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Posted to commits@airavata.apache.org by ch...@apache.org on 2014/11/11 21:12:10 UTC
[06/50] [abbrv] airavata git commit: Integrated appCatalog for ssh
and gsi modules, commented out old test classes, need to fix this
http://git-wip-us.apache.org/repos/asf/airavata/blob/2dd94e63/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
index 7ee5d6a..7e9fa89 100644
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
@@ -20,11 +20,13 @@
*/
package org.apache.airavata.gfac.ssh.util;
+import org.airavata.appcatalog.cpi.AppCatalog;
+import org.airavata.appcatalog.cpi.AppCatalogException;
+import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.ServerSettings;
import org.apache.airavata.common.utils.StringUtil;
import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.HostDescription;
import org.apache.airavata.commons.gfac.type.MappingFactory;
import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential;
import org.apache.airavata.gfac.Constants;
@@ -32,28 +34,36 @@ import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.RequestData;
import org.apache.airavata.gfac.core.context.JobExecutionContext;
import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
+import org.apache.airavata.gfac.core.states.GfacExperimentState;
import org.apache.airavata.gfac.ssh.context.SSHAuthWrapper;
import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
import org.apache.airavata.gfac.ssh.security.TokenizedSSHAuthInfo;
import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
import org.apache.airavata.gsi.ssh.api.ServerInfo;
-import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
import org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster;
import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
import org.apache.airavata.gsi.ssh.util.CommonUtils;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
+import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol;
import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.schemas.gfac.*;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.FileArrayType;
+import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+import org.apache.airavata.schemas.gfac.StringArrayType;
+import org.apache.airavata.schemas.gfac.URIArrayType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Set;
public class GFACSSHUtils {
private final static Logger logger = LoggerFactory.getLogger(GFACSSHUtils.class);
@@ -66,109 +76,113 @@ public class GFACSSHUtils {
public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
- HostDescription registeredHost = jobExecutionContext.getApplicationContext().getHostDescription();
- if (registeredHost.getType() instanceof GlobusHostType || registeredHost.getType() instanceof UnicoreHostType) {
+ JobSubmissionProtocol preferredJobSubmissionProtocol = jobExecutionContext.getPreferredJobSubmissionProtocol();
+ JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
+ if (preferredJobSubmissionProtocol == JobSubmissionProtocol.GLOBUS || preferredJobSubmissionProtocol == JobSubmissionProtocol.UNICORE) {
logger.error("This is a wrong method to invoke to non ssh host types,please check your gfac-config.xml");
- } else if (registeredHost.getType() instanceof SSHHostType
- || registeredHost.getType() instanceof GsisshHostType) {
- SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
- String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
- RequestData requestData = new RequestData(ServerSettings.getDefaultUserGateway());
- requestData.setTokenId(credentialStoreToken);
-
- ServerInfo serverInfo = new ServerInfo(null, registeredHost.getType().getHostAddress());
- SSHAuthWrapper sshAuth = (SSHAuthWrapper) jobExecutionContext.getProperty(ADVANCED_SSH_AUTH);
-
- Cluster pbsCluster = null;
+ } else if ( preferredJobSubmissionProtocol == JobSubmissionProtocol.SSH ) {
try {
- TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
- String installedParentPath = ((HpcApplicationDeploymentType)
- jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
- if (installedParentPath == null) {
- installedParentPath = "/";
- }
+ AppCatalog appCatalog = AppCatalogFactory.getAppCatalog();
+ SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(preferredJobSubmissionInterface.getJobSubmissionInterfaceId());
+ if (sshJobSubmission.getSecurityProtocol() == SecurityProtocol.GSI) {
+ SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+ String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
+ RequestData requestData = new RequestData(ServerSettings.getDefaultUserGateway());
+ requestData.setTokenId(credentialStoreToken);
+
+ ServerInfo serverInfo = new ServerInfo(null, jobExecutionContext.getHostName());
+ SSHAuthWrapper sshAuth = (SSHAuthWrapper) jobExecutionContext.getProperty(ADVANCED_SSH_AUTH);
+
+ Cluster pbsCluster = null;
+ try {
+ TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
+ String installedParentPath = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getExecutablePath();
+ if (installedParentPath == null) {
+ installedParentPath = "/";
+ }
- SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
