Author: lahiru
Date: Fri Aug 30 04:20:42 2013
New Revision: 1518890
URL: http://svn.apache.org/r1518890
Log:
adding error handling to the API.
Added:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
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/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java?rev=1518890&r1=1518889&r2=1518890&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
Fri Aug 30 04:20:42 2013
@@ -46,11 +46,29 @@ public interface SSHApi {
AuthenticationInfo authenticationInfo,
CommandOutput commandOutput) throws
SSHApiException;
- void submitAsyncJobWithPBS(ServerInfo serverInfo,
+ /**
+ * can be used to submit a job with a given pbs file
+ * @param serverInfo
+ * @param authenticationInfo
+ * @param pbsFilePath
+ * @param jobDescriptor
+ * @return The jobID
+ * @throws SSHApiException
+ */
+ String submitAsyncJobWithPBS(ServerInfo serverInfo,
AuthenticationInfo authenticationInfo,
String pbsFilePath, JobDescriptor
jobDescriptor) throws SSHApiException;
-//
- void submitAsyncJob(ServerInfo serverInfo,
+
+ /**
+ * can be used to submit a job without giving a pbs, but providing job
attributes
+ * @param serverInfo
+ * @param authenticationInfo
+ * @param jobDescriptor
+ * @return The jobID
+ * @throws SSHApiException
+ */
+
+ String submitAsyncJob(ServerInfo serverInfo,
AuthenticationInfo authenticationInfo,
JobDescriptor jobDescriptor) throws
SSHApiException;
}
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=1518890&r1=1518889&r2=1518890&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
Fri Aug 30 04:20:42 2013
@@ -41,9 +41,6 @@ public class JobDescriptor {
private JobDescriptorDocument jobDescriptionDocument;
- private CommandInfo commandInfo;
-
- private CommandOutput commandOutput;
public JobDescriptor() {
jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
@@ -58,7 +55,6 @@ public class JobDescriptor {
public JobDescriptor(CommandOutput commandOutput) {
jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
jobDescriptionDocument.addNewJobDescriptor();
- this.commandOutput = commandOutput;
}
@@ -78,21 +74,6 @@ public class JobDescriptor {
return jobDescriptor;
}
- public void setCommandInfo(CommandInfo commandInfo) {
- this.commandInfo = commandInfo;
- }
-
- public void setCommandOutput(CommandOutput commandOutput) {
- this.commandOutput = commandOutput;
- }
-
- public CommandInfo getCommandInfo() {
- return commandInfo;
- }
-
- public CommandOutput getCommandOutput() {
- return commandOutput;
- }
//todo write bunch of setter getters to set and get jobdescription
parameters
public void setWorkingDirectory(String workingDirectory) {
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=1518890&r1=1518889&r2=1518890&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
Fri Aug 30 04:20:42 2013
@@ -36,6 +36,8 @@ import javax.xml.transform.stream.Stream
import javax.xml.transform.stream.StreamSource;
import java.io.*;
import java.security.SecureRandom;
+import java.util.ArrayList;
+import java.util.List;
/**
* User: AmilaJ ([email protected])
@@ -50,7 +52,6 @@ public class DefaultSSHApi implements SS
private static final Logger log =
LoggerFactory.getLogger(DefaultSSHApi.class);
-
private ConfigReader configReader;
/**
@@ -67,6 +68,14 @@ public class DefaultSSHApi implements SS
}
}
+ /**
+ * @param commandInfo Encapsulated information about command. E.g
:- executable name
+ * parameters etc ...
+ * @param serverInfo The SSHing server information.
+ * @param authenticationInfo Security data needs to be communicated with
remote server.
+ * @param commandOutput The output of the command.
