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 0e92fe7ac30f71375f580d7eb682609c0310c744..38058e58e35ac021ab6a459c5344e9e21b53e7c3 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
@@ -9,6 +9,7 @@ import java.nio.file.StandardOpenOption;
import java.util.Calendar;
import java.util.Collections;
import java.util.EnumSet;
+import java.util.List;
import java.util.Properties;
import java.util.function.Predicate;
import java.util.function.Supplier;
@@ -49,73 +50,47 @@ public class Job {
private Boolean needsDownload;
private JobInfo jobInfo;
private Long jobId;
- private ProgressNotifier notifier;
+
- final private Progress dummy = new Progress() {
-
- @Override
- public void setTitle(String title) {
- }
-
- @Override
- public void setItemCount(int count, int total) {
- }
-
- @Override
- public void setCount(int count, int total) {
- }
-
- @Override
- public void itemDone(Object item) {
- }
-
- @Override
- public void done() {
- }
-
- @Override
- public void addItem(Object item) {
- }
- };
private String name;
- public Job(String name, Path basePath, Supplier<HaaSClient> haasClientSupplier, Progress progress)
+ public Job(String name, Path basePath, Supplier<HaaSClient> haasClientSupplier)
throws IOException {
- this(haasClientSupplier, progress);
+ this(haasClientSupplier);
HaaSClient client = this.haasClientSupplier.get();
- long id = client.createJob(name, Collections.emptyList(), notifier);
+ long id = client.createJob(name, Collections.emptyList());
jobDir = basePath.resolve("" + id);
this.name = name;
Files.createDirectory(jobDir);
- updateState();
+ updateNeedsDownload();
}
- public Job(Path p, Supplier<HaaSClient> haasClientSupplier, Progress progress) throws IOException {
- this(haasClientSupplier, progress);
+ public Job(Path p, Supplier<HaaSClient> haasClientSupplier) throws IOException {
+ this(haasClientSupplier);
jobDir = p;
loadJobInfo();
- updateState();
+ updateNeedsDownload();
}
- public void uploadFiles(Iterable<UploadingFile> files) {
+ public void uploadFiles(Iterable<UploadingFile> files, Progress notifier) {
HaaSClient client = this.haasClientSupplier.get();
- client.uploadFiles(jobId, files, notifier);
+
+ client.uploadFiles(jobId, files, new P_ProgressNotifierAdapter(notifier));
}
- public void uploadFilesByName(Iterable<String> files) {
+ public void uploadFilesByName(Iterable<String> files, Progress notifier) {
Iterable<UploadingFile> uploadingFiles = StreamSupport.stream(files.spliterator(), false)
.map((String name) -> HaaSClient.getUploadingFile(jobDir.resolve(name))).collect(Collectors.toList());
- uploadFiles(uploadingFiles);
+ uploadFiles(uploadingFiles, notifier);
}
public void submit() {
HaaSClient client = this.haasClientSupplier.get();
- client.submitJob(jobId, notifier);
+ client.submitJob(jobId);
}
- private Job(Supplier<HaaSClient> haasClientSupplier, Progress progress) throws IOException {
- notifier = new P_ProgressNotifierAdapter(progress);
+ private Job(Supplier<HaaSClient> haasClientSupplier) throws IOException {
this.haasClientSupplier = haasClientSupplier;
}
@@ -130,16 +105,10 @@ public class Job {
return jobId;
}
- synchronized public void updateState() throws IOException {
- if (needsDownload == null
- && EnumSet.of(JobState.Failed, JobState.Finished, JobState.Canceled).contains(getState())) {
- needsDownload = true;
- }
- saveJobinfo();
- }
+
- public void download() {
- download(x -> true, dummy);
+ public void download(Progress notifier) {
+ download(x -> true, notifier);
}
public Path storeDataInWorkdirectory(UploadingFile uploadingFile) throws IOException {
@@ -150,11 +119,11 @@ public class Job {
return result;
}
- synchronized public void download(Predicate<String> predicate, Progress progress) {
+ synchronized public void download(Predicate<String> predicate, Progress notifier) {
if (!needsDownload()) {
throw new IllegalStateException("Job: " + getJobId() + " doesn't need download");
}
- haasClientSupplier.get().download(getJobId(), jobDir, predicate, new P_ProgressNotifierAdapter(progress));
+ haasClientSupplier.get().download(getJobId(), jobDir, predicate, new P_ProgressNotifierAdapter(notifier));
needsDownload = false;
try {
saveJobinfo();
@@ -179,7 +148,7 @@ public class Job {
return jobInfo.getEndTime();
}
- public Iterable<String> getOutput(Iterable<JobSynchronizableFile> output) {
+ public List<String> getOutput(Iterable<JobSynchronizableFile> output) {
HaaSClient.SynchronizableFiles taskFileOffset = new HaaSClient.SynchronizableFiles();
long taskId = (Long) getJobInfo().getTasks().toArray()[0];
output.forEach(file -> taskFileOffset.addFile(taskId, file.getType(), file.getOffset()));
@@ -200,6 +169,22 @@ public class Job {
public String getProperty(String name) throws IOException {
return loadPropertiesIfExists().getProperty(name);
}
+
+ public void updateInfo() {
+ updateJobInfo();
+ }
+
+ public Path getDirectory() {
+ return jobDir;
+ }
+
+ synchronized private void updateNeedsDownload() throws IOException {
+ if (needsDownload == null
+ && EnumSet.of(JobState.Failed, JobState.Finished, JobState.Canceled).contains(getState())) {
+ needsDownload = true;
+ }
+ saveJobinfo();
+ }
private synchronized void saveJobinfo() throws IOException {
Properties prop = loadPropertiesIfExists();
@@ -244,6 +229,11 @@ public class Job {
private void updateJobInfo() {
jobInfo = haasClientSupplier.get().obtainJobInfo(getJobId());
+ try {
+ updateNeedsDownload();
+ } catch (IOException e) {
+ log.error(e.getMessage(), e);
+ }
}
private static boolean isValidPath(Path path) {
@@ -294,4 +284,6 @@ public class Job {
}
+
+
}
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 062f69260d4465940cce5e7d3599ddbfdaa64654..2b5d9913c8a98eb12aea9c969e014629b4c3eda5 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
@@ -8,6 +8,7 @@ import java.util.Calendar;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedList;
+import java.util.List;
import java.util.function.Predicate;
import java.util.stream.Collectors;
@@ -24,6 +25,7 @@ import net.imagej.updater.util.Progress;
public class JobManager {
+ @SuppressWarnings("unused")
private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.JobManager.class);
private Path workDirectory;
@@ -34,33 +36,29 @@ public class JobManager {
private Settings settings;
- public JobManager(Path workDirectory, Settings settings){
+ public JobManager(Path workDirectory, Settings settings) {
this.workDirectory = workDirectory;
this.settings = settings;
}
- public JobInfo createJob(Progress progress) throws IOException {
+ public JobInfo createJob() throws IOException {
Job job;
- if(jobs == null) {
+ if (jobs == null) {
jobs = new LinkedList<>();
}
- jobs.add(job = new Job(settings.getJobName(), workDirectory, this::getHaasClient, progress));
+ jobs.add(job = new Job(settings.getJobName(), workDirectory, this::getHaasClient));
return new JobInfo(job) {
@Override
public JobState getState() {
- try {
- job.updateState();
- } catch (IOException e) {
- log.error(e.getMessage(), e);
- }
+ job.updateInfo();
return super.getState();
}
};
}
- public JobInfo startJob(Iterable<UploadingFile> files, Progress progress) throws IOException {
- JobInfo result = createJob(progress);
- result.uploadFiles(files);
+ public JobInfo startJob(Iterable<UploadingFile> files, Progress notifier) throws IOException {
+ JobInfo result = createJob();
+ result.uploadFiles(files, notifier);
result.submit();
return result;
}
@@ -69,12 +67,12 @@ public class JobManager {
return () -> jobs.stream().filter(j -> j.needsDownload()).map(j -> new JobInfo(j)).iterator();
}
- public Collection<JobInfo> getJobs(Progress progress) throws IOException {
- if(jobs == null) {
+ public Collection<JobInfo> getJobs() throws IOException {
+ if (jobs == null) {
jobs = new LinkedList<>();
Files.list(this.workDirectory).filter(p -> Files.isDirectory(p) && Job.isJobPath(p)).forEach(p -> {
try {
- jobs.add(new Job(p, this::getHaasClient, progress));
+ jobs.add(new Job(p, this::getHaasClient));
} catch (IOException e) {
e.printStackTrace();
}
@@ -83,10 +81,10 @@ public class JobManager {
return jobs.stream().map(j -> new JobInfo(j)).collect(Collectors.toList());
}
- public void downloadJob(Long id) {
+ public void downloadJob(Long id, Progress notifier) {
Iterator<Job> job = jobs.stream().filter(j -> j.getJobId() == id).iterator();
assert job.hasNext();
- job.next().download();
+ job.next().download(notifier);
}
@@ -100,18 +98,21 @@ public class JobManager {
}
return haasClient;
}
-
+
public static class JobSynchronizableFile {
private SynchronizableFileType type;
private long offset;
+
public JobSynchronizableFile(SynchronizableFileType type, long offset) {
super();
this.type = type;
this.offset = offset;
}
+
public SynchronizableFileType getType() {
return type;
}
+
public long getOffset() {
return offset;
}
@@ -125,12 +126,12 @@ public class JobManager {
this.job = job;
}
- public void uploadFiles(Iterable<UploadingFile> files) {
- job.uploadFiles(files);
+ public void uploadFiles(Iterable<UploadingFile> files, Progress notifier) {
+ job.uploadFiles(files,notifier);
}
-
- public void uploadFilesByName(Iterable<String> files) {
- job.uploadFilesByName(files);
+
+ public void uploadFilesByName(Iterable<String> files, Progress notifier) {