- serverInfo.setUserName(credentials.getPortalUserName());
- jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
- // inside the pbsCluser object
+ SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
+ serverInfo.setUserName(credentials.getPortalUserName());
+ jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
+ // inside the pbsCluser object
- String key = credentials.getPortalUserName() + registeredHost.getType().getHostAddress() +
- serverInfo.getPort();
- if(sshAuth!=null){
- key=sshAuth.getKey();
- }
- boolean recreate = false;
- synchronized (clusters) {
- if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
- recreate = true;
- } else if (clusters.containsKey(key)) {
- int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
- if (clusters.get(key).get(i).getSession().isConnected()) {
- pbsCluster = clusters.get(key).get(i);
- } else {
- clusters.get(key).remove(i);
- recreate = true;
+ String key = credentials.getPortalUserName() + jobExecutionContext.getHostName() + serverInfo.getPort();
+ if(sshAuth!=null){
+ key=sshAuth.getKey();
}
- if (!recreate) {
- try {
- pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
- } catch (Exception e) {
- clusters.get(key).remove(i);
- logger.info("Connection found the connection map is expired, so we create from the scratch");
- maxClusterCount++;
- recreate = true; // we make the pbsCluster to create again if there is any exception druing connection
+ boolean recreate = false;
+ synchronized (clusters) {
+ if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
+ recreate = true;
+ } else if (clusters.containsKey(key)) {
+ int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
+ if (clusters.get(key).get(i).getSession().isConnected()) {
+ pbsCluster = clusters.get(key).get(i);
+ } else {
+ clusters.get(key).remove(i);
+ recreate = true;
+ }
+ if (!recreate) {
+ try {
+ pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
+ } catch (Exception e) {
+ clusters.get(key).remove(i);
+ logger.info("Connection found the connection map is expired, so we create from the scratch");
+ maxClusterCount++;
+ recreate = true; // we make the pbsCluster to create again if there is any exception druing connection
+ }
+ }
+ logger.info("Re-using the same connection used with the connection string:" + key);
+ } else {
+ recreate = true;
+ }
+ if (recreate) {
+ if (sshAuth != null) {
+ pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),
+ CommonUtils.getPBSJobManager(installedParentPath));
+ jobExecutionContext.setProperty(ADVANCED_SSH_AUTH,null); // some other provider might fail
+ key = sshAuth.getKey();
+ } else {
+ pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,
+ CommonUtils.getPBSJobManager(installedParentPath));
+ }
+ List<Cluster> pbsClusters = null;
+ if (!(clusters.containsKey(key))) {
+ pbsClusters = new ArrayList<Cluster>();
+ } else {
+ pbsClusters = clusters.get(key);
+ }
+ pbsClusters.add(pbsCluster);
+ clusters.put(key, pbsClusters);
}
}
- logger.info("Re-using the same connection used with the connection string:" + key);
- } else {
- recreate = true;
- }
- if (recreate) {
- if (sshAuth != null) {
- pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),
- CommonUtils.getPBSJobManager(installedParentPath));
- jobExecutionContext.setProperty(ADVANCED_SSH_AUTH,null); // some other provider might fail
- key = sshAuth.getKey();
- } else {
- pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,
- CommonUtils.getPBSJobManager(installedParentPath));
- }
- List<Cluster> pbsClusters = null;
- if (!(clusters.containsKey(key))) {
- pbsClusters = new ArrayList<Cluster>();
- } else {
- pbsClusters = clusters.get(key);
- }
- pbsClusters.add(pbsCluster);
- clusters.put(key, pbsClusters);
+ } catch (Exception e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
+ sshSecurityContext.setPbsCluster(pbsCluster);
+ jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT, sshSecurityContext);
}
- } catch (Exception e) {
- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ } catch (AppCatalogException e) {
+ throw new GFacException("Error while getting SSH Submission object from app catalog", e);
}
- sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT, sshSecurityContext);
}
}
- public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext,
- ApplicationDeploymentDescriptionType app, Cluster cluster) {
+ public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, Cluster cluster) {
JobDescriptor jobDescriptor = new JobDescriptor();
// this is common for any application descriptor
jobDescriptor.setCallBackIp(ServerSettings.getIp());
jobDescriptor.setCallBackPort(ServerSettings.getSetting(org.apache.airavata.common.utils.Constants.GFAC_SERVER_PORT, "8950"));
- jobDescriptor.setInputDirectory(app.getInputDataDirectory());
- jobDescriptor.setOutputDirectory(app.getOutputDataDirectory());
- jobDescriptor.setExecutablePath(app.getExecutableLocation());
- jobDescriptor.setStandardOutFile(app.getStandardOutput());
- jobDescriptor.setStandardErrorFile(app.getStandardError());
+ jobDescriptor.setInputDirectory(jobExecutionContext.getInputDir());
+ jobDescriptor.setOutputDirectory(jobExecutionContext.getOutputDir());
