diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/Job.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/Job.java
index 11c7654110f6848d990963f330a4e619cef09c21..330bb892da3866d92dae5e2f887329059628ad0d 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/Job.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/Job.java
@@ -437,7 +437,7 @@ public class Job {
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);
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/JobManager.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/JobManager.java
index 46f2d65f7099cf1e020de1bec579919ecebe4828..902780ceb5812c3d3f42d58cf3140c662ae47357 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/JobManager.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/JobManager.java
@@ -7,6 +7,7 @@ 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;
@@ -20,10 +21,14 @@ public class JobManager implements Closeable {
interface JobManager4Job {
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;
@@ -32,6 +37,8 @@ public class JobManager implements Closeable {
private final Settings settings;
+ private BiPredicate<Job, Path> uploadFilter = DUMMY_UPLOAD_FILTER;
+
private final JobManager4Job remover = new JobManager4Job() {
@Override
@@ -39,6 +46,11 @@ public class JobManager implements Closeable {
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) {
@@ -65,6 +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);
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/data_transfer/Synchronization.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/data_transfer/Synchronization.java
index 14c581b98ae17965e549280432393a7f03579982..f2f2181efb8e24e8db9ebd754ab58384fd78b9bc 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/data_transfer/Synchronization.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/data_transfer/Synchronization.java
@@ -12,6 +12,7 @@ import java.util.Collections;
import java.util.LinkedList;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
+import java.util.function.Predicate;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
@@ -48,14 +49,10 @@ public class Synchronization implements Closeable {
private final ExecutorService service;
-// public Synchronization(Supplier<HaaSFileTransfer> fileTransferSupplier, Path workingDirectory,
-// Runnable uploadFinishedNotifier, Runnable downloadFinishedNotifier) throws IOException {
-// this(fileTransferSupplier, workingDirectory, workingDirectory, workingDirectory, uploadFinishedNotifier,
-// downloadFinishedNotifier);
-// }
-
+ private final Predicate<Path> uploadFilter;
+
public Synchronization(Supplier<HaaSFileTransfer> fileTransferSupplier, Path workingDirectory, Path inputDirectory,
- Path outputDirectory, Runnable uploadFinishedNotifier, Runnable downloadFinishedNotifier)
+ Path outputDirectory, Runnable uploadFinishedNotifier, Runnable downloadFinishedNotifier, Predicate<Path> uploadFilter)
throws IOException {
this.workingDirectory = workingDirectory;
this.inputDirectory = inputDirectory;
@@ -65,6 +62,7 @@ public class Synchronization implements Closeable {
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) {
@@ -109,8 +107,8 @@ 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,
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
index d74cace55ffbc4b0bd170ea5652ce245ff48a9ba..e565d1d65a5c53e1bcee290802eb4d8bb731e336 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
@@ -25,6 +25,7 @@ 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;
@@ -252,13 +253,12 @@ public class BenchmarkJobManager implements Closeable {
public boolean needsUpload() {
return job.needsUpload();
}
-
@Override
public String toString() {
return "" + getId();
}
-
+
public void storeDataInWorkdirectory(UploadingFile file) throws IOException {
job.storeDataInWorkdirectory(file);
}
@@ -460,11 +460,12 @@ public class BenchmarkJobManager implements Closeable {
Stream<BenchmarkError> taskSpecificErrors = tasks.stream().flatMap(s -> s.getErrors().stream());
return Stream.concat(nonTaskSpecificErrors.stream(), taskSpecificErrors).collect(Collectors.toList());
}
-
+
}
public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
+ jobManager.setUploadFilter(this::canUpload);
}
public BenchmarkJob createJob(Function<Path, Path> inputDirectoryProvider,
@@ -583,7 +584,10 @@ public class BenchmarkJobManager implements Closeable {
jobManager.close();
}
-
+ private boolean canUpload(Job job, Path p) {
+ return job.getInputDirectory() == null || !p.equals(job.getInputDirectory().resolve(Constants.CONFIG_YAML));
+ }
+
private BenchmarkJob convertJob(Job job) {
return new BenchmarkJob(job);
}
@@ -591,9 +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");
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMController.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMController.java
index fd33cca18396606dab930e2ae0e5feaa5a4a94f8..cf34023108706defbe30d1456a720d107a8837c1 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMController.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMController.java
@@ -1,5 +1,7 @@
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;
@@ -21,7 +23,6 @@ import java.util.function.Function;
import javax.swing.WindowConstants;
-import org.apache.commons.lang3.NotImplementedException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -43,9 +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
@@ -171,8 +176,30 @@ public class BenchmarkSPIMController extends BorderPane implements CloseableCont
BenchmarkJob job = doCreateJob(wd -> newJobWindow.getInputDirectory(wd), wd -> newJobWindow.getOutputDirectory(wd));
if (job.isUseDemoData()) {
job.storeDataInWorkdirectory(getConfigYamlFile());
- } else if (Files.exists(job.getInputDirectory().resolve(Constants.CONFIG_YAML))) {
- throw new NotImplementedException("");
+ } 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);
+ }
+ }
+ }
+ });
+
}
}
}