Merge branch 'fixErrors'

haas-imagej-client/pom.xml

@@ -73,7 +73,7 @@
 		<dependency>
 			<groupId>cz.it4i.fiji</groupId>
 			<artifactId>haas-java-client</artifactId>
-			<version>0.0.1-SNAPSHOT</version>
+			<version>0.0.2-SNAPSHOT</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
 		<dependency>

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/Job.java

@@ -5,12 +5,14 @@ import java.io.InputStream;
 import java.io.InterruptedIOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.Calendar;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
+import java.util.function.Function;
 import java.util.function.Predicate;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
@@ -29,13 +31,24 @@ import cz.it4i.fiji.haas_java_client.ProgressNotifier;
 import cz.it4i.fiji.haas_java_client.TransferFileProgressForHaaSClient;
 import cz.it4i.fiji.haas_java_client.UploadingFile;
 import cz.it4i.fiji.scpclient.TransferFileProgress;
+
 /***
- * TASK - napojit na UI 
+ * TASK - napojit na UI
+ * 
  * @author koz01
  *
  */
 public class Job {
 
+	public static boolean isValidJobPath(Path path) {
+		try {
+			getJobId(path);
+		} catch (NumberFormatException e) {
+			return false;
+		}
+		return Files.isRegularFile(path.resolve(JOB_INFO_FILENAME));
+	}
+
 	private static final String JOB_NAME = "job.name";
 
 	private static final String JOB_NEEDS_UPLOAD = "job.needs_upload";
@@ -43,21 +56,18 @@ public class Job {
 	private static final String JOB_INFO_FILENAME = ".jobinfo";
 
 	private static final String JOB_NEEDS_DOWNLOAD = "job.needs_download";
-	
+
 	private static final String JOB_CAN_BE_DOWNLOADED = "job.can_be_downloaded";
-	
+
 	private static final String JOB_IS_DOWNLOADED = "job.downloaded";
-	
+
 	private static final String JOB_IS_UPLOADED = "job.uploaded";
 
-	public static boolean isValidJobPath(Path path) {
-		try {
-			getJobId(path);
-		} catch (NumberFormatException e) {
-			return false;
-		}
-		return Files.isRegularFile(path.resolve(JOB_INFO_FILENAME));
-	}
+	private static final String JOB_OUTPUT_DIRECTORY_PATH = "job.output_directory_path";
+
+	private static final String JOB_INPUT_DIRECTORY_PATH = "job.input_directory_path";
+
+	private static final String JOB_USE_DEMO_DATA = "job.use_demo_data";
 
 	private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.Job.class);
 
@@ -66,41 +76,50 @@ public class Job {
 	private final Supplier<HaaSClient> haasClientSupplier;
 
 	private JobInfo jobInfo;
-	
+
 	private Long jobId;
-	
+
 	private PropertyHolder propertyHolder;
-	
+
 	private final JobManager4Job jobManager;
-	
+
 	private Synchronization synchronization;
+
+	private Path inputDirectory;
+
+	private Path outputDirectory;
+
+	private boolean useDemoData;
+
 	
-	
-	public Job(JobManager4Job jobManager, String name, Path basePath, Supplier<HaaSClient> haasClientSupplier)
+
+	public Job(JobManager4Job jobManager, String name, Path basePath, Supplier<HaaSClient> haasClientSupplier,
+			Function<Path, Path> inputDirectoryProvider, Function<Path, Path> outputDirectoryProvider)
 			throws IOException {
 		this(jobManager, haasClientSupplier);
 		HaaSClient client = getHaaSClient();
 		long id = client.createJob(name, Collections.emptyList());
-		setJobDirectory(basePath.resolve("" + id));
+		setJobDirectory(basePath.resolve("" + id), inputDirectoryProvider, outputDirectoryProvider);
 		propertyHolder = new PropertyHolder(jobDir.resolve(JOB_INFO_FILENAME));
-		Files.createDirectory(jobDir);
+		Files.createDirectory(this.jobDir);
+		storeInputOutputDirectory();
 		setName(name);
-		
+
 	}
 
 	public Job(JobManager4Job jobManager, Path jobDirectory, Supplier<HaaSClient> haasClientSupplier) {
 		this(jobManager, haasClientSupplier);
-		setJobDirectory(jobDirectory);
-		propertyHolder = new PropertyHolder(jobDir.resolve(JOB_INFO_FILENAME));
+		propertyHolder = new PropertyHolder(jobDirectory.resolve(JOB_INFO_FILENAME));
+		useDemoData = getSafeBoolean(propertyHolder.getValue(JOB_USE_DEMO_DATA));
+		setJobDirectory(jobDirectory, jd -> useDemoData ? null : getDataDirectory(JOB_INPUT_DIRECTORY_PATH, jd),
+				jd -> getDataDirectory(JOB_OUTPUT_DIRECTORY_PATH, jd));
 	}
 
-	
 	private Job(JobManager4Job jobManager, Supplier<HaaSClient> haasClientSupplier) {
 		this.haasClientSupplier = haasClientSupplier;
 		this.jobManager = jobManager;
 	}
 
-
 	public void startUploadData() {
 		setProperty(JOB_NEEDS_UPLOAD, true);
 		try {
@@ -127,7 +146,7 @@ public class Job {
 				.collect(Collectors.toList());
 		synchronization.startDownload(files);
 	}
-	
+
 	public void stopDownloadData() {
 		setProperty(JOB_NEEDS_DOWNLOAD, false);
 		try {
@@ -137,14 +156,12 @@ public class Job {
 			throw new RuntimeException(e);
 		}
 	}
-	
+
 	public synchronized void resumeUpload() {
 		if (needsUpload()) {
 			synchronization.resumeUpload();
 		}
 	}
-	
-	
 
 	public synchronized void resumeDownload() {
 		if (needsDownload()) {
@@ -152,11 +169,10 @@ public class Job {
 		}
 	}
 
-	
 	public boolean canBeDownloaded() {
 		return Boolean.parseBoolean(getProperty(JOB_CAN_BE_DOWNLOADED));
 	}
-	
+
 	public void setUploaded(boolean b) {
 		setProperty(JOB_IS_UPLOADED, b);
 	}
@@ -164,23 +180,23 @@ public class Job {
 	public void setDownloaded(boolean b) {
 		setProperty(JOB_IS_DOWNLOADED, b);
 	}
-	
+
 	public boolean isUploaded() {
-		return  getSafeBoolean(getProperty(JOB_IS_UPLOADED));
+		return getSafeBoolean(getProperty(JOB_IS_UPLOADED));
 	}
 
 	public boolean isDownloaded() {
 		return getSafeBoolean(getProperty(JOB_IS_DOWNLOADED));
 	}
-	
+
 	public boolean needsDownload() {
 		return Boolean.parseBoolean(getProperty(JOB_NEEDS_DOWNLOAD));
 	}
-	
+
 	public boolean needsUpload() {
 		return Boolean.parseBoolean(getProperty(JOB_NEEDS_UPLOAD));
 	}
-	
+
 	public void uploadFile(String file, ProgressNotifier notifier) {
 		uploadFiles(Arrays.asList(file), notifier);
 	}
@@ -224,14 +240,16 @@ public class Job {
 		setCanBeDownloaded(true);
 	}
 
