Package org.apache.airavata.gsi.ssh.api

Examples of org.apache.airavata.gsi.ssh.api.Cluster

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                HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().
                        getApplicationDeploymentDescription().getType();
                JobDetails jobDetails = new JobDetails();
                String taskID = jobExecutionContext.getTaskData().getTaskID();
                try {
                    Cluster cluster = null;
                    if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) != null) {
                        cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
                    }
                    if (cluster == null) {
                        throw new GFacProviderException("Security context is not set properly");
                    } else {
                        log.info("Successfully retrieved the Security Context");
                    }
                    // This installed path is a mandetory field, because this could change based on the computing resource
                    JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, app, cluster);

                    log.info(jobDescriptor.toXML());

                    jobDetails.setJobDescription(jobDescriptor.toXML());

                    String jobID = cluster.submitBatchJob(jobDescriptor);
                    jobExecutionContext.setJobDetails(jobDetails);
                    if (jobID == null) {
                        jobDetails.setJobID("none");
                        GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
                    } else {
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                        this.passPhrase);
            }
            // Server info
            ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);

            Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
            outputPath = outputPath + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID()
                    + File.separator;
            pbsCluster.makeDirectory(outputPath);
            pbsCluster.scpTo(outputPath, standardError);
            pbsCluster.scpTo(outputPath, standardOutput);
            List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
            Set<String> keys = output.keySet();
            for (String paramName : keys) {
                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                  String downloadFile = MappingFactory.toString(actualParameter);
                  pbsCluster.scpTo(outputPath, downloadFile);
                    String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar)+1, downloadFile.length());
                    DataObjectType dataObjectType = new DataObjectType();
                    dataObjectType.setValue(outputPath + File.separatorChar + fileName);
                    dataObjectType.setKey(paramName);
                    dataObjectType.setType(DataType.URI);
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        TransferStatus status = new TransferStatus();

        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                .getApplicationDeploymentDescription().getType();
        try {
            Cluster cluster = null;
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
            } else {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
            }
            if (cluster == null) {
                throw new GFacProviderException("Security context is not set properly");
            } else {
                log.info("Successfully retrieved the Security Context");
            }

            // Get the Stdouts and StdErrs
            String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());

            TaskDetails taskData = jobExecutionContext.getTaskData();
            String outputDataDir = null;
            File localStdOutFile;
            File localStdErrFile;

            if (taskData.getAdvancedOutputDataHandling() != null) {
                outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
            }
            if (outputDataDir == null) {
                outputDataDir = File.separator + "tmp";
            }
            outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
            (new File(outputDataDir)).mkdirs();


            localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
            localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
//            cluster.makeDirectory(outputDataDir);
            cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
            Thread.sleep(1000);
            cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
            Thread.sleep(1000);

            String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
            String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDOUT:" + stdOutStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDERR:" + stdErrStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

            //todo this is a mess we have to fix this
            List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
            Set<String> keys = output.keySet();
            for (String paramName : keys) {
                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                if ("URI".equals(actualParameter.getType().getType().toString())) {

                    List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
                    if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
                        OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
                        Set<String> strings = output.keySet();
                        outputArray.clear();
                        for(String key:strings) {
                            ActualParameter actualParameter1 = (ActualParameter) output.get(key);
                            if("URI".equals(actualParameter1.getType().getType().toString())){
                              String downloadFile = MappingFactory.toString(actualParameter1);
                              cluster.scpFrom(downloadFile, outputDataDir);
                              String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar)+1, downloadFile.length());
                              String localFile = outputDataDir +  File.separator +fileName;
                jobExecutionContext.addOutputFile(localFile);
                MappingFactory.fromString(actualParameter1, localFile);
                DataObjectType dataObjectType = new DataObjectType();
                                dataObjectType.setValue(localFile);
                                dataObjectType.setKey(key);
                                dataObjectType.setType(DataType.URI);
                                outputArray.add(dataObjectType);
                            }
                        }
                        break;
                    } else {
                        String valueList = outputList.get(0);
                        cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
                        jobExecutionContext.addOutputFile(outputDataDir + File.separator + valueList);
                        DataObjectType dataObjectType = new DataObjectType();
                        dataObjectType.setValue(valueList);
                        dataObjectType.setKey(paramName);
                        dataObjectType.setType(DataType.URI);
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                GSIAuthenticationInfo authenticationInfo
                        = new MyProxyAuthenticationInfo(requestData.getMyProxyUserName(), requestData.getMyProxyPassword(), requestData.getMyProxyServerUrl(),
                        requestData.getMyProxyPort(), requestData.getMyProxyLifeTime(), System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY));
                ServerInfo serverInfo = new ServerInfo(requestData.getMyProxyUserName(), registeredHost.getType().getHostAddress());

