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Posted to commits@airavata.apache.org by sh...@apache.org on 2015/06/03 20:14:33 UTC
[16/39] airavata git commit: Refactored gfac sub modules,
merged gfac-ssh, gfac-gsissh, gfac-local,
gfac-monitor and gsissh modules and create gface-impl,
removed implementation from gfac-core to gfac-impl
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java
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diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java
new file mode 100644
index 0000000..002674c
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java
@@ -0,0 +1,262 @@
+/*
+ *
+ * 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.gfac.ssh.impl;
+
+import org.apache.airavata.gfac.ssh.api.*;
+import org.apache.airavata.gfac.core.authentication.AuthenticationInfo;
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
+import org.apache.airavata.gfac.ssh.util.CommonUtils;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+public class VanilaTestWithSSHAuth {
+
+ private String userName;
+ private String password;
+ private String passPhrase;
+ private String hostName;
+ private String workingDirectory;
+ private String privateKeyPath;
+ private String publicKeyPath;
+ private String path;
+
+ @BeforeTest
+ public void setUp() throws Exception {
+ System.out.println("Test case name " + this.getClass().getName());
+ //Trestles
+ this.hostName = "trestles.sdsc.xsede.org";
+ this.userName = "ogce";
+ this.path="/opt/torque/bin/";
+ //Stampede:
+// this.hostName = "stampede.tacc.xsede.org";
+// this.userName = "ogce";
+// this.path="/usr/bin";
+ //Lonestar:
+// this.hostName = "lonestar.tacc.utexas.edu";
+// this.userName = "us3";
+// this.path="/opt/sge6.2/bin/lx24-amd64";
+ //Alamo:
+// this.hostName = "alamo.uthscsa.edu";
+// this.userName = "raminder";
+// this.path="/opt/torque/bin/";
+ //Bigred:
+// this.hostName = "bigred2.uits.iu.edu";
+// this.userName = "cgateway";
+// this.path="/opt/torque/torque-5.0.1/bin/";
+
+ System.setProperty("ssh.host",hostName);
+ System.setProperty("ssh.username", userName);
+ System.setProperty("private.ssh.key", "/home/lginnali/.ssh/id_dsa");
+ System.setProperty("public.ssh.key", "/home/lginnali/.ssh/id_dsa.pub");
+ System.setProperty("ssh.working.directory", "/tmp");
+
+ this.hostName = System.getProperty("ssh.host");
+ this.userName = System.getProperty("ssh.username");
+ this.password = System.getProperty("ssh.password");
+ this.privateKeyPath = System.getProperty("private.ssh.key");
+ this.publicKeyPath = System.getProperty("public.ssh.key");
+
+ System.setProperty("ssh.keypass", "");
+ this.passPhrase = System.getProperty("ssh.keypass");
+ this.workingDirectory = System.getProperty("ssh.working.directory");
+
+
+ if (this.userName == null
+ || (this.password==null && (this.publicKeyPath == null || this.privateKeyPath == null)) || this.workingDirectory == null) {
+ System.out.println("########### In order to test you have to either username password or private,public keys");
+ System.out.println("Use -Dssh.user=xxx -Dssh.password=yyy -Dssh.private.key.passphrase=zzz " +
+ "-Dssh.private.key.path -Dssh.public.key.path -Dssh.working.directory ");
+ }
+ }
+
+
+ @Test
+ public void testSimplePBSJob() throws Exception {
+
+ AuthenticationInfo authenticationInfo = null;
+ if (password != null) {
+ authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+ } else {
+ authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
+ this.passPhrase);
+ }
+ // Server info
+ ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+ Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));
+
+ String date = new Date().toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
+
+ String pomFile = new File("").getAbsolutePath() + File.separator + "pom.xml";
+
+ workingDirectory = workingDirectory + File.separator
+ + date + "_" + UUID.randomUUID();
+ pbsCluster.makeDirectory(workingDirectory);
+ Thread.sleep(1000);
+ pbsCluster.makeDirectory(workingDirectory + File.separator + "inputs");
+ Thread.sleep(1000);
+ pbsCluster.makeDirectory(workingDirectory + File.separator + "outputs");
+
+
+ // doing file transfer to the remote resource
+ String remoteLocation = workingDirectory + File.separator + "inputs";
+ pbsCluster.scpTo(remoteLocation, pomFile);
+
+ int i = pomFile.lastIndexOf(File.separator);
+ String fileName = pomFile.substring(i + 1);
+ // constructing the job object
+ JobDescriptor jobDescriptor = new JobDescriptor();
+ jobDescriptor.setWorkingDirectory(workingDirectory);
+ jobDescriptor.setShellName("/bin/bash");
+ jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
+ jobDescriptor.setExecutablePath("/bin/echo");
+ jobDescriptor.setAllEnvExport(true);
+ jobDescriptor.setMailOptions("n");
+ jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
+ jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
+ jobDescriptor.setNodes(1);
+ jobDescriptor.setProcessesPerNode(1);
+ jobDescriptor.setQueueName("normal");
+ jobDescriptor.setMaxWallTime("5");
+ //jobDescriptor.setJobSubmitter("aprun -n 1");
+ List<String> inputs = new ArrayList<String>();
+ inputs.add(remoteLocation + File.separator + fileName);
+ jobDescriptor.setInputValues(inputs);
+ //finished construction of job object
+ System.out.println(jobDescriptor.toXML());
+ if(hostName.contains("trestles")){
+ String jobID = pbsCluster.submitBatchJob(jobDescriptor);
+ System.out.println("JobID returned : " + jobID);
+
+// Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
+ Thread.sleep(1000);
+ JobDescriptor jobById = pbsCluster.getJobDescriptorById(jobID);
+
+ //printing job data got from previous call
+ 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());
+ System.out.println(jobById.getVariableList());
+ }
+ }
+
+ @Test
+ public void testSimpleLSFJob() throws Exception {
+
+ AuthenticationInfo authenticationInfo = null;
+ if (password != null) {
+ authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+ } else {
+ authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
+ this.passPhrase);
+ }
+ // Server info
+ ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+
+
+ // constructing the job object
+ JobDescriptor jobDescriptor = new JobDescriptor();
+ jobDescriptor.setWorkingDirectory(workingDirectory);
+ jobDescriptor.setShellName("/bin/bash");
+ jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
+ jobDescriptor.setExecutablePath("/bin/echo");
+ jobDescriptor.setAllEnvExport(true);
+ jobDescriptor.setMailOptions("n");
+ jobDescriptor.setMailAddress("test@gmail.com");
+ jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
+ jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
+ jobDescriptor.setNodes(1);
+ jobDescriptor.setProcessesPerNode(1);
+ jobDescriptor.setQueueName("long");
+ jobDescriptor.setMaxWallTimeForLSF("5");
+ jobDescriptor.setJobSubmitter("mpiexec");
+ jobDescriptor.setModuleLoadCommands(new String[]{"module load openmpi/1.6.5"});
+ jobDescriptor.setUsedMemory("1000");
+ jobDescriptor.setChassisName("01");
+
+ //jobDescriptor.setJobSubmitter("aprun -n 1");
+ List<String> inputs = new ArrayList<String>();
+ jobDescriptor.setInputValues(inputs);
+ //finished construction of job object
+ System.out.println(jobDescriptor.toXML());
+ Cluster pbsCluster = new PBSCluster(CommonUtils.getLSFJobManager(""));