+ jobDescriptor.setExecutablePath(jobExecutionContext.getApplicationContext()
+ .getApplicationDeploymentDescription().getExecutablePath());
+ jobDescriptor.setStandardOutFile(jobExecutionContext.getStandardOutput());
+ jobDescriptor.setStandardErrorFile(jobExecutionContext.getStandardError());
Random random = new Random();
int i = random.nextInt(Integer.MAX_VALUE);
jobDescriptor.setJobName(String.valueOf(i + 99999999));
- jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());
-
-
+ jobDescriptor.setWorkingDirectory(jobExecutionContext.getWorkingDir());
List<String> inputValues = new ArrayList<String>();
MessageContext input = jobExecutionContext.getInMessageContext();
Map<String, Object> inputs = input.getParameters();
@@ -194,51 +208,6 @@ public class GFACSSHUtils {
}
jobDescriptor.setInputValues(inputValues);
- // this part will fill out the hpcApplicationDescriptor
- if (app instanceof HpcApplicationDeploymentType) {
- HpcApplicationDeploymentType applicationDeploymentType
- = (HpcApplicationDeploymentType) app;
- jobDescriptor.setUserName(((GSISSHAbstractCluster) cluster).getServerInfo().getUserName());
- jobDescriptor.setShellName("/bin/bash");
- jobDescriptor.setAllEnvExport(true);
- jobDescriptor.setMailOptions("n");
- jobDescriptor.setNodes(applicationDeploymentType.getNodeCount());
- jobDescriptor.setProcessesPerNode(applicationDeploymentType.getProcessorsPerNode());
- jobDescriptor.setMaxWallTime(String.valueOf(applicationDeploymentType.getMaxWallTime()));
- jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
- jobDescriptor.setCPUCount(applicationDeploymentType.getCpuCount());
- if (applicationDeploymentType.getProjectAccount() != null) {
- if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
- jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
- }
- }
- if (applicationDeploymentType.getQueue() != null) {
- if (applicationDeploymentType.getQueue().getQueueName() != null) {
- jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
- }
- }
- jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
- TaskDetails taskData = jobExecutionContext.getTaskData();
- if (taskData != null && taskData.isSetTaskScheduling()) {
- ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
- if (computionnalResource.getNodeCount() > 0) {
- jobDescriptor.setNodes(computionnalResource.getNodeCount());
- }
- if (computionnalResource.getComputationalProjectAccount() != null) {
- jobDescriptor.setAcountString(computionnalResource.getComputationalProjectAccount());
- }
- if (computionnalResource.getQueueName() != null) {
- jobDescriptor.setQueueName(computionnalResource.getQueueName());
- }
- if (computionnalResource.getTotalCPUCount() > 0) {
- jobDescriptor.setProcessesPerNode(computionnalResource.getTotalCPUCount());
- }
- if (computionnalResource.getWallTimeLimit() > 0) {
- jobDescriptor.setMaxWallTime(String.valueOf(computionnalResource.getWallTimeLimit()));
- }
- }
-
- }
return jobDescriptor;
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/2dd94e63/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
index e84848c..c65f386 100644
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
+++ b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
@@ -1,252 +1,252 @@
-/*
- *
- * 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.core.gfac.services.impl;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.commons.gfac.type.HostDescription;
-import org.apache.airavata.commons.gfac.type.ServiceDescription;
-import org.apache.airavata.gfac.GFacConfiguration;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.SecurityContext;
-import org.apache.airavata.gfac.core.context.ApplicationContext;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
-import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.ServerInfo;
-import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
-import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
-import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
-import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
-import org.apache.airavata.gsi.ssh.util.CommonUtils;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
-import org.apache.airavata.schemas.gfac.*;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-public class BigRed2TestWithSSHAuth {
- private JobExecutionContext jobExecutionContext;
-
- private String userName;
- private String password;
- private String passPhrase;
- private String hostName;
- private String workingDirectory;
- private String privateKeyPath;
- private String publicKeyPath;
-
- @BeforeClass
- public void setUp() throws Exception {
-
- System.out.println("Test case name " + this.getClass().getName());
-// System.setProperty("ssh.host","bigred2.uits.iu.edu"); //default ssh host
-// System.setProperty("ssh.user", "lginnali");
-// System.setProperty("ssh.private.key.path", "/Users/lahirugunathilake/.ssh/id_dsa");
-// System.setProperty("ssh.public.key.path", "/Users/lahirugunathilake/.ssh/id_dsa.pub");
-// System.setProperty("ssh.working.directory", "/tmp");
-
- this.hostName = "bigred2.uits.iu.edu";
- 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");
