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 <[email protected]> Authored: Fri Jun 5 11:45:22 2015 -0400 Committer: Shameera Rathanyaka <[email protected]> Committed: Fri Jun 5 11:45:22 2015 -0400 ---------------------------------------------------------------------- .../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(-) ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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);
