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Posted to commits@airavata.apache.org by sh...@apache.org on 2015/06/04 22:15:21 UTC
[08/81] [abbrv] 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-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
deleted file mode 100644
index b38a170..0000000
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ /dev/null
@@ -1,562 +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.ssh.util;
-
-import org.airavata.appcatalog.cpi.AppCatalog;
-import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential;
-import org.apache.airavata.gfac.Constants;
-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.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
-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.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.util.CommonUtils;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
-import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.apache.airavata.model.appcatalog.computeresource.*;
-import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
-import org.apache.airavata.model.workspace.experiment.ComputationalResourceScheduling;
-import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
-import org.apache.airavata.model.workspace.experiment.ErrorCategory;
-import org.apache.airavata.model.workspace.experiment.TaskDetails;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.*;
-
-public class GFACSSHUtils {
- private final static Logger logger = LoggerFactory.getLogger(GFACSSHUtils.class);
-
- public static Map<String, List<Cluster>> clusters = new HashMap<String, List<Cluster>>();
-
- public static final String PBS_JOB_MANAGER = "pbs";
- public static final String SLURM_JOB_MANAGER = "slurm";
- public static final String SUN_GRID_ENGINE_JOB_MANAGER = "UGE";
- public static final String LSF_JOB_MANAGER = "LSF";
-
- public static int maxClusterCount = 5;
-
- /**
- * This method is to add computing resource specific authentication, if its a third party machine, use the other addSecurityContext
- * @param jobExecutionContext
- * @throws GFacException
- * @throws ApplicationSettingsException
- */
- public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
- 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 (preferredJobSubmissionProtocol == JobSubmissionProtocol.SSH) {
- try {
- AppCatalog appCatalog = jobExecutionContext.getAppCatalog();
- SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(preferredJobSubmissionInterface.getJobSubmissionInterfaceId());
- SecurityProtocol securityProtocol = sshJobSubmission.getSecurityProtocol();
- if (securityProtocol == SecurityProtocol.GSI || securityProtocol == SecurityProtocol.SSH_KEYS) {
- SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
- String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
- RequestData requestData = new RequestData(jobExecutionContext.getGatewayID());
- requestData.setTokenId(credentialStoreToken);
-
- ServerInfo serverInfo = new ServerInfo(null, jobExecutionContext.getHostName());
-
- Cluster pbsCluster = null;
- try {
- AuthenticationInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
- String installedParentPath = jobExecutionContext.getResourceJobManager().getJobManagerBinPath();
- if (installedParentPath == null) {
- installedParentPath = "/";
- }
-
- SSHCredential credentials =((TokenizedSSHAuthInfo)tokenizedSSHAuthInfo).getCredentials();// this is just a call to get and set credentials in to this object,data will be used
- if(credentials.getPrivateKey()==null || credentials.getPublicKey()==null){
- // now we fall back to username password authentication
- Properties configurationProperties = ServerSettings.getProperties();
- tokenizedSSHAuthInfo = new DefaultPasswordAuthenticationInfo(configurationProperties.getProperty(Constants.SSH_PASSWORD));
- }
- // This should be the login user name from compute resource preference
- String loginUser = jobExecutionContext.getLoginUserName();
- if (loginUser == null) {
- loginUser = credentials.getPortalUserName();
- }
- serverInfo.setUserName(loginUser);
- jobExecutionContext.getExperiment().setUserName(loginUser);
-
-
- // inside the pbsCluser object
-
- String key = loginUser + jobExecutionContext.getHostName() + serverInfo.getPort();
- 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) {
- JobManagerConfiguration jConfig = null;
- String jobManager = sshJobSubmission.getResourceJobManager().getResourceJobManagerType().toString();
