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Updated project with changes since 2015 #1

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Updated project with changes since 2015 #1

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15 changes: 1 addition & 14 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,15 +1,2 @@
*.class

# Mobile Tools for Java (J2ME)
.mtj.tmp/

# Package Files #
*.jar
*.war
*.ear

# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*

target
/CDAGenerator/.jrebel_disabled
/CDAGenerator/src/main/resources/testCDA.xml
63 changes: 55 additions & 8 deletions CDAGenerator/pom.xml
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Expand Up @@ -3,24 +3,71 @@
<modelVersion>4.0.0</modelVersion>
<groupId>de.fhg.isst.ehealth.cda</groupId>
<artifactId>CDAGenerator</artifactId>
<version>1.1.4</version>
<version>1.2.0</version>
<packaging>jar</packaging>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<com.sun.xml.version>2.3.0</com.sun.xml.version>
</properties>

<repositories>
<repository>
<id>isst-artifactory</id>
<name>artifactory.isst.fraunhofer.de-releases</name>
<url>https://artifactory.isst.fraunhofer.de:443/artifactory/oe220-rzv-external-maven/</url>
</repository>
</repositories>
<distributionManagement>
<snapshotRepository>
<id>isst-artifactory</id>
<name>artifactory.isst.fraunhofer.de-snapshots</name>
<url>https://artifactory.isst.fraunhofer.de:443/artifactory/oe220-rzv-external-maven/</url>
</snapshotRepository>
<repository>
<id>isst-artifactory</id>
<name>artifactory.isst.fraunhofer.de-releases</name>
<url>https://artifactory.isst.fraunhofer.de:443/artifactory/oe220-rzv-external-maven/</url>
</repository>
</distributionManagement>

<dependencies>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<scope>test</scope>
</dependency>
<!--//Java10?-->
<!-- https://mvnrepository.com/artifact/com.sun.xml.bind/jaxb-impl -->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${com.sun.xml.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.sun.xml.bind/jaxb-core -->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>${com.sun.xml.version}</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>${com.sun.xml.version}</version>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>8</source>
<target>8</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
15 changes: 13 additions & 2 deletions CDAGenerator/src/main/java/de/fhg/isst/cda/choices/clinicalstatements/Observation.java
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Expand Up @@ -2,6 +2,7 @@

import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;

import de.fhg.isst.cda.classes.ClinicalStatement;
import de.fhg.isst.cda.classes.Code;
Expand All @@ -25,6 +26,9 @@ public class Observation extends ClinicalStatement {

/** The ids. */
private ArrayList<ID> ids;

/** The template ids */
private List<ID> templateId;

/** The code. */
private Code code;
Expand Down Expand Up @@ -111,10 +115,10 @@ public XActMoodDocumentObservation getMoodCode() {
public void setMoodCode(XActMoodDocumentObservation moodCode) {
this.moodCode = moodCode;
}

/**
* Gets the ids.
*
*
* @return the ids
*/
public ArrayList<ID> getIds() {
Expand All @@ -123,6 +127,13 @@ public ArrayList<ID> getIds() {
}
return ids;
}

public List<ID> getTemplateId() {
if (templateId==null){
templateId = new ArrayList<>();
}
return templateId;
}

/**
* Sets the ids.
Expand Down
76 changes: 57 additions & 19 deletions CDAGenerator/src/main/java/de/fhg/isst/cda/services/CDAService.java
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Expand Up @@ -17,9 +17,6 @@
import javax.xml.validation.SchemaFactory;
import javax.xml.validation.Validator;

import org.apache.log4j.LogManager;
import org.apache.log4j.Logger;
import org.apache.log4j.PropertyConfigurator;
import org.hl7.v3.cda.*;
import org.xml.sax.SAXException;

Expand Down Expand Up @@ -116,6 +113,10 @@
import de.fhg.isst.cda.classes.Telecom;
import de.fhg.isst.cda.exceptions.MissingAttributeException;
import de.fhg.isst.cda.exceptions.MissingNodeException;
import java.io.Serializable;
import java.io.StringWriter;
import org.w3c.dom.CDATASection;
import org.w3c.dom.Element;

