Author: lahiru
Date: Wed Sep 4 19:12:12 2013
New Revision: 1520111
URL: http://svn.apache.org/r1520111
Log:
adding more parameters to jobDescriptor.
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
airavata/sandbox/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java?rev=1520111&r1=1520110&r2=1520111&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
Wed Sep 4 19:12:12 2013
@@ -20,17 +20,10 @@
*/
package org.apache.airavata.gsi.ssh.api.job;
-import org.apache.airavata.gsi.ssh.api.CommandInfo;
import org.apache.airavata.gsi.ssh.api.CommandOutput;
-import org.apache.airavata.gsi.ssh.x2012.x12.InputList;
-import org.apache.airavata.gsi.ssh.x2012.x12.JobDescriptorDocument;
-import org.apache.airavata.gsi.ssh.x2012.x12.PbsParams;
-import org.apache.airavata.gsi.ssh.x2012.x12.impl.PbsParamsImpl;
+import org.apache.airavata.gsi.ssh.x2012.x12.*;
import org.apache.xmlbeans.XmlException;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
/**
@@ -128,7 +121,7 @@ public class JobDescriptor {
this.getJobDescriptorDocument().getJobDescriptor().setAcountString(name);
}
- public void setInputValues(List<String> inputValue){
+ public void setInputValues(List<String> inputValue) {
InputList inputList =
this.getJobDescriptorDocument().getJobDescriptor().addNewInputs();
inputList.setInputArray(inputValue.toArray(new
String[inputValue.size()]));
}
@@ -140,12 +133,151 @@ public class JobDescriptor {
public void setQueueName(String queueName) {
this.getJobDescriptorDocument().getJobDescriptor().setQueueName(queueName);
}
- public void setStatus(String queueName) {
+
+ public void setStatus(String queueName) {
this.getJobDescriptorDocument().getJobDescriptor().setStatus(queueName);
}
+ public void setAfterAnyList(String[] afterAnyList) {
+ AfterAnyList afterAny =
this.getJobDescriptorDocument().getJobDescriptor().addNewAfterAny();
+ afterAny.setAfterAnyArray(afterAnyList);
+ }
+
+ public void setAfterOKList(String[] afterOKList) {
+ AfterOKList afterAnyList =
this.getJobDescriptorDocument().getJobDescriptor().addNewAfterOKList();
+ afterAnyList.setAfterOKListArray(afterOKList);
+ }
+ public void setCTime(String cTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setCTime(cTime);
+ }
+ public void setQTime(String qTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setQTime(qTime);
+ }
+ public void setMTime(String mTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setMTime(mTime);
+ }
+ public void setSTime(String sTime) {
+ this.getJobDescriptorDocument().getJobDescriptor().setSTime(sTime);
+ }
+ public void setCompTime(String compTime) {
+
this.getJobDescriptorDocument().getJobDescriptor().setCompTime(compTime);
+ }
+ public void setOwner(String owner) {
+ this.getJobDescriptorDocument().getJobDescriptor().setOwner(owner);
+ }
+ public void setExecuteNode(String executeNode) {
+
this.getJobDescriptorDocument().getJobDescriptor().setExecuteNode(executeNode);
+ }
+ public void setEllapsedTime(String ellapsedTime) {
+
this.getJobDescriptorDocument().getJobDescriptor().setEllapsedTime(ellapsedTime);
+ }
+
+ public void setUsedCPUTime(String usedCPUTime) {
+
this.getJobDescriptorDocument().getJobDescriptor().setUsedCPUTime(usedCPUTime);
+ }
+ public void setUsedMemory(String usedMemory) {
+
this.getJobDescriptorDocument().getJobDescriptor().setUsedMem(usedMemory);
+ }
+ public void setVariableList(String variableList) {
+
this.getJobDescriptorDocument().getJobDescriptor().setVariableList(variableList);
+ }
+ public void setSubmitArgs(String submitArgs) {
+
this.getJobDescriptorDocument().getJobDescriptor().setSubmitArgs(submitArgs);
+ }
+
+
- public void getShellName() {
+ public String getExecutablePath() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getExecutablePath();
+ }
+
+ public boolean getAllEnvExport() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getAllEnvExport();
+ }
+
+ public String getMailOptions() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getMailOptions();
+ }
+
+ public String getStandardOutFile() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile();
+ }
+
+ public String getStandardErrorFile() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile();
+ }
+
+ public int getNodes(int name) {
+ return this.getJobDescriptorDocument().getJobDescriptor().getNodes();
+ }