+ ((PBSCluster) pbsCluster).generateJobScript(jobDescriptor);
+ }
+
+ @Test
+ public void testSCPFromAndSCPTo() throws Exception {
+
+ AuthenticationInfo authenticationInfo = null;
+ if (password != null) {
+ authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+ } else {
+ authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
+ this.passPhrase);
+ }
+ // Server info
+ ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+ Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));
+ new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));;
+
+ String date = new Date().toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
+
+ String pomFile = (new File(".")).getAbsolutePath() + File.separator + "pom.xml";
+ File file = new File(pomFile);
+ if(!file.exists()){
+ file.createNewFile();
+ }
+ // Constructing theworking directory for demonstration and creating directories in the remote
+ // resource
+ workingDirectory = workingDirectory + File.separator
+ + date + "_" + UUID.randomUUID();
+ pbsCluster.makeDirectory(workingDirectory);
+ pbsCluster.scpTo(workingDirectory, pomFile);
+ Thread.sleep(1000);
+ pbsCluster.scpFrom(workingDirectory + File.separator + "pom.xml", (new File(".")).getAbsolutePath());
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java
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diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java
new file mode 100644
index 0000000..29d6fca
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java
@@ -0,0 +1,207 @@
+/*
+ *
+ * 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.job;
+
+import com.google.common.eventbus.EventBus;
+import com.google.common.eventbus.Subscribe;
+import org.airavata.appcatalog.cpi.AppCatalog;
+import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
+import org.apache.airavata.common.utils.MonitorPublisher;
+import org.apache.airavata.gfac.core.monitor.MonitorID;
+import org.apache.airavata.gfac.monitor.impl.push.amqp.AMQPMonitor;
+import org.apache.airavata.gfac.ssh.api.Cluster;
+import org.apache.airavata.gfac.ssh.api.SSHApiException;
+import org.apache.airavata.gfac.ssh.api.ServerInfo;
+import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.impl.PBSCluster;
+import org.apache.airavata.gfac.ssh.impl.authentication.MyProxyAuthenticationInfo;
+import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
+import org.apache.airavata.model.appcatalog.computeresource.DataMovementInterface;
+import org.apache.airavata.model.appcatalog.computeresource.DataMovementProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.JobManagerCommand;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager;
+import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManagerType;
+import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
+import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol;
+import org.apache.airavata.model.messaging.event.JobStatusChangeEvent;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.LinkedBlockingQueue;
+
+public class AMQPMonitorTest {
+
+ private String myProxyUserName;
+ private String myProxyPassword;
+ private String certificateLocation;
+ private String pbsFilePath;
+ private String workingDirectory;
+ private MonitorPublisher monitorPublisher;
+ private BlockingQueue<MonitorID> finishQueue;
+ private BlockingQueue<MonitorID> pushQueue;
+ private Thread pushThread;
+ private String proxyFilePath;
+ private ComputeResourceDescription computeResourceDescription;
+ private final static Logger logger = LoggerFactory.getLogger(AMQPMonitorTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ System.setProperty("myproxy.username", "ogce");
+ System.setProperty("myproxy.password", "");
+ System.setProperty("basedir", "/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
+ System.setProperty("gsi.working.directory", "/home1/01437/ogce");
+ System.setProperty("trusted.cert.location", "/Users/lahirugunathilake/Downloads/certificates");
+ System.setProperty("proxy.file.path", "/Users/lahirugunathilake/Downloads/x509up_u503876");
+ myProxyUserName = System.getProperty("myproxy.username");
+ myProxyPassword = System.getProperty("myproxy.password");
+ workingDirectory = System.getProperty("gsi.working.directory");
+ certificateLocation = System.getProperty("trusted.cert.location");
+ proxyFilePath = System.getProperty("proxy.file.path");
+ System.setProperty("connection.name", "xsede");
+ if (myProxyUserName == null || myProxyPassword == null || workingDirectory == null) {
+ System.out.println(">>>>>> Please run tests with my proxy user name and password. " +
+ "E.g :- mvn clean install -Dmyproxy.user=xxx -Dmyproxy.password=xxx -Dgsi.working.directory=/path<<<<<<<");
+ throw new Exception("Need my proxy user name password to run tests.");
+ }
+
+ monitorPublisher = new MonitorPublisher(new EventBus());
+ pushQueue = new LinkedBlockingQueue<MonitorID>();
+ finishQueue = new LinkedBlockingQueue<MonitorID>();
+
+
+ final AMQPMonitor amqpMonitor = new
+ AMQPMonitor(monitorPublisher,
+ pushQueue, finishQueue,proxyFilePath,"xsede",
+ Arrays.asList("info1.dyn.teragrid.org,info2.dyn.teragrid.org".split(",")));
+ try {
+ (new Thread(){
+ public void run(){
+ amqpMonitor.run();
+ }
+ }).start();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+ computeResourceDescription = new ComputeResourceDescription("TestComputerResoruceId", "TestHostName");
+ computeResourceDescription.setHostName("stampede-host");
+ computeResourceDescription.addToIpAddresses("login1.stampede.tacc.utexas.edu");
+ ResourceJobManager resourceJobManager = new ResourceJobManager("1234", ResourceJobManagerType.SLURM);
+ Map<JobManagerCommand, String> commandMap = new HashMap<JobManagerCommand, String>();
+ commandMap.put(JobManagerCommand.SUBMISSION, "test");
+ resourceJobManager.setJobManagerCommands(commandMap);
+ resourceJobManager.setJobManagerBinPath("/usr/bin/");
+ resourceJobManager.setPushMonitoringEndpoint("push"); // TODO - add monitor mode
+ SSHJobSubmission sshJobSubmission = new SSHJobSubmission("TestSSHJobSubmissionInterfaceId", SecurityProtocol.GSI,
+ resourceJobManager);
+
+ AppCatalog appCatalog = AppCatalogFactory.getAppCatalog();
+ String jobSubmissionID = appCatalog.getComputeResource().addSSHJobSubmission(sshJobSubmission);
+
+ JobSubmissionInterface jobSubmissionInterface = new JobSubmissionInterface(jobSubmissionID, JobSubmissionProtocol.SSH, 1);
+
+ computeResourceDescription.addToJobSubmissionInterfaces(jobSubmissionInterface);
+ computeResourceDescription.addToDataMovementInterfaces(new DataMovementInterface("4532", DataMovementProtocol.SCP, 1));
+
+ }
+
+ @Test
+ public void testAMQPMonitor() throws SSHApiException {
+ /* now have to submit a job to some machine and add that job to the queue */
+ //Create authentication
+ GSIAuthenticationInfo authenticationInfo
+ = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
+ 7512, 17280000, certificateLocation);
+
+ // Server info
+ ServerInfo serverInfo = new ServerInfo("ogce", "login1.stampede.tacc.utexas.edu",2222);
+
+
+ Cluster pbsCluster = new
+ PBSCluster(serverInfo, authenticationInfo, org.apache.airavata.gfac.ssh.util.CommonUtils.getPBSJobManager("/usr/bin/"));
+
+
+ // Execute command
+ System.out.println("Target PBS file path: " + workingDirectory);
+ // constructing the job object
