Added the lacking try-with-resources.

Signed-off-by: Erwan Demairy <Erwan.Demairy@inria.fr>

modules/SemanticWebImport/src/main/java/fr/inria/edelweiss/semantic/analyzer/RdfAnalyzer.java

@@ -36,58 +36,58 @@ public class RdfAnalyzer implements LongTask, Runnable {
 	private ProgressTicket progressTicket;
 	private int fynLevel;
 
-	/**
-	 * Constructor.
-	 *
-	 * @param newModel Model to fill.
-	 * @param newSparqlRequest SPARQL request to fill with the model.
-	 */
-	public RdfAnalyzer(final GraphModel newModel, final String newSparqlRequest, final int fynLevel) {
-		super();
-		this.model = newModel;
-		this.sparqlRequest = newSparqlRequest;
-		this.fynLevel = fynLevel;
-		postProcessor = new EmptyPostProcessor();
-	}
-
-	@Override
-	public final void run() {
-		logger.info("Begin: Building the implementation relationships graph.");
-		int waitSeconds = 5;
-		Progress.start(progressTicket, waitSeconds);
-
-		try {
-			Progress.progress(progressTicket);
-			sparqlRequestResult = driver.sparqlQuery(sparqlRequest);
+    /**
+     * Constructor.
+     *
+     * @param newModel         Model to fill.
+     * @param newSparqlRequest SPARQL request to fill with the model.
+     */
+    public RdfAnalyzer(final GraphModel newModel, final String newSparqlRequest, final int fynLevel) {
+        super();
+        this.model = newModel;
+        this.sparqlRequest = newSparqlRequest;
+        this.fynLevel = fynLevel;
+        postProcessor = new EmptyPostProcessor();
+    }
+
+    @Override
+    public final void run() {
+        logger.info("Begin: Building the implementation relationships graph.");
+        int waitSeconds = 5;
+        Progress.start(progressTicket, waitSeconds);
+
+        try {
+            Progress.progress(progressTicket);
+            sparqlRequestResult = driver.sparqlQuery(sparqlRequest);
 
 			InputStream rdf = new ByteArrayInputStream(getSparqlRequestResult().getBytes(Charset.forName("UTF-8")));
 			RdfParser parser = new RdfParser(rdf, model, fynLevel);
 
-			Progress.progress(progressTicket);
-			parser.parse();
-			logger.log(Level.INFO, "Number of triples parsed: {0}", parser.getTripleNumber());
-		} catch (Exception e) {
-			logger.log(Level.INFO, "error when obtaining the nodes and edges: {0}", e.getMessage());
-			Exceptions.printStackTrace(e);
-		}
-
-		Progress.progress(progressTicket);
-		try {
-			saveResult(getSparqlRequestResult());
-		} catch (Exception e) {
-			logger.log(Level.INFO, "error when saving the result: {0}", e.getMessage());
-		}
-		Progress.progress(progressTicket);
-		postProcessor.setModel(model);
-		postProcessor.run();
-
-		logger.info("End: Building the implementation relationships graph.");
-		Progress.finish(progressTicket);
-	}
-
-	public final void setPostProcessing(final LayoutExamplePostProcessor newPostProcessor) {
-		this.postProcessor = newPostProcessor;
-	}
+            Progress.progress(progressTicket);
+            parser.parse();
+            logger.log(Level.INFO, "Number of triples parsed: {0}", parser.getTripleNumber());
+        } catch (Exception e) {
+            logger.log(Level.INFO, "error when obtaining the nodes and edges: {0}", e.getMessage());
+            Exceptions.printStackTrace(e);
+        }
+
+        Progress.progress(progressTicket);
+        try {
+            saveResult(getSparqlRequestResult());
+        } catch (Exception e) {
+            logger.log(Level.INFO, "error when saving the result: {0}", e.getMessage());
+        }
+        Progress.progress(progressTicket);
+        postProcessor.setModel(model);
+        postProcessor.run();
+
+        logger.info("End: Building the implementation relationships graph.");
+        Progress.finish(progressTicket);
+    }
+
+    public final void setPostProcessing(final LayoutExamplePostProcessor newPostProcessor) {
+        this.postProcessor = newPostProcessor;
+    }
 
 	public final void setSparqlEngine(final SparqlDriver newDriver) {
 		this.driver = newDriver;
@@ -101,30 +101,30 @@ public void setSaveResult(String saveResultName) {
 		this.saveResultName = saveResultName;
 	}
 