- if (jobManager == null) {
- logger.error("No Job Manager is configured, so we are picking pbs as the default job manager");
- jConfig = CommonUtils.getPBSJobManager(installedParentPath);
- } else {
- if (PBS_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getPBSJobManager(installedParentPath);
- } else if (SLURM_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getSLURMJobManager(installedParentPath);
- } else if (SUN_GRID_ENGINE_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getUGEJobManager(installedParentPath);
- } else if (LSF_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getLSFJobManager(installedParentPath);
- }
- }
-
- pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,jConfig);
- 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) {
- throw new GFacException("Error occurred...", e);
- }
- sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(jobExecutionContext.getHostName(), sshSecurityContext);
- }
- } catch (AppCatalogException e) {
- throw new GFacException("Error while getting SSH Submission object from app catalog", e);
- }
- }
- }
-
- /**
- * This method can be used to add third party resource security contexts
- * @param jobExecutionContext
- * @param sshAuth
- * @throws GFacException
- * @throws ApplicationSettingsException
- */
- public static void addSecurityContext(JobExecutionContext jobExecutionContext,SSHAuthWrapper sshAuth) throws GFacException, ApplicationSettingsException {
- try {
- if(sshAuth== null) {
- throw new GFacException("Error adding security Context, because sshAuthWrapper is null");
- }
- SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
- AppCatalog appCatalog = jobExecutionContext.getAppCatalog();
- JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
- SSHJobSubmission sshJobSubmission = null;
- try {
- sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(preferredJobSubmissionInterface.getJobSubmissionInterfaceId());
- } catch (Exception e1) {
- logger.error("Not able to get SSHJobSubmission from registry");
- }
-
- Cluster pbsCluster = null;
- String 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;
- }
- 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) {
- JobManagerConfiguration jConfig = null;
- String installedParentPath = null;
- if(jobExecutionContext.getResourceJobManager()!= null){
- installedParentPath = jobExecutionContext.getResourceJobManager().getJobManagerBinPath();
- }
- if (installedParentPath == null) {
- installedParentPath = "/";
- }
- if (sshJobSubmission != null) {
- String jobManager = sshJobSubmission.getResourceJobManager().getResourceJobManagerType().toString();
- if (jobManager == null) {
- logger.error("No Job Manager is configured, so we are picking pbs as the default job manager");
- jConfig = CommonUtils.getPBSJobManager(installedParentPath);
- } else {
- if (PBS_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getPBSJobManager(installedParentPath);
- } else if (SLURM_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getSLURMJobManager(installedParentPath);
- } else if (SUN_GRID_ENGINE_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
- jConfig = CommonUtils.getUGEJobManager(installedParentPath);
- } else if (LSF_JOB_MANAGER.equals(jobManager)) {
- jConfig = CommonUtils.getLSFJobManager(installedParentPath);
- }
- }
- }
- pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),jConfig);
- key = sshAuth.getKey();
- List<Cluster> pbsClusters = null;
- if (!(clusters.containsKey(key))) {
- pbsClusters = new ArrayList<Cluster>();
- } else {
- pbsClusters = clusters.get(key);
- }
- pbsClusters.add(pbsCluster);
- clusters.put(key, pbsClusters);
- }
- }
- sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(key, sshSecurityContext);
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw new GFacException("Error adding security Context", e);
- }
- }
-
-
- public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, Cluster cluster) throws AppCatalogException, ApplicationSettingsException {
- JobDescriptor jobDescriptor = new JobDescriptor();
- TaskDetails taskData = jobExecutionContext.getTaskData();
-
-
- // set email based job monitoring email address if monitor mode is JOB_EMAIL_NOTIFICATION_MONITOR
- boolean addJobNotifMail = isEmailBasedJobMonitor(jobExecutionContext);
- String emailIds = null;
- if (addJobNotifMail) {
- emailIds = ServerSettings.getEmailBasedMonitorAddress();
- }
- // add all configured job notification email addresses.
