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 658b31d6bb58c00d83e0f479e38e96e376250044..f55d820e4853d852b5b929f89459c49266126b62 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
@@ -258,6 +258,12 @@ public class Job {
}
}
+ public List<String> getFileContents(List<String> logs) {
+ try (HaaSFileTransfer transfer = haasClientSupplier.get().startFileTransfer(getId(), new DummyProgressNotifier())) {
+ return transfer.getContent(logs);
+ }
+ }
+
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransfer.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransfer.java
index e3b427f2a1cdbdfbaef67fbfa10b3a5d9bc789a8..c6c8a4b9b31142c0b5041b1ccf1882bae1a82b4d 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransfer.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransfer.java
@@ -18,4 +18,5 @@ public interface HaaSFileTransfer extends Closeable {
List<Long> obtainSize(List<String> files);
+ List<String> getContent(List<String> logs);
}
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransferImp.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransferImp.java
index 6d59b42f6240640ab78a8f692f43d17e00e39bad..bf07f5bda386340a0279b94f9e7e4b0fa8d52abb 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransferImp.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSFileTransferImp.java
@@ -1,9 +1,11 @@
package cz.it4i.fiji.haas_java_client;
+import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Path;
import java.rmi.RemoteException;
+import java.util.LinkedList;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
@@ -21,6 +23,7 @@ import cz.it4i.fiji.scpclient.ScpClient;
class HaaSFileTransferImp implements HaaSFileTransfer {
+ @SuppressWarnings("unused")
private static Logger log = LoggerFactory.getLogger(cz.it4i.fiji.haas_java_client.HaaSFileTransferImp.class);
private FileTransferMethodExt ft;
@@ -115,4 +118,37 @@ class HaaSFileTransferImp implements HaaSFileTransfer {
}
+ //TASK merge with download - stream provider for file, consumer for stream
+ @Override
+ public List<String> getContent(List<String> files) {
+ List<String> result = new LinkedList<>();
+ List<Long> fileSizes;
+ try {
+ fileSizes = HaaSClient.getSizes(StreamSupport.stream(files.spliterator(), false)
+ .map(filename -> "'" + ft.getSharedBasepath() + "/" + filename + "'").collect(Collectors.toList()),
+ scpClient, new P_ProgressNotifierDecorator4Size(notifier));
+
+ final long totalFileSize = fileSizes.stream().mapToLong(i -> i.longValue()).sum();
+ TransferFileProgressForHaaSClient progress = new TransferFileProgressForHaaSClient(totalFileSize, notifier);
+ int idx = 0;
+ for (String fileName : files) {
+ fileName = fileName.replaceFirst("/", "");
+ try(ByteArrayOutputStream os = new ByteArrayOutputStream()) {
+ String fileToDownload = "'" + ft.getSharedBasepath() + "/" + fileName + "'";
+ String item;
+ progress.addItem(item = fileName);
+ progress.startNewFile(fileSizes.get(idx));
+ scpClient.download(fileToDownload, os, progress);
+ os.flush();
+ progress.itemDone(item);
+ idx++;
+ result.add(os.toString());
+ }
+ }
+ } catch (JSchException | IOException e) {
+ throw new HaaSClientException(e);
+ }
+ return result;
+ }
+
}
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 fba4aba1cc71338aa91b4839f474f1fe678a249c..432729852937ac4330c0283b3f9b74286b52da36 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
@@ -374,6 +374,11 @@ public class BenchmarkJobManager {
@Override
public List<Long> getFileSizes(List<String> names) {
return job.getFileSizes(names);
+ }
+
+ @Override
+ public List<String> getFileContents(List<String> logs) {
+ return job.getFileContents(logs);
};
};
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
index 086f97440db414c27f0637c698c56939e77cacea..3b1a6a9bbd69528d4eabc6c1c9ec41dec980e383 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