+ String jobName = "GSI_SSH_SLEEP_JOB";
+ JobDescriptor jobDescriptor = new JobDescriptor();
+ jobDescriptor.setWorkingDirectory(workingDirectory);
+ jobDescriptor.setShellName("/bin/bash");
+ jobDescriptor.setJobName(jobName);
+ jobDescriptor.setExecutablePath("/bin/echo");
+ jobDescriptor.setAllEnvExport(true);
+ jobDescriptor.setMailOptions("n");
+ jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
+ jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
+ jobDescriptor.setNodes(1);
+ jobDescriptor.setProcessesPerNode(1);
+ jobDescriptor.setQueueName("normal");
+ jobDescriptor.setMaxWallTime("60");
+ jobDescriptor.setAcountString("TG-STA110014S");
+ List<String> inputs = new ArrayList<String>();
+ jobDescriptor.setOwner("ogce");
+ inputs.add("Hello World");
+ jobDescriptor.setInputValues(inputs);
+ //finished construction of job object
+ System.out.println(jobDescriptor.toXML());
+ String jobID = pbsCluster.submitBatchJob(jobDescriptor);
+ System.out.println(jobID);
+ try {
+ pushQueue.add(new MonitorID(computeResourceDescription, jobID,null,null,null, "ogce", jobName));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ try {
+ pushThread.join();
+ } catch (InterruptedException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+ class InnerClassAMQP{
+ @Subscribe
+ private void getStatus(JobStatusChangeEvent status){
+ Assert.assertNotNull(status);
+ pushThread.interrupt();
+ }
+ }
+ monitorPublisher.registerListener(new InnerClassAMQP());
+// try {
+// pushThread.join(5000);
+// Iterator<MonitorID> iterator = pushQueue.iterator();
+// MonitorID next = iterator.next();
+// org.junit.Assert.assertNotNull(next.getStatus());
+// } catch (Exception e) {
+// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+// }
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java
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diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java
new file mode 100644
index 0000000..c405e8c
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java
@@ -0,0 +1,172 @@
+///*
+// *
+// * 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.job;
+//
+//import java.io.File;
+//import java.util.ArrayList;
+//import java.util.List;
+//import java.util.concurrent.BlockingQueue;
+//import java.util.concurrent.LinkedBlockingQueue;
+//
+//import org.apache.airavata.common.utils.MonitorPublisher;
+//import org.apache.airavata.commons.gfac.type.HostDescription;
+//import org.apache.airavata.gfac.core.monitor.MonitorID;
+//import org.apache.airavata.gfac.monitor.HPCMonitorID;
+//import org.apache.airavata.gfac.monitor.UserMonitorData;
+//import org.apache.airavata.gfac.monitor.impl.pull.qstat.HPCPullMonitor;
+//import org.apache.airavata.gfac.ssh.api.Cluster;
+//import org.apache.airavata.gfac.ssh.api.SSHApiException;
+//import org.apache.airavata.gfac.ssh.api.ServerInfo;
+//import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo;
+//import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+//import org.apache.airavata.gfac.ssh.impl.PBSCluster;
+//import org.apache.airavata.gfac.ssh.impl.authentication.MyProxyAuthenticationInfo;
+//import org.apache.airavata.gfac.ssh.util.CommonUtils;
+//import org.apache.airavata.model.messaging.event.JobStatusChangeEvent;
+//import org.apache.airavata.schemas.gfac.GsisshHostType;
+//import org.junit.Assert;
+//import org.testng.annotations.Test;
+//
+//import com.google.common.eventbus.EventBus;
+//import com.google.common.eventbus.Subscribe;
+//
+//public class QstatMonitorTestWithMyProxyAuth {
+// private String myProxyUserName;
+// private String myProxyPassword;
+// private String certificateLocation;
+// private String pbsFilePath;
+// private String workingDirectory;
+// private HostDescription hostDescription;
+// private MonitorPublisher monitorPublisher;
+// private BlockingQueue<UserMonitorData> pullQueue;
+// private Thread monitorThread;
+//
+// @org.testng.annotations.BeforeClass
+// public void setUp() throws Exception {
+//// System.setProperty("myproxy.username", "ogce");
+//// System.setProperty("myproxy.password", "");
+//// System.setProperty("basedir", "/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
+//// System.setProperty("gsi.working.directory", "/home/ogce");
+//// System.setProperty("trusted.cert.location", "/Users/lahirugunathilake/Downloads/certificates");
+// myProxyUserName = System.getProperty("myproxy.username");
+// myProxyPassword = System.getProperty("myproxy.password");
+// workingDirectory = System.getProperty("gsi.working.directory");
+// certificateLocation = System.getProperty("trusted.cert.location");
+// if (myProxyUserName == null || myProxyPassword == null || workingDirectory == null) {
+// System.out.println(">>>>>> Please run tests with my proxy user name and password. " +
+// "E.g :- mvn clean install -Dmyproxy.username=xxx -Dmyproxy.password=xxx -Dgsi.working.directory=/path<<<<<<<");
+// throw new Exception("Need my proxy user name password to run tests.");
+// }
+//
+// monitorPublisher = new MonitorPublisher(new EventBus());
+// class InnerClassQstat {
+//
+// @Subscribe
+// private void getStatus(JobStatusChangeEvent status) {
+// Assert.assertNotNull(status);
+// System.out.println(status.getState().toString());
+// monitorThread.interrupt();
+// }
+// }
+// monitorPublisher.registerListener(this);
+// pullQueue = new LinkedBlockingQueue<UserMonitorData>();
+// final HPCPullMonitor qstatMonitor = new
+// HPCPullMonitor(pullQueue, monitorPublisher);
+// try {
+// (new Thread(){
+// public void run(){
+// qstatMonitor.run();
+// }
+// }).start();
+// } catch (Exception e) {
+// e.printStackTrace();
+// }
+//
+// hostDescription = new HostDescription(GsisshHostType.type);
+// hostDescription.getType().setHostAddress("trestles.sdsc.edu");
+// hostDescription.getType().setHostName("gsissh-gordon");
+// ((GsisshHostType) hostDescription.getType()).setPort(22);
+// ((GsisshHostType)hostDescription.getType()).setInstalledPath("/opt/torque/bin/");
+// }
+//
+// @Test
+// public void testQstatMonitor() throws SSHApiException {
+// /* now have to submit a job to some machine and add that job to the queue */
+// //Create authentication
+// GSIAuthenticationInfo authenticationInfo
+// = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
+// 7512, 17280000, certificateLocation);
+//
+// // Server info
+// ServerInfo serverInfo = new ServerInfo("ogce", hostDescription.getType().getHostAddress());
+//
+//
+// Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/"));
+//
+//
+// // Execute command
+// System.out.println("Target PBS file path: " + workingDirectory);
+// // constructing the job object
+// JobDescriptor jobDescriptor = new JobDescriptor();
+// jobDescriptor.setWorkingDirectory(workingDirectory);
+// jobDescriptor.setShellName("/bin/bash");
+// jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
+// jobDescriptor.setExecutablePath("/bin/echo");
+// jobDescriptor.setAllEnvExport(true);
+// jobDescriptor.setMailOptions("n");
+// jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
+// jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
+// jobDescriptor.setNodes(1);
+// jobDescriptor.setProcessesPerNode(1);
+// jobDescriptor.setQueueName("normal");
+// jobDescriptor.setMaxWallTime("60");
+// jobDescriptor.setAcountString("sds128");
