code: remove warning

haas-java-client/src/test/java/cz/it4i/fiji/haas_java_client/TestHaaSJavaClientWithSPIM.java

 package cz.it4i.fiji.haas_java_client;
 
+import static cz.it4i.fiji.haas_java_client.LambdaExceptionHandlerWrapper.wrap;
+
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -7,20 +9,17 @@ import java.nio.file.Paths;
 import java.util.Collections;
 import java.util.stream.StreamSupport;
 
-import javax.xml.rpc.ServiceException;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import cz.it4i.fiji.haas_java_client.HaaSClient.SynchronizableFiles;
 import cz.it4i.fiji.haas_java_client.proxy.JobFileContentExt;
-import static cz.it4i.fiji.haas_java_client.LambdaExceptionHandlerWrapper.wrap;
 
 public class TestHaaSJavaClientWithSPIM {
 
 	private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas_java_client.TestHaaSJavaClientWithSPIM.class);
 
-	public static void main(String[] args) throws ServiceException, IOException {
+	public static void main(String[] args) throws IOException {
 		HaaSClient client = new HaaSClient(SettingsProvider.getSettings("DD-17-31", TestingConstants.CONFIGURATION_FILE_NAME));
 		Path baseDir = Paths.get("/home/koz01/Work/vyzkumnik/fiji/work/aaa");
 

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/FileLock.java

 package cz.it4i.fiji.haas_spim_benchmark.commands;
 
 import java.io.Closeable;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.channels.FileChannel;
 import java.nio.channels.OverlappingFileLockException;
@@ -22,7 +21,7 @@ public class FileLock implements Closeable {
 
 	private java.nio.channels.FileLock lock;
 
-	public FileLock(Path lockPath) throws FileNotFoundException {
+	public FileLock(Path lockPath) {
 		this.localPath = lockPath;
 	}
 

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/ManageSPIMBenchmark.java

@@ -64,30 +64,26 @@ public class ManageSPIMBenchmark implements Command {
 			if (!Files.isDirectory(workingDirPath)) {
 				Files.createDirectories(workingDirPath);
 			}
+			@SuppressWarnings("resource")
 			final FileLock fl = new FileLock(workingDirPath.resolve(LOCK_FILE_NAME));
 			if(!fl.tryLock()) {
 				uiService.showDialog("Working directory is already used by someone else", MessageType.ERROR_MESSAGE);
 				return;
 			}
-			try {
-				final BenchmarkSPIMWindow dialog = new BenchmarkSPIMWindow(null,
-						new BenchmarkSPIMParametersImpl(userName, password, Constants.PHONE, email, workingDirPath));
-				dialog.executeAdjustment(() -> {
-					dialog.setTitle(Constants.MENU_ITEM_NAME + " " + Constants.SUBMENU_ITEM_NAME);
-					dialog.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
-					dialog.addWindowListener(new WindowAdapter() {
-						@Override
-						public void windowClosing(final WindowEvent e) {
-							super.windowClosing(e);
-							fl.close();
-						}
-					});
-					dialog.setVisible(true);
+			final BenchmarkSPIMWindow dialog = new BenchmarkSPIMWindow(null,
+					new BenchmarkSPIMParametersImpl(userName, password, Constants.PHONE, email, workingDirPath));
+			dialog.executeAdjustment(() -> {
+				dialog.setTitle(Constants.MENU_ITEM_NAME + " " + Constants.SUBMENU_ITEM_NAME);
+				dialog.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+				dialog.addWindowListener(new WindowAdapter() {
+					@Override
+					public void windowClosing(final WindowEvent e) {
+						super.windowClosing(e);
+						fl.close();
+					}
 				});
-			} catch(final IOException e) {
-				fl.close();
-				throw e;
-			}
+				dialog.setVisible(true);
+			});
 		} catch (final IOException e) {
 			log.error(e.getMessage(), e);
 		}

