Potential resource leaks closed

HIStream-i2b2/src/main/java/de/sekmi/histream/i2b2/PostgresPatientStore.java

@@ -141,9 +141,9 @@ public class PostgresPatientStore extends PostgresExtension<I2b2Patient> impleme
 
 
 	private void loadMaxPatientNum() throws SQLException{
-		Statement s = db.createStatement();
-		String sql = "SELECT MAX(patient_num) FROM patient_dimension";
-		try( ResultSet rs = s.executeQuery(sql) ){
+		try( Statement s = db.createStatement() ){
+			String sql = "SELECT MAX(patient_num) FROM patient_dimension";
+			ResultSet rs = s.executeQuery(sql);
 			if( rs.next() ){
 				maxPatientNum = rs.getInt(1);
 			}else{
@@ -151,6 +151,7 @@ public class PostgresPatientStore extends PostgresExtension<I2b2Patient> impleme
 				// start numbering patients with 1
 				maxPatientNum = 1;
 			}
+			rs.close();
 		}
 		log.info("MAX(patient_num) = "+maxPatientNum);
 	}

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

@@ -113,9 +113,9 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit>{
 	}
 	
 	private void loadMaxEncounterNum() throws SQLException{
-		Statement s = db.createStatement();
-		String sql = "SELECT MAX(encounter_num) FROM visit_dimension";
-		try( ResultSet rs = s.executeQuery(sql) ){
+		try( Statement s = db.createStatement() ){
+			String sql = "SELECT MAX(encounter_num) FROM visit_dimension";
+			ResultSet rs = s.executeQuery(sql);
 			if( rs.next() ){
 				maxEncounterNum = rs.getInt(1);
 			}else{
@@ -123,6 +123,7 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit>{
 				// start numbering patients with 1
 				maxEncounterNum = 1;
 			}
+			rs.close();
 		}
 		log.info("MAX(encounter_num) = "+maxEncounterNum);
 	}
@@ -143,6 +144,7 @@ public class PostgresVisitStore extends PostgresExtension<I2b2Visit>{
 				count ++;
 			}
 		}
+		stmt.close();
 		log.info("Loaded MAX(instance_num) for "+count+" encounters");
 		if( noMatch != 0 ){
 			log.warning("Encountered "+noMatch+" encounter_num in observation_fact without matching visits");

HIStream-i2b2/src/main/java/de/sekmi/histream/i2b2/ont/Import.java

@@ -4,6 +4,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.StringWriter;
 import java.sql.Connection;
 import java.sql.DriverManager;
@@ -75,14 +76,17 @@ public class Import implements AutoCloseable{
 		deleteConcepts.setString(1, sourceId);
 		count = deleteConcepts.executeUpdate();
 		System.out.println("Deleted "+count+" rows from "+getConceptTable());
+		deleteConcepts.close();
 
 		deleteAccess.setString(1, sourceId+"%");
 		count = deleteAccess.executeUpdate();
 		System.out.println("Deleted "+count+" rows from "+getAccessTable());
+		deleteAccess.close();
 
 		deleteOnt.setString(1, sourceId);
 		count = deleteOnt.executeUpdate();
 		System.out.println("Deleted "+count+" rows from "+getMetaTable());
+		deleteOnt.close();
 
 	}
 	
@@ -409,7 +413,9 @@ public class Import implements AutoCloseable{
 		}
 
 		Properties ont_props = new Properties();
-		ont_props.load(new FileInputStream(ontConfig));
+		try( InputStream in = new FileInputStream(ontConfig) ){
+			ont_props.load(in);
+		}
 
 		String ontClass = ont_props.getProperty("ontology.class");
 		if( ontClass == null ){
@@ -422,7 +428,10 @@ public class Import implements AutoCloseable{
 
 		// open database
 		props = new Properties();
-		props.load(new FileInputStream(impConfig));
+		try( InputStream in = new FileInputStream(impConfig) ){
+			props.load(in);
+		}
+		
 		try {
 			o.openDatabase((Map)props);
 		} catch (ClassNotFoundException e) {