+// List<String> inputs = new ArrayList<String>();
+// jobDescriptor.setOwner("ogce");
+// inputs.add("Hello World");
+// jobDescriptor.setInputValues(inputs);
+// //finished construction of job object
+// System.out.println(jobDescriptor.toXML());
+// for (int i = 0; i < 1; i++) {
+// String jobID = pbsCluster.submitBatchJob(jobDescriptor);
+// System.out.println("Job submitted successfully, Job ID: " + jobID);
+// MonitorID monitorID = new HPCMonitorID(hostDescription, jobID,null,null,null, "ogce","");
+// ((HPCMonitorID)monitorID).setAuthenticationInfo(authenticationInfo);
+// try {
+// org.apache.airavata.gfac.monitor.util.CommonUtils.addMonitortoQueue(pullQueue, monitorID, jobExecutionContext);
+// } catch (Exception e) {
+// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+// }
+// }
+// try {
+//
+// monitorThread.join();
+// } catch (Exception e) {
+// e.printStackTrace();
+// }
+// }
+//
+// @Subscribe
+// public void testCaseShutDown(JobStatusChangeEvent status) {
+// Assert.assertNotNull(status.getState());
+// monitorThread.stop();
+// }
+//}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/PBSTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/PBSTemplate.xslt b/modules/gfac/gfac-impl/src/test/resources/PBSTemplate.xslt
new file mode 100644
index 0000000..e749e9c
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/PBSTemplate.xslt
@@ -0,0 +1,73 @@
+<!--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 (theÏ "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. -->
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
+<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"/>
+ </xsl:when></xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:queueName">
+#PBS -q <xsl:value-of select="ns:queueName"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailOptions">
+#PBS -m <xsl:value-of select="ns:mailOptions"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+<xsl:when test="ns:acountString">
+#PBS -A <xsl:value-of select="ns:acountString"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:maxWallTime">
+#PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -o <xsl:value-of select="ns:standardOutFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -e <xsl:value-of select="ns:standardErrorFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
+#PBS -l nodes=<xsl:value-of select="ns:nodes"/>:ppn=<xsl:value-of select="ns:processesPerNode"/>
+<xsl:text>
</xsl:text>
+ </xsl:when>
+ </xsl:choose>
+<xsl:for-each select="ns:exports/ns:name">
+<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>
</xsl:text>
+export<xsl:text> </xsl:text><xsl:value-of select="."/>
+<xsl:text>
</xsl:text>
+</xsl:for-each>
+<xsl:for-each select="ns:preJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+cd <xsl:text> </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>
</xsl:text>
+ <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
+<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text>
+<xsl:for-each select="ns:inputs/ns:input">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+<xsl:for-each select="ns:postJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+</xsl:for-each>
+
+</xsl:template>
+
+</xsl:stylesheet>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/echo.bat
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/echo.bat b/modules/gfac/gfac-impl/src/test/resources/echo.bat
new file mode 100644
index 0000000..c6b849b
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/echo.bat
@@ -0,0 +1,22 @@
+::
+::
+:: 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.
+::
+::
+@echo off
+echo %1^=%2
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/gsissh.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/gsissh.properties b/modules/gfac/gfac-impl/src/test/resources/gsissh.properties
new file mode 100644
index 0000000..3fdf76d
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/gsissh.properties
@@ -0,0 +1,26 @@
+#
+#
+# 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.
+#
+
+###########################################################################
+# Specifies system level configurations as a key/value pairs.
+###########################################################################
+
+StrictHostKeyChecking=no
+ssh.session.timeout=360000
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/log4j.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/log4j.properties b/modules/gfac/gfac-impl/src/test/resources/log4j.properties
new file mode 100644
index 0000000..257802c
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/log4j.properties
@@ -0,0 +1,34 @@
+#
+# 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.
+#
+
+# Set root category priority to INFO and its only appender to CONSOLE.
+log4j.rootCategory=ALL, CONSOLE,LOGFILE
+log4j.rootLogger=ALL, CONSOLE, LOGFILE
+
+
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=[%p] %m%n
+
+# LOGFILE is set to be a File appender using a PatternLayout.
+log4j.appender.LOGFILE=org.apache.log4j.FileAppender
+log4j.appender.LOGFILE.File=./target/integration-tests.log
+log4j.appender.LOGFILE.Append=true
+log4j.appender.LOGFILE.layout=org.apache.log4j.PatternLayout
+log4j.appender.LOGFILE.layout.ConversionPattern=%d [%t] %-5p %c %x - %m%n
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/logging.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/logging.properties b/modules/gfac/gfac-impl/src/test/resources/logging.properties
new file mode 100644
index 0000000..0584d38
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/logging.properties
@@ -0,0 +1,42 @@
+#
+# 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.
+#
+#
+#default/fallback log4j configuration
+#
+
+# Set root logger level to WARN and its only appender to A1.
+log4j.rootLogger=INFO, A1, A2
+
+# A1 is set to be a rolling file appender with default params
+log4j.appender.A1=org.apache.log4j.RollingFileAppender
+log4j.appender.A1.File=target/seclogs.txt
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%d [%t] %-5p %c %x - %m%n
+
+# A2 is a console appender
+log4j.appender.A2=org.apache.log4j.ConsoleAppender
+
+# A2 uses PatternLayout.
+log4j.appender.A2.layout=org.apache.log4j.PatternLayout
+log4j.appender.A2.layout.ConversionPattern=%d [%t] %-5p %c{1} %x - %m%n
+
+log4j.logger.unicore.security=INFO
+
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/sleep.pbs
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/sleep.pbs b/modules/gfac/gfac-impl/src/test/resources/sleep.pbs
new file mode 100644
index 0000000..126e045
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/sleep.pbs
@@ -0,0 +1,32 @@
+#!/bin/bash
+#
+#
+# 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.
+#
+
+#$ -S /bin/bash
+#$ -V
+#$ -pe 1way 32
+#$ -m n
+#$ -q normal
+#$ -A
+#$ -l h_rt=0:60:00
+#$ -o application.stdout
+#$ -e application.stderr
+#PBS -N GSI_SSH_SLEEP_JOB
+/bin/sleep 60
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-impl/src/test/resources/test.pbs
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/test/resources/test.pbs b/modules/gfac/gfac-impl/src/test/resources/test.pbs
new file mode 100644
index 0000000..d18269b
--- /dev/null
+++ b/modules/gfac/gfac-impl/src/test/resources/test.pbs
@@ -0,0 +1,30 @@
+#!/bin/bash
+#
+#
+# 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.