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java

@@ -9,7 +9,6 @@ import static cz.it4i.fiji.haas_spim_benchmark.core.Constants.UI_TO_HAAS_FREQUEN
 
 import java.io.BufferedReader;
 import java.io.Closeable;
-import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
@@ -42,6 +41,8 @@ import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
 
+import net.imagej.updater.util.Progress;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
@@ -53,14 +54,13 @@ import cz.it4i.fiji.haas.HaaSOutputHolder;
 import cz.it4i.fiji.haas.HaaSOutputHolderImpl;
 import cz.it4i.fiji.haas.Job;
 import cz.it4i.fiji.haas.JobManager;
-import cz.it4i.fiji.haas_java_client.JobState;
-import cz.it4i.fiji.haas_java_client.ProgressNotifier;
 import cz.it4i.fiji.haas_java_client.HaaSClientSettings;
 import cz.it4i.fiji.haas_java_client.JobSettings;
 import cz.it4i.fiji.haas_java_client.JobSettingsBuilder;
+import cz.it4i.fiji.haas_java_client.JobState;
+import cz.it4i.fiji.haas_java_client.ProgressNotifier;
 import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
 import cz.it4i.fiji.haas_java_client.UploadingFile;
-import net.imagej.updater.util.Progress;
 
 public class BenchmarkJobManager implements Closeable {
 
@@ -88,8 +88,8 @@ public class BenchmarkJobManager implements Closeable {
 
 		public BenchmarkJob(Job job) {
 			this.job = job;
-			tasks = new LinkedList<Task>();
-			nonTaskSpecificErrors = new LinkedList<BenchmarkError>();
+			tasks = new LinkedList<>();
+			nonTaskSpecificErrors = new LinkedList<>();
 			computationAccessor = getComputationAccessor();
 		}
 
@@ -358,6 +358,7 @@ public class BenchmarkJobManager implements Closeable {
 			// If no job count definition has been found, search through the output and list
 			// all errors
 			if (!found) {
+				@SuppressWarnings("resource")
 				Scanner scanner = new Scanner(getSnakemakeOutput());
 				String currentLine;
 				while (scanner.hasNextLine()) {
@@ -380,6 +381,7 @@ public class BenchmarkJobManager implements Closeable {
 			}
 
 			// After the job count definition, task specification is expected
+			@SuppressWarnings("resource")
 			Scanner scanner = new Scanner(output.substring(processedOutputLength));
 			scanner.nextLine(); // Immediately after job count definition, task specification table header is
 								// expected
@@ -510,7 +512,7 @@ public class BenchmarkJobManager implements Closeable {
 				@Override
 				public List<String> getFileContents(List<String> logs) {
 					return job.getFileContents(logs);
-				};
+				}
 			};
 
 			result = new SPIMComputationAccessorDecoratorWithTimeout(result,
@@ -528,7 +530,7 @@ public class BenchmarkJobManager implements Closeable {
 
 	}
 
-	public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
+	public BenchmarkJobManager(BenchmarkSPIMParameters params) {
 		jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
 		jobManager.setUploadFilter(this::canUpload);
 	}
@@ -542,13 +544,13 @@ public class BenchmarkJobManager implements Closeable {
 		return convertJob(job);
 	}
 
-	public Collection<BenchmarkJob> getJobs() throws IOException {
+	public Collection<BenchmarkJob> getJobs() {
 		return jobManager.getJobs().stream().map(this::convertJob).collect(Collectors.toList());
 	}
 
-	public static void formatResultFile(Path filename) throws FileNotFoundException {
+	public static void formatResultFile(Path filename) {
 
-		List<ResultFileTask> identifiedTasks = new LinkedList<ResultFileTask>();
+		List<ResultFileTask> identifiedTasks = new LinkedList<>();
 
 		try {
 			String line = null;
@@ -639,8 +641,10 @@ public class BenchmarkJobManager implements Closeable {
 			log.error(e.getMessage(), e);
 		} finally {
 			try {
-				fileWriter.flush();
-				fileWriter.close();
+				if (fileWriter != null) {
+					fileWriter.flush();
+					fileWriter.close();
+				}
 			} catch (Exception e) {
 				log.error(e.getMessage(), e);
 			}