HIStream-i2b2/src/main/java/de/sekmi/histream/i2b2/services/HiveServer.java

@@ -3,6 +3,7 @@ package de.sekmi.histream.i2b2.services;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
+import java.io.Reader;
 import java.io.StringReader;
 import java.nio.file.FileSystem;
 import java.nio.file.FileSystems;
@@ -54,21 +55,14 @@ public class HiveServer implements Provider<Source>{
 		//scriptEngine = scriptManager.getEngineByName("nashorn");
 		// load scripts
 	}
-	public void loadMainScript(){
+	public void loadMainScript() throws IOException, ScriptException{
 		scriptEngine = scriptManager.getEngineByName("nashorn");
-		try {
-			scriptEngine.eval(new FileReader(scriptDir.resolve("main.js").toFile()));
+		try( Reader scriptFile = new FileReader(scriptDir.resolve("main.js").toFile()) ) {
+			scriptEngine.eval(scriptFile);
 			Object o = scriptEngine.eval("typeof httpRequest === 'function'");
 			if( o == null || !(o instanceof Boolean) || ((Boolean)o) != true ){
 				throw new ScriptException("global function 'httpRequest(?,?,?,?)' needed");
 			}
-		} catch (ScriptException e) {
-			e.printStackTrace();
-			scriptEngine = null;
-		} catch (FileNotFoundException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			scriptEngine = null;
 		}
 	}
 	
@@ -83,7 +77,12 @@ public class HiveServer implements Provider<Source>{
 				break;
 			}
 			System.out.println("Reloading scripts..");
-			loadMainScript();
+			try {
+				loadMainScript();
+			} catch (IOException | ScriptException e1) {
+				System.err.println("Error loading script");
+				e1.printStackTrace();
+			}
 			// pollEvents() is needed for the key to reset properly
 			for( WatchEvent<?> e : key.pollEvents() ){
 				if( e == null )continue;// noop
@@ -95,7 +94,9 @@ public class HiveServer implements Provider<Source>{
 			}
 		}
 	}
-	public void loadScipts()throws IOException{
+	@SuppressWarnings("resource") // cannot close default filesystem
+	public void loadScipts()throws IOException, ScriptException{
+		
 		FileSystem fs = FileSystems.getDefault();
 		scriptDir = fs.getPath("src", "main", "scripts", "i2b2-ws");
 		if( !Files.isDirectory(scriptDir) )throw new FileNotFoundException("Script dir not found: "+scriptDir);
@@ -118,7 +119,7 @@ public class HiveServer implements Provider<Source>{
 			}
 		}*/
 	}
-	public static void main(String args[]) throws IOException{
+	public static void main(String args[]) throws IOException, ScriptException{
 		HiveServer hs = new HiveServer();
 		hs.loadScipts();
 		Endpoint e = Endpoint.create(HTTPBinding.HTTP_BINDING, hs);

histream-core/src/main/java/de/sekmi/histream/impl/RunConfiguration.java

@@ -150,6 +150,7 @@ public class RunConfiguration implements Closeable{
 		if( inputStream != null ){
 			Properties props = new Properties();
 			props.load(inputStream);
+			inputStream.close();
 			version = props.getProperty("version","[unknown]");
 		}else{
 			// file is not run from jar
@@ -200,6 +201,7 @@ public class RunConfiguration implements Closeable{
 				if( p != null ){
 					System.out.println("ETL("+p.getMeta("etl.strategy")+"): "+file);
 					rc.processFile(p);
+					p.close();
 				}else{
 					System.err.println("Unable to find parser for file "+file);
 				}

histream-core/src/main/java/de/sekmi/histream/io/FlatProviderFactory.java

@@ -40,6 +40,7 @@ public class FlatProviderFactory implements FileObservationSupplierFactory, Plug
 		// don't need to close anything
 	}
 
+	@SuppressWarnings("resource")
 	@Override
 	public ObservationSupplier forFile(File file, ObservationFactory factory) throws IOException {
 		return new FlatObservationSupplier(factory, new FileInputStream(file));

histream-core/src/test/java/de/sekmi/histream/io/TransformerTest.java

@@ -9,18 +9,20 @@ import org.junit.Test;
 
 public class TransformerTest {
 	
+	@SuppressWarnings("resource")
 	@Test
 	public void testPullTransformerIdentity() throws FileNotFoundException, IOException{
 		FileObservationProviderTest f = new FileObservationProviderTest();
 		f.initializeObservationFactory();
 
 		Transformation t = Transformation.Identity;
-		FlatObservationSupplier sup = new FlatObservationSupplier(f.getFactory(), new FileInputStream("examples/dwh-flat.txt"));
-		PullTransformer p = new PullTransformer(sup, t);
-		
-		// validate content after identity transformation
-		f.initializeHandler();
-		f.validateExample(p);
-		f.closeHandler();
+		try( FlatObservationSupplier sup = new FlatObservationSupplier(f.getFactory(), new FileInputStream("examples/dwh-flat.txt")) ){
+			PullTransformer p = new PullTransformer(sup, t);
+			
+			// validate content after identity transformation
+			f.initializeHandler();
+			f.validateExample(p);
+			f.closeHandler();
+		}
 	}
 }