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Commit 6e4cb6c0 authored by Volker Thiemann's avatar Volker Thiemann
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Merge branch 'master' of gitlab.uni-oldenburg.de:AKTIN/dwh-import

parents f78712d8 721175dc
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cda-import/pom.xml
View file @ 6e4cb6c0
...@@ -5,7 +5,7 @@ ...@@ -5,7 +5,7 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-import</artifactId> <artifactId>cda-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<description> <description>
The CDA import module transforms received The CDA import module transforms received
...@@ -18,7 +18,7 @@ ...@@ -18,7 +18,7 @@
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</parent> </parent>
<properties> <properties>
...@@ -33,73 +33,25 @@ ...@@ -33,73 +33,25 @@
</resource> </resource>
</resources> </resources>
<plugins> <plugins>
<!-- <!-- copy dependencies for optional command line processing -->
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <artifactId>maven-dependency-plugin</artifactId>
<artifactId>maven-jar-plugin</artifactId> <executions>
<configuration> <execution>
<archive> <phase>install</phase>
<manifest> <goals>
<addClasspath>true</addClasspath> <goal>copy-dependencies</goal>
<classpathPrefix>lib/</classpathPrefix> </goals>
<mainClass>org.aktin.cda.etl.demo.Server</mainClass> <configuration>
</manifest> <outputDirectory>${project.build.directory}/dependencies</outputDirectory>
</archive> </configuration>
</configuration> </execution>
</plugin> </executions>
<plugin> </plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.3.6.v20151106</version>
<dependencies>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
<version>2.22.1</version>
</dependency>
</dependencies>
</plugin>
-->
<!--
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>unpack</id>
<phase>process-test-classes</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>org.jboss.as</groupId>
<artifactId>jboss-as-dist</artifactId>
<version>7.1.1.Final</version>
<type>zip</type>
<overWrite>false</overWrite>
<outputDirectory>target</outputDirectory>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
-->
</plugins> </plugins>
</build> </build>
<dependencyManagement> <dependencyManagement>
<!--
<dependencies>
<dependency>
<groupId>org.jboss.arquillian</groupId>
<artifactId>arquillian-bom</artifactId>
<version>1.1.10.Final</version>
<scope>import</scope>
<type>pom</type>
</dependency>
</dependencies>
-->
</dependencyManagement> </dependencyManagement>
<dependencies> <dependencies>
<dependency> <dependency>
...@@ -109,35 +61,13 @@ ...@@ -109,35 +61,13 @@
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-server</artifactId> <artifactId>cda-server</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-api</artifactId> <artifactId>dwh-api</artifactId>
<version>0.3-SNAPSHOT</version> <version>0.3</version>
</dependency>
<!--
<dependency>
<groupId>org.jboss.arquillian.junit</groupId>
<artifactId>arquillian-junit-container</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jboss.arquillian.container</groupId>
<artifactId>arquillian-weld-ee-embedded-1.1</artifactId>
<version>1.0.0.CR9</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jboss.weld</groupId>
<artifactId>weld-core</artifactId>
<version>2.3.2.Final</version>
<scope>test</scope>
</dependency> </dependency>
-->
<dependency> <dependency>
......
cda-import/src/main/java/org/aktin/cda/etl/CDAImporter.java
View file @ 6e4cb6c0
...@@ -50,6 +50,7 @@ public class CDAImporter extends AbstractCDAImporter implements AutoCloseable{ ...@@ -50,6 +50,7 @@ public class CDAImporter extends AbstractCDAImporter implements AutoCloseable{
* Construct a CDAImporter * Construct a CDAImporter
* @param factory observation factory * @param factory observation factory
* @param prefs preferences * @param prefs preferences
* @param anonymizer anonymizer interface
* @throws NamingException i2b2 data sources could not be found by their names * @throws NamingException i2b2 data sources could not be found by their names
* @throws SQLException initisiation errors with the database * @throws SQLException initisiation errors with the database
* @throws IOException unable to load CDA to ETL transformation script * @throws IOException unable to load CDA to ETL transformation script
......
cda-import/src/main/java/org/aktin/cda/etl/transform/Transformation.java
View file @ 6e4cb6c0
...@@ -41,6 +41,7 @@ public class Transformation { ...@@ -41,6 +41,7 @@ public class Transformation {
* @param moduleId module id * @param moduleId module id
* @param templateId template id * @param templateId template id
* @param xslt XSLT document * @param xslt XSLT document
* @param anonymizer anonzmiyer
* @throws TransformerFactoryConfigurationError if the transformer factory failed to initialize * @throws TransformerFactoryConfigurationError if the transformer factory failed to initialize
* @throws TransformerConfigurationException transformer setup error * @throws TransformerConfigurationException transformer setup error
*/ */
......