-	
-
 	synchronized public long getId() {
 		if (jobId == null) {
 			jobId = getJobId(jobDir);
 		}
 		return jobId;
 	}
+	
+	public boolean isUseDemoData() {
+		return useDemoData;
+	}
 
 	public Path storeDataInWorkdirectory(UploadingFile uploadingFile) throws IOException {
 		Path result;
@@ -242,8 +260,10 @@ public class Job {
 	}
 
 	synchronized public void download(Predicate<String> predicate, ProgressNotifier notifier) {
-		List<String> files = getHaaSClient().getChangedFiles(jobId).stream().filter(predicate).collect(Collectors.toList());
-		try (HaaSFileTransfer transfer =  haasClientSupplier.get().startFileTransfer(getId(), HaaSClient.DUMMY_TRANSFER_FILE_PROGRESS)) {
+		List<String> files = getHaaSClient().getChangedFiles(jobId).stream().filter(predicate)
+				.collect(Collectors.toList());
+		try (HaaSFileTransfer transfer = haasClientSupplier.get().startFileTransfer(getId(),
+				HaaSClient.DUMMY_TRANSFER_FILE_PROGRESS)) {
 			List<Long> fileSizes;
 			try {
 				fileSizes = transfer.obtainSize(files);
@@ -318,9 +338,9 @@ public class Job {
 		return jobDir;
 	}
 
-	public boolean remove() {
+	public boolean delete() {
 		boolean result;
-		if ((result = jobManager.remove(this)) && Files.isDirectory(jobDir)) {
+		if ((result = jobManager.deleteJob(this)) && Files.isDirectory(jobDir)) {
 			List<Path> pathsToDelete;
 			try {
 				pathsToDelete = Files.walk(jobDir).sorted(Comparator.reverseOrder()).collect(Collectors.toList());
@@ -369,41 +389,65 @@ public class Job {
 	public void setUploadNotifier(ProgressNotifier notifier) {
 		synchronization.setUploadNotifier(notifier);
 	}
-	
+
 	public void close() {
 		synchronization.close();
 	}
 
+	public Path getInputDirectory() {
+		return inputDirectory;
+	}
+
+	private void storeInputOutputDirectory() {
+		if (inputDirectory == null) {
+			useDemoData = true;
+			propertyHolder.setValue(JOB_USE_DEMO_DATA, "" + useDemoData);
+		} else {
+			storeDataDirectory(JOB_INPUT_DIRECTORY_PATH, inputDirectory);
+		}
+		storeDataDirectory(JOB_OUTPUT_DIRECTORY_PATH, outputDirectory);
+	}
+
+	private void storeDataDirectory(String directoryPropertyName, Path directory) {
+		if (!jobDir.equals(directory)) {
+			propertyHolder.setValue(directoryPropertyName, directory.toString());
+		}
+	}
+
+	private Path getDataDirectory(String typeOfDirectory, Path jobDirectory) {
+		String directory = propertyHolder.getValue(typeOfDirectory);
+		return directory != null ? Paths.get(directory) : jobDirectory;
+	}
+
 	private boolean getSafeBoolean(String value) {
 		return value != null ? Boolean.parseBoolean(value) : false;
 	}
 
-	private void setJobDirectory(Path jobDirectory) {
+	private void setJobDirectory(Path jobDirectory, Function<Path, Path> inputDirectoryProvider,
+			Function<Path, Path> outputDirectoryProvider) {
 		this.jobDir = jobDirectory;
+
 		try {
 			this.synchronization = new Synchronization(() -> startFileTransfer(HaaSClient.DUMMY_TRANSFER_FILE_PROGRESS),
-					jobDir, () -> {
+					jobDir, this.inputDirectory = inputDirectoryProvider.apply(jobDir),
+					this.outputDirectory = outputDirectoryProvider.apply(jobDir), () -> {
 						setProperty(JOB_NEEDS_UPLOAD, false);
 						setUploaded(true);
 					}, () -> {
 						setDownloaded(true);
 						setProperty(JOB_NEEDS_DOWNLOAD, false);
 						setCanBeDownloaded(false);
-					});
+					}, p -> jobManager.canUpload(Job.this, p));
 		} catch (IOException e) {
 			log.error(e.getMessage(), e);
 			throw new RuntimeException(e);
 		}
 	}
 
-
-
-	private HaaSFileTransfer startFileTransfer( TransferFileProgress progress) {
+	private HaaSFileTransfer startFileTransfer(TransferFileProgress progress) {
 		return haasClientSupplier.get().startFileTransfer(getId(), progress);
 	}
 
-	
-
 	private void setName(String name) {
 		setProperty(JOB_NAME, name);
 	}
@@ -426,7 +470,7 @@ public class Job {
 	private static long getJobId(Path path) {
 		return Long.parseLong(path.getFileName().toString());
 	}
-	
+
 	private void setCanBeDownloaded(boolean b) {
 		setProperty(JOB_CAN_BE_DOWNLOADED, b);
 	}

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/JobManager.java

@@ -7,6 +7,8 @@ import java.nio.file.Path;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedList;
+import java.util.function.BiPredicate;
+import java.util.function.Function;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -18,11 +20,15 @@ import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
 public class JobManager implements Closeable {
 
 	interface JobManager4Job {
-		boolean remove(Job job);
+		boolean deleteJob(Job job);
+
+		boolean canUpload(Job j, Path p);
 	}
 
 	private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.JobManager.class);
 
+	private static final BiPredicate<Job, Path> DUMMY_UPLOAD_FILTER = (X, Y) -> true;
+
 	private final Path workDirectory;
 
 	private Collection<Job> jobs;
@@ -31,12 +37,20 @@ public class JobManager implements Closeable {
 
 	private final Settings settings;
 
+	private BiPredicate<Job, Path> uploadFilter = DUMMY_UPLOAD_FILTER;
+
 	private final JobManager4Job remover = new JobManager4Job() {
 
 		@Override
-		public boolean remove(Job job) {
+		public boolean deleteJob(Job job) {
+			haasClient.deleteJob(job.getId());
 			return jobs.remove(job);
 		}
+
+		@Override
+		public boolean canUpload(Job j, Path p) {
+			return uploadFilter.test(j, p);
+		}
 	};
 
 	public JobManager(Path workDirectory, Settings settings) {
@@ -44,10 +58,12 @@ public class JobManager implements Closeable {
 		this.settings = settings;
 	}
 
-	public Job createJob() throws IOException {
+	public Job createJob(Function<Path, Path> inputDirectoryProvider, Function<Path, Path> outputDirectoryProvider)
+			throws IOException {
 		Job result;
 		initJobsIfNecessary();
-		jobs.add(result = new Job(remover, settings.getJobName(), workDirectory, this::getHaasClient));
+		jobs.add(result = new Job(remover, settings.getJobName(), workDirectory, this::getHaasClient,
+				inputDirectoryProvider, outputDirectoryProvider));
 		return result;
 	}
 
@@ -61,6 +77,10 @@ public class JobManager implements Closeable {
 		jobs.forEach(job -> job.close());
 	}
 