- if (ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_ENABLE).equalsIgnoreCase("true")) {
- String flags = ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_FLAGS);
- if (flags != null && jobExecutionContext.getApplicationContext().getComputeResourceDescription().getHostName().equals("stampede.tacc.xsede.org")) {
- flags = "ALL";
- }
- jobDescriptor.setMailOptions(flags);
-
- String userJobNotifEmailIds = ServerSettings.getSetting(ServerSettings.JOB_NOTIFICATION_EMAILIDS);
- if (userJobNotifEmailIds != null && !userJobNotifEmailIds.isEmpty()) {
- if (emailIds != null && !emailIds.isEmpty()) {
- emailIds += ("," + userJobNotifEmailIds);
- } else {
- emailIds = userJobNotifEmailIds;
- }
- }
-
- if (taskData.isEnableEmailNotification()) {
- List<String> emailList = jobExecutionContext.getTaskData().getEmailAddresses();
- String elist = GFacUtils.listToCsv(emailList, ',');
- if (elist != null && !elist.isEmpty()) {
- if (emailIds != null && !emailIds.isEmpty()) {
- emailIds = emailIds + "," + elist;
- } else {
- emailIds = elist;
- }
- }
- }
- }
- if (emailIds != null && !emailIds.isEmpty()) {
- logger.info("Email list: " + emailIds);
- jobDescriptor.setMailAddress(emailIds);
- }
- // 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(jobExecutionContext.getInputDir());
- jobDescriptor.setOutputDirectory(jobExecutionContext.getOutputDir());
- jobDescriptor.setExecutablePath(jobExecutionContext.getApplicationContext()
- .getApplicationDeploymentDescription().getExecutablePath());
- jobDescriptor.setStandardOutFile(jobExecutionContext.getStandardOutput());
- jobDescriptor.setStandardErrorFile(jobExecutionContext.getStandardError());
- String computationalProjectAccount = taskData.getTaskScheduling().getComputationalProjectAccount();
- if (computationalProjectAccount == null){
- ComputeResourcePreference computeResourcePreference = jobExecutionContext.getApplicationContext().getComputeResourcePreference();
- if (computeResourcePreference != null) {
- computationalProjectAccount = computeResourcePreference.getAllocationProjectNumber();
- }
- }
- if (computationalProjectAccount != null) {
- jobDescriptor.setAcountString(computationalProjectAccount);
- }
- // To make job name alpha numeric
- jobDescriptor.setJobName("A" + String.valueOf(generateJobName()));
- jobDescriptor.setWorkingDirectory(jobExecutionContext.getWorkingDir());
-
- List<String> inputValues = new ArrayList<String>();
- MessageContext input = jobExecutionContext.getInMessageContext();
-
- // sort the inputs first and then build the command ListR
- 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 : input.getParameters().values()) {
- if (object instanceof InputDataObjectType) {
- InputDataObjectType inputDOT = (InputDataObjectType) object;
- sortedInputSet.add(inputDOT);
- }
- }
- for (InputDataObjectType inputDataObjectType : sortedInputSet) {
- if (!inputDataObjectType.isRequiredToAddedToCommandLine()) {
- continue;
- }
- if (inputDataObjectType.getApplicationArgument() != null
- && !inputDataObjectType.getApplicationArgument().equals("")) {
- inputValues.add(inputDataObjectType.getApplicationArgument());
- }
-
- if (inputDataObjectType.getValue() != null
- && !inputDataObjectType.getValue().equals("")) {
- if (inputDataObjectType.getType() == DataType.URI) {
- // set only the relative path
- String filePath = inputDataObjectType.getValue();
- filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar) + 1, filePath.length());
- inputValues.add(filePath);
- }else {
- inputValues.add(inputDataObjectType.getValue());
- }
-
- }
- }
- Map<String, Object> outputParams = jobExecutionContext.getOutMessageContext().getParameters();
- for (Object outputParam : outputParams.values()) {
- if (outputParam instanceof OutputDataObjectType) {
- OutputDataObjectType output = (OutputDataObjectType) outputParam;
- if (output.getApplicationArgument() != null
