUsageContext("test usage context 3"); - org.LexGrid.concepts.Presentation presentation2 = new org.LexGrid.concepts.Presentation(); - presentation2.setDegreeOfFidelity("degree of fidelity"); - presentation2.setPropertyId("presentation 2"); - Text t2 = new Text(); - t2.setContent("2 content"); - t2.setDataType("string"); - - ref.getEntity().addPresentation(presentation1); - ref.getEntity().addPresentation(presentation2); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToAnonymousIndividualDescriptionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToAnonymousIndividualDescriptionTest.java deleted file mode 100644 index 176c801e5f..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToAnonymousIndividualDescriptionTest.java +++ /dev/null @@ -1,358 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedDegreeOfFidelity; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.SupportedNamespace; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.AnonymousIndividualDescription; -import org.cts2.entity.types.DesignationRole; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.DefinitionPreferredToDefinitionRoleConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionAboutConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionDefinitionListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionDesignationListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionNoteListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionPropertyListConverter; -import org.cts2.internal.mapper.converter.PresentationPreferredToDesignationRoleConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Before; -import org.junit.Test; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; - -public class ResolvedConceptReferenceToAnonymousIndividualDescriptionTest extends - BaseDozerBeanMapperTest { - @Resource - private NamedEntityDescriptionAboutConverter namedEntityDescriptionAboutConverter; - @Resource - private PresentationPreferredToDesignationRoleConverter presentationConverter; - @Resource - private DefinitionPreferredToDefinitionRoleConverter definitionConverter; - @Resource - private NamedEntityDescriptionPropertyListConverter namedEntityDescriptionPropertyListConverter; - @Resource - private NamedEntityDescriptionDesignationListConverter namedEntityDescriptionDesignationListConverter; - @Resource - private NamedEntityDescriptionDefinitionListConverter namedEntityDescriptionDefinitionListConverter; - @Resource - private NamedEntityDescriptionNoteListConverter namedEntityDescriptionNoteListConverter; - - private ResolvedConceptReference ref; - private AnonymousIndividualDescription mapped; - - @Before - public void initialize() { - ref = new ResolvedConceptReference(); - ref.setCode("testCode"); - ref.setCodeNamespace("testNamespace"); - ref.setCodingSchemeName("codingSchemeName"); - ref.setCodingSchemeURI("testUri"); - ref.setCodingSchemeVersion("testVersion"); - - Entity entity = new Entity(); - entity.setEntityCode("testCode"); - entity.setEntityCodeNamespace("testNamespace"); - - ref.setEntity(entity); - - // presentation - this.initPresentations(); - - // property - this.initProperties(); - - // comment - this.initComments(); - - // definition - this.initDefinitions(); - - CodingSchemeService css = EasyMock - .createMock(CodingSchemeService.class); - - CodingScheme cs = new CodingScheme(); - cs.setMappings(new Mappings()); - cs.getMappings().addSupportedNamespace(new SupportedNamespace()); - cs.getMappings().getSupportedNamespace(0).setLocalId("test-namespace"); - cs.getMappings().getSupportedNamespace(0).setUri("test-namespace-uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(0).setLocalId("test lang"); - cs.getMappings().getSupportedLanguage(0).setUri("test lang uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(1).setLocalId("en"); - cs.getMappings().getSupportedLanguage(1).setUri("en uri"); - cs.getMappings().addSupportedDataType(new SupportedDataType()); - cs.getMappings().getSupportedDataType(0).setLocalId("string"); - cs.getMappings().getSupportedDataType(0).setUri("string uri"); - cs.getMappings().addSupportedDegreeOfFidelity( - new SupportedDegreeOfFidelity()); - cs.getMappings().getSupportedDegreeOfFidelity(0).setLocalId("testFed"); - cs.getMappings().getSupportedDegreeOfFidelity(0).setUri("testFed uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(0) - .setLocalId("test usage context 1"); - cs.getMappings().getSupportedContext(0) - .setUri("test usage context 1 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(1) - .setLocalId("test usage context 2"); - cs.getMappings().getSupportedContext(1) - .setUri("test usage context 2 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(2) - .setLocalId("test usage context 3"); - cs.getMappings().getSupportedContext(2) - .setUri("test usage context 3 uri"); - - cs.setRepresentsVersion("testVersion"); - cs.setCodingSchemeURI("testUri"); - - EasyMock.expect( - css.getCodingSchemeByUriAndVersion("testUri", "testVersion")) - .andReturn(cs).times(5); - - EasyMock.replay(css); - - this.namedEntityDescriptionAboutConverter.setCodingSchemeService(css); - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.namedEntityDescriptionAboutConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - this.presentationConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - definitionConverter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - namedEntityDescriptionPropertyListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionPropertyListConverter.setCodingSchemeService(css); - namedEntityDescriptionDesignationListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionDesignationListConverter - .setCodingSchemeService(css); - namedEntityDescriptionDefinitionListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionDefinitionListConverter - .setCodingSchemeService(css); - namedEntityDescriptionNoteListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionNoteListConverter.setCodingSchemeService(css); - - mapped = baseDozerBeanMapper.map(ref, AnonymousIndividualDescription.class); - // mapped.setAbout(about) - // mapped.setDefinition(vDefinitionArray) - // mapped.setDesignation(vDesignationArray) - // mapped.setEntityType(vEntityTypeArray) - // mapped.setNote(vNoteArray) - // mapped.setEntryState(entryState) ? - // mapped.setProperty(vPropertyArray) - // mapped.setEquivalentEntities(vEquivalentEntitiesArray) - // mapped.setDescribingCodeSystemVersion(describingCodeSystemVersion) - // mapped.setInstances(instances) - - } - - @Test - public void testGetCode() { - assertEquals("testCode", mapped.getEntityId().getName()); - } - - @Test - public void testGetNamespace() { - assertEquals("testNamespace", mapped.getEntityId().getNamespace()); - } - - @Test - public void testGetCodingSchemeURI() { - assertEquals("testUri", mapped.getDescribingCodeSystemVersion() - .getMeaning()); - } - - @Test - public void testGetCodingSchemeName() { - assertEquals("codingSchemeName", mapped - .getDescribingCodeSystemVersion().getContent()); - } - - @Test - public void testGetAbout() { - assertEquals("testUri:testCode", mapped.getAbout()); - } - - @Test - public void testGetPresentationCount() { - assertEquals(2, mapped.getDesignationCount()); - } - - @Test - public void testGetPresentation() { - assertEquals("testFed", mapped.getDesignation(0).getDegreeOfFidelity() - .getContent()); - assertEquals("en", mapped.getDesignation(0).getLanguage().getContent()); - assertEquals("testPropertyID", mapped.getDesignation(0) - .getExternalIdentifier()); - assertEquals("testValue", mapped.getDesignation(0).getValue()); - assertEquals("test usage context 1", mapped.getDesignation(0) - .getUsageContext(0).getContent()); - assertEquals("test usage context 2", mapped.getDesignation(0) - .getUsageContext(1).getContent()); - assertEquals("test usage context 3", mapped.getDesignation(0) - .getUsageContext(2).getContent()); - assertEquals(DesignationRole.ALTERNATIVE, mapped.getDesignation(0) - .getDesignationRole()); - assertEquals("en uri", mapped.getDesignation(0).getLanguage() - .getMeaning()); - assertEquals("testFed uri", mapped.getDesignation(0) - .getDegreeOfFidelity().getMeaning()); - assertEquals("string uri", mapped.getDesignation(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDesignation(0) - .getUsageContext(0).getMeaning()); - assertEquals("test usage context 2 uri", mapped.getDesignation(0) - .getUsageContext(1).getMeaning()); - assertEquals("test usage context 3 uri", mapped.getDesignation(0) - .getUsageContext(2).getMeaning()); - } - - @Test - public void testGetPropertyCount() { - assertEquals(2, mapped.getPropertyCount()); - } - - @Test - public void testGetProperty() { - assertEquals("propertyId", mapped.getProperty(0) - .getExternalIdentifier()); - assertEquals("content", mapped.getProperty(0).getValue().getValue()); - assertEquals("string", mapped.getProperty(0).getValue().getFormat() - .getContent()); - assertEquals("string uri", mapped.getProperty(0).getValue().getFormat() - .getMeaning()); - assertEquals("test lang", mapped.getProperty(0).getValue() - .getLanguage().getContent()); - assertEquals("test lang uri", mapped.getProperty(0).getValue() - .getLanguage().getMeaning()); - } - - @Test - public void testGetCommentCount() { - assertEquals(2, mapped.getNoteCount()); - } - - @Test - public void testGetComment() { - assertEquals("content", mapped.getNote(0).getValue()); - assertEquals("test lang", mapped.getNote(0).getLanguage() - .getContent()); - assertEquals("string", mapped.getNote(0).getFormat().getContent()); - assertEquals("propertyId", mapped.getNote(0).getExternalIdentifier()); - assertEquals("string uri", mapped.getNote(0).getFormat().getMeaning()); - assertEquals("test lang uri", mapped.getNote(0).getLanguage().getMeaning()); - } - - @Test - public void testGetDefinitionCount() { - assertEquals(2, mapped.getDefinitionCount()); - } - - @Test - public void testGetDefinition() { - assertEquals("test propertyid", mapped.getDefinition(0) - .getExternalIdentifier()); - assertEquals("test lang", mapped.getDefinition(0).getLanguage() - .getContent()); - assertEquals("content", mapped.getDefinition(0).getValue()); - assertEquals("string", mapped.getDefinition(0).getFormat().getContent()); - assertEquals(DefinitionRole.INFORMATIVE, mapped.getDefinition(0) - .getDefinitionRole()); - assertEquals("test usage context 1", mapped.getDefinition(0) - .getUsageContext().getContent()); - assertEquals("test lang uri", mapped.getDefinition(0).getLanguage() - .getMeaning()); - assertEquals("string uri", mapped.getDefinition(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDefinition(0) - .getUsageContext().getMeaning()); - - } - - private void initProperties() { - org.LexGrid.commonTypes.Property prop1 = new org.LexGrid.commonTypes.Property(); - prop1.setPropertyId("propertyId"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - prop1.setValue(t); - prop1.setLanguage("test lang"); - org.LexGrid.commonTypes.Property prop2 = new org.LexGrid.commonTypes.Property(); - prop2.setPropertyId("prop2"); - - ref.getEntity().addProperty(prop1); - ref.getEntity().addProperty(prop2); - } - - private void initComments() { - org.LexGrid.concepts.Comment com1 = new org.LexGrid.concepts.Comment(); - com1.setLanguage("test lang"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - com1.setValue(t); - com1.setPropertyId("propertyId"); - org.LexGrid.concepts.Comment com2 = new org.LexGrid.concepts.Comment(); - com2.setLanguage("test lang2"); - com2.setPropertyId("propertyId2"); - - ref.getEntity().addComment(com1); - ref.getEntity().addComment(com2); - } - - private void initDefinitions() { - org.LexGrid.concepts.Definition def1 = new org.LexGrid.concepts.Definition(); - def1.setPropertyId("test propertyid"); - def1.setLanguage("test lang"); - Text t = new Text(); - t.setDataType("string"); - t.setContent("content"); - def1.setValue(t); - def1.addUsageContext("test usage context 1"); - def1.addUsageContext("test usage context 2"); - org.LexGrid.concepts.Definition def2 = new org.LexGrid.concepts.Definition(); - def2.setPropertyId("test propertyid 2"); - - ref.getEntity().addDefinition(def1); - ref.getEntity().addDefinition(def2); - } - - private void initPresentations() { - org.LexGrid.concepts.Presentation presentation1 = new org.LexGrid.concepts.Presentation(); - presentation1.setDegreeOfFidelity("testFed"); - presentation1.setPropertyId("testPropertyID"); - presentation1.setLanguage("en"); - Text value = new Text(); - value.setContent("testValue"); - value.setDataType("string"); - presentation1.setValue(value); - presentation1.setPropertyName("property name"); - presentation1.addUsageContext("test usage context 1"); - presentation1.addUsageContext("test usage context 2"); - presentation1.addUsageContext("test usage context 3"); - org.LexGrid.concepts.Presentation presentation2 = new org.LexGrid.concepts.Presentation(); - presentation2.setDegreeOfFidelity("degree of fidelity"); - presentation2.setPropertyId("presentation 2"); - Text t2 = new Text(); - t2.setContent("2 content"); - t2.setDataType("string"); - - ref.getEntity().addPresentation(presentation1); - ref.getEntity().addPresentation(presentation2); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToEntityDirectoryEntryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToEntityDirectoryEntryTest.java deleted file mode 100644 index fef382c406..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToEntityDirectoryEntryTest.java +++ /dev/null @@ -1,84 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedNamespace; -import org.cts2.entity.EntityDirectoryEntry; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.EntityDirectoryEntryAboutConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Before; -import org.junit.Test; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; - -public class ResolvedConceptReferenceToEntityDirectoryEntryTest extends BaseDozerBeanMapperTest { - - @Resource - private EntityDirectoryEntryAboutConverter entityDirectoryEntryAboutConverter; - - private ResolvedConceptReference ref; - private EntityDirectoryEntry mapped; - - - @Before - public void initialize() { - ref = new ResolvedConceptReference(); - ref.setCode("test code"); - ref.setCodeNamespace("test-namespace"); - ref.setCodingSchemeURI("testUri"); - ref.setCodingSchemeVersion("testVersion"); - - CodingSchemeService css = EasyMock.createMock(CodingSchemeService.class); - - CodingScheme cs = new CodingScheme(); - cs.setMappings(new Mappings()); - cs.getMappings().addSupportedNamespace(new SupportedNamespace()); - cs.getMappings().getSupportedNamespace(0).setLocalId("test-namespace"); - cs.getMappings().getSupportedNamespace(0).setUri("test-namespace-uri"); - cs.setRepresentsVersion("testVersion"); - cs.setCodingSchemeURI("testUri"); - - EasyMock.expect(css.getCodingSchemeByUriAndVersion("testUri", "testVersion")).andReturn(cs).times(1); - - EasyMock.replay(css); - - this.entityDirectoryEntryAboutConverter.setCodingSchemeService(css); - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.entityDirectoryEntryAboutConverter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - - mapped = baseDozerBeanMapper.map(ref, EntityDirectoryEntry.class); - - } - - @Test - public void converterIsNotNull(){ - assertNotNull(this.entityDirectoryEntryAboutConverter); - } - - @Test - public void testGetCode(){ - // map to local entity name - assertEquals("test code", mapped.getLocalEntityName().getName()); - // map to resource name - assertEquals("test code", mapped.getResourceName()); - } - - @Test - public void testGetNamespace(){ - assertEquals("test-namespace", mapped.getLocalEntityName().getNamespace()); - - } - - @Test - public void testCTS2About() { - assertEquals("test-namespace-uri:test code", mapped.getAbout()); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToNamedEntityDescriptionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToNamedEntityDescriptionTest.java deleted file mode 100644 index 0487af8f12..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToNamedEntityDescriptionTest.java +++ /dev/null @@ -1,358 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedDegreeOfFidelity; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.SupportedNamespace; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.entity.types.DesignationRole; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.DefinitionPreferredToDefinitionRoleConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionAboutConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionDefinitionListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionDesignationListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionNoteListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionPropertyListConverter; -import org.cts2.internal.mapper.converter.PresentationPreferredToDesignationRoleConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Before; -import org.junit.Test; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; - -public class ResolvedConceptReferenceToNamedEntityDescriptionTest extends - BaseDozerBeanMapperTest { - @Resource - private NamedEntityDescriptionAboutConverter namedEntityDescriptionAboutConverter; - @Resource - private PresentationPreferredToDesignationRoleConverter presentationConverter; - @Resource - private DefinitionPreferredToDefinitionRoleConverter definitionConverter; - @Resource - private NamedEntityDescriptionPropertyListConverter namedEntityDescriptionPropertyListConverter; - @Resource - private NamedEntityDescriptionDesignationListConverter namedEntityDescriptionDesignationListConverter; - @Resource - private NamedEntityDescriptionDefinitionListConverter namedEntityDescriptionDefinitionListConverter; - @Resource - private NamedEntityDescriptionNoteListConverter namedEntityDescriptionNoteListConverter; - - private ResolvedConceptReference ref; - private NamedEntityDescription mapped; - - @Before - public void initialize() { - ref = new ResolvedConceptReference(); - ref.setCode("testCode"); - ref.setCodeNamespace("testNamespace"); - ref.setCodingSchemeName("codingSchemeName"); - ref.setCodingSchemeURI("testUri"); - ref.setCodingSchemeVersion("testVersion"); - - Entity entity = new Entity(); - entity.setEntityCode("testCode"); - entity.setEntityCodeNamespace("testNamespace"); - - ref.setEntity(entity); - - // presentation - this.initPresentations(); - - // property - this.initProperties(); - - // comment - this.initComments(); - - // definition - this.initDefinitions(); - - CodingSchemeService css = EasyMock - .createMock(CodingSchemeService.class); - - CodingScheme cs = new CodingScheme(); - cs.setMappings(new Mappings()); - cs.getMappings().addSupportedNamespace(new SupportedNamespace()); - cs.getMappings().getSupportedNamespace(0).setLocalId("test-namespace"); - cs.getMappings().getSupportedNamespace(0).setUri("test-namespace-uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(0).setLocalId("test lang"); - cs.getMappings().getSupportedLanguage(0).setUri("test lang uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(1).setLocalId("en"); - cs.getMappings().getSupportedLanguage(1).setUri("en uri"); - cs.getMappings().addSupportedDataType(new SupportedDataType()); - cs.getMappings().getSupportedDataType(0).setLocalId("string"); - cs.getMappings().getSupportedDataType(0).setUri("string uri"); - cs.getMappings().addSupportedDegreeOfFidelity( - new SupportedDegreeOfFidelity()); - cs.getMappings().getSupportedDegreeOfFidelity(0).setLocalId("testFed"); - cs.getMappings().getSupportedDegreeOfFidelity(0).setUri("testFed uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(0) - .setLocalId("test usage context 1"); - cs.getMappings().getSupportedContext(0) - .setUri("test usage context 1 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(1) - .setLocalId("test usage context 2"); - cs.getMappings().getSupportedContext(1) - .setUri("test usage context 2 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(2) - .setLocalId("test usage context 3"); - cs.getMappings().getSupportedContext(2) - .setUri("test usage context 3 uri"); - - cs.setRepresentsVersion("testVersion"); - cs.setCodingSchemeURI("testUri"); - - EasyMock.expect( - css.getCodingSchemeByUriAndVersion("testUri", "testVersion")) - .andReturn(cs).times(5); - - EasyMock.replay(css); - - this.namedEntityDescriptionAboutConverter.setCodingSchemeService(css); - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.namedEntityDescriptionAboutConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - this.presentationConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - definitionConverter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - namedEntityDescriptionPropertyListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionPropertyListConverter.setCodingSchemeService(css); - namedEntityDescriptionDesignationListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionDesignationListConverter - .setCodingSchemeService(css); - namedEntityDescriptionDefinitionListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionDefinitionListConverter - .setCodingSchemeService(css); - namedEntityDescriptionNoteListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionNoteListConverter.setCodingSchemeService(css); - - mapped = baseDozerBeanMapper.map(ref, NamedEntityDescription.class); - // mapped.setAbout(about) - // mapped.setDefinition(vDefinitionArray) - // mapped.setDesignation(vDesignationArray) - // mapped.setEntityType(vEntityTypeArray) - // mapped.setNote(vNoteArray) - // mapped.setEntryState(entryState) ? - // mapped.setProperty(vPropertyArray) - // mapped.setEquivalentEntities(vEquivalentEntitiesArray) - // mapped.setDescribingCodeSystemVersion(describingCodeSystemVersion) - // mapped.setInstances(instances) - - } - - @Test - public void testGetCode() { - assertEquals("testCode", mapped.getEntityId().getName()); - } - - @Test - public void testGetNamespace() { - assertEquals("testNamespace", mapped.getEntityId().getNamespace()); - } - - @Test - public void testGetCodingSchemeURI() { - assertEquals("testUri", mapped.getDescribingCodeSystemVersion() - .getMeaning()); - } - - @Test - public void testGetCodingSchemeName() { - assertEquals("codingSchemeName", mapped - .getDescribingCodeSystemVersion().getContent()); - } - - @Test - public void testGetAbout() { - assertEquals("testUri:testCode", mapped.getAbout()); - } - - @Test - public void testGetPresentationCount() { - assertEquals(2, mapped.getDesignationCount()); - } - - @Test - public void testGetPresentation() { - assertEquals("testFed", mapped.getDesignation(0).getDegreeOfFidelity() - .getContent()); - assertEquals("en", mapped.getDesignation(0).getLanguage().getContent()); - assertEquals("testPropertyID", mapped.getDesignation(0) - .getExternalIdentifier()); - assertEquals("testValue", mapped.getDesignation(0).getValue()); - assertEquals("test usage context 1", mapped.getDesignation(0) - .getUsageContext(0).getContent()); - assertEquals("test usage context 2", mapped.getDesignation(0) - .getUsageContext(1).getContent()); - assertEquals("test usage context 3", mapped.getDesignation(0) - .getUsageContext(2).getContent()); - assertEquals(DesignationRole.ALTERNATIVE, mapped.getDesignation(0) - .getDesignationRole()); - assertEquals("en uri", mapped.getDesignation(0).getLanguage() - .getMeaning()); - assertEquals("testFed uri", mapped.getDesignation(0) - .getDegreeOfFidelity().getMeaning()); - assertEquals("string uri", mapped.getDesignation(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDesignation(0) - .getUsageContext(0).getMeaning()); - assertEquals("test usage context 2 uri", mapped.getDesignation(0) - .getUsageContext(1).getMeaning()); - assertEquals("test usage context 3 uri", mapped.getDesignation(0) - .getUsageContext(2).getMeaning()); - } - - @Test - public void testGetPropertyCount() { - assertEquals(2, mapped.getPropertyCount()); - } - - @Test - public void testGetProperty() { - assertEquals("propertyId", mapped.getProperty(0) - .getExternalIdentifier()); - assertEquals("content", mapped.getProperty(0).getValue().getValue()); - assertEquals("string", mapped.getProperty(0).getValue().getFormat() - .getContent()); - assertEquals("string uri", mapped.getProperty(0).getValue().getFormat() - .getMeaning()); - assertEquals("test lang", mapped.getProperty(0).getValue() - .getLanguage().getContent()); - assertEquals("test lang uri", mapped.getProperty(0).getValue() - .getLanguage().getMeaning()); - } - - @Test - public void testGetCommentCount() { - assertEquals(2, mapped.getNoteCount()); - } - - @Test - public void testGetComment() { - assertEquals("content", mapped.getNote(0).getValue()); - assertEquals("test lang", mapped.getNote(0).getLanguage() - .getContent()); - assertEquals("string", mapped.getNote(0).getFormat().getContent()); - assertEquals("propertyId", mapped.getNote(0).getExternalIdentifier()); - assertEquals("string uri", mapped.getNote(0).getFormat().getMeaning()); - assertEquals("test lang uri", mapped.getNote(0).getLanguage().getMeaning()); - } - - @Test - public void testGetDefinitionCount() { - assertEquals(2, mapped.getDefinitionCount()); - } - - @Test - public void testGetDefinition() { - assertEquals("test propertyid", mapped.getDefinition(0) - .getExternalIdentifier()); - assertEquals("test lang", mapped.getDefinition(0).getLanguage() - .getContent()); - assertEquals("content", mapped.getDefinition(0).getValue()); - assertEquals("string", mapped.getDefinition(0).getFormat().getContent()); - assertEquals(DefinitionRole.INFORMATIVE, mapped.getDefinition(0) - .getDefinitionRole()); - assertEquals("test usage context 1", mapped.getDefinition(0) - .getUsageContext().getContent()); - assertEquals("test lang uri", mapped.getDefinition(0).getLanguage() - .getMeaning()); - assertEquals("string uri", mapped.getDefinition(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDefinition(0) - .getUsageContext().getMeaning()); - - } - - private void initProperties() { - org.LexGrid.commonTypes.Property prop1 = new org.LexGrid.commonTypes.Property(); - prop1.setPropertyId("propertyId"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - prop1.setValue(t); - prop1.setLanguage("test lang"); - org.LexGrid.commonTypes.Property prop2 = new org.LexGrid.commonTypes.Property(); - prop2.setPropertyId("prop2"); - - ref.getEntity().addProperty(prop1); - ref.getEntity().addProperty(prop2); - } - - private void initComments() { - org.LexGrid.concepts.Comment com1 = new org.LexGrid.concepts.Comment(); - com1.setLanguage("test lang"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - com1.setValue(t); - com1.setPropertyId("propertyId"); - org.LexGrid.concepts.Comment com2 = new org.LexGrid.concepts.Comment(); - com2.setLanguage("test lang2"); - com2.setPropertyId("propertyId2"); - - ref.getEntity().addComment(com1); - ref.getEntity().addComment(com2); - } - - private void initDefinitions() { - org.LexGrid.concepts.Definition def1 = new org.LexGrid.concepts.Definition(); - def1.setPropertyId("test propertyid"); - def1.setLanguage("test lang"); - Text t = new Text(); - t.setDataType("string"); - t.setContent("content"); - def1.setValue(t); - def1.addUsageContext("test usage context 1"); - def1.addUsageContext("test usage context 2"); - org.LexGrid.concepts.Definition def2 = new org.LexGrid.concepts.Definition(); - def2.setPropertyId("test propertyid 2"); - - ref.getEntity().addDefinition(def1); - ref.getEntity().addDefinition(def2); - } - - private void initPresentations() { - org.LexGrid.concepts.Presentation presentation1 = new org.LexGrid.concepts.Presentation(); - presentation1.setDegreeOfFidelity("testFed"); - presentation1.setPropertyId("testPropertyID"); - presentation1.setLanguage("en"); - Text value = new Text(); - value.setContent("testValue"); - value.setDataType("string"); - presentation1.setValue(value); - presentation1.setPropertyName("property name"); - presentation1.addUsageContext("test usage context 1"); - presentation1.addUsageContext("test usage context 2"); - presentation1.addUsageContext("test usage context 3"); - org.LexGrid.concepts.Presentation presentation2 = new org.LexGrid.concepts.Presentation(); - presentation2.setDegreeOfFidelity("degree of fidelity"); - presentation2.setPropertyId("presentation 2"); - Text t2 = new Text(); - t2.setContent("2 content"); - t2.setDataType("string"); - - ref.getEntity().addPresentation(presentation1); - ref.getEntity().addPresentation(presentation2); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToNamedIndividualDescriptionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToNamedIndividualDescriptionTest.java deleted file mode 100644 index 0886e4e1ce..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ResolvedConceptReferenceToNamedIndividualDescriptionTest.java +++ /dev/null @@ -1,358 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.LexGrid.commonTypes.Text; -import org.LexGrid.concepts.Entity; -import org.LexGrid.naming.Mappings; -import org.LexGrid.naming.SupportedContext; -import org.LexGrid.naming.SupportedDataType; -import org.LexGrid.naming.SupportedDegreeOfFidelity; -import org.LexGrid.naming.SupportedLanguage; -import org.LexGrid.naming.SupportedNamespace; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.NamedIndividualDescription; -import org.cts2.entity.types.DesignationRole; -import org.cts2.internal.lexevs.identity.DefaultLexEvsIdentityConverter; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.internal.mapper.converter.DefinitionPreferredToDefinitionRoleConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionAboutConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionDefinitionListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionDesignationListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionNoteListConverter; -import org.cts2.internal.mapper.converter.NamedEntityDescriptionPropertyListConverter; -import org.cts2.internal.mapper.converter.PresentationPreferredToDesignationRoleConverter; -import org.easymock.classextension.EasyMock; -import org.junit.Before; -import org.junit.Test; -import org.lexevs.dao.database.service.codingscheme.CodingSchemeService; - -public class ResolvedConceptReferenceToNamedIndividualDescriptionTest extends - BaseDozerBeanMapperTest { - @Resource - private NamedEntityDescriptionAboutConverter namedEntityDescriptionAboutConverter; - @Resource - private PresentationPreferredToDesignationRoleConverter presentationConverter; - @Resource - private DefinitionPreferredToDefinitionRoleConverter definitionConverter; - @Resource - private NamedEntityDescriptionPropertyListConverter namedEntityDescriptionPropertyListConverter; - @Resource - private NamedEntityDescriptionDesignationListConverter namedEntityDescriptionDesignationListConverter; - @Resource - private NamedEntityDescriptionDefinitionListConverter namedEntityDescriptionDefinitionListConverter; - @Resource - private NamedEntityDescriptionNoteListConverter namedEntityDescriptionNoteListConverter; - - private ResolvedConceptReference ref; - private NamedIndividualDescription mapped; - - @Before - public void initialize() { - ref = new ResolvedConceptReference(); - ref.setCode("testCode"); - ref.setCodeNamespace("testNamespace"); - ref.setCodingSchemeName("codingSchemeName"); - ref.setCodingSchemeURI("testUri"); - ref.setCodingSchemeVersion("testVersion"); - - Entity entity = new Entity(); - entity.setEntityCode("testCode"); - entity.setEntityCodeNamespace("testNamespace"); - - ref.setEntity(entity); - - // presentation - this.initPresentations(); - - // property - this.initProperties(); - - // comment - this.initComments(); - - // definition - this.initDefinitions(); - - CodingSchemeService css = EasyMock - .createMock(CodingSchemeService.class); - - CodingScheme cs = new CodingScheme(); - cs.setMappings(new Mappings()); - cs.getMappings().addSupportedNamespace(new SupportedNamespace()); - cs.getMappings().getSupportedNamespace(0).setLocalId("test-namespace"); - cs.getMappings().getSupportedNamespace(0).setUri("test-namespace-uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(0).setLocalId("test lang"); - cs.getMappings().getSupportedLanguage(0).setUri("test lang uri"); - cs.getMappings().addSupportedLanguage(new SupportedLanguage()); - cs.getMappings().getSupportedLanguage(1).setLocalId("en"); - cs.getMappings().getSupportedLanguage(1).setUri("en uri"); - cs.getMappings().addSupportedDataType(new SupportedDataType()); - cs.getMappings().getSupportedDataType(0).setLocalId("string"); - cs.getMappings().getSupportedDataType(0).setUri("string uri"); - cs.getMappings().addSupportedDegreeOfFidelity( - new SupportedDegreeOfFidelity()); - cs.getMappings().getSupportedDegreeOfFidelity(0).setLocalId("testFed"); - cs.getMappings().getSupportedDegreeOfFidelity(0).setUri("testFed uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(0) - .setLocalId("test usage context 1"); - cs.getMappings().getSupportedContext(0) - .setUri("test usage context 1 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(1) - .setLocalId("test usage context 2"); - cs.getMappings().getSupportedContext(1) - .setUri("test usage context 2 uri"); - cs.getMappings().addSupportedContext(new SupportedContext()); - cs.getMappings().getSupportedContext(2) - .setLocalId("test usage context 3"); - cs.getMappings().getSupportedContext(2) - .setUri("test usage context 3 uri"); - - cs.setRepresentsVersion("testVersion"); - cs.setCodingSchemeURI("testUri"); - - EasyMock.expect( - css.getCodingSchemeByUriAndVersion("testUri", "testVersion")) - .andReturn(cs).times(5); - - EasyMock.replay(css); - - this.namedEntityDescriptionAboutConverter.setCodingSchemeService(css); - LexEvsIdentityConverter lexEvsIdentityConverter = new DefaultLexEvsIdentityConverter(); - this.namedEntityDescriptionAboutConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - this.presentationConverter - .setLexEvsIdentityConverter(lexEvsIdentityConverter); - definitionConverter.setLexEvsIdentityConverter(lexEvsIdentityConverter); - namedEntityDescriptionPropertyListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionPropertyListConverter.setCodingSchemeService(css); - namedEntityDescriptionDesignationListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionDesignationListConverter - .setCodingSchemeService(css); - namedEntityDescriptionDefinitionListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionDefinitionListConverter - .setCodingSchemeService(css); - namedEntityDescriptionNoteListConverter - .setBaseDozerBeanMapper(baseDozerBeanMapper); - namedEntityDescriptionNoteListConverter.setCodingSchemeService(css); - - mapped = baseDozerBeanMapper.map(ref, NamedIndividualDescription.class); - // mapped.setAbout(about) - // mapped.setDefinition(vDefinitionArray) - // mapped.setDesignation(vDesignationArray) - // mapped.setEntityType(vEntityTypeArray) - // mapped.setNote(vNoteArray) - // mapped.setEntryState(entryState) ? - // mapped.setProperty(vPropertyArray) - // mapped.setEquivalentEntities(vEquivalentEntitiesArray) - // mapped.setDescribingCodeSystemVersion(describingCodeSystemVersion) - // mapped.setInstances(instances) - - } - - @Test - public void testGetCode() { - assertEquals("testCode", mapped.getEntityId().getName()); - } - - @Test - public void testGetNamespace() { - assertEquals("testNamespace", mapped.getEntityId().getNamespace()); - } - - @Test - public void testGetCodingSchemeURI() { - assertEquals("testUri", mapped.getDescribingCodeSystemVersion() - .getMeaning()); - } - - @Test - public void testGetCodingSchemeName() { - assertEquals("codingSchemeName", mapped - .getDescribingCodeSystemVersion().getContent()); - } - - @Test - public void testGetAbout() { - assertEquals("testUri:testCode", mapped.getAbout()); - } - - @Test - public void testGetPresentationCount() { - assertEquals(2, mapped.getDesignationCount()); - } - - @Test - public void testGetPresentation() { - assertEquals("testFed", mapped.getDesignation(0).getDegreeOfFidelity() - .getContent()); - assertEquals("en", mapped.getDesignation(0).getLanguage().getContent()); - assertEquals("testPropertyID", mapped.getDesignation(0) - .getExternalIdentifier()); - assertEquals("testValue", mapped.getDesignation(0).getValue()); - assertEquals("test usage context 1", mapped.getDesignation(0) - .getUsageContext(0).getContent()); - assertEquals("test usage context 2", mapped.getDesignation(0) - .getUsageContext(1).getContent()); - assertEquals("test usage context 3", mapped.getDesignation(0) - .getUsageContext(2).getContent()); - assertEquals(DesignationRole.ALTERNATIVE, mapped.getDesignation(0) - .getDesignationRole()); - assertEquals("en uri", mapped.getDesignation(0).getLanguage() - .getMeaning()); - assertEquals("testFed uri", mapped.getDesignation(0) - .getDegreeOfFidelity().getMeaning()); - assertEquals("string uri", mapped.getDesignation(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDesignation(0) - .getUsageContext(0).getMeaning()); - assertEquals("test usage context 2 uri", mapped.getDesignation(0) - .getUsageContext(1).getMeaning()); - assertEquals("test usage context 3 uri", mapped.getDesignation(0) - .getUsageContext(2).getMeaning()); - } - - @Test - public void testGetPropertyCount() { - assertEquals(2, mapped.getPropertyCount()); - } - - @Test - public void testGetProperty() { - assertEquals("propertyId", mapped.getProperty(0) - .getExternalIdentifier()); - assertEquals("content", mapped.getProperty(0).getValue().getValue()); - assertEquals("string", mapped.getProperty(0).getValue().getFormat() - .getContent()); - assertEquals("string uri", mapped.getProperty(0).getValue().getFormat() - .getMeaning()); - assertEquals("test lang", mapped.getProperty(0).getValue() - .getLanguage().getContent()); - assertEquals("test lang uri", mapped.getProperty(0).getValue() - .getLanguage().getMeaning()); - } - - @Test - public void testGetCommentCount() { - assertEquals(2, mapped.getNoteCount()); - } - - @Test - public void testGetComment() { - assertEquals("content", mapped.getNote(0).getValue()); - assertEquals("test lang", mapped.getNote(0).getLanguage() - .getContent()); - assertEquals("string", mapped.getNote(0).getFormat().getContent()); - assertEquals("propertyId", mapped.getNote(0).getExternalIdentifier()); - assertEquals("string uri", mapped.getNote(0).getFormat().getMeaning()); - assertEquals("test lang uri", mapped.getNote(0).getLanguage().getMeaning()); - } - - @Test - public void testGetDefinitionCount() { - assertEquals(2, mapped.getDefinitionCount()); - } - - @Test - public void testGetDefinition() { - assertEquals("test propertyid", mapped.getDefinition(0) - .getExternalIdentifier()); - assertEquals("test lang", mapped.getDefinition(0).getLanguage() - .getContent()); - assertEquals("content", mapped.getDefinition(0).getValue()); - assertEquals("string", mapped.getDefinition(0).getFormat().getContent()); - assertEquals(DefinitionRole.INFORMATIVE, mapped.getDefinition(0) - .getDefinitionRole()); - assertEquals("test usage context 1", mapped.getDefinition(0) - .getUsageContext().getContent()); - assertEquals("test lang uri", mapped.getDefinition(0).getLanguage() - .getMeaning()); - assertEquals("string uri", mapped.getDefinition(0).getFormat() - .getMeaning()); - assertEquals("test usage context 1 uri", mapped.getDefinition(0) - .getUsageContext().getMeaning()); - - } - - private void initProperties() { - org.LexGrid.commonTypes.Property prop1 = new org.LexGrid.commonTypes.Property(); - prop1.setPropertyId("propertyId"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - prop1.setValue(t); - prop1.setLanguage("test lang"); - org.LexGrid.commonTypes.Property prop2 = new org.LexGrid.commonTypes.Property(); - prop2.setPropertyId("prop2"); - - ref.getEntity().addProperty(prop1); - ref.getEntity().addProperty(prop2); - } - - private void initComments() { - org.LexGrid.concepts.Comment com1 = new org.LexGrid.concepts.Comment(); - com1.setLanguage("test lang"); - Text t = new Text(); - t.setContent("content"); - t.setDataType("string"); - com1.setValue(t); - com1.setPropertyId("propertyId"); - org.LexGrid.concepts.Comment com2 = new org.LexGrid.concepts.Comment(); - com2.setLanguage("test lang2"); - com2.setPropertyId("propertyId2"); - - ref.getEntity().addComment(com1); - ref.getEntity().addComment(com2); - } - - private void initDefinitions() { - org.LexGrid.concepts.Definition def1 = new org.LexGrid.concepts.Definition(); - def1.setPropertyId("test propertyid"); - def1.setLanguage("test lang"); - Text t = new Text(); - t.setDataType("string"); - t.setContent("content"); - def1.setValue(t); - def1.addUsageContext("test usage context 1"); - def1.addUsageContext("test usage context 2"); - org.LexGrid.concepts.Definition def2 = new org.LexGrid.concepts.Definition(); - def2.setPropertyId("test propertyid 2"); - - ref.getEntity().addDefinition(def1); - ref.getEntity().addDefinition(def2); - } - - private void initPresentations() { - org.LexGrid.concepts.Presentation presentation1 = new org.LexGrid.concepts.Presentation(); - presentation1.setDegreeOfFidelity("testFed"); - presentation1.setPropertyId("testPropertyID"); - presentation1.setLanguage("en"); - Text value = new Text(); - value.setContent("testValue"); - value.setDataType("string"); - presentation1.setValue(value); - presentation1.setPropertyName("property name"); - presentation1.addUsageContext("test usage context 1"); - presentation1.addUsageContext("test usage context 2"); - presentation1.addUsageContext("test usage context 3"); - org.LexGrid.concepts.Presentation presentation2 = new org.LexGrid.concepts.Presentation(); - presentation2.setDegreeOfFidelity("degree of fidelity"); - presentation2.setPropertyId("presentation 2"); - Text t2 = new Text(); - t2.setContent("2 content"); - t2.setDataType("string"); - - ref.getEntity().addPresentation(presentation1); - ref.getEntity().addPresentation(presentation2); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ValueSetDefinitionToValueSetDefinitionTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ValueSetDefinitionToValueSetDefinitionTest.java deleted file mode 100644 index 19fc8898d1..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/mapper/ValueSetDefinitionToValueSetDefinitionTest.java +++ /dev/null @@ -1,60 +0,0 @@ -package org.cts2.internal.mapper; - -import static org.junit.Assert.assertEquals; - -import org.LexGrid.LexBIG.Utility.Constructors; -import org.LexGrid.valueSets.DefinitionEntry; -import org.LexGrid.valueSets.types.DefinitionOperator; -import org.cts2.core.types.SetOperator; -import org.cts2.valueset.ValueSetDefinitionEntry; -import org.junit.Test; - -public class ValueSetDefinitionToValueSetDefinitionTest extends BaseDozerBeanMapperTest { - - @Test - public void testEntityDescription(){ - org.LexGrid.valueSets.ValueSetDefinition vsdLg = new org.LexGrid.valueSets.ValueSetDefinition(); - vsdLg.setEntityDescription(Constructors.createEntityDescription("test desc")); - - org.cts2.valueset.ValueSetDefinition mapped = - baseDozerBeanMapper.map(vsdLg, org.cts2.valueset.ValueSetDefinition.class); - - assertEquals("test desc", mapped.getResourceSynopsis().getValue()); - } - - @Test - public void testDefinitionOperatorForward(){ - DefinitionOperator[] defOperators = {DefinitionOperator.AND,DefinitionOperator.OR,DefinitionOperator.SUBTRACT}; - SetOperator[] setOperators = {SetOperator.INTERSECT,SetOperator.UNION,SetOperator.SUBTRACT}; - - for(int i=0;i handler; - - @Before - public void buildTestHandler(){ - this.handler = - new AbstractIterableLexEvsBackedRestrictionHandler(){ - - @Override - public List> registerSupportedModelAttributeReferences() { - List> returnList = new ArrayList>(); - - ResolvableModelAttributeReference ref = new ResolvableModelAttributeReference( - new AttributeResolver(){ - - @Override - public String resolveAttribute( - TestThing modelObject) { - return modelObject.testAttribute; - } - }); - - ResolvableModelAttributeReference ref2 = new ResolvableModelAttributeReference( - new AttributeResolver(){ - - @Override - public String resolveAttribute( - TestThing modelObject) { - return modelObject.testOtherAttribute; - } - }); - - ref.setContent("firstAttribute"); - returnList.add(ref); - - ref2.setContent("secondAttribute"); - returnList.add(ref2); - - return returnList; - } - - @Override - public List registerSupportedMatchAlgorithmReferences() { - return null; - } - - @Override - public List> processOtherRestictions( - TestDirectoryURI directoryUri) { - return null; - } - }; - - MatchAlgorithm testAlgorithm = new MatchAlgorithm(){ - - @Override - public float matchScore(String matchText, String compareString) { - if(matchText.equals(compareString)){ - return 1; - } else { - return 0; - } - } - - @Override - public String getName() { - return "test-algorithm"; - } - - }; - - this.handler.setMatchAlgorithms(Arrays.asList(testAlgorithm)); - } - - @Test - public void testDoRestrict(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - - FilterComponent testFilterComponent = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "this"); - - Collection returnList = - this.handler.doRestrict(Arrays.asList(one,two), testFilterComponent, 1); - - assertEquals(1, returnList.size()); - - assertEquals("this", returnList.iterator().next().testAttribute); - } - - @Test - public void testDoRestrictNoMatch(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - - FilterComponent testFilterComponent = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "__INVALID__"); - - Collection returnList = - this.handler.doRestrict(Arrays.asList(one,two), testFilterComponent, 1); - - assertEquals(0, returnList.size()); - } - - @Test - public void testSimpleRestrict(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - TestThing three = new TestThing("run", "jump"); - - FilterComponent testFilterComponent = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "run"); - - Filter filter = TestUtils.buildFilter(testFilterComponent); - - List returnList = new ArrayList(); - - TestRestrictionState restrictionState = new TestRestrictionState(); - restrictionState.getFilters().add(filter); - - IterableRestriction restriction = this.handler.compile(new DefaultTestDirectoryURI(restrictionState)); - - Iterables.addAll(returnList, restriction.processRestriction(Arrays.asList(one,two,three))); - - assertEquals(1, returnList.size()); - - assertEquals("run", returnList.get(0).testAttribute); - } - - @Test - public void testUnionRestrict(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - TestThing three = new TestThing("run", "jump"); - - FilterComponent testFilterComponent1 = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "run"); - - FilterComponent testFilterComponent2 = TestUtils.buildFilterComponent( - "secondAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "else"); - - Filter filter1 = TestUtils.buildFilter(testFilterComponent1); - Filter filter2 = TestUtils.buildFilter(testFilterComponent2); - - List returnList = new ArrayList(); - - TestRestrictionState restrictionState = new TestRestrictionState(); - restrictionState.setSetComposite(new SetComposite()); - restrictionState.getSetComposite().setSetOperator(SetOperator.UNION); - restrictionState.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(filter1)); - restrictionState.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(filter2)); - - IterableRestriction restriction = this.handler.compile(new DefaultTestDirectoryURI(restrictionState)); - - Iterables.addAll(returnList, restriction.processRestriction(Arrays.asList(one,two,three))); - - assertEquals(2, returnList.size()); - } - - @Test - public void testSubtractRestrict(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - TestThing three = new TestThing("run", "jump"); - - FilterComponent testFilterComponent1 = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "run"); - - FilterComponent testFilterComponent2 = TestUtils.buildFilterComponent( - "secondAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "jump"); - - Filter filter1 = TestUtils.buildFilter(testFilterComponent1); - Filter filter2 = TestUtils.buildFilter(testFilterComponent2); - - List returnList = new ArrayList(); - - TestRestrictionState restrictionState = new TestRestrictionState(); - restrictionState.setSetComposite(new SetComposite()); - restrictionState.getSetComposite().setSetOperator(SetOperator.INTERSECT); - restrictionState.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(filter1)); - restrictionState.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(filter2)); - - IterableRestriction restriction = this.handler.compile(new DefaultTestDirectoryURI(restrictionState)); - - Iterables.addAll(returnList, restriction.processRestriction(Arrays.asList(one,two,three))); - - assertEquals(1, returnList.size()); - - assertEquals("run", returnList.get(0).testAttribute); - } - - @Test - public void test2DeepSetOperationsIntersect(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - TestThing three = new TestThing("run", "jump"); - - FilterComponent testFilterComponent1 = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "run"); - - FilterComponent testFilterComponent2 = TestUtils.buildFilterComponent( - "secondAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "jump"); - - FilterComponent testFilterComponent3 = TestUtils.buildFilterComponent( - "secondAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "that"); - - Filter filter1 = TestUtils.buildFilter(testFilterComponent1); - Filter filter2 = TestUtils.buildFilter(testFilterComponent2); - Filter filter3 = TestUtils.buildFilter(testFilterComponent3); - - List returnList = new ArrayList(); - - TestRestrictionState restrictionState1 = new TestRestrictionState(); - restrictionState1.setSetComposite(new SetComposite()); - restrictionState1.getSetComposite().setSetOperator(SetOperator.UNION); - restrictionState1.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(filter1)); - restrictionState1.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(filter3)); - - TestRestrictionState restrictionState2 = new TestRestrictionState(); - restrictionState2.setSetComposite(new SetComposite()); - restrictionState2.getSetComposite().setSetOperator(SetOperator.INTERSECT); - restrictionState2.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(filter1)); - restrictionState2.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(filter2)); - - TestRestrictionState restrictionState3 = new TestRestrictionState(); - restrictionState3.setSetComposite(new SetComposite()); - restrictionState3.getSetComposite().setSetOperator(SetOperator.INTERSECT); - restrictionState3.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(restrictionState1)); - restrictionState3.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(restrictionState2)); - - IterableRestriction restriction = this.handler.compile(new DefaultTestDirectoryURI(restrictionState3)); - - Iterables.addAll(returnList, restriction.processRestriction(Arrays.asList(one,two,three))); - - assertEquals(1, returnList.size()); - - assertEquals("run", returnList.get(0).testAttribute); - } - - @Test - public void test2DeepSetOperationsSubtract(){ - TestThing one = new TestThing("this", "that"); - TestThing two = new TestThing("something", "else"); - TestThing three = new TestThing("run", "jump"); - - FilterComponent testFilterComponent1 = TestUtils.buildFilterComponent( - "firstAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "run"); - - FilterComponent testFilterComponent2 = TestUtils.buildFilterComponent( - "secondAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "jump"); - - FilterComponent testFilterComponent3 = TestUtils.buildFilterComponent( - "secondAttribute", TargetReferenceType.ATTRIBUTE, "test-algorithm", "that"); - - Filter filter1 = TestUtils.buildFilter(testFilterComponent1); - Filter filter2 = TestUtils.buildFilter(testFilterComponent2); - Filter filter3 = TestUtils.buildFilter(testFilterComponent3); - - List returnList = new ArrayList(); - - TestRestrictionState restrictionState1 = new TestRestrictionState(); - restrictionState1.setSetComposite(new SetComposite()); - restrictionState1.getSetComposite().setSetOperator(SetOperator.UNION); - restrictionState1.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(filter1)); - restrictionState1.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(filter3)); - - TestRestrictionState restrictionState2 = new TestRestrictionState(); - restrictionState2.setSetComposite(new SetComposite()); - restrictionState2.getSetComposite().setSetOperator(SetOperator.INTERSECT); - restrictionState2.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(filter1)); - restrictionState2.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(filter2)); - - TestRestrictionState restrictionState3 = new TestRestrictionState(); - restrictionState3.setSetComposite(new SetComposite()); - restrictionState3.getSetComposite().setSetOperator(SetOperator.SUBTRACT); - restrictionState3.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(restrictionState1)); - restrictionState3.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(restrictionState2)); - - IterableRestriction restriction = this.handler.compile(new DefaultTestDirectoryURI(restrictionState3)); - - Iterables.addAll(returnList, restriction.processRestriction(Arrays.asList(one,two,three))); - - assertEquals(1, returnList.size()); - - assertEquals("this", returnList.get(0).testAttribute); - } - - private static class TestThing { - private String testAttribute; - private String testOtherAttribute; - - private TestThing(){ - super(); - } - - private TestThing(String testAttribute, String testOtherAttribute) { - super(); - this.testAttribute = testAttribute; - this.testOtherAttribute = testOtherAttribute; - } - - } - - private static class TestRestrictionState extends RestrictionState { - - } - - private static interface TestDirectoryURI extends DirectoryURI { - - public TestRestrictionState getRestrictionState(); - } - - - private static class DefaultTestDirectoryURI implements TestDirectoryURI { - - private TestRestrictionState restrictionState = new TestRestrictionState(); - - private DefaultTestDirectoryURI(TestRestrictionState restrictionState){ - this.restrictionState = restrictionState; - } - - private DefaultTestDirectoryURI(Filter filter){ - this.restrictionState.getFilters().add(filter); - } - - private DefaultTestDirectoryURI(TestRestrictionState state1, TestRestrictionState state2, SetOperator setOperator){ - this.restrictionState.setSetComposite(new SetComposite()); - - this.restrictionState.getSetComposite().setDirectoryUri1(new DefaultTestDirectoryURI(state1)); - this.restrictionState.getSetComposite().setDirectoryUri2(new DefaultTestDirectoryURI(state2)); - } - - @Override - public TestRestrictionState getRestrictionState() { - return this.restrictionState; - } - - @Override - public > T get(QueryControl queryControl, - ReadContext readContext, Class content) { - // TODO Auto-generated method stub - return null; - } - - @Override - public int count(ReadContext readContext) { - // TODO Auto-generated method stub - return 0; - } - - @Override - public DirectoryURI restrict(Filter filter) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String marshall() { - // TODO Auto-generated method stub - return null; - } - - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/model/uri/restrict/ValueSetDefinitionRestrictionHandlerTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/model/uri/restrict/ValueSetDefinitionRestrictionHandlerTest.java deleted file mode 100644 index 9cd27c61ec..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/model/uri/restrict/ValueSetDefinitionRestrictionHandlerTest.java +++ /dev/null @@ -1,67 +0,0 @@ -package org.cts2.internal.model.uri.restrict; - -import static org.junit.Assert.assertEquals; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -import org.LexGrid.valueSets.ValueSetDefinition; -import org.cts2.core.Filter; -import org.cts2.core.FilterComponent; -import org.cts2.core.types.TargetReferenceType; -import org.cts2.internal.match.BaseCompositeMatchAlgorithm; -import org.cts2.internal.match.ExactMatcher; -import org.cts2.internal.match.MatchAlgorithm; -import org.cts2.test.TestUtils; -import org.cts2.uri.ValueSetDefinitionDirectoryURI; -import org.cts2.uri.restriction.ValueSetDefinitionRestrictionState; -import org.easymock.classextension.EasyMock; -import org.junit.Test; - -import com.google.common.collect.Iterables; - -public class ValueSetDefinitionRestrictionHandlerTest { - - @Test - public void testUnionRestrict(){ - ValueSetDefinitionRestrictionHandler handler = new ValueSetDefinitionRestrictionHandler(); - - MatchAlgorithm matchAlgorithm = new BaseCompositeMatchAlgorithm("exactMatch", new ExactMatcher()); - - handler.setMatchAlgorithms(Arrays.asList(matchAlgorithm)); - - FilterComponent filterComponent = - TestUtils.buildFilterComponent("valueSetDefinitionName", TargetReferenceType.ATTRIBUTE, "exactMatch", "test_name"); - - ValueSetDefinition vsd1 = new ValueSetDefinition(); - vsd1.setValueSetDefinitionName("some_name"); - - ValueSetDefinition vsd2 = new ValueSetDefinition(); - vsd2.setValueSetDefinitionName("test_name"); - - List definitions = Arrays.asList(vsd1,vsd2); - - Filter filter = TestUtils.buildFilter(filterComponent); - - ValueSetDefinitionRestrictionState restrictionState = new ValueSetDefinitionRestrictionState(); - restrictionState.getFilters().add(filter); - - ValueSetDefinitionDirectoryURI uri = EasyMock.createMock(ValueSetDefinitionDirectoryURI.class); - EasyMock.expect(uri.getRestrictionState()).andReturn(restrictionState); - - EasyMock.replay(uri); - - IterableRestriction restriction = handler.compile(uri); - - Iterable restrictedDefs = restriction.processRestriction(definitions); - - List returnList = new ArrayList(); - - Iterables.addAll(returnList, restriction.processRestriction(restrictedDefs)); - - assertEquals(1,returnList.size()); - - assertEquals("test_name", returnList.get(0).getValueSetDefinitionName()); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEVSAssociationQueryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEVSAssociationQueryTest.java deleted file mode 100644 index 777ea63eab..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEVSAssociationQueryTest.java +++ /dev/null @@ -1,68 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.association.AssociationDirectory; -import org.cts2.internal.model.uri.factory.CodeSystemDirectoryURIFactory; -import org.cts2.internal.profile.query.LexEvsAssociationQueryService; -import org.cts2.profile.BaseService; -import org.cts2.test.BaseCts2UnitTest; -import org.cts2.uri.AssociationDirectoryURI; -import org.easymock.classextension.EasyMock; -import org.junit.Ignore; -import org.junit.Test; - -public class LexEVSAssociationQueryTest extends BaseCts2UnitTest { - - @Resource - private LexEvsAssociationQueryService associationQuery; - - @Resource - private BaseService baseService; - - @Resource - private CodeSystemDirectoryURIFactory codeSystemDirectoryURIFactory; - - @Test - public void testInit(){ - assertNotNull(associationQuery); - } - - @Test - public void testIsAvailableThroughBaseService(){ - assertNotNull(baseService.getQueryService().getCodeSystemQueryService()); - } - - /* - @Test - @Ignore - public void testResolveDirectoryURINotNull() throws LBInvocationException{ - LexBIGService lbs = EasyMock.createMock(LexBIGService.class); - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new CodingSchemeRendering(); - csr.setCodingSchemeSummary(new CodingSchemeSummary()); - csr.getCodingSchemeSummary().setCodingSchemeURI("testURI"); - csrl.addCodingSchemeRendering(csr); - - EasyMock.expect(lbs.getSupportedCodingSchemes()).andReturn(csrl).anyTimes(); - EasyMock.replay(lbs); - - associationQuery.setLexBigService(lbs); - codeSystemDirectoryURIFactory.setLexBigService(lbs); - - AssociationDirectoryURI directoryUri = associationQuery.getAllAssociations(); - AssociationDirectory ad = directoryUri.get(null, null, AssociationDirectory.class); - assertNotNull(ad); - assertTrue(ad.getEntryCount() > 0); - } - */ -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryTest.java deleted file mode 100644 index 2589c908d3..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsCodeSystemQueryTest.java +++ /dev/null @@ -1,73 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.codesystem.CodeSystemDirectory; -import org.cts2.internal.model.uri.factory.CodeSystemDirectoryURIFactory; -import org.cts2.internal.profile.query.LexEvsCodeSystemQueryService; -import org.cts2.profile.BaseService; -import org.cts2.test.BaseCts2UnitTest; -import org.cts2.uri.CodeSystemDirectoryURI; -import org.easymock.classextension.EasyMock; -import org.junit.Ignore; -import org.junit.Test; - -public class LexEvsCodeSystemQueryTest extends BaseCts2UnitTest { - - @Resource - private LexEvsCodeSystemQueryService lexEvsCodeSystemQuery; - - @Resource - private BaseService baseService; - - @Resource - private CodeSystemDirectoryURIFactory codeSystemDirectoryURIFactory; - - @Test - public void testInit(){ - assertNotNull(lexEvsCodeSystemQuery); - } - - @Test - public void testIsAvailableThroughBaseService(){ - assertNotNull(baseService.getQueryService().getCodeSystemQueryService()); - } - - /* - @Test - @Ignore - public void testResolveDirectoryURINotNull() throws LBInvocationException{ - LexBIGService lbs = EasyMock.createMock(LexBIGService.class); - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new CodingSchemeRendering(); - csr.setCodingSchemeSummary(new CodingSchemeSummary()); - csr.getCodingSchemeSummary().setCodingSchemeURI("testURI"); - csrl.addCodingSchemeRendering(csr); - - EasyMock.expect(lbs.getSupportedCodingSchemes()).andReturn(csrl).anyTimes(); - EasyMock.replay(lbs); - - lexEvsCodeSystemQuery.setLexBigService(lbs); - codeSystemDirectoryURIFactory.setLexBigService(lbs); - - CodeSystemDirectoryURI directoryUri = lexEvsCodeSystemQuery.getAllCodeSystems(); - - CodeSystemDirectory csd = directoryUri.get(null, null, CodeSystemDirectory.class); - assertNotNull(csd); - assertTrue(csd.getEntryCount() > 0); - - CodeSystemDirectory directory = lexEvsCodeSystemQuery.resolve(directoryUri, null, null); - - assertNotNull(directory); - } - */ -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryTest.java deleted file mode 100644 index ce240aef07..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsCodeSystemVersionQueryTest.java +++ /dev/null @@ -1,129 +0,0 @@ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.cts2.codesystemversion.CodeSystemVersionDirectory; -import org.cts2.internal.model.uri.factory.CodeSystemVersionDirectoryURIFactory; -import org.cts2.internal.profile.query.LexEvsCodeSystemVersionQueryService; -import org.cts2.profile.BaseService; -import org.cts2.service.core.QueryControl; -import org.cts2.test.BaseCts2UnitTest; -import org.cts2.uri.CodeSystemVersionDirectoryURI; -import org.easymock.classextension.EasyMock; -import org.junit.Test; - -public class LexEvsCodeSystemVersionQueryTest extends BaseCts2UnitTest { - - @Resource - private LexEvsCodeSystemVersionQueryService lexEvsCodeSystemVersionQuery; - - @Resource - private BaseService baseService; - - @Resource - private CodeSystemVersionDirectoryURIFactory codeSystemVersonDirectoryURIFactory; - - @Test - public void testInit(){ - assertNotNull(lexEvsCodeSystemVersionQuery); - } - - @Test - public void testIsAvailableThroughBaseService(){ - assertNotNull(baseService.getQueryService().getCodeSystemQueryService()); - } - - @Test - public void testResolveDirectoryURINotNull() throws LBInvocationException{ - LexBIGService lbs = EasyMock.createMock(LexBIGService.class); - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new CodingSchemeRendering(); - csr.setCodingSchemeSummary(new CodingSchemeSummary()); - csr.getCodingSchemeSummary().setCodingSchemeURI("testURI"); - csrl.addCodingSchemeRendering(csr); - - EasyMock.expect(lbs.getSupportedCodingSchemes()).andReturn(csrl).anyTimes(); - EasyMock.replay(lbs); - - lexEvsCodeSystemVersionQuery.setLexBigService(lbs); - codeSystemVersonDirectoryURIFactory.setLexBigService(lbs); - - CodeSystemVersionDirectoryURI directoryUri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - - CodeSystemVersionDirectory directory = lexEvsCodeSystemVersionQuery.resolve(directoryUri, null, null); - - assertNotNull(directory); - } - - public static class TimeoutCodingSchemeRendering extends CodingSchemeRendering{ - - private static final long serialVersionUID = 1L; - - @Override - public CodingSchemeSummary getCodingSchemeSummary() { - try { - Thread.sleep(500); - } catch (InterruptedException e) { - throw new RuntimeException(e); - } - - return null; - } - }; - - @Test(expected=Exception.class) - public void testResolveDirectoryWithTimeout() throws LBInvocationException{ - LexBIGService lbs = EasyMock.createMock(LexBIGService.class); - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new TimeoutCodingSchemeRendering(); - - csrl.addCodingSchemeRendering(csr); - - EasyMock.expect(lbs.getSupportedCodingSchemes()).andReturn(csrl).anyTimes(); - EasyMock.replay(lbs); - - lexEvsCodeSystemVersionQuery.setLexBigService(lbs); - codeSystemVersonDirectoryURIFactory.setLexBigService(lbs); - - CodeSystemVersionDirectoryURI directoryUri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - - QueryControl queryControl = new QueryControl(); - queryControl.setTimeLimit(100l); - - lexEvsCodeSystemVersionQuery.resolve(directoryUri, queryControl, null); - } - - @Test(expected=Exception.class) - public void testResolveDirectoryBeforeTimeout() throws LBInvocationException{ - LexBIGService lbs = EasyMock.createMock(LexBIGService.class); - - CodingSchemeRenderingList csrl = new CodingSchemeRenderingList(); - CodingSchemeRendering csr = new TimeoutCodingSchemeRendering(); - - csrl.addCodingSchemeRendering(csr); - - EasyMock.expect(lbs.getSupportedCodingSchemes()).andReturn(csrl).anyTimes(); - EasyMock.replay(lbs); - - lexEvsCodeSystemVersionQuery.setLexBigService(lbs); - codeSystemVersonDirectoryURIFactory.setLexBigService(lbs); - - CodeSystemVersionDirectoryURI directoryUri = lexEvsCodeSystemVersionQuery.getCodeSystemVersions(); - - QueryControl queryControl = new QueryControl(); - queryControl.setTimeLimit(600l); - - CodeSystemVersionDirectory directory = lexEvsCodeSystemVersionQuery.resolve(directoryUri, queryControl, null); - - assertNotNull(directory); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryTest.java deleted file mode 100644 index 6afa112ec4..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/query/LexEvsValueSetDefinitionQueryTest.java +++ /dev/null @@ -1,84 +0,0 @@ -/** - * - */ -package org.cts2.internal.profile.query; - -import static org.junit.Assert.*; - -import javax.annotation.Resource; - -import org.cts2.internal.profile.query.LexEvsCodeSystemVersionQueryService; -import org.cts2.profile.BaseService; -import org.junit.Test; - -/** - * - * @author Sridhar Dwarkanath - * - * - */ -public class LexEvsValueSetDefinitionQueryTest { - - @Resource - private LexEvsCodeSystemVersionQueryService lexEvsCodeSystemVersionQuery; - - @Resource - private BaseService baseService; - - /** - * Test method for {@link org.cts2.internal.profile.query.LexEvsValueSetDefinitionQueryService#resolve(org.cts2.uri.ValueSetDefinitionDirectoryURI, org.cts2.service.core.QueryControl, org.apache.commons.betwixt.io.read.ReadContext)}. - */ - @Test - public void testResolve() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.query.LexEvsValueSetDefinitionQueryService#resolveAsList(org.cts2.uri.ValueSetDefinitionDirectoryURI, org.cts2.service.core.QueryControl, org.apache.commons.betwixt.io.read.ReadContext)}. - */ - @Test - public void testResolveAsList() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.query.LexEvsValueSetDefinitionQueryService#restrictToEntities(org.cts2.uri.ValueSetDefinitionDirectoryURI, java.util.List)}. - */ - @Test - public void testRestrictToEntities() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.query.AbstractBaseQueryService#count(org.cts2.uri.DirectoryURI, org.cts2.service.core.ReadContext)}. - */ - @Test - public void testCount() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.query.AbstractBaseQueryService#restrict(org.cts2.uri.DirectoryURI, org.cts2.core.Filter)}. - */ - @Test - public void testRestrict() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.query.AbstractBaseQueryService#setDirectoryURIFactory(org.cts2.internal.model.uri.factory.DirectoryURIFactory)}. - */ - @Test - public void testSetDirectoryURIFactory() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.query.AbstractBaseQueryService#getDirectoryURIFactory()}. - */ - @Test - public void testGetDirectoryURIFactory() { - fail("Not yet implemented"); - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadServiceTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadServiceTest.java deleted file mode 100644 index 84a8756867..