Merge pull request #9 from qbicsoftware/development

Prepare release 1.6.0

.travis.yml

@@ -31,7 +31,8 @@ before_script: if [ "$VAADIN_CHARTS_LICENSE_CODE" != "" ]; then
                fi;
 
 # as agreed in our SOP, build everything (don't deploy, just try to 'mvn install' locally, which covers all phases)
-script: mvn --quiet --activate-profiles !development-build,!release-build --settings .travis.settings.xml clean cobertura:cobertura install
+script: mvn build-helper:parse-version versions:set -DnewVersion=\${parsedVersion.majorVersion}.\${parsedVersion.minorVersion}.\${parsedVersion.incrementalVersion}-SNAPSHOT versions:update-child-modules && mvn versions:commit &&
+        mvn --quiet --activate-profiles !development-build,!release-build --settings .travis.settings.xml clean cobertura:cobertura install
 # upload code coverage report, generate maven site (javadocs, documentation, static code analysis, etc.)
 after_success: 
 - bash <(curl -s https://codecov.io/bash)
@@ -53,7 +54,8 @@ deploy:
   # artifact will be installed in our testing instance if it is a .war file
 - skip_cleanup: true
   provider: script
-  script: mvn --quiet --activate-profiles !development-build,release-build --settings .travis.settings.xml deploy
+  script: mvn build-helper:parse-version versions:set -DnewVersion=$TRAVIS_TAG -DprocessAllModules && mvn versions:commit &&
+          mvn --quiet --activate-profiles !development-build,release-build --settings .travis.settings.xml deploy
   on:
     branch: master
     condition: '"$TRAVIS_EVENT_TYPE" = "push"'

pom.xml

@@ -8,8 +8,8 @@
 		<version>1.5.1</version>
 	</parent>
 	<artifactId>data-model-lib</artifactId>
+	<version>1.6.0-SNAPSHOT</version>
 	<packaging>jar</packaging>
-	<version>1.5.2</version>
 	<name>Data Model Library</name>
 	<url>http://github.com/qbicsoftware/data-model-lib</url>
 	<description>A collection of QBiC data models.</description>

src/main/groovy/life/qbic/datamodel/Constants.groovy

@@ -0,0 +1,7 @@
+package life.qbic.datamodel
+
+class Constants {
+
+    static final public String ISO_8601_DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ss'Z'"
+
+}

src/main/groovy/life/qbic/datamodel/services/Status.groovy

@@ -1,5 +1,5 @@
 package life.qbic.datamodel.services;
 
 public enum Status {
-  WAITING, PROCESSING, PROCESSED, FAILED_QC, DATA_AT_QBIC
-}
+  WAITING, PROCESSING, PROCESSED, FAILED_QC, DATA_AT_QBIC, METADATA_REGISTERED
+}

src/main/groovy/life/qbic/datamodel/workflows/MetaData.groovy

@@ -0,0 +1,40 @@
+package life.qbic.datamodel.workflows
+
+import com.fasterxml.jackson.annotation.JsonProperty
+import groovy.transform.EqualsAndHashCode
+
+@EqualsAndHashCode()
+class MetaData {
+
+    @JsonProperty('metadata')
+    private final Map metadata
+
+    MetaData() {
+        metadata = [:].asImmutable()
+    }
+
+    MetaData(Map metadata){
+        this.metadata = metadata.asImmutable()
+    }
+
+    @Override
+    Object getProperty(String s) {
+        return this.metadata.get(s)
+    }
+
+    @Override
+    boolean equals(Object o) {
+        if( !o instanceof MetaData ) {
+            return false
+        }
+        def trace = o as MetaData
+        for( String key in this.metadata.keySet() ) {
+            def thisProperty = this.getProperty(key)
+            def otherProperty = trace.getProperty(key)
+            if( ! otherProperty || ( otherProperty != thisProperty ) ) {
+                return false
+            }
+        }
+        return true
+    }
+}