cda-import/src/main/java/org/aktin/cda/etl/transform/fun/OneWayHashFunction.java
View file @ 6e4cb6c0
...@@ -37,7 +37,7 @@ public abstract class OneWayHashFunction extends ExtensionFunctionDefinition { ...@@ -37,7 +37,7 @@ public abstract class OneWayHashFunction extends ExtensionFunctionDefinition {
/** /**
* Implements a call to the hash function with variable arguments. * Implements a call to the hash function with variable arguments.
* For the algorithm, see {@link OneWayHashFunction#calculateHash(String...)} * The algorithm is delegated to the implementation of {@link Anonymizer}
* *
* @author R.W.Majeed * @author R.W.Majeed
* *
......
cda-import/src/test/java/org/aktin/cda/etl/CDAImporterMockUp.java
View file @ 6e4cb6c0
...@@ -4,6 +4,7 @@ import java.io.IOException; ...@@ -4,6 +4,7 @@ import java.io.IOException;
import java.time.ZoneId; import java.time.ZoneId;
import java.util.Iterator; import java.util.Iterator;
import java.util.function.Consumer; import java.util.function.Consumer;
import java.util.logging.Logger;
import javax.annotation.PreDestroy; import javax.annotation.PreDestroy;
import javax.inject.Singleton; import javax.inject.Singleton;
...@@ -20,12 +21,13 @@ import de.sekmi.histream.impl.SimpleVisitExtension; ...@@ -20,12 +21,13 @@ import de.sekmi.histream.impl.SimpleVisitExtension;
@Singleton @Singleton
public class CDAImporterMockUp extends AbstractCDAImporter implements Consumer<Observation>, AutoCloseable{ public class CDAImporterMockUp extends AbstractCDAImporter implements Consumer<Observation>, AutoCloseable{
private static final Logger log = Logger.getLogger(CDAImporterMockUp.class.getName());
private ObservationFactory factory; private ObservationFactory factory;
private int insertCount; private int insertCount;
public CDAImporterMockUp() throws IOException{ public CDAImporterMockUp() throws IOException{
super(new ConcatAnonymizer()); super(new ConcatAnonymizer());
System.out.println("CONSTRUCT CDAImporterMockUp"); log.info("CONSTRUCT CDAImporterMockUp");
factory = new ObservationFactoryImpl(new SimplePatientExtension(), new SimpleVisitExtension()); factory = new ObservationFactoryImpl(new SimplePatientExtension(), new SimpleVisitExtension());
insertCount = 0; insertCount = 0;
} }
...@@ -33,7 +35,7 @@ public class CDAImporterMockUp extends AbstractCDAImporter implements Consumer<O ...@@ -33,7 +35,7 @@ public class CDAImporterMockUp extends AbstractCDAImporter implements Consumer<O
@PreDestroy @PreDestroy
@Override @Override
public void close() { public void close() {
System.out.println("CLOSE CDAImporterMockUp (insertCount="+insertCount+")"); log.info("CLOSE CDAImporterMockUp (insertCount="+insertCount+")");
} }
@Override @Override
......
cda-import/src/test/java/org/aktin/cda/etl/TestTransformToEAV.java
View file @ 6e4cb6c0
...@@ -20,6 +20,22 @@ import de.sekmi.histream.ext.Patient; ...@@ -20,6 +20,22 @@ import de.sekmi.histream.ext.Patient;
import de.sekmi.histream.ext.Visit; import de.sekmi.histream.ext.Visit;
import de.sekmi.histream.io.GroupedXMLReader; import de.sekmi.histream.io.GroupedXMLReader;
/**
* Test the template transformations from CDA to EAV-XML. Multiple template ids
* and AKTIN modules are supported.
