diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolder.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolder.java
new file mode 100644
index 0000000000000000000000000000000000000000..c54b0f5c00ecdd9a2497ac0ed36982271189e48d
--- /dev/null
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolder.java
@@ -0,0 +1,7 @@
+package cz.it4i.fiji.haas;
+
+public interface HaaSOutputHolder {
+
+ String getActualOutput();
+
+}
\ No newline at end of file
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolderImpl.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolderImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..b2a5b68aab9b4e281678297c6d00f14ed97990fb
--- /dev/null
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolderImpl.java
@@ -0,0 +1,31 @@
+package cz.it4i.fiji.haas;
+
+import java.util.Arrays;
+
+import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
+import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
+
+public class HaaSOutputHolderImpl implements HaaSOutputHolder {
+ private StringBuilder result = new StringBuilder();
+ private HaaSOutputSource source;
+ private SynchronizableFileType type;
+ public HaaSOutputHolderImpl(HaaSOutputSource source, SynchronizableFileType typeForHold) {
+ super();
+ this.source = source;
+ this.type = typeForHold;
+ }
+
+ /* (non-Javadoc)
+ * @see cz.it4i.fiji.haas.HaaSOutputHolder#getActualOutput()
+ */
+ @Override
+ public String getActualOutput () {
+ updateData();
+ return result.toString();
+ }
+
+ private void updateData() {
+ JobSynchronizableFile file = new JobSynchronizableFile(type, result.length());
+ result.append(source.getOutput(Arrays.asList(file)).get(0));
+ }
+}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputSource.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputSource.java
new file mode 100644
index 0000000000000000000000000000000000000000..904258f0f2acfef95184b07073b82823b68b750e
--- /dev/null
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputSource.java
@@ -0,0 +1,9 @@
+package cz.it4i.fiji.haas;
+
+import java.util.List;
+
+import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
+
+public interface HaaSOutputSource {
+ public List<String> getOutput(List<JobSynchronizableFile> files);
+}
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java
index 515310a6cdf1587d0e3b2f95fe38f7c6d187c4cb..374481004f6c13fb6f4dcccee151dc97b4cb0ab3 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java
@@ -1,11 +1,12 @@
package cz.it4i.fiji.haas_java_client;
public enum JobState {
- Configuring ,
- Submitted ,
- Queued ,
- Running ,
- Finished ,
- Failed ,
+ Unknown,
+ Configuring,
+ Submitted,
+ Queued,
+ Running,
+ Finished,
+ Failed,
Canceled;
}
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 081027d5c5fa89f6dcd3fdd8866718c5c6c522ea..e0480df0a77b883760209b3065c3c9925c46733d 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
@@ -1,6 +1,7 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
@@ -9,12 +10,14 @@ import java.nio.file.Files;
import java.nio.file.InvalidPathException;
import java.nio.file.Path;
import java.nio.file.Paths;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
+import java.util.Scanner;
import java.util.function.Predicate;
import java.util.stream.Collectors;
@@ -22,6 +25,9 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.yaml.snakeyaml.Yaml;
+import cz.it4i.fiji.haas.HaaSOutputHolder;
+import cz.it4i.fiji.haas.HaaSOutputHolderImpl;
+import cz.it4i.fiji.haas.HaaSOutputSource;
import cz.it4i.fiji.haas.Job;
import cz.it4i.fiji.haas.JobManager;
import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
@@ -29,6 +35,7 @@ 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 cz.it4i.fiji.haas_java_client.SynchronizableFileType;
import javafx.beans.value.ObservableValueBase;
import net.imagej.updater.util.Progress;
@@ -39,10 +46,33 @@ public class BenchmarkJobManager {
private static Logger log = LoggerFactory
.getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
- public final class BenchmarkJob extends ObservableValueBase<BenchmarkJob> {
+ private JobManager jobManager;
+
+
+ public final class BenchmarkJob extends ObservableValueBase<BenchmarkJob> implements HaaSOutputSource {
private Job job;
+
private JobState oldState;
+
+ private List<Task> tasks;
+
+ private SPIMComputationAccessor computationAccessor = new SPIMComputationAccessor() {
+
+ private HaaSOutputHolder outputOfSnakemake =
