Author: lahiru
Date: Thu Oct 17 19:04:10 2013
New Revision: 1533215
URL: http://svn.apache.org/r1533215
Log:
gsissh tool to handle standard out and standard error and give higher
preference to standard out.
Removed:
airavata/trunk/tools/gsissh/src/main/resources/gsissh.properties
Modified:
airavata/trunk/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
airavata/trunk/tools/gsissh/src/main/resources/PBSTemplate.xslt
Modified:
airavata/trunk/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java?rev=1533215&r1=1533214&r2=1533215&view=diff
==============================================================================
---
airavata/trunk/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
(original)
+++
airavata/trunk/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
Thu Oct 17 19:04:10 2013
@@ -82,13 +82,16 @@ public class PBSCluster implements Clust
System.setProperty(X509_CERT_DIR, (String)
((GSIAuthenticationInfo) authenticationInfo).getProperties().
get("X509_CERT_DIR"));
}
-
+ if(installedPath == null) {
+ throw new SSHApiException("Installed path cannot be null !!");
+ }
if (installedPath.endsWith("/")) {
this.installedPath = installedPath;
} else {
this.installedPath = installedPath + "/";
}
+
try {
this.configReader = new ConfigReader();
} catch (IOException e) {
@@ -233,12 +236,30 @@ public class PBSCluster implements Clust
//Check whether pbs submission is successful or not, if it failed
throw and exception in submitJob method
// with the error thrown in qsub command
//
+ String stdOutputString =
getOutputifAvailable(jobIDReaderCommandOutput, "Error submitting job to
resource");
+ return stdOutputString;
- if (!jobIDReaderCommandOutput.getStdErrorString().equals("")) {
- throw new
SSHApiException(jobIDReaderCommandOutput.getStandardError().toString());
- } else {
- return jobIDReaderCommandOutput.getStdOutputString();
+ }
+
+ /**
+ * This method will read standard output and if there's any it will be
parsed
+ * @param jobIDReaderCommandOutput
+ * @param errorMsg
+ * @return
+ * @throws SSHApiException
+ */
+ private String getOutputifAvailable(StandardOutReader
jobIDReaderCommandOutput, String errorMsg) throws SSHApiException {
+ String stdOutputString = jobIDReaderCommandOutput.getStdOutputString();
+ String stdErrorString = jobIDReaderCommandOutput.getStdErrorString();
+
+ if(stdOutputString == null){
+ throw new SSHApiException(errorMsg + stdErrorString);
+ }else{
+ if(stdErrorString != null){
+ log.error("Standard Error output : " + stdErrorString);
+ }
}
+ return stdOutputString;
}
public String submitBatchJob(JobDescriptor jobDescriptor) throws
SSHApiException {
@@ -299,10 +320,8 @@ public class PBSCluster implements Clust
StandardOutReader stdOutReader = new StandardOutReader();
CommandExecutor.executeCommand(rawCommandInfo, this.getSession(),
stdOutReader);
- if (stdOutReader.getStdErrorString() != null) {
- throw new
SSHApiException(stdOutReader.getStandardError().toString());
- }
- String result = stdOutReader.getStdOutputString();
+
+ String result = getOutputifAvailable(stdOutReader, "Error getting
cluster information !");
String[] Nodes = result.split("\n");
String[] line;
String header, value;
@@ -367,10 +386,8 @@ public class PBSCluster implements Clust
StandardOutReader stdOutReader = new StandardOutReader();
CommandExecutor.executeCommand(rawCommandInfo, this.getSession(),
stdOutReader);
- if (!stdOutReader.getStdErrorString().equals("")) {
- throw new
SSHApiException(stdOutReader.getStandardError().toString());
- }
- String result = stdOutReader.getStdOutputString();
+
+ String result = getOutputifAvailable(stdOutReader, "Error getting job
information from the resource !");;
String[] info = result.split("\n");
JobDescriptor jobDescriptor = new JobDescriptor();
String[] line;
@@ -459,7 +476,7 @@ public class PBSCluster implements Clust
public void scpTo(String remoteFile, String localFile) throws
SSHApiException {
try {
- SSHUtils.scpTo(remoteFile, localFile, session);
+ SSHUtils.scpTo(remoteFile, localFile, session);
} catch (IOException e) {
throw new SSHApiException("Failed during scping local file:" +
localFile + " to remote file "
+ serverInfo.getHost() + ":rFile", e);
@@ -471,7 +488,7 @@ public class PBSCluster implements Clust
public void scpFrom(String remoteFile, String localFile) throws
SSHApiException {
try {
- SSHUtils.scpFrom(remoteFile, localFile, session);
+ SSHUtils.scpFrom(remoteFile, localFile, session);
} catch (IOException e) {
throw new SSHApiException("Failed during scping local file:" +
localFile + " to remote file "
+ serverInfo.getHost() + ":rFile", e);
@@ -552,11 +569,9 @@ public class PBSCluster implements Clust
StandardOutReader stdOutReader = new StandardOutReader();
CommandExecutor.executeCommand(rawCommandInfo, this.getSession(),
stdOutReader);
- // check the standard error, incase user gave wrong jobID
- if (!stdOutReader.getStdErrorString().equals("")) {
- throw new
SSHApiException(stdOutReader.getStandardError().toString());
- }
- String result = stdOutReader.getStdOutputString();
+
+
+ String result = getOutputifAvailable(stdOutReader,"Error getting job
status with job ID: " + jobID);
String[] info = result.split("\n");
String[] line = null;
for (String anInfo : info) {
@@ -577,9 +592,8 @@ public class PBSCluster implements Clust
StandardOutReader stdOutReader = new StandardOutReader();
CommandExecutor.executeCommand(rawCommandInfo, this.getSession(),
stdOutReader);
- if (!stdOutReader.getStdErrorString().equals("")) {
- throw new
SSHApiException(stdOutReader.getStandardError().toString());
- }
+
+ getOutputifAvailable(stdOutReader, "Error cancelling job with Job ID :
" + jobID);
JobDescriptor jobById = this.getJobDescriptorById(jobID);
if (CommonUtils.isJobFinished(jobById)) {
Modified: airavata/trunk/tools/gsissh/src/main/resources/PBSTemplate.xslt
URL:
http://svn.apache.org/viewvc/airavata/trunk/tools/gsissh/src/main/resources/PBSTemplate.xslt?rev=1533215&r1=1533214&r2=1533215&view=diff
==============================================================================
--- airavata/trunk/tools/gsissh/src/main/resources/PBSTemplate.xslt (original)
+++ airavata/trunk/tools/gsissh/src/main/resources/PBSTemplate.xslt Thu Oct 17
19:04:10 2013
@@ -9,7 +9,6 @@
<xsl:output method="text" />
<xsl:template match="/ns:JobDescriptor">
#! /bin/sh
-# PBS batch job script built by Globus job manager
# <xsl:choose>
<xsl:when test="ns:shellName">
##PBS -S <xsl:value-of select="ns:shellName"/>