src/main/groovy/life/qbic/datamodel/workflows/RunInfo.groovy

@@ -0,0 +1,64 @@
+package life.qbic.datamodel.workflows
+
+import com.fasterxml.jackson.annotation.JsonFormat
+import com.fasterxml.jackson.annotation.JsonProperty
+import groovy.transform.EqualsAndHashCode
+import life.qbic.datamodel.Constants
+
+import java.text.SimpleDateFormat
+
+enum NextflowEventType
+{
+    STARTED, PROCESS_SUBMITTED, PROCESS_STARTED, PROCESS_COMPLETED, ERROR, COMPLETED, UNKNOWN
+}
+
+@EqualsAndHashCode()
+class RunInfo {
+
+    @JsonProperty("event")
+    private NextflowEventType event
+
+    @JsonProperty("runName")
+    private String name
+
+    @JsonProperty("runStatus")
+    private String status
+
+    @JsonProperty("runId")
+    private String id
+
+    @JsonProperty("utcTime")
+    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = Constants.ISO_8601_DATETIME_FORMAT)
+    private Date time
+
+    RunInfo() {
+        event = NextflowEventType.UNKNOWN
+        name = ""
+        status = ""
+        id = ""
+        time = new Date()
+    }
+
+    RunInfo(Map weblogRunInformation) {
+        event = convertEventStringToEventType(weblogRunInformation.get('event') as String)
+        name = weblogRunInformation.get('runName') ?: ""
+        status = weblogRunInformation.get('runStatus') ?: ""
+        id = weblogRunInformation.get('runId') ?: ""
+        time = convertStringToDate(weblogRunInformation.get('utcTime') as String)
+    }
+
+    private static Date convertStringToDate(String s) {
+        Date date = new SimpleDateFormat(Constants.ISO_8601_DATETIME_FORMAT).parse(s)
+        return date
+    }
+
+    private static NextflowEventType convertEventStringToEventType(String event) {
+        try {
+            def eventType = event.toUpperCase() as NextflowEventType
+            return eventType
+        } catch (IllegalArgumentException e) {
+            return NextflowEventType.UNKNOWN
+        }
+    }
+
+}

src/main/groovy/life/qbic/datamodel/workflows/Trace.groovy

@@ -0,0 +1,39 @@
+package life.qbic.datamodel.workflows
+
+import com.fasterxml.jackson.annotation.JsonProperty
+
+
+class Trace {
+
+    @JsonProperty("properties")
+    private final Map traceInformation
+
+    Trace() {
+        traceInformation = [:].asImmutable()
+    }
+
+    Trace(Map trace) {
+        traceInformation = trace.asImmutable()
+    }
+
+    @Override
+    Object getProperty(String s) {
+        return traceInformation.get(s)
+    }
+
+    @Override
+    boolean equals(Object o) {
+        if( !o instanceof Trace ) {
+            return false
+        }
+        def trace = o as Trace
+        for( String key in this.traceInformation.keySet() ) {
+            def thisProperty = this.getProperty(key)
+            def otherProperty = trace.getProperty(key)
+            if( ! otherProperty || ( otherProperty != thisProperty ) ) {
+                return false
+            }
+        }
+        return true
+    }
+}

src/main/java/life/qbic/datamodel/identifiers/SampleCodeFunctions.java

@@ -61,7 +61,7 @@ public static boolean isQbicBarcode(String code) {
    * @return true if String is a QBiC entity code, false if not
    */
   public static boolean isQbicEntityCode(String code) {
-    Pattern entityPattern = Pattern.compile("Q[A-X0-9]{4}ENTITY-[0-9]*$", Pattern.CASE_INSENSITIVE);
+    Pattern entityPattern = Pattern.compile("Q[A-X0-9]{4}ENTITY-[1-9][0-9]*", Pattern.CASE_INSENSITIVE);
     Matcher matcher = entityPattern.matcher(code);
     return matcher.find();
   }