// TODO: Auto-generated Javadoc
/**
Expand All @@ -129,22 +130,13 @@ public class CDAService {
/** The factory. */
private ObjectFactory factory;

private Logger logger;

/**
* Instantiates a new CDA Service.
*/
public CDAService() {
this.logger = LogManager.getLogger(CDAService.class.getName());
this.log4j();
}

private void log4j() {

PropertyConfigurator.configureAndWatch("log4j.properties");
this.factory = new ObjectFactory();
}

/**
* Save.
*
Expand Down Expand Up @@ -175,6 +167,43 @@ public void save(String xmlPath, CDADocument mapDocument) throws MissingAttribut
marshaller.marshal(saveDoc, os);
os.close();
}
/**
* Save.
*
* @param file
* @param mapDocument
* @throws MissingAttributeException
* @throws MissingNodeException
* @throws FileNotFoundException
* @throws JAXBException
* @throws IOException
*/
public void save(File file, CDADocument mapDocument)throws MissingAttributeException, MissingNodeException, FileNotFoundException,
JAXBException, IOException {
POCDMT000040ClinicalDocument saveDoc = this.generate(mapDocument);

OutputStream os = new FileOutputStream(file);
JAXBContext jaxbcontext = JAXBContext.newInstance(POCDMT000040ClinicalDocument.class);
Marshaller marshaller = jaxbcontext.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);

marshaller.marshal(saveDoc, os);
os.close();
}

public String getCdaString(CDADocument mapDocument)throws MissingAttributeException, MissingNodeException, FileNotFoundException,
JAXBException, IOException {
POCDMT000040ClinicalDocument saveDoc = this.generate(mapDocument);

StringWriter writer = new StringWriter();
JAXBContext jaxbcontext = JAXBContext.newInstance(POCDMT000040ClinicalDocument.class);
Marshaller marshaller = jaxbcontext.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);

marshaller.marshal(saveDoc, writer);

return writer.toString();
}

/**
* Prints the.
Expand Down Expand Up @@ -212,7 +241,6 @@ public void print(CDADocument mapDocument) throws MissingAttributeException, Mis
* @return true, if successful
*/
public boolean validate(String xsdPath, String xmlPath) {
this.logger.trace("Entering CDA Validation");
boolean state = false;
try {
SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Expand All @@ -221,10 +249,8 @@ public boolean validate(String xsdPath, String xmlPath) {
validator.validate(new StreamSource(new File(xmlPath)));
state = true;
} catch (SAXException | IOException e) {
this.logger.error("CDA Validation Error");
this.logger.error(e.getMessage());
e.printStackTrace();
}
this.logger.trace("Exiting CDA Validation");
return state;
}

Expand Down Expand Up @@ -3287,6 +3313,13 @@ private POCDMT000040Observation createCDAObservation(Observation mapObservation)
}
}

if (!mapObservation.getTemplateId().isEmpty()){
for (ID templateId : mapObservation.getTemplateId())
{
cdaObservation.getTemplateId().add(createCDAId(templateId));
}
}

if (mapObservation.getCode() != null) {
cdaObservation.setCode(this.createCDACE(mapObservation.getCode()));
}
Expand Down Expand Up @@ -3334,10 +3367,15 @@ private POCDMT000040Observation createCDAObservation(Observation mapObservation)
}

if (mapObservation.getValue()!=null) {

if (mapObservation.getValue() instanceof String) {
ED mapObservationValue = factory.createED();
mapObservationValue.getContent().add((String)mapObservation.getValue());
String value = (String) mapObservation.getValue();
if(value.equals("CDA_CONSENT_SAML"))
{
mapObservationValue.setMediaType("text/xml");
mapObservationValue.setRepresentation(BinaryDataEncoding.TXT);
}
mapObservationValue.getContent().add(value);
cdaObservation.getValue().add(mapObservationValue);
}
else if (mapObservation.getValue() instanceof Code) {
Expand Down