+#
+
+#PBS -q normal
+#PBS -A sds128
+#PBS -l nodes=1:ppn=1
+#PBS -l walltime=00:00:01
+#PBS -o job_output
+#PBS -N GSI_SSH_JOB
+#PBS -V
+
+/bin/date
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/pom.xml b/modules/gfac/gfac-local/pom.xml
deleted file mode 100644
index 081dfd8..0000000
--- a/modules/gfac/gfac-local/pom.xml
+++ /dev/null
@@ -1,65 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!--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 (theÏ "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. -->
-
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <parent>
- <groupId>org.apache.airavata</groupId>
- <artifactId>gfac</artifactId>
- <version>0.16-SNAPSHOT</version>
- <relativePath>../pom.xml</relativePath>
- </parent>
-
- <modelVersion>4.0.0</modelVersion>
- <artifactId>airavata-gfac-local</artifactId>
- <name>Airavata GFac Local implementation</name>
- <description>This is the extension of GFAC Local.</description>
- <url>http://airavata.apache.org/</url>
-
- <dependencies>
-
- <!-- Logging -->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- </dependency>
-
- <!-- GFAC schemas -->
- <dependency>
- <groupId>org.apache.airavata</groupId>
- <artifactId>airavata-gfac-core</artifactId>
- <version>${project.version}</version>
- </dependency>
-
- <!-- Test -->
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.testng</groupId>
- <artifactId>testng</artifactId>
- <version>6.1.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>jcl-over-slf4j</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-log4j12</artifactId>
- <scope>test</scope>
- </dependency>
-
- </dependencies>
-
-</project>
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalDirectorySetupHandler.java b/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalDirectorySetupHandler.java
deleted file mode 100644
index 2f9e3b0..0000000
--- a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalDirectorySetupHandler.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- *
- * 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.gfac.local.handler;
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.GFacHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.util.Properties;
-
-public class LocalDirectorySetupHandler implements GFacHandler {
- private static final Logger log = LoggerFactory.getLogger(LocalDirectorySetupHandler.class);
-
- public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
- log.info("Invoking LocalDirectorySetupHandler ...");
- log.debug("working directory = " + jobExecutionContext.getWorkingDir());
- log.debug("temp directory = " + jobExecutionContext.getWorkingDir());
-
- makeFileSystemDir(jobExecutionContext.getWorkingDir());
- makeFileSystemDir(jobExecutionContext.getInputDir());
- makeFileSystemDir(jobExecutionContext.getOutputDir());
- }
-
- @Override
- public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
- // TODO: Auto generated method body.
- }
-
- private void makeFileSystemDir(String dir) throws GFacHandlerException {
- File f = new File(dir);
- if (f.isDirectory() && f.exists()) {
- return;
- } else if (!new File(dir).mkdir()) {
- throw new GFacHandlerException("Cannot create directory " + dir);
- }
- }
-
- public void initProperties(Properties properties) throws GFacHandlerException {
-
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java b/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
deleted file mode 100644
index 884ccd5..0000000
--- a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/handler/LocalInputHandler.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- *
- * 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.gfac.local.handler;
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.AbstractHandler;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.commons.io.FileUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Map;
-import java.util.Properties;
-
-
-public class LocalInputHandler extends AbstractHandler {
- private static final Logger logger = LoggerFactory.getLogger(LocalInputHandler.class);
- @Override
- public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
- super.invoke(jobExecutionContext);
- Map<String, Object> inputParameters = jobExecutionContext.getInMessageContext().getParameters();
- for (Map.Entry<String, Object> inputParamEntry : inputParameters.entrySet()) {
- if (inputParamEntry.getValue() instanceof InputDataObjectType) {
- InputDataObjectType inputDataObject = (InputDataObjectType) inputParamEntry.getValue();
- if (inputDataObject.getType() == DataType.URI
- && inputDataObject != null
- && !inputDataObject.getValue().equals("")) {
- try {
- inputDataObject.setValue(stageFile(jobExecutionContext.getInputDir(), inputDataObject.getValue()));
- } catch (IOException e) {
- throw new GFacHandlerException("Error while data staging sourceFile= " + inputDataObject.getValue());
- }
- }
- }
- }
- }
-
- private String stageFile(String inputDir, String sourceFilePath) throws IOException {
- int i = sourceFilePath.lastIndexOf(File.separator);
- String substring = sourceFilePath.substring(i + 1);
- if (inputDir.endsWith("/")) {
- inputDir = inputDir.substring(0, inputDir.length() - 1);
- }
- String targetFilePath = inputDir + File.separator + substring;
-
- if (sourceFilePath.startsWith("file")) {
- sourceFilePath = sourceFilePath.substring(sourceFilePath.indexOf(":") + 1, sourceFilePath.length());
- }
-
- File sourceFile = new File(sourceFilePath);
- File targetFile = new File(targetFilePath);
- if (targetFile.exists()) {
- targetFile.delete();
- }
- logger.info("staging source file : " + sourceFilePath + " to target file : " + targetFilePath);
- FileUtils.copyFile(sourceFile, targetFile);
-
- return targetFilePath;
- }
-
- @Override
- public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
-
- }
-
- @Override
- public void initProperties(Properties properties) throws GFacHandlerException {
-
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java b/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
deleted file mode 100644
index 871193a..0000000
--- a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
+++ /dev/null
@@ -1,311 +0,0 @@
-/*
- *
- * 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.gfac.local.provider.impl;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import org.apache.airavata.gfac.Constants;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.notification.events.StartExecutionEvent;
-import org.apache.airavata.gfac.core.provider.AbstractProvider;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gfac.core.utils.OutputUtils;
-import org.apache.airavata.gfac.local.utils.InputStreamToFileWriter;
-import org.apache.airavata.gfac.local.utils.InputUtils;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
-import org.apache.airavata.model.appcatalog.appdeployment.SetEnvPaths;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.messaging.event.JobIdentifier;
-import org.apache.airavata.model.messaging.event.JobStatusChangeEvent;
-import org.apache.airavata.model.messaging.event.TaskIdentifier;
-import org.apache.airavata.model.messaging.event.TaskOutputChangeEvent;
-import org.apache.airavata.model.workspace.experiment.JobDetails;
-import org.apache.airavata.model.workspace.experiment.JobState;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.registry.cpi.RegistryModelType;
-import org.apache.xmlbeans.XmlException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
-
-public class LocalProvider extends AbstractProvider {
- private static final Logger log = LoggerFactory.getLogger(LocalProvider.class);
- private ProcessBuilder builder;
- private List<String> cmdList;
- private String jobId;
-
- public static class LocalProviderJobData{
- private String applicationName;
