integration tests with i2b2 database

i2b2-integration-tests/.gitignore

+.settings/
+.classpath
+.project
+target/

i2b2-integration-tests/pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<name>HIStream : i2b2 integration tests</name>
+	
+	<groupId>de.sekmi.histream</groupId>
+	<artifactId>i2b2-intregration-tests</artifactId>
+	<version>0.5-SNAPSHOT</version>
+
+	<parent>
+		<groupId>de.sekmi.histream</groupId>
+		<artifactId>histream</artifactId>
+		<version>0.5-SNAPSHOT</version>
+	</parent>
+  
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-failsafe-plugin</artifactId>
+				<version>2.18.1</version>
+				<executions>
+					<execution>
+						<goals>
+							<goal>integration-test</goal>
+							<goal>verify</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-i2b2</artifactId>
+			<version>0.5-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-skos</artifactId>
+			<version>0.5-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-import</artifactId>
+			<version>0.5-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-import</artifactId>
+			<version>0.5-SNAPSHOT</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.maven.plugins</groupId>
+			<artifactId>maven-failsafe-plugin</artifactId>
+			<version>2.18.1</version>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+</project>
\ No newline at end of file

i2b2-integration-tests/src/test/java/de/sekmi/histream/i2b2/ITImportData.java

+package de.sekmi.histream.i2b2;
+
+import java.io.InputStream;
+import java.io.UncheckedIOException;
+import java.util.Map;
+import java.util.Properties;
+import java.util.function.Supplier;
+
+import org.junit.Test;
+
+import de.sekmi.histream.Observation;
+import de.sekmi.histream.ObservationFactory;
+import de.sekmi.histream.ObservationSupplier;
+import de.sekmi.histream.etl.ETLObservationSupplier;
+import de.sekmi.histream.impl.ObservationFactoryImpl;
+import de.sekmi.histream.io.Streams;
+
+public class ITImportData {
+
+	@Test
+	public void importData() throws Exception{
+		Properties i2b2 = new Properties();
+		try( InputStream in = getClass().getResourceAsStream("/i2b2.properties") ){
+			i2b2.load(in);
+		}
+		PostgresPatientStore patients = new PostgresPatientStore((Map)i2b2);
+		PostgresVisitStore visits = new PostgresVisitStore((Map)i2b2);
+		I2b2Inserter inserter = new I2b2Inserter((Map)i2b2);
+		ObservationFactory factory = new ObservationFactoryImpl();
+		factory.registerExtension(patients);
+		factory.registerExtension(visits);
+
+		ObservationSupplier data = ETLObservationSupplier.load(ETLObservationSupplier.class.getResource("/test-1-datasource.xml"), factory);
+		inserter.setMeta(ObservationSupplier.META_ETL_STRATEGY, data.getMeta(ObservationSupplier.META_ETL_STRATEGY));
+		Supplier<Observation> source = data;
+		// XXX test transformation later
+		//source = new PullTransformer(source, mapping);
+		try{
+			Streams.transfer(source, inserter);
+		}catch( UncheckedIOException e ){
+			// unwrap unchecked IO exception
+			throw e.getCause();
+		}finally{
+			data.close();
+			inserter.close();
+			patients.close();
+			visits.close();
+		}
+	}
+}

i2b2-integration-tests/src/test/java/de/sekmi/histream/i2b2/ITImportOntology.java

+package de.sekmi.histream.i2b2;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URL;
+import java.sql.SQLException;
+import java.util.Map;
+import java.util.Properties;
+
+import org.junit.Test;
+
+import de.sekmi.histream.i2b2.ont.Import;
+import de.sekmi.histream.ontology.skos.Store;
+
+public class ITImportOntology {
+
+	@Test
+	public void importOntology() throws Exception{
+		Properties i2b2 = new Properties();
+		try( InputStream in = getClass().getResourceAsStream("/i2b2.properties") ){
+			i2b2.load(in);
+		}
+		Store store = new Store(new File("../histream-skos/examples/test-ontology.ttl"));
+		try( Import i = new Import((Map)i2b2) ){
+			i.setOntology(store);
+			i.processOntology();
+		}
+		store.close();
+	}
+}

i2b2-integration-tests/src/test/resources/i2b2.properties

+jdbc.host = localhost
+jdbc.database = i2b2
+jdbc.port = 15432
+
+# all keys beginning with meta.jdbc. are passed to the JDBC driver
+meta.jdbc.user = i2b2metadata
+meta.jdbc.password =
+# metadata table
+meta.table=i2b2metadata.i2b2
+# metadata table access
+meta.access=i2b2metadata.table_access
+meta.basepath=\\i2b2\\
+# Before each import, data for this sourcesystem_cd will be deleted
+meta.sourcesystem_cd=test
+
+
+# concept dimension
+# all keys beginning with data.jdbc. are passed to the JDBC driver
+data.jdbc.user = i2b2demodata
+data.jdbc.password =
+data.concept.table=i2b2demodata.concept_dimension
+project = test
+
+# language to use for accessing ontology
+ont.language=EN

i2b2-integration-tests/src/test/resources/skos-ontology.properties

+ontology.class = de.sekmi.histream.ontology.skos.Store
+rdf.file.1 = ../histream-skos/examples/test-ontology.ttl

pom.xml

@@ -56,6 +56,7 @@
 		<!--<module>histream-hl7</module>-->
 		<module>histream-skos</module>
 		<module>histream-import</module>
+		<module>i2b2-integration-tests</module>
 		<module>distribution</module>
 	</modules>
 	<build>
@@ -155,6 +156,17 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<executions>
+					<execution>
+						<goals>
+							<goal>test-jar</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 	</build>
 	<reporting>