+	public void setUploadFilter(BiPredicate<Job, Path> filter) {
+		uploadFilter = filter != null ? filter : DUMMY_UPLOAD_FILTER;
+	}
+
 	private HaaSClient getHaasClient() {
 		if (haasClient == null) {
 			haasClient = new HaaSClient(settings);

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/data_transfer/Synchronization.java

@@ -6,12 +6,13 @@ import java.io.InterruptedIOException;
 import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedList;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
-import java.util.function.Function;
+import java.util.function.Predicate;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
@@ -24,20 +25,22 @@ import cz.it4i.fiji.haas_java_client.ProgressNotifier;
 import cz.it4i.fiji.haas_java_client.UploadingFile;
 import cz.it4i.fiji.haas_java_client.UploadingFileImpl;
 
-public class Synchronization implements Closeable{
+public class Synchronization implements Closeable {
 
 	public static final Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.data_transfer.Synchronization.class);
-	
+
 	private static final String FILE_INDEX_TO_UPLOAD_FILENAME = ".toUploadFiles";
-	
+
 	private static final String FILE_INDEX_TO_DOWNLOAD_FILENAME = ".toDownloadFiles";
-	
+
 	private static final String FILE_INDEX_DOWNLOADED_FILENAME = ".downloaded";
-	
+
 	private final Path workingDirectory;
-	
-	private final Function<String,Path> pathResolver;
-	
+
+	private final Path inputDirectory;
+
+	private final Path outputDirectory;
+
 	private final PersistentIndex<Path> filesDownloaded;
 
 	private final PersistentSynchronizationProcess<Path> uploadProcess;
@@ -45,31 +48,36 @@ public class Synchronization implements Closeable{
 	private final P_PersistentDownloadProcess downloadProcess;
 
 	private final ExecutorService service;
-	
-	public Synchronization(Supplier<HaaSFileTransfer> fileTransferSupplier, Path workingDirectory,
-			 Runnable uploadFinishedNotifier, Runnable downloadFinishedNotifier) throws IOException {
-		this.service = Executors.newFixedThreadPool(2);
+
+	private final Predicate<Path> uploadFilter;
+
+	public Synchronization(Supplier<HaaSFileTransfer> fileTransferSupplier, Path workingDirectory, Path inputDirectory,
+			Path outputDirectory, Runnable uploadFinishedNotifier, Runnable downloadFinishedNotifier, Predicate<Path> uploadFilter)
+			throws IOException {
 		this.workingDirectory = workingDirectory;
-		this.pathResolver = name -> workingDirectory.resolve(name);
+		this.inputDirectory = inputDirectory;
+		this.outputDirectory = outputDirectory;
+		this.service = Executors.newFixedThreadPool(2);
 		this.filesDownloaded = new PersistentIndex<>(workingDirectory.resolve(FILE_INDEX_DOWNLOADED_FILENAME),
-				pathResolver);
+				name -> Paths.get(name));
 		this.uploadProcess = createUploadProcess(fileTransferSupplier, service, uploadFinishedNotifier);
 		this.downloadProcess = createDownloadProcess(fileTransferSupplier, service, downloadFinishedNotifier);
+		this.uploadFilter = uploadFilter;
 	}
 
 	public synchronized void setUploadNotifier(ProgressNotifier notifier) {
 		uploadProcess.setNotifier(notifier);
 	}
-	
+
 	public void setDownloadNotifier(ProgressNotifier notifier) {
 		downloadProcess.setNotifier(notifier);
-		
+
 	}
 
 	public synchronized void startUpload() throws IOException {
 		uploadProcess.start();
 	}
-	
+
 	public void stopUpload() throws IOException {
 		uploadProcess.stop();
 	}
@@ -77,16 +85,16 @@ public class Synchronization implements Closeable{
 	public void resumeUpload() {
 		uploadProcess.resume();
 	}
-	
+
 	public synchronized void startDownload(Collection<String> files) throws IOException {
 		this.downloadProcess.setItems(files);
 		this.downloadProcess.start();
 	}
-	
+
 	public synchronized void stopDownload() throws IOException {
 		this.downloadProcess.stop();
 	}
-	
+
 	public synchronized void resumeDownload() {
 		this.downloadProcess.resume();
 	}
@@ -99,23 +107,24 @@ public class Synchronization implements Closeable{
 	}
 
 	private boolean canUpload(Path file) {
-		
-		return !file.getFileName().toString().matches("[.][^.]+") && !filesDownloaded.contains(file);
+		return uploadFilter.test(file) && !file.getFileName().toString().matches("[.][^.]+")
+				&& !filesDownloaded.contains(file);
 	}
 
 	private PersistentSynchronizationProcess<Path> createUploadProcess(Supplier<HaaSFileTransfer> fileTransferSupplier,
 			ExecutorService service, Runnable uploadFinishedNotifier) throws IOException {
 		return new PersistentSynchronizationProcess<Path>(service, fileTransferSupplier, uploadFinishedNotifier,
-				workingDirectory.resolve(FILE_INDEX_TO_UPLOAD_FILENAME), pathResolver) {
+				workingDirectory.resolve(FILE_INDEX_TO_UPLOAD_FILENAME), name -> inputDirectory.resolve(name)) {
 
 			@Override
 			protected Iterable<Path> getItems() throws IOException {
-				try(DirectoryStream<Path> ds = Files.newDirectoryStream(workingDirectory,Synchronization.this::canUpload)) {
-					return StreamSupport.stream(ds.spliterator(), false).collect(Collectors.toList()); 
+				try (DirectoryStream<Path> ds = Files.newDirectoryStream(inputDirectory,
+						Synchronization.this::canUpload)) {
+					return StreamSupport.stream(ds.spliterator(), false).collect(Collectors.toList());
 				}
-				
+
 			}
-	
+
 			@Override
 			protected void processItem(HaaSFileTransfer tr, Path p) throws InterruptedIOException {
 				UploadingFile uf = new UploadingFileImpl(p);
@@ -124,29 +133,28 @@ public class Synchronization implements Closeable{
 
 			@Override
 			protected long getTotalSize(Iterable<Path> items, HaaSFileTransfer tr) {
-				return StreamSupport.stream(items.spliterator(), false).map(p->{
+				return StreamSupport.stream(items.spliterator(), false).map(p -> {
 					try {
 						return Files.size(p);
 					} catch (IOException e) {
 						log.error(e.getMessage(), e);
-						return 0; 
+						return 0;
 					}
-				}).collect(Collectors.summingLong(val->val.longValue()));
+				}).collect(Collectors.summingLong(val -> val.longValue()));
 			}
 		};
 	}
 