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/ResultFileTask.java

@@ -25,7 +25,7 @@ public class ResultFileTask {
 
 	public ResultFileTask(String name) {
 		this.name = name;
-		this.jobs = new LinkedList<ResultFileJob>();
+		this.jobs = new LinkedList<>();
 	}
 
 	public String getName() {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessorDecoratorWithTimeout.java

@@ -25,7 +25,7 @@ public class SPIMComputationAccessorDecoratorWithTimeout implements SPIMComputat
 		this.intervalForQueryInMs = intervalForQueryInMs;
 		this.decorated = decorated;
 		initAllowedTypes(allowedTypes);
-		outputCache = new P_ResultCacheHolder<List<String>>(x -> decorated.getActualOutput(this.allowedTypes));
+		outputCache = new P_ResultCacheHolder<>(x -> decorated.getActualOutput(this.allowedTypes));
 		changedFilesCache = new P_ResultCacheHolder<>(set -> {
 			if (set == null) {
 				set = new HashSet<>();
@@ -61,8 +61,8 @@ public class SPIMComputationAccessorDecoratorWithTimeout implements SPIMComputat
 		return decorated.getFileContents(logs);
 	}
 
-	private void initAllowedTypes(Set<SynchronizableFileType> allowedTypes) {
-		for (SynchronizableFileType type : allowedTypes) {
+	private void initAllowedTypes(Set<SynchronizableFileType> usedAllowedTypes) {
+		for (SynchronizableFileType type : usedAllowedTypes) {
 			this.allowedTypes.add(type);
 			this.allowedTypesIndices.put(type, this.allowedTypes.size() - 1);
 		}

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java

@@ -28,7 +28,7 @@ public class Task {
 	 * Looks up next task computation (i.e. with lowest timepoint) of the current
 	 * task and populates its parameters
 	 * 
-	 * @param positionInOutput:
+	 * @param positionInOutput
 	 *            Index of the output position to search from
 	 * @return success flag
 	 */

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java

@@ -36,27 +36,32 @@ public class TaskComputation {
 			return content;
 		}
 
+		@Override
+		public int hashCode() {
+			final int prime = 31;
+			int result = 1;
+			result = prime * result + ((content == null) ? 0 : content.hashCode());
+			result = prime * result + ((name == null) ? 0 : name.hashCode());
+			return result;
+		}
+
 		@Override
 		public boolean equals(Object obj) {
-			if (this == obj)
-				return true;
-			if (obj == null)
-				return false;
-			if (getClass() != obj.getClass())
-				return false;
+			if (this == obj) return true;
+			if (obj == null) return false;
+			if (getClass() != obj.getClass()) return false;
 			Log other = (Log) obj;
 			if (content == null) {
-				if (other.content != null)
-					return false;
-			} else if (!content.equals(other.content))
-				return false;
+				if (other.content != null) { return false;}
+			}
+			else if (!content.equals(other.content)) return false;
 			if (name == null) {
-				if (other.name != null)
-					return false;
-			} else if (!name.equals(other.name))
-				return false;
+				if (other.name != null) return false;
+			}
+			else if (!name.equals(other.name)) return false;
 			return true;
 		}
+		
 	}
 
 	public static class File {
@@ -99,7 +104,7 @@ public class TaskComputation {
 		this.computationAccessor = computationAccessor;
 		this.taskDescription = taskDescription;
 		this.timepoint = timepoint;
-		this.errors = new LinkedList<BenchmarkError>();
+		this.errors = new LinkedList<>();
 		this.state = JobState.Unknown;
 		updateState();
 	}
@@ -147,11 +152,11 @@ public class TaskComputation {
 	/**
 	 * Populates parameters of the current object by searching the output
 	 * 
-	 * @param positionInOutput:
+	 * @param actualPositionInOutput
 	 *            Index of the output position to search from
 	 * @return success flag
 	 */
-	public boolean populateParameters(int positionInOutput) {
+	public boolean populateParameters(int actualPositionInOutput) {
 