+ job.uploadFilesByName(files, notifier);
}
public void submit() {
@@ -161,14 +162,14 @@ public class JobManager {
return getStringFromTimeSafely(job.getEndTime());
}
- public void downloadData(Progress progress) {
- downloadData(x->true, progress);
+ public void downloadData(Progress notifier) {
+ downloadData(x -> true, notifier);
}
-
- public void downloadData(Predicate<String> predicate, Progress progress) {
- job.download(predicate,progress);
+
+ public void downloadData(Predicate<String> predicate, Progress notifier) {
+ job.download(predicate, notifier);
fireValueChangedEvent();
-
+
}
public void waitForStart() {
@@ -176,8 +177,8 @@ public class JobManager {
}
- public void updateInfo() throws IOException {
- job.updateState();
+ public void updateInfo() {
+ job.updateInfo();
}
@Override
@@ -188,11 +189,11 @@ public class JobManager {
public Path storeDataInWorkdirectory(UploadingFile uploadingFile) throws IOException {
return job.storeDataInWorkdirectory(uploadingFile);
}
-
- public Iterable<String> getOutput(Iterable<JobSynchronizableFile> files) {
+
+ public List<String> getOutput(Iterable<JobSynchronizableFile> files) {
return job.getOutput(files);
}
-
+
private String getStringFromTimeSafely(Calendar time) {
return time != null ? time.getTime().toString() : "N/A";
}
@@ -203,15 +204,16 @@ public class JobManager {
public void setProperty(String name, String value) throws IOException {
job.setProperty(name, value);
-
+
}
public String getProperty(String name) throws IOException {
return job.getProperty(name);
}
-
-
+ public Path getDirectory() {
+ return job.getDirectory();
+ }
}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/DummyProgress.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/DummyProgress.java
new file mode 100644
index 0000000000000000000000000000000000000000..d91a0beb69b97af2c4dbe4c9aa8ee3dd5a74991e
--- /dev/null
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/DummyProgress.java
@@ -0,0 +1,37 @@
+package cz.it4i.fiji.haas.ui;
+
+import net.imagej.updater.util.Progress;
+
+public class DummyProgress implements Progress {
+
+ @Override
+ public void setTitle(String title) {
+
+ }
+
+ @Override
+ public void setCount(int count, int total) {
+
+ }
+
+ @Override
+ public void addItem(Object item) {
+
+ }
+
+ @Override
+ public void setItemCount(int count, int total) {
+
+ }
+
+ @Override
+ public void itemDone(Object item) {
+
+ }
+
+ @Override
+ public void done() {
+
+ }
+
+}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java
index f3601be3950eeea7c3e7bd1d741b731bb988bd75..d52a841d02d62a04709a509316187212a1faddab 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java
@@ -3,21 +3,35 @@ package cz.it4i.fiji.haas.ui;
import java.awt.Dimension;
import java.awt.Frame;
import java.awt.Window;
+import java.awt.im.InputMethodRequests;
import java.io.IOException;
import java.net.URL;
import java.util.function.Consumer;
import javax.swing.JDialog;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import javafx.application.Platform;
import javafx.embed.swing.JFXPanel;
import javafx.fxml.FXMLLoader;
import javafx.scene.Parent;
import javafx.scene.Scene;
-
public class FXFrame<C extends FXFrame.Controller> extends JDialog {
+ @SuppressWarnings("unused")
+ private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.ui.FXFrame.class);
+
+ static public void runOnFxThread(Runnable runnable) {
+ if (Platform.isFxApplicationThread()) {
+ runnable.run();
+ } else {
+ Platform.runLater(runnable);
+ }
+ }
+
public interface Controller {
void init(Window frame);
}
@@ -42,18 +56,12 @@ public class FXFrame<C extends FXFrame.Controller> extends JDialog {
*/
protected void init(Consumer<C> controlerInit) {
this.controlerInit = controlerInit;
- this.fxPanel = new JFXPanel();
+ this.fxPanel = new P_JFXPanel();
Platform.setImplicitExit(false);
this.add(this.fxPanel);
// The call to runLater() avoid a mix between JavaFX thread and Swing thread.
- Platform.runLater(new Runnable() {
- @Override
- public void run() {
- initFX(fxPanel);
- }
-
- });
+ runOnFxThread(() -> initFX(fxPanel));
}
@@ -69,10 +77,6 @@ public class FXFrame<C extends FXFrame.Controller> extends JDialog {
loader.setLocation(res);
Parent rootLayout = (Parent) loader.load();
- // Get the controller and add an ImageJ context to it.
- controller = loader.<C>getController();
- controlerInit.accept(controller);
- controller.init(this);
// Show the scene containing the root layout.
Scene scene = new Scene(rootLayout);
this.fxPanel.setScene(scene);
@@ -85,6 +89,10 @@ public class FXFrame<C extends FXFrame.Controller> extends JDialog {
this.fxPanel.setPreferredSize(dim);
// this.setSize((int) scene.getWidth(), (int) scene.getHeight());
this.pack();
+ // Get the controller and add an ImageJ context to it.
+ controller = loader.<C>getController();
+ controlerInit.accept(controller);
+ controller.init(this);
} catch (IOException e) {
e.printStackTrace();
@@ -92,4 +100,22 @@ public class FXFrame<C extends FXFrame.Controller> extends JDialog {
}
+ private static class P_JFXPanel extends JFXPanel {
+ private static final long serialVersionUID = 1L;
+
+
+ @Override
+ public synchronized InputMethodRequests getInputMethodRequests() {
+ try {
+ return super.getInputMethodRequests();
+ } catch(NullPointerException e) {
+ //IGNORE FIX ISSUE https://bugs.openjdk.java.net/browse/JDK-8098836
+ return null;
+ }
+ }
+
+
+
+ };
+
}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java
index de2a03a50f10377d00c540e7bb6f0e1b3440ab83..1a1cb4b54bf5eb3011c92704f1c77346b1dbe065 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java
@@ -1,12 +1,19 @@
package cz.it4i.fiji.haas.ui;
+import java.util.concurrent.CompletableFuture;
+
import javax.swing.JDialog;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public class ModalDialogs {
+ @SuppressWarnings("unused")
+ private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.ui.ModalDialogs.class);
public static <T extends JDialog>T doModal(T dialog, int operation) {
dialog.setModal(true);
dialog.setDefaultCloseOperation(operation);
- new Thread(()->dialog.setVisible(true)).start();
+ CompletableFuture.runAsync(()->dialog.setVisible(true));
return dialog;
}
}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java
index acd8050822221d2b14cec5c934b6129e4c539d73..6b7b453d5c418640bf3c111a0b2a0e75f7ccb5e0 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java
@@ -1,5 +1,4 @@
- package cz.it4i.fiji.haas.ui;
-
+package cz.it4i.fiji.haas.ui;
import java.awt.Adjustable;
import java.awt.Container;
@@ -20,17 +19,22 @@ import javax.swing.JProgressBar;
import javax.swing.JScrollPane;
import javax.swing.ScrollPaneConstants;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import net.imagej.ui.swing.updater.SwingTools;
import net.imagej.updater.util.Progress;
import net.imagej.updater.util.UpdateCanceledException;
/**
-* TODO
-*
-* @author Johannes Schindelin
-*/
+ * TODO
+ *
+ * @author Johannes Schindelin
+ */
@SuppressWarnings("serial")
public class ProgressDialog extends JDialog implements Progress {
+ @SuppressWarnings("unused")
+ private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.ui.ProgressDialog.class);
JProgressBar progress;
JButton detailsToggle;
@@ -47,7 +51,7 @@ public class ProgressDialog extends JDialog implements Progress {
}
public ProgressDialog(final Window owner, final String title) {
- super(owner);
+ super(owner, title);
final Container root = getContentPane();
root.setLayout(new BoxLayout(root, BoxLayout.Y_AXIS));
@@ -75,14 +79,12 @@ public class ProgressDialog extends JDialog implements Progress {
ProgressDialog.this.dispose();
}
});
- buttons.add(cancel);
+ // buttons.add(cancel);
buttons.setMaximumSize(buttons.getMinimumSize());
root.add(buttons);
details = new Details();
- detailsScrollPane =
- new JScrollPane(details,
- ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED,
+ detailsScrollPane = new JScrollPane(details, ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
detailsScrollPane.getVerticalScrollBar().addAdjustmentListener(new AdjustmentListener() {
@@ -98,7 +100,8 @@ public class ProgressDialog extends JDialog implements Progress {
detailsScrollPane.setVisible(false);
root.add(detailsScrollPane);
- if (title != null) setTitle(title);
+ if (title != null)
+ setTitle(title);
pack();
if (owner != null) {
@@ -108,15 +111,15 @@ public class ProgressDialog extends JDialog implements Progress {
size.width = o.width / 2;
setSize(size);
}
- setLocation(owner.getX() + (o.width - size.width) / 2, owner.getY() +
- (o.height - size.height) / 2);
+ setLocation(owner.getX() + (o.width - size.width) / 2, owner.getY() + (o.height - size.height) / 2);
}
final KeyAdapter keyAdapter = new KeyAdapter() {
@Override
public void keyReleased(final KeyEvent e) {
- if (e.getKeyCode() == KeyEvent.VK_ESCAPE) cancel();
+ if (e.getKeyCode() == KeyEvent.VK_ESCAPE)
+ cancel();
}
};
root.addKeyListener(keyAdapter);
@@ -124,7 +127,8 @@ public class ProgressDialog extends JDialog implements Progress {
cancel.addKeyListener(keyAdapter);
setLocationRelativeTo(null);
- if (title != null) setVisible(true);
+ if (title != null)
+ setVisible(true);
}
public void cancel() {