-	private P_PersistentDownloadProcess createDownloadProcess(
-			Supplier<HaaSFileTransfer> fileTransferSupplier,  ExecutorService service,
-			Runnable uploadFinishedNotifier) throws IOException {
-		
+	private P_PersistentDownloadProcess createDownloadProcess(Supplier<HaaSFileTransfer> fileTransferSupplier,
+			ExecutorService service, Runnable uploadFinishedNotifier) throws IOException {
+
 		return new P_PersistentDownloadProcess(service, fileTransferSupplier, uploadFinishedNotifier);
 	}
-	
-	private class P_PersistentDownloadProcess extends PersistentSynchronizationProcess<String>{
+
+	private class P_PersistentDownloadProcess extends PersistentSynchronizationProcess<String> {
 
 		private Collection<String> items = Collections.emptyList();
-		
+
 		public P_PersistentDownloadProcess(ExecutorService service, Supplier<HaaSFileTransfer> fileTransferSupplier,
 				Runnable processFinishedNotifier) throws IOException {
 			super(service, fileTransferSupplier, processFinishedNotifier,
@@ -156,7 +164,7 @@ public class Synchronization implements Closeable{
 		private synchronized void setItems(Collection<String> items) {
 			this.items = new LinkedList<>(items);
 		}
-		
+
 		@Override
 		protected synchronized Iterable<String> getItems() throws IOException {
 			return items;
@@ -164,19 +172,20 @@ public class Synchronization implements Closeable{
 
 		@Override
 		protected void processItem(HaaSFileTransfer tr, String file) throws InterruptedIOException {
-			filesDownloaded.insert(workingDirectory.resolve(file));
+			filesDownloaded.insert(outputDirectory.resolve(file));
 			try {
 				filesDownloaded.storeToWorkingFile();
 			} catch (IOException e) {
 				log.error(e.getMessage(), e);
 			}
-			tr.download(file, workingDirectory);
+			tr.download(file, outputDirectory);
 		}
 
 		@Override
 		protected long getTotalSize(Iterable<String> items, HaaSFileTransfer tr) throws InterruptedIOException {
-			return tr.obtainSize( StreamSupport.stream(items.spliterator(), false).collect(Collectors.toList())).stream().collect(Collectors.summingLong(val->val));
+			return tr.obtainSize(StreamSupport.stream(items.spliterator(), false).collect(Collectors.toList())).stream()
+					.collect(Collectors.summingLong(val -> val));
 		}
-		
+
 	}
 }

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/JavaFXRoutines.java

@@ -28,7 +28,7 @@ public interface JavaFXRoutines {
 			void accept(TableCell<?, ?> cell, B value, boolean empty);
 		}
 
-		private TableCellUpdater<S, T> updater;
+		private final TableCellUpdater<S, T> updater;
 
 		public TableCellAdapter(TableCellUpdater<S, T> updater) {
 			this.updater = updater;
@@ -36,14 +36,18 @@ public interface JavaFXRoutines {
 
 		@Override
 		protected void updateItem(T item, boolean empty) {
-			updater.accept(this, item, empty);
+			if(empty) {
+				this.setText("");
+			} else {
+				updater.accept(this, item, empty);
+			}
 		}
 	}
 
 	static public class FutureValueUpdater<S, T, U extends CompletableFuture<T>> implements TableCellUpdater<S, U> {
 
-		private TableCellUpdater<S, T> inner;
-		private Executor executor;
+		private final TableCellUpdater<S, T> inner;
+		private final Executor executor;
 
 		public FutureValueUpdater(TableCellUpdater<S, T> inner, Executor exec) {
 			this.inner = inner;

haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ObservableValueRegistry.java

@@ -30,16 +30,16 @@ public abstract class ObservableValueRegistry<K, V extends UpdatableObservableVa
 		};
 	}
 	
-	public V addIfAbsent(K key) {
+	public synchronized V addIfAbsent(K key) {
 		V uov = map.computeIfAbsent(key, k -> constructObservableValue(k));
 		return uov;
 	}
 	
-	public V get(K key) {
+	public synchronized V get(K key) {
 		return map.get(key);
 	}
 
-	public Collection<V> getAllItems() {
+	public synchronized Collection<V> getAllItems() {
 		return map.values().stream().map(val -> val).collect(Collectors.toList());
 	}
 	

haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java

@@ -298,6 +298,14 @@ public class HaaSClient {
 		}
 	}
 
+	public void deleteJob(long id) {
+		try {
+			getJobManagement().deleteJob(id, getSessionID());
+		} catch (RemoteException | ServiceException e) {
+			throw new HaaSClientException(e);
+		}
+	}
+
 	private HaaSFileTransferImp getFileTransferMethod(long jobId, TransferFileProgress progress)
 			throws RemoteException, UnsupportedEncodingException, ServiceException, JSchException {
 		P_FileTransferPool pool = filetransferPoolMap.computeIfAbsent(jobId, id -> new P_FileTransferPool(id));
@@ -327,7 +335,7 @@ public class HaaSClient {
 	private long doCreateJob(String name, int numberOfNodes, Collection<Entry<String, String>> templateParameters)
 			throws RemoteException, ServiceException {
 		Collection<TaskSpecificationExt> taskSpec = Arrays
-				.asList(createTaskSpecification(name + ": ", templateId, numberOfNodes, templateParameters));
+				.asList(createTaskSpecification(name + "-task", templateId, numberOfNodes, templateParameters));
 		JobSpecificationExt jobSpecification = createJobSpecification(name, numberOfNodes, taskSpec);
 		SubmittedJobInfoExt job = getJobManagement().createJob(jobSpecification, getSessionID());
 		return job.getId();

haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java

@@ -8,5 +8,6 @@ public enum JobState {
     Running,
     Finished,
     Failed,
-    Canceled;
+    Canceled, 
+    Disposed;
 }

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

@@ -25,9 +25,11 @@ import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.Scanner;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.Executor;
+import java.util.function.Function;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -40,7 +42,6 @@ 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.UploadingFileFromResource;
 import cz.it4i.fiji.haas_java_client.JobState;
 import cz.it4i.fiji.haas_java_client.ProgressNotifier;
 import cz.it4i.fiji.haas_java_client.Settings;
@@ -48,9 +49,8 @@ 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{
+public class BenchmarkJobManager implements Closeable {
 
-	
 	private static Logger log = LoggerFactory
 			.getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
 
@@ -59,7 +59,11 @@ public class BenchmarkJobManager implements Closeable{
 	public final class BenchmarkJob implements HaaSOutputHolder {
 
 		private final Job job;
-		
+
+		public boolean isUseDemoData() {
+			return job.isUseDemoData();
+		}
+
 		private final List<Task> tasks;
 		private final List<BenchmarkError> nonTaskSpecificErrors;
 		private final SPIMComputationAccessor computationAccessor;
@@ -84,14 +88,14 @@ public class BenchmarkJobManager implements Closeable{
 		}
 
 		public synchronized void startJob(Progress progress) throws IOException {
-			job.uploadFile(Constants.CONFIG_YAML,  new P_ProgressNotifierAdapter(progress));
+			job.uploadFile(Constants.CONFIG_YAML, new P_ProgressNotifierAdapter(progress));
 			String outputName = getOutputName(job.openLocalFile(Constants.CONFIG_YAML));
 			verifiedState = null;
 			verifiedStateProcessed = false;
 			running = null;
 			job.submit();
 			job.setProperty(SPIM_OUTPUT_FILENAME_PATTERN, outputName);
-		
+
 		}
 
 		public JobState getState() {
@@ -106,7 +110,6 @@ public class BenchmarkJobManager implements Closeable{
 			job.stopUploadData();
 		}
 