- && !output.getApplicationArgument().equals("")) {
- inputValues.add(output.getApplicationArgument());
- }
- if (output.getValue() != null && !output.getValue().equals("") && output.isRequiredToAddedToCommandLine()) {
- if (output.getType() == DataType.URI){
- String filePath = output.getValue();
- filePath = filePath.substring(filePath.lastIndexOf(File.separatorChar) + 1, filePath.length());
- inputValues.add(filePath);
- }
- }
- }
- }
-
- jobDescriptor.setInputValues(inputValues);
- jobDescriptor.setUserName(((GSISSHAbstractCluster) cluster).getServerInfo().getUserName());
- jobDescriptor.setShellName("/bin/bash");
- jobDescriptor.setAllEnvExport(true);
- jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
-
- ResourceJobManager resourceJobManager = jobExecutionContext.getResourceJobManager();
-
-
- ComputationalResourceScheduling taskScheduling = taskData.getTaskScheduling();
- if (taskScheduling != null) {
- int totalNodeCount = taskScheduling.getNodeCount();
- int totalCPUCount = taskScheduling.getTotalCPUCount();
-
-
- if (taskScheduling.getComputationalProjectAccount() != null) {
- jobDescriptor.setAcountString(taskScheduling.getComputationalProjectAccount());
- }
- if (taskScheduling.getQueueName() != null) {
- jobDescriptor.setQueueName(taskScheduling.getQueueName());
- }
-
- if (totalNodeCount > 0) {
- jobDescriptor.setNodes(totalNodeCount);
- }
- if (taskScheduling.getComputationalProjectAccount() != null) {
- jobDescriptor.setAcountString(taskScheduling.getComputationalProjectAccount());
- }
- if (taskScheduling.getQueueName() != null) {
- jobDescriptor.setQueueName(taskScheduling.getQueueName());
- }
- if (totalCPUCount > 0) {
- int ppn = totalCPUCount / totalNodeCount;
- jobDescriptor.setProcessesPerNode(ppn);
- jobDescriptor.setCPUCount(totalCPUCount);
- }
- if (taskScheduling.getWallTimeLimit() > 0) {
- jobDescriptor.setMaxWallTime(String.valueOf(taskScheduling.getWallTimeLimit()));
- if(resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)){
- jobDescriptor.setMaxWallTimeForLSF(String.valueOf(taskScheduling.getWallTimeLimit()));
- }
- }
- if (taskScheduling.getTotalPhysicalMemory() > 0) {
- jobDescriptor.setUsedMemory(taskScheduling.getTotalPhysicalMemory() + "");
- }
- } else {
- logger.error("Task scheduling cannot be null at this point..");
- }
- ApplicationDeploymentDescription appDepDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
- List<String> moduleCmds = appDepDescription.getModuleLoadCmds();
- if (moduleCmds != null) {
- for (String moduleCmd : moduleCmds) {
- jobDescriptor.addModuleLoadCommands(moduleCmd);
- }
- }
- List<String> preJobCommands = appDepDescription.getPreJobCommands();
- if (preJobCommands != null) {
- for (String preJobCommand : preJobCommands) {
- jobDescriptor.addPreJobCommand(parseCommand(preJobCommand, jobExecutionContext));
- }
- }
-
- List<String> postJobCommands = appDepDescription.getPostJobCommands();
- if (postJobCommands != null) {
- for (String postJobCommand : postJobCommands) {
- jobDescriptor.addPostJobCommand(parseCommand(postJobCommand, jobExecutionContext));
- }
- }
-
- ApplicationParallelismType parallelism = appDepDescription.getParallelism();
- if (parallelism != null){
- if (parallelism == ApplicationParallelismType.MPI || parallelism == ApplicationParallelismType.OPENMP || parallelism == ApplicationParallelismType.OPENMP_MPI){
- Map<JobManagerCommand, String> jobManagerCommands = resourceJobManager.getJobManagerCommands();
- if (jobManagerCommands != null && !jobManagerCommands.isEmpty()) {
- for (JobManagerCommand command : jobManagerCommands.keySet()) {
- if (command == JobManagerCommand.SUBMISSION) {
- String commandVal = jobManagerCommands.get(command);
- jobDescriptor.setJobSubmitter(commandVal);
- }
- }
- }
- }
- }
- return jobDescriptor;
- }
-
- public static boolean isEmailBasedJobMonitor(JobExecutionContext jobExecutionContext) throws AppCatalogException {