+ new HaaSOutputHolderImpl(getValue(), SynchronizableFileType.StandardErrorFile);
+
+ @Override
+ public String getActualOutput() {
+ return outputOfSnakemake.getActualOutput();
+ }
+
+ @Override
+ public boolean fileExists(Path filePath) {
+ File f = new File(filePath.toString());
+ return f.exists() && !f.isDirectory();
+ }
+ };
public BenchmarkJob(Job job) {
super();
@@ -73,7 +103,7 @@ public class BenchmarkJobManager {
setDownloaded(true);
}
- public void downloadStatistics(Progress progress) throws IOException {
+ public void downloadStatistics(Progress progress) throws IOException {
job.download(BenchmarkJobManager.downloadStatistics(), progress);
fireValueChangedEvent();
Path resultFile = job.getDirectory().resolve(Constants.BENCHMARK_RESULT_FILE);
@@ -84,7 +114,7 @@ public class BenchmarkJobManager {
public List<String> getOutput(List<JobSynchronizableFile> files) {
return job.getOutput(files);
}
-
+
public long getId() {
return job.getId();
}
@@ -118,8 +148,7 @@ public class BenchmarkJobManager {
@Override
public boolean equals(Object obj) {
if (obj instanceof BenchmarkJob) {
- BenchmarkJob job = (BenchmarkJob) obj;
- return job.getId() == getId();
+ return ((BenchmarkJob) obj).getId() == getId();
}
return false;
}
@@ -145,6 +174,40 @@ public class BenchmarkJobManager {
return job.getDirectory();
}
+ public List<Task> getTasks() {
+ if (tasks == null) {
+ fillTasks();
+ }
+ return tasks;
+ }
+
+ private void fillTasks() {
+
+ final String OUTPUT_PARSING_JOB_COUNTS = "Job counts:";
+ final String OUTPUT_PARSING_TAB_DELIMITER = "\\t";
+ final int OUTPUT_PARSING_EXPECTED_NUMBER_OF_WORDS_PER_LINE = 2;
+
+ tasks = new ArrayList<>();
+ Scanner scanner = new Scanner(computationAccessor.getActualOutput());
+ while (scanner.hasNextLine()) {
+ if (!scanner.nextLine().equals(OUTPUT_PARSING_JOB_COUNTS)) {
+ continue;
+ }
+ scanner.nextLine();
+
+ while (true) {
+ List<String> lineWords = Arrays.stream(scanner.nextLine().split(OUTPUT_PARSING_TAB_DELIMITER))
+ .filter(word -> word.length() > 0).collect(Collectors.toList());
+ if (lineWords.size() != OUTPUT_PARSING_EXPECTED_NUMBER_OF_WORDS_PER_LINE) {
+ break;
+ }
+ tasks.add(new Task(computationAccessor, lineWords.get(1), Integer.parseInt(lineWords.get(0))));
+ }
+ break;
+ }
+ scanner.close();
+ }
+
private void setDownloaded(boolean b) {
job.setProperty(JOB_HAS_DATA_TO_DOWNLOAD_PROPERTY, b + "");
}
@@ -155,8 +218,6 @@ public class BenchmarkJobManager {
}
}
- private JobManager jobManager;
-
public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
}
@@ -331,7 +392,6 @@ public class BenchmarkJobManager {
}
private static Settings constructSettingsFromParams(BenchmarkSPIMParameters params) {
- // TODO Auto-generated method stub
return new Settings() {
@Override
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/PipelineBase.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/PipelineBase.java
new file mode 100644
index 0000000000000000000000000000000000000000..1e3fc82ddf6815d1058d3832643cf6407409bb86
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/PipelineBase.java
@@ -0,0 +1,29 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.util.Collection;
+
+abstract public class PipelineBase<T extends PipelineBase<?,?>,S> {
+ private Collection<T> successors;
+ private S id;
+
+
+
+ public PipelineBase( S id) {
+ super();
+ this.id = id;
+ }
+
+
+ public Collection<T> getSuccessors() {
+ if(successors == null) {
+ successors = fillSuccesors();
+ }
+ return successors;
+ }
+
+ public S getId() {
+ return id;
+ }
+
+ abstract protected Collection<T> fillSuccesors();
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..39151ca434b506f873741dae844360934863ffbb
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
@@ -0,0 +1,9 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.nio.file.Path;
+
+import cz.it4i.fiji.haas.HaaSOutputHolder;
+
+public interface SPIMComputationAccessor extends HaaSOutputHolder {
+ boolean fileExists(Path fileName);
+}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
new file mode 100644
index 0000000000000000000000000000000000000000..17e74f89bc0e381b6da22fbc4168b41e930ddd2a
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
@@ -0,0 +1,26 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.util.Collection;
+import java.util.LinkedList;
+
+public class Task {
+ private final String description;
+ private final Collection<TaskComputation> computations;