- private List<String> inputParameters;
- private String workingDir;
- private String inputDir;
- private String outputDir;
- public String getApplicationName() {
- return applicationName;
- }
- public void setApplicationName(String applicationName) {
- this.applicationName = applicationName;
- }
- public List<String> getInputParameters() {
- return inputParameters;
- }
- public void setInputParameters(List<String> inputParameters) {
- this.inputParameters = inputParameters;
- }
- public String getWorkingDir() {
- return workingDir;
- }
- public void setWorkingDir(String workingDir) {
- this.workingDir = workingDir;
- }
- public String getInputDir() {
- return inputDir;
- }
- public void setInputDir(String inputDir) {
- this.inputDir = inputDir;
- }
- public String getOutputDir() {
- return outputDir;
- }
- public void setOutputDir(String outputDir) {
- this.outputDir = outputDir;
- }
- }
- public LocalProvider(){
- cmdList = new ArrayList<String>();
- }
-
- public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
- super.initialize(jobExecutionContext);
-
- // build command with all inputs
- buildCommand();
- initProcessBuilder(jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription());
-
- // extra environment variables
- builder.environment().put(Constants.INPUT_DATA_DIR_VAR_NAME, jobExecutionContext.getInputDir());
- builder.environment().put(Constants.OUTPUT_DATA_DIR_VAR_NAME, jobExecutionContext.getOutputDir());
-
- // set working directory
- builder.directory(new File(jobExecutionContext.getWorkingDir()));
-
- // log info
- log.info("Command = " + InputUtils.buildCommand(cmdList));
- log.info("Working dir = " + builder.directory());
- /*for (String key : builder.environment().keySet()) {
- log.info("Env[" + key + "] = " + builder.environment().get(key));
- }*/
- }
-
- public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException {
- jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
- JobDetails jobDetails = new JobDetails();
- try {
- jobId = jobExecutionContext.getTaskData().getTaskID();
- jobDetails.setJobID(jobId);
- jobDetails.setJobDescription(jobExecutionContext.getApplicationContext()
- .getApplicationDeploymentDescription().getAppDeploymentDescription());
- jobExecutionContext.setJobDetails(jobDetails);
- GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.SETUP);
- // running cmd
- Process process = builder.start();
-
- Thread standardOutWriter = new InputStreamToFileWriter(process.getInputStream(), jobExecutionContext.getStandardOutput());
- Thread standardErrorWriter = new InputStreamToFileWriter(process.getErrorStream(), jobExecutionContext.getStandardError());
-
- // start output threads
- standardOutWriter.setDaemon(true);
- standardErrorWriter.setDaemon(true);
- standardOutWriter.start();
- standardErrorWriter.start();
-
- int returnValue = process.waitFor();
-
- // make sure other two threads are done
- standardOutWriter.join();
- standardErrorWriter.join();
-
- /*
- * check return value. usually not very helpful to draw conclusions based on return values so don't bother.
- * just provide warning in the log messages
- */
- if (returnValue != 0) {
- log.error("Process finished with non zero return value. Process may have failed");
- } else {
- log.info("Process finished with return value of zero.");
- }
-
- StringBuffer buf = new StringBuffer();
- buf.append("Executed ").append(InputUtils.buildCommand(cmdList))
- .append(" on the localHost, working directory = ").append(jobExecutionContext.getWorkingDir())
- .append(" tempDirectory = ").append(jobExecutionContext.getScratchLocation()).append(" With the status ")
- .append(String.valueOf(returnValue));
-
- log.info(buf.toString());
-
- // updating the job status to complete because there's nothing to monitor in local jobs
-// MonitorID monitorID = createMonitorID(jobExecutionContext);
- JobIdentifier jobIdentity = new JobIdentifier(jobExecutionContext.getJobDetails().getJobID(),
- jobExecutionContext.getTaskData().getTaskID(),
- jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(),
- jobExecutionContext.getExperimentID(),
- jobExecutionContext.getGatewayID());
- jobExecutionContext.getMonitorPublisher().publish(new JobStatusChangeEvent(JobState.COMPLETE, jobIdentity));
- } catch (IOException io) {
- throw new GFacProviderException(io.getMessage(), io);
- } catch (InterruptedException e) {
- throw new GFacProviderException(e.getMessage(), e);
- }catch (GFacException e) {
- throw new GFacProviderException(e.getMessage(), e);
- }
- }
-
-// private MonitorID createMonitorID(JobExecutionContext jobExecutionContext) {
-// MonitorID monitorID = new MonitorID(jobExecutionContext.getApplicationContext().getHostDescription(), jobId,
-// jobExecutionContext.getTaskData().getTaskID(),
-// jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(), jobExecutionContext.getExperimentID(),
-// jobExecutionContext.getExperiment().getUserName(),jobId);
-// return monitorID;
-// }
-
-// private void saveApplicationJob(JobExecutionContext jobExecutionContext)
-// throws GFacProviderException {
-// ApplicationDeploymentDescriptionType app = jobExecutionContext.
-// getApplicationContext().getApplicationDeploymentDescription().getType();
-// ApplicationJob appJob = GFacUtils.createApplicationJob(jobExecutionContext);
-// appJob.setJobId(jobId);
-// LocalProviderJobData data = new LocalProviderJobData();
-// data.setApplicationName(app.getExecutableLocation());
-// data.setInputDir(app.getInputDataDirectory());
-// data.setOutputDir(app.getOutputDataDirectory());
-// data.setWorkingDir(builder.directory().toString());
-// data.setInputParameters(ProviderUtils.getInputParameters(jobExecutionContext));
-// ByteArrayOutputStream stream = new ByteArrayOutputStream();
-// JAXB.marshal(data, stream);
-// appJob.setJobData(stream.toString());
-// appJob.setSubmittedTime(Calendar.getInstance().getTime());
-// appJob.setStatus(ApplicationJobStatus.SUBMITTED);
-// appJob.setStatusUpdateTime(appJob.getSubmittedTime());
-// GFacUtils.recordApplicationJob(jobExecutionContext, appJob);
-// }
-
- public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException {
- try {
- List<OutputDataObjectType> outputArray = new ArrayList<OutputDataObjectType>();
- String stdOutStr = GFacUtils.readFileToString(jobExecutionContext.getStandardOutput());
- String stdErrStr = GFacUtils.readFileToString(jobExecutionContext.getStandardError());
- Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
- OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
- TaskDetails taskDetails = (TaskDetails)registry.get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
- if (taskDetails != null){
- taskDetails.setApplicationOutputs(outputArray);
- registry.update(RegistryModelType.TASK_DETAIL, taskDetails, taskDetails.getTaskID());
- }
- registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
- TaskIdentifier taskIdentity = new TaskIdentifier(jobExecutionContext.getTaskData().getTaskID(),
- jobExecutionContext.getWorkflowNodeDetails().getNodeInstanceId(),
- jobExecutionContext.getExperimentID(),
- jobExecutionContext.getGatewayID());
- jobExecutionContext.getMonitorPublisher().publish(new TaskOutputChangeEvent(outputArray, taskIdentity));
- } catch (XmlException e) {
- throw new GFacProviderException("Cannot read output:" + e.getMessage(), e);
- } catch (IOException io) {
- throw new GFacProviderException(io.getMessage(), io);
- } catch (Exception e){
- throw new GFacProviderException("Error in retrieving results",e);
- }
- }
-
- public boolean cancelJob(JobExecutionContext jobExecutionContext) throws GFacException {
- throw new NotImplementedException();
- }
-
- @Override
- public void recover(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
- // TODO: Auto generated method body.