 		// Should the state be different than unknown, there is no need to populate
 		// parameters
@@ -159,7 +164,7 @@ public class TaskComputation {
 			return false;
 		}
 
-		this.positionInOutput = positionInOutput;
+		this.positionInOutput = actualPositionInOutput;
 		if (!resolveJobParameters()) {
 			return false;
 		}
@@ -200,6 +205,7 @@ public class TaskComputation {
 			final String OUTPUT_PARSING_ERRONEOUS_JOB = "Error in job ";
 			final String desiredPatternErroneousJob = OUTPUT_PARSING_ERRONEOUS_JOB + taskDescription;
 
+			@SuppressWarnings("resource")
 			Scanner scanner = new Scanner(getSnakemakeOutput().substring(positionInOutput));
 			String currentLine;
 			while (scanner.hasNextLine()) {
@@ -225,6 +231,7 @@ public class TaskComputation {
 		final String OUTPUT_PARSING_LOGS = "log: ";
 		final String OUTPUT_PARSING_JOB_ID = "jobid: ";
 
+		@SuppressWarnings("resource")
 		Scanner scanner = new Scanner(getSnakemakeOutput().substring(positionInOutput));
 		String currentLine;
 		while (scanner.hasNextLine()) {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMControl.java

@@ -23,6 +23,8 @@ import java.util.function.Function;
 
 import javax.swing.WindowConstants;
 
+import net.imagej.updater.util.Progress;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -62,7 +64,6 @@ import javafx.scene.control.Tooltip;
 import javafx.scene.layout.BorderPane;
 import javafx.scene.layout.Region;
 import mpicbg.spim.data.SpimDataException;
-import net.imagej.updater.util.Progress;
 
 public class BenchmarkSPIMControl extends BorderPane implements CloseableControl, InitiableControl {
 
@@ -96,8 +97,8 @@ public class BenchmarkSPIMControl extends BorderPane implements CloseableControl
 	}
 
 	@Override
-	public void init(Window root) {
-		this.root = root;
+	public void init(Window rootWindow) {
+		this.root = rootWindow;
 		executorServiceWS = Executors.newSingleThreadExecutor();
 		executorServiceUI = Executors.newSingleThreadExecutor();
 		timer = new Timer();
@@ -274,28 +275,22 @@ public class BenchmarkSPIMControl extends BorderPane implements CloseableControl
 				: new DummyProgress();
 
 		executorServiceWS.execute(() -> {
-
-			try {
-				List<BenchmarkJob> jobs = new LinkedList<>(manager.getJobs());
-				jobs.sort((bj1, bj2) -> (int) (bj1.getId() - bj2.getId()));
-				for (BenchmarkJob bj : jobs) {
-					registry.addIfAbsent(bj);
-				}
-				registry.update();
-				Set<ObservableValue<BenchmarkJob>> actual = new HashSet<>(this.jobs.getItems());
-
-				executorServiceFX.execute(() -> {
-					for (ObservableBenchmarkJob value : registry.getAllItems()) {
-						if (!actual.contains(value)) {
-							addJobToItems(value);
-						}
-					}
-				});
-				progress.done();
-			} catch (IOException e) {
-				log.error(e.getMessage(), e);
+			List<BenchmarkJob> inspectedJobs = new LinkedList<>(manager.getJobs());
+			inspectedJobs.sort((bj1, bj2) -> (int) (bj1.getId() - bj2.getId()));
+			for (BenchmarkJob bj : inspectedJobs) {
+				registry.addIfAbsent(bj);
 			}
+			registry.update();
+			Set<ObservableValue<BenchmarkJob>> actual = new HashSet<>(this.jobs.getItems());
 
