From 45bd29ae08fb2186fbeb6a9dd8883b81aa465cec Mon Sep 17 00:00:00 2001
From: Petr Bainar <petr.bainar@hotmail.com>
Date: Tue, 30 Jan 2018 12:56:51 +0100
Subject: [PATCH] iss1011: implementing Task parsing from the snakeMake output
---
.../core/BenchmarkJobManager.java | 58 +++++++++++--------
1 file changed, 34 insertions(+), 24 deletions(-)
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 ef0058bd..8e706e96 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
@@ -9,12 +9,14 @@ 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;
@@ -49,13 +51,16 @@ public class BenchmarkJobManager {
public final class BenchmarkJob extends ObservableValueBase<BenchmarkJob> implements HaaSOutputSource {
private Job job;
+
private JobState oldState;
- private HaaSOutputHolder outputOfSnakemake;
-
private List<Task> tasks;
private SPIMComputationAccessor computationAccessor = new SPIMComputationAccessor() {
+
+ private HaaSOutputHolder outputOfSnakemake =
+ new HaaSOutputHolderImpl(getValue(), SynchronizableFileType.StandardErrorFile);
+
@Override
public String getActualOutput() {
return outputOfSnakemake.getActualOutput();
@@ -71,7 +76,6 @@ public class BenchmarkJobManager {
public BenchmarkJob(Job job) {
super();
this.job = job;
- outputOfSnakemake = new HaaSOutputHolderImpl(getValue(), SynchronizableFileType.StandardErrorFile);
}
public void startJob(Progress progress) throws IOException {
@@ -98,7 +102,7 @@ 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);
@@ -171,33 +175,39 @@ public class BenchmarkJobManager {
}
public List<Task> getTasks() {
- if(tasks == null) {
+ if (tasks == null) {
fillTasks();
}
return tasks;
- }
-
+ }
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
+ 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 + "");
}
--
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