-		
 		public synchronized CompletableFuture<JobState> getStateAsync(Executor executor) {
 			if (running != null) {
 				return running;
@@ -121,12 +124,12 @@ public class BenchmarkJobManager implements Closeable{
 		public void startDownload() throws IOException {
 			if (job.getState() == JobState.Finished) {
 				String filePattern = job.getProperty(SPIM_OUTPUT_FILENAME_PATTERN);
-				job.startDownload(downloadFinishedData(filePattern) );
+				job.startDownload(downloadFinishedData(filePattern));
 			} else if (job.getState() == JobState.Failed || job.getState() == JobState.Canceled) {
 				job.startDownload(downloadFailedData());
 			}
 		}
-		
+
 		public boolean canBeDownloaded() {
 			return job.canBeDownloaded();
 		}
@@ -205,8 +208,8 @@ public class BenchmarkJobManager implements Closeable{
 			return computationAccessor.getActualOutput(Arrays.asList(SynchronizableFileType.StandardErrorFile)).get(0);
 		}
 
-		public boolean remove() {
-			return job.remove();
+		public boolean delete() {
+			return job.delete();
 		}
 
 		public void cancelJob() {
@@ -223,11 +226,47 @@ public class BenchmarkJobManager implements Closeable{
 			job.resumeUpload();
 		}
 
+		public void setDownloaded(Boolean val) {
+			job.setDownloaded(val);
+		}
+
+		public void setUploaded(boolean b) {
+			job.setUploaded(b);
+		}
+
+		public boolean isDownloaded() {
+			return job.isDownloaded();
+		}
+
+		public boolean isUploaded() {
+			return job.isUploaded();
+		}
+
+		public void stopDownload() {
+			job.stopDownloadData();
+		}
+
+		public boolean needsDownload() {
+			return job.needsDownload();
+		}
+
+		public boolean needsUpload() {
+			return job.needsUpload();
+		}
+
 		@Override
 		public String toString() {
 			return "" + getId();
 		}
 
+		public void storeDataInWorkdirectory(UploadingFile file) throws IOException {
+			job.storeDataInWorkdirectory(file);
+		}
+
+		public Path getInputDirectory() {
+			return job.getInputDirectory();
+		}
+
 		private ProgressNotifier convertTo(Progress progress) {
 			return progress == null ? null : new P_ProgressNotifierAdapter(progress);
 		}
@@ -385,7 +424,8 @@ public class BenchmarkJobManager implements Closeable{
 		private SPIMComputationAccessor getComputationAccessor() {
 			SPIMComputationAccessor result = new SPIMComputationAccessor() {
 
-				private final HaaSOutputHolder outputOfSnakemake = new HaaSOutputHolderImpl(list -> job.getOutput(list));
+				private final HaaSOutputHolder outputOfSnakemake = new HaaSOutputHolderImpl(
+						list -> job.getOutput(list));
 
 				@Override
 				public List<String> getActualOutput(List<SynchronizableFileType> content) {
@@ -421,42 +461,16 @@ public class BenchmarkJobManager implements Closeable{
 			return Stream.concat(nonTaskSpecificErrors.stream(), taskSpecificErrors).collect(Collectors.toList());
 		}
 
-		public void setDownloaded(Boolean val) {
-			job.setDownloaded(val);
-		}
-		
-		public void setUploaded(boolean b) {
-			job.setUploaded(b);
-		}
-
-		public boolean isDownloaded() {
-			return job.isDownloaded();
-		}
-
-		public boolean isUploaded() {
-			return job.isUploaded();
-		}
-
-		public void stopDownload() {
-			job.stopDownloadData();
-		}
-
-		public boolean needsDownload() {
-			return job.needsDownload();
-		}
-
-		public boolean needsUpload() {
-			return job.needsUpload();
-		}
 	}
 
 	public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
 		jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
+		jobManager.setUploadFilter(this::canUpload);
 	}
 
-	public BenchmarkJob createJob() throws IOException {
-		Job job = jobManager.createJob();
-		job.storeDataInWorkdirectory(getUploadingFile());
+	public BenchmarkJob createJob(Function<Path, Path> inputDirectoryProvider,
+			Function<Path, Path> outputDirectoryProvider) throws IOException {
+		Job job = jobManager.createJob(inputDirectoryProvider, outputDirectoryProvider);
 		return convertJob(job);
 	}
 
@@ -570,8 +584,8 @@ public class BenchmarkJobManager implements Closeable{
 		jobManager.close();
 	}
 
-	private UploadingFile getUploadingFile() {
-		return new UploadingFileFromResource("", Constants.CONFIG_YAML);
+	private boolean canUpload(Job job, Path p) {
+		return job.getInputDirectory() == null || !p.equals(job.getInputDirectory().resolve(Constants.CONFIG_YAML));
 	}
 
 	private BenchmarkJob convertJob(Job job) {
@@ -581,9 +595,9 @@ public class BenchmarkJobManager implements Closeable{
 	private String getOutputName(InputStream openLocalFile) throws IOException {
 		try (InputStream is = openLocalFile) {
 			Yaml yaml = new Yaml();
-
 			Map<String, Map<String, String>> map = yaml.load(is);
-			String result = map.get("common").get("hdf5_xml_filename");
+			String result = Optional.ofNullable(map).map(m -> m.get("common")).map(m -> m.get("hdf5_xml_filename"))
+					.orElse(null);
 			if (result == null) {
 				throw new IllegalArgumentException("hdf5_xml_filename not found");
 			}
@@ -688,6 +702,11 @@ public class BenchmarkJobManager implements Closeable{
 			public long getClusterNodeType() {
 				return Constants.HAAS_CLUSTER_NODE_TYPE;
 			}
+
+			@Override
+			public int getNumberOfCoresPerNode() {
+				return Constants.CORES_PER_NODE;
+			}
 		};
 	}
 

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

@@ -10,7 +10,7 @@ public interface Constants {
 	String HAAS_JOB_NAME = "HaaSSPIMBenchmark";
 	int HAAS_CLUSTER_NODE_TYPE = 6;
 	int HAAS_TEMPLATE_ID = 4;
-	String HAAS_PROJECT_ID = "DD-17-31";
+	String HAAS_PROJECT_ID = "OPEN-12-20";
 	int HAAS_TIMEOUT = 9600; //Walltime in seconds
 	
 	final String NEW_LINE_SEPARATOR = "\n";
@@ -52,5 +52,6 @@ public interface Constants {
 	String STATISTICS_SUMMARY_FILENAME = "summary.csv";
 	String SUMMARY_FILE_HEADER = "Task;AvgMemoryUsage;AvgWallTime;MaxWallTime;TotalTime;JobCount";
 	String DONE_TASK = "done";
+	int CORES_PER_NODE = 24;
 	