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsCodeSystemVersionReadServiceTest.java +++ /dev/null @@ -1,199 +0,0 @@ -package org.cts2.internal.profile.read; - -import static org.junit.Assert.*; - -import javax.annotation.Resource; - -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.cts2.codesystemversion.CodeSystemVersion; -import org.cts2.internal.model.resource.factory.CodeSystemVersionFactory; -import org.cts2.internal.model.uri.factory.CodeSystemDirectoryURIFactory; -import org.cts2.internal.profile.read.LexEvsCodeSystemVersionReadService; -import org.cts2.profile.BaseService; -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.test.BaseCts2UnitTest; -import org.easymock.classextension.EasyMock; -import org.junit.Test; - -public class LexEvsCodeSystemVersionReadServiceTest extends BaseCts2UnitTest { - - @Resource - private LexEvsCodeSystemVersionReadService lexEvsCodeSystemVersionReadService; - - @Resource - private BaseService baseService; - - @Resource - private CodeSystemDirectoryURIFactory codeSystemDirectoryURIFactory; - - @Test - public void testInit(){ - assertNotNull(lexEvsCodeSystemVersionReadService); - } - - @Test - public void testIsAvailableThroughBaseService(){ - assertNotNull(baseService.getQueryService().getCodeSystemQueryService()); - } - - @Test - public void testResolveDirectoryURINotNull() throws LBInvocationException{ - - CodeSystemVersionFactory factory = - EasyMock.createMock(CodeSystemVersionFactory.class); - - NameOrURI id = new NameOrURI(); - - EasyMock.expect(factory.getCurrentCodeSystemVersion(id)).andReturn(new CodeSystemVersion()); - - - EasyMock.replay(factory); - lexEvsCodeSystemVersionReadService.setCodeSystemVersionFactory(factory); - - assertNotNull( - lexEvsCodeSystemVersionReadService.read(id, null, null)); - } - - @Test - public void Get_correct_About_CodeSystemVersion() throws LBInvocationException{ - - CodeSystemVersionFactory factory = - EasyMock.createMock(CodeSystemVersionFactory.class); - - NameOrURI id = new NameOrURI(); - - CodeSystemVersion csv = new CodeSystemVersion(); - csv.setAbout("test_about"); - - EasyMock.expect(factory.getCurrentCodeSystemVersion(id)).andReturn(csv); - - - EasyMock.replay(factory); - lexEvsCodeSystemVersionReadService.setCodeSystemVersionFactory(factory); - - CodeSystemVersion returned = - lexEvsCodeSystemVersionReadService.read(id, null, null); - - assertEquals("test_about", returned.getAbout()); - } - - @Test - public void Test_Read_CodeSystemVersion_By_Name() throws LBInvocationException{ - - CodeSystemVersionFactory factory = - EasyMock.createMock(CodeSystemVersionFactory.class); - - NameOrURI id = new NameOrURI(); - - CodeSystemVersion csv = new CodeSystemVersion(); - csv.setCodeSystemVersionName("test:name"); - csv.setDocumentURI("doc:uri"); - - EasyMock.expect(factory.getCurrentCodeSystemVersion(id)).andReturn(csv); - - - EasyMock.replay(factory); - lexEvsCodeSystemVersionReadService.setCodeSystemVersionFactory(factory); - - CodeSystemVersion returned = - lexEvsCodeSystemVersionReadService.read(id, null, null); - - assertEquals("test:name", returned.getCodeSystemVersionName()); - assertEquals("doc:uri", returned.getDocumentURI()); - } - - @Test - public void Test_Read_CodeSystemVersion_By_DocumentURI() throws LBInvocationException{ - - CodeSystemVersionFactory factory = - EasyMock.createMock(CodeSystemVersionFactory.class); - - NameOrURI id = new NameOrURI(); - id.setName("test:name"); - - CodeSystemVersion csv = new CodeSystemVersion(); - csv.setCodeSystemVersionName("test:name"); - csv.setDocumentURI("doc:uri"); - - EasyMock.expect(factory.getCurrentCodeSystemVersion(id)).andReturn(csv); - - - EasyMock.replay(factory); - lexEvsCodeSystemVersionReadService.setCodeSystemVersionFactory(factory); - - CodeSystemVersion returned = - lexEvsCodeSystemVersionReadService.read(id, null, null); - - assertEquals("test:name", returned.getCodeSystemVersionName()); - assertEquals("doc:uri", returned.getDocumentURI()); - } - - @Test(expected=Exception.class) - public void Test_Exceed_Timeout() throws LBInvocationException{ - - final CodeSystemVersion csv = new CodeSystemVersion(); - csv.setAbout("test_about"); - - CodeSystemVersionFactory factory = - new CodeSystemVersionFactory(){ - - @Override - public CodeSystemVersion getCurrentCodeSystemVersion( - NameOrURI nameOrUri) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - throw new RuntimeException(e); - } - - return csv; - } - - }; - - NameOrURI id = new NameOrURI(); - QueryControl queryControl = new QueryControl(); - queryControl.setTimeLimit(50l); - - lexEvsCodeSystemVersionReadService.setCodeSystemVersionFactory(factory); - - CodeSystemVersion returned = - lexEvsCodeSystemVersionReadService.read(id, queryControl, null); - } - - @Test - public void Test_Exceed_Timeout_Not_Exceeded() throws LBInvocationException{ - - final CodeSystemVersion csv = new CodeSystemVersion(); - csv.setAbout("test_about"); - - CodeSystemVersionFactory factory = - new CodeSystemVersionFactory(){ - - @Override - public CodeSystemVersion getCurrentCodeSystemVersion( - NameOrURI nameOrUri) { - try { - Thread.sleep(1000); - } catch (InterruptedException e) { - throw new RuntimeException(e); - } - - return csv; - } - - }; - - NameOrURI id = new NameOrURI(); - QueryControl queryControl = new QueryControl(); - queryControl.setTimeLimit(2000l); - - lexEvsCodeSystemVersionReadService.setCodeSystemVersionFactory(factory); - - CodeSystemVersion returned = - lexEvsCodeSystemVersionReadService.read(id, queryControl, null); - - assertEquals("test_about", returned.getAbout()); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsEntityDescriptionReadServiceTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsEntityDescriptionReadServiceTest.java deleted file mode 100644 index a64207153a..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsEntityDescriptionReadServiceTest.java +++ /dev/null @@ -1,110 +0,0 @@ -package org.cts2.internal.profile.read; - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; - -import javax.annotation.Resource; - -import org.cts2.core.EntityReference; -import org.cts2.entity.EntityDescription; -import org.cts2.entity.EntityList; -import org.cts2.entity.NamedEntityDescription; -import org.cts2.internal.model.resource.factory.EntityDescriptionFactory; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; -import org.cts2.test.BaseCts2UnitTest; -import org.easymock.classextension.EasyMock; -import org.junit.Test; - -public class LexEvsEntityDescriptionReadServiceTest extends BaseCts2UnitTest { - @Resource - private LexEvsEntityDescriptionReadService lexEvsEntityDescriptionReadService; - @Resource - private EntityDescriptionFactory entityDescriptionFactory; - - @Test - public void testRead() { - - EntityNameOrURI id = new EntityNameOrURI(); - NameOrURI csId = new NameOrURI(); - - EntityDescription ed = new NamedEntityDescription(); - ed.setAbout("test about"); - - entityDescriptionFactory = EasyMock - .createMock(EntityDescriptionFactory.class); - EasyMock.expect(entityDescriptionFactory.getEntityDescription(id, csId)) - .andReturn(ed); - EasyMock.replay(entityDescriptionFactory); - lexEvsEntityDescriptionReadService - .setEntityDescriptionFactory(entityDescriptionFactory); - - assertEquals("test about", - lexEvsEntityDescriptionReadService.read(id, csId, null, null) - .getAbout()); - } - - @Test - public void testExists() { - EntityNameOrURI id = new EntityNameOrURI(); - NameOrURI codeSystemVersion = new NameOrURI(); - EntityDescription ed = new NamedEntityDescription(); - - entityDescriptionFactory = EasyMock - .createMock(EntityDescriptionFactory.class); - EasyMock.expect( - entityDescriptionFactory.getEntityDescription(id, - codeSystemVersion)).andReturn(ed); - EasyMock.replay(entityDescriptionFactory); - - lexEvsEntityDescriptionReadService - .setEntityDescriptionFactory(entityDescriptionFactory); - - assertEquals(true, lexEvsEntityDescriptionReadService.exists(id, - codeSystemVersion, null, null)); - - } - - @Test - public void testAvailableDescriptions() { - EntityNameOrURI id = new EntityNameOrURI(); - - entityDescriptionFactory = EasyMock - .createMock(EntityDescriptionFactory.class); - EasyMock.expect(entityDescriptionFactory.availableDescriptions(id)) - .andReturn(new EntityReference()); - EasyMock.replay(entityDescriptionFactory); - - lexEvsEntityDescriptionReadService - .setEntityDescriptionFactory(entityDescriptionFactory); - - assertNotNull(lexEvsEntityDescriptionReadService.availableDescriptions(id, null)); - - } - - @Test - public void testReadEntityDescriptions() { - EntityNameOrURI id = new EntityNameOrURI(); - - entityDescriptionFactory = EasyMock.createMock(EntityDescriptionFactory.class); - EasyMock.expect(entityDescriptionFactory.getEntityDescriptionList(id)).andReturn(new EntityList()); - EasyMock.replay(entityDescriptionFactory); - - lexEvsEntityDescriptionReadService.setEntityDescriptionFactory(entityDescriptionFactory); - - assertNotNull(lexEvsEntityDescriptionReadService.readEntityDescriptions(id, null, null)); - - } - - @Test - public void testExistsInCodeSystem() { - // lexEvsEntityDescriptionReadService.existsInCodeSystem(id, codeSystem, - // tag, context); - } - - @Test - public void testReadByCodeSystem() { - // lexEvsEntityDescriptionReadService.readByCodeSystem(id, codeSystem, - // tag, queryControl, context); - } -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsValueSetDefinitionReadServiceTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsValueSetDefinitionReadServiceTest.java deleted file mode 100644 index 62391a9f15..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/profile/read/LexEvsValueSetDefinitionReadServiceTest.java +++ /dev/null @@ -1,87 +0,0 @@ -/** - * - */ -package org.cts2.internal.profile.read; - -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; - -import java.net.URI; -import java.net.URISyntaxException; - -import javax.annotation.Resource; - -import org.cts2.service.core.NameOrURI; -import org.cts2.service.core.QueryControl; -import org.cts2.test.BaseCts2UnitTest; -import org.cts2.valueset.ValueSetDefinition; -import org.cts2.valueset.ValueSetDefinitionEntry; -import org.junit.Test; -/** - * - * @author Sridhar Dwarkanath - * - * - */ -public class LexEvsValueSetDefinitionReadServiceTest extends BaseCts2UnitTest { - - @Resource - private LexEvsValueSetDefinitionReadService lexEvsValueSetDefinitionReadService; - - @Test - public void testInit(){ - assertNotNull(lexEvsValueSetDefinitionReadService); - } - - /** - * Test method for {@link org.cts2.internal.profile.read.LexEvsValueSetDefinitionReadService#exists(java.net.URI, org.cts2.service.core.ReadContext)}. - * @throws URISyntaxException - */ - @Test - public void testExists() throws URISyntaxException { - assertTrue(lexEvsValueSetDefinitionReadService.exists(new URI("SRITEST:AUTO:Ford"), null)); - } - - /** - * Test method for {@link org.cts2.internal.profile.read.LexEvsValueSetDefinitionReadService#existsDefinitionForValueSet(org.cts2.core.NameOrURI, org.cts2.core.NameOrURI, org.cts2.service.core.ReadContext)}. - */ - @Test - public void testExistsDefinitionForValueSet() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.read.LexEvsValueSetDefinitionReadService#getDefinitionForValueSet(org.cts2.core.NameOrURI, org.cts2.core.NameOrURI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext)}. - */ - @Test - public void testGetDefinitionForValueSet() { - fail("Not yet implemented"); - } - - /** - * Test method for {@link org.cts2.internal.profile.read.LexEvsValueSetDefinitionReadService#read(java.net.URI, org.cts2.service.core.QueryControl, org.cts2.service.core.ReadContext)}. - * @throws URISyntaxException - */ - @Test - public void testRead() throws URISyntaxException { - QueryControl qc = new QueryControl(); - qc.setTimeLimit(10000L); - qc.setMaxToReturn(null); - NameOrURI nameOrURI = new NameOrURI(); - nameOrURI.setName("XML"); - qc.setFormat(nameOrURI); - - ValueSetDefinition vsd = this.lexEvsValueSetDefinitionReadService.read(new URI/*("SRITEST:AUTO:PropertyRefTest1") */("CTS2TESTVSD"), qc, null); - - System.out.println("vsd.about : " + vsd.getAbout()); - System.out.println("vsd.formal name : " + vsd.getFormalName()); - - for (ValueSetDefinitionEntry de : vsd.getEntry()) - { - System.out.println("ENTRY TYPE : " + de.getEntryType()); - System.out.println("OPERATOR : " + de.getOperator()); - } - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/internal/util/PagingListTest.java b/cts2Impl/src/test/unit/java/org/cts2/internal/util/PagingListTest.java deleted file mode 100644 index 5c6f0efbd0..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/internal/util/PagingListTest.java +++ /dev/null @@ -1,94 +0,0 @@ -package org.cts2.internal.util; - -import static org.junit.Assert.*; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Iterator; -import java.util.List; - -import org.cts2.internal.util.PagingList; -import org.junit.Test; - -public class PagingListTest { - - @Test - public void testEmptyIterator(){ - List list = new ArrayList(); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - assertEquals(0, plist.size()); - } - - @Test(expected=IndexOutOfBoundsException.class) - public void testEmptyIteratorException(){ - List list = new ArrayList(); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - plist.get(0); - } - - @Test - public void testGetLast(){ - List list = Arrays.asList("one","two","three"); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - assertEquals("three",plist.get(2)); - } - - @Test(expected=IndexOutOfBoundsException.class) - public void testGetLastPlusOne(){ - List list = Arrays.asList("one","two","three"); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - plist.get(3); - } - - @Test - public void testGetCached(){ - List list = Arrays.asList("one","two","three", "four"); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - assertEquals("four", plist.get(3)); - - assertEquals("two", plist.get(1)); - } - - @Test - public void testIterate(){ - List list = Arrays.asList("one","two","three", "four"); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - Iterator itr = plist.iterator(); - - assertEquals("one", itr.next()); - assertEquals("two", itr.next()); - assertEquals("three", itr.next()); - assertEquals("four", itr.next()); - assertFalse(itr.hasNext()); - } - - @Test - public void testIterateTwice(){ - List list = Arrays.asList("one","two","three", "four"); - - PagingList plist = new PagingList(list.iterator(), list.size()); - - for(int i=0;i<2;i++){ - Iterator itr = plist.iterator(); - - assertEquals("one", itr.next()); - assertEquals("two", itr.next()); - assertEquals("three", itr.next()); - assertEquals("four", itr.next()); - assertFalse(itr.hasNext()); - } - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/BaseCts2UnitTest.java b/cts2Impl/src/test/unit/java/org/cts2/test/BaseCts2UnitTest.java deleted file mode 100644 index df7d98ef3a..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/BaseCts2UnitTest.java +++ /dev/null @@ -1,18 +0,0 @@ -package org.cts2.test; - -import org.junit.Test; -import org.junit.runner.RunWith; -import org.springframework.test.context.ContextConfiguration; -import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; - -@RunWith(SpringJUnit4ClassRunner.class) -@ContextConfiguration( - value = "/cts2-application-config-unit-test.xml") -public class BaseCts2UnitTest { - - @Test - public void testInit(){ - //test to check initialization of test context - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/LexBIGServiceNoOp.java b/cts2Impl/src/test/unit/java/org/cts2/test/LexBIGServiceNoOp.java deleted file mode 100644 index 4a70df2372..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/LexBIGServiceNoOp.java +++ /dev/null @@ -1,131 +0,0 @@ -package org.cts2.test; - -import java.util.Date; - -import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList; -import org.LexGrid.LexBIG.DataModel.Collections.ExtensionDescriptionList; -import org.LexGrid.LexBIG.DataModel.Collections.LocalNameList; -import org.LexGrid.LexBIG.DataModel.Collections.ModuleDescriptionList; -import org.LexGrid.LexBIG.DataModel.Collections.SortDescriptionList; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.types.SortContext; -import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; -import org.LexGrid.LexBIG.Extensions.Generic.GenericExtension; -import org.LexGrid.LexBIG.Extensions.Query.Filter; -import org.LexGrid.LexBIG.Extensions.Query.Sort; -import org.LexGrid.LexBIG.History.HistoryService; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph; -import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet; -import org.LexGrid.LexBIG.LexBIGService.LexBIGService; -import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; -import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceMetadata; -import org.LexGrid.codingSchemes.CodingScheme; - -public class LexBIGServiceNoOp implements LexBIGService{ - - private static final long serialVersionUID = 1L; - - @Override - public CodedNodeSet getCodingSchemeConcepts(String codingScheme, - CodingSchemeVersionOrTag versionOrTag) throws LBException { - return null; - } - - @Override - public CodedNodeSet getCodingSchemeConcepts(String codingScheme, - CodingSchemeVersionOrTag versionOrTag, boolean activeOnly) - throws LBException { - return null; - } - - @Override - public Filter getFilter(String name) throws LBException { - return null; - } - - @Override - public ExtensionDescriptionList getFilterExtensions() { - return null; - } - - @Override - public GenericExtension getGenericExtension(String name) throws LBException { - return null; - } - - @Override - public ExtensionDescriptionList getGenericExtensions() { - return null; - } - - @Override - public HistoryService getHistoryService(String codingScheme) - throws LBException { - return null; - } - - @Override - public Date getLastUpdateTime() throws LBInvocationException { - return null; - } - - @Override - public ModuleDescriptionList getMatchAlgorithms() { - return null; - } - - @Override - public CodedNodeGraph getNodeGraph(String codingScheme, - CodingSchemeVersionOrTag versionOrTag, String relationContainerName) - throws LBException { - return null; - } - - @Override - public CodedNodeSet getNodeSet(String codingScheme, - CodingSchemeVersionOrTag versionOrTag, LocalNameList entityTypes) - throws LBException { - return null; - } - - @Override - public LexBIGServiceManager getServiceManager(Object credentials) - throws LBException { - return null; - } - - @Override - public LexBIGServiceMetadata getServiceMetadata() throws LBException { - return null; - } - - @Override - public Sort getSortAlgorithm(String name) throws LBException { - return null; - } - - @Override - public SortDescriptionList getSortAlgorithms(SortContext context) { - return null; - } - - @Override - public CodingSchemeRenderingList getSupportedCodingSchemes() - throws LBInvocationException { - return null; - } - - @Override - public CodingScheme resolveCodingScheme(String codingScheme, - CodingSchemeVersionOrTag versionOrTag) throws LBException { - return null; - } - - @Override - public String resolveCodingSchemeCopyright(String codingScheme, - CodingSchemeVersionOrTag versionOrTag) throws LBException { - return null; - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/LexEvsIdentityConverterNoOp.java b/cts2Impl/src/test/unit/java/org/cts2/test/LexEvsIdentityConverterNoOp.java deleted file mode 100644 index cafd2c6455..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/LexEvsIdentityConverterNoOp.java +++ /dev/null @@ -1,96 +0,0 @@ -package org.cts2.test; - -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; -import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.Core.ConceptReference; -import org.LexGrid.codingSchemes.CodingScheme; -import org.cts2.core.types.DefinitionRole; -import org.cts2.entity.types.DesignationRole; -import org.cts2.internal.lexevs.identity.LexEvsIdentityConverter; -import org.cts2.service.core.EntityNameOrURI; -import org.cts2.service.core.NameOrURI; - -public class LexEvsIdentityConverterNoOp implements LexEvsIdentityConverter { - - @Override - public AbsoluteCodingSchemeVersionReference nameOrUriToAbsoluteCodingSchemeVersionReference( - NameOrURI nameOrUri) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String codingSchemeSummaryToCodeSystemVersionName( - CodingSchemeSummary codingSchemeSummary) { - // TODO Auto-generated method stub - return null; - } - - - @Override - public ConceptReference entityNameOrUriToConceptReference( - EntityNameOrURI nameOrUri) { - // TODO Auto-generated method stub - return null; - } - - @Override - public AbsoluteCodingSchemeVersionReference codeSystemVersionNameToCodingSchemeReference( - String codeSystemVersionName) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String codingSchemeReferenceToCodeSystemVersionName( - AbsoluteCodingSchemeVersionReference ref) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String codingSchemeToCodeSystemVersionName(CodingScheme codingScheme) { - // TODO Auto-generated method stub - return null; - } - - public String codingSchemeToCodeSystemVersionDocumentUri( - CodingScheme codingScheme) { - // TODO Auto-generated method stub - return null; - } - - @Override - public AbsoluteCodingSchemeVersionReference codeSystemVersionDocumentUriToCodingSchemeReference( - String codeSystemVersionDocumentUri) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String codingSchemeReferenceToCodeSystemVersionDocumentUri( - AbsoluteCodingSchemeVersionReference ref) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String nsUriAndCodeToUri(String nsUri, String code) { - // TODO Auto-generated method stub - return null; - } - - @Override - public DesignationRole preferredtoDestinationRole(boolean b) { - // TODO Auto-generated method stub - return null; - } - - @Override - public DefinitionRole preferredtoDefinitionRole(boolean b) { - // TODO Auto-generated method stub - return null; - } - - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/LexEvsServiceLocatorNoOp.java b/cts2Impl/src/test/unit/java/org/cts2/test/LexEvsServiceLocatorNoOp.java deleted file mode 100644 index 11ed9d72d9..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/LexEvsServiceLocatorNoOp.java +++ /dev/null @@ -1,7 +0,0 @@ -package org.cts2.test; - -import org.lexevs.locator.LexEvsServiceLocator; - -public class LexEvsServiceLocatorNoOp extends LexEvsServiceLocator { - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/NoOpLogger.java b/cts2Impl/src/test/unit/java/org/cts2/test/NoOpLogger.java deleted file mode 100644 index 77d4b22df3..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/NoOpLogger.java +++ /dev/null @@ -1,134 +0,0 @@ -package org.cts2.test; - -import org.LexGrid.LexBIG.Utility.logging.LgLoggerIF; - -public class NoOpLogger implements LgLoggerIF { - - @Override - public void busy() { - // TODO Auto-generated method stub - - } - - @Override - public String info(String message) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String debug(String message) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String warn(String message) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String warn(String message, Throwable sourceException) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String error(String message) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String error(String message, Throwable sourceException) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String fatal(String message) { - // TODO Auto-generated method stub - return null; - } - - @Override - public String fatal(String message, Throwable sourceException) { - // TODO Auto-generated method stub - return null; - } - - @Override - public void fatalAndThrowException(String message) throws Exception { - // TODO Auto-generated method stub - - } - - @Override - public void fatalAndThrowException(String message, Throwable sourceException) - throws Exception { - // TODO Auto-generated method stub - - } - - @Override - public void logMethod() { - // TODO Auto-generated method stub - - } - - @Override - public void logMethod(Object[] params) { - // TODO Auto-generated method stub - - } - - @Override - public void loadLogDebug(String message) { - // TODO Auto-generated method stub - - } - - @Override - public void loadLogError(String message, Throwable e) { - // TODO Auto-generated method stub - - } - - @Override - public void loadLogError(String message) { - // TODO Auto-generated method stub - - } - - @Override - public void loadLogWarn(String message, Throwable e) { - // TODO Auto-generated method stub - - } - - @Override - public void exportLogDebug(String message) { - // TODO Auto-generated method stub - - } - - @Override - public void exportLogError(String message, Throwable e) { - // TODO Auto-generated method stub - - } - - @Override - public void exportLogError(String message) { - // TODO Auto-generated method stub - - } - - @Override - public void exportLogWarn(String message, Throwable e) { - // TODO Auto-generated method stub - - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/TestLoggableClass.java b/cts2Impl/src/test/unit/java/org/cts2/test/TestLoggableClass.java deleted file mode 100644 index cf6d587624..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/TestLoggableClass.java +++ /dev/null @@ -1,17 +0,0 @@ -package org.cts2.test; - -import org.cts2.internal.logging.annotation.Loggable; - -@Loggable -public class TestLoggableClass { - - @Loggable - public void loggableMethod(){ - - } - - public void unLoggableMethod(){ - - } - -} diff --git a/cts2Impl/src/test/unit/java/org/cts2/test/TestUtils.java b/cts2Impl/src/test/unit/java/org/cts2/test/TestUtils.java deleted file mode 100644 index e3cc4ceef9..0000000000 --- a/cts2Impl/src/test/unit/java/org/cts2/test/TestUtils.java +++ /dev/null @@ -1,46 +0,0 @@ -package org.cts2.test; - -import org.cts2.core.Filter; -import org.cts2.core.FilterComponent; -import org.cts2.core.MatchAlgorithmReference; -import org.cts2.core.NameOrURI; -import org.cts2.core.PropertyReference; -import org.cts2.core.types.TargetReferenceType; - -public class TestUtils { - - public static Filter buildFilter(FilterComponent... filterComponents){ - Filter filter = new Filter(); - filter.setComponent(filterComponents); - - return filter; - } - - public static FilterComponent buildFilterComponent( - String propetyRefName, - TargetReferenceType type, - String matchAlgorithm, - String matchValue){ - - FilterComponent testFilterComponent = new FilterComponent(); - - PropertyReference pref = new PropertyReference(); - pref.setReferenceType(type); - - NameOrURI nameOrURI = new NameOrURI(); - nameOrURI.setName(propetyRefName); - - pref.setReferenceTarget(nameOrURI); - - testFilterComponent.setFilterComponent(pref); - - MatchAlgorithmReference ref = new MatchAlgorithmReference(); - ref.setContent(matchAlgorithm); - - testFilterComponent.setMatchAlgorithm(ref); - - testFilterComponent.setMatchValue(matchValue); - - return testFilterComponent; - } -} diff --git a/cts2Impl/src/test/unit/resources/cts2-application-config-unit-test.xml b/cts2Impl/src/test/unit/resources/cts2-application-config-unit-test.xml deleted file mode 100755 index 75d5a238bb..0000000000 --- a/cts2Impl/src/test/unit/resources/cts2-application-config-unit-test.xml +++ /dev/null @@ -1,21 +0,0 @@ - - - - - - - - - - - - - - - - diff --git a/lbAdmin/scripts/CleanUpMetadata.sh b/lbAdmin/scripts/CleanUpMetadata.sh old mode 100644 new mode 100755 index c98f48c36a..9739a57b9e --- a/lbAdmin/scripts/CleanUpMetadata.sh +++ b/lbAdmin/scripts/CleanUpMetadata.sh @@ -1,15 +1,14 @@ -@echo off -REM CleanUpMetadata -REM Clean up metadata entries that are orphaned. -REM -REM Options: -REM -REM -h, --help, Prints usage information -REM -REM -f,--force, Force removal without prompting of metadata that doesn't have a corresponding coding scheme entry(orphaned). -REM -REM -REM Example: -REM -REM CleanUpMetadata -r +# CleanUpMetadata +# Clean up metadata entries that are orphaned. +# +# Options: +# +# -h, --help, Prints usage information +# +# -f,--force, Force removal without prompting of metadata that doesn't have a corresponding coding scheme entry(orphaned). +# +# +# Example: +# +# CleanUpMetadata -r java -Xmx800m -XX:PermSize=256m -cp "..\runtime\lbPatch.jar:..\runtime\lbRuntime.jar" org.LexGrid.LexBIG.admin.CleanUpMetadata %* \ No newline at end of file diff --git a/lbAdmin/scripts/Load.bat b/lbAdmin/scripts/Load.bat new file mode 100644 index 0000000000..492265ffd7 --- /dev/null +++ b/lbAdmin/scripts/Load.bat @@ -0,0 +1,13 @@ +@echo off +REM A generic loader script that allows for the selection of a Loader Extension. +REM +REM Options: +REM -in,--input URI or path specifying location of the source file +REM -l, --loader LexGrid Load Extension name +REM -mf,--manifest URI or path specifying location of the manifest file +REM -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated +REM -t, --tag An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. +REM +REM Example: LoadText -in "file:///path/to/file.txt" -a +REM +java -Xmx1000m -cp "..\runtime\lbPatch.jar;..\runtime\lbRuntime.jar" org.LexGrid.LexBIG.admin.Load %* \ No newline at end of file diff --git a/lbAdmin/scripts/Load.sh b/lbAdmin/scripts/Load.sh new file mode 100644 index 0000000000..0282300f34 --- /dev/null +++ b/lbAdmin/scripts/Load.sh @@ -0,0 +1,13 @@ +# A generic loader script that allows for the selection of a Loader Extension. +# +# Options: +# -in,--input URI or path specifying location of the source file +# -l, --loader LexGrid Load Extension name +# -mf,--manifest URI or path specifying location of the manifest file +# -a, --activate ActivateScheme on successful load; if unspecified the +# vocabulary is loaded but not activated. +# -t, --tag An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. +# +# Example: LoadText -in "file:///path/to/file.txt" -a +# +java -Xmx1000m -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.Load $@ diff --git a/lbAdmin/scripts/LoadAllTestScripts.sh b/lbAdmin/scripts/LoadAllTestScripts.sh new file mode 100755 index 0000000000..9bce685f04 --- /dev/null +++ b/lbAdmin/scripts/LoadAllTestScripts.sh @@ -0,0 +1,34 @@ +#Test script to test working order of other load scripts. +#Choose NCI Thesaurus for the metadata and manifest interactive load. +echo ***Loading Terminologies**** +echo ***Loading LexgridXML**** +./LoadLgXML.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/Automobiles.xml +echo ***Loading OBO**** +./LoadOBO.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/cell.obo +echo ***Loading OWL**** +./LoadOWL.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/sample.owl +echo ***Loading Owl2**** +./LoadOWL2.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/owl2/owl2-snippet-data.owl +echo ***Loading RRF**** +./LoadUmlsBatch.sh -in file:///home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/sampleUMLS-AIR -s AIR +echo ***Loading NCI Meta*** +./LoadMetaBatch.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/sampleNciMeta +echo ***Loading Map**** +./LoadMrMap.sh -inMap /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/mrmap_mapping/NCIt-to-ICD9mappings.MRMAP.RRF -inSat /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/mrmap_mapping/MRSAT_NCI2ICD9.RRF +echo ***Load Metadata*** +./LoadMetadata.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/metadata1.xml +echo ***Load NCI History*** +./LoadNCIHistory.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/Filtered_pipe_out_12f.txt -vf /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/SystemReleaseHistory.txt +echo ***Load UMLS History*** +./LoadUMLSHistory.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/sampleNciMetaHistory +echo ***Load Manifest***** +./LoadManifest.sh -mf /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/sample-manifest.xml +echo ***Load Pick List**** +./LoadPickListDefinition.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/valueDomain/pickListTestData.xml +echo ***Load Value Set**** +./LoadValueSetDefinition.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/valueDomain/VSDOnlyTest.xml +echo ***Load HL7 Mif**** +./LoadMIFVocabulary.