- if (jobExecutionContext.getPreferredJobSubmissionProtocol() == JobSubmissionProtocol.SSH) {
- String jobSubmissionInterfaceId = jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionInterfaceId();
- SSHJobSubmission sshJobSubmission = jobExecutionContext.getAppCatalog().getComputeResource().getSSHJobSubmission(jobSubmissionInterfaceId);
- MonitorMode monitorMode = sshJobSubmission.getMonitorMode();
- return monitorMode != null && monitorMode == MonitorMode.JOB_EMAIL_NOTIFICATION_MONITOR;
- } else {
- return false;
- }
- }
-
- private static int generateJobName() {
- Random random = new Random();
- int i = random.nextInt(Integer.MAX_VALUE);
- i = i + 99999999;
- if(i<0) {
- i = i * (-1);
- }
- return i;
- }
-
- private static String parseCommand(String value, JobExecutionContext jobExecutionContext) {
- String parsedValue = value.replaceAll("\\$workingDir", jobExecutionContext.getWorkingDir());
- parsedValue = parsedValue.replaceAll("\\$inputDir", jobExecutionContext.getInputDir());
- parsedValue = parsedValue.replaceAll("\\$outputDir", jobExecutionContext.getOutputDir());
- return parsedValue;
- }
- /**
- * This method can be used to set the Security Context if its not set and later use it in other places
- * @param jobExecutionContext
- * @param authenticationInfo
- * @param userName
- * @param hostName
- * @param port
- * @return
- * @throws GFacException
- */
- public static String prepareSecurityContext(JobExecutionContext jobExecutionContext, AuthenticationInfo authenticationInfo
- , String userName, String hostName, int port) throws GFacException {
- ServerInfo serverInfo = new ServerInfo(userName, hostName);
- String key = userName+hostName+port;
- SSHAuthWrapper sshAuthWrapper = new SSHAuthWrapper(serverInfo, authenticationInfo, key);
- if (jobExecutionContext.getSecurityContext(key) == null) {
- try {
- GFACSSHUtils.addSecurityContext(jobExecutionContext, sshAuthWrapper);
- } catch (ApplicationSettingsException e) {
- logger.error(e.getMessage());
- try {
- StringWriter errors = new StringWriter();
- e.printStackTrace(new PrintWriter(errors));
- GFacUtils.saveErrorDetails(jobExecutionContext, errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
- } catch (GFacException e1) {
- logger.error(e1.getLocalizedMessage());
- }
- throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
- }
- }
- return key;
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java
deleted file mode 100644
index 704528f..0000000
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package org.apache.airavata.gfac.ssh.util;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.airavata.gfac.core.context.JobExecutionContext;
-import org.apache.airavata.gfac.core.handler.GFacHandlerException;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
-import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.model.appcatalog.appinterface.DataType;
-import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * To handle outputs of different data types
- *
- */
-public class HandleOutputs {
- private static final Logger log = LoggerFactory.getLogger(HandleOutputs.class);
-
- public static List<OutputDataObjectType> handleOutputs(JobExecutionContext jobExecutionContext, Cluster cluster) throws GFacHandlerException {
- List<OutputDataObjectType> outputArray = new ArrayList<OutputDataObjectType>();
- try {
- String outputDataDir = File.separator + "tmp" + File.separator + jobExecutionContext.getExperimentID();
- (new File(outputDataDir)).mkdirs();
-
- List<OutputDataObjectType> outputs = jobExecutionContext.getTaskData().getApplicationOutputs();
- List<String> outputList = cluster.listDirectory(jobExecutionContext.getWorkingDir());
- boolean missingOutput = false;
-
- for (OutputDataObjectType output : outputs) {
- // FIXME: Validation of outputs based on required and optional and search based on REGEX provided in search.