+			executorServiceFX.execute(() -> {
+				for (ObservableBenchmarkJob value : registry.getAllItems()) {
+					if (!actual.contains(value)) {
+						addJobToItems(value);
+					}
+				}
+			});
+			progress.done();
 		});
 	}
 
@@ -337,11 +332,11 @@ public class BenchmarkSPIMControl extends BorderPane implements CloseableControl
 	private void setCellValueFactoryCompletable(int index, Function<BenchmarkJob, CompletableFuture<String>> mapper) {
 		JavaFXRoutines.setCellValueFactory(jobs, index, mapper);
 		((TableColumn<ObservableBenchmarkJob, CompletableFuture<String>>) jobs.getColumns().get(index))
-				.setCellFactory(column -> new TableCellAdapter<ObservableBenchmarkJob, CompletableFuture<String>> //
+				.setCellFactory(column -> new TableCellAdapter<> //
 				(//
 						new P_TableCellUpdaterDecoratorWithToolTip<>//
 						(//
-								new FutureValueUpdater<ObservableBenchmarkJob, String, CompletableFuture<String>>//
+								new FutureValueUpdater<>//
 								(//
 										new StringValueUpdater<ObservableBenchmarkJob>(), executorServiceFX//
 								), //
@@ -349,11 +344,7 @@ public class BenchmarkSPIMControl extends BorderPane implements CloseableControl
 	}
 
 	private void openJobDetailsWindow(BenchmarkJob job) {
-		try {
-			new JobDetailWindow(root, job).setVisible(true);
-		} catch (IOException e) {
-			log.error(e.getMessage(), e);
-		}
+		new JobDetailWindow(root, job).setVisible(true);
 	}
 
 	private void openBigDataViewer(BenchmarkJob job) {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMWindow.java

 package cz.it4i.fiji.haas_spim_benchmark.ui;
 
 import java.awt.Window;
-import java.io.IOException;
 
 import cz.it4i.fiji.haas.ui.FXFrame;
 import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager;
@@ -12,13 +11,9 @@ public class BenchmarkSPIMWindow extends FXFrame<BenchmarkSPIMControl>{
 
 	private static final long serialVersionUID = 1L;
 		
-	public BenchmarkSPIMWindow(Window parentWindow, BenchmarkSPIMParameters params) throws IOException {
+	public BenchmarkSPIMWindow(Window parentWindow, BenchmarkSPIMParameters params) {
 		super(parentWindow,()->{
-			try {
-				return new BenchmarkSPIMControl(new BenchmarkJobManager(params));
-			} catch (IOException e) {
-				throw new RuntimeException(e);
-			}
+			return new BenchmarkSPIMControl(new BenchmarkJobManager(params));
 		});
 		
 	}

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/HaaSOutputObservableValueRegistry.java

@@ -78,11 +78,11 @@ public class HaaSOutputObservableValueRegistry implements Closeable {
 
 		String value;
 
-		private synchronized void update(String value) {
+		private synchronized void update(String newValue) {
 			String oldValue = this.value;
-			this.value = value;
-			if (value != null && oldValue == null || value == null && oldValue != null
-					|| value != null && !value.equals(oldValue)) {
+			this.value = newValue;
+			if (newValue != null && oldValue == null || newValue == null && oldValue != null
+					|| newValue != null && !newValue.equals(oldValue)) {
 				fireValueChangedEvent();
 			}
 		}

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/JobDetailControl.java

@@ -57,13 +57,13 @@ public class JobDetailControl extends TabPane implements CloseableControl, Initi
 	
 	
 	private void enableOnlySpecificTab(Tab tabToLeaveEnabled) {
-		getTabs().stream().filter(node -> node != jobPropertiesTab).forEach(node -> node.setDisable(true));
+		getTabs().stream().filter(node -> node != tabToLeaveEnabled).forEach(node -> node.setDisable(true));
 		getSelectionModel().select(jobPropertiesTab);
 	}
 