@@ -132,7 +136,8 @@ public class ProgressDialog extends JDialog implements Progress {
}
protected void checkIfCanceled() {
- if (canceled) throw new UpdateCanceledException();
+ if (canceled)
+ throw new UpdateCanceledException();
}
@Override
@@ -147,9 +152,10 @@ public class ProgressDialog extends JDialog implements Progress {
SwingTools.invokeOnEDT(new Runnable() {
@Override
public void run() {
- if (detailsScrollPane.isVisible() || latestDetail == null) progress
- .setString(title);
- else progress.setString(title + ": " + latestDetail.getString());
+ if (detailsScrollPane.isVisible() || latestDetail == null)
+ progress.setString(title);
+ else
+ progress.setString(title + ": " + latestDetail.getString());
}
});
repaint();
@@ -158,7 +164,8 @@ public class ProgressDialog extends JDialog implements Progress {
@Override
public void setCount(final int count, final int total) {
checkIfCanceled();
- if (updatesTooFast()) return;
+ if (updatesTooFast())
+ return;
SwingTools.invokeOnEDT(new Runnable() {
@Override
public void run() {
@@ -173,7 +180,8 @@ public class ProgressDialog extends JDialog implements Progress {
public void addItem(final Object item) {
checkIfCanceled();
details.addDetail(item.toString());
- if (itemUpdatesTooFast() && !detailsScrollPane.isVisible()) return;
+ if (itemUpdatesTooFast() && !detailsScrollPane.isVisible())
+ return;
setTitle();
validate();
repaint();
@@ -182,7 +190,8 @@ public class ProgressDialog extends JDialog implements Progress {
@Override
public void setItemCount(final int count, final int total) {
checkIfCanceled();
- if (itemUpdatesTooFast()) return;
+ if (itemUpdatesTooFast())
+ return;
SwingTools.invokeOnEDT(new Runnable() {
@Override
public void run() {
@@ -196,7 +205,9 @@ public class ProgressDialog extends JDialog implements Progress {
@Override
public void itemDone(final Object item) {
checkIfCanceled();
- if (itemUpdatesTooFast() && !detailsScrollPane.isVisible()) return;
+ if (itemUpdatesTooFast() && !detailsScrollPane.isVisible())
+ return;
+
SwingTools.invokeOnEDT(new Runnable() {
@Override
public void run() {
@@ -207,7 +218,8 @@ public class ProgressDialog extends JDialog implements Progress {
@Override
public void done() {
- if (latestDetail != null) latestDetail.setValue(latestDetail.getMaximum());
+ if (latestDetail != null)
+ latestDetail.setValue(latestDetail.getMaximum());
SwingTools.invokeOnEDT(new Runnable() {
@Override
public void run() {
@@ -228,7 +240,8 @@ public class ProgressDialog extends JDialog implements Progress {
setTitle();
final Dimension dimension = getSize();
- if (toggleHeight == -1) toggleHeight = dimension.height + 100;
+ if (toggleHeight == -1)
+ toggleHeight = dimension.height + 100;
setSize(new Dimension(dimension.width, toggleHeight));
toggleHeight = dimension.height;
}
@@ -260,13 +273,15 @@ public class ProgressDialog extends JDialog implements Progress {
}
protected boolean updatesTooFast() {
- if (System.currentTimeMillis() - latestUpdate < 50) return true;
+ if (System.currentTimeMillis() - latestUpdate < 50)
+ return true;
latestUpdate = System.currentTimeMillis();
return false;
}
protected boolean itemUpdatesTooFast() {
- if (System.currentTimeMillis() - itemLatestUpdate < 50) return true;
+ if (System.currentTimeMillis() - itemLatestUpdate < 50)
+ return true;
itemLatestUpdate = System.currentTimeMillis();
return false;
}
@@ -277,4 +292,3 @@ public class ProgressDialog extends JDialog implements Progress {
dialog.setVisible(true);
}
}
-
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/TableViewContextMenu.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/TableViewContextMenu.java
new file mode 100644
index 0000000000000000000000000000000000000000..78acda8aa157379f6f30299a2e06635c76995a6e
--- /dev/null
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/TableViewContextMenu.java
@@ -0,0 +1,65 @@
+package cz.it4i.fiji.haas.ui;
+
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.function.Consumer;
+import java.util.function.Predicate;
+
+import javafx.event.EventHandler;
+import javafx.scene.control.ContextMenu;
+import javafx.scene.control.MenuItem;
+import javafx.scene.control.TableView;
+import javafx.scene.input.ContextMenuEvent;
+
+public class TableViewContextMenu<T> {
+ private Collection<P_MenuItem> items = new LinkedList<TableViewContextMenu<T>.P_MenuItem>();
+ private ContextMenu cm;
+ private TableView<T> tableView;
+
+ public TableViewContextMenu(TableView<T> tableView) {
+ this.cm = new ContextMenu();
+ this.tableView = tableView;
+ tableView.setContextMenu(cm);
+ tableView.setOnContextMenuRequested(new EventHandler<ContextMenuEvent>() {
+ @Override
+ public void handle(ContextMenuEvent event) {
+ T selected = getSelectedItem();
+ for (P_MenuItem item : items) {
+ item.updateEnable(selected);
+ }
+ }
+ });
+ }
+
+ public void addItem(String text, Consumer<T> eventHandler, Predicate<T> enableHandler) {
+ items.add(new P_MenuItem(text, eventHandler, enableHandler));
+ }
+
+ private T getSelectedItem() {
+ T result = null;
+ if (tableView.getSelectionModel().getSelectedCells().size() >= 0) {
+ result = tableView.getSelectionModel().getSelectedItem();
+ }
+ return result;
+ }
+
+ private class P_MenuItem {
+
+ private MenuItem item;
+ private Predicate<T> enableHandler;
+
+ public P_MenuItem(String text, Consumer<T> eventHandler, Predicate<T> enableHandler) {
+ super();
+ this.enableHandler = enableHandler;
+ item = new MenuItem(text);
+ item.setOnAction(e -> eventHandler.accept(getSelectedItem()));
+ cm.getItems().add(item);
+ }
+
+ public void updateEnable(T selected) {
+ item.setDisable(!enableHandler.test(selected));
+ }
+
+ }
+
+}
diff --git a/haas-java-client/.classpath b/haas-java-client/.classpath
index af1430be15836d78425a795565a49fcd23d562b4..8433ca6cd09c102eb627ee07ccba5210fb875e64 100644
--- a/haas-java-client/.classpath
+++ b/haas-java-client/.classpath
@@ -22,5 +22,15 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/.gitignore b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/.gitignore
index 702c8b4dfc8d2cf814f8eaa495f6397ba279a113..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/.gitignore
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/.gitignore
@@ -1 +0,0 @@
-/Constants.java
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Configuration.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Configuration.java
new file mode 100644
index 0000000000000000000000000000000000000000..363f497302a446de7e8ca749e8eda894cf8911dd
--- /dev/null
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Configuration.java
@@ -0,0 +1,26 @@
+package cz.it4i.fiji.haas_java_client;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
+public class Configuration {
+
+ private Properties properties;
+
+ public Configuration(String configFile) {
+ try(InputStream is = this.getClass().getClassLoader().getResourceAsStream(configFile)) {
+ if(is == null) {
+ throw new IllegalArgumentException("Resource " + configFile + " does not exists. Copy " + configFile + ".template and fill it, please!");
+ }
+ this.properties = new Properties();
+ this.properties.load(is);
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ protected String getValue(String key) {
+ return this.properties.getProperty(key);
+ }
+}
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Constants.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..35f602ac95f040ba9912f83bc9596754673025be
--- /dev/null
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Constants.java
@@ -0,0 +1,28 @@
+package cz.it4i.fiji.haas_java_client;
+
+class Constants extends Configuration{
+
+
+ public Constants() {
+ super("configuration.properties");
+ }
+
+ public String getUserName() {
+ return getValue("USER_NAME");
+ }
+
+ public String getPhone() {
+ return getValue("PHONE");
+ }
+
+ public String getPassword() {
+ return getValue("PASSWORD");
+ }
+
+ public String getEmail() {
+ return getValue("EMAIL");
+ }
+
+
+
+}
\ No newline at end of file
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Constants.java.templ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Constants.java.templ
deleted file mode 100644
index e2d5e13f220e429b17f68193ceb9cb5041fd6caf..0000000000000000000000000000000000000000
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/Constants.java.templ
+++ /dev/null
@@ -1,8 +0,0 @@
-package cz.it4i.fiji.haas_java_client;
-
-interface Constants {
- String USER_NAME = "";
- String PASSWORD = "";
- String EMAIL = "";
- String PHONE = "";
-}
\ No newline at end of file
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java
index daa379cfe2eb74610c5daefa40ba5593934348ab..a08e3a1626fbed22b99a2ba35378354ddbb5a3e9 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java
@@ -162,17 +162,18 @@ public class HaaSClient {
}
public long start(Iterable<Path> files, String name, Collection<Entry<String, String>> templateParameters) {
- Iterable<UploadingFile> uploadingFiles = StreamSupport.stream(files.spliterator(), false).map(HaaSClient::getUploadingFile).collect(Collectors.toList());
+ Iterable<UploadingFile> uploadingFiles = StreamSupport.stream(files.spliterator(), false)
+ .map(HaaSClient::getUploadingFile).collect(Collectors.toList());