-
- if (DataType.URI == output.getType()) {
- // for failed jobs outputs are not generated. So we should not download outputs
- if (GFacUtils.isFailedJob(jobExecutionContext)){
- continue;
- }
- String outputFile = output.getValue();
- String fileName = outputFile.substring(outputFile.lastIndexOf(File.separatorChar) + 1, outputFile.length());
-
- if (output.getLocation() == null && !outputList.contains(fileName) && output.isIsRequired()) {
- missingOutput = true;
- } else {
- cluster.scpFrom(outputFile, outputDataDir);
- String localFile = outputDataDir + File.separator + fileName;
- jobExecutionContext.addOutputFile(localFile);
- output.setValue(localFile);
- outputArray.add(output);
- }
-
- } else if (DataType.STDOUT == output.getType()) {
- String downloadFile = jobExecutionContext.getStandardOutput();
- String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length());
- cluster.scpFrom(downloadFile, outputDataDir);
- String localFile = outputDataDir + File.separator + fileName;
- jobExecutionContext.addOutputFile(localFile);
- jobExecutionContext.setStandardOutput(localFile);
- output.setValue(localFile);
- outputArray.add(output);
-
- } else if (DataType.STDERR == output.getType()) {
- String downloadFile = jobExecutionContext.getStandardError();
- String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length());
- cluster.scpFrom(downloadFile, outputDataDir);
- String localFile = outputDataDir + File.separator + fileName;
- jobExecutionContext.addOutputFile(localFile);
- jobExecutionContext.setStandardError(localFile);
- output.setValue(localFile);
- outputArray.add(output);
-
- }
- }
- if (outputArray == null || outputArray.isEmpty()) {
- log.error("Empty Output returned from the Application, Double check the application and ApplicationDescriptor output Parameter Names");
- if (jobExecutionContext.getTaskData().getAdvancedOutputDataHandling() == null) {
- throw new GFacHandlerException("Empty Output returned from the Application, Double check the application"
- + "and ApplicationDescriptor output Parameter Names");
- }
- }
-
- if (missingOutput) {
- String arrayString = Arrays.deepToString(outputArray.toArray());
- log.error(arrayString);
- throw new GFacHandlerException("Required output is missing");
- }
- } catch (Exception e) {
- throw new GFacHandlerException(e);
- }
- jobExecutionContext.getTaskData().setApplicationOutputs(outputArray);
- return outputArray;
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-ssh/src/main/resources/errors.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/resources/errors.properties b/modules/gfac/gfac-ssh/src/main/resources/errors.properties
deleted file mode 100644
index 88c41b8..0000000
--- a/modules/gfac/gfac-ssh/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
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-ssh/src/main/resources/service.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/main/resources/service.properties b/modules/gfac/gfac-ssh/src/main/resources/service.properties
deleted file mode 100644
index 391bfea..0000000
--- a/modules/gfac/gfac-ssh/src/main/resources/service.properties
+++ /dev/null
@@ -1,58 +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.
-#
-#
-
-
-#
-# Class which implemented Scheduler interface. It will be used to determine a Provider
-#
-scheduler.class= org.apache.airavata.core.gfac.scheduler.impl.SchedulerImpl
-
-#
-# Data Service Plugins classes
-#
-datachain.classes= org.apache.airavata.core.gfac.extension.data.RegistryDataService
-
-#
-# Pre execution Plugins classes. For example, GridFTP Input Staging
-#
-prechain.classes= org.apache.airavata.core.gfac.extension.pre.GridFtpInputStaging
-prechain.classes= org.apache.airavata.core.gfac.extension.pre.HttpInputStaging
-
-#
-# Post execution Plugins classes. For example, GridFTP Output Staging
-#
-postchain.classes= org.apache.airavata.core.gfac.extension.post.GridFtpOutputStaging
-postchain.classes= org.apache.airavata.core.gfac.extension.post.OutputRegister
-
-#
-# SSH private key location. It will be used by SSHProvider
-#
-# ssh.key=/home/user/.ssh/id_rsa
-# ssh.keypass=
-# ssh.username=usernameAtHost
-
-#
-# MyProxy credential. It will be used by GridFTP Plugins and GramProvider.