@@ -15,4 +15,6 @@ public interface SPIMComputationAccessor extends HaaSOutputHolder {
Collection<String> getChangedFiles();
List<Long> getFileSizes(List<String> names);
+
+ List<String> getFileContents(List<String> logs);
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessorDecoratorWithTimeout.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessorDecoratorWithTimeout.java
index 11e132499ce68a9ee53b562413575b232c642de5..3f9b2ce48d1a6a3a2832d13241891cdf8613d3af 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessorDecoratorWithTimeout.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessorDecoratorWithTimeout.java
@@ -55,6 +55,11 @@ public class SPIMComputationAccessorDecoratorWithTimeout implements SPIMComputat
public List<Long> getFileSizes(List<String> names) {
return decorated.getFileSizes(names);
}
+
+ @Override
+ public List<String> getFileContents(List<String> logs) {
+ return decorated.getFileContents(logs);
+ }
private void initAllowedTypes(Set<SynchronizableFileType> allowedTypes) {
for (SynchronizableFileType type : allowedTypes) {
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
index 39802fe262facf4522329945e3ec2b64c49a63ea..f34934f4f6b9de56e192c09ba1a359c892c11a81 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
@@ -14,7 +14,6 @@ import com.google.common.collect.Streams;
import cz.it4i.fiji.haas_java_client.JobState;
import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
-import io.scif.jj2000.j2k.NotImplementedError;
public class TaskComputation {
@@ -34,6 +33,28 @@ public class TaskComputation {
public String getContent() {
return content;
}
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ Log other = (Log) obj;
+ if (content == null) {
+ if (other.content != null)
+ return false;
+ } else if (!content.equals(other.content))
+ return false;
+ if (name == null) {
+ if (other.name != null)
+ return false;
+ } else if (!name.equals(other.name))
+ return false;
+ return true;
+ }
}
public static class File {
@@ -62,7 +83,6 @@ public class TaskComputation {
private int positionInOutput;
private Collection<String> inputs;
- @SuppressWarnings("unused")
private Collection<String> outputs;
private Collection<String> logs;
private Long id;
@@ -116,7 +136,10 @@ public class TaskComputation {
}
public Collection<Log> getLogs() {
- throw new NotImplementedError();
+ List<String> logNames = new LinkedList<>(logs);
+ List<String> contents = computationAccessor.getFileContents(logNames);
+ return Streams.<String, String, Log>zip(logNames.stream(), contents.stream(),
+ (name, content) -> new Log(name, content)).collect(Collectors.toList());
}
/**
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/SPIMPipelineProgressViewController.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/SPIMPipelineProgressViewController.java
index a50ce0cdfe7227e5d03cb3ffd70e3d62685eac1b..57813409aefdf5daa4a805de5ed0fb4f622cdb61 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/SPIMPipelineProgressViewController.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/SPIMPipelineProgressViewController.java
@@ -123,7 +123,7 @@ public class SPIMPipelineProgressViewController extends BorderPane implements Cl
Window w = new Window();
w.addWindowListener(new WindowAdapter() {
@Override
- public void windowClosed(WindowEvent e) {
+ public void windowClosing(WindowEvent e) {
adapter.close();
}
});
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/TaskComputationAdapter.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/TaskComputationAdapter.java
index 10ae4fdeae86bf6087dd66f7d4fb5f6d3f7eadf1..40750677982308c630b1d48ec805b2e96bd61f42 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/TaskComputationAdapter.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/ui/TaskComputationAdapter.java
@@ -6,23 +6,31 @@ import java.util.List;
import java.util.Map;
import java.util.Timer;
import java.util.TimerTask;