return start(uploadingFiles, name, templateParameters, dummyNotifier);
}
- public long start(Iterable<UploadingFile> files, String name,
- Collection<Entry<String, String>> templateParameters, ProgressNotifier notifier) {
+ public long start(Iterable<UploadingFile> files, String name, Collection<Entry<String, String>> templateParameters,
+ ProgressNotifier notifier) {
notifier.setTitle("Starting job");
try {
- long jobId = doCreateJob(name, templateParameters, notifier);
+ long jobId = doCreateJob(name, templateParameters);
doUploadFiles(jobId, files, notifier);
- doSubmitJob(jobId, notifier);
+ doSubmitJob(jobId);
return jobId;
} catch (ServiceException | JSchException | IOException e) {
throw new RuntimeException(e);
@@ -180,10 +181,9 @@ public class HaaSClient {
}
- public long createJob(String name, Collection<Entry<String, String>> templateParameters,
- ProgressNotifier notifier) {
+ public long createJob(String name, Collection<Entry<String, String>> templateParameters) {
try {
- return doCreateJob(name, templateParameters, notifier);
+ return doCreateJob(name, templateParameters);
} catch (RemoteException | ServiceException e) {
throw new RuntimeException(e);
}
@@ -197,9 +197,9 @@ public class HaaSClient {
}
}
- public void submitJob(long jobId, ProgressNotifier notifier) {
+ public void submitJob(long jobId) {
try {
- doSubmitJob(jobId, notifier);
+ doSubmitJob(jobId);
} catch (RemoteException | ServiceException e) {
throw new RuntimeException(e);
}
@@ -262,7 +262,8 @@ public class HaaSClient {
FileTransferMethodExt ft = getFileTransfer().getFileTransferMethod(jobId, getSessionID());
try (ScpClient scpClient = getScpClient(ft)) {
String[] filesArray = getFileTransfer().listChangedFilesForJob(jobId, getSessionID());
- Collection<String> files = Arrays.asList(filesArray).stream().filter(function).collect(Collectors.toList());
+ Collection<String> files = Arrays.asList(filesArray).stream().filter(function)
+ .collect(Collectors.toList());
List<Long> fileSizes = getSizes(
files.stream().map(filename -> "'" + ft.getSharedBasepath() + "/" + filename + "'").collect(
Collectors.toList()),
@@ -335,10 +336,8 @@ public class HaaSClient {
};
}
- private void doSubmitJob(long jobId, ProgressNotifier notifier) throws RemoteException, ServiceException {
+ private void doSubmitJob(long jobId) throws RemoteException, ServiceException {
getJobManagement().submitJob(jobId, getSessionID());
- notifier.itemDone(getNotificationItem4JobId(jobId));
- notifier.done();
}
private void doUploadFiles(long jobId, Iterable<UploadingFile> files, ProgressNotifier notifier)
@@ -368,20 +367,15 @@ public class HaaSClient {
getFileTransfer().endFileTransfer(jobId, fileTransfer, getSessionID());
}
- private long doCreateJob(String name, Collection<Entry<String, String>> templateParameters,
- ProgressNotifier notifier) throws RemoteException, ServiceException {
+ private long doCreateJob(String name, Collection<Entry<String, String>> templateParameters)
+ throws RemoteException, ServiceException {
TaskSpecificationExt taskSpec = createTaskSpecification(name, templateId, templateParameters);
JobSpecificationExt jobSpecification = createJobSpecification(name, Arrays.asList(taskSpec));
SubmittedJobInfoExt job = getJobManagement().createJob(jobSpecification, getSessionID());
- notifier.addItem(getNotificationItem4JobId(job.getId()));
return job.getId();
}
- private String getNotificationItem4JobId(long jobId) {
- return String.format("Created job: %d\n", jobId);
- }
-
- private List<Long> getSizes(List<String> asList, ScpClient scpClient, ProgressNotifier notifier)
+ private List<Long> getSizes(List<String> asList, ScpClient scpClient, ProgressNotifier notifier)
throws JSchException, IOException {
List<Long> result = new LinkedList<>();
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/TestingConstants.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/TestingConstants.java
index 6b91d662a3f7e041a4e9c6dc29693f387ddd7456..389ebe716048fbbcbe0f683c3908ad6b3a415db9 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/TestingConstants.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/TestingConstants.java
@@ -1,32 +1,29 @@
package cz.it4i.fiji.haas_java_client;
interface TestingConstants {
- String USER_NAME = "testuser";
- String PASSWORD = "57f9caaf84";
- String EMAIL = "jan.kozusznik@vsb.cz";
- String PHONE = "999111000";
static Settings getSettings(long templateId, int timeOut, long clusterNodeType, String projectId) {
+ Constants constants = new Constants();
return new Settings() {
@Override
public String getUserName() {
- return USER_NAME;
+ return constants.getUserName();
}
@Override
public String getPhone() {
- return PHONE;
+ return constants.getPhone();
}
@Override
public String getPassword() {
- return PASSWORD;
+ return constants.getPassword();
}
@Override
public String getEmail() {
- return EMAIL;
+ return constants.getEmail();
}
@Override
diff --git a/haas-java-client/src/main/resources/.gitignore b/haas-java-client/src/main/resources/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..b5285f5f9fb3ae9423696a524c0fcf6c5a8d5d0c
--- /dev/null
+++ b/haas-java-client/src/main/resources/.gitignore
@@ -0,0 +1 @@
+/configuration.properties
diff --git a/haas-java-client/src/main/resources/configuration.properties.template b/haas-java-client/src/main/resources/configuration.properties.template
new file mode 100644
index 0000000000000000000000000000000000000000..892ed0d0a691608a7070d5beb4c3c8e539c074ef
--- /dev/null
+++ b/haas-java-client/src/main/resources/configuration.properties.template
@@ -0,0 +1,4 @@
+USER_NAME=
+PASSWORD=
+EMAIL=
+PHONE=
\ No newline at end of file
diff --git a/haas-java-client/src/test/resources/.gitignore b/haas-java-client/src/test/resources/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..b5285f5f9fb3ae9423696a524c0fcf6c5a8d5d0c
--- /dev/null
+++ b/haas-java-client/src/test/resources/.gitignore
@@ -0,0 +1 @@
+/configuration.properties
diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/.gitignore b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/Constants.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..984071e8fd57bc3f8c3e2fcf500987ed3ffd3066
--- /dev/null
+++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/Constants.java
@@ -0,0 +1,31 @@
+package cz.it4i.fiji.haas_snakemake_spim;
+
+import cz.it4i.fiji.haas_java_client.Configuration;
+
+public class Constants extends Configuration {
+
+ public Constants() {
+ super("configuration.properties");
+ }
+
+ public String getProjectId() {
+ return getValue("PROJECT_ID");
+ }
+
+ public String getPassword() {
+ return getValue("PASSWORD");
+ }
+
+ public String getUserName() {
+ return getValue("USER_NAME");
+ }
+
+ public String getPhone() {
+ return getValue("PHONE");
+ }
+
+ public String getEmail() {
+ return getValue("EMAIL");
+ }
+
+}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/TestingConstants.template b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/TestingConstants.java
similarity index 64%
rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/TestingConstants.template
rename to haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/TestingConstants.java
index 6e89e500814d9ffd5ecef6a5d6dd6e9aaa0f9c56..a82879df1059f432a7eed31781d79a7a1936ceb8 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/TestingConstants.template
+++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/TestingConstants.java
@@ -1,39 +1,36 @@
-package cz.it4i.fiji.haas;
+package cz.it4i.fiji.haas_snakemake_spim;
import cz.it4i.fiji.haas_java_client.Settings;
-interface TestingConstants {
- String USER_NAME = <user name to haas>;
- String PASSWORD = <password to haas>;
- String EMAIL = ;
- String PHONE = ;
-
+public interface TestingConstants {
static Settings getSettings() {
+ Constants constants = new Constants();
long templateId = 2l;
int timeOut = 9600;
long clusterNodeType = 6l;
- String projectId = "DD-17-31";
+
+
return new Settings() {
@Override
public String getUserName() {
- return USER_NAME;
+ return constants.getUserName();
}
@Override
public String getPhone() {
- return PHONE;
+ return constants.getPhone();
}
@Override
public String getPassword() {
- return PASSWORD;
+ return constants.getPassword();
}
@Override
public String getEmail() {
- return EMAIL;
+ return constants.getEmail();
}
@Override
@@ -53,7 +50,12 @@ interface TestingConstants {
@Override
public String getProjectId() {
- return projectId;
+ return constants.getProjectId();
+ }
+
+ @Override
+ public String getJobName() {
+ return "HaaS-Snakemake-SPIM";
}
};
}
diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java
index 3ea5e71cd4fb5da950249b31f1ffd429bce20977..28961641813b04c9b9ee8f359c500197489c93ae 100644
--- a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java
+++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java
@@ -19,10 +19,11 @@ import org.scijava.ui.UIService;
import org.scijava.widget.UIComponent;
import cz.it4i.fiji.haas.JobManager;
-import cz.it4i.fiji.haas.TestingConstants;
import cz.it4i.fiji.haas.JobManager.JobInfo;
+import cz.it4i.fiji.haas.ui.DummyProgress;
import cz.it4i.fiji.haas.ui.ModalDialogs;
import cz.it4i.fiji.haas.ui.ProgressDialog;