 }

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

@@ -185,7 +185,8 @@ public class TaskComputation {
 
 		// Should the state be queued, try to find out whether a log file exists
 		if (state == JobState.Queued) {
-			if (null != logs && !logs.stream().anyMatch(logFile -> computationAccessor.fileExists(logFile))) {
+			if (!taskDescription.equals(Constants.DONE_TASK) && null != logs
+					&& !logs.stream().anyMatch(logFile -> computationAccessor.fileExists(logFile))) {
 				return; // No log file exists yet
 			}
 			state = JobState.Running;

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

 package cz.it4i.fiji.haas_spim_benchmark.ui;
 
+import static cz.it4i.fiji.haas_spim_benchmark.core.Constants.CONFIG_YAML;
+
 import java.awt.Desktop;
 import java.awt.Window;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.EnumSet;
 import java.util.HashSet;
 import java.util.LinkedList;
@@ -22,6 +26,7 @@ import javax.swing.WindowConstants;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import cz.it4i.fiji.haas.UploadingFileFromResource;
 import cz.it4i.fiji.haas.ui.CloseableControl;
 import cz.it4i.fiji.haas.ui.DummyProgress;
 import cz.it4i.fiji.haas.ui.InitiableControl;
@@ -30,6 +35,7 @@ import cz.it4i.fiji.haas.ui.ModalDialogs;
 import cz.it4i.fiji.haas.ui.ProgressDialog;
 import cz.it4i.fiji.haas.ui.TableViewContextMenu;
 import cz.it4i.fiji.haas_java_client.JobState;
+import cz.it4i.fiji.haas_java_client.UploadingFile;
 import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager;
 import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.BenchmarkJob;
 import cz.it4i.fiji.haas_spim_benchmark.core.Constants;
@@ -38,9 +44,13 @@ import cz.it4i.fiji.haas_spim_benchmark.core.ObservableBenchmarkJob;
 import cz.it4i.fiji.haas_spim_benchmark.core.ObservableBenchmarkJob.TransferProgress;
 import javafx.beans.value.ObservableValue;
 import javafx.fxml.FXML;
+import javafx.scene.control.Alert;
+import javafx.scene.control.Alert.AlertType;
+import javafx.scene.control.ButtonType;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.TableView;
 import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.Region;
 import net.imagej.updater.util.Progress;
 
 //FIXME: fix Exception during context menu request on task with N/A state
@@ -50,21 +60,21 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 	private TableView<ObservableBenchmarkJob> jobs;
 
 	private final BenchmarkJobManager manager;
-	
+
 	private final ExecutorService executorServiceJobState = Executors.newWorkStealingPool();
-	
+
 	private final Executor executorServiceFX = new FXFrameExecutorService();
-	
+
 	private Window root;
 
 	private ExecutorService executorServiceUI;
-	
+
 	private ExecutorService executorServiceWS;
-	
+
 	private Timer timer;
-	
+
 	private ObservableBenchmarkJobRegistry registry;
-	
+
 	private static Logger log = LoggerFactory
 			.getLogger(cz.it4i.fiji.haas_spim_benchmark.ui.BenchmarkSPIMController.class);
 
@@ -102,7 +112,7 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 
 	private void initMenu() {
 		TableViewContextMenu<ObservableBenchmarkJob> menu = new TableViewContextMenu<>(jobs);
-		menu.addItem("Create job", x -> executeWSCallAsync("Creating job", p -> manager.createJob()), j -> true);
+		menu.addItem("Create job", x -> askForCreateJob(), j -> true);
 		menu.addItem("Start job", job -> executeWSCallAsync("Starting job", p -> {
 			job.getValue().startJob(p);
 			job.getValue().update();
@@ -112,7 +122,8 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 		menu.addItem("Cancel job", job -> executeWSCallAsync("Canceling job", p -> {
 			job.getValue().cancelJob();
 			job.getValue().update();
-		}), job -> JavaFXRoutines.notNullValue(job, j -> j.getState() == JobState.Running || j.getState() == JobState.Queued ));
+		}), job -> JavaFXRoutines.notNullValue(job,
+				j -> j.getState() == JobState.Running || j.getState() == JobState.Queued));
 
 		menu.addItem("Execution details", job -> {
 			try {
@@ -126,16 +137,16 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 
 		menu.addItem("Upload data", job -> executeWSCallAsync("Uploading data", p -> job.getValue().startUpload()),
 				job -> executeWSCallAsync("Stop uploading data", p -> job.getValue().stopUpload()),
-				job -> JavaFXRoutines.notNullValue(job, j -> !EnumSet.of(JobState.Running).contains(j.getState())),
+				job -> JavaFXRoutines.notNullValue(job,
+						j -> !j.isUseDemoData() && !EnumSet.of(JobState.Running, JobState.Disposed).contains(j.getState())),
 				job -> job.getUploadProgress().isWorking());
-		
-		
 		menu.addItem("Download result",
 				job -> executeWSCallAsync("Downloading data", p -> job.getValue().startDownload()),
 				job -> executeWSCallAsync("Stop downloading data", p -> job.getValue().stopDownload()),
-				job -> JavaFXRoutines.notNullValue(job,
-						j -> EnumSet.of(JobState.Failed, JobState.Finished, JobState.Canceled).contains(j.getState())
-								&& j.canBeDownloaded()),
+				job -> JavaFXRoutines
+						.notNullValue(job,
+								j -> EnumSet.of(JobState.Failed, JobState.Finished, JobState.Canceled)
+										.contains(j.getState()) && j.canBeDownloaded()),
 				job -> job.getDownloadProgress().isWorking());
 
 		menu.addItem("Download statistics",
@@ -146,6 +157,71 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 				job -> JavaFXRoutines.notNullValue(job, j -> j.getState().equals(JobState.Failed)));
 
 		menu.addItem("Open working directory", j -> open(j.getValue()), x -> JavaFXRoutines.notNullValue(x, j -> true));
+		
+		menu.addItem("Delete", j -> deleteJob(j.getValue()), x -> JavaFXRoutines.notNullValue(x, j -> true));
+	}
+
+	private void deleteJob(BenchmarkJob bj) {
+		bj.delete();
+		registry.update();
+	}
+
+	private void askForCreateJob() {
+		NewJobWindow newJobWindow = new NewJobWindow(null);
+		ModalDialogs.doModal(newJobWindow, WindowConstants.DISPOSE_ON_CLOSE);
+		newJobWindow.setCreatePressedNotifier(() -> executeWSCallAsync("Creating job", false,
+				new P_JobAction() {
+					@Override
+					public void doAction(Progress p) throws IOException {
+						BenchmarkJob job = doCreateJob(wd -> newJobWindow.getInputDirectory(wd), wd -> newJobWindow.getOutputDirectory(wd));
+						if (job.isUseDemoData()) {
+							job.storeDataInWorkdirectory(getConfigYamlFile());
+						} else if (Files.exists(job.getInputDirectory().resolve(CONFIG_YAML))) {
+							executorServiceFX.execute(new Runnable() {
+								
+								@Override
+								public void run() {
+									Alert al = new Alert(AlertType.CONFIRMATION,
+											"Main file \"" + CONFIG_YAML + "\" found in input directory \""
+													+ job.getInputDirectory()
+													+ "\". Would you like to copy it into job subdirectory \""
+													+ job.getDirectory() + "\"?",
+											ButtonType.YES, ButtonType.NO);
+									al.setHeaderText(null);
+									al.setTitle("Copy " + CONFIG_YAML + "?");
+									al.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
+									if (al.showAndWait().get() == ButtonType.YES) {
+										try {
+											Files.copy(job.getInputDirectory().resolve(CONFIG_YAML), job.getDirectory().resolve(CONFIG_YAML));
+										} catch (IOException e) {
+											log.error(e.getMessage(), e);
+										}
+									}
+								}
+							});
+							
+						}
+					}
+				}
+		));
+
+		
+	}
+
+	private UploadingFile getConfigYamlFile() {
+		return new UploadingFileFromResource("", Constants.CONFIG_YAML);
+	}
+	
+	private BenchmarkJob doCreateJob(Function<Path,Path> inputProvider, Function<Path,Path> outputProvider) throws IOException {
+		BenchmarkJob bj = manager.createJob(inputProvider, outputProvider);
+		ObservableBenchmarkJob obj = registry.addIfAbsent(bj);
+		addJobToItems(obj);
+		jobs.refresh();
+		return bj;
+	}
+
+	private synchronized void addJobToItems(ObservableBenchmarkJob obj) {
+		jobs.getItems().add(obj);
 	}
 