                Cluster pbsCluster = null;
                try {
                    String installedParentPath = ((HpcApplicationDeploymentType)
                            jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
                    pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
                            (CommonUtils.getPBSJobManager(installedParentPath)));
                } catch (SSHApiException e) {
                    e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                }

                context.setPbsCluster(pbsCluster);
            }

            jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT, context);
        //Adding Amanzon Keys
            if (this.configuration.getAmazonSecurityContext() != null) {
                jobExecutionContext.addSecurityContext(AmazonSecurityContext.AMAZON_SECURITY_CONTEXT,
                        this.configuration.getAmazonSecurityContext());
         }
      //Adding SSH security
            String sshUserName = configurationProperties.getProperty(Constants.SSH_USER_NAME);
            String sshPrivateKey = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY);
            String sshPrivateKeyPass = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
            String sshPassword = configurationProperties.getProperty(Constants.SSH_PASSWORD);
            String sshPublicKey = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
            SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
            if (((SSHHostType) registeredHost.getType()).getHpcResource()) {
                AuthenticationInfo authenticationInfo = null;
                // we give higher preference to the password over keypair ssh authentication
                if (sshPassword != null) {
                    authenticationInfo = new DefaultPasswordAuthenticationInfo(sshPassword);
                } else {
                    authenticationInfo = new DefaultPublicKeyFileAuthentication(sshPublicKey, sshPrivateKey, sshPrivateKeyPass);
                }
                ServerInfo serverInfo = new ServerInfo(sshUserName, registeredHost.getType().getHostAddress());

                Cluster pbsCluster = null;
                try {
                    String installedParentPath = ((HpcApplicationDeploymentType)
                            jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
                    pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
                            (CommonUtils.getPBSJobManager(installedParentPath)));
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                    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);
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        }
        jobExecutionContext.setInMessageContext(inputNew);
    }

    private static String stageInputFiles(JobExecutionContext jobExecutionContext, String paramValue) throws IOException, GFacException {
        Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
        if (cluster == null) {
            throw new GFacException("Security context is not set properly");
        } else {
            log.info("Successfully retrieved the Security Context");
        }
        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
        int i = paramValue.lastIndexOf(File.separator);
        String substring = paramValue.substring(i + 1);
        try {
            String targetFile = app.getInputDataDirectory() + File.separator + substring;
            if(paramValue.startsWith("scp:")){
              paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
              cluster.scpThirdParty(paramValue, targetFile);
            }else{
            if(paramValue.startsWith("file")){
                paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
            }
            cluster.scpTo(targetFile, paramValue);
            }
            return targetFile;
        } catch (SSHApiException e) {
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
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        makeDirectory(jobExecutionContext);

  }
  private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
        try{
        Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
        if (cluster == null) {
            throw new GFacHandlerException("Security context is not set properly");
        } else {
            log.info("Successfully retrieved the Security Context");
        }
        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
            String workingDirectory = app.getScratchWorkingDirectory();
            cluster.makeDirectory(workingDirectory);
            cluster.makeDirectory(app.getScratchWorkingDirectory());
            cluster.makeDirectory(app.getInputDataDirectory());
            cluster.makeDirectory(app.getOutputDataDirectory());
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            status.setTransferState(TransferState.DIRECTORY_SETUP);
            detail.setTransferStatus(status);
            detail.setTransferDescription("Working directory = " + workingDirectory);
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                = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
                7512, 17280000, certificateLocation);

        // Server info
        ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
        Cluster pbsCluster = null;
        try {
            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(app.getInstalledParentPath()));
        } catch (SSHApiException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
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        // Server info
        ServerInfo serverInfo = new ServerInfo("ogce", hostDescription.getType().getHostAddress());


        Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/"));


        // Execute command
        System.out.println("Target PBS file path: " + workingDirectory);
        // constructing the job object
        JobDescriptor jobDescriptor = new JobDescriptor();
        jobDescriptor.setWorkingDirectory(workingDirectory);
        jobDescriptor.setShellName("/bin/bash");
        jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
        jobDescriptor.setExecutablePath("/bin/echo");
        jobDescriptor.setAllEnvExport(true);
        jobDescriptor.setMailOptions("n");
        jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
        jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
        jobDescriptor.setNodes(1);
        jobDescriptor.setProcessesPerNode(1);
        jobDescriptor.setQueueName("normal");
        jobDescriptor.setMaxWallTime("60");
        jobDescriptor.setAcountString("sds128");
        List<String> inputs = new ArrayList<String>();
        jobDescriptor.setOwner("ogce");
        inputs.add("Hello World");
        jobDescriptor.setInputValues(inputs);
        //finished construction of job object
        System.out.println(jobDescriptor.toXML());
        for (int i = 0; i < 1; i++) {
            String jobID = pbsCluster.submitBatchJob(jobDescriptor);
            System.out.println("Job submitted successfully, Job ID: " +  jobID);
            MonitorID monitorID = new HPCMonitorID(hostDescription, jobID,null,null,null, "ogce");
            ((HPCMonitorID)monitorID).setAuthenticationInfo(authenticationInfo);
            try {
                org.apache.airavata.gfac.monitor.util.CommonUtils.addMonitortoQueue(pullQueue, monitorID);
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        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().
                getApplicationDeploymentDescription().getType();
        JobDetails jobDetails = new JobDetails();
       String taskID = jobExecutionContext.getTaskData().getTaskID();
        try {
            Cluster cluster = null;
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
            }
            if (cluster == null) {
                throw new GFacProviderException("Security context is not set properly");
            } else {
                log.info("Successfully retrieved the Security Context");
            }
            // This installed path is a mandetory field, because this could change based on the computing resource
            JobDescriptor jobDescriptor = GFACGSISSHUtils.createJobDescriptor(jobExecutionContext, app, cluster);

            log.info(jobDescriptor.toXML());
           
            jobDetails.setJobDescription(jobDescriptor.toXML());
           
            String jobID = cluster.submitBatchJob(jobDescriptor);
            jobExecutionContext.setJobDetails(jobDetails);
            if(jobID == null){
                jobDetails.setJobID("none");
                GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.FAILED);
            }else{
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