From 5c6541de450de328c4da799e344f53ec9558a6b1 Mon Sep 17 00:00:00 2001
From: Jan Kozusznik <jan@kozusznik.cz>
Date: Mon, 29 Jan 2018 15:21:47 +0100
Subject: [PATCH] basic definitions
---
.../cz/it4i/fiji/haas/HaaSOutputHolder.java | 27 +++++++++++++++++++
.../cz/it4i/fiji/haas/HaaSOutputSource.java | 9 +++++++
.../core/BenchmarkJobManager.java | 22 ++++++++++++++-
.../fiji/haas_spim_benchmark/core/Task.java | 24 +++++++++++++++++
.../core/TaskComputation.java | 5 ++++
5 files changed, 86 insertions(+), 1 deletion(-)
create mode 100644 haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolder.java
create mode 100644 haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputSource.java
create mode 100644 haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
create mode 100644 haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
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 00000000..5c8da0e6
--- /dev/null
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/HaaSOutputHolder.java
@@ -0,0 +1,27 @@
+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 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));
+ }
+}
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 00000000..904258f0
--- /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-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 4fb7751e..3b720588 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
@@ -21,6 +21,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.yaml.snakeyaml.Yaml;
+import cz.it4i.fiji.haas.HaaSOutputHolder;
+import cz.it4i.fiji.haas.HaaSOutputSource;
import cz.it4i.fiji.haas.JobManager;
import cz.it4i.fiji.haas.JobManager.JobInfo;
import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
@@ -28,6 +30,7 @@ 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;
@@ -38,14 +41,19 @@ public class BenchmarkJobManager {
private static Logger log = LoggerFactory
.getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
- public final class Job extends ObservableValueBase<Job> {
+ public final class Job extends ObservableValueBase<Job> implements HaaSOutputSource {
private JobInfo jobInfo;
private JobState oldState;
+
+ private HaaSOutputHolder outputOfSnakemake;
+
+ private Collection<Task> tasks;
public Job(JobInfo ji) {
super();
this.jobInfo = ji;
+ outputOfSnakemake = new HaaSOutputHolder(getValue(), SynchronizableFileType.StandardErrorFile);
}
public void startJob(Progress progress) throws IOException {
@@ -139,6 +147,18 @@ public class BenchmarkJobManager {
return jobInfo.getDirectory();
}
+ public Collection<Task> getTasks() {
+ if(tasks == null) {
+ fillTasks();
+ }
+ return tasks;
+ }
+
+
+ private void fillTasks() {
+ String snakeMakeoutput = outputOfSnakemake.getActualOutput();
+
+ }
private void setDownloaded(boolean b) {
jobInfo.setProperty(JOB_HAS_DATA_TO_DOWNLOAD_PROPERTY, b + "");
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 00000000..95ac6f0a
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
@@ -0,0 +1,24 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+import java.util.Collection;
+
+import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.Job;
+
+public class Task {
+ private String description;
+ private Job job;
+ private Collection<TaskComputation> computations;
+
+ public Task(Job job,String description) {
+ this.description = description;
+ this.job = job;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+ public Collection<Task> getPredecessors() {
+ return null;
+ }
+}
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 00000000..497e2fd1
--- /dev/null
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
@@ -0,0 +1,5 @@
+package cz.it4i.fiji.haas_spim_benchmark.core;
+
+public class TaskComputation {
+
+}
--
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