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/hl7MifVocabulary/DEFN=UV=VO=1189-20121121.coremif/ +echo ***Load MedDRA**** +./LoadMedDRA.sh -in /home/m029206/LexEVS_6.1.0.RC1/test/resources/testData/medDRA +echo ***Done**** diff --git a/lbAdmin/scripts/LoadMedDRA.sh b/lbAdmin/scripts/LoadMedDRA.sh index 3c3aaf532a..6aec433e7c 100644 --- a/lbAdmin/scripts/LoadMedDRA.sh +++ b/lbAdmin/scripts/LoadMedDRA.sh @@ -1 +1,19 @@ -# Loads a file specified in the Medical Dictionary for Regulatory Activities (MedDRA) format. # # Options: # -in,--input URI or path specifying location of the source file # -mf,--manifest URI or path specifying location of the manifest file # -v, --validate Perform validation of the candidate # resource without loading data. If specified, the '-a' and '-t' # options are ignored. Supported levels of validation include: # 0 = Verify document is valid # -a, --activate ActivateScheme on successful load; if unspecified the # vocabulary is loaded but not activated. # -t, --tag An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. # -cui Uri to MRCONSO.RRF from the NCI Metathesaurus allows loading of CUI's # for a given term. (Slows load time considerably) # # Example: LoadMedDRA -in "file:///path/to/file.asc" -a # LoadMedDRA -in "file:///path/to/file.asc" -v 0 # LoadMedDRA -in "file:///path/to/file.asc" -cui "file:///path/to/MRCONSO.RRF java -Xmx1000m -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadMedDRA $@ \ No newline at end of file +# Loads a file specified in the Medical Dictionary for Regulatory Activities (MedDRA) format. +# +# Options: +# -in,--input URI or path specifying location of the source file +# -mf,--manifest URI or path specifying location of the manifest file +# -v, --validate Perform validation of the candidate +# resource without loading data. If specified, the '-a' and '-t' +# options are ignored. Supported levels of validation include: +# 0 = Verify document is valid +# -a, --activate ActivateScheme on successful load; if unspecified the +# vocabulary is loaded but not activated. +# -t, --tag An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. +# -cui Uri to MRCONSO.RRF from the NCI Metathesaurus allows loading of CUI's +# for a given term. (Slows load time considerably) +# +# Example: LoadMedDRA -in "file:///path/to/file.asc" -a +# LoadMedDRA -in "file:///path/to/file.asc" -v 0 +# LoadMedDRA -in "file:///path/to/file.asc" -cui "file:///path/to/MRCONSO.RRF +java -Xmx1000m -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadMedDRA $@ diff --git a/lbAdmin/scripts/LoadOWL.sh b/lbAdmin/scripts/LoadOWL.sh index 96640fbe27..df34225a4e 100644 --- a/lbAdmin/scripts/LoadOWL.sh +++ b/lbAdmin/scripts/LoadOWL.sh @@ -1,5 +1,5 @@ # Loads an OWL file. You can provide a manifest file to configure coding scheme -# meta data. +# meta data. # # Options: # -in,--input URI or path specifying location of the source file @@ -17,4 +17,4 @@ # Example: LoadOWL -in "file:///path/to/somefile.owl" -a # LoadOWL -in "file:///path/to/somefile.owl" -v 0 # -java -Xmx3000m -XX:MaxPermSize=256M -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadOWL $@ +java -Xmx3000m -XX:MaxPermSize=256M -Djava.awt.headless=true -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadOWL $@ diff --git a/lbAdmin/scripts/LoadText.bat b/lbAdmin/scripts/LoadText.bat new file mode 100644 index 0000000000..d6472c4929 --- /dev/null +++ b/lbAdmin/scripts/LoadText.bat @@ -0,0 +1,19 @@ +@echo off +REM Loads a file in LexGrid Text format. +REM +REM Options: +REM -in,--input URI or path specifying location of the source file +REM -d, --delimiter defaults to tab the character used to delimit pair +REM or triple components and the nesting. +REM -mf,--manifest URI or path specifying location of the manifest file +REM -v, --validate Perform validation of the candidate +REM resource without loading data. If specified, the '-a' and '-t' +REM options are ignored. Supported levels of validation include: +REM 0 = Verify document is valid +REM -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated +REM -t, --tag An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. +REM +REM Example: LoadText -in "file:///path/to/file.txt" -a +REM LoadText -in "file:///path/to/file.txt" -v 0 +REM +java -Xmx1000m -cp "..\runtime\lbPatch.jar;..\runtime\lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadText %* \ No newline at end of file diff --git a/lbAdmin/scripts/LoadText.sh b/lbAdmin/scripts/LoadText.sh new file mode 100644 index 0000000000..ea6d6c37ae --- /dev/null +++ b/lbAdmin/scripts/LoadText.sh @@ -0,0 +1,19 @@ +# Loads a file in LexGrid Text format. +# +# Options: +# -in,--input URI or path specifying location of the source file +# -d, --delimiter defaults to tab the character used to delimit pair +# or triple components and the nesting. +# -mf,--manifest URI or path specifying location of the manifest file +# -v, --validate Perform validation of the candidate +# resource without loading data. If specified, the '-a' and '-t' +# options are ignored. Supported levels of validation include: +# 0 = Verify document is valid +# -a, --activate ActivateScheme on successful load; if unspecified the +# vocabulary is loaded but not activated. +# -t, --tag An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. +# +# Example: LoadText -in "file:///path/to/file.txt" -a +# LoadText -in "file:///path/to/file.txt" -v 0 +# +java -Xmx1000m -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadText $@ diff --git a/lbAdmin/scripts/RemoveTagScheme.bat b/lbAdmin/scripts/RemoveTagScheme.bat new file mode 100644 index 0000000000..6137b184fd --- /dev/null +++ b/lbAdmin/scripts/RemoveTagScheme.bat @@ -0,0 +1,14 @@ +@echo off +REM Removes a tag ID (e.g. 'PRODUCTION' or 'TEST') from a coding scheme URN and version. +REM +REM Options: +REM -u,--urn URN uniquely identifying the code system. +REM -v,--version Version identifier. +REM +REM Note: If the URN and version values are unspecified, a +REM list of available coding schemes will be presented for +REM user selection. +REM +REM Example: RemoveTagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" +REM +java -Xmx1000m -cp "..\runtime\lbPatch.jar;..\runtime\lbRuntime.jar" org.LexGrid.LexBIG.admin.RemoveTagScheme %* \ No newline at end of file diff --git a/lbAdmin/scripts/RemoveTagScheme.sh b/lbAdmin/scripts/RemoveTagScheme.sh new file mode 100644 index 0000000000..732420d9dc --- /dev/null +++ b/lbAdmin/scripts/RemoveTagScheme.sh @@ -0,0 +1,13 @@ +# Removes a tag ID (e.g. 'PRODUCTION' or 'TEST') from a coding scheme URN and version. +# +# Options: +# -u,--urn URN uniquely identifying the code system. +# -v,--version Version identifier. +# +# Note: If the URN and version values are unspecified, a +# list of available coding schemes will be presented for +# user selection. +# +# Example: RemoveTagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" +# +java -Xmx1000m -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.RemoveTagScheme $@ diff --git a/lbAdmin/src/org/LexGrid/LexBIG/admin/ExportLgXML.java b/lbAdmin/src/org/LexGrid/LexBIG/admin/ExportLgXML.java index 1c1448150b..5050a5d573 100644 --- a/lbAdmin/src/org/LexGrid/LexBIG/admin/ExportLgXML.java +++ b/lbAdmin/src/org/LexGrid/LexBIG/admin/ExportLgXML.java @@ -18,21 +18,18 @@ */ package org.LexGrid.LexBIG.admin; -import java.io.File; -import java.io.FileNotFoundException; import java.net.URI; -import java.util.Enumeration; -import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; -import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; +import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag; +import org.LexGrid.LexBIG.Exceptions.LBParameterException; import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; -import org.LexGrid.LexBIG.Extensions.Export.LexGrid_Exporter; import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; import org.LexGrid.LexBIG.Impl.exporters.LexGridExport; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; import org.LexGrid.LexBIG.Utility.Constructors; +import org.LexGrid.codingSchemes.CodingScheme; import org.apache.commons.cli.BasicParser; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.Option; @@ -110,44 +107,69 @@ public void run(String[] args) throws Exception { LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); - - // Find in list of registered vocabularies ... + + CodingScheme codingScheme = null; CodingSchemeSummary css = null; + + // Find in list of registered vocabularies ... if (urn != null && ver != null) { urn = urn.trim(); ver = ver.trim(); - Enumeration schemes = lbs.getSupportedCodingSchemes() - .enumerateCodingSchemeRendering(); - while (schemes.hasMoreElements() && css == null) { - CodingSchemeSummary summary = schemes.nextElement().getCodingSchemeSummary(); - if (urn.equalsIgnoreCase(summary.getCodingSchemeURI()) - && ver.equalsIgnoreCase(summary.getRepresentsVersion())) - css = summary; + + // Try to resolve the CodingScheme + CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag(); + versionOrTag.setVersion(ver); + + try { + codingScheme = lbs.resolveCodingScheme(urn, versionOrTag); } + catch (LBParameterException lbpe) { + codingScheme = null; + } } - // Found it? If not, prompt... - if (css == null) { + // If the CodingScheme was not found, prompt for a CodingSchemeSummary + if (codingScheme == null) { if (urn != null || ver != null) { Util.displayMessage("No matching coding scheme was found for the given URN or version."); Util.displayMessage(""); } css = Util.promptForCodeSystem(); + if (css == null) return; } - - // Find the registered extension handling this type of export ... - LexGridExport exporter = (LexGridExport) lbsm.getExporter(LexGridExport.name); - - // Perform the requested action ... - CnsCngPair cngCngPair = FilterParser.parse(lbs, css.getCodingSchemeURI(), css.getRepresentsVersion(), cl); - exporter.setCng(cngCngPair.getCng()); - exporter.setCns(cngCngPair.getCns()); + else { + // Find the registered extension handling this type of export ... + LexGridExport exporter = (LexGridExport) lbsm.getExporter(LexGridExport.name); + + // Perform the requested action ... + CnsCngPair cngCngPair = FilterParser.parse(lbs, codingScheme.getCodingSchemeURI(), + codingScheme.getRepresentsVersion(), cl); + exporter.setCng(cngCngPair.getCng()); + exporter.setCns(cngCngPair.getCns()); + + exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(codingScheme.getCodingSchemeURI(), + codingScheme.getRepresentsVersion()), destination, overwrite, + false, true); + Util.displayExporterStatus(exporter); + } - exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(css), destination, overwrite, - false, true); - Util.displayExporterStatus(exporter); + if (css != null) { + // Find the registered extension handling this type of export ... + LexGridExport exporter = (LexGridExport) lbsm.getExporter(LexGridExport.name); + + // Perform the requested action ... + CnsCngPair cngCngPair = FilterParser.parse(lbs, css.getCodingSchemeURI(), + css.getRepresentsVersion(), cl); + exporter.setCng(cngCngPair.getCng()); + exporter.setCns(cngCngPair.getCns()); + + exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(css), + destination, overwrite, + false, true); + Util.displayExporterStatus(exporter); + } } } diff --git a/lbAdmin/src/org/LexGrid/LexBIG/admin/Load.java b/lbAdmin/src/org/LexGrid/LexBIG/admin/Load.java new file mode 100644 index 0000000000..ead876c0ba --- /dev/null +++ b/lbAdmin/src/org/LexGrid/LexBIG/admin/Load.java @@ -0,0 +1,167 @@ +/* + * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and + * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the + * triple-shield Mayo logo are trademarks and service marks of MFMER. + * + * Except as contained in the copyright notice above, or as used to identify + * MFMER as the author of this software, the trade names, trademarks, service + * marks, or product names of the copyright holder shall not be used in + * advertising, promotion or otherwise in connection with this software without + * prior written authorization of the copyright holder. + * + * Licensed under the Eclipse Public License, Version 1.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.eclipse.org/legal/epl-v10.html + * + */ +package org.LexGrid.LexBIG.admin; + +import java.net.URI; + +import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; +import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; +import org.LexGrid.LexBIG.Extensions.Load.Loader; +import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; +import org.LexGrid.LexBIG.LexBIGService.LexBIGService; +import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; +import org.LexGrid.annotations.LgAdminFunction; +import org.apache.commons.cli.BasicParser; +import org.apache.commons.cli.CommandLine; +import org.apache.commons.cli.Option; +import org.apache.commons.cli.Options; +import org.apache.commons.cli.ParseException; +import org.lexevs.system.ResourceManager; + +import edu.mayo.informatics.resourcereader.core.StringUtils; + +@LgAdminFunction +public class Load { + + public static void main(String[] args) { + try { + new Load().run(args); + } catch (LBResourceUnavailableException e) { + Util.displayTaggedMessage(e.getMessage()); + } catch (Exception e) { + Util.displayAndLogError("REQUEST FAILED !!!", e); + } + } + + public Load() { + super(); + } + + /** + * Primary entry point for the program. + * + * @throws Exception + */ + public void run(String[] args) throws Exception { + synchronized (ResourceManager.instance()) { + + // Parse the command line ... + CommandLine cl = null; + Options options = getCommandOptions(); + try { + cl = new BasicParser().parse(options, args); + } catch (ParseException e) { + Util + .displayCommandOptions( + "Load", + options, + "\n Load -in \"file:///path/to/file.txt\" -a" + + "\n Load -in \"file:///path/to/file.txt\" -mf \"file:///path/to/myCodingScheme-manifest.xml\" -a" + + Util.getURIHelp(), e); + return; + } + + // Interpret provided values ... + boolean activate = cl.hasOption("a"); + + String loaderExtension = cl.getOptionValue("l"); + + String manUriStr = cl.getOptionValue("mf"); + URI manifest = null; + + if (!StringUtils.isNull(manUriStr)) + manifest = Util.string2FileURI(manUriStr); + + URI source = Util.string2FileURI(cl.getOptionValue("in")); + + Util.displayTaggedMessage("LOADING FROM URI: " + source.toString()); + + // Find the registered extension handling this type of load ... + LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); + LexBIGServiceManager lbsm = lbs.getServiceManager(null); + Loader loader = lbsm.getLoader(loaderExtension); + + loader.setCodingSchemeManifestURI(manifest); + loader.load(source); + Util.displayLoaderStatus(loader); + + // If specified, set the associated tag on the newly loaded + // scheme(s) ... + if (cl.hasOption("t")) { + String tag = cl.getOptionValue("t"); + AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); + for (int i = 0; i < refs.length; i++) { + AbsoluteCodingSchemeVersionReference ref = refs[i]; + lbsm.setVersionTag(ref, tag); + Util.displayTaggedMessage("Tag assigned>> " + ref.getCodingSchemeURN() + " Version>> " + + ref.getCodingSchemeVersion()); + } + } + + // If requested, activate the newly loaded scheme(s) ... + if (activate) { + AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); + for (int i = 0; i < refs.length; i++) { + AbsoluteCodingSchemeVersionReference ref = refs[i]; + lbsm.activateCodingSchemeVersion(ref); + Util.displayTaggedMessage("Scheme activated>> " + ref.getCodingSchemeURN() + " Version>> " + + ref.getCodingSchemeVersion()); + } + } + } + } + + /** + * Return supported command options. + * + * @return org.apache.commons.cli.Options + */ + private Options getCommandOptions() { + Options options = new Options(); + Option o; + + o = new Option("l", "loader", true, "LexEVS Loader Extension to use."); + o.setArgName("name"); + o.setRequired(true); + options.addOption(o); + + o = new Option("in", "input", true, "URI or path specifying location of the source file."); + o.setArgName("uri"); + o.setRequired(true); + options.addOption(o); + + o = new Option("mf", "manifest", true, "URI or path specifying location of the manifest file."); + o.setArgName("uri"); + o.setRequired(false); + options.addOption(o); + + o = new Option("a", "activate", false, "ActivateScheme on successful load; if unspecified the " + + "vocabulary is loaded but not activated."); + o.setRequired(false); + options.addOption(o); + + o = new Option("t", "tag", true, "An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign."); + o.setArgName("id"); + o.setRequired(false); + options.addOption(o); + + return options; + } + +} \ No newline at end of file diff --git a/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadMedDRA.java b/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadMedDRA.java index 124e492d48..bfe9a72ae3 100644 --- a/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadMedDRA.java +++ b/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadMedDRA.java @@ -1 +1 @@ -package org.LexGrid.LexBIG.admin; import java.net.URI; import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; import org.LexGrid.LexBIG.Extensions.Load.MedDRA_Loader; import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; import org.LexGrid.annotations.LgAdminFunction; import org.apache.commons.cli.BasicParser; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.lexevs.system.ResourceManager; import edu.mayo.informatics.resourcereader.core.StringUtils; @SuppressWarnings("deprecation") @LgAdminFunction public class LoadMedDRA { public static void main(String[] args) { try { new LoadMedDRA().run(args); } catch (LBResourceUnavailableException e) { Util.displayTaggedMessage(e.getMessage()); } catch (Exception e) { Util.displayAndLogError("REQUEST FAILED !!!", e); } } public LoadMedDRA() { super(); } /** * Primary entry point for the program. * * @throws Exception */ public void run(String[] args) throws Exception { synchronized (ResourceManager.instance()) { // Parse the command line ... CommandLine cl = null; Options options = getCommandOptions(); int vl = -1; try { cl = new BasicParser().parse(options, args); if (cl.hasOption("v")) vl = Integer.parseInt(cl.getOptionValue("v")); } catch (ParseException e) { Util .displayCommandOptions( "LoadMedDRA", options, "\n LoadMedDRA -in \"file:///path/\" -a" + "\n LoadMedDRA -in \"file:///path/\" -mf \"file:///path/to/myCodingScheme-manifest.xml\" -a" + "\n LoadMedDRA -in \"file:///path/\" -cui \"file:///path/to/MRCONSO\"" + "\n LoadMedDRA -in \"file:///path/\" -v 0" + Util.getURIHelp(), e); return; } // Interpret provided values ... String manUriStr = cl.getOptionValue("mf"); URI manifest = null; if (!StringUtils.isNull(manUriStr)) manifest = Util.string2FileURI(manUriStr); URI source = Util.string2FileURI(cl.getOptionValue("in")); boolean activate = vl < 0 && cl.hasOption("a"); URI cui = Util.string2FileURI(cl.getOptionValue("cui")); if (vl >= 0) { Util.displayTaggedMessage("VALIDATING SOURCE URI: " + source.toString()); } else { Util.displayTaggedMessage("LOADING FROM URI: " + source.toString()); Util.displayTaggedMessage(activate ? "ACTIVATE ON SUCCESS" : "NO ACTIVATION"); } // Find the registered extension handling this type of load ... LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); MedDRA_Loader loader = (MedDRA_Loader) lbsm.getLoader(org.LexGrid.LexBIG.Impl.loaders.MedDRALoaderImpl.name); // Perform the requested load or validate action ... // TODO: Unclear what I need here if (vl >= 0) { loader.validate(source, vl); Util.displayTaggedMessage("VALIDATION SUCCESSFUL"); } else { loader.setCodingSchemeManifestURI(manifest); loader.load(source, cui,false, true); Util.displayLoaderStatus(loader); } // If specified, set the associated tag on the newly loaded // scheme(s) ... if (vl < 0 && cl.hasOption("t")) { String tag = cl.getOptionValue("t"); AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); for (int i = 0; i < refs.length; i++) { AbsoluteCodingSchemeVersionReference ref = refs[i]; lbsm.setVersionTag(ref, tag); Util.displayTaggedMessage("Tag assigned>> " + ref.getCodingSchemeURN() + " Version>> " + ref.getCodingSchemeVersion()); } } // If requested, activate the newly loaded scheme(s) ... if (activate) { AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); for (int i = 0; i < refs.length; i++) { AbsoluteCodingSchemeVersionReference ref = refs[i]; lbsm.activateCodingSchemeVersion(ref); Util.displayTaggedMessage("Scheme activated>> " + ref.getCodingSchemeURN() + " Version>> " + ref.getCodingSchemeVersion()); } } } } /** * Return supported command options. * * @return org.apache.commons.cli.Options */ private Options getCommandOptions() { Options options = new Options(); Option o; o = new Option("in", "input", true, "URI or path specifying location of the source files."); o.setArgName("uri"); o.setRequired(true); options.addOption(o); o = new Option("cui", "umlscui", true, "URI or path specifying location of the cui source file."); o.setArgName("uri"); o.setRequired(false); options.addOption(o); o = new Option("mf", "manifest", true, "URI or path specifying location of the manifest file."); o.setArgName("uri"); o.setRequired(false); options.addOption(o); o = new Option("v", "validate", true, "Validation only; no load. If specified, 'a' and 't' " + "are ignored. 0 to verify the file conforms to the OBO format."); o.setArgName("int"); o.setRequired(false); options.addOption(o); o = new Option("a", "activate", false, "ActivateScheme on successful load; if unspecified the " + "vocabulary is loaded but not activated."); o.setRequired(false); options.addOption(o); o = new Option("t", "tag", true, "An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign."); o.setArgName("id"); o.setRequired(false); options.addOption(o); return options; } } \ No newline at end of file +package org.LexGrid.LexBIG.admin; import java.net.URI; import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; import org.LexGrid.LexBIG.Extensions.Load.MedDRA_Loader; import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; import org.LexGrid.annotations.LgAdminFunction; import org.apache.commons.cli.BasicParser; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.lexevs.system.ResourceManager; import edu.mayo.informatics.resourcereader.core.StringUtils; @SuppressWarnings("deprecation") @LgAdminFunction public class LoadMedDRA { public static void main(String[] args) { try { new LoadMedDRA().run(args); } catch (LBResourceUnavailableException e) { Util.displayTaggedMessage(e.getMessage()); } catch (Exception e) { Util.displayAndLogError("REQUEST FAILED !!!", e); } } public LoadMedDRA() { super(); } /** * Primary entry point for the program. * * @throws Exception */ public void run(String[] args) throws Exception { synchronized (ResourceManager.instance()) { // Parse the command line ... CommandLine cl = null; Options options = getCommandOptions(); int vl = -1; try { cl = new BasicParser().parse(options, args); if (cl.hasOption("v")) vl = Integer.parseInt(cl.getOptionValue("v")); } catch (ParseException e) { Util .displayCommandOptions( "LoadMedDRA", options, "\n LoadMedDRA -in \"file:///path/\" -a" + "\n LoadMedDRA -in \"file:///path/\" -mf \"file:///path/to/myCodingScheme-manifest.xml\" -a" + "\n LoadMedDRA -in \"file:///path/\" -cui \"file:///path/to/MRCONSO\"" + "\n LoadMedDRA -in \"file:///path/\" -v 0" + Util.getURIHelp(), e); return; } // Interpret provided values ... String manUriStr = cl.getOptionValue("mf"); URI manifest = null; if (!StringUtils.isNull(manUriStr)) manifest = Util.string2FileURI(manUriStr); URI source = Util.string2FileURI(cl.getOptionValue("in")); boolean activate = vl < 0 && cl.hasOption("a"); String cuiURI = cl.getOptionValue("cui"); URI cui = null; if(!StringUtils.isNull(cuiURI)){ cui = Util.string2FileURI(cuiURI); } if (vl >= 0) { Util.displayTaggedMessage("VALIDATING SOURCE URI: " + source.toString()); } else { Util.displayTaggedMessage("LOADING FROM URI: " + source.toString()); Util.displayTaggedMessage(activate ? "ACTIVATE ON SUCCESS" : "NO ACTIVATION"); } // Find the registered extension handling this type of load ... LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); MedDRA_Loader loader = (MedDRA_Loader) lbsm.getLoader(org.LexGrid.LexBIG.Impl.loaders.MedDRALoaderImpl.name); // Perform the requested load or validate action ... // TODO: Unclear what I need here if (vl >= 0) { loader.validate(source, vl); Util.displayTaggedMessage("VALIDATION SUCCESSFUL"); } else { loader.setCodingSchemeManifestURI(manifest); loader.load(source, cui,false, true); Util.displayLoaderStatus(loader); } // If specified, set the associated tag on the newly loaded // scheme(s) ... if (vl < 0 && cl.hasOption("t")) { String tag = cl.getOptionValue("t"); AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); for (int i = 0; i < refs.length; i++) { AbsoluteCodingSchemeVersionReference ref = refs[i]; lbsm.setVersionTag(ref, tag); Util.displayTaggedMessage("Tag assigned>> " + ref.getCodingSchemeURN() + " Version>> " + ref.getCodingSchemeVersion()); } } // If requested, activate the newly loaded scheme(s) ... if (activate) { AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); for (int i = 0; i < refs.length; i++) { AbsoluteCodingSchemeVersionReference ref = refs[i]; lbsm.activateCodingSchemeVersion(ref); Util.displayTaggedMessage("Scheme activated>> " + ref.getCodingSchemeURN() + " Version>> " + ref.getCodingSchemeVersion()); } } } } /** * Return supported command options. * * @return org.apache.commons.cli.Options */ private Options getCommandOptions() { Options options = new Options(); Option o; o = new Option("in", "input", true, "URI or path specifying location of the source files."); o.setArgName("uri"); o.setRequired(true); options.addOption(o); o = new Option("cui", "umlscui", true, "URI or path specifying location of the cui source file."); o.setArgName("uri"); o.setRequired(false); options.addOption(o); o = new Option("mf", "manifest", true, "URI or path specifying location of the manifest file."); o.setArgName("uri"); o.setRequired(false); options.addOption(o); o = new Option("v", "validate", true, "Validation only; no load. If specified, 'a' and 't' " + "are ignored. 0 to verify the file conforms to the OBO format."); o.setArgName("int"); o.setRequired(false); options.addOption(o); o = new Option("a", "activate", false, "ActivateScheme on successful load; if unspecified the " + "vocabulary is loaded but not activated."); o.setRequired(false); options.addOption(o); o = new Option("t", "tag", true, "An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign."); o.setArgName("id"); o.setRequired(false); options.addOption(o); return options; } } \ No newline at end of file diff --git a/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadText.java b/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadText.java new file mode 100644 index 0000000000..88056719b9 --- /dev/null +++ b/lbAdmin/src/org/LexGrid/LexBIG/admin/LoadText.java @@ -0,0 +1,197 @@ +/* + * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and + * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the + * triple-shield Mayo logo are trademarks and service marks of MFMER. + * + * Except as contained in the copyright notice above, or as used to identify + * MFMER as the author of this software, the trade names, trademarks, service + * marks, or product names of the copyright holder shall not be used in + * advertising, promotion or otherwise in connection with this software without + * prior written authorization of the copyright holder. + * + * Licensed under the Eclipse Public License, Version 1.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.eclipse.org/legal/epl-v10.html + * + */ +package org.LexGrid.LexBIG.admin; + +import java.net.URI; + +import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; +import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; +import org.LexGrid.LexBIG.Extensions.Load.Text_Loader; +import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; +import org.LexGrid.LexBIG.LexBIGService.LexBIGService; +import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; +import org.LexGrid.annotations.LgAdminFunction; +import org.apache.commons.cli.BasicParser; +import org.apache.commons.cli.CommandLine; +import org.apache.commons.cli.Option; +import org.apache.commons.cli.Options; +import org.apache.commons.cli.ParseException; +import org.lexevs.system.ResourceManager; + +import edu.mayo.informatics.resourcereader.core.StringUtils; + +@LgAdminFunction +public class LoadText { + + public static void main(String[] args) { + try { + new LoadText().run(args); + } catch (LBResourceUnavailableException e) { + Util.displayTaggedMessage(e.getMessage()); + } catch (Exception e) { + Util.displayAndLogError("REQUEST FAILED !!!", e); + } + } + + public LoadText() { + super(); + } + + /** + * Primary entry point for the program. + * + * @throws Exception + */ + public void run(String[] args) throws Exception { + synchronized (ResourceManager.instance()) { + + // Parse the command line ... + CommandLine cl = null; + Options options = getCommandOptions(); + int vl = -1; + try { + cl = new BasicParser().parse(options, args); + if (cl.hasOption("v")) + vl = Integer.parseInt(cl.getOptionValue("v")); + } catch (ParseException e) { + Util + .displayCommandOptions( + "LoadText", + options, + "\n LoadText -in \"file:///path/to/file.txt\" -a" + + "\n LoadText -in \"file:///path/to/file.txt\" -mf \"file:///path/to/myCodingScheme-manifest.xml\" -a" + + "\n LoadText -in \"file:///path/to/file.txt\" -v 0" + Util.getURIHelp(), e); + return; + } + + // Interpret provided values ... + String manUriStr = cl.getOptionValue("mf"); + URI manifest = null; + + if (!StringUtils.isNull(manUriStr)) + manifest = Util.string2FileURI(manUriStr); + + URI source; + if(cl.hasOption("in")){ + source = Util.string2FileURI(cl.getOptionValue("in")); + } else { + source = new URI(Text_Loader.STD_IN_URI); + } + boolean activate = vl < 0 && cl.hasOption("a"); + if (vl >= 0) { + Util.displayTaggedMessage("VALIDATING SOURCE URI: " + source.toString()); + } else { + Util.displayTaggedMessage("LOADING FROM URI: " + source.toString()); + Util.displayTaggedMessage(activate ? "ACTIVATE ON SUCCESS" : "NO ACTIVATION"); + } + + String delimiterArg = cl.getOptionValue("d", null); + if(delimiterArg != null && delimiterArg.length() != 1){ + Util.displayMessage("Delimiter character ('d') must be exactly 1 character in size."); + System.exit(1); + } + + Character delimeter = delimiterArg == null ? null : delimiterArg.charAt(0); + + // Find the registered extension handling this type of load ... + LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); + LexBIGServiceManager lbsm = lbs.getServiceManager(null); + Text_Loader loader = (Text_Loader) lbsm.getLoader(org.LexGrid.LexBIG.Extensions.Load.Text_Loader.name); + + // Perform the requested load or validate action ... + if (vl >= 0) { + loader.validate(source, delimeter, true, vl); + Util.displayTaggedMessage("VALIDATION SUCCESSFUL"); + } else { + loader.setCodingSchemeManifestURI(manifest); + loader.load(source, delimeter, true, true, true); + Util.displayLoaderStatus(loader); + } + + // If specified, set the associated tag on the newly loaded + // scheme(s) ... + if (vl < 0 && cl.hasOption("t")) { + String tag = cl.getOptionValue("t"); + AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); + for (int i = 0; i < refs.length; i++) { + AbsoluteCodingSchemeVersionReference ref = refs[i]; + lbsm.setVersionTag(ref, tag); + Util.displayTaggedMessage("Tag assigned>> " + ref.getCodingSchemeURN() + " Version>> " + + ref.getCodingSchemeVersion()); + } + } + + // If requested, activate the newly loaded scheme(s) ... + if (activate) { + AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); + for (int i = 0; i < refs.length; i++) { + AbsoluteCodingSchemeVersionReference ref = refs[i]; + lbsm.activateCodingSchemeVersion(ref); + Util.displayTaggedMessage("Scheme activated>> " + ref.getCodingSchemeURN() + " Version>> " + + ref.getCodingSchemeVersion()); + } + } + } + } + + /** + * Return supported command options. + * + * @return org.apache.commons.cli.Options + */ + private Options getCommandOptions() { + Options options = new Options(); + Option o; + + o = new Option("in", "input", true, "URI or path specifying location of the source file."); + o.setArgName("uri"); + o.setRequired(false); + options.addOption(o); + + o = new Option("d", "delimiter", true, "Optional - defaults to tab the character used to delimit pair " + + " or triple components and the nesting."); + o.setArgName("d"); + o.setRequired(false); + options.addOption(o); + + o = new Option("mf", "manifest", true, "URI or path specifying location of the manifest file."); + o.setArgName("uri"); + o.setRequired(false); + options.addOption(o); + + o = new Option("v", "validate", true, "Validation only; no load. If specified, 'a' and 't' " + + "are ignored. 0 to verify the file conforms to the OBO format."); + o.setArgName("int"); + o.setRequired(false); + options.addOption(o); + + o = new Option("a", "activate", false, "ActivateScheme on successful load; if unspecified the " + + "vocabulary is loaded but not activated."); + o.setRequired(false); + options.addOption(o); + + o = new Option("t", "tag", true, "An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign."); + o.setArgName("id"); + o.setRequired(false); + options.addOption(o); + + return options; + } + +} \ No newline at end of file diff --git a/lbAdmin/src/org/LexGrid/LexBIG/admin/RemoveTagScheme.java b/lbAdmin/src/org/LexGrid/LexBIG/admin/RemoveTagScheme.java new file mode 100644 index 0000000000..eb4ddc6883 --- /dev/null +++ b/lbAdmin/src/org/LexGrid/LexBIG/admin/RemoveTagScheme.java @@ -0,0 +1,154 @@ +/* + * Copyright: (c) 2004-2014 Mayo Foundation for Medical Education and + * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the + * triple-shield Mayo logo are trademarks and service marks of MFMER. + * + * Except as contained in the copyright notice above, or as used to identify + * MFMER as the author of this software, the trade names, trademarks, service + * marks, or product names of the copyright holder shall not be used in + * advertising, promotion or otherwise in connection with this software without + * prior written authorization of the copyright holder. + * + * Licensed under the Eclipse Public License, Version 1.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.eclipse.org/legal/epl-v10.html + * + */ +package org.LexGrid.LexBIG.admin; + +import java.util.Enumeration; + +import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; +import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; +import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; +import org.LexGrid.LexBIG.LexBIGService.LexBIGService; +import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; +import org.LexGrid.LexBIG.Utility.Constructors; +import org.LexGrid.annotations.LgAdminFunction; +import org.apache.commons.cli.BasicParser; +import org.apache.commons.cli.CommandLine; +import org.apache.commons.cli.Option; +import org.apache.commons.cli.Options; +import org.apache.commons.cli.ParseException; +import org.lexevs.system.ResourceManager; + +/** + * Removes a tag ID (e.g. 'PRODUCTION' or 'TEST') from a coding scheme URN + * and version. + * + * 
+ * Example: java org.LexGrid.LexBIG.admin.RemoveTagScheme
+ *  -u,--urn &lturn&gt; URN uniquely identifying the code system.