- 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.username=xxx -Dssh.password=yyy -Dssh.keypass=zzz " +
- "-Dprivate.ssh.key -Dpublic.ssh.key -Dssh.working.directory ");
- }
- URL resource = BigRed2TestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
- assert resource != null;
- System.out.println(resource.getFile());
- GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null);
-
-// gFacConfiguration.setMyProxyLifeCycle(3600);
-// gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
-// gFacConfiguration.setMyProxyUser("*****");
-// gFacConfiguration.setMyProxyPassphrase("*****");
-// gFacConfiguration.setTrustedCertLocation("./certificates");
-// //have to set InFlwo Handlers and outFlowHandlers
-// gFacConfiguration.setInHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
-// gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
-
- /*
- * Host
- */
- HostDescription host = new HostDescription(SSHHostType.type);
- host.getType().setHostAddress(hostName);
- host.getType().setHostName(hostName);
- ((SSHHostType)host.getType()).setHpcResource(true);
- /*
- * App
- */
- ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
- HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
- ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
- name.setStringValue("EchoLocal");
- app.setApplicationName(name);
-
- app.setCpuCount(1);
- app.setJobType(JobTypeType.SERIAL);
- app.setNodeCount(1);
- app.setProcessorsPerNode(1);
-
- /*
- * Use bat file if it is compiled on Windows
- */
- app.setExecutableLocation("/bin/echo");
-
- /*
- * Default tmp location
- */
- String tempDir = "/tmp";
- String date = (new Date()).toString();
- date = date.replaceAll(" ", "_");
- date = date.replaceAll(":", "_");
-
- tempDir = tempDir + File.separator
- + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
-
- System.out.println(tempDir);
- app.setScratchWorkingDirectory(tempDir);
- app.setStaticWorkingDirectory(tempDir);
- app.setInputDataDirectory(tempDir + File.separator + "inputData");
- app.setOutputDataDirectory(tempDir + File.separator + "outputData");
- app.setStandardOutput(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stdout");
- app.setStandardError(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stderr");
- app.setMaxWallTime(5);
- app.setJobSubmitterCommand("aprun -n 1");
- app.setInstalledParentPath("/opt/torque/torque-4.2.3.1/bin/");
-
- /*
- * Service
- */
- ServiceDescription serv = new ServiceDescription();
- serv.getType().setName("SimpleEcho");
-
- List<InputParameterType> inputList = new ArrayList<InputParameterType>();
-
- InputParameterType input = InputParameterType.Factory.newInstance();
- input.setParameterName("echo_input");
- input.setParameterType(StringParameterType.Factory.newInstance());
- inputList.add(input);
-
- InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
-
- .size()]);
- List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
- OutputParameterType output = OutputParameterType.Factory.newInstance();
- output.setParameterName("echo_output");
- output.setParameterType(StringParameterType.Factory.newInstance());
- outputList.add(output);
-
- OutputParameterType[] outputParamList = outputList
- .toArray(new OutputParameterType[outputList.size()]);
-
- serv.getType().setInputParametersArray(inputParamList);
- serv.getType().setOutputParametersArray(outputParamList);
-
- jobExecutionContext = new JobExecutionContext(gFacConfiguration, serv.getType().getName());
- // Adding security context
- jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext(app));
- ApplicationContext applicationContext = new ApplicationContext();
- jobExecutionContext.setApplicationContext(applicationContext);
- applicationContext.setServiceDescription(serv);
- applicationContext.setApplicationDeploymentDescription(appDesc);
- applicationContext.setHostDescription(host);
-
- MessageContext inMessage = new MessageContext();
- ActualParameter echo_input = new ActualParameter();
- ((StringParameterType) echo_input.getType()).setValue("echo_output=hello");
- inMessage.addParameter("echo_input", echo_input);
-
-
- jobExecutionContext.setInMessageContext(inMessage);
-
- MessageContext outMessage = new MessageContext();
- ActualParameter echo_out = new ActualParameter();
-// ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
- outMessage.addParameter("echo_output", echo_out);
- jobExecutionContext.setRegistry(RegistryFactory.getLoggingRegistry());
- jobExecutionContext.setTaskData(new TaskDetails("11323"));
- jobExecutionContext.setOutMessageContext(outMessage);
-
- }
-
-
- private SecurityContext getSecurityContext(HpcApplicationDeploymentType app) {
- try {
-
- 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 = null;
- SSHSecurityContext sshSecurityContext = null;
-
- JobManagerConfiguration pbsJobManager = CommonUtils.getPBSJobManager(app.getInstalledParentPath());
- pbsCluster = new PBSCluster(serverInfo, authenticationInfo, pbsJobManager);
-
-
- sshSecurityContext = new SSHSecurityContext();
- sshSecurityContext.setPbsCluster(pbsCluster);
- sshSecurityContext.setUsername(userName);
- sshSecurityContext.setKeyPass(passPhrase);