-	private void saveResult(String sparqlRequestResult) throws FileNotFoundException, IOException {
-		if (this.saveResultName.isEmpty()) {
-			return;
-		}
-		FileOutputStream fSave = new FileOutputStream(saveResultName);
-		fSave.write(sparqlRequestResult.getBytes());
-		fSave.close();
-	}
-
-	/**
-	 * @return the sparqlRequestResult
-	 */
-	public String getSparqlRequestResult() {
-		return sparqlRequestResult;
-	}
-
-	@Override
-	public boolean cancel() {
-		return true;
-	}
-
-	@Override
-	public void setProgressTicket(ProgressTicket pt) {
-		this.progressTicket = pt;
-	}
+    private void saveResult(String sparqlRequestResult) throws IOException {
+        if (this.saveResultName.isEmpty()) {
+            return;
+        }
+        try (var fSave = new FileOutputStream(saveResultName)) {
+            fSave.write(sparqlRequestResult.getBytes());
+        }
+    }
+
+    /**
+     * @return the sparqlRequestResult
+     */
+    public String getSparqlRequestResult() {
+        return sparqlRequestResult;
+    }
+
+    @Override
+    public boolean cancel() {
+        return true;
+    }
+
+    @Override
+    public void setProgressTicket(ProgressTicket pt) {
+        this.progressTicket = pt;
+    }
 
 }

modules/SemanticWebImport/src/main/java/fr/inria/edelweiss/semantic/configurationmanager/ConfigurationManager.java

@@ -200,20 +200,21 @@ static protected ArrayList<String> listFilesInJar(String jarName, String path) t
             path = path.substring(1);
         }
         ArrayList<String> result = new ArrayList<String>();
-        JarFile jar = new JarFile(jarName);
-        Enumeration<JarEntry> entries = jar.entries();
-        while (entries.hasMoreElements()) {
-            String name = entries.nextElement().getName();
-            logger.log(Level.INFO, "{0}", name);
-            if (name.startsWith(path)) { //filter according to the path
-                String entry = name.substring(path.length());
-                int checkSubdir = entry.indexOf("/");
-                if (checkSubdir >= 0) {
-                    // if it is a subdirectory, we just return the directory name
-                    entry = entry.substring(0, checkSubdir);
-                }
-                if (!entry.isEmpty()) {
-                    result.add(entry);
+        try (JarFile jar = new JarFile(jarName)) {
+            var entries = jar.entries();
+            while (entries.hasMoreElements()) {
+                var name = entries.nextElement().getName();
+                logger.log(Level.INFO, "{0}", name);
+                if (name.startsWith(path)) { //filter according to the path
+                    var entry = name.substring(path.length());
+                    int checkSubdir = entry.indexOf("/");
+                    if (checkSubdir >= 0) {
+                        // if it is a subdirectory, we just return the directory name
+                        entry = entry.substring(0, checkSubdir);
+                    }
+                    if (!entry.isEmpty()) {
+                        result.add(entry);
+                    }
                 }
             }
         }

modules/SemanticWebImport/src/main/java/fr/inria/edelweiss/semantic/importer/SemanticWebImportParser.java

@@ -63,104 +63,103 @@ public final void setRdfRequest(String nodeRdfRequest) {
 		}
 	}
 