+
+ public int getProcessesPerNode() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getProcessesPerNode();
+ }
+
+ public String getMaxWallTime() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getMaxWallTime();
+ }
+
+ public String getAcountString() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getAcountString();
+ }
+
+ public String[] getInputValues() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getInputs().getInputArray();
+ }
+
+ public String getJobID() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+
+ public String getQueueName() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getQueueName();
+ }
+
+ public String getStatus() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getStatus();
+ }
+
+ public String[] getAfterAnyList() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getAfterAny().getAfterAnyArray();
+ }
+
+ public String[] getAfterOKList() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getAfterOKList().getAfterOKListArray();
+ }
+ public String getCTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getCTime();
+ }
+ public String getQTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getQTime();
+ }
+ public String getMTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getMTime();
+ }
+ public String getSTime() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getSTime();
+ }
+ public String getCompTime() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getCompTime();
+ }
+ public String getOwner() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getOwner();
+ }
+ public String getExecuteNode() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getExecuteNode();
+ }
+ public String getEllapsedTime() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getEllapsedTime();
+ }
+
+ public String getUsedCPUTime() {
+ return
this.getJobDescriptorDocument().getJobDescriptor().getUsedCPUTime();
+ }
+ public String getUsedMemory() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getUsedMem();
+ }
+ public void getShellName() {
this.getJobDescriptorDocument().getJobDescriptor().getShellName();
}
@@ -153,9 +285,18 @@ public class JobDescriptor {
return this.getJobDescriptorDocument().getJobDescriptor().getJobName();
}
- public String getJobId(){
+ public String getJobId() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+
+
+ public String getVariableList() {
+ return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+ }
+ public String getSubmitArgs() {
return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
}
+
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java?rev=1520111&r1=1520110&r2=1520111&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
Wed Sep 4 19:12:12 2013
@@ -248,6 +248,9 @@ public class DefaultSSHApi implements SS
StandardOutReader stdOutReader = new StandardOutReader();
this.executeCommand(rawCommandInfo, serverInfo, authenticationInfo,
stdOutReader);
+ if (!stdOutReader.getErrorifAvailable().equals("")) {
+ throw new
SSHApiException(stdOutReader.getStandardError().toString());
+ }
String result = stdOutReader.getStdOutput();
String[] Nodes = result.split("\n");
String[] line;
@@ -312,6 +315,9 @@ public class DefaultSSHApi implements SS
StandardOutReader stdOutReader = new StandardOutReader();
this.executeCommand(rawCommandInfo, serverInfo, authenticationInfo,
stdOutReader);
+ if (!stdOutReader.getErrorifAvailable().equals("")) {
+ throw new
SSHApiException(stdOutReader.getStandardError().toString());
+ }
String result = stdOutReader.getStdOutput();
String[] info = result.split("\n");
JobDescriptor jobDescriptor = new JobDescriptor();
@@ -338,36 +344,38 @@ public class DefaultSSHApi implements SS
value = value.replaceAll("\t", "");
// jobDescriptor.VariablesList=value;
// jobDescriptor.analyzeVariableList(value);
- } else if ("Job Id".equals(header))
+ } else if ("Job Id".equals(header)){
jobDescriptor.setJobID(value);
- else if ("Job_Name".equals(header))
+ }else if ("Job_Name".equals(header)){
jobDescriptor.setJobName(value);
-
- else if ("Job_Owner".equals(header)) {
-// jobDescriptor.setOwner(value);
+ }else if ("Account_Name".equals(header)){
+ jobDescriptor.setAcountString(value);
+ }else if ("job_state".equals(header)){
+ jobDescriptor.setStatus(value);
+ }else if ("Job_Owner".equals(header)) {