- sshSecurityContext.setPrivateKeyLoc(privateKeyPath);
- return sshSecurityContext;
- } catch (SSHApiException e) {
- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
- }
- return null;
- }
-
- @Test
- public void testSSHProvider() throws GFacException {
- BetterGfacImpl gFacAPI = new BetterGfacImpl();
- gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
- org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobDescription());
- org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobID());
- }
-
-}
+///*
+// *
+// * 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.core.gfac.services.impl;
+//
+//import org.apache.airavata.commons.gfac.type.ActualParameter;
+//import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+//import org.apache.airavata.commons.gfac.type.HostDescription;
+//import org.apache.airavata.commons.gfac.type.ServiceDescription;
+//import org.apache.airavata.gfac.GFacConfiguration;
+//import org.apache.airavata.gfac.GFacException;
+//import org.apache.airavata.gfac.SecurityContext;
+//import org.apache.airavata.gfac.core.context.ApplicationContext;
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.context.MessageContext;
+//import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
+//import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
+//import org.apache.airavata.gsi.ssh.api.Cluster;
+//import org.apache.airavata.gsi.ssh.api.SSHApiException;
+//import org.apache.airavata.gsi.ssh.api.ServerInfo;
+//import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
+//import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
+//import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+//import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+//import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
+//import org.apache.airavata.gsi.ssh.util.CommonUtils;
+//import org.apache.airavata.model.workspace.experiment.TaskDetails;
+//import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
+//import org.apache.airavata.schemas.gfac.*;
+//import org.testng.annotations.BeforeClass;
+//import org.testng.annotations.Test;
+//
+//import java.io.File;
+//import java.net.URL;
+//import java.util.ArrayList;
+//import java.util.Date;
+//import java.util.List;
+//import java.util.UUID;
+//
+//public class BigRed2TestWithSSHAuth {
+// private JobExecutionContext jobExecutionContext;
+//
+// private String userName;
+// private String password;
+// private String passPhrase;
+// private String hostName;
+// private String workingDirectory;
+// private String privateKeyPath;
+// private String publicKeyPath;
+//
+// @BeforeClass
+// public void setUp() throws Exception {
+//
+// System.out.println("Test case name " + this.getClass().getName());
+//// System.setProperty("ssh.host","bigred2.uits.iu.edu"); //default ssh host
+//// System.setProperty("ssh.user", "lginnali");
+//// System.setProperty("ssh.private.key.path", "/Users/lahirugunathilake/.ssh/id_dsa");
+//// System.setProperty("ssh.public.key.path", "/Users/lahirugunathilake/.ssh/id_dsa.pub");
+//// System.setProperty("ssh.working.directory", "/tmp");
+//
+// this.hostName = "bigred2.uits.iu.edu";
+// 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");
+// 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.username=xxx -Dssh.password=yyy -Dssh.keypass=zzz " +
+// "-Dprivate.ssh.key -Dpublic.ssh.key -Dssh.working.directory ");
+// }
+// URL resource = BigRed2TestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+// assert resource != null;
+// System.out.println(resource.getFile());
+// GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null);
+//
+//// gFacConfiguration.setMyProxyLifeCycle(3600);
+//// gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+//// gFacConfiguration.setMyProxyUser("*****");
+//// gFacConfiguration.setMyProxyPassphrase("*****");
+//// gFacConfiguration.setTrustedCertLocation("./certificates");
+//// //have to set InFlwo Handlers and outFlowHandlers
+//// gFacConfiguration.setInHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
+//// gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
+//
+// /*
+// * Host
+// */
+// HostDescription host = new HostDescription(SSHHostType.type);
+// host.getType().setHostAddress(hostName);
+// host.getType().setHostName(hostName);
+// ((SSHHostType)host.getType()).setHpcResource(true);
+// /*
+// * App
+// */
+// ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
+// HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
+// ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+// name.setStringValue("EchoLocal");
+// app.setApplicationName(name);
+//
+// app.setCpuCount(1);
+// app.setJobType(JobTypeType.SERIAL);
+// app.setNodeCount(1);
+// app.setProcessorsPerNode(1);
+//
+// /*
+// * Use bat file if it is compiled on Windows
+// */
+// app.setExecutableLocation("/bin/echo");
+//
+// /*
+// * Default tmp location
+// */
+// String tempDir = "/tmp";
+// String date = (new Date()).toString();
+// date = date.replaceAll(" ", "_");
+// date = date.replaceAll(":", "_");
+//
+// tempDir = tempDir + File.separator
+// + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