+import cz.it4i.fiji.haas_snakemake_spim.TestingConstants;
import cz.it4i.fiji.haas_snakemake_spim.ui.CheckStatusOfHaaSWindow;
import net.imagej.ImageJ;
@@ -59,16 +60,11 @@ public class CheckStatusOfHaaS implements Command {
window = ModalDialogs.doModal(new CheckStatusOfHaaSWindow(getFrame(), context),WindowConstants.DISPOSE_ON_CLOSE);
ProgressDialog dialog = ModalDialogs.doModal(new ProgressDialog(window),WindowConstants.DO_NOTHING_ON_CLOSE);
dialog.setTitle("Downloading info about jobs");
- Collection<JobInfo> jobs = jobManager.getJobs(dialog);
+ Collection<JobInfo> jobs = jobManager.getJobs();
int count = 0;
for (JobInfo ji : jobs) {
String item;
dialog.addItem(item = "job id:" + ji.getId());
- try {
- ji.updateInfo();
- } catch (IOException e) {
- log.error(e);
- }
window.addJob(ji);
dialog.itemDone(item);
dialog.setCount(count, jobs.size());
@@ -98,7 +94,7 @@ public class CheckStatusOfHaaS implements Command {
private void downloadAll() {
for (JobInfo id : jobManager.getJobsNeedingDownload()) {
System.out.println("Job " + id.getId() + " needs download");
- jobManager.downloadJob(id.getId());
+ jobManager.downloadJob(id.getId(), new DummyProgress());
}
}
diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java
index 3576aa7f8b4b2a25a425ec11f9d29c9c604ab25f..8fc4df618bac9bdbeef26bc3a4ff3777df3967fc 100644
--- a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java
+++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java
@@ -21,10 +21,10 @@ import org.scijava.ui.UIService;
import org.scijava.widget.UIComponent;
import cz.it4i.fiji.haas.JobManager;
-import cz.it4i.fiji.haas.TestingConstants;
import cz.it4i.fiji.haas.ui.ModalDialogs;
import cz.it4i.fiji.haas.ui.ProgressDialog;
import cz.it4i.fiji.haas_java_client.HaaSClient;
+import cz.it4i.fiji.haas_snakemake_spim.TestingConstants;
import net.imagej.ImageJ;
/**
@@ -56,9 +56,13 @@ public class RunWithHaaS implements Command {
public void run() {
try {
jobManager = new JobManager(getWorkingDirectoryPath(), TestingConstants.getSettings());
+ ProgressDialog dialog = ModalDialogs.doModal(new ProgressDialog(getFrame(), "Starting job"),
+ WindowConstants.DO_NOTHING_ON_CLOSE);
+
jobManager.startJob(
getContent(dataDirectory).stream().map(HaaSClient::getUploadingFile).collect(Collectors.toList()),
- ModalDialogs.doModal(new ProgressDialog(getFrame()), WindowConstants.DO_NOTHING_ON_CLOSE));
+ dialog);
+ dialog.done();
} catch (IOException e) {
log.error(e);
}
diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/.gitignore b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..702c8b4dfc8d2cf814f8eaa495f6397ba279a113
--- /dev/null
+++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/.gitignore
@@ -0,0 +1 @@
+/Constants.java
diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java
index 4763b20336d312ac689c0b3bb8405f72dc1ed6b5..38092ad763dcea820b46ae9e882b6e27b710a8a0 100644
--- a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java
+++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java
@@ -22,8 +22,9 @@ import javafx.scene.control.MenuItem;
import javafx.scene.control.TableColumn;
import javafx.scene.control.TableView;
import javafx.scene.input.ContextMenuEvent;
+import net.imagej.updater.util.Progress;
-public class CheckStatusOfHaaSController implements FXFrame.Controller{
+public class CheckStatusOfHaaSController implements FXFrame.Controller {
@Parameter
private LogService logService;
@@ -42,14 +43,15 @@ public class CheckStatusOfHaaSController implements FXFrame.Controller{
}
public void init(Window root) {
+ this.root = root;
initTable();
initMenu();
- this.root = root;
}
private void downloadData(ActionEvent event) {
- Platform.runLater(() -> jobs.getSelectionModel().getSelectedItem()
- .downloadData(ModalDialogs.doModal(new ProgressDialog(root), WindowConstants.DO_NOTHING_ON_CLOSE)));
+ Progress progress = ModalDialogs.doModal(new ProgressDialog(root, "Downloading data"), WindowConstants.DO_NOTHING_ON_CLOSE);
+ Platform.runLater(() -> jobs.getSelectionModel().getSelectedItem().downloadData(progress));
+ progress.done();
}
private void initMenu() {
diff --git a/haas-snakemake-spim/src/main/resources/.gitignore b/haas-snakemake-spim/src/main/resources/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..b5285f5f9fb3ae9423696a524c0fcf6c5a8d5d0c
--- /dev/null
+++ b/haas-snakemake-spim/src/main/resources/.gitignore
@@ -0,0 +1 @@
+/configuration.properties
diff --git a/haas-snakemake-spim/src/main/resources/configuration.properties.template b/haas-snakemake-spim/src/main/resources/configuration.properties.template
new file mode 100644
index 0000000000000000000000000000000000000000..5db03d89f48785d3b2c31be4322b12aced25d6b1
--- /dev/null
+++ b/haas-snakemake-spim/src/main/resources/configuration.properties.template
@@ -0,0 +1,5 @@
+PROJECT_ID=DD-17-31
+USER_NAME=
+PASSWORD=
+EMAIL=
+PHONE=
\ No newline at end of file
diff --git a/haas-spim-benchmark/pom.xml b/haas-spim-benchmark/pom.xml
index 9a7a84fb8b45c33872e5cc4b1a9df97c7527248e..1dd914065cd78b18f350bb346d1cb29e3beaf6e4 100644
--- a/haas-spim-benchmark/pom.xml
+++ b/haas-spim-benchmark/pom.xml
@@ -61,7 +61,13 @@
<system>None</system>
</ciManagement>
+ <properties>
+ <license.licenseName>cc0</license.licenseName>
+ <license.copyrightOwners>N/A</license.copyrightOwners>
+ <license.projectName>Plugins for running SPIM automated workflow by
+ IT4I HaaS.</license.projectName>
+ </properties>
<repositories>
<repository>
<id>imagej.public</id>
@@ -73,8 +79,9 @@
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
+ <scope>compile</scope>
</dependency>
-
+
<dependency>
<groupId>cz.it4i.fiji</groupId>
<artifactId>haas-imagej-client</artifactId>
@@ -91,4 +98,7 @@
<artifactId>slf4j-simple</artifactId>
</dependency>
</dependencies>
-</project>
\ No newline at end of file
+ <build>
+
+ </build>
+</project>
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/BenchmarkSPIMParametersImpl.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/BenchmarkSPIMParametersImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..70ece8d7350cd6baa982801e87aa21650655112d
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/BenchmarkSPIMParametersImpl.java
@@ -0,0 +1,41 @@
+package cz.it4i.fiji.haas_spim_benchmark.commands;
+
+import java.nio.file.Path;
+
+import cz.it4i.fiji.haas_java_client.Configuration;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkSPIMParameters;
+
+class BenchmarkSPIMParametersImpl extends Configuration implements BenchmarkSPIMParameters{
+
+ private Path workingDirectory;
+
+ public BenchmarkSPIMParametersImpl(Path workingDirectory) {
+ super("configuration.properties");
+ this.workingDirectory = workingDirectory;
+ }
+
+ @Override
+ public Path workingDirectory() {
+ return workingDirectory;
+ }
+
+ @Override
+ public String username() {
+ return getValue("USER_NAME");
+ }
+
+ @Override
+ public String password() {
+ return getValue("PASSWORD");
+ }
+
+ @Override
+ public String phone() {
+ return getValue("PHONE");
+ }
+
+ @Override
+ public String email() {
+ return getValue("EMAIL");
+ }
+}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/ManageSPIMBenchmark.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/ManageSPIMBenchmark.java
new file mode 100644
index 0000000000000000000000000000000000000000..75eab35b14172e2c2a52df7984e6dfa3c1c239bf
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/ManageSPIMBenchmark.java
@@ -0,0 +1,78 @@
+package cz.it4i.fiji.haas_spim_benchmark.commands;
+
+import java.awt.Frame;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import javax.swing.WindowConstants;
+
+import org.scijava.Context;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.ui.ApplicationFrame;
+import org.scijava.ui.UIService;
+import org.scijava.widget.UIComponent;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import cz.it4i.fiji.haas.ui.ModalDialogs;
+import cz.it4i.fiji.haas_spim_benchmark.ui.BenchmarkSPIMWindow;
+import net.imagej.ImageJ;
+
+/**
+ *
+ * @author koz01
+ *
+ */
+@Plugin(type = Command.class, headless = false, menuPath = "Plugins>SPIM benchmark")
+public class ManageSPIMBenchmark implements Command {
+
+ private static Logger log = LoggerFactory
+ .getLogger(cz.it4i.fiji.haas_spim_benchmark.commands.ManageSPIMBenchmark.class);
+
+ @Parameter(label = "Work directory", persist = true, style = "directory")
+ private File workDirectory;
+
+ @Parameter
+ private UIService uiService;
+
+ @Parameter
+ private Context context;
+
+ @Override
+ public void run() {
+ try {
+ ModalDialogs.doModal(
+ new BenchmarkSPIMWindow(getFrame(), new BenchmarkSPIMParametersImpl(Paths.get(workDirectory.getPath()))),
+ WindowConstants.DISPOSE_ON_CLOSE);
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ log.error(e.getMessage(), e);
+ }
+
+ }
+
+ private Frame getFrame() {
+ ApplicationFrame af = uiService.getDefaultUI().getApplicationFrame();
+ if (af instanceof Frame) {
+ return (Frame) af;
+ } else if (af instanceof UIComponent) {
+ Object component = ((UIComponent<?>) af).getComponent();
+ if (component instanceof Frame) {
+ return (Frame) component;
+ }
+ }
+ return null;
+ }
+
+ public static void main(final String... args) {
+ // Launch ImageJ as usual.