+ jobDescriptor.setOwner(value);
} else if ("resources_used.cput".equals(header)) {
-// jobDescriptor.setUsedcput(value);
+ jobDescriptor.setUsedCPUTime(value);
} else if ("resources_used.mem".equals(header)) {
-// jobDescriptor.setUsedMem(value);
+ jobDescriptor.setUsedMemory(value);
} else if ("resources_used.walltime".equals(header)) {
-// jobDescriptor.setEllapsedTime(value);
- } else if ("job_state".equals(header))
+ jobDescriptor.setEllapsedTime(value);
+ } else if ("job_state".equals(header)){
jobDescriptor.setStatus(value);
-
- else if ("queue".equals(header))
+ }else if ("queue".equals(header))
jobDescriptor.setQueueName(value);
else if ("ctime".equals(header)) {
-// jobDescriptor.setCtime(value);
+ jobDescriptor.setCTime(value);
} else if ("qtime".equals(header)) {
-// jobDescriptor.setQtime(value);
+ jobDescriptor.setQTime(value);
} else if ("mtime".equals(header)) {
-// jobDescriptor.setMtime(value);
+ jobDescriptor.setMTime(value);
} else if ("start_time".equals(header)) {
-// jobDescriptor.setStime(value);
+ jobDescriptor.setSTime(value);
} else if ("comp_time".equals(header)) {
-// jobDescriptor.setComp_time(value);
+ jobDescriptor.setCompTime(value);
} else if ("exec_host".equals(header)) {
-// jobDescriptor.setExecuteNode(value);
+ jobDescriptor.setExecuteNode(value);
} else if ("Output_Path".equals(header)) {
if (info[i + 1].contains("=") || info[i + 1].contains(":"))
jobDescriptor.setStandardOutFile(value);
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java?rev=1520111&r1=1520110&r2=1520111&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
Wed Sep 4 19:12:12 2013
@@ -49,7 +49,6 @@ public class StandardOutReader implement
break;
}
try {
- Thread.sleep(1000);
} catch (Exception ignored) {
}
}
Modified:
airavata/sandbox/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd?rev=1520111&r1=1520110&r2=1520111&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd
(original)
+++ airavata/sandbox/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd Wed
Sep 4 19:12:12 2013
@@ -33,6 +33,20 @@
<element name="inputs" type="gsissh:inputList" minOccurs="1"
maxOccurs="1"/>
<element name="exports" type="gsissh:exportProperties"
minOccurs="1" maxOccurs="1"/>
<element name="status" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="afterAny" type="gsissh:afterAnyList" minOccurs="0"
maxOccurs="1"/>
+ <element name="afterOKList" type="gsissh:afterOKList"
minOccurs="0" maxOccurs="1"/>
+ <element name="cTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="qTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="mTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="sTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="compTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="owner" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="executeNode" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="ellapsedTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="usedCPUTime" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="usedMem" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="submitArgs" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
+ <element name="variableList" type="xsd:string" minOccurs="0"
maxOccurs="1"/>
</sequence>
</complexType>
<complexType name="inputList">
@@ -40,6 +54,18 @@
<element name="input" type="xsd:string" minOccurs="0"
maxOccurs="unbounded" />
</sequence>
</complexType>
+ <complexType name="afterAnyList">
+ <sequence>
+ <element name="afterAny" type="xsd:string"
minOccurs="0" maxOccurs="unbounded" />
+ </sequence>
+ </complexType>
+
+ <complexType name="afterOKList">
+ <sequence>
+ <element name="afterOKList" type="xsd:string"
minOccurs="0" maxOccurs="unbounded" />
+ </sequence>
+ </complexType>
+
<complexType name="exportProperties">
<sequence>
Modified:
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java?rev=1520111&r1=1520110&r2=1520111&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
(original)
+++
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Wed Sep 4 19:12:12 2013
@@ -23,16 +23,11 @@ package org.apache.airavata.gsi.ssh.impl
import org.apache.airavata.gsi.ssh.api.*;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.ssh.x2012.x12.ExportProperties;
-import org.apache.airavata.gsi.ssh.x2012.x12.InputList;
