database testing with embedded hsql database.

junit tests for visit and patient store

histream-i2b2/pom.xml

@@ -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

@@ -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

@@ -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

+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

+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();
+	}
+}

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

@@ -25,11 +25,54 @@ import java.io.Closeable;
 import java.io.IOException;
 import java.sql.DriverManager;
 import java.sql.SQLException;
+import java.time.Instant;
 
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.i2b2.PostgresPatientStore;
+import de.sekmi.histream.impl.ExternalSourceImpl;
 public class TestPostgresPatientStore implements Closeable {
 	PostgresPatientStore store;
+	LocalHSQLDataSource ds;
+	
+	@Before
+	public void createDatabase() throws SQLException, IOException {
+		ds = new LocalHSQLDataSource();
+		ds.delete();
+		ds.createI2b2();
+	}
+
+	private void openPatientStore() throws SQLException {
+		store = new PostgresPatientStore();
+		store.open(ds.getConnection(), "test", new DataDialect());
+	}
+	@After
+	public void cleanupDatabase() throws SQLException, IOException {
+		if( store != null ) {
+			store.close();
+		}
+		ds.delete();
+	}
 	
+	@Test
+	public void insertPatient() throws IOException, SQLException {
+		ExternalSourceType t = new ExternalSourceImpl("junit", Instant.now());
+		openPatientStore();
+		store.createInstance("ABC001", t);
+		store.flush();
+		store.close();
+		store = null;
+		// reload store from database
+		openPatientStore();
+		// attempt to load previously stored patient
+		I2b2Patient p = store.retrieve("ABC001");
+		Assert.assertNotNull(p);
+	}
+
 	public void open(String  host, int port, String user, String password, String projectId) throws ClassNotFoundException, SQLException{
 		store = new PostgresPatientStore();
 		store.open(DriverManager.getConnection("jdbc:postgresql://"+host+":"+port+"/i2b2", user, password),projectId, new DataDialect());

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

@@ -25,15 +25,76 @@ import java.io.Closeable;
 import java.io.IOException;
 import java.sql.DriverManager;
 import java.sql.SQLException;
+import java.time.Instant;
 
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import de.sekmi.histream.DateTimeAccuracy;
+import de.sekmi.histream.ext.ExternalSourceType;
 import de.sekmi.histream.i2b2.PostgresVisitStore;
+import de.sekmi.histream.impl.ExternalSourceImpl;
 
 public class TestPostgresVisitStore implements Closeable {
-	private PostgresVisitStore store;
+	private PostgresVisitStore vs;
+	private PostgresPatientStore ps;
+	LocalHSQLDataSource ds;
+	
+	@Before
+	public void createDatabase() throws SQLException, IOException {
+		ds = new LocalHSQLDataSource();
+		ds.delete();
+		ds.createI2b2();
+	}
+
+	private void openVisitStore() throws SQLException {
+		ps = new PostgresPatientStore();
+		ps.open(ds.getConnection(), "test", new DataDialect());
+		vs = new PostgresVisitStore();
+		vs.open(ds.getConnection(), "test", new DataDialect());
+	}
+	@After
+	public void cleanupDatabase() throws SQLException, IOException {
+		if( vs != null ) {
+			vs.close();
+		}
+		if( ps != null ) {
+			ps.close();
+		}
+		ds.delete();
+	}
+
+	@Test
+	public void insertVisit() throws IOException, SQLException {
+		ExternalSourceType t = new ExternalSourceImpl("junit", Instant.now());
+		openVisitStore();
+
+		// create patient
+		I2b2Patient pat = ps.createInstance("ABC001", t);
+		I2b2Visit v = vs.createInstance("VIS001", pat, t);
+		v.setStartTime(new DateTimeAccuracy(Instant.now()));
+		v = vs.findVisit("VIS001");
+		Assert.assertEquals("ABC001",v.getPatientId());
+		// TODO reload store from database
+		vs.close();
+		vs = null;
+		ps.close();
+		ps = null;
+
+		// attempt to load previously stored patient
+		openVisitStore();
+		v = vs.findVisit("VIS001");		
+		Assert.assertNotNull(v);
+		Assert.assertEquals("ABC001",v.getPatientId());
+	}
+
+
 
 	public void open(String  host, int port) throws ClassNotFoundException, SQLException{
-		store = new PostgresVisitStore();
-		store.open(DriverManager.getConnection("jdbc:postgresql://"+host+":"+port+"/i2b2", "i2b2demodata", "demodata"), "demo", new DataDialect());
+		vs = new PostgresVisitStore();
+		vs.open(DriverManager.getConnection("jdbc:postgresql://"+host+":"+port+"/i2b2", "i2b2demodata", "demodata"), "demo", new DataDialect());
 	}
 	
 	private void open()throws Exception{
@@ -42,15 +103,15 @@ public class TestPostgresVisitStore implements Closeable {
 	
 	@Override
 	public void close() throws IOException{
-		store.close();
+		vs.close();
 	}
 	