-#
-# myproxy.server=myproxy.teragrid.org
-# myproxy.user=username
-# myproxy.pass=password
-# myproxy.life=3600
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/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
deleted file mode 100644
index c65f386..0000000
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
+++ /dev/null
@@ -1,252 +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.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/7b809747/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java b/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java
deleted file mode 100644
index d42ea52..0000000
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java
+++ /dev/null
@@ -1,135 +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.core.gfac.services.impl;
-//
-//import junit.framework.Assert;
-//import org.apache.airavata.client.AiravataAPIFactory;
-//import org.apache.airavata.client.api.AiravataAPI;
-//import org.apache.airavata.client.api.exception.AiravataAPIInvocationException;
-//import org.apache.airavata.common.exception.AiravataConfigurationException;
-//import org.apache.airavata.common.exception.ApplicationSettingsException;
-//import org.apache.airavata.common.utils.ClientSettings;
-//import org.apache.airavata.common.utils.DBUtil;
-//import org.apache.airavata.common.utils.ServerSettings;
-//import org.apache.airavata.credential.store.credential.impl.ssh.SSHCredential;
-//import org.apache.airavata.credential.store.store.CredentialReader;
-//import org.apache.airavata.credential.store.store.impl.CredentialReaderImpl;
-//import org.apache.airavata.gfac.GFacException;
-//import org.apache.airavata.gfac.RequestData;
-//import org.apache.airavata.gfac.ssh.security.TokenizedSSHAuthInfo;
-//import org.apache.airavata.gsi.ssh.api.SSHApiException;
-//import org.apache.airavata.gsi.ssh.api.ServerInfo;
-//import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-//import org.apache.airavata.gsi.ssh.util.CommonUtils;
-//import org.apache.airavata.registry.api.AiravataRegistry2;
-//import org.apache.airavata.registry.api.AiravataRegistryFactory;
-//import org.apache.airavata.registry.api.AiravataUser;
-//import org.apache.airavata.registry.api.Gateway;
-//import org.apache.airavata.registry.api.exception.RegAccessorInstantiateException;
-//import org.apache.airavata.registry.api.exception.RegAccessorInvalidException;
-//import org.apache.airavata.registry.api.exception.RegAccessorUndefinedException;
-//import org.apache.airavata.registry.api.exception.RegException;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//import org.testng.annotations.BeforeTest;
-//import org.testng.annotations.Test;
-//
-//import java.util.UUID;
-//
-//public class CredentialStoreTest {
-// private final static Logger logger = LoggerFactory.getLogger(CredentialStoreTest.class);
-//
-// @BeforeTest
-// public void testGSISSHProvider() throws GFacException, IllegalAccessException, ClassNotFoundException, InstantiationException, ApplicationSettingsException, SSHApiException {
-// System.setProperty("credential.store.keystore.url", "/Users/lahirugunathilake/Downloads/airavata_sym.jks");
-// System.setProperty("credential.store.keystore.alias", "airavata");
-// System.setProperty("credential.store.keystore.password", "airavata");
-// System.setProperty("myproxy.username", "ogce");
-// System.setProperty("myproxy.password", "");
-// System.setProperty("trusted.cert.location", "/Users/lahirugunathilake/Downloads/certificates");
-// System.setProperty("credential.store.jdbc.url","jdbc:mysql://gw85.iu.xsede.org:3306/airavata_gta_prod");
-// System.setProperty("credential.store.jdbc.user","gtaAiravataUser");
-// System.setProperty("credential.store.jdbc.password","gtaAiravataPWD");
-// System.setProperty("credential.store.jdbc.driver","com.mysql.jdbc.Driver");
-//
-//
-//
-// UUID uuid = UUID.randomUUID();
-// System.out.println("TokenId: " + uuid.toString());
-//// String publicKey = registry.createCredential("default",uuid.toString(),"lginnali" );
-//// System.out.println("Public-Key: " +publicKey);
-//// String tokenId = uuid.toString();
-// String tokenId = "2c308fa9-99f8-4baa-92e4-d062e311483c";
-// CredentialReader credentialReader = new CredentialReaderImpl(new DBUtil("jdbc:mysql://gw85.iu.xsede.org:3306/airavata_gta_prod",
-// "ptaAiravataUser", "ptaAiravataPWD", "com.mysql.jdbc.Driver"));
-//
-//
-// RequestData requestData = new RequestData();
-// requestData.setMyProxyUserName("cgateway");
-// requestData.setTokenId(tokenId);
-// requestData.setGatewayId("default");
-// TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(credentialReader, requestData);
-//
-// SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();
-// ServerInfo serverInfo = new ServerInfo("cgateway", "bigred2.uits.iu.edu");
-//
-// PBSCluster pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/"));
-// Assert.assertNotNull(pbsCluster);
-// return;
-//
-// }
-//
-// @Test
-// public static void main(String[] args) {
-// try {
-// new CredentialStoreTest().testGSISSHProvider();
-// } catch (GFacException e) {