-import org.apache.commons.io.FilenameUtils;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
import java.io.File;
-import java.net.URI;
-import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
@@ -54,9 +49,9 @@ public class DefaultSSHApiTest {
@BeforeTest
public void setUp() throws Exception {
-// System.setProperty("myproxy.user", "ogce");
-// System.setProperty("myproxy.password", "");
-// System.setProperty("basedir",
"/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
+ System.setProperty("myproxy.user", "ogce");
+ System.setProperty("myproxy.password", "Jdas7wph");
+ System.setProperty("basedir",
"/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
myProxyUserName = System.getProperty("myproxy.user");
myProxyPassword = System.getProperty("myproxy.password");
@@ -194,25 +189,72 @@ public class DefaultSSHApiTest {
// Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
JobDescriptor jobById = sshApi.getJobById(serverInfo,
authenticationInfo, jobID);
- AssertJUnit.assertEquals(jobById.getJobId(),jobID);
+ AssertJUnit.assertEquals(jobById.getJobId(), jobID);
+ System.out.println(jobById.getAcountString());
+ System.out.println(jobById.getAllEnvExport());
+ System.out.println(jobById.getCompTime());
+ System.out.println(jobById.getExecutablePath());
+ System.out.println(jobById.getEllapsedTime());
+ System.out.println(jobById.getQueueName());
+ System.out.println(jobById.getExecuteNode());
+ System.out.println(jobById.getJobName());
+ System.out.println(jobById.getCTime());
+ System.out.println(jobById.getSTime());
+ System.out.println(jobById.getMTime());
+ System.out.println(jobById.getCompTime());
+ System.out.println(jobById.getOwner());
+ System.out.println(jobById.getQTime());
+ System.out.println(jobById.getUsedCPUTime());
+ System.out.println(jobById.getUsedMemory());
}
@Test
public void testGetCluster()throws Exception{
-// AuthenticationInfo authenticationInfo
-// = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
-// 7512, 17280000);
-// // Server info
-// ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
-// // Get the API
-// SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
-// Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
-// System.out.println(cluster.getNodes()[0].getName());
-// System.out.println(cluster.getNodes()[0].getNp());
-// System.out.println(cluster.getNodes()[0].getState());
-// System.out.println(cluster.getNodes()[0].getCores()[0].getId());
-// System.out.println(cluster.getNodes()[0].getName());
+ AuthenticationInfo authenticationInfo
+ = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
+ 7512, 17280000);
+ // Server info
+ ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
+ // Get the API
+ SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+ Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
+ System.out.println(cluster.getNodes()[0].getName());
+ System.out.println(cluster.getNodes()[0].getNp());
+ System.out.println(cluster.getNodes()[0].getState());
+ System.out.println(cluster.getNodes()[0].getCores()[0].getId());
+ System.out.println(cluster.getNodes()[0].getName());
+
+ }
+
+ @Test
+ public void testGetJob() throws Exception {
+ String jobID = "1584665";
+ AuthenticationInfo authenticationInfo
+ = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
+ 7512, 17280000);
+ // Server info
+ ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
+
+
+ // Get the API
+ SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+ JobDescriptor jobById = sshApi.getJobById(serverInfo,
authenticationInfo, jobID);
+ System.out.println(jobById.getAcountString());
+ System.out.println(jobById.getAllEnvExport());
+ System.out.println(jobById.getCompTime());
+ System.out.println(jobById.getExecutablePath());
+ System.out.println(jobById.getEllapsedTime());
+ System.out.println(jobById.getQueueName());
+ System.out.println(jobById.getJobName());
+ System.out.println(jobById.getCTime());
+ System.out.println(jobById.getSTime());
+ System.out.println(jobById.getMTime());
+ System.out.println(jobById.getCompTime());
+ System.out.println(jobById.getOwner());
+ System.out.println(jobById.getQTime());
+ System.out.println(jobById.getUsedCPUTime());
+ System.out.println(jobById.getUsedMemory());
}
@Test
public void testsubmitAsyncJobWithFailure() throws Exception {