+
+ public Task(SPIMComputationAccessor outputHolder, String description, int numComputations) {
+ this.description = description;
+ this.computations = new LinkedList<>();
+
+ for (int i = 0; i < numComputations; i++) {
+ computations.add(new TaskComputation(outputHolder, this, i + 1));
+ }
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+ public Collection<TaskComputation> getComputations() {
+ return computations;
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..af0bec0717d9dc9bc247805d93c57f0bebfab6a4
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
@@ -0,0 +1,112 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.Scanner;
+
+import cz.it4i.fiji.haas_java_client.JobState;
+
+public class TaskComputation {
+
+ // A single-purpose class dedicated to help with TaskComputation members initialization
+ private class ParsedTaskComputationValues {
+ private final Collection<String> logs;
+ private final Collection<String> inputs;
+ private final Collection<String> outputs;
+ private final Long id;
+
+ public ParsedTaskComputationValues(Collection<String> inputs, Collection<String> outputs, Collection<String> logs, Long id) {
+ this.inputs = inputs;
+ this.outputs = outputs;
+ this.logs = logs;
+ this.id = id;
+ }
+ }
+
+ private final Task task;
+ private final int timepoint;
+ private final Collection<String> inputs;
+ private final Collection<String> outputs;
+ private final Collection<String> logs;
+ private final Long id;
+
+ //TASK 1011 what states will be defined and how it will be defined
+ private JobState state = JobState.Unknown;
+
+ public TaskComputation(SPIMComputationAccessor outputHolder, Task task, int timepoint) {
+ this.task = task;
+ this.timepoint = timepoint;
+ ParsedTaskComputationValues parsedValues = parseStuff(outputHolder);
+ this.inputs = parsedValues.inputs;
+ this.outputs = parsedValues.outputs;
+ this.logs = parsedValues.logs;
+ this.id = parsedValues.id;
+ }
+
+ public JobState getState() {
+ updateState();//TASK 1011 it is not good idea update every time when state is requested
+ return state;
+ }
+
+ private void updateState() {
+ //TASK 1011 This should never happen, add some error handling to resolveId()
+ if (id == null) {
+ return;
+ }
+
+ //String snakeOutput = outputHolder.getActualOutput();
+
+ //TASK 1011
+ //resolve if job is queued (defined id), started (exists log file), finished (in log is Finished job 10.) or
+ //or failed (some error in log)
+ }
+
+ private Long getId() {
+ return id;
+ }
+
+ private ParsedTaskComputationValues parseStuff(SPIMComputationAccessor outputHolder) {
+
+ final String OUTPUT_PARSING_RULE = "rule ";
+ final String OUTPUT_PARSING_COLON = ":";
+ final String OUTPUT_PARSING_COMMA_SPACE = ", ";
+ final String desiredPattern = OUTPUT_PARSING_RULE + task.getDescription() + OUTPUT_PARSING_COLON;
+
+ final String OUTPUT_PARSING_INPUTS = "input: ";
+ final String OUTPUT_PARSING_OUTPUTS = "output: ";
+ final String OUTPUT_PARSING_LOGS = "log: ";
+ final String OUTPUT_PARSING_JOB_ID = "jobid: ";
+
+ Scanner scanner = new Scanner(outputHolder.getActualOutput());
+ int jobsToSkip = timepoint;
+ while (scanner.hasNextLine() && jobsToSkip > 0) {
+ if (scanner.nextLine().equals(desiredPattern)) {
+ jobsToSkip--;
+ }
+ }
+
+ String currentLine;
+ Collection<String> resolvedInputs = new LinkedList<>();
+ Collection<String> resolvedOutputs = new LinkedList<>();
+ Collection<String> resolvedLogs = new LinkedList<>();
+ Long resolvedId = null;
+ while (scanner.hasNextLine()) {
+ currentLine = scanner.nextLine();
+ if (currentLine.contains(OUTPUT_PARSING_INPUTS)) {
+ resolvedInputs = Arrays.asList(currentLine.split(OUTPUT_PARSING_INPUTS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
+ } else if (currentLine.contains(OUTPUT_PARSING_OUTPUTS)) {
+ resolvedOutputs = Arrays.asList(currentLine.split(OUTPUT_PARSING_OUTPUTS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
+ } else if (currentLine.contains(OUTPUT_PARSING_LOGS)) {
+ resolvedLogs = Arrays.asList(currentLine.split(OUTPUT_PARSING_LOGS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
+ } else if (currentLine.contains(OUTPUT_PARSING_JOB_ID)) {
+ resolvedId = Long.parseLong(currentLine.split(OUTPUT_PARSING_JOB_ID)[1]);
+ } else if (currentLine.trim().isEmpty()) {
+ break;
+ }
+ }
+ scanner.close();
+
+ return new ParsedTaskComputationValues(resolvedInputs, resolvedOutputs, resolvedLogs, resolvedId);
+ }
+}