 	private void open(BenchmarkJob j) {
@@ -174,8 +250,9 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 			}
 			return null;
 		}, x -> {
-			if (update)
+			if (update) {
 				updateJobs();
+			}
 		});
 	}
 
@@ -201,11 +278,11 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 				}
 				registry.update();
 				Set<ObservableValue<BenchmarkJob>> actual = new HashSet<>(this.jobs.getItems());
-				
+
 				executorServiceFX.execute(() -> {
 					for (ObservableBenchmarkJob value : registry.getAllItems()) {
 						if (!actual.contains(value)) {
-							this.jobs.getItems().add(value);
+							addJobToItems(value);
 						}
 					}
 				});
@@ -242,7 +319,6 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 
 	private void remove(BenchmarkJob bj) {
 		jobs.getItems().remove(registry.get(bj));
-		bj.remove();
 	}
 
 	private void setCellValueFactory(int index, Function<BenchmarkJob, String> mapper) {
@@ -252,12 +328,10 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
 	@SuppressWarnings("unchecked")
 	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 JavaFXRoutines.TableCellAdapter<ObservableBenchmarkJob, CompletableFuture<String>>(
-								new JavaFXRoutines.FutureValueUpdater<ObservableBenchmarkJob, String, CompletableFuture<String>>(
-										new JavaFXRoutines.StringValueUpdater<ObservableBenchmarkJob>(),
-										executorServiceFX)));
+		((TableColumn<ObservableBenchmarkJob, CompletableFuture<String>>) jobs.getColumns().get(index)).setCellFactory(
+				column -> new JavaFXRoutines.TableCellAdapter<ObservableBenchmarkJob, CompletableFuture<String>>(
+						new JavaFXRoutines.FutureValueUpdater<ObservableBenchmarkJob, String, CompletableFuture<String>>(
+								new JavaFXRoutines.StringValueUpdater<ObservableBenchmarkJob>(), executorServiceFX)));
 	}
 
 	private interface P_JobAction {

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

+package cz.it4i.fiji.haas_spim_benchmark.ui;
+
+import java.awt.Window;
+import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+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;
+import javafx.scene.control.Alert.AlertType;
+import javafx.scene.control.Button;
+import javafx.scene.control.RadioButton;
+import javafx.scene.control.TextField;
+import javafx.scene.control.Toggle;
+import javafx.scene.control.ToggleGroup;
+import javafx.scene.layout.BorderPane;
+import javafx.stage.DirectoryChooser;
+
+public class NewJobController extends BorderPane implements CloseableControl, InitiableControl {
+
+	public enum DataLocation {
+		DEMONSTRATION_ON_SERVER, WORK_DIRECTORY, CUSTOM_DIRECTORY
+	}
+
+	private static final Runnable EMPTY_NOTIFIER = () -> {
+	};
+
+	@SuppressWarnings("unused")
+	private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas_spim_benchmark.ui.NewJobController.class);
+
+	@FXML
+	private Button bt_create;
+
+	@FXML
+	private ToggleGroup tg_inputDataLocation;
+
+	@FXML
+	private ToggleGroup tg_outputDataLocation;
+
+	@FXML
+	private RadioButton rb_ownInput;
+
+	@FXML
+	private RadioButton rb_ownOutput;
+
+	@FXML
+	private TextField et_inputDirectory;
+
+	@FXML
+	private TextField et_outputDirectory;
+
+	private DataLocation inputDataLocation;
+
+	private DataLocation outputDataLocation;
+
+	private FXFrame<?> ownerWindow;
+
+	private Runnable createPressedNotifier;
+
+	@FXML
+	private Button bt_selectInput;
+
+	@FXML
+	private Button bt_selectOutput;
+	
+	public NewJobController() {
+		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));
+		initSelectButton(et_inputDirectory, bt_selectInput);
+		initSelectButton(et_outputDirectory, bt_selectOutput);
+	}
+
+	@Override
+	public void close() {
+	}
+
+	@Override
+	public void init(Window parameter) {
+		ownerWindow = (FXFrame<?>) parameter;
+	}
+
+	public Path getInputDirectory(Path workingDirectory) {
+		return getDirectory(inputDataLocation, et_inputDirectory.getText(), workingDirectory);
+	}
+
+	public Path getOutputDirectory(Path workingDirectory) {
+		return getDirectory(outputDataLocation, et_outputDirectory.getText(), workingDirectory);
+	}
+
+	public void setCreatePressedNotifier(Runnable createPressedNotifier) {
+		if (createPressedNotifier != null) {
+			this.createPressedNotifier = createPressedNotifier;
+		} else {
+			this.createPressedNotifier = EMPTY_NOTIFIER;
+		}
+	}
+
+	private void initSelectButton(TextField textField, Button button) {
+		button.setOnAction(x -> {
+			Path p = Paths.get(textField.getText());
+			DirectoryChooser dch = new DirectoryChooser();
+			if (Files.exists(p)) {
+				dch.setInitialDirectory(p.toAbsolutePath().toFile());
+			}
+			File result = dch.showDialog(ownerWindow.getFxPanel().getScene().getWindow());
+			if (result != null) {
+				textField.setText(result.toString());
+			}
+		});
+	}
+
+	private Path getDirectory(DataLocation dataLocation, String selectedDirectory, Path workingDirectory) {
+		switch (dataLocation) {
+		case DEMONSTRATION_ON_SERVER:
+			return null;
+		case WORK_DIRECTORY:
+			return workingDirectory;
+		case CUSTOM_DIRECTORY:
+			return Paths.get(selectedDirectory).toAbsolutePath();
+		default:
+			throw new UnsupportedOperationException("Not support " + dataLocation);
+		}
+	}
+
+	private void createPressed() {
+		obtainValues();
+		if (checkDirectoryLocationIfNeeded()) {
+			ownerWindow.setVisible(false);
+			ownerWindow.dispose();
+			createPressedNotifier.run();
+		}
+	}
+
+	private boolean checkDirectoryLocationIfNeeded() {
+		return checkDataLocationValue(inputDataLocation, et_inputDirectory.getText(), "input")
+				&& checkDataLocationValue(outputDataLocation, et_outputDirectory.getText(), "output");
+
+	}
+
+	private boolean checkDataLocationValue(DataLocation dataLocation, String directory, String type) {
+		Path directoryPath = Paths.get(directory);
+		if (dataLocation == DataLocation.CUSTOM_DIRECTORY && (!Files.exists(directoryPath) || directory.isEmpty())) {
+			Alert alert = new Alert(AlertType.WARNING);
+			alert.setTitle("Invalid input provided");
+			alert.setHeaderText(null);
+			String message = !directory.isEmpty() ? "Directory %s for %s not exists"
+					: "Directory for %2$s is not selected.";
+			alert.setContentText(String.format(message, directoryPath.toAbsolutePath(), type));
+			alert.showAndWait();
+			return false;
+		}
+		return true;
+	}
+
+	private void obtainValues() {
+		inputDataLocation = obtainDataLocation(tg_inputDataLocation);
+		outputDataLocation = obtainDataLocation(tg_outputDataLocation);
+	}
+
+	private DataLocation obtainDataLocation(ToggleGroup group) {
+		int backawardOrderOfSelected = group.getToggles().size()
+				- group.getToggles().indexOf(group.getSelectedToggle());
+		return DataLocation.values()[DataLocation.values().length - backawardOrderOfSelected];
+	}
+
+	private void selected(ObservableValue<? extends Toggle> v, Toggle o, 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/NewJobWindow.java