-	private boolean isExecutionDetailsAvailable(BenchmarkJob job) {
-		return job.getState() == JobState.Running || job.getState() == JobState.Finished
-				|| job.getState() == JobState.Failed || job.getState() == JobState.Canceled;
+	private boolean isExecutionDetailsAvailable(BenchmarkJob inspectedJob) {
+		return inspectedJob.getState() == JobState.Running || inspectedJob.getState() == JobState.Finished
+				|| inspectedJob.getState() == JobState.Failed || inspectedJob.getState() == JobState.Canceled;
 	}
 
 	@Override

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/JobDetailWindow.java

 package cz.it4i.fiji.haas_spim_benchmark.ui;
 
 import java.awt.Window;
-import java.io.IOException;
 
 import cz.it4i.fiji.haas.ui.FXFrame;
 import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.BenchmarkJob;
@@ -12,7 +11,7 @@ public class JobDetailWindow extends FXFrame<JobDetailControl>{
 	
 
 	
-	public JobDetailWindow(Window parentWindow, BenchmarkJob job) throws IOException {
+	public JobDetailWindow(Window parentWindow, BenchmarkJob job) {
 		super(parentWindow,()->{
 			return new JobDetailControl(job);
 			

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/JobPropertiesControl.java

@@ -57,13 +57,13 @@ public class JobPropertiesControl extends BorderPane implements Closeable {
 
 	private void fillTable() {
 		properties.getItems()
-				.add(new UpdatableObservableValue<JobPropertiesControl.P_Value>(
+				.add(new UpdatableObservableValue<>(
 						new P_Value("Input", job.getInputDirectory(), "Demo data on the Salomon IT4I cluster"),
 						x -> UpdateStatus.NotUpdated, x -> x));
-		properties.getItems().add(new UpdatableObservableValue<JobPropertiesControl.P_Value>(
+		properties.getItems().add(new UpdatableObservableValue<>(
 				new P_Value("Output", job.getOutputDirectory(), "N/A"), x -> UpdateStatus.NotUpdated, x -> x));
 
-		properties.getItems().add(new UpdatableObservableValue<JobPropertiesControl.P_Value>(
+		properties.getItems().add(new UpdatableObservableValue<>(
 				new P_Value("Working", job.getDirectory(), "N/A"), x -> UpdateStatus.NotUpdated, x -> x));
 
 	}

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/NewJobController.java

@@ -13,7 +13,6 @@ import cz.it4i.fiji.haas.ui.CloseableControl;
 import cz.it4i.fiji.haas.ui.FXFrame;
 import cz.it4i.fiji.haas.ui.InitiableControl;
 import cz.it4i.fiji.haas.ui.JavaFXRoutines;
-import javafx.beans.value.ObservableValue;
 import javafx.fxml.FXML;
 import javafx.scene.Parent;
 import javafx.scene.control.Alert;
@@ -77,8 +76,8 @@ public class NewJobController extends BorderPane implements CloseableControl, In
 		JavaFXRoutines.initRootAndController("NewJobView.fxml", this);
 		getStylesheets().add(getClass().getResource("NewJobView.css").toExternalForm());
 		bt_create.setOnMouseClicked(X -> createPressed());
-		tg_inputDataLocation.selectedToggleProperty().addListener((v, old, n) -> selected(v, old, n, rb_ownInput));
-		tg_outputDataLocation.selectedToggleProperty().addListener((v, o, n) -> selected(v, o, n, rb_ownOutput));
+		tg_inputDataLocation.selectedToggleProperty().addListener((v, old, n) -> selected(n, rb_ownInput));
+		tg_outputDataLocation.selectedToggleProperty().addListener((v, o, n) -> selected(n, rb_ownOutput));
 		initSelectButton(et_inputDirectory, bt_selectInput);
 		initSelectButton(et_outputDirectory, bt_selectOutput);
 	}
@@ -176,7 +175,7 @@ public class NewJobController extends BorderPane implements CloseableControl, In
 		return DataLocation.values()[DataLocation.values().length - backawardOrderOfSelected];
 	}
 