+ *  -v,--version &ltversionId&gt; Version identifier.
+ * 
+ * Note: If the URN and version values are unspecified, a
+ * list of available coding schemes will be presented for
+ * user selection.
+ * 
+ * Example: java -Xmx512m -cp lgRuntime.jar
+ * org.LexGrid.LexBIG.admin.RemoteTagScheme
+ *   -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
+ *
+ * + * @author Cory Endle + */ +@LgAdminFunction +public class RemoveTagScheme { + + public static void main(String[] args) { + try { + new RemoveTagScheme().run(args); + } catch (Exception e) { + Util.displayAndLogError("REQUEST FAILED !!!", e); + } + } + + public RemoveTagScheme() { + super(); + } + + /** + * Primary entry point for the program. + * + * @throws Exception + */ + public void run(String[] args) throws Exception { + synchronized (ResourceManager.instance()) { + + // Parse the command line ... + CommandLine cl = null; + Options options = getCommandOptions(); + try { + cl = new BasicParser().parse(options, args); + } catch (ParseException e) { + Util.displayCommandOptions("RemoveTagScheme", options, + "RemoveTagScheme -u \"urn:oid:2.16.840.1.113883.3.26.1.1\" -v \"05.09e\"", e); + Util.displayMessage(Util.getPromptForSchemeHelp()); + return; + } + + // Interpret provided values ... + String urn = cl.getOptionValue("u"); + String ver = cl.getOptionValue("v"); + CodingSchemeSummary css = null; + + // Find in list of registered vocabularies ... + if (urn != null && ver != null) { + urn = urn.trim(); + ver = ver.trim(); + LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); + Enumeration schemes = lbs.getSupportedCodingSchemes() + .enumerateCodingSchemeRendering(); + while (schemes.hasMoreElements() && css == null) { + CodingSchemeSummary summary = schemes.nextElement().getCodingSchemeSummary(); + if (urn.equalsIgnoreCase(summary.getCodingSchemeURI()) + && ver.equalsIgnoreCase(summary.getRepresentsVersion())) + css = summary; + } + } + + // Found it? If not, prompt... + if (css == null) { + if (urn != null || ver != null) { + Util.displayMessage("No matching coding scheme was found for the given URN or version."); + Util.displayMessage(""); + } + css = Util.promptForCodeSystem(); + if (css == null) + return; + } + + // Continue and perform the action ... + Util.displayTaggedMessage("A matching coding scheme was found ..."); + LexBIGServiceManager lbsm = LexBIGServiceImpl.defaultInstance().getServiceManager(new Object()); + // Pass in a null tag to have it removed. + lbsm.setVersionTag(Constructors.createAbsoluteCodingSchemeVersionReference(css), null); + Util.displayTaggedMessage("Request complete"); + } + } + + /** + * Return supported command options. + * + * @return org.apache.commons.cli.Options + */ + private Options getCommandOptions() { + Options options = new Options(); + Option o; + + o = new Option("u", "urn", true, "URN uniquely identifying the code system."); + o.setArgName("name"); + o.setRequired(false); + options.addOption(o); + + o = new Option("v", "version", true, "Version identifier."); + o.setArgName("id"); + o.setRequired(false); + options.addOption(o); + + return options; + } + +} \ No newline at end of file diff --git a/lbGUI/ivy.xml b/lbGUI/ivy.xml index edfb3a7964..7e1b55c804 100755 --- a/lbGUI/ivy.xml +++ b/lbGUI/ivy.xml @@ -12,7 +12,6 @@ - diff --git a/lbGUI/launch/[lbGUI] LB_GUI_OSX 64.launch b/lbGUI/launch/[lbGUI] LB_GUI_OSX 64.launch index 773f6d318e..7663e19d28 100644 --- a/lbGUI/launch/[lbGUI] LB_GUI_OSX 64.launch +++ b/lbGUI/launch/[lbGUI] LB_GUI_OSX 64.launch @@ -11,6 +11,7 @@ + diff --git a/lbGUI/src/org/LexGrid/LexBIG/gui/CodeSystemDetails.java b/lbGUI/src/org/LexGrid/LexBIG/gui/CodeSystemDetails.java index 811985bde4..13c55ce561 100644 --- a/lbGUI/src/org/LexGrid/LexBIG/gui/CodeSystemDetails.java +++ b/lbGUI/src/org/LexGrid/LexBIG/gui/CodeSystemDetails.java @@ -70,33 +70,33 @@ public void buildComponents(final CodingScheme codeSystemDetails) { | SWT.READ_ONLY | SWT.H_SCROLL | SWT.V_SCROLL); results_.setLayoutData(new GridData(GridData.FILL_BOTH)); - Button editButton = new Button(shell_, SWT.BUTTON1); - editButton - .setText("Edit Coding Scheme"); - editButton.addSelectionListener(new SelectionListener() { +// Button editButton = new Button(shell_, SWT.BUTTON1); +// editButton +// .setText("Edit Coding Scheme"); +// editButton.addSelectionListener(new SelectionListener() { +// +// public void widgetDefaultSelected(SelectionEvent arg0) { +// // +// } - public void widgetDefaultSelected(SelectionEvent arg0) { - // - } - - public void widgetSelected(SelectionEvent arg0) { - CodingSchemeEditDialog editDialog; - try { - editDialog = new CodingSchemeEditDialog(lbGui, null, false, "Edit CodingScheme", shell_, codeSystemDetails, new DialogHandler(shell_)); - } catch (Exception e) { - throw new RuntimeException(e); - } - - editDialog.addItemUpdateListener(new ItemUpdateListener() { - - public void onItemUpdate(CodingScheme item) { - results_.setText(ObjectToString.toString(item)); - lbGui.refreshCodingSchemeList(); - } - - }); - editDialog.open(); - } - }); +// public void widgetSelected(SelectionEvent arg0) { +// CodingSchemeEditDialog editDialog; +// try { +// editDialog = new CodingSchemeEditDialog(lbGui, null, false, "Edit CodingScheme", shell_, codeSystemDetails, new DialogHandler(shell_)); +// } catch (Exception e) { +// throw new RuntimeException(e); +// } +// +// editDialog.addItemUpdateListener(new ItemUpdateListener() { +// +// public void onItemUpdate(CodingScheme item) { +// results_.setText(ObjectToString.toString(item)); +// lbGui.refreshCodingSchemeList(); +// } +// +// }); +// editDialog.open(); +// } +// }); } } \ No newline at end of file diff --git a/lbGUI/src/org/LexGrid/LexBIG/gui/displayResults/DisplayCodedNodeSet.java b/lbGUI/src/org/LexGrid/LexBIG/gui/displayResults/DisplayCodedNodeSet.java index f8814a9f42..6f77e0115a 100644 --- a/lbGUI/src/org/LexGrid/LexBIG/gui/displayResults/DisplayCodedNodeSet.java +++ b/lbGUI/src/org/LexGrid/LexBIG/gui/displayResults/DisplayCodedNodeSet.java @@ -127,7 +127,7 @@ public class DisplayCodedNodeSet { private ConceptTreeView primaryTree; private final boolean twoGraphs; private TabFolder tabs; - private Button editButton; + //private Button editButton; /* * The subsetGraph/Tree are used only in the Coded Node Graph case (ie, not @@ -300,42 +300,42 @@ private void init() { showSecondaryRel_button.setSelection(showSecondaryRel_selected); showSecondaryRel_button.addSelectionListener(graphingCheckboxListener); - editButton = new Button(graphChoices, SWT.BUTTON1); - editButton - .setText("Edit Entity"); - editButton.addSelectionListener(new SelectionListener() { - - public void widgetDefaultSelected(SelectionEvent arg0) { - // - } - - public void widgetSelected(SelectionEvent arg0) { - - int index = displayedCodeList_.getSelectionIndex(); - ResolvedConceptReference rcr = displayedResults_.get(index); - try { - EntityEditDialog editDialog = - new EntityEditDialog(lb_gui_, null, false, "Edit Entity", shell_, dialog_, rcr); - editDialog.open(); - - editDialog.addItemUpdateListener(new ItemUpdateListener() { - - public void onItemUpdate(ResolvedConceptReference ref) { - displayConceptDetails(ref); - updateGraphForConceptSelection(ref); - addOrUpdateDisplayedResults(ref, -1, -1, -1, SWT.NONE, -1, -1, true); - editButton.setEnabled(false); - } - }); - } catch (Exception e) { - throw new RuntimeException(e); - } - - } - - }); - - editButton.setEnabled(false); +// editButton = new Button(graphChoices, SWT.BUTTON1); +// editButton +// .setText("Edit Entity"); +// editButton.addSelectionListener(new SelectionListener() { +// +// public void widgetDefaultSelected(SelectionEvent arg0) { +// // +// } +// +// public void widgetSelected(SelectionEvent arg0) { +// +// int index = displayedCodeList_.getSelectionIndex(); +// ResolvedConceptReference rcr = displayedResults_.get(index); +// try { +// EntityEditDialog editDialog = +// new EntityEditDialog(lb_gui_, null, false, "Edit Entity", shell_, dialog_, rcr); +// editDialog.open(); +// +// editDialog.addItemUpdateListener(new ItemUpdateListener() { +// +// public void onItemUpdate(ResolvedConceptReference ref) { +// displayConceptDetails(ref); +// updateGraphForConceptSelection(ref); +// addOrUpdateDisplayedResults(ref, -1, -1, -1, SWT.NONE, -1, -1, true); +// editButton.setEnabled(false); +// } +// }); +// } catch (Exception e) { +// throw new RuntimeException(e); +// } +// +// } +// +// }); +// +// editButton.setEnabled(false); // Add graph viewer ... // Graph graph = new Graph(true); @@ -492,10 +492,10 @@ public void widgetDefaultSelected(SelectionEvent e) { public void widgetSelected(SelectionEvent e) { int index = displayedCodeList_.getSelectionIndex(); - if (index == -1) { - editButton.setEnabled(false); - return; - } +// if (index == -1) { +// editButton.setEnabled(false); +// return; +// } if (index == displayedResults_.size()) { if (displayedCodeList_.getItem(index).equals(FETCHING_MORE)) { // in the process of fetching more... do nothing. @@ -510,7 +510,7 @@ public void widgetSelected(SelectionEvent e) { } else { if(lb_gui_.isAdminEnabled()) { - editButton.setEnabled(true); +// editButton.setEnabled(true); } ResolvedConceptReference rcr = displayedResults_.get(index); diff --git a/lbGUI/src/org/LexGrid/LexBIG/gui/edit/AbstractEditDialog.java b/lbGUI/src/org/LexGrid/LexBIG/gui/edit/AbstractEditDialog.java index 42ba849581..eb19206590 100644 --- a/lbGUI/src/org/LexGrid/LexBIG/gui/edit/AbstractEditDialog.java +++ b/lbGUI/src/org/LexGrid/LexBIG/gui/edit/AbstractEditDialog.java @@ -43,7 +43,7 @@ import org.eclipse.swt.widgets.MessageBox; import org.eclipse.swt.widgets.Shell; import org.eclipse.swt.widgets.Text; -import org.lexevs.cts2.core.update.RevisionInfo; +//import org.lexevs.cts2.core.update.RevisionInfo; public abstract class AbstractEditDialog implements ItemUpdateListener { @@ -63,15 +63,15 @@ public abstract class AbstractEditDialog implements ItemUpdateListener { public List> listeners = new ArrayList>(); - protected RevisionInfo buildRevisionInfo(){ - RevisionInfo revisionInfo = new RevisionInfo(); - if(getRevisionEditing()) { - revisionInfo.setRevisionId(getRevisionId()); - } else { - revisionInfo.setRevisionId(createRandomRevisionId()); - } - return revisionInfo; - } +// protected RevisionInfo buildRevisionInfo(){ +// RevisionInfo revisionInfo = new RevisionInfo(); +// if(getRevisionEditing()) { +// revisionInfo.setRevisionId(getRevisionId()); +// } else { +// revisionInfo.setRevisionId(createRandomRevisionId()); +// } +// return revisionInfo; +// } private String createRandomRevisionId() { return UUID.randomUUID().toString(); @@ -127,7 +127,7 @@ public void shellIconified(ShellEvent arg0) { }); } - protected abstract T updateItem(); +// protected abstract T updateItem(); public void addItemUpdateListener(ItemUpdateListener listener) { this.listeners.add(listener); @@ -201,26 +201,26 @@ public void widgetSelected(SelectionEvent arg0) { } }); - Button saveButton = new Button(buttonComposite, SWT.BUTTON1); - saveButton.setText("Save"); - saveButton.addSelectionListener(new SelectionListener() { - - public void widgetDefaultSelected(SelectionEvent arg0) { - // - } - - public void widgetSelected(SelectionEvent arg0) { - T updatedItem = updateItem(); - - dialogHandler.showInfo("Update", "Item has been Updated sucessfully", true); - - for(ItemUpdateListener listener : listeners) { - listener.onItemUpdate(updatedItem); - } - - hasBeenEdited = false; - } - }); +// Button saveButton = new Button(buttonComposite, SWT.BUTTON1); +// saveButton.setText("Save"); +// saveButton.addSelectionListener(new SelectionListener() { +// +// public void widgetDefaultSelected(SelectionEvent arg0) { +// // +// } +// +// public void widgetSelected(SelectionEvent arg0) { +// T updatedItem = updateItem(); +// +// dialogHandler.showInfo("Update", "Item has been Updated sucessfully", true); +// +// for(ItemUpdateListener listener : listeners) { +// listener.onItemUpdate(updatedItem); +// } +// +// hasBeenEdited = false; +// } +// }); GridData gridData = new GridData(); gridData.horizontalAlignment = GridData.HORIZONTAL_ALIGN_BEGINNING; @@ -229,7 +229,7 @@ public void widgetSelected(SelectionEvent arg0) { buttonComposite.setLayoutData(gridData); buttonComposite.setEnabled(true); buttonComposite.setVisible(true); - saveButton.setVisible(true); +// saveButton.setVisible(true); this.hasBeenEdited = false; diff --git a/lbGUI/src/org/LexGrid/LexBIG/gui/edit/CodingSchemeEditDialog.java b/lbGUI/src/org/LexGrid/LexBIG/gui/edit/CodingSchemeEditDialog.java index d8f2461318..b6910e7ee4 100644 --- a/lbGUI/src/org/LexGrid/LexBIG/gui/edit/CodingSchemeEditDialog.java +++ b/lbGUI/src/org/LexGrid/LexBIG/gui/edit/CodingSchemeEditDialog.java @@ -33,8 +33,8 @@ import org.eclipse.swt.layout.GridLayout; import org.eclipse.swt.widgets.Composite; import org.eclipse.swt.widgets.Shell; -import org.lexevs.cts2.LexEvsCTS2Impl; -import org.lexevs.cts2.author.CodeSystemAuthoringOperation; +//import org.lexevs.cts2.LexEvsCTS2Impl; +//import org.lexevs.cts2.author.CodeSystemAuthoringOperation; import org.lexevs.dao.database.utility.DaoUtility; import org.lexevs.locator.LexEvsServiceLocator; @@ -46,8 +46,8 @@ public class CodingSchemeEditDialog extends AbstractEditDialog{ private static String FORMAL_NAME_KEY = "formalName"; private static String NUM_OF_CONCEPTS_KEY = "approxNumConcepts"; - private CodeSystemAuthoringOperation codeSystemAuthoringOperation = - LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); +// private CodeSystemAuthoringOperation codeSystemAuthoringOperation = +// LexEvsCTS2Impl.defaultInstance().getAuthoringOperation().getCodeSystemAuthoringOperation(); public CodingSchemeEditDialog( LB_GUI lbGui, @@ -88,36 +88,36 @@ protected void initComponents(Composite composite) { String.valueOf(codingScheme.getApproxNumConcepts())); } - @Override - protected CodingScheme updateItem() { - - String numOfConceptsText = super.getTextBoxContent(NUM_OF_CONCEPTS_KEY); - long numOfConcepts = Long.parseLong(numOfConceptsText); - Text copyRight = DaoUtility.createText(super.getTextBoxContent(COPYRIGHT_TEXT_KEY)); - String formalName = super.getTextBoxContent(FORMAL_NAME_KEY); - - try { - this.codeSystemAuthoringOperation.updateCodeSystem( - this.buildRevisionInfo(), - this.codingScheme.getCodingSchemeName(), - this.codingScheme.getCodingSchemeURI(), - formalName, - null, - numOfConcepts, - this.codingScheme.getRepresentsVersion(), - null, - null, - copyRight, - null); - } catch (LBException e) { - this.getDialogHandler().showError("Update Error", e.getMessage()); - } - - return LexEvsServiceLocator.getInstance(). - getDatabaseServiceManager(). - getCodingSchemeService(). - getCodingSchemeByUriAndVersion( - this.codingScheme.getCodingSchemeURI(), - this.codingScheme.getRepresentsVersion()); - } +// @Override +// protected CodingScheme updateItem() { +// +// String numOfConceptsText = super.getTextBoxContent(NUM_OF_CONCEPTS_KEY); +// long numOfConcepts = Long.parseLong(numOfConceptsText); +// Text copyRight = DaoUtility.createText(super.getTextBoxContent(COPYRIGHT_TEXT_KEY)); +// String formalName = super.getTextBoxContent(FORMAL_NAME_KEY); +// +// try { +// this.codeSystemAuthoringOperation.updateCodeSystem( +// this.buildRevisionInfo(), +// this.codingScheme.getCodingSchemeName(), +// this.codingScheme.getCodingSchemeURI(), +// formalName, +// null, +// numOfConcepts, +// this.codingScheme.getRepresentsVersion(), +// null, +// null, +// copyRight, +// null); +// } catch (LBException e) { +// this.getDialogHandler().showError("Update Error", e.getMessage()); +// } +// +// return LexEvsServiceLocator.getInstance(). +// getDatabaseServiceManager(). +// getCodingSchemeService(). +// getCodingSchemeByUriAndVersion( +// this.codingScheme.getCodingSchemeURI(), +// this.codingScheme.getRepresentsVersion()); +// } } \ No newline at end of file diff --git a/lbGUI/src/org/LexGrid/LexBIG/gui/edit/EntityEditDialog.java b/lbGUI/src/org/LexGrid/LexBIG/gui/edit/EntityEditDialog.java index 534c0b6e45..f4e3f1a7c7 100644 --- a/lbGUI/src/org/LexGrid/LexBIG/gui/edit/EntityEditDialog.java +++ b/lbGUI/src/org/LexGrid/LexBIG/gui/edit/EntityEditDialog.java @@ -43,9 +43,9 @@ import org.eclipse.swt.widgets.Combo; import org.eclipse.swt.widgets.Composite; import org.eclipse.swt.widgets.Shell; -import org.lexevs.cts2.LexEvsCTS2Impl; -import org.lexevs.cts2.author.CodeSystemAuthoringOperation; -import org.lexevs.cts2.core.update.RevisionInfo; +//import org.lexevs.cts2.LexEvsCTS2Impl; +//import org.lexevs.cts2.author.CodeSystemAuthoringOperation; +//import org.lexevs.cts2.core.update.RevisionInfo; import org.lexevs.dao.database.utility.DaoUtility; public class EntityEditDialog extends AbstractEditDialog { @@ -57,8 +57,8 @@ public class EntityEditDialog extends AbstractEditDialogDan Armbrust * @version subversion $Revision: $ checked in on $Date: $ diff --git a/lbImpl/src/org/LexGrid/LexBIG/Impl/Extensions/GenericExtensions/search/SearchExtensionImpl.java b/lbImpl/src/org/LexGrid/LexBIG/Impl/Extensions/GenericExtensions/search/SearchExtensionImpl.java index 921c820976..5bc7949144 100644 --- a/lbImpl/src/org/LexGrid/LexBIG/Impl/Extensions/GenericExtensions/search/SearchExtensionImpl.java +++ b/lbImpl/src/org/LexGrid/LexBIG/Impl/Extensions/GenericExtensions/search/SearchExtensionImpl.java @@ -61,6 +61,22 @@ public ResolvedConceptReferencesIterator search( MatchAlgorithm matchAlgorithm) throws LBParameterException { return this.search(text, codeSystemsToInclude, codeSystemsToExclude, matchAlgorithm, false); } + + @Override + public ResolvedConceptReferencesIterator search( + final String text, + Set codeSystemsToInclude, + Set codeSystemsToExclude, + MatchAlgorithm matchAlgorithm, + boolean includeAnonymous) throws LBParameterException { + return this.search( + text, + codeSystemsToInclude, + codeSystemsToExclude, + matchAlgorithm, + includeAnonymous, + false); + } @Override public ResolvedConceptReferencesIterator search( @@ -68,7 +84,8 @@ public ResolvedConceptReferencesIterator search( Set codeSystemsToInclude, Set codeSystemsToExclude, MatchAlgorithm matchAlgorithm, - boolean includeAnonymous) throws LBParameterException { + boolean includeAnonymous, + boolean includeInactive) throws LBParameterException { LexEvsServiceLocator lexEvsServiceLocator = LexEvsServiceLocator.getInstance(); List entries = @@ -97,14 +114,20 @@ public ResolvedConceptReferencesIterator search( Query query = this.parseQuery(this.decorateQueryString(text, analyzer, matchAlgorithm), analyzer); - if(! includeAnonymous){ + if(! includeAnonymous || ! includeInactive){ BooleanQuery booleanQuery = new BooleanQuery(); booleanQuery.add(query, Occur.MUST); - booleanQuery.add(new TermQuery(new Term("anonymous", "true")), Occur.MUST_NOT); + + if(! includeAnonymous){ + booleanQuery.add(new TermQuery(new Term("anonymous", "true")), Occur.MUST_NOT); + } + if(! includeInactive){ + booleanQuery.add(new TermQuery(new Term("active", "false")), Occur.MUST_NOT); + } query = booleanQuery; } - + List scoreDocs = lexEvsServiceLocator. getIndexServiceManager(). getSearchIndexService(). diff --git a/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/RadLexProtegeFramesLoaderImpl.java b/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/RadLexProtegeFramesLoaderImpl.java index 573c9423d2..1db67a740d 100644 --- a/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/RadLexProtegeFramesLoaderImpl.java +++ b/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/RadLexProtegeFramesLoaderImpl.java @@ -40,7 +40,7 @@ /** * Validates and/or loads RadLex content, provided by the - * Radiological Society of North America in Protégé frame format. + * Radiological Society of North America in Protégé frame format. * * @author Dan Armbrust * @version subversion $Revision: $ checked in on $Date: $ diff --git a/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/TextLoaderImpl.java b/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/TextLoaderImpl.java index 9562a2a328..e46b6dbbb0 100644 --- a/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/TextLoaderImpl.java +++ b/lbImpl/src/org/LexGrid/LexBIG/Impl/loaders/TextLoaderImpl.java @@ -24,7 +24,6 @@ import org.LexGrid.LexBIG.DataModel.InterfaceElements.ExtensionDescription; import org.LexGrid.LexBIG.DataModel.InterfaceElements.types.ProcessState; import org.LexGrid.LexBIG.Exceptions.LBException; -import org.LexGrid.LexBIG.Exceptions.LBInvocationException; import org.LexGrid.LexBIG.Exceptions.LBParameterException; import org.LexGrid.LexBIG.Extensions.Load.OntologyFormat; import org.LexGrid.LexBIG.Extensions.Load.Text_Loader; @@ -61,7 +60,7 @@ public void validate(URI uri, Character delimiter, boolean triplesFormat, int va public void load(URI source, Character delimiter, boolean readDoublesAsTriples, boolean stopOnErrors, boolean async) throws LBException { - this.getOptions().getStringOption(DELIMITER_OPTION).setOptionValue(String.valueOf(delimiter)); + this.getOptions().getStringOption(DELIMITER_OPTION).setOptionValue(delimiter == null ? null : String.valueOf(delimiter)); this.getOptions().getBooleanOption(FORCE_FORMAT_B_OPTION).setOptionValue(readDoublesAsTriples); this.getOptions().getBooleanOption(FAIL_ON_ERROR_OPTION).setOptionValue(stopOnErrors); this.getOptions().getBooleanOption(ASYNC_OPTION).setOptionValue(async); diff --git a/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Generic/SearchExtension.java b/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Generic/SearchExtension.java index b846705235..4cb6a72c2b 100644 --- a/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Generic/SearchExtension.java +++ b/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Generic/SearchExtension.java @@ -133,4 +133,44 @@ public ResolvedConceptReferencesIterator search( Set codingSchemesToExclude, MatchAlgorithm matchAlgorithm, boolean includeAnonymous) throws LBParameterException; + + + /** + * Search based on a given text string over given coding schemes, excluding + * the listed. + * + * NOTE: If a coding scheme appears in both codingSchemesToInclude + * and codingSchemesToExclude, the exclude will be given priority. + * + * @param text + * The search text + * @param codingSchemesToInclude + * The coding schemes to include in the search + * @param codingSchemesToExclude + * The coding schemes to include in the search + * @param matchAlgorithm + * The match algorithm to use for matching + * @param includeAnonymous + * Whether or not to include Anonymous Entities + * Default: 'false' + * NOTE: 'false' -> include "anonymous != 'true'" + * 'true' -> include all + * + * @param includeInactive + * Whether or not to include Inactive Entities + * Default: 'false' + * NOTE: 'false' -> include "active != 'true'" + * 'true' -> include all + * @return + * A ResolvedConceptReferencesIterator + * + * @throws LBParameterException + */ + public ResolvedConceptReferencesIterator search( + String text, + Set codingSchemesToInclude, + Set codingSchemesToExclude, + MatchAlgorithm matchAlgorithm, + boolean includeAnonymous, + boolean includeInactive) throws LBParameterException; } diff --git a/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/RadlexProtegeFrames_Loader.java b/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/RadlexProtegeFrames_Loader.java index a7cd9b308b..918e7a2da2 100644 --- a/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/RadlexProtegeFrames_Loader.java +++ b/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/RadlexProtegeFrames_Loader.java @@ -24,12 +24,12 @@ /** * Validates and/or loads RadLex content, provided by the - * Radiological Society of North America in Protégé frame format. + * Radiological Society of North America in Protégé frame format. */ public interface RadlexProtegeFrames_Loader extends Loader { /** - * Load the Radiological Lexicon (RadLex) ontology from a Protégé + * Load the Radiological Lexicon (RadLex) ontology from a Protégé * Frames (.pprj) file format. This will also result in implicit * generation of standard indices required by the LexBIG runtime. *

@@ -37,7 +37,7 @@ public interface RadlexProtegeFrames_Loader extends Loader { * operation is already in progress. * * @param source - * URI corresponding to the Protégé project (typically .pprj) file. + * URI corresponding to the Protégé project (typically .pprj) file. * @param stopOnErrors * True means stop if any load error is detected. False means * attempt to load what can be loaded if recoverable errors are @@ -60,7 +60,7 @@ public interface RadlexProtegeFrames_Loader extends Loader { * @throws LBException * * @param source - * URI corresponding to the Protégé project (typically .pprj) file. + * URI corresponding to the Protégé project (typically .pprj) file. * @param validationLevel * Supported levels of validation include: 0 = Verify the source file * exists. diff --git a/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/Text_Loader.java b/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/Text_Loader.java index abbc43e615..f7a841e845 100644 --- a/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/Text_Loader.java +++ b/lbInterfaces/src/org/LexGrid/LexBIG/Extensions/Load/Text_Loader.java @@ -35,6 +35,9 @@ * @created 09-Feb-2006 10:22:07 PM */ public interface Text_Loader extends Loader { + + public static String STD_IN_URI = "std:in"; + public static final String name = "TextLoader"; public static final String description = "This loader loads LexGrid Text files into the LexGrid database."; diff --git a/lbPackager/build.properties b/lbPackager/build.properties index d25e81c072..ea256421c8 100755 --- a/lbPackager/build.properties +++ b/lbPackager/build.properties @@ -2,13 +2,13 @@ vMajor=6 #Product version - minor release -vMinor=1 +vMinor=2 #Product version - patch level vPatch=0 #Product version - candidate status (e.g. a= alpha, b=beta, rc=release candidate ) -vCStat=.RC1 +vCStat= #Product build id vBuild=${vMajor}.${vMinor}.${vPatch}${vCStat} diff --git a/lbPackager/build.xml b/lbPackager/build.xml index 3ca2e90bcb..c13d1d7ae3 100644 --- a/lbPackager/build.xml +++ b/lbPackager/build.xml @@ -65,7 +65,6 @@ You may obtain a copy of the License at - @@ -549,22 +548,6 @@ You may obtain a copy of the License at - - - - - - - - - - - @@ -653,8 +636,8 @@ pause java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=linux/ -cp lbGUI.jar:linux/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_GUI - -java -d32 -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=OSX/ -XstartOnFirstThread -cp lbGUI.jar:OSX/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_GUI + +java -Xmx3000M -XX:MaxPermSize=256M -d64 -Djava.library.path=OSX/ -XstartOnFirstThread -cp lbGUI.jar:OSX/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_GUI java -Xmx6000M -XX:MaxPermSize=256M -Djava.library.path=linux_x86_64/ -cp lbGUI.jar:linux_x86_64/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_GUI @@ -671,7 +654,7 @@ pause java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=linux/ -cp lbGUI.jar:linux/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_GUI -d - + java -d32 -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=OSX/ -XstartOnFirstThread -cp lbGUI.jar:OSX/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_GUI -d @@ -680,14 +663,14 @@ java -Xmx6000M -XX:MaxPermSize=256M -Djava.library.path=linux_x86_64/ -cp lbGUI. - java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=windows/ -cp lbGUI.jar;windows/swt.jar;../runtime/lbPatch.jar;../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI +java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=windows/ -cp lbGUI.jar;windows/swt.jar;../runtime/lbPatch.jar;../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI pause - java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=linux/ -cp lbGUI.jar:linux/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI +java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=linux/ -cp lbGUI.jar:linux/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI - - java -d32 -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=OSX/ -XstartOnFirstThread -cp lbGUI.jar:OSX/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI + +java -Xmx3000M -XX:MaxPermSize=256M -Djava.library.path=OSX/ -XstartOnFirstThread -cp lbGUI.jar:OSX/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI java -Xmx1000M -XX:MaxPermSize=256M -cp lbGUI.jar;windows_64/swt.jar;../runtime/lbPatch.jar;../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI @@ -698,21 +681,18 @@ java -Xmx1000M -XX:MaxPermSize=256M -cp lbGUI.jar;windows_64/swt.jar;../runtime/ pause - java -Xmx6000M -XX:MaxPermSize=256M -Djava.library.path=linux_x86_64/ -cp lbGUI.jar:linux_x86_64/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI +java -Xmx6000M -XX:MaxPermSize=256M -Djava.library.path=linux_x86_64/ -cp lbGUI.jar:linux_x86_64/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI - java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=windows/ -cp lbGUI.jar;windows/swt.jar;../runtime/lbPatch.jar;../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d +java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=windows/ -cp lbGUI.jar;windows/swt.jar;../runtime/lbPatch.jar;../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d pause - java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=linux/ -cp lbGUI.jar:linux/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d - - - java -d32 -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=OSX/ -XstartOnFirstThread -cp lbGUI.jar:OSX/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d +java -Xmx1000M -XX:MaxPermSize=256M -Djava.library.path=linux/ -cp lbGUI.jar:linux/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d - java -Xmx6000M -XX:MaxPermSize=256M -Djava.library.path=linux_x86_64/ -cp lbGUI.jar:linux_x86_64/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d +java -Xmx6000M -XX:MaxPermSize=256M -Djava.library.path=linux_x86_64/ -cp lbGUI.jar:linux_x86_64/swt.jar:../runtime/lbPatch.jar:../runtime/lbRuntime.jar org.LexGrid.LexBIG.gui.LB_VSD_GUI -d @@ -769,7 +749,7 @@ pause lexevs-dao, lgConverter, lexrdf, lbImpl, lbAdmin, Indexer, lgResourceReader, lgValueSets,lbExamples, loader-framework-core, abstract-rrf-loader, - umls-loader, meta-loader, rxnorm-loader, cts2-model, cts2, lbGUI, lbTest"> + umls-loader, meta-loader, rxnorm-loader, lbGUI, lbTest"> @@ -917,36 +897,7 @@ pause - - - - - - - - - - - - - - - - - - - - - - - + @@ -1092,7 +1043,7 @@ pause + build-lexbig-jar, javadoc, pack"/> Installs the graphical interface for OSX. - + - + diff --git a/lbPackager/files/license.txt b/lbPackager/files/license.txt index de32d4ded6..207047a501 100644 --- a/lbPackager/files/license.txt +++ b/lbPackager/files/license.txt @@ -2,9 +2,9 @@ Software User Agreement 12 October, 2010 -=============================================================================== +=========================================================================== Usage of Content -=============================================================================== +=========================================================================== THIS PRODUCTS MAKES AVAILABLE SOFTWARE, DOCUMENTATION, INFORMATION AND/OR OTHER MATERIALS (COLLECTIVELY "CONTENT"). USE OF THE CONTENT IS GOVERNED BY THE TERMS AND CONDITIONS OF THIS AGREEMENT AND/OR THE TERMS AND CONDITIONS OF LICENSE @@ -15,15 +15,15 @@ REFERENCED BELOW. IF YOU DO NOT AGREE TO THE TERMS AND CONDITIONS OF THIS AGREEMENT AND THE TERMS AND CONDITIONS OF ANY APPLICABLE LICENSE AGREEMENTS OR NOTICES INDICATED OR REFERENCED BELOW, THEN YOU MAY NOT USE THE CONTENT. -=============================================================================== +=========================================================================== Applicable Licenses -=============================================================================== +=========================================================================== Unless otherwise noted, content is provided to you under terms and conditions of the following agreement: Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and -Research (MFMER).  All rights reserved.  MAYO, MAYO CLINIC, and the +Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the triple-shield Mayo logo are trademarks and service marks of MFMER. Except as contained in the copyright notice above, or as used to @@ -35,10 +35,10 @@ without prior written authorization of the copyright holder. Licensed under the Eclipse Public License, Version 1.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at -  -              http://www.eclipse.org/legal/epl-v10.html -================================================================================ +http://www.eclipse.org/legal/epl-v10.html + +========================================================================= Content includes redistribution of additional 3rd party software modules, placed in the '/runtime-components/extlib' folder of the installation root directory. @@ -49,11 +49,11 @@ Modules include, but are not limited to, those listed below. IT IS YOUR OBLIGATION TO READ AND ACCEPT ALL SUCH TERMS AND CONDITIONS PRIOR TO USE OF THE CONTENT. -================================================================================ +========================================================================= Included materials: -================================================================================ +========================================================================= This product incorporates code and other materials created with NCI funding as -part of the LexGrid Vocabulary Services for caBIG™ (LexEVS) project, with +part of the LexGrid Vocabulary Services for caBIG (LexEVS) project, with additional funding provided by the National Center for Biomedical Ontology (NCBO) as part of the LexGrid Vocabulary Services for NCBO (LexBIO) project. @@ -66,7 +66,7 @@ readable source code form and machine readable, binary, object code form. lbRuntime ======================================== The LexEVS runtime code, including all necessary code and dependencies required -for direct Java-to-Java invocation of the LexEVS API.  This consolidates LexEVS +for direct Java-to-Java invocation of the LexEVS API. This consolidates LexEVS code and 3rd party modules in order to simplify configuration for program execution. @@ -98,8 +98,8 @@ ARQ is a query engine for Jena that supports the SPARQL RDF Query language. ======================================== caGrid ======================================== -Grid infrastructure to support the caBIG™ community. Contains tools for -creating and deploying caBIG™ compliant grid services. +Grid infrastructure to support the caBIG community. Contains tools for +creating and deploying caBIG compliant grid services. ======================================== castor @@ -237,7 +237,7 @@ Used for graph representations in the LexEVS GUI. protege, protege-owl ======================================== This product incorporates (or builds upon) [part of] the license open source -Protégé system. +Protg system. ======================================== saxpath @@ -249,11 +249,11 @@ xerces ======================================== XML parsing services -================================================================================ -================================================================================ +======================================================================== +======================================================================== Additional License Terms and Conditions -================================================================================ -================================================================================ +======================================================================== +======================================================================== ======================================== caGrid @@ -396,59 +396,59 @@ commons-cli commons-discovery ======================================== - * ==================================================================== - * +* =================================================================== +* * The Apache Software License, Version 1.1 - * - * Copyright (c) 1999-2001 The Apache Software Foundation.  All rights - * reserved. - * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions - * are met: - * - * 1. Redistributions of source code must retain the above copyright - *    notice, this list of conditions and the following disclaimer. - * - * 2. Redistributions in binary form must reproduce the above copyright - *    notice, this list of conditions and the following disclaimer in - *    the documentation and/or other materials provided with the - *    distribution. - * - * 3. The end-user documentation included with the redistribution, if - *    any, must include the following acknowlegement: - *       "This product includes software developed by the - *        Apache Software Foundation (http://www.apache.org/)." - *    Alternately, this acknowlegement may appear in the software itself, - *    if and wherever such third-party acknowlegements normally appear. - * - * 4. The names "The Jakarta Project", "Commons", and "Apache Software - *    Foundation" must not be used to endorse or promote products derived - *    from this software without prior written permission. For written - *    permission, please contact apache@apache.org. - * - * 5. Products derived from this software may not be called "Apache" - *    nor may "Apache" appear in their names without prior written - *    permission of the Apache Group. - * - * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED - * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES - * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED.  IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR - * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF - * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND - * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, - * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT - * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF - * SUCH DAMAGE. - * ==================================================================== - * - * This software consists of voluntary contributions made by many - * individuals on behalf of the Apache Software Foundation.  For more - * information on the Apache Software Foundation, please see - * . +* +* Copyright (c) 1999-2001 The Apache Software Foundation. All rights +* reserved. +* +* Redistribution and use in source and binary forms, with or without +* modification, are permitted provided that the following conditions +* are met: +* +* 1. Redistributions of source code must retain the above copyright +* notice, this list of conditions and the following disclaimer. +* +* 2. Redistributions in binary form must reproduce the above copyright +* notice, this list of conditions and the following disclaimer in +* the documentation and/or other materials provided with the +* distribution. +* +* 3. The end-user documentation included with the redistribution, if +* any, must include the following acknowlegement: +* "This product includes software developed by the +* Apache Software Foundation (http://www.apache.org/)." +* Alternately, this acknowlegement may appear in the software itself, +* if and wherever such third-party acknowlegements normally appear. +* +* 4. The names "The Jakarta Project", "Commons", and "Apache Software +* Foundation" must not be used to endorse or promote products derived +* from this software without prior written permission. For written +* permission, please contact apache@apache.org. +* +* 5. Products derived from this software may not be called "Apache" +* nor may "Apache" appear in their names without prior written +* permission of the Apache Group. +* +* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED +* WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES +* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +* DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR +* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF +* USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND +* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT +* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF +* SUCH DAMAGE. +* ==================================================================== +* +* This software consists of voluntary contributions made by many +* individuals on behalf of the Apache Software Foundation. For more +* information on the Apache Software Foundation, please see +* . ======================================== commons-codec @@ -620,16 +620,16 @@ CopyOnWriteArrayList and ConcurrentReaderHashMap classes are adapted from Sun JDK source code. These are copyright of Sun Microsystems, Inc, and are used with their kind permission, as described in the following license: -=============================================================================== +=========================================================================== TECHNOLOGY LICENSE FROM SUN MICROSYSTEMS, INC. TO DOUG LEA Whereas Doug Lea desires to utlized certain Java Software technologies in the -util.concurrent technology; and Whereas Sun Microsystems, Inc. (“Sun”) desires +util.concurrent technology; and Whereas Sun Microsystems, Inc. (Sun) desires that Doug Lea utilize certain Java Software technologies in the util.concurrent technology; Therefore the parties agree as follows, effective May 31, 2002: -“Java Software technologies” means +Java Software technologies means classes/java/util/ArrayList.java, and classes/java/util/HashMap.java. The Java Software technologies are Copyright (c) 1994-2000 Sun Microsystems, @@ -907,7 +907,7 @@ ini ======================================== Unless otherwise noted, the following copyright statement applies: -© Copyright 2000, 2001, 2002, 2003, 2004, 2005 Hewlett-Packard Development + Copyright 2000, 2001, 2002, 2003, 2004, 2005 Hewlett-Packard Development Company, LP Redistribution and use in source and binary forms, with or without modification, @@ -939,11 +939,11 @@ Jena is built on top of other sub-systems which we gratefully acknowledge: details of these systems and their version numbers (see http://jena.sourceforge.net/Licenses/index.html) -• Xerces -• JUnit -• Jakarta ORO -• ICU4J -• util.concurrent from Doug Lea + Xerces + JUnit + Jakarta ORO + ICU4J + util.concurrent from Doug Lea ======================================== junit @@ -1316,7 +1316,7 @@ Third Party Content The Content includes items that have been sourced from third parties as set out below. If you did not receive this Content directly from the Eclipse Foundation, the following is provided for informational purposes only, and you should look -to the Redistributor’s license for terms and conditions of use. +to the Redistributors license for terms and conditions of use. OSGi Materials @@ -1347,7 +1347,7 @@ Alliance and its members are not responsible and shall not be held responsible in any manner for identifying or failing to identify any or all such third party intellectual property rights. -OSGi™ is a trademark, registered trademark, or service mark of The OSGi Alliance +OSGi is a trademark, registered trademark, or service mark of The OSGi Alliance in the US and other countries. Java is a trademark, registered trademark, or service mark of Sun Microsystems, Inc. in the US and other countries. All other trademarks, registered trademarks, or service marks used in the Content are the diff --git a/lbPackager/files/readme-lexbig.txt b/lbPackager/files/readme-lexbig.txt index 58e264cab1..49958ed3ad 100644 --- a/lbPackager/files/readme-lexbig.txt +++ b/lbPackager/files/readme-lexbig.txt @@ -1,528 +1,2 @@ - -Cumulative Release notes for LexEVS 6.0.4 and it's predecessors, 6.0.3, 6.0.2, 6.0.1 and 6.0 -Craig Stancl -Pradip Kanjamala -Scott Bauer -Sridhar Yadav - -This release includes previous patch items from 6.0.1 and 6.0.2: - -== Version 6.0.1 == -1) RRF relation directionality is no longer reversed. - https://tracker.nci.nih.gov/browse/LEXEVS-451 -2) Resolves missing HL7 relations. - https://tracker.nci.nih.gov/browse/LEXEVS-449 - -== Version 6.0.2 == -1) RRF loader now allows 9 characters in the staging -table for LUI's -2) changed the default collation used in MySql from -utf8_general_ci to utf8_bin -3) Fixed error in intersection and difference -function -4) Fixed error in mapping functions to allow -concepts to be resolved properly. -5) The LexEVS OWL export code has been updated to -ensure that the the CUI and TUI properties are -present in the OWL exported content. -6) Admin scripts cleaned up to match documentation -to functionality -7) Updated MeDRA security files. -8) Users can now set collation table values from -configuration file. - -== Version 6.0.3 == - -1) Corrects a problem where isMappingScheme method returns -true when given no relations. - https://tracker.nci.nih.gov/browse/LEXEVS-4661) -2) PropertyId on Property is Required. Altered the code to check if the PropertyId field is null. - https://tracker.nci.nih.gov/browse/LEXEVS-453 -3) Updated swt jars to allow the GUI to work in later OSX and 64 bit Linux -4) Downgraded jena jars for OWL export to fix OWL export error. -5) Corrected the URI for HL7V3.0 and HL7V2.5 - https://tracker.nci.nih.gov/browse/LEXEVS-453 -6) Corrects an issue where OWL and OBO headers are loaded as source - https://tracker.nci.nih.gov/browse/LEXEVS-487 - - -== Version 6.0.4 == - - -1) This release contains an RXNORM loader which is a community contributed (PGRN PHONT) project. As such, it is unsupported. -2) Contains updated launcher's for Value Set GUI for 64bit Windows and Linux. -3) Set DB_PRIMARY_KEY_STRATEGY=SEQUENTIAL_INTEGER as default for generating primary keys in the database. -https://tracker.nci.nih.gov/browse/LEXEVS-494 -4) Corrected an issue with the RRF loader that failed when loading ICD-10. -5) Modified the UmlsRootNodeResolver to only mark codes that have V-SAB value as being root nodes. -6) Updated build for OSX to allow GUI to work with newer versions. (Not backward compatible with powerpc Macs.) -7) Updated loader descriptions to better match function. -https://tracker.nci.nih.gov/browse/LEXEVS-454 -8) Updated build dependencies to point to NCI Nexus server. - - -LexEVS 6.0.0 Release Notes - - - - - -Craig Stancl -Deepak Sharma -Kevin Peterson -Scott Bauer -Sridhar Dwarkanath -Zonghui Lian - -Division of Biomedical Statistics and Informatics -Department of Health Science Research -Mayo Foundation -Rochester, MN - - - - -Table of Contents - - - -Table of Contents 2 -Introduction 2 -CTS2 Implementation 2 -OWL/RDF Export 3 -Integer Primary Keys 4 -Mapping Extension 4 -Supplement Extension 4 -Value Sets (gForge # 26650) 5 -Versioning (gForge # 26651) 6 -XML Loaders 7 -XML Exporter 8 -GForge Items 9 -LexGrid model changes 10 - - -Introduction -This document contains major functionalities that are included in LexEVS 6.0.0 -Release. - -CTS2 Implementation -� Initial Interfaces - The initial set of Interface and API has been created. Input parameters and - output values are still evolving, but interfaces are in place reflect the - functionality of CTS2. -� CTS2 Administration Development (see: org.lexevs.cts2.admin.AdminOperation ) - Import Code System - (see: org.lexevs.cts2.admin.load.CodeSystemLoadOperation) - Loads a �NEW� Revision of a Coding Scheme into the System. If Revision info - is not supplied by the user (such as Revision Id), it will be generated. - Utilizes existing LexEVS loader functionality. - Change Code System Status - (see: org.lexevs.cts2.author.CodeSystemAuthoringOperation) - Import Value Set Version - (see: org.lexevs.cts2.admin.load.ValueSetLoadOperation) - Export Code System Content - (see: org.lexevs.cts2.admin.load.CodeSystemLoadOperation) - Register for Notification - (see: org.lexevs.cts2.admin.NotificationAdminOperation) - Allows the user to register for notification of a System State Change. - There are various events that occur in the system, and a user may choose to - listen for one or more of them. - Update Notification Registration - (see: org.lexevs.cts2.admin.NotificationAdminOperation) - Allows the user to alter an existing Notification Registration. - Update Notification Registration Status - (see: org.lexevs.cts2.admin.NotificationAdminOperation) - Allows the user to �SUSPEND�, �REINSTATE�, or �REMOVE� a notification from - the system. - -� CTS2 Authoring Development (see: org.lexevs.cts2.author.AuthoringOperation ) - Association Authoring Operations - (see: org.lexevs.cts2.author.AssociationAuthoringOperation) - Create association in an established coding scheme using the Revision model. - Create association in an established mapping dedicated coding scheme using - the Revision model. - Create association mapping. Create mappings between coding schemes and - persist as new coding scheme with default metadata settings. Persist using - the Revision model. - Create association mapping. Create mappings between coding schemes and - persist as a coding scheme with user defined metadata values. Persist - using the Revision model. - Create association mapping: Create mappings between coding schemes with - persisted concept values pulled from target schemes current in a LexEVS - service instance. Persist using the Revision model. - Create association type. Create a new AssociationPredicate value and - persist is using the Revision model. - ValueSet Authoring - (see: org.lexevs.cts2.author.ValueSetAuthoringOperation) - -OWL/RDF Export -� OWL/RDF Export functionality has been added, allowing the export of loaded -LexEVS content into OWL format. - (see: org.LexGrid.LexBIG.Extensions.Export.OWL_Exporter) - -Know issues/restrictions: - GForge #30058: AssociationData is not exported. Thus, the owl/rdf exporter - cannot handle the owl:hasValue, owl:maxCardinality, owl:minCardinality, - owl:cardinality constraints. - - - -Integer Primary Keys -� Primary keys are now configurable � either a GUID or a Sequential Integer -scheme can be used. Sequential Integers offer better performance, while GUIDs - enable portability between databases. - -The configuration will appear as such in the lbconfig.props file: - -# DB_PRIMARY_KEY_STRATEGY indicates which strategy will be used -# for the primary key of the database tables. -# WARNING - This cannot be change after the initial -# schema installation. -# -# Allowable values include: -# -# "GUID" -# - Primary Keys are implemented as random GUIDs. -# "SEQUENTIAL_INTEGER" -# - Primary Keys will be sequentially incremented -# - as Integer values. -DB_PRIMARY_KEY_STRATEGY=GUID - -Mapping Extension -(see: org.LexGrid.LexBIG.Extensions.Generic.MappingExtension) -� A general purpose Generic Extension for Mapping Coding Schemes has been -introduced. - -The main implemented features are: - Faster retrieval of Mapping ontology relationships as compared to standard - CodedNodeGraph methods - Expanded Sorting capabilities to include: - Source Code - Target Code - Source Entity Description - Target Entity Description - Relationship Name - A Named Qualifier - Ability to count the number of codes that participate in a mapping ontology - without having to traverse - Determine whether or not an Ontology can be considered a �Mapping� Ontology. - A �Mapping� Ontology is defined in this case as having at least ALL - Relations containers marked as �isMapping=true� - -Supplement Extension -(see: org.LexGrid.LexBIG.Extensions.Generic.SupplementExtension) -� A general purpose Generic Extension for Coding Scheme Supplements has been - introduced. - -The main implemented features are: - Determine whether or not a giving Coding Scheme is acting as a Coding Scheme - Supplement. - Resolve the Parent Coding Scheme of a given Coding Scheme Supplement. - -Value Sets (gForge # 26650) -� Administrative functions : - Ability to load Value Set and Pick List Definitions in to LexGrid repository - Ability to remove Value Set and Pick List Definitions from LexGrid repository. - Ability to export Value Set and Pick List Definition in LexGrid XML format. -� Query functions : - Ability to list all the Value Set and Pick List Definitions loaded in the - system. - Ability to dynamically resolve Value Set and Pick List Definition with/without - user supplied restrictions. - Ability to check if a concept code is part of given Value Set. - Ability to check if one Value Set is sub set of other Value Set. - Ability to apply restrictions like term, coding scheme version, etc and - resolve Value Set and Pick List Definition. - Ability to list all the coding schemes referenced by a Value Set Definition. - Ability to list all Value Set Definition URIs that references a Coding Scheme. - Etc. -� Authoring functions : - Ability to load/update/remove Value Set Definition, DefinitionEntry and - Properties using Versioning API. -� Scripts : - LoadValueSetDefinition(.bat and .sh) �Loads Value Set Definition in LexGrid - XML file into repository. - LoadPickListDefinition(.bat and .sh) � Loads Pick List Definition in LexGrid - XML file into repository. -� GUI : - New GUI (LB_VSD_GUI in gui folder of LexEVS API install directory) is - developed to test all the functionalities that are available for Value Set - Definitions. This tool should mainly be used for testing purpose and not in - production. Here are few major functions available through this GUI tool: - Create new Value Set Definition - Update existing Value Set Definition - Remove existing Value Set Definition - Load Value Set and Pick List Definition from LexGrid XML file - List all Value Set and Pick List Definitions present in the system - Add/update/remove DefinitionEntries (rule sets) - Add/update/remove properties - Resolve Value Set and Pick List Definition using specific set of coding - scheme and version that are loaded in the system - Ability to validate if the changes made returns desired result before saving - changes to the database - Export Value Set and Pick List Definitions in LexGrid XML format - Following query functions are also available: -� Filter by Coding Scheme Reference -� Filter by Concept Domain -� Check if concept code is valid entry in Value Set Resolution -� Filter by a term -� Check if one Value Set is subset of other -� Filter by Value Set Definition Name -� JUnit : - Junit to test all the Value Set functionalities are included in lbTest java - package. - Org.LexGrid.valuedomain.test.VDAllTests.java � Loads test data, runs both - Value Set and Pick list functionality tests, and removes loaded test data. - -Note: Usage Context and Concept Domain is not included in this release, but -will be in next release. - -Versioning (gForge # 26651) -Versioning is a new functionality that has been added to LexEVS API in this -release. Versioning API is divided into two parts, loader and query API. For -this release, loader API is included; query API will be included in next -release. -� Loader functions: -� Loader enables the editing capability of a codingScheme, valueset and picklist. -� Changes can be applied in XML format. -� Changes can be applied in the form of LexGrid Java castor objects as well. -� Loader maintains the history of changes applied to the versionable objects. -� Types of changes that can be applied on a versionable object are -NEW � to create a new versionable element -MODIFY � to change the attributes of an existing versionable element -VERSIONABLE � to change (or schedule a change of) the status of a versionable -element within the context of the containing service. -REMOVE � to remove a versionable element from the service. (Note that the -versionable object will be removed completely from the system including the -history. VERSIONABLE Retire should be used if the element and its history -should remain) -DEPENDENT � no changes are to be made to the named element itself, but a -versionable element whose identity is dependent upon this element is to undergo - a change. -� Loader validates each of the versionable object before loading it. Below are - the criteria for a valid versionable object. -� EntryState must be present. -� If the change type is NEW -� The object being loaded should not exist in lexEVS system. (Exception : The - being added already exist.) -� prevRevision of entryState should be null. (Exception : Changes of type NEW -are not allowed to have previous revisions.) -� If the change type is other than NEW -� The object being revised should be present in the lexEVS system. (Exception : - The codingScheme being revised doesn't exist.) -� The object must have prevRevision, except when the versionable object is -revised first time after the "initial load". (Initial load : -CodingScheme/ValueSet/PickList loaded with out a user defined revision) -� The prevRevision should match the newest revision id of the given versionable - object that is already loaded in the lexEVS system. (Exception : Revision - source is not in sync with the database revisions. Previous revision id does - not match with the latest revision id of the . Please update - the authoring instance with all the revisions and regenerate the source. ) -� JUnit : - VersionableEventAuthoringTest in lbTest package. - - -XML Loaders -� Streaming XML (gForge # 26652): Ability to stream vocabulary contents in -LexGrid XML format into LexGrid repository. -� Ability to load contents at following entry points: - Coding Scheme - Value Set Definition - Pick List Definition - Revision -� JUnit : - Junit to test above functionalities are included in lbTest java package. - -XML Exporter -� Content can be exported to a LexGrid XML file by use of the LexGrid XML -Exporter. -� The LexGrid XML Exporter can be accessed from a command line or from the -LexGrid GUI. -� As of Prototype 3, the following content export scenarios are supported from - the command line, GUI or both: - Entire code system (both) - Concepts only (GUI) - Associations only (GUI) - Specific Association (GUI) - -� Accessing function within the GUI: - Entire code system: - At the menu: Commands -> Enable Admin Options - Select code system - At the menu: Export Terminology -> Export as LexGrid XML - - Concepts only: - Select code system - Click 'Get Code Set' button - Select the CodedNodeSet (CS) from the list - Click the 'LgExport' button - - Associations only: - Select code system - Click 'Get Code Graph' button - Select the CodedNodeGraph (CG) from the list - Note: restrict the set of associations by name: - Click the 'Add' button in the Restrictions frame - Then, in the 'Configure LexBIG' window: - Select 'Restrict to Associations' in the 'Restriction Type' drop down - Select the association name in the 'Associations' selection box - Click the OK button - Click the 'LgExport' button - -Know issues/restrictions: - Command line - Does not currently support the same level of function as the GUI. Only entire - code systems can be exported via the command line. Additional filtering options - will be available from the command line at a later date (Alpha 1). - When calling the XML Exporter from the command line always specify the force - option �-f�. Otherwise the export will fail saying the output file already - exists. This is a bug and will fixed during Alpha1 development. - - Scaling issues. Exporting of concepts should take place via streaming the - content to the file and so should not be constrained by memory. At this - time, however, associations are loaded into memory and so memory may be - a factor in exporting code systems with many associations. This will - be addressed during Alpha 1 development. - - - - - -GForge Items -21720 � Load MRMAP data - MRMAP data is now loaded as a Mapping Coding Scheme - -21935 � OWL loader processing of - -29177 Value Set query enhancement - -27844 ISO 21090 Data Type Support - All Analytical Grid Service methods use ISO 21090 Data Types - -23770 - OBI.owl loading � incorrect curation status - -23806 - OBI.owl loading � incorrect Imported from - -22036 - Focus code not found when referencing external coding scheme - -28645 - Manifest loader/metadata loader - -26637 - Page CodedNodeGraph Results: -� CodedNodeGraph results are retrieved on demand from the database. Depth and -Breath of the graph are both expanded on demand, so graph traversal time -should not be effected by ontology, number of AssociatedConcepts, resolve depth, - etc. -� AssociatedConcepts (and Resolved Entities, if needed) are retrieved in batches, - instead of individually. -Limitations -� Duplicate AssociatedConcepts may exist in the graph to prevent cycles. This -is consistent with LexEVS 5.x. - -28460 - Load source qualifiers for generic properties in NCI-META RRF loader -� This was implemented in the 5.1.x meta loader, and will be included in the -6.0 meta loader (which is in progress -- not included in prototype 3) - -23643 - Java 1.6 -� LexEVS 6.0 is required to be compiled and run in a Java 6.0 environment. - -27026 - Modify Meta Browser Extension to support browsing and searching of -other.. -� Meta Browser Extension now pages Associated Concepts (much like the NCI Term -Browser Extension) and includes a JSON processor for outputting path-to-root -and neighborhood Entities. Implemented initially for LexEVS 5.1.x - -25681 - Problem loading MeSH and Spanish version of SNOMED -� All RRF loaders are adjusted to load in UTF8 format - allowing for -Spanish/French/etc characters. - -28167 - ClaML Loader update for LexEVS 6.0 -� Converted the model framework from emf to castor. - -26975 - PropertyLinks won't load without namespace being supplied - Fixed by adding a validation function, which can fix the null -entity entitycodenamespace field issue - -26976 - Loader should not shut down on a duplicate property - Fixed by adding a validation function which can handle the duplicated -property issue by removing one of them - -26977 - Loader should not shut down on missing propertylink reference - Fixed by adding a validation function which removed the propertylink -if the property does not exist - -26072 -Incorrect Hibernate mappings of Oracle CLOB database type in caCORE SDK -functions - Fixed by changing the clob type to text in the hibernate mapping -files. - -27021 � Rename Value Domain - Renamed Value Domain to Value Set Definition and Value Set Resolution. - -24037 � Include immediate parent/children when Value Set Definition has -transitiveClosure as 'false' and referenceAssociation is present. - -22296 - OWL loader does not load concepts with paranthesis - This issue has been resolved in LexEVS 6.0 Prototype 3 and later releases. - Tested and verified. - - JUnit Test case is created and successfully executed with implementation - class "org.LexGrid.LexBIG.Impl.bugs.GForge22296" in project lbTest. - - -LexGrid model changes -Package ValueSets: - Renamed element ValueDomainDefinition to ValueSetDefinition and container - ValueDomains to ValueSets. GForge # 27021. - Added attribute 'conceptDomain' of type 'conceptDomain' to class - 'valueSetDefinition' to support CTS 2 SFM. - Added class 'propertyReference' and 'propertyMatchValue' to support CTS 2 - SFM. - propetyReference contains : 'codingScheme'(Required), 'propertyName', - 'propertyMatchValue' - propertyMatchValue extends from 'text' and contains attribute 'matchAlgorithm' - Made 'definitionEntry' versionable to support CTS 2 SFM. - Made class 'valueSetDefinition' and 'pickListDefinition' as entry point. - his change allows to load and export Value Set Definition and Pick List Definition individually. - -Package Naming: - Added 'supportedConceptDomain' to support CTS 2 SFM. - Added attributes 'codingScheme', 'entityCodeNamespace' and 'entityCode' to - 'SupportedAssociation'. This was added to make it earier to get an - AssociationEntity instance for a given associationPredicate. - Added attribute 'propertyType' to 'SupportedProperty'. This provides an easy - way to find all supportedProperties information by propertyType which are - 'presentation','definition','comment' and 'property'. NCI requirement Gforge # 24699. - -Package CommonTypes: - Added 'conceptDomain' in localIds. Since ConceptDomain has been added to - the model, we will need to maintain all the ConceptDomain used in the system - in our SupportedAttributes mappings. - Changed 'owner' in 'versionable' from 'source' to 'tsCaseIgnoreIA5String'. - This was changed since other attributes of Source were never used. - -Package Concept: - Removed elements 'Concept' and 'Instance'. These first class elements are - not required anymore as an 'Entity' can represent either 'concept' or 'instance' or any other type by specifying it in its EntityType. - -Package Relations: - Made class 'relation' versionable to Support CTS 2 SFM. - Added 'isMapping', 'sourceCodingScheme', 'sourceCodingSchemeVersion', - 'targetCodingScheme', 'targetCodingSchemeVersion' to class 'relation' to - support loading of MRMAP RRF file. - Added 'properties' container to 'relation' container to supported loading - of MRMAP RRF file. - Removed 'isNative' and 'source' from 'relation' as they were never used. - Added new class 'associationPredicate' with required attribute 'associationName' - to supported loading of MRMAP RRF file. - Renamed class 'association' to 'associationEntity'. Removed all Booleans except - 'isTransitive', and 'isNavigable. And made 'associationEntity' subclass - of 'Entity'. This change was also made to supported loading of MRMAP RRF file. - -Package Versions: - Changed 'changeAgent' in class 'revision' from 'source' to 'tsCaseIgnoreIA5String' - as none of the 'Source' attributes were used. - - Added unique key constraint to relaseURI column of systemRelease table. - - Added missing entryStateGuid to propertyLinks table. - +Release notes are available here: +https://wiki.nci.nih.gov/display/LexEVS/LexEVS+6.2+Release+Notes \ No newline at end of file diff --git a/lbPackager/resources/lbPackager build.xml [build-lexbig].launch b/lbPackager/resources/lbPackager build.xml [build-lexbig].launch index 797f93124e..b409e4f017 100644 --- a/lbPackager/resources/lbPackager build.xml [build-lexbig].launch +++ b/lbPackager/resources/lbPackager build.xml [build-lexbig].launch @@ -1,6 +1,6 @@ - + - + @@ -8,7 +8,10 @@ + + + diff --git a/lbTest/ivy.xml b/lbTest/ivy.xml index 2f295fa622..d81252a643 100755 --- a/lbTest/ivy.xml +++ b/lbTest/ivy.xml @@ -14,7 +14,6 @@ - diff --git a/lbTest/logs/protege_0.log b/lbTest/logs/protege_0.log new file mode 100644 index 0000000000..0379122f37 --- /dev/null +++ b/lbTest/logs/protege_0.log @@ -0,0 +1,4454 @@ +2014.05.05 16:21:22.833 CDT INFO: *** SYSTEM START *** +2014.05.05 16:21:24.466 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:21:24.622 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:21:26.895 CDT INFO: Completed triple loading after 2006 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:21:27.339 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.05 16:21:27.995 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.05 16:21:28.013 CDT INFO: Completed triple loading after 17 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:21:28.015 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:21:28.016 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:21:28.016 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:21:28.016 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:21:28.016 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:21:28.016 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:21:28.017 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:21:28.019 CDT INFO: 2 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:21:28.020 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:21:28.050 CDT INFO: 26 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:21:28.060 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:21:28.075 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:21:28.075 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:21:28.075 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:21:28.075 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:21:28.075 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:21:28.076 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:21:28.120 CDT INFO: 44 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:21:28.121 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:21:28.121 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:21:28.122 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:23:50.575 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:23:50.691 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:23:51.248 CDT INFO: Completed triple loading after 556 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:23:51.249 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:23:51.249 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:23:51.249 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:23:51.249 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:23:51.249 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:23:51.249 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:23:51.250 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:23:51.348 CDT INFO: 98 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:23:51.349 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:23:51.349 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:23:51.349 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:23:51.543 CDT INFO: 193 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:23:51.543 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:23:51.544 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:23:51.544 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:23:51.544 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:23:51.544 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:23:51.546 CDT INFO: 1 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:23:51.546 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:23:51.546 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:23:51.546 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:24:34.237 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:24:34.314 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:24:34.332 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:24:34.332 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:24:34.332 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:24:34.332 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:24:34.332 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:24:34.332 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:24:34.333 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:24:34.333 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:24:34.334 CDT INFO: 1 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:24:34.336 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:24:34.336 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:24:34.336 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:24:34.337 CDT INFO: 1 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:24:34.337 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:24:34.337 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:24:34.337 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:24:34.337 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:24:34.337 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:24:34.340 CDT INFO: 3 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:24:34.340 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:24:34.341 CDT INFO: 1 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:24:34.341 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:27:51.357 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:27:51.455 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:27:51.576 CDT INFO: Completed triple loading after 120 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:27:51.576 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:27:51.576 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:27:51.576 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:27:51.577 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:27:51.577 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:27:51.577 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:27:51.577 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:27:51.581 CDT INFO: 4 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:27:51.584 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:27:51.584 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:27:51.585 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:27:51.586 CDT INFO: 1 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:27:51.586 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:27:51.586 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:27:51.586 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:27:51.586 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:27:51.587 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:27:51.598 CDT INFO: 11 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:27:51.598 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:27:51.599 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:27:51.600 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:28:26.810 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:28:26.907 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:28:26.918 CDT INFO: Completed triple loading after 10 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:28:26.919 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:28:26.919 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:28:26.919 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:28:26.919 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:28:26.919 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:28:26.919 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:28:26.919 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:28:26.920 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:28:26.920 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:28:26.920 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:28:26.920 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:28:26.921 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:28:26.921 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:28:26.921 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:28:26.921 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:28:26.921 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:28:26.921 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:28:26.922 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:28:26.923 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:28:26.923 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:28:26.923 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:29:01.841 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:29:01.902 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:29:02.171 CDT INFO: Completed triple loading after 269 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:29:02.171 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:29:02.171 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:29:02.171 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:29:02.171 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:29:02.172 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:29:02.172 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:29:02.172 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:29:02.173 CDT INFO: 1 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:29:02.173 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:29:02.173 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:29:02.174 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:29:02.174 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:29:02.174 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:29:02.174 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:29:02.174 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:29:02.175 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:29:02.175 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:29:02.175 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:29:02.175 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:29:02.175 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:29:02.176 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:29:33.529 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:29:33.630 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:29:33.653 CDT INFO: Completed triple loading after 23 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:29:33.653 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:29:33.653 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:29:33.653 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:29:33.654 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:29:33.654 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:29:33.654 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:29:33.654 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:29:33.654 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:29:33.655 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:29:33.655 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:29:33.655 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:29:33.655 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:29:33.655 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:29:33.655 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:29:33.655 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:29:33.655 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:29:33.655 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:29:33.673 CDT INFO: 17 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:29:33.673 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:29:33.673 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:29:33.673 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.05 16:43:36.009 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.05 16:43:36.031 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.05 16:43:36.168 CDT INFO: Completed triple loading after 136 ms -- ProtegeOWLParser.loadTriples() +2014.05.05 16:43:36.168 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:43:36.169 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.05 16:43:36.169 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:43:36.169 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.05 16:43:36.169 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:43:36.169 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.05 16:43:36.169 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:43:36.170 CDT INFO: 1 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.05 16:43:36.170 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:43:36.171 CDT INFO: 1 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.05 16:43:36.171 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:43:36.172 CDT INFO: 1 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.05 16:43:36.172 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:43:36.172 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.05 16:43:36.172 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:43:36.172 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.05 16:43:36.172 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:43:36.173 CDT INFO: 1 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.05 16:43:36.173 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:43:36.173 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.05 16:43:36.173 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:45:08.332 CDT INFO: *** SYSTEM START *** +2014.05.06 08:45:09.939 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:45:10.049 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:45:11.484 CDT INFO: Completed triple loading after 1217 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:45:11.500 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:45:11.500 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:45:11.500 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:45:11.500 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:45:11.500 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:45:11.500 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:45:11.500 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:45:11.500 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:45:11.563 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:45:11.579 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:45:11.579 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:45:11.594 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:45:11.594 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:45:11.594 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:45:11.594 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:45:11.594 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:45:11.594 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:45:11.610 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:45:11.610 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:45:11.610 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:45:11.610 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:45:48.349 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:45:48.397 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:45:48.459 CDT INFO: Completed triple loading after 62 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:45:48.459 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:45:48.459 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:45:48.459 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:45:48.459 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:45:48.459 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:45:48.459 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:45:48.459 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:45:48.459 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:45:48.459 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:45:48.459 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:45:48.459 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:45:48.459 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:45:48.475 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:45:48.475 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:45:48.475 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:45:48.475 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:45:48.475 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:45:48.475 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:45:48.475 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:45:48.475 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:45:48.475 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:46:20.737 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:46:20.987 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:46:21.206 CDT INFO: Completed triple loading after 219 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:46:21.206 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:46:21.206 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:46:21.206 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:46:21.206 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:46:21.206 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:46:21.206 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:46:21.206 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:46:21.221 CDT INFO: 15 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:46:21.221 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:46:21.221 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:46:21.221 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:46:21.221 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:46:21.221 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:46:21.221 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:46:21.221 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:46:21.221 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:46:21.221 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:46:21.221 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:46:21.221 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:46:21.221 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:46:21.221 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:46:51.813 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:46:51.861 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:46:51.892 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:46:51.892 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:46:51.892 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:46:51.892 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:56:10.568 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:56:10.663 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:56:11.209 CDT INFO: Completed triple loading after 546 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:56:11.209 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:56:11.209 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:56:11.209 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:56:11.209 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:56:11.209 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:56:11.209 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:56:11.209 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:56:11.271 CDT INFO: 62 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:56:11.271 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:56:11.271 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:56:11.271 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:56:11.443 CDT INFO: 172 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:56:11.443 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:56:11.443 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:56:11.443 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:56:11.443 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:56:11.443 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:56:11.443 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:56:11.443 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:56:11.458 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:56:11.458 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:56:48.415 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:56:48.494 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:56:48.509 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:56:48.509 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:56:48.509 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:56:48.525 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:56:48.525 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:56:48.525 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:56:48.525 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 08:57:59.913 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 08:58:00.008 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 08:58:00.211 CDT INFO: Completed triple loading after 203 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:58:00.725 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.06 08:58:00.757 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.06 08:58:00.772 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 08:58:00.772 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:58:00.772 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 08:58:00.772 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:58:00.772 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 08:58:00.772 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:58:00.772 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 08:58:00.772 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:58:00.772 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 08:58:00.788 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:58:00.788 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 08:58:00.788 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:58:00.788 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 08:58:00.788 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:58:00.788 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 08:58:00.788 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:58:00.788 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 08:58:00.788 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:58:00.788 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 08:58:00.788 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:58:00.788 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 08:58:00.788 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 09:01:49.874 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 09:01:49.875 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 09:01:49.999 CDT INFO: Completed triple loading after 124 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 09:01:49.999 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 09:01:49.999 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 09:01:49.999 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 09:01:49.999 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 09:01:49.999 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 09:01:49.999 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 09:01:49.999 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 09:01:50.015 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 09:01:50.015 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 09:01:50.015 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 09:01:50.015 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 09:01:50.015 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 09:01:50.015 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 09:01:50.015 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 09:01:50.015 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 09:01:50.015 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 09:01:50.015 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 09:01:50.015 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 09:01:50.015 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 09:01:50.015 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 09:01:50.015 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:12:32.313 CDT INFO: *** SYSTEM START *** +2014.05.06 10:12:33.873 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:12:34.124 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:12:35.622 CDT INFO: Completed triple loading after 1233 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:12:36.093 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.06 10:12:36.124 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.06 10:12:36.155 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:12:36.155 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:12:36.155 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:12:36.155 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:12:36.155 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:12:36.155 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:12:36.155 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:12:36.155 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:12:36.171 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:12:36.171 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:12:36.186 CDT INFO: 15 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:12:36.202 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:12:36.217 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:12:36.217 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:12:36.217 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:12:36.217 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:12:36.217 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:12:36.217 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:12:36.249 CDT INFO: 32 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:12:36.249 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:12:36.249 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:12:36.249 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:18:21.194 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:18:21.258 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:18:21.367 CDT INFO: Completed triple loading after 94 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:18:21.367 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:18:21.367 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:18:21.367 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:18:21.367 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:18:21.367 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:18:21.367 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:18:21.367 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:18:21.383 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:18:21.383 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:18:21.383 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:18:21.383 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:18:21.383 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:18:21.383 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:18:21.383 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:18:21.383 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:18:21.383 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:18:21.383 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:18:21.398 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:18:21.398 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:18:21.398 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:18:21.398 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:18:56.702 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:18:56.766 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:18:56.781 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:18:56.781 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:18:56.781 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:18:56.781 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:19:28.450 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:19:28.545 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:19:28.686 CDT INFO: Completed triple loading after 141 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:19:28.686 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:19:28.686 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:19:28.686 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:19:57.670 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:19:57.703 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:19:57.734 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:19:57.734 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:19:57.734 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:19:57.734 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:27:07.115 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:27:07.163 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:27:07.475 CDT INFO: Completed triple loading after 312 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:27:07.475 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:27:07.475 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:27:07.475 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:27:07.475 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:27:07.475 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:27:07.475 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:27:07.475 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:27:07.522 CDT INFO: 47 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:27:07.522 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:27:07.522 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:27:07.522 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:27:07.724 CDT INFO: 202 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:27:07.724 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:27:07.724 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:27:07.724 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:27:07.724 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:27:07.724 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:27:07.724 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:27:07.724 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:27:07.724 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:27:07.724 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:27:42.045 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:27:42.077 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:27:42.092 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:27:42.092 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:27:42.092 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:27:42.092 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:27:42.092 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:27:42.092 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:27:42.092 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:27:42.092 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:27:42.092 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:27:42.108 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:27:42.108 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:27:42.108 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:27:42.108 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:27:42.108 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:27:42.108 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:27:42.108 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:27:42.108 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:27:42.108 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:27:42.108 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:27:42.108 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:27:42.108 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:27:42.108 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 10:32:41.359 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 10:32:41.360 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 10:32:41.485 CDT INFO: Completed triple loading after 125 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 10:32:41.485 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:32:41.485 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 10:32:41.501 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:22:35.397 CDT INFO: *** SYSTEM START *** +2014.05.06 11:22:37.066 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:22:37.145 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:22:38.534 CDT INFO: Completed triple loading after 1186 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:22:38.847 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.06 11:22:38.894 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.06 11:22:38.925 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:22:38.925 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:22:38.925 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:22:38.925 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:22:38.925 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:22:38.925 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:22:38.925 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:22:38.925 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:22:38.940 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:22:38.940 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:22:39.003 CDT INFO: 63 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:22:39.003 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:22:39.018 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:22:39.018 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:22:39.018 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:22:39.018 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:22:39.018 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:22:39.018 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:22:39.065 CDT INFO: 47 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:22:39.065 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:22:39.065 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:22:39.065 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:24:48.388 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:24:48.592 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:24:48.935 CDT INFO: Completed triple loading after 343 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:24:48.935 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:24:48.935 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:24:48.935 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:24:48.935 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:24:48.935 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:24:48.935 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:24:48.935 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:24:48.982 CDT INFO: 47 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:24:48.982 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:24:48.982 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:24:48.982 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:24:49.169 CDT INFO: 187 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:24:49.184 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:24:49.184 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:24:49.184 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:24:49.184 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:24:49.184 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:24:49.184 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:24:49.184 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:24:49.184 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:24:49.184 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:25:25.782 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:25:25.861 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:25:25.893 CDT INFO: Completed triple loading after 32 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:25:25.893 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:25:25.893 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:25:25.908 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:25:25.908 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:25:25.908 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:25:25.908 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:28:32.402 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:28:32.497 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:28:32.590 CDT INFO: Completed triple loading after 93 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:28:32.590 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:28:32.590 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:28:32.590 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:28:32.590 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:28:32.590 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:28:32.590 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:28:32.590 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:28:32.606 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:28:32.606 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:28:32.606 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:28:32.606 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:28:32.606 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:28:32.606 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:28:32.606 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:28:32.606 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:28:32.606 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:28:32.606 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:28:32.621 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:28:32.621 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:28:32.621 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:28:32.621 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:29:06.116 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:29:06.210 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:29:06.226 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:29:06.226 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:29:06.226 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:29:06.226 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:29:35.274 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:29:35.353 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:29:35.541 CDT INFO: Completed triple loading after 188 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:29:35.541 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:29:35.541 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:29:35.541 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:30:01.327 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:30:01.360 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:30:01.375 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:30:01.375 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:30:01.375 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:30:01.391 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:30:01.391 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:30:01.391 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:30:01.391 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:40:02.704 CDT INFO: *** SYSTEM START *** +2014.05.06 11:40:04.046 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:40:04.109 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:40:05.935 CDT INFO: Completed triple loading after 1544 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:40:06.330 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:40:06.330 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:40:06.330 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:40:06.330 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:40:06.330 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:40:06.330 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:40:06.330 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:40:06.626 CDT INFO: 296 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:40:06.626 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:40:06.626 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:40:06.642 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:40:06.907 CDT INFO: 265 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:40:06.907 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:40:06.923 CDT INFO: 16 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:40:06.923 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:40:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:40:06.923 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:40:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:40:06.923 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:40:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:40:06.923 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:40:53.008 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:40:53.056 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:40:53.072 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:40:53.072 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:40:53.072 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:40:53.072 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:40:53.072 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:40:53.072 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:40:53.072 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:40:53.072 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:40:53.072 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:40:53.072 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:40:53.072 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:40:53.072 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:40:53.087 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:40:53.087 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:40:53.087 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:40:53.087 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:40:53.087 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:40:53.087 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:40:53.087 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:40:53.087 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:40:53.087 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:40:53.087 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:41:25.352 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:41:25.352 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:41:25.945 CDT INFO: Completed triple loading after 593 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:41:26.414 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.06 11:41:26.445 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.06 11:41:26.461 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:41:26.461 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:41:26.461 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:41:26.461 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:41:26.461 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:41:26.461 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:41:26.461 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:41:26.461 