+import java.util.stream.Collectors;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import cz.it4i.fiji.haas_spim_benchmark.core.Constants;
import cz.it4i.fiji.haas_spim_benchmark.core.TaskComputation;
+import cz.it4i.fiji.haas_spim_benchmark.core.TaskComputation.Log;
import javafx.beans.value.ObservableValue;
import javafx.beans.value.ObservableValueBase;
-//TASK: Dodělat naplnění logs, aktualizace a getXXX
-// Pokračovat zapojením do UI - akce v SPIMPipelineProgressViewWindow
-// pro zobrazení TaskComputation
+//TASK: Pokračovat zapojením do UI - upravit pro TaskComputation
+//TASK: dodělat progress dialog + modalita
+//
public class TaskComputationAdapter implements Closeable {
+ @SuppressWarnings("unused")
+ private static Logger log = LoggerFactory
+ .getLogger(cz.it4i.fiji.haas_spim_benchmark.ui.TaskComputationAdapter.class);
+
private final TaskComputation computation;
private final List<ObservableValue<RemoteFileInfo>> outputs = new LinkedList<>();
- @SuppressWarnings("unused")
- private final List<ObservableValue<String>> logs = new LinkedList<>();
+ private final List<ObservableLog> logs = new LinkedList<>();
private final Timer timer;
@@ -31,6 +39,7 @@ public class TaskComputationAdapter implements Closeable {
timer = new Timer();
Map<String, Long> sizes = computation.getOutFileSizes();
computation.getOutputs().forEach(outputFile -> addOutputFile(outputFile, sizes.get(outputFile)));
+ computation.getLogs().forEach(log->logs.add(new ObservableLog(log)));
timer.scheduleAtFixedRate(new P_TimerTask(), Constants.HAAS_TIMEOUT, Constants.HAAS_TIMEOUT);
}
@@ -42,22 +51,16 @@ public class TaskComputationAdapter implements Closeable {
public List<ObservableValue<RemoteFileInfo>> getOutputs() {
return outputs;
}
+
+ public List<ObservableLog> getLogs() {
+ return logs;
+ }
private void addOutputFile(String outputFile, Long size) {
outputs.add(new ObservableOutputFile(outputFile, size));
}
- public static class Log {
- public String getName() {
- return null;
- }
-
- public ObservableValue<String> getContent() {
- return null;
- }
- }
-
- public class ObservableOutputFile extends ObservableValueBase<RemoteFileInfo> {
+ private class ObservableOutputFile extends ObservableValueBase<RemoteFileInfo> {
private final String name;
@@ -95,11 +98,65 @@ public class TaskComputationAdapter implements Closeable {
}
}
+ public static class ObservableLog {
+
+ private final String name;
+
+ private final P_ObservableString value;
+
+ public ObservableLog(Log content) {
+ this.value = new P_ObservableString(content.getContent());
+ this.name = log.getName();
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public ObservableValue<String> getContent() {
+ return value;
+ }
+
+ public void setContentValue(Log log) {
+ if (!log.getName().equals(log.getName())) {
+ throw new IllegalArgumentException(
+ "this.name=" + getName() + ", log.name=" + log.getName());
+ }
+ value.setValue(log.getContent());
+ }
+
+ private class P_ObservableString extends ObservableValueBase<String> {
+
+ private String value;
+
+ public P_ObservableString(String value) {
+ this.value = value;
+ }
+
+ @Override
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ if(this.value != null && !this.value.equals(value) ||
+ value != null && !value.equals(this.value)) {
+ this.value = value;
+ fireValueChangedEvent();
+ }
+ }
+ }
+
+ }
+
private class P_TimerTask extends TimerTask {
@Override
public void run() {
Map<String, Long> sizes = computation.getOutFileSizes();
+ Map<String, Log> logs = computation.getLogs().stream()
+ .collect(Collectors.<Log, String, Log>toMap((Log log) -> log.getName(), (Log log) -> log));
+ TaskComputationAdapter.this.logs.forEach(log->((ObservableLog) log).setContentValue(logs.get(log.getName())));
outputs.forEach(value -> ((ObservableOutputFile) value).setSize(sizes.get(value.getValue().getName())));
}