+ * @throws SSHApiException
+ */
public void executeCommand(CommandInfo commandInfo, ServerInfo serverInfo,
AuthenticationInfo authenticationInfo,
CommandOutput commandOutput) throws
SSHApiException {
@@ -144,9 +153,16 @@ public class DefaultSSHApi implements SS
}
- public void submitAsyncJobWithPBS(ServerInfo serverInfo,
- AuthenticationInfo authenticationInfo,
- String pbsFilePath, JobDescriptor
jobDescriptor) throws SSHApiException {
+ /**
+ * @param serverInfo
+ * @param authenticationInfo
+ * @param pbsFilePath
+ * @param jobDescriptor
+ * @throws SSHApiException
+ */
+ public String submitAsyncJobWithPBS(ServerInfo serverInfo,
+ AuthenticationInfo authenticationInfo,
+ String pbsFilePath, JobDescriptor
jobDescriptor) throws SSHApiException {
try {
SCPTo scpTo = new SCPTo(serverInfo, authenticationInfo, new
ConfigReader());
@@ -163,21 +179,35 @@ public class DefaultSSHApi implements SS
" connecting user name - "
+ serverInfo.getUserName(), e);
}
-
// since this is a constant we do not ask users to fill this
RawCommandInfo rawCommandInfo = new
RawCommandInfo("/opt/torque/bin/qsub " +
jobDescriptor.getWorkingDirectory() + File.separator +
FilenameUtils.getName(pbsFilePath));
- this.executeCommand(rawCommandInfo, serverInfo, authenticationInfo,
jobDescriptor.getCommandOutput());
+ StandardOutReader jobIDReaderCommandOutput = new StandardOutReader();
+ this.executeCommand(rawCommandInfo, serverInfo, authenticationInfo,
jobIDReaderCommandOutput);
+
+ //Check whether pbs submission is successful or not, if it failed
throw and exception in submitJob method
+ // with the error thrown in qsub command
+ if (jobIDReaderCommandOutput.getErrorifAvailable().equals("")) {
+ return jobIDReaderCommandOutput.getStdOutput();
+ } else {
+ throw new
SSHApiException(jobIDReaderCommandOutput.getStandardError().toString());
+ }
}
- public void submitAsyncJob(ServerInfo serverInfo, AuthenticationInfo
authenticationInfo, JobDescriptor jobDescriptor) throws SSHApiException {
+ /**
+ * @param serverInfo
+ * @param authenticationInfo
+ * @param jobDescriptor
+ * @throws SSHApiException
+ */
+ public String submitAsyncJob(ServerInfo serverInfo, AuthenticationInfo
authenticationInfo, JobDescriptor jobDescriptor) throws SSHApiException {
TransformerFactory factory = TransformerFactory.newInstance();
String xsltPath = "src" + File.separator + "main" + File.separator +
"resources" + File.separator + "PBSTemplate.xslt";
Source xslt = new StreamSource(new File(xsltPath));
Transformer transformer = null;
StringWriter results = new StringWriter();
-
+ File tempPBSFile = null;
try {
// generate the pbs script using xslt
transformer = factory.newTransformer(xslt);
@@ -192,13 +222,13 @@ public class DefaultSSHApi implements SS
int number = new SecureRandom().nextInt();
number = (number < 0 ? -number : number);
- File tempPBSFile = new File(Integer.toString(number) + ".pbs");
+ tempPBSFile = new File(Integer.toString(number) + ".pbs");
FileUtils.writeStringToFile(tempPBSFile, results.toString());
//reusing submitAsyncJobWithPBS method to submit a job
- this.submitAsyncJobWithPBS(serverInfo, authenticationInfo,
tempPBSFile.getAbsolutePath(), jobDescriptor);
- tempPBSFile.delete();
+ String jobID = this.submitAsyncJobWithPBS(serverInfo,
authenticationInfo, tempPBSFile.getAbsolutePath(), jobDescriptor);
+ return jobID;
} catch (TransformerConfigurationException e) {
throw new SSHApiException("Error parsing PBS transformation", e);
} catch (TransformerException e) {
@@ -208,6 +238,8 @@ public class DefaultSSHApi implements SS
"Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
" connecting user name - "
+ serverInfo.getUserName(), e);
+ } finally {
+ tempPBSFile.delete();
}
Added:
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=1518890&view=auto
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
(added)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/StandardOutReader.java