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:41:26.461 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:41:26.461 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:41:26.554 CDT INFO: 93 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:41:26.554 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:41:26.554 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:41:26.554 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:41:26.554 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:41:26.554 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:41:26.554 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:41:26.554 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:41:26.554 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:41:26.554 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:41:26.554 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:41:26.554 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:47:00.583 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:47:00.647 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:47:00.771 CDT INFO: Completed triple loading after 124 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:47:00.771 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:47:00.771 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:47:00.787 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:47:00.787 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:47:00.787 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:47:00.787 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:47:36.451 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:47:36.499 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:47:36.514 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:47:36.514 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:47:36.514 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:47:36.530 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:47:36.530 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:47:36.530 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:48:08.512 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:48:08.575 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:48:08.716 CDT INFO: Completed triple loading after 141 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:48:08.716 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:48:08.716 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:48:08.716 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:48:38.763 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:48:38.810 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:48:38.826 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:48:38.826 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:48:38.826 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:48:38.842 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:48:38.842 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:48:38.842 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:48:38.842 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.06 11:59:45.747 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.06 11:59:45.748 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.06 11:59:45.888 CDT INFO: Completed triple loading after 140 ms -- ProtegeOWLParser.loadTriples() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.06 11:59:45.888 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:59:45.888 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.06 11:59:45.888 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:29:07.808 CDT INFO: *** SYSTEM START *** +2014.05.08 14:29:09.493 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:29:09.650 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:29:11.288 CDT INFO: Completed triple loading after 1435 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:29:11.773 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.08 14:29:11.929 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.08 14:29:11.929 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:29:11.929 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:29:11.929 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:29:11.929 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:29:11.929 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:29:11.929 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:29:11.929 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:29:11.929 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:29:11.944 CDT INFO: 15 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:29:11.944 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:29:11.960 CDT INFO: 16 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:29:11.975 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:29:11.975 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:29:11.975 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:29:11.975 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:29:11.975 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:29:11.975 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:29:11.975 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:29:11.991 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:29:11.991 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:29:11.991 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:29:11.991 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:31:19.511 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:31:19.606 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:31:19.996 CDT INFO: Completed triple loading after 390 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:31:19.996 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:31:19.996 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:31:19.996 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:31:19.996 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:31:19.996 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:31:19.996 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:31:19.996 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:31:20.058 CDT INFO: 62 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:31:20.058 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:31:20.058 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:31:20.058 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:31:20.261 CDT INFO: 203 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:31:20.261 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:31:20.261 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:31:20.261 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:31:20.261 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:31:20.261 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:31:20.261 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:31:20.261 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:31:20.261 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:31:20.261 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:31:53.801 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:31:53.802 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:31:53.833 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:31:53.833 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:31:53.833 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:31:53.833 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:31:53.833 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:31:53.833 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:31:53.833 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:31:53.833 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:31:53.849 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:31:53.849 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:31:53.849 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:31:53.849 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:31:53.849 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:31:53.849 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:31:53.849 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:31:53.849 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:31:53.849 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:31:53.849 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:31:53.849 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:31:53.849 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:31:53.849 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:31:53.849 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:35:09.092 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:35:09.140 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:35:09.249 CDT INFO: Completed triple loading after 109 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:35:09.249 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:35:09.249 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:35:09.249 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:35:09.249 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:35:09.249 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:35:09.249 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:35:09.249 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:35:09.249 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:35:09.265 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:35:09.265 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:35:09.265 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:35:09.265 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:35:09.265 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:35:09.265 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:35:09.265 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:35:09.265 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:35:09.265 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:35:09.265 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:35:09.265 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:35:09.265 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:35:09.265 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:35:44.507 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:35:44.570 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:35:44.586 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:35:44.586 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:35:44.586 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:35:44.586 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:36:20.545 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:36:20.671 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:36:20.795 CDT INFO: Completed triple loading after 124 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:36:20.795 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:36:20.795 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:36:20.795 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:36:20.795 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:36:20.795 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:36:20.811 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:36:20.811 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:36:20.811 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:36:50.576 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:36:50.608 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:36:50.639 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:36:50.639 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:36:50.639 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:36:50.639 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.08 14:47:34.072 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.08 14:47:34.073 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.08 14:47:34.214 CDT INFO: Completed triple loading after 141 ms -- ProtegeOWLParser.loadTriples() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.08 14:47:34.214 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:47:34.214 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.08 14:47:34.214 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:34:11.142 CDT INFO: *** SYSTEM START *** +2014.05.13 12:34:12.952 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:34:13.093 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:34:14.981 CDT INFO: Completed triple loading after 1607 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:34:14.996 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:34:14.996 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:34:14.996 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:34:14.996 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:34:14.996 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:34:14.996 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:34:14.996 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:34:15.153 CDT INFO: 157 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:34:15.153 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:34:15.153 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:34:15.216 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:34:15.450 CDT INFO: 234 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:34:15.450 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:34:15.450 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:34:15.450 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:34:15.450 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:34:15.450 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:34:15.450 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:34:15.450 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:34:15.450 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:34:15.450 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:35:03.890 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:35:03.953 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:35:03.984 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:35:03.984 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:35:03.984 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:35:03.984 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:38:32.195 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:38:32.242 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:38:32.352 CDT INFO: Completed triple loading after 110 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:38:32.352 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:38:32.352 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:38:32.352 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:38:32.352 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:38:32.352 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:38:32.352 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:38:32.352 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:38:32.352 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:38:32.367 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:38:32.367 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:38:32.367 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:38:32.367 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:38:32.367 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:38:32.367 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:38:32.367 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:38:32.367 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:38:32.367 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:38:32.367 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:38:32.367 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:38:32.383 CDT INFO: 16 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:38:32.383 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:39:06.844 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:39:06.876 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:39:06.908 CDT INFO: Completed triple loading after 32 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:39:06.908 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:39:06.908 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:39:06.908 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:39:06.908 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:39:06.908 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:39:06.908 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:39:06.908 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:39:06.908 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:39:06.908 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:39:06.923 CDT INFO: 15 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:39:06.923 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:39:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:39:06.923 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:39:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:39:06.923 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:39:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:39:06.923 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:39:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:39:06.923 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:39:06.923 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:39:06.923 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:39:36.377 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:39:36.456 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:39:36.612 CDT INFO: Completed triple loading after 156 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:39:36.612 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:39:36.612 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:39:36.612 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:39:36.612 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:39:36.612 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:39:36.612 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:39:36.612 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:39:36.612 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:39:36.612 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:39:36.612 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:39:36.612 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:39:36.612 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:39:36.628 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:39:36.628 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:39:36.628 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:39:36.628 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:39:36.628 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:39:36.628 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:39:36.628 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:39:36.628 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:39:36.628 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:40:05.753 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:40:05.769 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:40:05.801 CDT INFO: Completed triple loading after 32 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:40:05.801 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:40:05.801 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:40:05.801 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:48:26.144 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:48:26.223 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:48:26.410 CDT INFO: Completed triple loading after 187 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:48:27.190 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.13 12:48:27.222 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.13 12:48:27.222 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:48:27.222 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:48:27.222 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:48:27.222 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:48:27.222 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:48:27.222 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:48:27.222 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:48:27.222 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:48:27.222 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:48:27.222 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:48:27.222 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:48:27.222 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:48:27.238 CDT INFO: 16 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:48:27.238 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:48:27.238 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:48:27.238 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:48:27.238 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:48:27.238 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:48:27.253 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:48:27.253 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:48:27.253 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:48:27.253 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 12:52:52.250 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 12:52:52.266 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 12:52:52.406 CDT INFO: Completed triple loading after 140 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 12:52:52.406 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:52:52.406 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 12:52:52.406 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 13:52:06.112 CDT INFO: *** SYSTEM START *** +2014.05.13 13:52:07.298 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 13:52:07.361 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 13:52:08.547 CDT INFO: Completed triple loading after 936 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 13:52:08.656 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:52:08.656 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:52:08.656 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:52:08.656 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:52:08.656 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:52:08.656 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:52:08.656 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:52:08.656 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:52:08.672 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:52:08.672 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:52:08.672 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:52:08.704 CDT INFO: 32 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:52:08.704 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:52:08.704 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:52:08.704 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:52:08.704 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:52:08.704 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:52:08.719 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:52:08.719 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:52:08.719 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:52:08.719 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 13:52:57.891 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 13:52:57.955 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 13:52:58.017 CDT INFO: Completed triple loading after 62 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 13:52:58.017 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:52:58.017 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:52:58.017 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:52:58.017 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:52:58.017 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:52:58.017 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:52:58.017 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:52:58.017 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:52:58.017 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:52:58.064 CDT INFO: 47 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:52:58.064 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:52:58.064 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:52:58.064 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:52:58.064 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:52:58.064 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:52:58.064 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:52:58.064 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:52:58.064 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:52:58.064 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:52:58.064 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:52:58.064 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 13:53:27.627 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 13:53:27.628 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 13:53:27.846 CDT INFO: Completed triple loading after 218 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:53:27.846 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:53:27.846 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:53:27.846 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 13:54:05.349 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 13:54:05.380 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 13:54:05.412 CDT INFO: Completed triple loading after 32 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:54:05.412 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 13:54:05.412 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:54:05.428 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 13:54:05.428 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:54:05.428 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 13:54:05.428 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 14:02:22.948 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 14:02:22.949 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 14:02:23.277 CDT INFO: Completed triple loading after 328 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:02:23.277 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:02:23.277 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:02:23.277 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:02:23.277 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:02:23.277 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:02:23.277 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:02:23.277 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:02:23.323 CDT INFO: 46 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:02:23.323 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:02:23.323 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:02:23.323 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:02:23.511 CDT INFO: 188 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:02:23.511 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:02:23.511 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:02:23.511 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:02:23.511 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:02:23.511 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:02:23.511 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:02:23.511 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:02:23.511 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:02:23.511 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 14:02:59.921 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 14:02:59.922 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 14:02:59.953 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:02:59.953 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:02:59.953 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:02:59.953 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 14:04:10.810 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 14:04:10.810 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 14:04:11.014 CDT INFO: Completed triple loading after 204 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:04:11.342 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.13 14:04:11.373 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.13 14:04:11.389 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:04:11.389 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:04:11.389 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:04:11.389 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:04:11.389 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:04:11.389 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:04:11.389 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:04:11.389 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:04:11.389 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:04:11.389 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:04:11.404 CDT INFO: 15 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:04:11.404 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:04:11.404 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:04:11.404 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:04:11.404 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:04:11.404 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:04:11.404 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:04:11.404 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:04:11.404 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:04:11.420 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:04:11.420 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:04:11.420 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 14:08:26.323 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 14:08:26.324 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 14:08:26.464 CDT INFO: Completed triple loading after 140 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:08:26.464 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:08:26.464 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:08:26.464 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 14:57:12.583 CDT INFO: *** SYSTEM START *** +2014.05.13 14:57:13.769 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 14:57:13.832 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 14:57:15.330 CDT INFO: Completed triple loading after 1295 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:57:15.518 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.13 14:57:15.596 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.13 14:57:15.596 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 14:57:15.596 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:57:15.596 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 14:57:15.596 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:57:15.612 CDT INFO: 16 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 14:57:15.612 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:57:15.612 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 14:57:15.612 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:57:15.612 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 14:57:15.612 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:57:15.643 CDT INFO: 31 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 14:57:15.674 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:57:15.690 CDT INFO: 16 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 14:57:15.690 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:57:15.690 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 14:57:15.690 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:57:15.690 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 14:57:15.690 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:57:15.690 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 14:57:15.690 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:57:15.690 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 14:57:15.690 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:02:55.282 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:02:55.298 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:02:55.408 CDT INFO: Completed triple loading after 110 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:02:55.408 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:02:55.408 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:02:55.424 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:02:55.424 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:02:55.424 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:02:55.424 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:03:30.516 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:03:30.548 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:03:30.548 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:03:30.548 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:03:30.548 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:03:30.564 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:03:30.564 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:03:30.564 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:03:30.564 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:04:02.205 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:04:02.205 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:04:02.377 CDT INFO: Completed triple loading after 172 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:04:02.377 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:04:02.377 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:04:02.377 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:04:02.377 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:04:02.377 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:04:02.377 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:04:02.377 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:04:02.377 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:04:02.377 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:04:02.377 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:04:02.393 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:04:02.393 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:04:02.393 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:04:02.393 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:04:02.393 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:04:02.393 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:04:02.393 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:04:02.393 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:04:02.393 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:04:02.393 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:04:02.393 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:04:32.220 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:04:32.221 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:04:32.268 CDT INFO: Completed triple loading after 47 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:04:32.268 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:04:32.268 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:04:32.268 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:11:57.589 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:11:57.590 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:11:57.917 CDT INFO: Completed triple loading after 327 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:11:57.917 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:11:57.917 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:11:57.917 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:11:57.917 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:11:57.917 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:11:57.917 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:11:57.917 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:11:57.980 CDT INFO: 63 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:11:57.980 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:11:57.980 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:11:57.980 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:11:58.167 CDT INFO: 187 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:11:58.167 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:11:58.167 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:11:58.167 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:11:58.167 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:11:58.167 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:11:58.167 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:11:58.167 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:11:58.167 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:11:58.167 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:12:33.688 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:12:33.688 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:12:33.689 CDT INFO: Completed triple loading after 1 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:12:33.689 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:12:33.689 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:12:33.689 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:12:33.689 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:12:33.689 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:12:33.689 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:12:33.689 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:12:33.705 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:12:33.720 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:12:33.720 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:12:33.720 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:12:33.720 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:12:33.720 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:12:33.720 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:12:33.720 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:12:33.720 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:12:33.720 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:12:33.720 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:12:33.720 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:12:33.720 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:12:33.720 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:17:19.667 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:17:19.667 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:17:19.808 CDT INFO: Completed triple loading after 141 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:17:19.808 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:17:19.808 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:17:19.808 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:47:41.960 CDT INFO: *** SYSTEM START *** +2014.05.13 15:47:43.146 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:47:43.209 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:47:44.879 CDT INFO: Completed triple loading after 1467 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:47:45.463 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:47:45.463 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:47:45.463 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:47:45.463 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:47:45.463 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:47:45.463 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:47:45.463 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:47:45.744 CDT INFO: 281 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:47:45.744 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:47:45.744 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:47:45.759 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:47:46.024 CDT INFO: 265 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:47:46.040 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:47:46.040 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:47:46.040 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:47:46.040 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:47:46.040 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:47:46.040 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:47:46.040 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:47:46.040 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:47:46.040 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:48:28.567 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:48:28.617 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:48:28.664 CDT INFO: Completed triple loading after 47 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:48:28.664 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:48:28.664 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:48:28.664 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:48:28.664 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:48:28.664 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:48:28.664 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:48:28.664 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:48:28.664 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:48:28.680 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:48:28.680 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:48:28.680 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:48:28.680 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:48:28.680 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:48:28.680 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:48:28.680 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:48:28.680 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:48:28.680 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:48:28.680 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:48:28.680 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:48:28.680 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:48:28.680 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:51:54.797 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:51:54.845 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:51:54.969 CDT INFO: Completed triple loading after 124 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:51:54.969 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:51:54.969 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:51:54.969 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:51:54.969 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:51:54.969 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:51:54.969 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:51:54.969 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:51:54.969 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:51:54.985 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:51:54.985 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:51:54.985 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:51:54.985 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:51:54.985 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:51:54.985 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:51:54.985 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:51:54.985 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:51:54.985 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:51:55.001 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:51:55.001 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:51:55.001 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:51:55.001 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:52:29.353 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:52:29.463 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:52:29.510 CDT INFO: Completed triple loading after 47 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:52:29.510 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:52:29.510 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:52:29.510 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:52:29.510 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:52:29.510 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:52:29.510 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:52:29.510 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:52:29.510 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:52:29.510 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:52:29.525 CDT INFO: 15 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:52:29.525 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:52:29.525 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:52:29.525 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:52:29.525 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:52:29.525 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:52:29.525 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:52:29.525 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:52:29.525 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:52:29.525 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:52:29.525 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:52:29.525 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 15:55:41.425 CDT INFO: *** SYSTEM START *** +2014.05.13 15:55:42.595 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 15:55:42.659 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 15:55:44.141 CDT INFO: Completed triple loading after 1186 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:55:44.391 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.13 15:55:44.469 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.13 15:55:44.469 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 15:55:44.485 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:55:44.485 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 15:55:44.485 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:55:44.485 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 15:55:44.485 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:55:44.485 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 15:55:44.485 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:55:44.485 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 15:55:44.485 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:55:44.500 CDT INFO: 15 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 15:55:44.500 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:55:44.516 CDT INFO: 16 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 15:55:44.516 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:55:44.516 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 15:55:44.516 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:55:44.516 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 15:55:44.516 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:55:44.516 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 15:55:44.516 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:55:44.516 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 15:55:44.532 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:00:24.157 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:00:24.189 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:00:24.314 CDT INFO: Completed triple loading after 125 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:00:24.314 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:00:24.314 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:00:24.314 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:00:24.314 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:00:24.314 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:00:24.314 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:00:24.314 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:00:24.330 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:00:24.330 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:00:24.330 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:00:24.330 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:00:24.330 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:00:24.330 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:00:24.330 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:00:24.330 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:00:24.330 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:00:24.330 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:00:24.345 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:00:24.345 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:00:24.345 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:00:24.345 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:00:58.151 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:00:58.152 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:00:58.152 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:00:58.152 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:00:58.152 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:00:58.168 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:00:58.168 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:01:29.275 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:01:29.323 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:01:29.479 CDT INFO: Completed triple loading after 156 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:01:29.479 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:01:29.479 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:01:29.479 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:02:03.456 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:02:03.504 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:02:03.535 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:02:03.535 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:02:03.535 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:02:03.535 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:10:44.408 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:10:44.409 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:10:44.721 CDT INFO: Completed triple loading after 312 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:10:44.721 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:10:44.721 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:10:44.721 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:10:44.721 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:10:44.721 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:10:44.721 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:10:44.721 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:10:44.784 CDT INFO: 63 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:10:44.784 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:10:44.784 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:10:44.784 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:10:44.987 CDT INFO: 203 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:10:44.987 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:10:44.987 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:10:44.987 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:10:44.987 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:10:44.987 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:10:44.987 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:10:44.987 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:10:44.987 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:10:44.987 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:11:21.881 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:11:21.882 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:11:21.913 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:11:21.913 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:11:21.913 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:11:21.913 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.13 16:15:35.432 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.13 16:15:35.433 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.13 16:15:35.573 CDT INFO: Completed triple loading after 140 ms -- ProtegeOWLParser.loadTriples() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.13 16:15:35.573 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:15:35.573 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.13 16:15:35.573 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:36:35.602 CDT INFO: *** SYSTEM START *** +2014.05.14 10:36:37.068 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:36:37.256 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:36:39.160 CDT INFO: Completed triple loading after 1576 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:36:39.582 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.14 10:36:39.644 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.14 10:36:39.644 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:36:39.660 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:36:39.660 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:36:39.660 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:36:39.660 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:36:39.660 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:36:39.660 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:36:39.660 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:36:39.660 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:36:39.660 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:36:39.691 CDT INFO: 31 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:36:39.707 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:36:39.707 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:36:39.707 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:36:39.707 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:36:39.707 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:36:39.707 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:36:39.707 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:36:39.722 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:36:39.722 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:36:39.722 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:36:39.722 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:38:50.301 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:38:50.552 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:38:50.989 CDT INFO: Completed triple loading after 437 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:38:50.989 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:38:50.989 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:38:50.989 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:38:50.989 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:38:50.989 