+//
+// System.out.println(tempDir);
+// app.setScratchWorkingDirectory(tempDir);
+// app.setStaticWorkingDirectory(tempDir);
+// app.setInputDataDirectory(tempDir + File.separator + "inputData");
+// app.setOutputDataDirectory(tempDir + File.separator + "outputData");
+// app.setStandardOutput(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stdout");
+// app.setStandardError(tempDir + File.separator + app.getApplicationName().getStringValue() + ".stderr");
+// app.setMaxWallTime(5);
+// app.setJobSubmitterCommand("aprun -n 1");
+// app.setInstalledParentPath("/opt/torque/torque-4.2.3.1/bin/");
+//
+// /*
+// * Service
+// */
+// ServiceDescription serv = new ServiceDescription();
+// serv.getType().setName("SimpleEcho");
+//
+// List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+//
+// InputParameterType input = InputParameterType.Factory.newInstance();
+// input.setParameterName("echo_input");
+// input.setParameterType(StringParameterType.Factory.newInstance());
+// inputList.add(input);
+//
+// InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+//
+// .size()]);
+// List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+// OutputParameterType output = OutputParameterType.Factory.newInstance();
+// output.setParameterName("echo_output");
+// output.setParameterType(StringParameterType.Factory.newInstance());
+// outputList.add(output);
+//
+// OutputParameterType[] outputParamList = outputList
+// .toArray(new OutputParameterType[outputList.size()]);
+//
+// serv.getType().setInputParametersArray(inputParamList);
+// serv.getType().setOutputParametersArray(outputParamList);
+//
+// jobExecutionContext = new JobExecutionContext(gFacConfiguration, serv.getType().getName());
+// // Adding security context
+// jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext(app));
+// ApplicationContext applicationContext = new ApplicationContext();
+// jobExecutionContext.setApplicationContext(applicationContext);
+// applicationContext.setServiceDescription(serv);
+// applicationContext.setApplicationDeploymentDescription(appDesc);
+// applicationContext.setHostDescription(host);
+//
+// MessageContext inMessage = new MessageContext();
+// ActualParameter echo_input = new ActualParameter();
+// ((StringParameterType) echo_input.getType()).setValue("echo_output=hello");
+// inMessage.addParameter("echo_input", echo_input);
+//
+//
+// jobExecutionContext.setInMessageContext(inMessage);
+//
+// MessageContext outMessage = new MessageContext();
+// ActualParameter echo_out = new ActualParameter();
+//// ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+// outMessage.addParameter("echo_output", echo_out);
+// jobExecutionContext.setRegistry(RegistryFactory.getLoggingRegistry());
+// jobExecutionContext.setTaskData(new TaskDetails("11323"));
+// jobExecutionContext.setOutMessageContext(outMessage);
+//
+// }
+//
+//
+// private SecurityContext getSecurityContext(HpcApplicationDeploymentType app) {
+// try {
+//
+// 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 = null;
+// SSHSecurityContext sshSecurityContext = null;
+//
+// JobManagerConfiguration pbsJobManager = CommonUtils.getPBSJobManager(app.getInstalledParentPath());
+// pbsCluster = new PBSCluster(serverInfo, authenticationInfo, pbsJobManager);
+//
+//
+// sshSecurityContext = new SSHSecurityContext();
+// sshSecurityContext.setPbsCluster(pbsCluster);
+// sshSecurityContext.setUsername(userName);
+// sshSecurityContext.setKeyPass(passPhrase);
+// sshSecurityContext.setPrivateKeyLoc(privateKeyPath);
+// return sshSecurityContext;
+// } catch (SSHApiException e) {
+// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+// }
+// return null;
+// }
+//
+// @Test
+// public void testSSHProvider() throws GFacException {
+// BetterGfacImpl gFacAPI = new BetterGfacImpl();
+// gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
+// org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobDescription());
+// org.junit.Assert.assertNotNull(jobExecutionContext.getJobDetails().getJobID());
+// }
+//
+//}
http://git-wip-us.apache.org/repos/asf/airavata/blob/2dd94e63/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
index 5cb1200..b115b6c 100644
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
+++ b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
@@ -1,172 +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.core.gfac.services.impl;
-
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.commons.gfac.type.HostDescription;
-import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.commons.gfac.type.ServiceDescription;
-import org.apache.airavata.gfac.GFacConfiguration;
-import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.core.context.ApplicationContext;
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
-import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.InputParameterType;
-import org.apache.airavata.schemas.gfac.OutputParameterType;
-import org.apache.airavata.schemas.gfac.SSHHostType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.commons.lang.SystemUtils;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SSHProviderTestWithSSHAuth {