-	private void selected(ObservableValue<? extends Toggle> v, Toggle o, Toggle n, Parent disableIfNotSelected) {
+	private void selected(Toggle n, Parent disableIfNotSelected) {
 		disableIfNotSelected.getChildrenUnmodifiable().forEach(node -> node.setDisable(n != disableIfNotSelected));
 	}
 

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/ObservableTaskRegistry.java

@@ -30,7 +30,7 @@ public class ObservableTaskRegistry extends ObservableValueRegistry<Task, Updata
 	
 	@Override
 	protected UpdatableObservableValue<Task> constructObservableValue(Task task) {
-		return new UpdatableObservableValue<Task>(task, getUpdateFunction(), getStateProvider());
+		return new UpdatableObservableValue<>(task, getUpdateFunction(), getStateProvider());
 	}
 
 	private static UpdateStatus update(Task t) {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/SPIMPipelineProgressViewController.java

@@ -119,7 +119,7 @@ public class SPIMPipelineProgressViewController extends BorderPane implements Cl
 		tasks.setPrefWidth(PREFERRED_WIDTH);
 		timer = new Timer();
 		registry = new ObservableTaskRegistry(()-> job, task -> tasks.getItems().remove(registry.get(task)));
-		TableViewContextMenu<ObservableValue<Task>> menu = new TableViewContextMenu<ObservableValue<Task>>(this.tasks);
+		TableViewContextMenu<ObservableValue<Task>> menu = new TableViewContextMenu<>(this.tasks);
 		menu.addItem("Open view", (task, columnIndex) -> proof(task, columnIndex),
 				(x, columnIndex) -> check(x, columnIndex));
 	}
@@ -160,8 +160,8 @@ public class SPIMPipelineProgressViewController extends BorderPane implements Cl
 	}
 
 	private void fillTable() {
-		List<Task> tasks = job.getTasks();
-		if (tasks == null) {
+		List<Task> processedTasks = job.getTasks();
+		if (processedTasks == null) {
 			timer.schedule(new TimerTask() {
 				@Override
 				public void run() {
@@ -170,13 +170,13 @@ public class SPIMPipelineProgressViewController extends BorderPane implements Cl
 			}, Constants.HAAS_UPDATE_TIMEOUT / Constants.UI_TO_HAAS_FREQUENCY_UPDATE_RATIO);
 		} else {
 
-			Optional<List<TaskComputation>> optional = tasks.stream().map(task -> task.getComputations())
+			Optional<List<TaskComputation>> optional = processedTasks.stream().map(task -> task.getComputations())
 					.collect(Collectors.<List<TaskComputation>>maxBy((a, b) -> a.size() - b.size()));
 			if (!optional.isPresent()) {
 				return;
 			}
 			List<TaskComputation> computations = optional.get();
-			List<ObservableValue<Task>> taskList = (tasks.stream().map(task -> registry.addIfAbsent(task))
+			List<ObservableValue<Task>> taskList = (processedTasks.stream().map(task -> registry.addIfAbsent(task))
 					.collect(Collectors.toList()));
 			executorFx.execute(() -> {
 				int i = 0;
@@ -204,9 +204,8 @@ public class SPIMPipelineProgressViewController extends BorderPane implements Cl
 		JavaFXRoutines.setCellValueFactory(this.tasks, index, (Function<Task, TaskComputation>) v -> {
 			if (v.getComputations().size() >= index) {
 				return v.getComputations().get(index - 1);
-			} else {
-				return null;
-			}
+			} 
+			return null;
 		});
 		((TableColumn<ObservableValue<Task>, TaskComputation>) this.tasks.getColumns().get(index))
 				.setCellFactory(column -> new TableCellAdapter<>((cell, val, empty) -> {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/TaskComputationAdapter.java