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:38:50.989 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:38:50.989 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:38:51.051 CDT INFO: 62 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:38:51.051 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:38:51.051 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:38:51.051 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:38:51.285 CDT INFO: 234 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:38:51.285 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:38:51.285 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:38:51.285 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:38:51.285 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:38:51.285 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:38:51.285 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:38:51.285 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:38:51.285 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:38:51.285 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:39:27.462 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:39:27.526 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:39:27.541 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:39:27.541 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:39:27.541 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:39:27.541 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:42:40.245 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:42:40.308 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:42:40.417 CDT INFO: Completed triple loading after 109 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:42:40.417 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:42:40.417 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:42:40.433 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:42:40.433 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:42:40.433 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:42:40.433 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:43:18.764 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:43:18.796 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:43:18.812 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:43:18.812 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:43:18.812 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:43:18.812 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:43:49.047 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:43:49.094 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:43:49.266 CDT INFO: Completed triple loading after 172 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:43:49.266 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:43:49.266 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:43:49.266 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:43:49.266 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:43:49.266 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:43:49.266 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:43:49.266 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:43:49.266 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:43:49.266 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:43:49.282 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:43:49.282 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:43:49.282 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:43:49.282 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:43:49.282 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:43:49.282 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:43:49.282 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:43:49.282 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:43:49.282 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:43:49.282 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:43:49.282 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:43:49.282 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:44:17.877 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:44:17.988 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:44:18.003 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:44:18.003 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:44:18.003 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:44:18.003 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 10:55:00.041 CDT INFO: *** SYSTEM START *** +2014.05.14 10:55:01.445 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 10:55:01.508 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 10:55:03.130 CDT INFO: Completed triple loading after 1326 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:55:07.094 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.14 10:55:14.957 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.14 10:55:14.989 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 10:55:14.989 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:55:14.989 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 10:55:14.989 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:55:14.989 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 10:55:14.989 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:55:14.989 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 10:55:14.989 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:55:14.989 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 10:55:14.989 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:55:15.021 CDT INFO: 32 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 10:55:15.021 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:55:15.036 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 10:55:15.036 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:55:15.036 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 10:55:15.036 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:55:15.052 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 10:55:15.052 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:55:15.052 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 10:55:15.068 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:55:15.068 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 10:55:15.068 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:00:04.313 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:00:04.328 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:00:04.470 CDT INFO: Completed triple loading after 141 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:00:04.470 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:00:04.470 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:00:04.470 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:00:04.470 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:00:04.470 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:00:04.470 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:00:04.470 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:00:04.470 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:00:04.470 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:00:04.485 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:00:04.485 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:00:04.485 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:00:04.485 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:00:04.485 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:00:04.485 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:00:04.485 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:00:04.485 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:00:04.501 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:00:04.501 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:00:04.501 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:00:04.501 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:00:43.751 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:00:43.767 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:00:43.768 CDT INFO: Completed triple loading after 1 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:00:43.768 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:00:43.768 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:00:43.768 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:01:13.893 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:01:13.894 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:01:14.050 CDT INFO: Completed triple loading after 156 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:01:14.050 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:01:14.050 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:01:14.050 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:01:44.251 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:01:44.252 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:01:44.283 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:01:44.283 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:01:44.283 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:01:44.283 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:09:59.542 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:09:59.574 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:09:59.886 CDT INFO: Completed triple loading after 312 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:09:59.886 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:09:59.886 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:09:59.886 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:09:59.886 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:09:59.886 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:09:59.886 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:09:59.886 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:09:59.933 CDT INFO: 47 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:09:59.933 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:09:59.933 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:09:59.933 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:10:00.167 CDT INFO: 234 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:10:00.167 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:10:00.167 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:10:00.167 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:10:00.167 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:10:00.167 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:10:00.167 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:10:00.167 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:10:00.167 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:10:00.182 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:10:36.515 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:10:36.516 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:10:36.547 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:10:36.547 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:10:36.547 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:10:36.547 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 11:14:20.181 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 11:14:20.181 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 11:14:20.307 CDT INFO: Completed triple loading after 126 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 11:14:20.307 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:14:20.307 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 11:14:20.307 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:14:20.307 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 11:14:20.307 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:14:20.307 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 11:14:20.307 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:14:20.307 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 11:14:20.307 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:14:20.307 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 11:14:20.307 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:14:20.322 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 11:14:20.322 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:14:20.322 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 11:14:20.322 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:14:20.322 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 11:14:20.322 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:14:20.322 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 11:14:20.322 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:14:20.322 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 11:14:20.322 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:18:22.609 CDT INFO: *** SYSTEM START *** +2014.05.14 12:18:23.888 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:18:24.014 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:18:25.652 CDT INFO: Completed triple loading after 1310 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:18:25.762 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.14 12:18:25.794 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.14 12:18:25.840 CDT INFO: Completed triple loading after 46 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:18:25.840 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:18:25.840 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:18:25.840 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:18:25.840 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:18:25.840 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:18:25.840 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:18:25.840 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:18:25.840 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:18:25.840 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:18:25.903 CDT INFO: 63 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:18:25.903 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:18:25.918 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:18:25.918 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:18:25.918 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:18:25.918 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:18:25.918 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:18:25.918 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:18:25.965 CDT INFO: 47 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:18:25.965 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:18:25.965 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:18:25.965 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:20:28.149 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:20:28.166 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:20:28.540 CDT INFO: Completed triple loading after 374 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:20:28.540 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:20:28.540 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:20:28.540 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:20:28.540 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:20:28.540 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:20:28.540 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:20:28.540 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:20:28.587 CDT INFO: 47 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:20:28.587 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:20:28.587 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:20:28.587 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:20:28.837 CDT INFO: 250 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:20:28.837 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:20:28.837 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:20:28.837 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:20:28.837 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:20:28.837 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:20:28.837 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:20:28.837 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:20:28.837 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:20:28.837 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:21:03.016 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:21:03.095 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:21:03.111 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:21:03.111 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:21:03.111 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:21:03.111 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:21:03.111 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:21:03.111 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:21:03.111 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:21:03.111 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:21:03.127 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:21:03.127 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:21:03.127 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:21:03.127 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:21:03.127 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:21:03.127 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:21:03.127 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:21:03.127 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:21:03.127 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:21:03.127 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:21:03.127 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:21:03.127 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:21:03.127 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:21:03.127 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:25:11.654 CDT INFO: *** SYSTEM START *** +2014.05.14 12:25:12.996 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:25:13.059 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:25:14.682 CDT INFO: Completed triple loading after 1389 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:25:14.682 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:25:14.682 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:25:14.682 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:25:14.682 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:25:14.682 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:25:14.682 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:25:14.682 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:25:14.919 CDT INFO: 237 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:25:14.919 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:25:14.919 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:25:14.950 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:25:15.215 CDT INFO: 265 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:25:15.215 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:25:15.231 CDT INFO: 16 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:25:15.231 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:25:15.231 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:25:15.231 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:25:15.231 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:25:15.231 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:25:15.231 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:25:15.231 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:26:00.271 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:26:00.271 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:26:00.304 CDT INFO: Completed triple loading after 33 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:26:00.304 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:26:00.304 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:26:00.304 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:30:04.553 CDT INFO: *** SYSTEM START *** +2014.05.14 12:30:05.801 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:30:05.864 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:30:07.627 CDT INFO: Completed triple loading after 1560 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:30:07.737 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.14 12:30:07.893 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.14 12:30:07.940 CDT INFO: Completed triple loading after 47 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:30:07.940 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:30:07.940 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:30:07.940 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:30:07.940 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:30:07.940 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:30:07.940 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:30:07.940 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:30:07.940 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:30:07.940 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:30:08.002 CDT INFO: 62 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:30:08.018 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:30:08.018 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:30:08.018 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:30:08.018 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:30:08.018 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:30:08.018 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:30:08.018 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:30:08.034 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:30:08.034 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:30:08.034 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:30:08.034 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:34:43.557 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:34:43.611 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:34:43.720 CDT INFO: Completed triple loading after 109 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:34:43.720 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:34:43.720 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:34:43.720 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:34:43.720 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:34:43.720 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:34:43.720 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:34:43.720 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:34:43.720 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:34:43.736 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:34:43.736 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:34:43.736 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:34:43.736 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:34:43.736 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:34:43.736 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:34:43.736 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:34:43.736 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:34:43.736 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:34:43.751 CDT INFO: 15 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:34:43.751 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:34:43.751 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:34:43.751 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:35:18.712 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:35:18.760 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:35:18.775 CDT INFO: Completed triple loading after 15 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:35:18.775 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:35:18.775 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:35:18.775 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:35:48.073 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:35:48.137 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:35:48.324 CDT INFO: Completed triple loading after 187 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:35:48.324 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:35:48.324 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:35:48.324 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:36:15.093 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:36:15.172 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:36:15.188 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:36:15.188 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:36:15.188 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:36:15.204 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:36:15.204 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:36:15.204 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:36:15.204 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:44:43.893 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:44:43.894 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:44:44.206 CDT INFO: Completed triple loading after 312 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:44:44.206 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:44:44.222 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:44:44.222 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:44:44.222 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:44:44.222 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:44:44.222 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:44:44.222 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:44:44.269 CDT INFO: 47 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:44:44.269 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:44:44.269 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:44:44.269 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:44:44.472 CDT INFO: 203 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:44:44.472 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:44:44.472 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:44:44.472 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:44:44.472 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:44:44.472 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:44:44.472 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:44:44.472 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:44:44.472 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:44:44.472 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:45:22.225 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:45:22.226 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:45:22.257 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:45:22.257 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:45:22.257 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:45:22.257 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 12:49:42.823 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 12:49:42.824 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 12:49:42.980 CDT INFO: Completed triple loading after 156 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 12:49:42.980 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:49:42.980 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 12:49:42.980 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:49:42.980 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 12:49:42.980 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:49:42.980 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 12:49:42.980 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:49:42.980 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 12:49:42.996 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:49:42.996 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 12:49:42.996 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:49:42.996 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 12:49:42.996 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:49:42.996 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 12:49:42.996 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:49:42.996 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 12:49:42.996 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:49:42.996 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 12:49:42.996 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:49:42.996 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 12:49:42.996 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 14:55:39.771 CDT INFO: *** SYSTEM START *** +2014.05.14 14:55:41.175 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 14:55:41.270 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 14:55:43.454 CDT INFO: Completed triple loading after 1825 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 14:55:43.502 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 14:55:43.502 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 14:55:43.502 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 14:55:43.502 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 14:55:43.502 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 14:55:43.502 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 14:55:43.502 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 14:55:43.502 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 14:55:43.502 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 14:55:43.568 CDT INFO: 66 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 14:55:43.568 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 14:55:43.584 CDT INFO: 16 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 14:55:43.584 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 14:55:43.584 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 14:55:43.584 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 14:55:43.584 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 14:55:43.584 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 14:55:43.584 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 14:55:43.584 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 14:55:43.584 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 14:55:43.584 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:10:55.504 CDT INFO: *** SYSTEM START *** +2014.05.14 15:10:56.736 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:10:56.862 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:10:58.453 CDT INFO: Completed triple loading after 1310 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:10:58.828 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.14 15:10:58.906 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.14 15:10:58.922 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:10:58.922 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:10:58.922 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:10:58.922 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:10:58.922 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:10:58.922 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:10:58.922 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:10:58.922 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:10:58.922 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:10:58.922 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:10:58.938 CDT INFO: 16 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:10:58.953 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:10:58.969 CDT INFO: 16 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:10:58.969 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:10:58.969 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:10:58.969 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:10:58.969 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:10:58.969 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:10:58.969 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:10:58.969 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:10:58.969 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:10:58.969 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:15:42.727 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:15:42.806 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:15:42.931 CDT INFO: Completed triple loading after 125 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:15:42.931 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:15:42.931 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:15:42.947 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:15:42.947 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:15:42.947 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:15:42.947 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:16:22.759 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:16:22.791 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:16:22.791 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:16:22.791 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:16:22.791 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:16:22.791 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:16:22.791 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:16:22.791 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:16:22.791 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:16:22.791 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:16:22.791 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:16:22.791 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:16:22.791 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:16:22.807 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:16:22.807 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:16:22.807 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:16:22.807 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:16:22.807 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:16:22.807 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:16:22.807 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:16:22.807 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:16:22.807 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:16:22.807 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:16:22.807 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:16:54.304 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:16:54.305 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:16:54.461 CDT INFO: Completed triple loading after 156 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:16:54.461 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:16:54.477 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:16:54.477 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:16:54.477 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:17:23.805 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:17:23.884 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:17:23.915 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:17:23.915 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:17:23.915 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:17:23.915 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:17:23.915 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:17:23.915 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:17:23.915 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:17:23.915 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:17:23.915 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:17:23.930 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:17:23.930 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:17:23.930 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:17:23.930 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:17:23.930 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:17:23.930 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:17:23.930 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:17:23.930 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:17:23.930 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:17:23.930 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:17:23.930 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:17:23.930 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:17:23.930 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:25:38.611 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:25:38.612 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:25:39.018 CDT INFO: Completed triple loading after 406 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:25:39.018 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:25:39.018 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:25:39.018 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:25:39.018 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:25:39.018 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:25:39.018 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:25:39.018 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:25:39.065 CDT INFO: 47 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:25:39.065 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:25:39.065 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:25:39.065 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:25:39.283 CDT INFO: 218 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:25:39.283 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:25:39.283 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:25:39.283 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:25:39.283 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:25:39.283 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:25:39.283 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:25:39.283 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:25:39.283 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:25:39.283 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:26:19.999 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:26:20.047 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:26:20.063 CDT INFO: Completed triple loading after 16 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:26:20.063 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:26:20.063 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:26:20.063 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.14 15:30:35.502 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.14 15:30:35.503 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.14 15:30:35.675 CDT INFO: Completed triple loading after 172 ms -- ProtegeOWLParser.loadTriples() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.14 15:30:35.675 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:30:35.675 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.14 15:30:35.675 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:14:53.888 CDT INFO: *** SYSTEM START *** +2014.05.15 08:14:55.292 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:14:55.527 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:14:57.399 CDT INFO: Completed triple loading after 1560 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:14:57.414 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:14:57.414 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:14:57.414 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:14:57.414 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:14:57.414 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:14:57.414 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:14:57.414 CDT INFO: Postprocess: Instances with multiple types (74 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:14:57.414 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:14:57.493 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:14:57.493 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:14:57.509 CDT INFO: Postprocess: Process orphan classes (67 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:14:57.509 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:14:57.509 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:14:57.509 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:14:57.509 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:14:57.509 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:14:57.509 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:14:57.540 CDT INFO: 31 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:14:57.540 CDT INFO: Postprocess: Possibly typed entities (7 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:14:57.540 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:14:57.540 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:15:37.259 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:15:37.369 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/camera.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:15:37.462 CDT INFO: Completed triple loading after 78 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Instances with multiple types (5 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Process orphan classes (12 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:15:37.462 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:15:37.462 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:15:37.478 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:15:37.478 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:15:37.478 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:15:37.478 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:16:08.492 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:16:08.571 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:16:08.758 CDT INFO: Completed triple loading after 187 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:16:08.758 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:16:08.758 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:16:08.758 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:16:37.649 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:16:37.681 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/sample.cp.2.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:16:37.728 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:16:37.728 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:16:37.728 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:16:37.728 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Instances with multiple types (0 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:16:37.728 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:16:37.728 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Process orphan classes (2 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:16:37.728 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:16:37.728 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:16:37.744 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:16:37.744 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:16:37.744 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:16:37.744 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:16:37.744 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:16:37.744 CDT INFO: Postprocess: Possibly typed entities (1 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:16:37.744 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:16:37.744 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:24:20.992 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:24:21.227 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/OvarianMass_SNOMED_ValueSets.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:24:21.664 CDT INFO: Completed triple loading after 437 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:24:21.664 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:24:21.664 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:24:21.664 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:24:21.664 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:24:21.664 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:24:21.664 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:24:21.664 CDT INFO: Postprocess: Instances with multiple types (158 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:24:21.742 CDT INFO: 78 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:24:21.742 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:24:21.742 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:24:21.742 CDT INFO: Postprocess: Process orphan classes (121 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:24:21.960 CDT INFO: 218 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:24:21.960 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:24:21.960 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:24:21.960 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:24:21.960 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:24:21.960 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:24:21.960 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:24:21.960 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:24:21.960 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:24:21.960 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:24:56.577 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:24:56.640 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/npotest.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:24:56.671 CDT INFO: Completed triple loading after 31 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Instances with multiple types (11 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Process orphan classes (3 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:24:56.671 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:24:56.671 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:24:56.687 CDT INFO: 16 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:24:56.687 CDT INFO: Postprocess: Possibly typed entities (2 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:24:56.687 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:24:56.687 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:26:07.435 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:26:07.545 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/pizza.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:26:07.779 CDT INFO: Completed triple loading after 234 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:26:08.232 CDT INFO: Importing http://protege.stanford.edu/plugins/owl/protege from location: http://protege.stanford.edu/plugins/owl/protege -- AbstractOWLModel.loadImportedAssertions() +2014.05.15 08:26:08.263 CDT INFO: Loading triples for: http://protege.stanford.edu/plugins/owl/protege -- ProtegeOWLParser.loadTriples() +2014.05.15 08:26:08.278 CDT INFO: Completed triple loading after 0 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:26:08.278 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:26:08.278 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:26:08.278 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:26:08.278 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:26:08.278 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:26:08.278 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:26:08.278 CDT INFO: Postprocess: Instances with multiple types (101 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:26:08.294 CDT INFO: 16 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:26:08.294 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:26:08.294 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:26:08.294 CDT INFO: Postprocess: Process orphan classes (97 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:26:08.294 CDT INFO: 0 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:26:08.294 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:26:08.294 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:26:08.294 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:26:08.294 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:26:08.294 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:26:08.294 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:26:08.294 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:26:08.294 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:26:08.294 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 08:31:46.486 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 08:31:46.487 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 08:31:46.612 CDT INFO: Completed triple loading after 125 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 08:31:46.612 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:31:46.612 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 08:31:46.612 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:31:46.612 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 08:31:46.612 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:31:46.612 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 08:31:46.612 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:31:46.612 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 08:31:46.612 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:31:46.612 CDT INFO: 0 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 08:31:46.612 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:31:46.627 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 08:31:46.627 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:31:46.627 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 08:31:46.627 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:31:46.627 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 08:31:46.627 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:31:46.627 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 08:31:46.627 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:31:46.627 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 08:31:46.627 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() +2014.05.15 12:20:06.801 CDT INFO: *** SYSTEM START *** +2014.05.15 12:20:08.486 CDT WARNING: [Local Folder Repository] The specified file must be a directory. (C:\git\lexevs\lbTest\plugins\edu.stanford.smi.protegex.owl) -- LocalFolderRepository.update() +2014.05.15 12:20:08.612 CDT INFO: Loading triples for: file:/C:/git/lexevs/lbTest/resources/testData/amino-acid.owl -- ProtegeOWLParser.loadTriples() +2014.05.15 12:20:09.938 CDT INFO: Completed triple loading after 1061 ms -- ProtegeOWLParser.loadTriples() +2014.05.15 12:20:09.954 CDT INFO: Postprocess: Process entities with incorrect Java type (0 entities) ... -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 12:20:09.954 CDT INFO: 0 ms + -- TriplePostProcessor.processFramesWithWrongJavaType() +2014.05.15 12:20:09.954 CDT INFO: Postprocess: Process metaclasses (3 metaclasses) ... -- TriplePostProcessor.processMetaclasses() +2014.05.15 12:20:09.954 CDT INFO: 0 ms + -- TriplePostProcessor.processMetaclasses() +2014.05.15 12:20:09.955 CDT INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 12:20:09.955 CDT INFO: 0 ms + -- TriplePostProcessor.processSubclassesOfRdfList() +2014.05.15 12:20:09.955 CDT INFO: Postprocess: Instances with multiple types (44 instances) ... -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 12:20:09.955 CDT INFO: 0 ms + -- TriplePostProcessor.processInstancesWithMultipleTypes() +2014.05.15 12:20:09.955 CDT INFO: Postprocess: Add inferred superclasses ... -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 12:20:09.986 CDT INFO: 31 ms + -- TriplePostProcessor.processInferredSuperclasses() +2014.05.15 12:20:09.986 CDT INFO: Postprocess: Process orphan classes (46 classes) ... -- TriplePostProcessor.processOrphanClses() +2014.05.15 12:20:10.001 CDT INFO: 15 ms + -- TriplePostProcessor.processOrphanClses() +2014.05.15 12:20:10.001 CDT INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 12:20:10.001 CDT INFO: 0 ms + -- TriplePostProcessor.processGeneralizedConceptInclusions() +2014.05.15 12:20:10.001 CDT INFO: Postprocess: Abstract classes... -- TriplePostProcessor.processAbstractClasses() +2014.05.15 12:20:10.001 CDT INFO: 0 ms + -- TriplePostProcessor.processAbstractClasses() +2014.05.15 12:20:10.001 CDT INFO: Postprocess: Domain and range of properties... -- TriplePostProcessor.processDomainAndRange() +2014.05.15 12:20:10.001 CDT INFO: 0 ms + -- TriplePostProcessor.processDomainAndRange() +2014.05.15 12:20:10.001 CDT INFO: Postprocess: Possibly typed entities (0 resources) ... -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 12:20:10.001 CDT INFO: 0 ms + -- TriplePostProcessor.processPossiblyTypedResources() +2014.05.15 12:20:10.001 CDT INFO: Updating underlying frames model in 0 ms -- ProtegeOWLParser.doFinalPostProcessing() diff --git a/lbTest/resources/[lbImpl] All Tests - NormalConfig.launch b/lbTest/resources/[lbImpl] All Tests - NormalConfig.launch index ce59fb5523..3bb8d8e934 100644 --- a/lbTest/resources/[lbImpl] All Tests - NormalConfig.launch +++ b/lbTest/resources/[lbImpl] All Tests - NormalConfig.launch @@ -17,5 +17,5 @@ - + diff --git a/lbTest/resources/testData/testExport/null_1.0.xml b/lbTest/resources/testData/testExport/null_1.0.xml new file mode 100644 index 0000000000..e69de29bb2 diff --git a/lbTest/resources/testData/testLoadLongsource.obo b/lbTest/resources/testData/testLoadLongsource.obo new file mode 100644 index 0000000000..f55ab63062 --- /dev/null +++ b/lbTest/resources/testData/testLoadLongsource.obo @@ -0,0 +1,44 @@ +format-version: 1.0 +date: 21:07:2007 19:08 +saved-by: m029451 +auto-generated-by: OBO-Edit 1.100-beta1 +default-namespace: test + + +[Term] +id: A +name: A + +[Term] +id: A1 +name: A1 +is_a: A ! A + +[Term] +id: A12 +name: A12 +is_a: A1 ! A1 + +[Term] +id: A13 +name: A13 +is_a: A12 ! A12 + +[Term] +id: A2 +name: A2 +is_a: A + + +[Term] +id: A22 +name: A22 +is_a: A2 ! A2 + +[Term] +id: DOID:0050777 +name: Joubert syndrome +def: "An autosomal recessive disease that is characterized by congenital malformation of the brainstem and agenesis or hypoplasia of the cerebellar vermis leading to an abnormal respiratory pattern, nystagmus, hypotonia, ataxia, and delay in achieving motor milestones resulting from dysfunction of ciliary proteins (ciliopathy)." [url:http\://en.wikipedia.org/wiki/Joubert_syndrome, url:http\://omim.org/entry/213300?search=joubert&highlight=joubert, url:http\://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=1022&Disease_Disease_Search_diseaseGroup=Joubert-syndrome&Disease_Disease_Search_diseaseType=Pat&Disease%28s%29/group%20of%20diseases=Joubert-syndrome--Joubert-Boltshauser-syndrome-&title=Joubert-syndrome--Joubert-Boltshauser-syndrome-&search=Disease_Search_Simple] +xref: OMIM:213300 +created_by: lschriml +creation_date: 2013-04-04T11:25:32Z diff --git a/lbTest/resources/testData/valueDomain/vdTestData.xml b/lbTest/resources/testData/valueDomain/vdTestData.xml index ad13cb7290..e50c9d041c 100755 --- a/lbTest/resources/testData/valueDomain/vdTestData.xml +++ b/lbTest/resources/testData/valueDomain/vdTestData.xml @@ -135,6 +135,19 @@ + + + + + Domestic Auto Makers Long Name + + + + + + + +