- private JobExecutionContext jobExecutionContext;
- @Before
- public void setUp() throws Exception {
-
- URL resource = SSHProviderTestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
- GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null);
-// gFacConfiguration.s
- //have to set InFlwo Handlers and outFlowHandlers
- ApplicationContext applicationContext = new ApplicationContext();
- HostDescription host = new HostDescription(SSHHostType.type);
- host.getType().setHostName("bigred");
- host.getType().setHostAddress("bigred2.uits.iu.edu");
- applicationContext.setHostDescription(host);
- /*
- * App
- */
- ApplicationDescription appDesc = new ApplicationDescription();
- ApplicationDeploymentDescriptionType app = appDesc.getType();
- ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
- name.setStringValue("EchoSSH");
- app.setApplicationName(name);
-
- /*
- * Use bat file if it is compiled on Windows
- */
- if (SystemUtils.IS_OS_WINDOWS) {
- URL url = this.getClass().getClassLoader().getResource("echo.bat");
- app.setExecutableLocation(url.getFile());
- } else {
- //for unix and Mac
- app.setExecutableLocation("/bin/echo");
- }
-
- /*
- * Job location
- */
- String tempDir = "/tmp";
- String date = (new Date()).toString();
- date = date.replaceAll(" ", "_");
- date = date.replaceAll(":", "_");
-
- tempDir = tempDir + File.separator
- + "EchoSSH" + "_" + date + "_" + UUID.randomUUID();
-
- app.setScratchWorkingDirectory(tempDir);
- app.setStaticWorkingDirectory(tempDir);
- app.setInputDataDirectory(tempDir + File.separator + "input");
- app.setOutputDataDirectory(tempDir + File.separator + "output");
- app.setStandardOutput(tempDir + File.separator + "echo.stdout");
- app.setStandardError(tempDir + File.separator + "echo.stderr");
-
- applicationContext.setApplicationDeploymentDescription(appDesc);
-
- /*
- * Service
- */
- ServiceDescription serv = new ServiceDescription();
- serv.getType().setName("EchoSSH");
-
- List<InputParameterType> inputList = new ArrayList<InputParameterType>();
- InputParameterType input = InputParameterType.Factory.newInstance();
- input.setParameterName("echo_input");
- input.setParameterType(StringParameterType.Factory.newInstance());
- inputList.add(input);
- InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
- .size()]);
-
- List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
- OutputParameterType output = OutputParameterType.Factory.newInstance();
- output.setParameterName("echo_output");
- output.setParameterType(StringParameterType.Factory.newInstance());
- outputList.add(output);
- OutputParameterType[] outputParamList = outputList
- .toArray(new OutputParameterType[outputList.size()]);
-
- serv.getType().setInputParametersArray(inputParamList);
- serv.getType().setOutputParametersArray(outputParamList);
-
- jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
- jobExecutionContext.setApplicationContext(applicationContext);
-
- // Add security context
- jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext());
- /*
- * Host
- */
- applicationContext.setServiceDescription(serv);
-
- MessageContext inMessage = new MessageContext();
- ActualParameter echo_input = new ActualParameter();
- ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
- inMessage.addParameter("echo_input", echo_input);
-
- jobExecutionContext.setInMessageContext(inMessage);
-
- MessageContext outMessage = new MessageContext();
- ActualParameter echo_out = new ActualParameter();
+///*
+// *
+// * 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.core.gfac.services.impl;
+//
+//import java.io.File;
+//import java.net.URL;
+//import java.util.ArrayList;
+//import java.util.Date;
+//import java.util.List;
+//import java.util.UUID;
+//
+//import org.apache.airavata.commons.gfac.type.ActualParameter;
+//import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+//import org.apache.airavata.commons.gfac.type.HostDescription;
+//import org.apache.airavata.commons.gfac.type.MappingFactory;
+//import org.apache.airavata.commons.gfac.type.ServiceDescription;
+//import org.apache.airavata.gfac.GFacConfiguration;
+//import org.apache.airavata.gfac.GFacException;
+//import org.apache.airavata.gfac.core.context.ApplicationContext;
+//import org.apache.airavata.gfac.core.context.JobExecutionContext;
+//import org.apache.airavata.gfac.core.context.MessageContext;
+//import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
+//import org.apache.airavata.gfac.ssh.security.SSHSecurityContext;
+//import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+//import org.apache.airavata.schemas.gfac.InputParameterType;
+//import org.apache.airavata.schemas.gfac.OutputParameterType;
+//import org.apache.airavata.schemas.gfac.SSHHostType;
+//import org.apache.airavata.schemas.gfac.StringParameterType;
+//import org.apache.commons.lang.SystemUtils;
+//import org.junit.Assert;
+//import org.junit.Before;
+//import org.junit.Test;
+//
+//public class SSHProviderTestWithSSHAuth {
+// private JobExecutionContext jobExecutionContext;
+// @Before
+// public void setUp() throws Exception {
+//
+// URL resource = SSHProviderTestWithSSHAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+// GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null);
+//// gFacConfiguration.s
+// //have to set InFlwo Handlers and outFlowHandlers
+// ApplicationContext applicationContext = new ApplicationContext();
+// HostDescription host = new HostDescription(SSHHostType.type);
+// host.getType().setHostName("bigred");
+// host.getType().setHostAddress("bigred2.uits.iu.edu");
+// applicationContext.setHostDescription(host);
+// /*
+// * App
+// */
+// ApplicationDescription appDesc = new ApplicationDescription();
+// ApplicationDeploymentDescriptionType app = appDesc.getType();
+// ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+// name.setStringValue("EchoSSH");
+// app.setApplicationName(name);
+//
+// /*
+// * Use bat file if it is compiled on Windows
+// */
+// if (SystemUtils.IS_OS_WINDOWS) {
+// URL url = this.getClass().getClassLoader().getResource("echo.bat");
+// app.setExecutableLocation(url.getFile());
+// } else {
+// //for unix and Mac
+// app.setExecutableLocation("/bin/echo");
+// }
+//
+// /*
+// * Job location
+// */
+// String tempDir = "/tmp";
+// String date = (new Date()).toString();
+// date = date.replaceAll(" ", "_");
+// date = date.replaceAll(":", "_");
+//
+// tempDir = tempDir + File.separator
+// + "EchoSSH" + "_" + date + "_" + UUID.randomUUID();
+//
+// app.setScratchWorkingDirectory(tempDir);
+// app.setStaticWorkingDirectory(tempDir);
+// app.setInputDataDirectory(tempDir + File.separator + "input");
+// app.setOutputDataDirectory(tempDir + File.separator + "output");
+// app.setStandardOutput(tempDir + File.separator + "echo.stdout");
+// app.setStandardError(tempDir + File.separator + "echo.stderr");
+//
+// applicationContext.setApplicationDeploymentDescription(appDesc);
+//
+// /*
+// * Service
+// */
+// ServiceDescription serv = new ServiceDescription();
+// serv.getType().setName("EchoSSH");
+//
+// List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+// InputParameterType input = InputParameterType.Factory.newInstance();
+// input.setParameterName("echo_input");
+// input.setParameterType(StringParameterType.Factory.newInstance());
+// inputList.add(input);
+// InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
+// .size()]);
+//
+// List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+// OutputParameterType output = OutputParameterType.Factory.newInstance();
+// output.setParameterName("echo_output");
+// output.setParameterType(StringParameterType.Factory.newInstance());
+// outputList.add(output);
+// OutputParameterType[] outputParamList = outputList
+// .toArray(new OutputParameterType[outputList.size()]);
+//
+// serv.getType().setInputParametersArray(inputParamList);
+// serv.getType().setOutputParametersArray(outputParamList);
+//
+// jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
+// jobExecutionContext.setApplicationContext(applicationContext);
+//
+// // Add security context
+// jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, getSecurityContext());
+// /*
+// * Host
+// */
+// applicationContext.setServiceDescription(serv);
+//
+// MessageContext inMessage = new MessageContext();
+// ActualParameter echo_input = new ActualParameter();
// ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
- outMessage.addParameter("echo_output", echo_out);
-
- jobExecutionContext.setOutMessageContext(outMessage);
-
- }
-
- private SSHSecurityContext getSecurityContext() {
- SSHSecurityContext context = new SSHSecurityContext();
- context.setUsername("lginnali");
- context.setPrivateKeyLoc("~/.ssh/id_dsa");
- context.setKeyPass("i want to be free");
- return context;
- }
-
- @Test
- public void testLocalProvider() throws GFacException {
- BetterGfacImpl gFacAPI = new BetterGfacImpl();
- gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
- MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
- Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")), "hello");
- }
-}
+// inMessage.addParameter("echo_input", echo_input);
+//
+// jobExecutionContext.setInMessageContext(inMessage);
+//
+// MessageContext outMessage = new MessageContext();
+// ActualParameter echo_out = new ActualParameter();
+//// ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+// outMessage.addParameter("echo_output", echo_out);
+//
+// jobExecutionContext.setOutMessageContext(outMessage);
+//
+// }
+//
+// private SSHSecurityContext getSecurityContext() {
+// SSHSecurityContext context = new SSHSecurityContext();
+// context.setUsername("lginnali");
+// context.setPrivateKeyLoc("~/.ssh/id_dsa");
+// context.setKeyPass("i want to be free");
+// return context;
+// }
+//
+// @Test
+// public void testLocalProvider() throws GFacException {
+// BetterGfacImpl gFacAPI = new BetterGfacImpl();
+// gFacAPI.submitJob(jobExecutionContext.getExperimentID(), jobExecutionContext.getTaskData().getTaskID(), jobExecutionContext.getGatewayID());
+// MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
+// Assert.assertEquals(MappingFactory.toString((ActualParameter)outMessageContext.getParameter("echo_output")), "hello");
+// }
+//}