-	public PostgresVisitStore getStore(){ return store; }
+	public PostgresVisitStore getStore(){ return vs; }
 	
 	public static void main(String args[]) throws Exception{
 		TestPostgresVisitStore t = new TestPostgresVisitStore();
 		t.open();
-		System.out.println("Current visit cache size: "+t.store.size());
+		System.out.println("Current visit cache size: "+t.vs.size());
 		t.close();
 	}
 }

histream-i2b2/src/test/resources/i2b2_hsqldb_data.sql

+-- demo data for testing query executions via SQL
+
+INSERT INTO patient_dimension(patient_num,vital_status_cd,birth_date,sex_cd)VALUES(1001, NULL, '2001-01-01','F');
+INSERT INTO patient_dimension(patient_num,vital_status_cd,birth_date,sex_cd)VALUES(1002, NULL, '2002-02-02','M');
+INSERT INTO patient_dimension(patient_num,vital_status_cd,birth_date,sex_cd)VALUES(1003, NULL, '2003-03-03','F');
+
+INSERT INTO visit_dimension(encounter_num,patient_num,active_status_cd,start_date)VALUES(2001, 1001, NULL, '2011-01-01 01:00:00');
+INSERT INTO visit_dimension(encounter_num,patient_num,active_status_cd,start_date)VALUES(2002, 1001, NULL, '2011-01-02 02:00:00');
+INSERT INTO visit_dimension(encounter_num,patient_num,active_status_cd,start_date)VALUES(2003, 1001, NULL, '2011-01-03 03:00:00');
+INSERT INTO visit_dimension(encounter_num,patient_num,active_status_cd,start_date)VALUES(2004, 1002, NULL, '2011-01-01 01:00:00');
+INSERT INTO visit_dimension(encounter_num,patient_num,active_status_cd,start_date)VALUES(2005, 1002, NULL, '2011-01-02 02:00:00');
+
+INSERT INTO observation_fact(encounter_num,patient_num,start_date,concept_cd)VALUES(2001,1001,'2011-01-01 01:01:00','ICD10GM:F30.0');
+INSERT INTO observation_fact(encounter_num,patient_num,start_date,concept_cd)VALUES(2001,1001,'2011-01-01 01:02:00','ICD10GM:F30.8');
+INSERT INTO observation_fact(encounter_num,patient_num,start_date,concept_cd)VALUES(2002,1001,'2011-01-02 01:01:00','ICD10GM:Y36.9!');
+INSERT INTO observation_fact(encounter_num,patient_num,start_date,concept_cd)VALUES(2004,1002,'2011-01-01 01:01:00','ICD10GM:Y36.9!');
+COMMIT;

histream-i2b2/src/test/resources/i2b2_hsqldb_ddl_create.sql

+-- demo data for testing query executions via SQL
+
+CREATE TABLE observation_fact(
+	encounter_num INTEGER NOT NULL, 
+	patient_num INTEGER NOT NULL, 
+	concept_cd VARCHAR(50) NOT NULL,
+	provider_id VARCHAR(50) NULL,
+	start_date DATETIME NOT NULL,
+	modifier_cd VARCHAR(50) NULL,
+	instance_num INTEGER NULL,
+	valtype_cd VARCHAR(50) NULL,
+	tval_char VARCHAR(255) NULL,
+	nval_num DECIMAL(18,5) NULL,
+	units_cd VARCHAR(50) NULL,
+	end_date DATETIME NULL,
+	location_cd VARCHAR(50) NULL,
+	update_date DATETIME NULL,
+	download_date DATETIME NULL,
+	import_date DATETIME NULL,
+	sourcesystem_cd VARCHAR(50) NULL
+);
+CREATE TABLE patient_dimension(
+	patient_num INTEGER NOT NULL,
+	vital_status_cd VARCHAR(3) NULL,
+	birth_date DATETIME NULL,
+	death_date DATETIME NULL,
+	sex_cd VARCHAR(8) NULL,
+	update_date DATETIME NULL,
+	download_date DATETIME NULL,
+	import_date DATETIME NULL,
+	sourcesystem_cd VARCHAR(50) NULL
+);
+CREATE TABLE patient_mapping(
+	patient_ide VARCHAR(200) NOT NULL,
+	patient_ide_source VARCHAR(50) NOT NULL,
+	patient_num INTEGER NOT NULL,
+	patient_ide_status VARCHAR(50) NULL,
+	project_id VARCHAR(50) NOT NULL,
+	update_date DATETIME NULL,
+	download_date DATETIME NULL,
+	import_date DATETIME NULL,
+	sourcesystem_cd VARCHAR(50) NULL
+);
+
+CREATE TABLE visit_dimension(
+	encounter_num INTEGER NOT NULL,
+	patient_num INTEGER NOT NULL,
+	active_status_cd VARCHAR(3) NULL,
+	start_date DATETIME NULL,
+	end_date DATETIME NULL,
+	inout_cd VARCHAR(8) NULL,
+	location_cd VARCHAR(64) NULL,
+	update_date DATETIME NULL,
+	download_date DATETIME NULL,
+	import_date DATETIME NULL,
+	sourcesystem_cd VARCHAR(50) NULL
+);
+-- references to patient_ide, patient_ide_source NULL??
+CREATE TABLE encounter_mapping(
+	encounter_ide VARCHAR(200) NOT NULL,
+	encounter_ide_source VARCHAR(50) NOT NULL,
+	project_id VARCHAR(50) NOT NULL,
+	encounter_num INTEGER NOT NULL,
+	patient_ide VARCHAR(200) NULL, 
+	patient_ide_source VARCHAR(50) NULL,
+	encounter_ide_status VARCHAR(50) NULL,
+	update_date DATETIME NULL,
+	download_date DATETIME NULL,
+	import_date DATETIME NULL,
+	sourcesystem_cd VARCHAR(50) NULL
+);

histream-i2b2/src/test/resources/i2b2_hsqldb_ddl_drop.sql

+DROP TABLE observation_fact;
+DROP TABLE patient_dimension;
+DROP TABLE visit_dimension;