+ final ImageJ ij = new ImageJ();
+ ij.launch(args);
+
+ ij.command().run(ManageSPIMBenchmark.class, true);
+ }
+
+}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/package-info.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..dcfbfc4ce8e10a519f9405f30cd0c0b801db3800
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/commands/package-info.java
@@ -0,0 +1,8 @@
+/**
+ *
+ */
+/**
+ * @author koz01
+ *
+ */
+package cz.it4i.fiji.haas_spim_benchmark.commands;
\ No newline at end of file
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 26e65fd2383d11ec62863db01cdf811cfed7e34d..375a00fbcb06bc230b287d3413ac4c9963665560 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
@@ -6,91 +6,167 @@ import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.Collection;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.Predicate;
import java.util.stream.Collectors;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import org.yaml.snakeyaml.Yaml;
import cz.it4i.fiji.haas.JobManager;
-import cz.it4i.fiji.haas.TestingConstants;
-import cz.it4i.fiji.haas.UploadingFileFromResource;
import cz.it4i.fiji.haas.JobManager.JobInfo;
import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
+import cz.it4i.fiji.haas.UploadingFileFromResource;
import cz.it4i.fiji.haas_java_client.HaaSClient;
import cz.it4i.fiji.haas_java_client.JobState;
+import cz.it4i.fiji.haas_java_client.Settings;
+import javafx.beans.value.ObservableValueBase;
import net.imagej.updater.util.Progress;
public class BenchmarkJobManager {
- private static final String SPIM_OUTPUT_FILENAME_PATTERN = "spim.outputFilenamePattern";
- private static final int HAAS_TEMPLATE_ID = 4;
- private static final String CONFIG_YAML = "config.yaml";
- private JobManager jobManager;
- private Progress progress;
- private Map<Long, JobInfo> jobs = new HashMap<>();
+
+ @SuppressWarnings("unused")
+ private static Logger log = LoggerFactory
+ .getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
+
+ public final class Job extends ObservableValueBase<Job> {
+ private JobInfo jobInfo;
+
+ private JobState oldState;
+ public Job(JobInfo ji) {
+ super();
+ this.jobInfo = ji;
+ }
- public BenchmarkJobManager(Path workDirectory, Progress progress) throws IOException {
- jobManager = new JobManager(workDirectory, TestingConstants.getSettings(HAAS_TEMPLATE_ID, 6));
- this.progress = progress;
- }
+ public void startJob(Progress progress) throws IOException {
+ jobInfo.uploadFilesByName(Arrays.asList(CONFIG_YAML), progress);
+ String outputName = getOutputName(jobInfo.openLocalFile(CONFIG_YAML));
+ jobInfo.submit();
+ jobInfo.setProperty(SPIM_OUTPUT_FILENAME_PATTERN, outputName);
+ }
- public long createJob() throws IOException {
- JobInfo jobInfo = jobManager.createJob(progress);
- jobInfo.storeDataInWorkdirectory(getUploadingFile());
- return indexJob(jobInfo);
- }
+ public JobState getState() {
+ return oldState = jobInfo.getState();
+ }
- public void startJob(long jobId) throws IOException {
- JobInfo jobInfo = jobs.get(jobId);
- jobInfo.uploadFilesByName(Arrays.asList(CONFIG_YAML));
- String outputName = getOutputName(jobInfo.openLocalFile(CONFIG_YAML));
- jobInfo.submit();
- jobInfo.setProperty(SPIM_OUTPUT_FILENAME_PATTERN, outputName);
- }
+ public void downloadData(Progress progress) throws IOException {
+ JobInfo ji = jobInfo;
+ if (ji.needsDownload()) {
+ if (ji.getState() == JobState.Finished) {
+ String filePattern = ji.getProperty(SPIM_OUTPUT_FILENAME_PATTERN);
+ ji.downloadData(downloadFinishedData(filePattern), progress);
+ } else if (ji.getState() == JobState.Failed) {
+ ji.downloadData(downloadFailedData(), progress);
+ }
+ }
- public Collection<Long> getJobs() throws IOException {
- return jobManager.getJobs(progress).stream().map(this::indexJob).collect(Collectors.toList());
- }
+ }
- public JobState getState(long jobId) {
- return jobs.get(jobId).getState();
- }
+ public List<String> getOutput(List<JobSynchronizableFile> files) {
+ return jobInfo.getOutput(files);
+ }
+
+ public long getId() {
+ return jobInfo.getId();
+ }
+
+ public String getCreationTime() {
+ return jobInfo.getCreationTime();
+ }
+
+ public String getStartTime() {
+ return jobInfo.getStartTime();
+ }
+
+ public String getEndTime() {
+ return jobInfo.getEndTime();
+ }
+
+ @Override
+ public Job getValue() {
+ return this;
+ }
+
+ @Override
+ public int hashCode() {
+ return jobInfo.getId().hashCode();
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (obj instanceof Job) {
+ Job job = (Job) obj;
+ return job.getId() == getId();
- public void downloadData(long jobId) throws IOException {
- JobInfo ji = jobs.get(jobId);
- if (ji.needsDownload()) {
- if (ji.getState() == JobState.Finished) {
- String filePattern = ji.getProperty(SPIM_OUTPUT_FILENAME_PATTERN);
- ji.downloadData(downloadFinishedData(filePattern), progress);
- } else if (ji.getState() == JobState.Failed) {
- ji.downloadData(downloadFailedData(), progress);
}
+ return false;
+ }
+
+ public void update(Job job) {
+ jobInfo = job.jobInfo;
+ if (jobInfo.getState() != oldState) {
+ fireValueChangedEvent();
+ }
+ }
+
+
+
+ public boolean downloaded() {
+ return !jobInfo.needsDownload();
+ }
+
+ public Job update() {
+ jobInfo.updateInfo();
+ return this;
+ }
+
+ public Path getDirectory() {
+ return jobInfo.getDirectory();
}
+ }
+
+ private static final String HAAS_JOB_NAME = "HaaSSPIMBenchmark";
+ private static final int HAAS_CLUSTER_NODE_TYPE = 6;
+ private static final int HAAS_TEMPLATE_ID = 4;
+ private static final String HAAS_PROJECT_ID = "DD-17-31";
+ private static final int HAAS_TIMEOUT = 9600;
+
+ private static final String SPIM_OUTPUT_FILENAME_PATTERN = "spim.outputFilenamePattern";
+ private static final String CONFIG_YAML = "config.yaml";
+ private JobManager jobManager;
+
+ public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
+ jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
}
- public Iterable<String> getOutput(long jobId, List<JobSynchronizableFile> files) {
- return jobs.get(jobId).getOutput(files);
+ public Job createJob() throws IOException {
+ JobInfo jobInfo = jobManager.createJob();
+ jobInfo.storeDataInWorkdirectory(getUploadingFile());
+ return convertJob(jobInfo);
+ }
+
+ public Collection<Job> getJobs() throws IOException {
+
+ return jobManager.getJobs().stream().map(this::convertJob).collect(Collectors.toList());
}
private HaaSClient.UploadingFile getUploadingFile() {
return new UploadingFileFromResource("", CONFIG_YAML);
}
- private long indexJob(JobInfo jobInfo) {
- jobs.put(jobInfo.getId(), jobInfo);
- return jobInfo.getId();
+ private Job convertJob(JobInfo jobInfo) {
+ return new Job(jobInfo);
}
- @SuppressWarnings("rawtypes")
private String getOutputName(InputStream openLocalFile) throws IOException {
try (InputStream is = openLocalFile) {
Yaml yaml = new Yaml();
- Map map = yaml.load(is);
- String result = (String) ((Map) map.get("common")).get("hdf5_xml_filename");
+ Map<String, Map<String, String>> map = yaml.load(is);
+ String result = map.get("common").get("hdf5_xml_filename");
if (result == null) {
throw new IllegalArgumentException("hdf5_xml_filename not found");
}
@@ -122,4 +198,55 @@ public class BenchmarkJobManager {
|| p.getParent().getFileName().toString().equals("logs");
};
}
+
+ private static Settings constructSettingsFromParams(BenchmarkSPIMParameters params) {
+ // TODO Auto-generated method stub
+ return new Settings() {
+
+ @Override
+ public String getUserName() {
+ return params.username();
+ }
+
+ @Override
+ public int getTimeout() {
+ return HAAS_TIMEOUT;
+ }
+
+ @Override
+ public long getTemplateId() {
+ return HAAS_TEMPLATE_ID;
+ }
+
+ @Override
+ public String getProjectId() {
+ return HAAS_PROJECT_ID;
+ }
+
+ @Override
+ public String getPhone() {
+ return params.phone();
+ }
+
+ @Override
+ public String getPassword() {
+ return params.password();
+ }
+
+ @Override
+ public String getJobName() {
+ return HAAS_JOB_NAME;
+ }
+
+ @Override
+ public String getEmail() {
+ return params.email();
+ }
+
+ @Override
+ public long getClusterNodeType() {
+ return HAAS_CLUSTER_NODE_TYPE;
+ }
+ };
+ }
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkSPIMParameters.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkSPIMParameters.java
new file mode 100644
index 0000000000000000000000000000000000000000..abbafc2c0db434162b7166c36d457086e896512c
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkSPIMParameters.java
@@ -0,0 +1,11 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.nio.file.Path;
+
+public interface BenchmarkSPIMParameters {
+ Path workingDirectory();
+ String username();
+ String password();
+ String phone();
+ String email();
+}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..367ef54df3ca69b2dc82e879f4c0088737adf470
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Constants.java
@@ -0,0 +1,5 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+public interface Constants {
+ long HAAS_UPDATE_TIMEOUT = 1000;
+}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIM.fxml b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIM.fxml
index 07201409776731fd9033a79207a24241f760665b..27eff777e379056574c46ec623441f321a668d56 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIM.fxml
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIM.fxml
@@ -4,7 +4,7 @@
<?import javafx.scene.control.TableView?>