-	public SemanticWebImportParser() {
-		this(new RequestParameters(""));
-	}
-
-	public SemanticWebImportParser(RequestParameters requests) {
-		this.parameters = requests;
-	}
-
-	/**
-	 * Asynchronous operation that fills the current workspace.
-	 *
-	 * @sa waitEndpopulateRDFGraph
-	 *
-	 * @param driverUsed SPARQL request driver.
-	 * @param properties Parameters to use.
-	 */
-	public final void populateRDFGraph(SparqlDriver driverUsed, Properties properties, LongTaskListener listener) {
-		this.listener = listener;
-		boolean resetWorkspace = Boolean.parseBoolean(properties.getProperty(PluginProperties.RESET_WORKSPACE.getValue(), "false"));
-		boolean postProcessing = Boolean.parseBoolean(properties.getProperty(PluginProperties.POST_PROCESSING.getValue(), "false"));
-		String saveResultName = properties.getProperty(PluginProperties.SAVE_SPARQL_RESULT.getValue(), "");
-		int fynLevel = Integer.parseInt(properties.getProperty(PluginProperties.FYN_LEVEL.getValue(), "0"));
-
-		logger.log(Level.INFO, "resetWorkspace = {0}", resetWorkspace);
-		logger.log(Level.INFO, "postProcessing = {0}", postProcessing);
-
-		this.driver = driverUsed;
-		this.driver.setPluginProperties(properties);
-
-		GephiUtils.createProjectIfEmpty();
-		GephiUtils.createWorkspaceIfEmpty();
-
-		pc = Lookup.getDefault().lookup(ProjectController.class);
-		Workspace dataWorkspace = pc.getCurrentWorkspace();
-		GraphModel model = getCurrentGraphModel(dataWorkspace);
-		// @TODO how to reset the graph
+    public SemanticWebImportParser() {
+        this(new RequestParameters(""));
+    }
+
+    public SemanticWebImportParser(RequestParameters requests) {
+        this.parameters = requests;
+    }
+
+    /**
+     * Asynchronous operation that fills the current workspace.
+     *
+     * @param driverUsed SPARQL request driver.
+     * @param properties Parameters to use.
+     * @sa waitEndpopulateRDFGraph
+     */
+    public final void populateRDFGraph(SparqlDriver driverUsed, Properties properties, LongTaskListener listener) {
+        this.listener = listener;
+        boolean resetWorkspace = Boolean.parseBoolean(properties.getProperty(PluginProperties.RESET_WORKSPACE.getValue(), "false"));
+        boolean postProcessing = Boolean.parseBoolean(properties.getProperty(PluginProperties.POST_PROCESSING.getValue(), "false"));
+        String saveResultName = properties.getProperty(PluginProperties.SAVE_SPARQL_RESULT.getValue(), "");
+        int fynLevel = Integer.parseInt(properties.getProperty(PluginProperties.FYN_LEVEL.getValue(), "0"));
+
+        logger.log(Level.INFO, "resetWorkspace = {0}", resetWorkspace);
+        logger.log(Level.INFO, "postProcessing = {0}", postProcessing);
+
+        this.driver = driverUsed;
+        this.driver.setPluginProperties(properties);
+
+        GephiUtils.createProjectIfEmpty();
+        GephiUtils.createWorkspaceIfEmpty();
+
+        pc = Lookup.getDefault().lookup(ProjectController.class);
+        Workspace dataWorkspace = pc.getCurrentWorkspace();
+        GraphModel model = getCurrentGraphModel(dataWorkspace);
+        // @TODO how to reset the graph
 //        if (resetWorkspace) {
 //            model.getNodeTable().clear();
 //        }
-		Table nodeTable = model.getNodeTable();
-		if (!nodeTable.hasColumn("namespace")) {
-			nodeTable.addColumn("namespace", String.class);
-		}
-
-		analyzer = initAnalyzer(model, parameters.getRdfRequest(), fynLevel);
-		analyzer.setSaveResult(saveResultName);
-		if (postProcessing) {
-			LayoutExamplePostProcessor postProcessor = new LayoutExamplePostProcessor();
-			analyzer.setPostProcessing(postProcessor);
-		}
-		executor.setLongTaskListener(this);
-		executor.execute(analyzer, analyzer, "Importing Semantic Graph", new LongTaskErrorHandler() {
-			@Override
-			public void fatalError(Throwable thrwbl) {
-				thrwbl.printStackTrace();
-			}
-		});
-
-	}
-
-	@Override
-	public void taskFinished(LongTask lt) {
-		if (waitEndPopulate.availablePermits() < 1) {
-			waitEndPopulate.release();
-		}
-		listener.taskFinished(lt);
-	}
-
-	public final void waitEndpopulateRDFGraph() throws InterruptedException {
-		waitEndPopulate.acquire();
-	}
-
-	private RdfAnalyzer initAnalyzer(GraphModel model, String rdfRequest, int fynLevel) {
-		driver.init();
-		RdfAnalyzer localAnalyzer = new RdfAnalyzer(model, rdfRequest, fynLevel);
-		localAnalyzer.setSparqlEngine(driver);
-		return localAnalyzer;
-	}
-
-	public RequestParameters getParameters() {
-		return parameters;
-	}
-
-	public void setParameters(RequestParameters newParameters) {
-		this.parameters = newParameters;
-	}
-
-	private GraphModel getCurrentGraphModel(final Workspace currentWorkspace) {
-		final GraphController currentGraphController = Lookup.getDefault().lookup(GraphController.class);
-		return currentGraphController.getGraphModel(currentWorkspace);
-	}
-
-	/**
-	 * @return the rdfGraph
-	 */
-	public Graph getRdfGraph() {
-		return this.rdfGraph;
-	}
+        Table nodeTable = model.getNodeTable();
+        if (!nodeTable.hasColumn("namespace")) {
+            nodeTable.addColumn("namespace", String.class);
+        }
+
+        analyzer = initAnalyzer(model, parameters.getRdfRequest(), fynLevel);
+        analyzer.setSaveResult(saveResultName);
+        if (postProcessing) {
+            LayoutExamplePostProcessor postProcessor = new LayoutExamplePostProcessor();
+            analyzer.setPostProcessing(postProcessor);
+        }
+        executor.setLongTaskListener(this);
+        executor.execute(analyzer, analyzer, "Importing Semantic Graph", new LongTaskErrorHandler() {
+            @Override
+            public void fatalError(Throwable thrwbl) {
+                thrwbl.printStackTrace();
+            }
+        });
+
+    }
+
+    @Override
+    public void taskFinished(LongTask lt) {
+        if (waitEndPopulate.availablePermits() < 1) {
+            waitEndPopulate.release();
+        }
+        listener.taskFinished(lt);
+    }
+
+    public final void waitEndpopulateRDFGraph() throws InterruptedException {
+        waitEndPopulate.acquire();
+    }
+
+    private RdfAnalyzer initAnalyzer(GraphModel model, String rdfRequest, int fynLevel) {
+        driver.init();
+        RdfAnalyzer localAnalyzer = new RdfAnalyzer(model, rdfRequest, fynLevel);
+        localAnalyzer.setSparqlEngine(driver);
+        return localAnalyzer;
+    }
+
+    public RequestParameters getParameters() {
+        return parameters;
+    }
+
+    public void setParameters(RequestParameters newParameters) {
+        this.parameters = newParameters;
+    }
+
+    private GraphModel getCurrentGraphModel(final Workspace currentWorkspace) {
+        final GraphController currentGraphController = Lookup.getDefault().lookup(GraphController.class);
+        return currentGraphController.getGraphModel(currentWorkspace);
+    }
+
+    /**
+     * @return the rdfGraph
+     */
+    public Graph getRdfGraph() {
+        return this.rdfGraph;
+    }
 
