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Posted to commits@airavata.apache.org by sh...@apache.org on 2015/06/05 17:45:25 UTC
airavata git commit: Fixed partial jobId retrieve from PBS resource
at validation step.
Repository: airavata
Updated Branches:
refs/heads/airavata-0.15-release-branch 58af590d3 -> 97135ad33
Fixed partial jobId retrieve from PBS resource at validation step.
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/97135ad3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/97135ad3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/97135ad3
Branch: refs/heads/airavata-0.15-release-branch
Commit: 97135ad33c057b4f54ccf873e7a14cac8f286f56
Parents: 58af590
Author: Shameera Rathanyaka <sh...@gmail.com>
Authored: Fri Jun 5 11:45:22 2015 -0400
Committer: Shameera Rathanyaka <sh...@gmail.com>
Committed: Fri Jun 5 11:45:22 2015 -0400
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.../apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java | 2 +-
.../org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java | 6 +++++-
.../apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java | 1 +
3 files changed, 7 insertions(+), 2 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata/blob/97135ad3/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
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diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
index b658b16..7e8db3b 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSJobConfiguration.java
@@ -99,7 +99,7 @@ public class PBSJobConfiguration implements JobManagerConfiguration {
@Override
public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
// For PBS there is no option to get jobDetails by JobName, so we search with userName
- return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
+ return new RawCommandInfo(this.installedPath + "qstat -u " + userName + " -f | grep \"Job_Name = " + jobName + "\" -B1");
}
@Override
http://git-wip-us.apache.org/repos/asf/airavata/blob/97135ad3/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
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diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
index 1458f4c..81f241d 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java
@@ -194,8 +194,12 @@ public class PBSOutputParser implements OutputParser {
@Override
public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
+ /* output will look like
+ Job Id: 2080802.gordon-fe2.local
+ Job_Name = A312402627
+ */
String regJobId = "jobId";
- Pattern pattern = Pattern.compile("\\s*(?<" + regJobId + ">[^\\s]*).* " + jobName + " "); // regex , JOB_ID will come as first column
+ Pattern pattern = Pattern.compile("(?<" + regJobId + ">[^\\s]*)\\s*.* " + jobName);
if (rawOutput != null) {
Matcher matcher = pattern.matcher(rawOutput);
if (matcher.find()) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/97135ad3/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
index 7a04f11..f8b46c8 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/GSISSHAbstractCluster.java
@@ -630,6 +630,7 @@ public class GSISSHAbstractCluster implements Cluster {
return files;
}
+ @Deprecated
public synchronized void getJobStatuses(String userName, Map<String,JobStatus> jobIDs)throws SSHApiException {
int retry = 3;
RawCommandInfo rawCommandInfo = jobManagerConfiguration.getUserBasedMonitorCommand(userName);