<?import javafx.scene.layout.BorderPane?>
-<BorderPane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="400.0" prefWidth="912.0" xmlns="http://javafx.com/javafx/8.0.65" xmlns:fx="http://javafx.com/fxml/1" fx:controller="cz.it4i.fiji.haas_snakemake_spim.ui.CheckStatusOfHaaSController">
+<BorderPane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="400.0" prefWidth="912.0" xmlns="http://javafx.com/javafx/8.0.65" xmlns:fx="http://javafx.com/fxml/1" fx:controller="cz.it4i.fiji.haas_spim_benchmark.ui.BenchmarkSPIMController">
<center>
<TableView fx:id="jobs" prefHeight="400.0" prefWidth="675.0" BorderPane.alignment="CENTER">
<columns>
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 8e8feade02c1274450e3cb2ac47e5d06d852db25..9010a3b02a52cf5ba5c70e42bca2078ab235cfbd 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
@@ -1,15 +1,192 @@
package cz.it4i.fiji.haas_spim_benchmark.ui;
+import java.awt.Desktop;
import java.awt.Window;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.util.EnumSet;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.Timer;
+import java.util.TimerTask;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.function.Function;
+import java.util.function.Predicate;
+import java.util.stream.Collectors;
+import javax.swing.WindowConstants;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import cz.it4i.fiji.haas.ui.DummyProgress;
import cz.it4i.fiji.haas.ui.FXFrame;
+import cz.it4i.fiji.haas.ui.ModalDialogs;
+import cz.it4i.fiji.haas.ui.ObservableValueAdapter;
+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_spim_benchmark.core.BenchmarkJobManager;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.Job;
+import cz.it4i.fiji.haas_spim_benchmark.core.Constants;
+import javafx.fxml.FXML;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableView;
+import net.imagej.updater.util.Progress;
+
+public class BenchmarkSPIMController implements FXFrame.Controller {
+
+ private static boolean notNullValue(Job j, Predicate<Job> pred) {
+ if (j == null) {
+ return false;
+ } else {
+ return pred.test(j);
+ }
+ }
+
+ @FXML
+ private TableView<Job> jobs;
+
+ private BenchmarkJobManager manager;
+
+ private Window root;
+
+ private ExecutorService executorService;
-public class BenchmarkSPIMController implements FXFrame.Controller{
+ private Timer timer;
+
+ private static Logger log = LoggerFactory
+ .getLogger(cz.it4i.fiji.haas_spim_benchmark.ui.BenchmarkSPIMController.class);
@Override
public void init(Window frame) {
- // TODO Auto-generated method stub
-
+ executorService = Executors.newSingleThreadExecutor();
+ timer = new Timer();
+ timer.scheduleAtFixedRate(new TimerTask() {
+ @Override
+ public void run() {
+ updateJobs(false);
+ }
+ }, Constants.HAAS_UPDATE_TIMEOUT, Constants.HAAS_UPDATE_TIMEOUT);
+ root = frame;
+ initTable();
+ initMenu();
+ updateJobs();
+ root.addWindowListener(new WindowAdapter() {
+ @Override
+ public void windowClosed(WindowEvent e) {
+ super.windowClosed(e);
+ dispose();
+ }
+ });
+ }
+
+ public void setManager(BenchmarkJobManager manager) {
+ this.manager = manager;
+
}
+ private void initMenu() {
+ TableViewContextMenu<Job> menu = new TableViewContextMenu<>(jobs);
+ menu.addItem("Create job", x -> executeJobActionAsync("Creating job", p -> manager.createJob()), j -> true);
+ menu.addItem("Start job", job -> executeJobActionAsync("Starting job", p -> job.startJob(p)),
+ job -> notNullValue(job, j -> j.getState() == JobState.Configuring));
+ menu.addItem("Download", job -> executeJobActionAsync("Downloading data", p -> job.downloadData(p)),
+ job -> notNullValue(job,
+ j -> EnumSet.of(JobState.Failed, JobState.Finished).contains(j.getState()) && !j.downloaded()));
+ menu.addItem("Show output", j -> new JobOutputView(root, executorService, j, Constants.HAAS_UPDATE_TIMEOUT),
+ job -> notNullValue(job,
+ j -> EnumSet.of(JobState.Failed, JobState.Finished, JobState.Running).contains(j.getState())));
+ menu.addItem("Open", j->open(j), x->true);
+ menu.addItem("Update table", job -> updateJobs(), j -> true);
+
+ }
+
+ private void open(Job j) {
+ executorService.execute(() -> {
+ Desktop desktop = Desktop.getDesktop();
+ try {
+ desktop.open(j.getDirectory().toFile());
+ } catch (IOException e) {
+ log.error(e.getMessage(), e);
+ }});
+ }
+
+ private void executeJobActionAsync(String title, P_JobAction action) {
+ executorService.execute(() -> {
+ try {
+ ProgressDialog dialog = ModalDialogs.doModal(new ProgressDialog(root, title),
+ WindowConstants.DO_NOTHING_ON_CLOSE);
+ action.doAction(dialog);
+ dialog.done();
+ updateJobs();
+ } catch (IOException e) {
+ log.error(e.getMessage(), e);
+ }
+ });
+ }
+
+ private void updateJobs() {
+ updateJobs(true);
+ }
+
+ private void updateJobs(boolean showProgress) {
+ executorService.execute(() -> {
+ Progress progress = showProgress
+ ? ModalDialogs.doModal(new ProgressDialog(root, "Updating jobs"),
+ WindowConstants.DO_NOTHING_ON_CLOSE)
+ : new DummyProgress();
+
+ Set<Job> old = new HashSet<Job>(jobs.getItems());
+ Map<Job, Job> actual;
+ try {
+ actual = manager.getJobs().stream().map(job -> job.update())
+ .collect(Collectors.toMap(job -> job, job -> job));
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ }
+ for (Job job : old) {
+ if (!actual.containsKey(job)) {
+ jobs.getItems().remove(job);
+ } else {
+ job.update(actual.get(job));
+ }
+ }
+ progress.done();
+ FXFrame.runOnFxThread(() -> {
+ for (Job job : actual.keySet()) {
+ if (!old.contains(job)) {
+ jobs.getItems().add(job);
+ }
+ }
+ });
+ });
+ }
+
+ private void initTable() {
+ setCellValueFactory(0, j -> j.getId() + "");
+ setCellValueFactory(1, j -> j.getState().toString());
+ setCellValueFactory(2, j -> j.getCreationTime().toString());
+ setCellValueFactory(3, j -> j.getStartTime().toString());
+ setCellValueFactory(4, j -> j.getEndTime().toString());
+ }
+
+ @SuppressWarnings("unchecked")
+ private void setCellValueFactory(int index, Function<Job, String> mapper) {
+ ((TableColumn<Job, String>) jobs.getColumns().get(index))
+ .setCellValueFactory(f -> new ObservableValueAdapter<Job, String>(f.getValue(), mapper));
+
+ }
+
+ private interface P_JobAction {
+ public void doAction(Progress p) throws IOException;
+ }
+
+ private void dispose() {
+ executorService.shutdown();
+ timer.cancel();
+ }
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMWindow.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMWindow.java
index 206e707499937f08a6cfba9bfa30f77c6657d0be..b15fadcdc0d6ec5ef6c79c59d235a534f0899b5d 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMWindow.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIMWindow.java
@@ -1,16 +1,21 @@
package cz.it4i.fiji.haas_spim_benchmark.ui;
import java.awt.Frame;
+import java.io.IOException;
import cz.it4i.fiji.haas.ui.FXFrame;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkSPIMParameters;
public class BenchmarkSPIMWindow extends FXFrame<BenchmarkSPIMController> {
private static final long serialVersionUID = 1L;
- public BenchmarkSPIMWindow(Frame applicationFrame) {
+ public BenchmarkSPIMWindow(Frame applicationFrame, BenchmarkSPIMParameters params) throws IOException {
super(applicationFrame, "/cz/it4i/fiji/haas_spim_benchmark/ui/BenchmarkSPIM.fxml");
- init(x->{});
+ BenchmarkJobManager manager = new BenchmarkJobManager(params);
+ init(controller->controller.setManager(manager));
}
+
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/JobOutputView.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/JobOutputView.java
new file mode 100644
index 0000000000000000000000000000000000000000..3da6d260f6756ce10a0dfaf76611d2c21de87e1e
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/JobOutputView.java
@@ -0,0 +1,102 @@
+package cz.it4i.fiji.haas_spim_benchmark.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.Window;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Arrays;
+import java.util.Timer;
+import java.util.TimerTask;
+import java.util.concurrent.ExecutorService;
+
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
+import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.Job;
+
+public class JobOutputView {
+ @SuppressWarnings("unused")
+ private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas_spim_benchmark.ui.JobOutputView.class);
+ private Timer timer;
+ private JDialog theDialog;
+ private JTextArea theText;
+ private Job job;
+ private ExecutorService executor;
+ private long readedChars = 0;
+
+ public JobOutputView(Window parent, ExecutorService executor, Job job, long refreshTimeout) {
+ this.job = job;
+ this.executor = executor;
+ constructFrame(parent);
+ parent.addWindowListener(new WindowAdapter() {
+ @Override
+ public void windowClosed(WindowEvent e) {
+ dispose();
+ }
+ });
+ timer = new Timer();
+ timer.schedule(new TimerTask() {
+ @Override
+ public void run() {
+ updateView();
+ }
+ }, refreshTimeout, refreshTimeout);
+ updateView();
+ }
+
+ private void dispose() {
+ timer.cancel();
+ theDialog.dispose();
+ }
+
+ private void constructFrame(Window parent) {
+ theDialog = new JDialog(parent, "Output of job: " + (job!=null?job.getId():"N/A"));
+ theDialog.setPreferredSize(new Dimension(500, 500));
+ theDialog.setLocation(550, 400);
+ JPanel jPanel = new JPanel(new BorderLayout());
+ theDialog.setContentPane(jPanel);
+ //Create the text area used for output. Request
+ //enough space for 5 rows and 30 columns.