+package cz.it4i.fiji.haas_spim_benchmark.ui;
+
+import java.awt.Window;
+import java.nio.file.Path;
+
+import cz.it4i.fiji.haas.ui.FXFrame;
+
+public class NewJobWindow extends FXFrame<NewJobController>{
+
+	private static final long serialVersionUID = 1L;
+	
+
+	
+	public NewJobWindow(Window parentWindow) {
+		super(parentWindow,()->{
+			return new NewJobController();
+			
+		});
+		setTitle("Create job");
+	}
+	
+	public Path getInputDirectory(Path workingDirectory) {
+		return getFxPanel().getControl().getInputDirectory(workingDirectory);
+	}
+	
+	public Path getOutputDirectory(Path workingDirectory) {
+		return getFxPanel().getControl().getOutputDirectory(workingDirectory);
+	}
+
+
+	public void setCreatePressedNotifier(Runnable runnable) {
+		getFxPanel().getControl().setCreatePressedNotifier(runnable);
+	}
+}
\ No newline at end of file

haas-spim-benchmark/src/main/resources/cz/it4i/fiji/haas_spim_benchmark/ui/NewJobView.css

+{
+	-fx-padding: 3 3 3 3;
+	
+}
\ No newline at end of file

haas-spim-benchmark/src/main/resources/cz/it4i/fiji/haas_spim_benchmark/ui/NewJobView.fxml

+<?xml version="1.0" encoding="UTF-8"?>
+
+<?import javafx.geometry.Insets?>
+<?import javafx.scene.control.Button?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.RadioButton?>
+<?import javafx.scene.control.TextField?>
+<?import javafx.scene.control.TitledPane?>
+<?import javafx.scene.control.ToggleGroup?>
+<?import javafx.scene.layout.AnchorPane?>
+<?import javafx.scene.layout.BorderPane?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+
+<fx:root maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" type="BorderPane" xmlns="http://javafx.com/javafx/8.0.65" xmlns:fx="http://javafx.com/fxml/1" fx:controller="cz.it4i.fiji.haas_spim_benchmark.ui.NewJobController">
+   <center>
+      <VBox BorderPane.alignment="CENTER">
+         <children>
+            <TitledPane animated="false" collapsible="false" text="Input">
+               <content>
+                  <AnchorPane>
+                     <children>
+                        <VBox>
+                           <children>
+                              <RadioButton mnemonicParsing="false" selected="true">
+                                 <toggleGroup>
+                                    <ToggleGroup fx:id="tg_inputDataLocation" />
+                                 </toggleGroup>
+                                 <graphic>
+                                    <Label maxHeight="1.7976931348623157E308" text="Demonstration data on IT4I cluster" />
+                                 </graphic>
+                              </RadioButton>
+                              <RadioButton maxHeight="1.7976931348623157E308" mnemonicParsing="false" toggleGroup="$tg_inputDataLocation">
+                                 <graphic>
+                                    <Label maxHeight="1.7976931348623157E308" text="Job subdirectory" />
+                                 </graphic>
+                              </RadioButton>
+                              <RadioButton fx:id="rb_ownInput" mnemonicParsing="false" toggleGroup="$tg_inputDataLocation">
+                                 <graphic>
+                                    <HBox disable="true">
+                                       <children>
+                                          <TextField fx:id="et_inputDirectory" prefWidth="350.0" />
+                                          <Button fx:id="bt_selectInput" mnemonicParsing="false" text="Select" />
+                                       </children>
+                                    </HBox>
+                                 </graphic>
+                              </RadioButton>
+                           </children>
+                        </VBox>
+                     </children>
+                  </AnchorPane>
+               </content>
+            </TitledPane>
+            <TitledPane animated="false" collapsible="false" text="Output">
+               <content>
+                  <AnchorPane minHeight="0.0" minWidth="0.0">
+                     <children>
+                        <VBox>
+                           <children>
+                              <HBox>
+                                 <children>
+                                    <RadioButton maxHeight="1.7976931348623157E308" mnemonicParsing="false" selected="true">
+                                       <toggleGroup>
+                                          <ToggleGroup fx:id="tg_outputDataLocation" />
+                                       </toggleGroup>
+                                       <graphic>
+                                          <Label maxHeight="1.7976931348623157E308" text="Job subdirectory" />
+                                       </graphic>
+                                    </RadioButton>
+                                 </children>
+                              </HBox>
+                              <HBox>
+                                 <children>
+                                    <RadioButton fx:id="rb_ownOutput" mnemonicParsing="false" toggleGroup="$tg_outputDataLocation">
+                                       <graphic>
+                                          <HBox disable="true">
+                                             <children>
+                                                <TextField fx:id="et_outputDirectory" prefWidth="350.0" />
+                                                <Button fx:id="bt_selectOutput" mnemonicParsing="false" text="Select" />
+                                             </children>
+                                          </HBox>
+                                       </graphic>
+                                    </RadioButton>
+                                 </children>
+                              </HBox>
+                           </children>
+                        </VBox>
+                     </children>
+                  </AnchorPane>
+               </content>
+            </TitledPane>
+         </children>
+      </VBox>
+   </center>
+   <bottom>
+      <BorderPane BorderPane.alignment="CENTER">
+         <right>
+            <Button fx:id="bt_create" mnemonicParsing="false" prefHeight="22.0" prefWidth="71.0" text="Create" BorderPane.alignment="CENTER">
+               <BorderPane.margin>
+                  <Insets right="3.0" />
+               </BorderPane.margin></Button>
+         </right>
+      </BorderPane>
+   </bottom>
+</fx:root>