@@ -38,7 +38,7 @@ public class TaskComputationAdapter implements Closeable {
 	public void init() {
 		Map<String, Long> sizes = computation.getOutFileSizes();
 		computation.getOutputs().forEach(outputFile -> addOutputFile(outputFile, sizes.get(outputFile)));
-		computation.getLogs().forEach(log -> logs.add(new ObservableLog(log)));
+		computation.getLogs().forEach(decoratedLog -> logs.add(new ObservableLog(decoratedLog)));
 		synchronized (this) {
 			if(timer != null) {
 				timer.schedule(new P_TimerTask(), Constants.HAAS_TIMEOUT, Constants.HAAS_TIMEOUT);
@@ -94,21 +94,21 @@ public class TaskComputationAdapter implements Closeable {
 	
 		private class P_ObservableString extends ObservableValueBase<String> {
 	
-			private String value;
+			private String innerValue;
 	
 			public P_ObservableString(String value) {
-				this.value = value;
+				this.innerValue = value;
 			}
 	
 			@Override
 			public String getValue() {
-				return value;
+				return innerValue;
 			}
 			
 			public void setValue(String value) {
-				if(this.value != null && !this.value.equals(value) ||
-					value != null && !value.equals(this.value)) {
-					this.value = value;
+				if(this.innerValue != null && !this.innerValue.equals(value) ||
+					value != null && !value.equals(this.innerValue)) {
+					this.innerValue = value;
 					fireValueChangedEvent();
 				}
 			}
@@ -159,10 +159,10 @@ public class TaskComputationAdapter implements Closeable {
 		@Override
 		public void run() {
 			Map<String, Long> sizes = computation.getOutFileSizes();
-			Map<String, Log> logs = computation.getLogs().stream()
-					.collect(Collectors.<Log, String, Log>toMap((Log log) -> log.getName(), (Log log) -> log));
+			Map<String, Log> computationLogs = computation.getLogs().stream()
+					.collect(Collectors.<Log, String, Log>toMap((Log l) -> l.getName(), (Log l) -> l));
 			TaskComputationAdapter.this.logs
-					.forEach(log -> log.setContentValue(logs.get(log.getName())));
+					.forEach(processedLog -> processedLog.setContentValue(computationLogs.get(processedLog.getName())));
 			outputs.forEach(value -> ((ObservableOutputFile) value).setSize(sizes.get(value.getValue().getName())));
 		}
 

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/TaskComputationControl.java

@@ -59,10 +59,10 @@ public class TaskComputationControl extends TabPane implements CloseableControl,
 			remoteFilesInfo.setFiles(adapter.getOutputs());
 			remoteFilesInfo.init(parameter);
 			Collection<Runnable> runs = new LinkedList<>();
-			for (ObservableLog log : adapter.getLogs()) {
+			for (ObservableLog observableLog : adapter.getLogs()) {
 				LogViewControl logViewControl = new LogViewControl();
-				logViewControl.setObservable(log.getContent());
-				runs.add(() -> addTab(log.getName(), logViewControl));
+				logViewControl.setObservable(observableLog.getContent());
+				runs.add(() -> addTab(observableLog.getName(), logViewControl));
 			}
 			uiExecutor.execute(() -> runs.forEach(r -> r.run()));
 		});

haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/FormatResultFileRun.java

 package cz.it4i.fiji.haas;
 
-import java.io.FileNotFoundException;
 import java.nio.file.Paths;
 
 import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager;
 
 public class FormatResultFileRun {
-	public static void main(String[] args) throws FileNotFoundException {
+	public static void main(String[] args) {
 		BenchmarkJobManager.formatResultFile(Paths.get(args[0]));
 	}
 }