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 (theà "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 {