-// e.printStackTrace();
-// } catch (IllegalAccessException e) {
-// e.printStackTrace();
-// } catch (ClassNotFoundException e) {
-// e.printStackTrace();
-// } catch (InstantiationException e) {
-// e.printStackTrace();
-// } catch (ApplicationSettingsException e) {
-// e.printStackTrace();
-// } catch (SSHApiException e) {
-// e.printStackTrace();
-// }
-// }
-//
-// private static AiravataAPI getAiravataAPI() throws AiravataAPIInvocationException, ApplicationSettingsException {
-// AiravataAPI airavataAPI;
-// try {
-// String sysUser = ClientSettings.getSetting("admin");
-// String gateway = ClientSettings.getSetting("default");
-// airavataAPI = AiravataAPIFactory.getAPI(gateway, sysUser);
-// } catch (AiravataAPIInvocationException e) {
-// logger.error("Unable to create airavata API", e.getMessage());
-// throw new AiravataAPIInvocationException(e);
-// } catch (ApplicationSettingsException e) {
-// logger.error("Unable to create airavata API", e.getMessage());
-// throw new ApplicationSettingsException(e.getMessage());
-// }
-// return airavataAPI;
-// }
-//
-//}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/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
deleted file mode 100644
index b115b6c..0000000
--- a/modules/gfac/gfac-ssh/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTestWithSSHAuth.java
+++ /dev/null
@@ -1,172 +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.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();
-//// ((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");
-// }
-//}
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt b/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt
deleted file mode 100644
index cf8dfb6..0000000
--- a/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt
+++ /dev/null
@@ -1,75 +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 (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 submission script generated by Apache Airavata
-# <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:value-of select="ns:cpuCount"/><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-ssh/src/test/resources/logging.properties
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-ssh/src/test/resources/logging.properties b/modules/gfac/gfac-ssh/src/test/resources/logging.properties
deleted file mode 100644
index 0584d38..0000000
--- a/modules/gfac/gfac-ssh/src/test/resources/logging.properties
+++ /dev/null
@@ -1,42 +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.
-#
-#
-#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/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/pom.xml b/modules/gfac/pom.xml
index 7f661ae..0414afc 100644
--- a/modules/gfac/pom.xml
+++ b/modules/gfac/pom.xml
@@ -31,14 +31,11 @@
<activeByDefault>true</activeByDefault>
</activation>
<modules>
+ <module>gfac-service</module>
+ <module>gfac-client</module>
<module>gfac-core</module>
- <module>gfac-ssh</module>
- <module>gfac-local</module>
- <module>gfac-gsissh</module>
+ <module>gfac-impl</module>
<module>gfac-bes</module>
- <module>gfac-monitor</module>
- <module>airavata-gfac-service</module>
- <module>airavata-gfac-stubs</module>
<module>gfac-application-specific-handlers</module>
</modules>
</profile>
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACEmbeddedJobSubmitter.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACEmbeddedJobSubmitter.java b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACEmbeddedJobSubmitter.java
index e93ae71..e506556 100644
--- a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACEmbeddedJobSubmitter.java
+++ b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACEmbeddedJobSubmitter.java
@@ -21,24 +21,17 @@
package org.apache.airavata.orchestrator.core.impl;
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.MonitorPublisher;
import org.apache.airavata.common.utils.ServerSettings;
import org.apache.airavata.credential.store.store.CredentialReader;
import org.apache.airavata.gfac.client.GFACInstance;
-import org.apache.airavata.gfac.core.cpi.BetterGfacImpl;
-import org.apache.airavata.gfac.core.cpi.GFac;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
+import org.apache.airavata.gfac.core.GFac;
+import org.apache.airavata.gfac.core.GFacUtils;
import org.apache.airavata.orchestrator.core.context.OrchestratorContext;
import org.apache.airavata.orchestrator.core.exception.OrchestratorException;
import org.apache.airavata.orchestrator.core.job.JobSubmitter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import com.google.common.eventbus.EventBus;
-
-import java.io.IOException;
-
/**
* This is the simplest implementation for JobSubmitter,
* This is calling gfac invocation methods to invoke the gfac embedded mode,so this does not really implement
@@ -54,7 +47,6 @@ public class GFACEmbeddedJobSubmitter implements JobSubmitter {
public void initialize(OrchestratorContext orchestratorContext) throws OrchestratorException {
this.orchestratorContext = orchestratorContext;
- gfac = BetterGfacImpl.getInstance();
}
public GFACInstance selectGFACInstance() throws OrchestratorException {