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
index 5c8da0e69ed27d513448e98bb099246daf27d291..c54b0f5c00ecdd9a2497ac0ed36982271189e48d 100644
--- 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
@@ -1,27 +1,7 @@
package cz.it4i.fiji.haas;
-import java.util.Arrays;
+public interface HaaSOutputHolder {
-import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
-import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
+ String getActualOutput();
-public class HaaSOutputHolder {
- private StringBuilder result = new StringBuilder();
- private HaaSOutputSource source;
- private SynchronizableFileType type;
- public HaaSOutputHolder(HaaSOutputSource source, SynchronizableFileType typeForHold) {
- super();
- this.source = source;
- this.type = typeForHold;
- }
-
- 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));
- }
-}
+}
\ 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-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 a5b6ce893c40a657fecde4061c0e717756fe7b33..ef0058bd2819e88c09a48aeb92023f70794d3b31 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
@@ -22,8 +22,10 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.yaml.snakeyaml.Yaml;
-import cz.it4i.fiji.haas.Job;
+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;
import cz.it4i.fiji.haas.UploadingFileFromResource;
@@ -41,6 +43,9 @@ public class BenchmarkJobManager {
private static Logger log = LoggerFactory
.getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
+ private JobManager jobManager;
+
+
public final class BenchmarkJob extends ObservableValueBase<BenchmarkJob> implements HaaSOutputSource {
private Job job;
@@ -48,12 +53,25 @@ public class BenchmarkJobManager {
private HaaSOutputHolder outputOfSnakemake;
- private Collection<Task> tasks;
+ private List<Task> tasks;
+
+ private SPIMComputationAccessor computationAccessor = new SPIMComputationAccessor() {
+ @Override
+ public String getActualOutput() {
+ return outputOfSnakemake.getActualOutput();
+ }
+
+ @Override
+ public boolean fileExists(String fileName) {
+ // TASK 1011 modify interface of job for checking of file existence
+ return false;
+ }
+ };
public BenchmarkJob(Job job) {
super();
this.job = job;
- outputOfSnakemake = new HaaSOutputHolder(getValue(), SynchronizableFileType.StandardErrorFile);
+ outputOfSnakemake = new HaaSOutputHolderImpl(getValue(), SynchronizableFileType.StandardErrorFile);
}
public void startJob(Progress progress) throws IOException {
@@ -91,7 +109,7 @@ public class BenchmarkJobManager {
public List<String> getOutput(List<JobSynchronizableFile> files) {
return job.getOutput(files);
}
-
+
public long getId() {
return job.getId();
}
@@ -152,7 +170,7 @@ public class BenchmarkJobManager {
return job.getDirectory();
}
- public Collection<Task> getTasks() {
+ public List<Task> getTasks() {
if(tasks == null) {
fillTasks();
}
@@ -161,7 +179,23 @@ public class BenchmarkJobManager {
private void fillTasks() {
+ SPIMComputationAccessor accessor = computationAccessor;
String snakeMakeoutput = outputOfSnakemake.getActualOutput();
+ //TASK 1011 parse snakeOutput, create tasks base part:
+//Job counts:
+// count jobs
+// 1 define_output
+// 1 define_xml_tif
+// 1 done
+// 2 fusion
+// 1 hdf5_xml
+// 1 hdf5_xml_output
+// 2 registration
+// 2 resave_hdf5
+// 2 resave_hdf5_output
+// 1 timelapse
+// 1 xml_merge
+// 15
}
private void setDownloaded(boolean b) {
@@ -174,8 +208,6 @@ public class BenchmarkJobManager {
}
}
- private JobManager jobManager;
-
public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
}
@@ -350,7 +382,6 @@ 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..0ba6590109e4406f0d99e247ac8757d25af4e908
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
@@ -0,0 +1,7 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import cz.it4i.fiji.haas.HaaSOutputHolder;
+
+public interface SPIMComputationAccessor extends HaaSOutputHolder {
+ boolean fileExists(String 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
index 95ac6f0ab1d1cef69ff66e9f5e8d5ae6483306ff..84af6203020fe9a90b10200c869d33eb2ee07516 100644
--- 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
@@ -1,24 +1,36 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
import java.util.Collection;
-
-import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.Job;
+import java.util.LinkedList;
public class Task {
+ private SPIMComputationAccessor outputHolder;
private String description;
- private Job job;
private Collection<TaskComputation> computations;
-
- public Task(Job job,String description) {
+ private int numComputations;
+
+ public Task(SPIMComputationAccessor outputHolder, String description, int numComputations) {
this.description = description;
- this.job = job;
+ this.outputHolder = outputHolder;
+ this.numComputations = numComputations;
+ }
+
+ public Collection<TaskComputation> getComputations() {
+ if (computations == null) {
+ fillComputations();
+ }
+ return computations;
}
public String getDescription() {
return description;
}
-
- public Collection<Task> getPredecessors() {
- return null;
+
+ private void fillComputations() {
+ computations = new LinkedList<>();
+ for (int i = 0; i < numComputations; i++) {
+ computations.add(new TaskComputation(outputHolder, this, i + 1));
+ }
}
+
}
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 497e2fd107bd2a358d30b82f16e046e92e158848..2d1c7b221d415bac344dbd9221a164108eac5ed7 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
@@ -1,5 +1,69 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
+import java.util.Collection;
+import java.util.LinkedList;
+
+import cz.it4i.fiji.haas_java_client.JobState;
+
+
public class TaskComputation {
+ private SPIMComputationAccessor outputHolder;
+ private int timepoint;
+ private Long id;
+ //TASK 1011 what states will be defined and how it will be defined
+ private JobState state;
+ private Task task;
+ private Collection<String> logs = new LinkedList<>();
+ private Collection<String> outputs = new LinkedList<>();
+ private Collection<String> inputs = new LinkedList<>();
+
+
+ public TaskComputation(SPIMComputationAccessor outputHolder,Task task, int timepoint) {
+ this.outputHolder = outputHolder;
+ this.timepoint = timepoint;
+ this.task = task;
+ }
+
+ public JobState getState() {
+ updateState();//TASK 1011 it is not good idea update every time when state is requested
+ return state != null?state:JobState.Configuring;
+ }
+
+ private void updateState() {
+ String snakeOutput = outputHolder.getActualOutput();
+ Long id = getId();
+ if(id == null) {
+ return;
+ }
+ //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() {
+ if(id == null) {
+ fillId();
+ }
+ return id;
+ }
+
+ private void fillId() {
+ //TASK 1011
+ //find timepoint-th occurence of
+//rule resave_hdf5:
+// input: HisRFP_test-01-00.h5_xml, HisRFP_test_first.xml
+// output: HisRFP_test-01-00.h5, HisRFP_test-01-00.h5_hdf5
+// log: logs/b2_resave_hdf5-01.log
+// jobid: 7
+// wildcards: xml_base=HisRFP_test, file_id=01
+
+ //resave_hdf5 == task.getDescription()
+ //jobid -> id
+ //input->inputs
+ //...
+ //
+ //or return
+ }
+
}