* <p>
* For standalone transformation testing, build the {@code cda-import} module
* with {@code mvn clean install}. When needed, run the build command from the
* parent directory.<br/>
* When the build ist complete, the transformation can be tested with
* a command line application. E.g. from within the {@code cda-import/target/} directory:
* <pre>
* java -classpath "test-classes;classes;dependencies/*" org.aktin.cda.etl.TestTransformToEAV "../../cda-validation/src/main/resources/Additional Examples/basismodul-beispiel-storyboard01-complete.xml"
* </pre>
* </p>
* @author R.W.Majeed
*
*/
public class TestTransformToEAV { public class TestTransformToEAV {
@Test @Test
...@@ -32,6 +48,7 @@ public class TestTransformToEAV { ...@@ -32,6 +48,7 @@ public class TestTransformToEAV {
Assert.assertTrue(templateId.length() > 0); Assert.assertTrue(templateId.length() > 0);
} }
} }
@SuppressWarnings("deprecation")
@Test @Test
public void transformExample1() throws Exception{ public void transformExample1() throws Exception{
CDAParser parser = new CDAParser(); CDAParser parser = new CDAParser();
...@@ -72,7 +89,7 @@ public class TestTransformToEAV { ...@@ -72,7 +89,7 @@ public class TestTransformToEAV {
/** /**
* Transform a CDA file to a EAV which is output on stdout. * Transform a CDA file to a EAV which is output on stdout.
* Call with {@code java -classpath "cda-import/target/test-classes;cda-import/target/classes;cda-server/target/classes;cda-validation/target/classes;histream-core/target/classes" org.aktin.cda.etl.TestTransformToEAV filename} * Call with {@code java -classpath "test-classes;classes;dependencies/*" org.aktin.cda.etl.TestTransformToEAV filename}
* @param args file name argument * @param args file name argument
* @throws Exception error * @throws Exception error
*/ */
......
cda-ontology/pom.xml
View file @ 6e4cb6c0
...@@ -4,14 +4,14 @@ ...@@ -4,14 +4,14 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-ontology</artifactId> <artifactId>cda-ontology</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<description> <description>
CDA Ontology definitions CDA Ontology definitions
</description> </description>
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</parent> </parent>
<build> <build>
<resources> <resources>
......
cda-server/pom.xml
View file @ 6e4cb6c0
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-server</artifactId> <artifactId>cda-server</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<description> <description>
The CDA server provides web service interfaces The CDA server provides web service interfaces
...@@ -16,7 +16,7 @@ ...@@ -16,7 +16,7 @@
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</parent> </parent>
<properties> <properties>
...@@ -77,7 +77,7 @@ ...@@ -77,7 +77,7 @@
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-api</artifactId> <artifactId>dwh-api</artifactId>
<version>0.2</version> <version>0.3</version>
</dependency> </dependency>
<!-- dependency injection --> <!-- dependency injection -->
...@@ -98,7 +98,7 @@ ...@@ -98,7 +98,7 @@
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-validation</artifactId> <artifactId>cda-validation</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</dependency> </dependency>
</dependencies> </dependencies>
</project> </project>
\ No newline at end of file
cda-validation/pom.xml
View file @ 6e4cb6c0
...@@ -4,12 +4,12 @@ ...@@ -4,12 +4,12 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-validation</artifactId> <artifactId>cda-validation</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</parent> </parent>
<properties> <properties>
<schematronVersion>20170302T140447</schematronVersion> <schematronVersion>20170302T140447</schematronVersion>
......
demo-distribution/pom.xml
View file @ 6e4cb6c0
...@@ -6,19 +6,19 @@ ...@@ -6,19 +6,19 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>demo-distribution</artifactId> <artifactId>demo-distribution</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</parent> </parent>
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>demo-server</artifactId> <artifactId>demo-server</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</dependency> </dependency>
</dependencies> </dependencies>
......
demo-server/pom.xml
View file @ 6e4cb6c0
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>demo-server</artifactId> <artifactId>demo-server</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<description> <description>
Demo server application. The demo server can receive Demo server application. The demo server can receive
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</parent> </parent>
<properties> <properties>
...@@ -52,12 +52,12 @@ ...@@ -52,12 +52,12 @@
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-validation</artifactId> <artifactId>cda-validation</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>cda-server</artifactId> <artifactId>cda-server</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
</dependency> </dependency>
</dependencies> </dependencies>
</project> </project>
\ No newline at end of file
pom.xml
View file @ 6e4cb6c0
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>dwh-import</artifactId> <artifactId>dwh-import</artifactId>
<version>0.9-SNAPSHOT</version> <version>0.9rc2-SNAPSHOT</version>
<name>AKTIN : DWH Import</name> <name>AKTIN : DWH Import</name>
<description>AKTIN Software</description> <description>AKTIN Software</description>
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
<parent> <parent>
<groupId>org.aktin</groupId> <groupId>org.aktin</groupId>
<artifactId>aktin</artifactId> <artifactId>aktin</artifactId>
<version>0.7-SNAPSHOT</version> <version>0.7</version>
</parent> </parent>
<properties> <properties>
......
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