 	public String getLastRdfResult() {
 		return analyzer.getSparqlRequestResult();

modules/SemanticWebImport/src/main/java/fr/inria/edelweiss/semantic/importer/SemanticWebImporterPanel.java

@@ -7,6 +7,7 @@
 package fr.inria.edelweiss.semantic.importer;
 
 import fr.inria.edelweiss.sparql.corese.CoreseDriver;
+
 import java.util.List;
 
 /**

modules/SemanticWebImport/src/main/java/fr/inria/edelweiss/sparql/GephiUtils.java

@@ -95,17 +95,17 @@ public static float convertFloat(final String id) {
 		return decodedNum;
 	}
 
-	// Get values of color size RGB (0->1)
-	public static float convertFloatColor(final String id) {
-		float decodedNum = 0, temp;
-		try {
-			temp = Float.parseFloat(id.replaceAll("\"", "\\\""));
-			decodedNum = (temp % 256) / 255;
-		} catch (NumberFormatException ex) {
-			Exceptions.printStackTrace(ex);
-		}
-		return decodedNum;
-	}
+    // Get values of color size RGB (0->1)
+    public static float convertFloatColor(final String id) {
+        float decodedNum = 0, temp;
+        try {
+            temp = Float.parseFloat(id.replaceAll("\"", "\\\""));
+            decodedNum = (temp % 256) / 255;
+        } catch (NumberFormatException ex) {
+            Exceptions.printStackTrace(ex);
+        }
+        return decodedNum;
+    }
 
 	//Split color values RGB (0,0,0)
 	public static String[] stringSplit(final String id) {

modules/SemanticWebImport/src/main/java/fr/inria/edelweiss/sparql/corese/CoreseDriver.java

@@ -154,15 +154,15 @@ private void load_resource(final String fileName) throws LoadException {
      */
     private void load_resource_workaround(final String fileName) throws IOException, LoadException {
         int dotPos = fileName.lastIndexOf('.');
-        File tempFile = File.createTempFile("corese_input", '.' + fileName.substring(dotPos + 1, fileName.length()));
-        FileWriter outputTempFile = new FileWriter(tempFile);
-        final BufferedReader resource = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(fileName)));
-        String currentLine;
-        while ((currentLine = resource.readLine()) != null) {
-            outputTempFile.write(currentLine + '\n');
+        var tempFile = File.createTempFile("corese_input", '.' + fileName.substring(dotPos + 1, fileName.length()));
+        try (FileWriter outputTempFile = new FileWriter(tempFile);
+             var resource = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(fileName)))
+        ) {
+            String currentLine;
+            while ((currentLine = resource.readLine()) != null) {
+                outputTempFile.write(currentLine + '\n');
+            }
         }
-        resource.close();
-        outputTempFile.close();
         loader.parse(tempFile.getAbsolutePath());
     }
 

modules/SemanticWebImport/src/main/java/fr/inria/wimmics/semanticweb/filter/instance/InstanceFilter.java

