database testing with embedded hsql database. (ff135840) · Commits · Raphael Majeed / histream

histream-i2b2/pom.xml

+12 −5

Original line number	Diff line number	Diff line
		@@ -17,11 +17,6 @@
		</plugins>
		</build>
		<dependencies>
		<dependency>
		<groupId>junit</groupId>
		<artifactId>junit</artifactId>
		<scope>test</scope>
		</dependency>
		<dependency>
		<groupId>org.postgresql</groupId>
		<artifactId>postgresql</artifactId>
		@@ -33,5 +28,17 @@
		<artifactId>histream-core</artifactId>
		<version>0.16-SNAPSHOT</version>
		</dependency>
		<dependency>
		<groupId>junit</groupId>
		<artifactId>junit</artifactId>
		<scope>test</scope>
		</dependency>
		<dependency>
		<groupId>org.hsqldb</groupId>
		<artifactId>hsqldb</artifactId>
		<version>2.4.1</version>
		<scope>test</scope>
		</dependency>

		</dependencies>
		</project>
		No newline at end of file

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/I2b2Visit.java

+2 −0

Original line number	Diff line number	Diff line
		@@ -73,6 +73,8 @@ public class I2b2Visit extends VisitImpl {
		// also set the patient_num
		int patient_num = ((I2b2Patient)patient).getNum();
		this.patient_num = patient_num;
		}else {
		throw new IllegalArgumentException("Patient expected of instanceOf I2b2Patient");
		}
		}

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/PostgresVisitStore.java

+4 −0

Original line number	Diff line number	Diff line
		@@ -43,6 +43,7 @@ import java.util.logging.Logger;
		import de.sekmi.histream.DateTimeAccuracy;
		import de.sekmi.histream.Observation;
		import de.sekmi.histream.ext.ExternalSourceType;
		import de.sekmi.histream.ext.Patient;
		import de.sekmi.histream.ext.StoredExtensionType;
		import de.sekmi.histream.ext.Visit;
		import de.sekmi.histream.ext.Visit.Status;
		@@ -476,6 +477,9 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit> implements
		return getOrCreateInstance(fact.getEncounterId(), fact.getExtension(I2b2Patient.class), fact.getSource());
		}

		public I2b2Visit createInstance(String encounterId, Patient patient, ExternalSourceType source) {
		return getOrCreateInstance(encounterId, (I2b2Patient)patient, source);
		}
		@Override
		public Iterable<Class<? super I2b2Visit>> getInstanceTypes() {
		return INSTANCE_TYPES;

histream-i2b2/src/test/java/de/sekmi/histream/i2b2/LocalHSQLDataSource.java

0 → 100644

+140 −0

Original line number	Diff line number	Diff line
		package de.sekmi.histream.i2b2;

		import java.io.BufferedReader;
		import java.io.IOException;
		import java.io.InputStream;
		import java.io.InputStreamReader;
		import java.io.PrintWriter;
		import java.nio.charset.StandardCharsets;
		import java.sql.Connection;
		import java.sql.DriverManager;
		import java.sql.ResultSet;
		import java.sql.SQLException;
		import java.sql.SQLFeatureNotSupportedException;
		import java.sql.Statement;
		import java.util.logging.Logger;

		import javax.sql.DataSource;

		// TODO move to query-i2b2-sql
		public class LocalHSQLDataSource implements DataSource{

		private PrintWriter pw;
		private static final String JDBC_URI = "jdbc:hsqldb:file:target/testdb_crcdata";

		public void delete() throws SQLException {
		try( Connection c = getConnection() ){
		Statement s = c.createStatement();
		s = c.createStatement();
		s.executeQuery("DROP SCHEMA PUBLIC CASCADE");
		s.close();
		}
		}

		private static void executeSQL(Connection dbc, BufferedReader lines) throws SQLException, IOException {
		StringBuilder stmt = new StringBuilder();
		String line;
		while( (line = lines.readLine()) != null ) {
		line = line.trim();
		if( line.trim().startsWith("--") ) {
		// ignore comment lines
		continue;
		}
		if( line.endsWith(";") ) {
		// append without ;
		stmt.append(line.substring(0, line.length()-1));
		// execute
		try( Statement s = dbc.createStatement() ){
		s.executeUpdate(stmt.toString());
		}
		// clear
		stmt = new StringBuilder();
		}else {
		stmt.append(line);
		}
		}
		}
		/**
		* Create the database and initialize it with the specified DDL statements
		* @param sql_ddl SQL DDL statements
		* @throws SQLException SQL error
		* @throws IOException IO error reading the DDL
		*/
		public void create(BufferedReader ... sql_ddl) throws SQLException, IOException {
		try( Connection dbc = DriverManager.getConnection(JDBC_URI+";create=true", "SA", "") ){
		for( BufferedReader ddl : sql_ddl ) {
		executeSQL(dbc, ddl);
		}
		}
		}

		public void createI2b2() throws SQLException, IOException {
		try( InputStream in = TestHSQLDataSource.class.getResourceAsStream("/i2b2_hsqldb_ddl_create.sql");
		BufferedReader rd = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8)) )
		{
		this.create(rd);
		}
		}
		public Integer executeCountQuery(String sql) throws SQLException {
		Integer ret = null;
		try( Connection c = getConnection();
		Statement s = c.createStatement();
		ResultSet rs = s.executeQuery(sql) )
		{
		if( rs.next() ) {
		ret = rs.getInt(1);
		}
		}
		return ret;
		}
		public LocalHSQLDataSource() {
		pw = new PrintWriter(System.out);
		}
		@Override
		public PrintWriter getLogWriter() throws SQLException {
		return pw;
		}

		@Override
		public void setLogWriter(PrintWriter out) throws SQLException {
		this.pw = out;
		}

		@Override
		public void setLoginTimeout(int seconds) throws SQLException {
		// TODO Auto-generated method stub

		}

		@Override
		public int getLoginTimeout() throws SQLException {
		// TODO Auto-generated method stub
		return 0;
		}

		@Override
		public Logger getParentLogger() throws SQLFeatureNotSupportedException {
		throw new SQLFeatureNotSupportedException();
		}

		@Override
		public <T> T unwrap(Class<T> iface) throws SQLException {
		throw new UnsupportedOperationException();
		}

		@Override
		public boolean isWrapperFor(Class<?> iface) throws SQLException {
		throw new UnsupportedOperationException();
		}

		@Override
		public Connection getConnection() throws SQLException {
		return getConnection("SA","");
		}

		@Override
		public Connection getConnection(String username, String password) throws SQLException {
		return DriverManager.getConnection(JDBC_URI+";ifexists=true", username, password);
		}

		}

histream-i2b2/src/test/java/de/sekmi/histream/i2b2/TestHSQLDataSource.java

0 → 100644

+20 −0

Original line number	Diff line number	Diff line
		package de.sekmi.histream.i2b2;

		import java.io.IOException;
		import java.sql.SQLException;

		import org.junit.Assert;
		import org.junit.Test;

		public class TestHSQLDataSource {

		@Test
		public void testCreateTables() throws IOException, SQLException {
		LocalHSQLDataSource ds = new LocalHSQLDataSource();
		ds.createI2b2();
		// perform queries
		Assert.assertEquals(0, ds.executeCountQuery("SELECT COUNT(*) FROM observation_fact").intValue());
		// drop database
		ds.delete();
		}
		}