- }
-
- @Override
- public void monitor(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
- // TODO: Auto generated method body.
- }
-
-
- private void buildCommand() {
- cmdList.add(jobExecutionContext.getExecutablePath());
- Map<String, Object> inputParameters = jobExecutionContext.getInMessageContext().getParameters();
-
- // sort the inputs first and then build the command List
- Comparator<InputDataObjectType> inputOrderComparator = new Comparator<InputDataObjectType>() {
- @Override
- public int compare(InputDataObjectType inputDataObjectType, InputDataObjectType t1) {
- return inputDataObjectType.getInputOrder() - t1.getInputOrder();
- }
- };
- Set<InputDataObjectType> sortedInputSet = new TreeSet<InputDataObjectType>(inputOrderComparator);
- for (Object object : inputParameters.values()) {
- if (object instanceof InputDataObjectType) {
- InputDataObjectType inputDOT = (InputDataObjectType) object;
- sortedInputSet.add(inputDOT);
- }
- }
- for (InputDataObjectType inputDataObjectType : sortedInputSet) {
- if (inputDataObjectType.getApplicationArgument() != null
- && !inputDataObjectType.getApplicationArgument().equals("")) {
- cmdList.add(inputDataObjectType.getApplicationArgument());
- }
-
- if (inputDataObjectType.getValue() != null
- && !inputDataObjectType.getValue().equals("")) {
- cmdList.add(inputDataObjectType.getValue());
- }
- }
-
- }
-
- private void initProcessBuilder(ApplicationDeploymentDescription app){
- builder = new ProcessBuilder(cmdList);
-
- List<SetEnvPaths> setEnvironment = app.getSetEnvironment();
- if (setEnvironment != null) {
- for (SetEnvPaths envPath : setEnvironment) {
- Map<String,String> builderEnv = builder.environment();
- builderEnv.put(envPath.getName(), envPath.getValue());
- }
- }
- }
-
- public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
-
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputStreamToFileWriter.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputStreamToFileWriter.java b/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputStreamToFileWriter.java
deleted file mode 100644
index 2467ce8..0000000
--- a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputStreamToFileWriter.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- *
- * 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.gfac.local.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.*;
-
-public class InputStreamToFileWriter extends Thread{
- protected final Logger log = LoggerFactory.getLogger(this.getClass());
-
- private BufferedReader in;
- private BufferedWriter out;
-
- public InputStreamToFileWriter(InputStream in, String out) throws IOException {
- this.in = new BufferedReader(new InputStreamReader(in));
- this.out = new BufferedWriter(new FileWriter(out));
- }
-
- public void run() {
- try {
- String line = null;
- while ((line = in.readLine()) != null) {
- if (log.isDebugEnabled()) {
- log.debug(line);
- }
- out.write(line);
- out.newLine();
- }
- } catch (Exception e) {
- log.error(e.getMessage(), e);
- } finally {
- if (in != null) {
- try {
- in.close();
- } catch (Exception e) {
- log.error(e.getMessage(), e);
- }
- }
- if (out != null) {
- try {
- out.close();
- } catch (Exception e) {
- log.error(e.getMessage(), e);
- }
- }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputUtils.java b/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputUtils.java
deleted file mode 100644
index 98671fd..0000000
--- a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/InputUtils.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- *
- * 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.gfac.local.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.List;
-
-public class InputUtils {
-
- private static final Logger logger = LoggerFactory.getLogger(InputUtils.class);
-
- private static final String SPACE = " ";
-
- private InputUtils() {
- }
-
- public static String buildCommand(List<String> cmdList) {
- StringBuffer buff = new StringBuffer();
- for (String string : cmdList) {
- logger.debug("Build Command --> " + string);
- buff.append(string);
- buff.append(SPACE);
- }
- return buff.toString();
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java b/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
deleted file mode 100644
index 2b45df7..0000000
--- a/modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/utils/LocalProviderUtil.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- *
- * 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.gfac.local.utils;
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.provider.GFacProviderException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-
-public class LocalProviderUtil {
- private static final Logger log = LoggerFactory.getLogger(LocalProviderUtil.class);
-
- private void makeFileSystemDir(String dir) throws GFacProviderException {
- File f = new File(dir);
- if (f.isDirectory() && f.exists()) {
- return;
- } else if (!new File(dir).mkdir()) {
- throw new GFacProviderException("Cannot make directory " + dir);
- }
- }
-
- public void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacProviderException {
- log.info("working diectroy = " + jobExecutionContext.getWorkingDir());
- log.info("temp directory = " + jobExecutionContext.getScratchLocation());
- makeFileSystemDir(jobExecutionContext.getWorkingDir());
- makeFileSystemDir(jobExecutionContext.getScratchLocation());
- makeFileSystemDir(jobExecutionContext.getInputDir());
- makeFileSystemDir(jobExecutionContext.getOutputDir());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-local/src/main/resources/errors.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-local/src/main/resources/errors.properties b/modules/gfac/gfac-local/src/main/resources/errors.properties
deleted file mode 100644
index 88c41b8..0000000
--- a/modules/gfac/gfac-local/src/main/resources/errors.properties
+++ /dev/null
@@ -1,197 +0,0 @@
-#
-#
-# 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.
-#
-
-# Directly copied from jglobus. Not a good way to manager error properties.