@@ -59,14 +59,15 @@ public void setType(String newType) {
 
     @Override
     public Graph filter(Graph graph) {
-        Formatter getSubtypesOfrequest = new Formatter().format(GET_ALLTYPES_OF, type);
-        String[][] nodesToKeepList = SemanticWebImportMainWindowTopComponent.getSparqlRequester().selectOnGraph(getSubtypesOfrequest.toString());
-        HashSet<String> nodesToKeepSet = convertStringArrayToSet(nodesToKeepList);
+        try (Formatter getSubtypesOfrequest = new Formatter().format(GET_ALLTYPES_OF, type)) {
+            String[][] nodesToKeepList = SemanticWebImportMainWindowTopComponent.getSparqlRequester().selectOnGraph(getSubtypesOfrequest.toString());
+            HashSet<String> nodesToKeepSet = convertStringArrayToSet(nodesToKeepList);
 
-        Node[] nodes = graph.getNodes().toArray();
-        for (Node node : nodes) {
-            if (!nodesToKeepSet.contains((String)node.getId())) {
-                graph.removeNode(node);
+            Node[] nodes = graph.getNodes().toArray();
+            for (Node node : nodes) {
+                if (!nodesToKeepSet.contains((String) node.getId())) {
+                    graph.removeNode(node);
+                }
             }
         }
         return graph;

modules/SemanticWebImport/src/main/java/fr/inria/wimmics/semanticweb/filter/sparql/SPARQLFilterPanel.java

@@ -9,6 +9,7 @@
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
+
 /**
  *
  * @author Erwan Demairy <Erwan.Demairy@inria.fr>
@@ -51,22 +52,22 @@ private void initComponents() {
         javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
         this.setLayout(layout);
         layout.setHorizontalGroup(
-            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addGroup(layout.createSequentialGroup()
-                .addContainerGap()
-                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addComponent(sparqlRequestEditor, javax.swing.GroupLayout.DEFAULT_SIZE, 431, Short.MAX_VALUE)
-                    .addComponent(updateButton, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
-                .addContainerGap())
+                layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                        .addGroup(layout.createSequentialGroup()
+                                .addContainerGap()
+                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                                        .addComponent(sparqlRequestEditor, javax.swing.GroupLayout.DEFAULT_SIZE, 431, Short.MAX_VALUE)
+                                        .addComponent(updateButton, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                                .addContainerGap())
         );
         layout.setVerticalGroup(
-            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addGroup(layout.createSequentialGroup()
-                .addContainerGap()
-                .addComponent(sparqlRequestEditor, javax.swing.GroupLayout.PREFERRED_SIZE, 128, javax.swing.GroupLayout.PREFERRED_SIZE)
-                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addComponent(updateButton)
-                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                        .addGroup(layout.createSequentialGroup()
+                                .addContainerGap()
+                                .addComponent(sparqlRequestEditor, javax.swing.GroupLayout.PREFERRED_SIZE, 128, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                                .addComponent(updateButton)
+                                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
     }// </editor-fold>//GEN-END:initComponents
 

modules/SemanticWebImport/src/main/java/fr/inria/wimmics/semanticweb/filter/type/TypeFilter.java

@@ -66,18 +66,18 @@ public void setType(String newType) {
 
     @Override
     public Graph filter(Graph graph) {
-        Formatter getSubtypesOfrequest = new Formatter().format(GET_SUBTYPES_OF, type);
+        try (Formatter getSubtypesOfrequest = new Formatter().format(GET_SUBTYPES_OF, type)) {
 
-        String[][] nodesToKeepList = SemanticWebImportMainWindowTopComponent.getSparqlRequester().selectOnGraph(getSubtypesOfrequest.toString());
-        HashSet<String> nodesToKeepSet = convertStringArrayToSet(nodesToKeepList);
+            String[][] nodesToKeepList = SemanticWebImportMainWindowTopComponent.getSparqlRequester().selectOnGraph(getSubtypesOfrequest.toString());
+            HashSet<String> nodesToKeepSet = convertStringArrayToSet(nodesToKeepList);
 
-        Node[] nodes = graph.getNodes().toArray();
-        for (Node node : nodes) {
-            if (!nodesToKeepSet.contains((String)node.getId())) {
-                graph.removeNode(node);
+            Node[] nodes = graph.getNodes().toArray();
+            for (Node node : nodes) {
+                if (!nodesToKeepSet.contains((String) node.getId())) {
+                    graph.removeNode(node);
+                }
             }
         }
-
         return graph;
     }