integration tests with i2b2 database

.settings/

.classpath

.project

target/

<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

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();

		}

	}

}

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();

	}

}

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