From 1928b9d79c88a28d42e302ac17f48459857c06b8 Mon Sep 17 00:00:00 2001
From: Petr Bainar <petr.bainar@hotmail.com>
Date: Tue, 30 Jan 2018 15:53:02 +0100
Subject: [PATCH] iss1011: implementing id resolving
---
.../core/TaskComputation.java | 58 ++++++++++++-------
1 file changed, 36 insertions(+), 22 deletions(-)
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 3ee8bb11..36a81feb 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
@@ -2,6 +2,7 @@ package cz.it4i.fiji.haas_spim_benchmark.core;
import java.util.Collection;
import java.util.LinkedList;
+import java.util.Scanner;
import cz.it4i.fiji.haas_java_client.JobState;
@@ -10,10 +11,11 @@ public class TaskComputation {
private final SPIMComputationAccessor outputHolder;
private final Task task;
private final int timepoint;
+ private final Long id;
- private Long id;
//TASK 1011 what states will be defined and how it will be defined
private JobState state = JobState.Unknown;
+
private Collection<String> logs = new LinkedList<>();
private Collection<String> outputs = new LinkedList<>();
private Collection<String> inputs = new LinkedList<>();
@@ -23,6 +25,7 @@ public class TaskComputation {
this.outputHolder = outputHolder;
this.task = task;
this.timepoint = timepoint;
+ this.id = resolveId();
}
public JobState getState() {
@@ -31,39 +34,50 @@ public class TaskComputation {
}
private void updateState() {
- String snakeOutput = outputHolder.getActualOutput();
- Long id = getId();
- if(id == null) {
+ //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() {
- 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
+ private Long resolveId() {
+
+ final String OUTPUT_PARSING_RULE = "rule ";
+ final String OUTPUT_PARSING_JOB_ID = "jobid: ";
+ final String OUTPUT_PARSING_COLON = ":";
+ final String desiredPattern = OUTPUT_PARSING_RULE + task.getDescription() + OUTPUT_PARSING_COLON;
+
+ Scanner scanner = new Scanner(outputHolder.getActualOutput());
+ int jobsToSkip = timepoint - 1;
+ do {
+ if (scanner.nextLine().equals(desiredPattern)) {
+ jobsToSkip--;
+ }
+ } while (jobsToSkip >= 0 && scanner.hasNextLine());
+
+ String currentLine;
+ Long resolvedId = null;
+ while (scanner.hasNextLine()) {
+ currentLine = scanner.nextLine();
+ if (!currentLine.contains(OUTPUT_PARSING_JOB_ID)) {
+ continue;
+ }
+ resolvedId = Long.parseLong(currentLine.split(OUTPUT_PARSING_JOB_ID)[1]);
+ break;
+ }
+ scanner.close();
- //resave_hdf5 == task.getDescription()
- //jobid -> id
- //input->inputs
- //...
- //
- //or return
+ return resolvedId;
}
}
--
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