+ theText = new JTextArea(5, 30);
+ theText.setEditable(false);
+ JScrollPane scrollPane = new JScrollPane(theText);
+
+ //Lay out the main panel.
+ jPanel.setPreferredSize(new Dimension(450, 130));
+ jPanel.add(scrollPane, BorderLayout.CENTER);
+
+ theDialog.pack();
+ theDialog.addWindowListener(new WindowAdapter() {
+ @Override
+ public void windowClosing(WindowEvent e) {
+ super.windowClosing(e);
+ dispose();
+ }
+ });
+ theDialog.setVisible(true);
+ }
+
+ private void updateView() {
+ executor.execute(() -> {
+ JobSynchronizableFile file = new JobSynchronizableFile(SynchronizableFileType.StandardErrorFile,
+ readedChars);
+ String output;
+ if (job != null) {
+ output = job.getOutput(Arrays.asList(file)).get(0);
+ } else {
+ output = "This is testing line\n";
+ }
+ readedChars += output.length();
+ theText.append(output);
+ theText.setCaretPosition(theText.getDocument().getLength());
+ });
+ }
+}
diff --git a/haas-spim-benchmark/src/main/resources/.gitignore b/haas-spim-benchmark/src/main/resources/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..b5285f5f9fb3ae9423696a524c0fcf6c5a8d5d0c
--- /dev/null
+++ b/haas-spim-benchmark/src/main/resources/.gitignore
@@ -0,0 +1 @@
+/configuration.properties
diff --git a/haas-spim-benchmark/src/main/resources/configuration.properties.template b/haas-spim-benchmark/src/main/resources/configuration.properties.template
new file mode 100644
index 0000000000000000000000000000000000000000..892ed0d0a691608a7070d5beb4c3c8e539c074ef
--- /dev/null
+++ b/haas-spim-benchmark/src/main/resources/configuration.properties.template
@@ -0,0 +1,4 @@
+USER_NAME=
+PASSWORD=
+EMAIL=
+PHONE=
\ No newline at end of file
diff --git a/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/.gitignore b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/BenchmarkSPIMParametersImpl.java b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/BenchmarkSPIMParametersImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..f9af043a0662da9ee9b5ada72d093ac70d35737d
--- /dev/null
+++ b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/BenchmarkSPIMParametersImpl.java
@@ -0,0 +1,48 @@
+package cz.it4i.fiji.haas;
+
+import java.nio.file.Path;
+
+import cz.it4i.fiji.haas_java_client.Configuration;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkSPIMParameters;
+
+class BenchmarkSPIMParametersImpl extends Configuration implements BenchmarkSPIMParameters{
+
+ String USER_NAME = "testuser";
+ String PASSWORD = "57f9caaf84";
+
+ String EMAIL = "aaa@vsb.cz";
+ String PHONE = "123456789";
+
+
+ private Path workingDirectory;
+
+ public BenchmarkSPIMParametersImpl(Path workingDirectory) {
+ super("configuration.properties");
+ this.workingDirectory = workingDirectory;
+ }
+
+ @Override
+ public Path workingDirectory() {
+ return workingDirectory;
+ }
+
+ @Override
+ public String username() {
+ return getValue("USER_NAME");
+ }
+
+ @Override
+ public String password() {
+ return getValue("PASSWORD");
+ }
+
+ @Override
+ public String phone() {
+ return getValue("PHONE");
+ }
+
+ @Override
+ public String email() {
+ return getValue("EMAIL");
+ }
+}
diff --git a/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java
index 3a36e0e82d5df1cbd9fd9d3624a35318068d76b4..15c76cad21e1c948a5024d2551232a2952b50ee3 100644
--- a/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java
+++ b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java
@@ -9,73 +9,50 @@ import java.util.Arrays;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
+import cz.it4i.fiji.haas.ui.DummyProgress;
import cz.it4i.fiji.haas_java_client.JobState;
import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager;
-import net.imagej.updater.util.Progress;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.Job;
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkSPIMParameters;
public class RunBenchmark {
private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas.RunBenchmark.class);
public static class CreateJob {
public static void main(String[] args) throws IOException {
- Path p = Paths.get("/tmp/benchmark");
- if (!Files.exists(p)) {
- Files.createDirectory(p);
- }
- BenchmarkJobManager benchmarkJobManager = new BenchmarkJobManager(p, new P_Progress());
- long ji = benchmarkJobManager.createJob();
- log.info("job: " + ji + " created.");
+ BenchmarkJobManager benchmarkJobManager = new BenchmarkJobManager(getBenchmarkSPIMParameters());
+ Job ji = benchmarkJobManager.createJob();
+ log.info("job: " + ji.getId() + " created.");
}
}
public static class ProcessJobs {
public static void main(String[] args) throws IOException {
- Path p = Paths.get("/tmp/benchmark");
- if (!Files.exists(p)) {
- Files.createDirectory(p);
- }
- BenchmarkJobManager benchmarkJobManager = new BenchmarkJobManager(p, new P_Progress());
- for (long jobId : benchmarkJobManager.getJobs()) {
+ BenchmarkJobManager benchmarkJobManager = new BenchmarkJobManager(getBenchmarkSPIMParameters());
+ for (Job job : benchmarkJobManager.getJobs()) {
JobState state;
- log.info("job: " + jobId + " hasStatus " + (state = benchmarkJobManager.getState(jobId)));
+ log.info("job: " + job.getId() + " hasStatus " + (state = job.getState()));
if (state == JobState.Configuring) {
- benchmarkJobManager.startJob(jobId);
+ job.startJob(new DummyProgress());
} else if (state != JobState.Running && state != JobState.Queued) {
- benchmarkJobManager.downloadData(jobId);
+ job.downloadData(new DummyProgress());
} else if (state == JobState.Running) {
- log.info(benchmarkJobManager.getOutput(jobId,Arrays.asList(
- new JobManager.JobSynchronizableFile(SynchronizableFileType.StandardErrorFile, 0))).iterator().next());
- }
+ JobSynchronizableFile file = new JobSynchronizableFile(SynchronizableFileType.StandardErrorFile, 0);
+ log.info(job.getOutput(Arrays.asList(file)).iterator().next());
+ }
}
}
}
- private static class P_Progress implements Progress {
-
- @Override
- public void setTitle(String title) {
- }
+
- @Override
- public void setCount(int count, int total) {
+ private static BenchmarkSPIMParameters getBenchmarkSPIMParameters() throws IOException {
+ Path p = Paths.get("/tmp/benchmark");
+ if (!Files.exists(p)) {
+ Files.createDirectory(p);
}
-
- @Override
- public void addItem(Object item) {
- }
-
- @Override
- public void setItemCount(int count, int total) {
- }
-
- @Override
- public void itemDone(Object item) {
- }
-
- @Override
- public void done() {
- }
-
+ return new BenchmarkSPIMParametersImpl(p);
}
}
diff --git a/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunView.java b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunView.java
new file mode 100644
index 0000000000000000000000000000000000000000..0ffd4000e349a5801f5b58b9630e7e75be87cea1
--- /dev/null
+++ b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunView.java
@@ -0,0 +1,13 @@
+package cz.it4i.fiji.haas;
+
+import java.util.concurrent.Executors;
+
+import javax.swing.JFrame;
+
+import cz.it4i.fiji.haas_spim_benchmark.ui.JobOutputView;
+
+public class RunView {
+ public static void main(String[] args) {
+ new JobOutputView(new JFrame(), Executors.newSingleThreadExecutor(), null, 3000);
+ }
+}
diff --git a/java-scpclient/src/test/java/TestSCP.java b/java-scpclient/src/test/java/TestSCP.java
index 5c20cd53e61f46a0e06f76b1ca474e52d7efc68e..6762e37bdb19ce65089570420175d5dc1355139d 100644
--- a/java-scpclient/src/test/java/TestSCP.java
+++ b/java-scpclient/src/test/java/TestSCP.java
@@ -1,5 +1,4 @@
import java.io.IOException;
-import java.nio.file.Paths;
import com.jcraft.jsch.JSchException;
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..04d107ebb35ec5f9c2122eb7050b5cebb8437d4e
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,34 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+ http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>cz.it4i.fiji</groupId>
+ <artifactId>haas-parent</artifactId>
+ <version>0.0.1-SNAPSHOT</version>
+ <name>Multi Chapter Simple Parent Project</name>
+ <packaging>pom</packaging>
+ <modules>
+ <module>java-scpclient</module>
+ <module>haas-java-client</module>
+ <module>haas-imagej-client</module>
+ <module>haas-spim-benchmark</module>
+
+ </modules>
+
+ <build>
+ <pluginManagement>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.5</source>
+ <target>1.5</target>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+
+</project>