-1 = Parameter not supported
-2 = The RSL length is greater than the maximum allowed
-3 = No resources available
-4 = Bad directory specified
-5 = The executable does not exist
-6 = Insufficient funds
-7 = Authentication with the remote server failed
-8 = Job cancelled by user
-9 = Job cancelled by system
-
-10 = Data transfer to the server failed
-11 = The stdin file does not exist
-12 = The connection to the server failed (check host and port)
-13 = The provided RSL 'maxtime' value is invalid (not an integer or must be greater than 0)
-14 = The provided RSL 'count' value is invalid (not an integer or must be greater than 0)
-15 = The job manager received an invalid RSL
-16 = Could not connect to job manager
-17 = The job failed when the job manager attempted to run it
-18 = Paradyn error
-19 = The provided RSL 'jobtype' value is invalid
-
-20 = The provided RSL 'myjob' value is invalid
-21 = The job manager failed to locate an internal script argument file
-22 = The job manager failed to create an internal script argument file
-23 = The job manager detected an invalid job state
-24 = The job manager detected an invalid script response
-25 = The job manager detected an invalid job state
-26 = The provided RSL 'jobtype' value is not supported by this job manager
-27 = Unimplemented
-28 = The job manager failed to create an internal script submission file
-29 = The job manager cannot find the user proxy
-
-30 = The job manager failed to open the user proxy
-31 = The job manager failed to cancel the job as requested
-32 = System memory allocation failed
-33 = The interprocess job communication initialization failed
-34 = The interprocess job communication setup failed
-35 = The provided RSL 'host count' value is invalid
-36 = One of the provided RSL parameters is unsupported
-37 = The provided RSL 'queue' parameter is invalid
-38 = The provided RSL 'project' parameter is invalid
-39 = The provided RSL string includes variables that could not be identified
-
-40 = The provided RSL 'environment' parameter is invalid
-41 = The provided RSL 'dryrun' parameter is invalid
-42 = The provided RSL is invalid (an empty string)
-43 = The job manager failed to stage the executable
-44 = The job manager failed to stage the stdin file
-45 = The requested job manager type is invalid
-46 = The provided RSL 'arguments' parameter is invalid
-47 = The gatekeeper failed to run the job manager
-48 = The provided RSL could not be properly parsed
-49 = There is a version mismatch between GRAM components
-
-50 = The provided RSL 'arguments' parameter is invalid
-51 = The provided RSL 'count' parameter is invalid
-52 = The provided RSL 'directory' parameter is invalid
-53 = The provided RSL 'dryrun' parameter is invalid
-54 = The provided RSL 'environment' parameter is invalid
-55 = The provided RSL 'executable' parameter is invalid
-56 = The provided RSL 'host_count' parameter is invalid
-57 = The provided RSL 'jobtype' parameter is invalid
-58 = The provided RSL 'maxtime' parameter is invalid
-59 = The provided RSL 'myjob' parameter is invalid
-
-60 = The provided RSL 'paradyn' parameter is invalid
-61 = The provided RSL 'project' parameter is invalid
-62 = The provided RSL 'queue' parameter is invalid
-63 = The provided RSL 'stderr' parameter is invalid
-64 = The provided RSL 'stdin' parameter is invalid
-65 = The provided RSL 'stdout' parameter is invalid
-66 = The job manager failed to locate an internal script
-67 = The job manager failed on the system call pipe()
-68 = The job manager failed on the system call fcntl()
-69 = The job manager failed to create the temporary stdout filename
-
-70 = The job manager failed to create the temporary stderr filename
-71 = The job manager failed on the system call fork()
-72 = The executable file permissions do not allow execution
-73 = The job manager failed to open stdout
-74 = The job manager failed to open stderr
-75 = The cache file could not be opened in order to relocate the user proxy
-76 = Cannot access cache files in ~/.globus/.gass_cache, check permissions, quota, and disk space
-77 = The job manager failed to insert the contact in the client contact list
-78 = The contact was not found in the job manager's client contact list
-79 = Connecting to the job manager failed. Possible reasons: job terminated, invalid job contact, network problems, ...
-
-80 = The syntax of the job contact is invalid
-81 = The executable parameter in the RSL is undefined
-82 = The job manager service is misconfigured. condor arch undefined
-83 = The job manager service is misconfigured. condor os undefined
-84 = The provided RSL 'min_memory' parameter is invalid
-85 = The provided RSL 'max_memory' parameter is invalid
-86 = The RSL 'min_memory' value is not zero or greater
-87 = The RSL 'max_memory' value is not zero or greater
-88 = The creation of a HTTP message failed
-89 = Parsing incoming HTTP message failed
-
-90 = The packing of information into a HTTP message failed
-91 = An incoming HTTP message did not contain the expected information
-92 = The job manager does not support the service that the client requested
-93 = The gatekeeper failed to find the requested service
-94 = The jobmanager does not accept any new requests (shutting down)
-95 = The client failed to close the listener associated with the callback URL
-96 = The gatekeeper contact cannot be parsed
-97 = The job manager could not find the 'poe' command
-98 = The job manager could not find the 'mpirun' command
-99 = The provided RSL 'start_time' parameter is invalid"
-100 = The provided RSL 'reservation_handle' parameter is invalid
-
-101 = The provided RSL 'max_wall_time' parameter is invalid
-102 = The RSL 'max_wall_time' value is not zero or greater
-103 = The provided RSL 'max_cpu_time' parameter is invalid
-104 = The RSL 'max_cpu_time' value is not zero or greater
-105 = The job manager is misconfigured, a scheduler script is missing
-106 = The job manager is misconfigured, a scheduler script has invalid permissions
-107 = The job manager failed to signal the job
-108 = The job manager did not recognize/support the signal type
-109 = The job manager failed to get the job id from the local scheduler
-
-110 = The job manager is waiting for a commit signal
-111 = The job manager timed out while waiting for a commit signal
-112 = The provided RSL 'save_state' parameter is invalid
-113 = The provided RSL 'restart' parameter is invalid
-114 = The provided RSL 'two_phase' parameter is invalid
-115 = The RSL 'two_phase' value is not zero or greater
-116 = The provided RSL 'stdout_position' parameter is invalid
-117 = The RSL 'stdout_position' value is not zero or greater
-118 = The provided RSL 'stderr_position' parameter is invalid
-119 = The RSL 'stderr_position' value is not zero or greater
-
-120 = The job manager restart attempt failed
-121 = The job state file doesn't exist
-122 = Could not read the job state file
-123 = Could not write the job state file
-124 = The old job manager is still alive
-125 = The job manager state file TTL expired
-126 = It is unknown if the job was submitted
-127 = The provided RSL 'remote_io_url' parameter is invalid
-128 = Could not write the remote io url file
-129 = The standard output/error size is different
-
-130 = The job manager was sent a stop signal (job is still running)
-131 = The user proxy expired (job is still running)
-132 = The job was not submitted by original jobmanager
-133 = The job manager is not waiting for that commit signal
-134 = The provided RSL scheduler specific parameter is invalid
-135 = The job manager could not stage in a file
-136 = The scratch directory could not be created
-137 = The provided 'gass_cache' parameter is invalid
-138 = The RSL contains attributes which are not valid for job submission
-139 = The RSL contains attributes which are not valid for stdio update
-
-140 = The RSL contains attributes which are not valid for job restart
-141 = The provided RSL 'file_stage_in' parameter is invalid
-142 = The provided RSL 'file_stage_in_shared' parameter is invalid
-143 = The provided RSL 'file_stage_out' parameter is invalid
-144 = The provided RSL 'gass_cache' parameter is invalid
-145 = The provided RSL 'file_cleanup' parameter is invalid
-146 = The provided RSL 'scratch_dir' parameter is invalid
-147 = The provided scheduler-specific RSL parameter is invalid
-148 = A required RSL attribute was not defined in the RSL spec
-149 = The gass_cache attribute points to an invalid cache directory
-
-150 = The provided RSL 'save_state' parameter has an invalid value
-151 = The job manager could not open the RSL attribute validation file
-152 = The job manager could not read the RSL attribute validation file
-153 = The provided RSL 'proxy_timeout' is invalid
-154 = The RSL 'proxy_timeout' value is not greater than zero
-155 = The job manager could not stage out a file
-156 = The job contact string does not match any which the job manager is handling
-157 = Proxy delegation failed
-158 = The job manager could not lock the state lock file
-
-1000 = Failed to start up callback handler
-1003 = Job contact not set