Fri Aug 30 04:20:42 2013
@@ -0,0 +1,82 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.gsi.ssh.impl;
+
+import com.jcraft.jsch.Channel;
+import org.apache.airavata.gsi.ssh.api.CommandOutput;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+public class StandardOutReader implements CommandOutput {
+
+ String stdOutput = null;
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ public void onOutput(Channel channel) {
+ try {
+ StringBuffer pbsOutput = new StringBuffer("");
+ InputStream inputStream = channel.getInputStream();
+ byte[] tmp = new byte[1024];
+ while (true) {
+ while (inputStream.available() > 0) {
+ int i = inputStream.read(tmp, 0, 1024);
+ if (i < 0) break;
+ pbsOutput.append(new String(tmp, 0, i));
+ }
+ if (channel.isClosed()) {
+ String output = pbsOutput.toString();
+ this.setStdOutput(output);
+ break;
+ }
+ try {
+ Thread.sleep(1000);
+ } catch (Exception ignored) {
+ }
+ }
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ public OutputStream getStandardError() {
+ return os;
+ }
+
+ public String getErrorifAvailable(){
+ return os.toString();
+ }
+
+ public void exitCode(int code) {
+ System.out.println("Program exit code - " + code);
+ }
+
+ public String getStdOutput() {
+ return stdOutput;
+ }
+
+ public void setStdOutput(String stdOutput) {
+ this.stdOutput = stdOutput;
+ }
+}
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=1518890&r1=1518889&r2=1518890&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
Fri Aug 30 04:20:42 2013
@@ -135,14 +135,9 @@ public class DefaultSSHApiTest {
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
7512, 17280000);
- // Create command
- CommandInfo commandInfo = new RawCommandInfo("/opt/torque/bin/qsub
/home/ogce/sleep1.pbs");
-
// Server info
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- // Output
- CommandOutput commandOutput = new SystemCommandOutput();
// Get the API
SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
@@ -150,12 +145,12 @@ public class DefaultSSHApiTest {
// Execute command
System.out.println("Target PBS file path: " + workingDirectory);
System.out.println("Local PBS File path: " + pbsFilePath);
- JobDescriptor jobDescriptor = new JobDescriptor(commandOutput);
+ JobDescriptor jobDescriptor = new JobDescriptor();
//Here we give working directory as a file name to replace the file,
to allow multiple test runs with the same
//file name
jobDescriptor.setWorkingDirectory(workingDirectory);
- sshApi.submitAsyncJobWithPBS(serverInfo, authenticationInfo,
pbsFilePath, jobDescriptor);
- System.out.println(jobDescriptor.toXML());
+ String jobID = sshApi.submitAsyncJobWithPBS(serverInfo,
authenticationInfo, pbsFilePath, jobDescriptor);
+ System.out.println("JobID returned : " + jobID);
}
@Test
@@ -168,8 +163,6 @@ public class DefaultSSHApiTest {
// Server info
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- // Output
- CommandOutput commandOutput = new SystemCommandOutput();
// Get the API
SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
@@ -178,7 +171,7 @@ public class DefaultSSHApiTest {
System.out.println("Target PBS file path: " + workingDirectory);
System.out.println("Local PBS File path: " + pbsFilePath);
String workingDirectory = File.separator + "home" + File.separator +
"ogce" + File.separator + "gsissh";
- JobDescriptor jobDescriptor = new JobDescriptor(commandOutput);
+ JobDescriptor jobDescriptor = new JobDescriptor();
jobDescriptor.setWorkingDirectory(workingDirectory);
jobDescriptor.setShellName("/bin/bash");
jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
@@ -195,6 +188,7 @@ public class DefaultSSHApiTest {
inputs.add("Hello World");
jobDescriptor.setInputValues(inputs);
System.out.println(jobDescriptor.toXML());
- sshApi.submitAsyncJob(serverInfo, authenticationInfo, jobDescriptor);
+ String jobID = sshApi.submitAsyncJob(serverInfo, authenticationInfo,
jobDescriptor);
+ System.out.println("JobID returned : " + jobID);
}
}
