Examples with ProcessContext org.apache.airavata.gfac.core.context.ProcessContext used on opensource projects

Example 6 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class BESJobSubmissionTask method copyInputFilesToLocal.

private void copyInputFilesToLocal(TaskContext taskContext) throws GFacException {
    ProcessContext pc = taskContext.getParentProcessContext();
    StorageResourceDescription storageResource = pc.getStorageResource();
    if (storageResource != null) {
        hostName = storageResource.getHostName();
    } else {
        throw new GFacException("Storage Resource is null");
    }
    inputPath = pc.getStorageFileSystemRootLocation();
    inputPath = (inputPath.endsWith(File.separator) ? inputPath : inputPath + File.separator);
    String remoteFilePath = null, fileName = null, localFilePath = null;
    URI remoteFileURI = null;
    try {
        authenticationInfo = Factory.getStorageSSHKeyAuthentication(pc);
        ServerInfo serverInfo = pc.getStorageResourceServerInfo();
        Session sshSession = Factory.getSSHSession(authenticationInfo, serverInfo);
        List<InputDataObjectType> processInputs = pc.getProcessModel().getProcessInputs();
        for (InputDataObjectType input : processInputs) {
            if (input.getType() == DataType.URI) {
                remoteFileURI = new URI(input.getValue());
                remoteFilePath = remoteFileURI.getPath();
                fileName = remoteFilePath.substring(remoteFilePath.lastIndexOf("/") + 1);
                localFilePath = pc.getInputDir() + File.separator + fileName;
                log.info("SCP remote file :{} -> to local :{}", remoteFilePath, localFilePath);
                SSHUtils.scpFrom(remoteFilePath, localFilePath, sshSession);
                input.setValue("file:/" + localFilePath);
            }
        }
    } catch (IOException | JSchException | SSHApiException | URISyntaxException e) {
        log.error("Error while coping remote file " + remoteFilePath + " to local " + localFilePath, e);
        throw new GFacException("Error while scp input files to local file location", e);
    } catch (CredentialStoreException e) {
        String msg = "Authentication issue, make sure you are passing valid credential token";
        log.error(msg, e);
        throw new GFacException(msg, e);
    }
}

Example 7 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class DefaultJobSubmissionTask method cancel.

@Override
public JobStatus cancel(TaskContext taskcontext) throws TaskException {
    ProcessContext processContext = taskcontext.getParentProcessContext();
    RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
    JobModel jobModel = processContext.getJobModel();
    int retryCount = 0;
    if (jobModel != null) {
        if (processContext.getProcessState() == ProcessState.EXECUTING) {
            while (jobModel.getJobId() == null) {
                log.info("Cancellation pause {} secs until process get jobId", pauseTimeInSec);
                try {
                    Thread.sleep(waitForProcessIdmillis);
                } catch (InterruptedException e) {
                // ignore
                }
            }
        }
        try {
            JobStatus oldJobStatus = remoteCluster.getJobStatus(jobModel.getJobId());
            while (oldJobStatus == null && retryCount <= 5) {
                retryCount++;
                Thread.sleep(retryCount * 1000);
                oldJobStatus = remoteCluster.getJobStatus(jobModel.getJobId());
            }
            if (oldJobStatus != null) {
                oldJobStatus = remoteCluster.cancelJob(jobModel.getJobId());
                return oldJobStatus;
            } else {
                throw new TaskException("Cancel operation failed, Job status couldn't find in resource, JobId " + jobModel.getJobId());
            }
        } catch (GFacException | InterruptedException e) {
            throw new TaskException("Error while cancelling job " + jobModel.getJobId(), e);
        }
    } else {
        throw new TaskException("Couldn't complete cancel operation, JobModel is null in ProcessContext.");
    }
}

Example 8 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class ForkJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus taskStatus = new TaskStatus(TaskState.CREATED);
    try {
        ProcessContext processContext = taskContext.getParentProcessContext();
        JobModel jobModel = processContext.getJobModel();
        jobModel.setTaskId(taskContext.getTaskId());
        RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        jobModel.setJobName(groovyMap.get(Script.JOB_NAME).toString());
        ResourceJobManager resourceJobManager = GFacUtils.getResourceJobManager(processContext);
        JobManagerConfiguration jConfig = null;
        if (resourceJobManager != null) {
            jConfig = Factory.getJobManagerConfiguration(resourceJobManager);
        }
        JobStatus jobStatus = new JobStatus();
        File jobFile = GFacUtils.createJobFile(groovyMap, taskContext, jConfig);
        if (jobFile != null && jobFile.exists()) {
            jobModel.setJobDescription(FileUtils.readFileToString(jobFile));
            JobSubmissionOutput jobSubmissionOutput = remoteCluster.submitBatchJob(jobFile.getPath(), processContext.getWorkingDir());
            jobModel.setExitCode(jobSubmissionOutput.getExitCode());
            jobModel.setStdErr(jobSubmissionOutput.getStdErr());
            jobModel.setStdOut(jobSubmissionOutput.getStdOut());
            String jobId = jobSubmissionOutput.getJobId();
            if (jobId != null && !jobId.isEmpty()) {
                jobModel.setJobId(jobId);
                GFacUtils.saveJobModel(processContext, jobModel);
                jobStatus.setJobState(JobState.SUBMITTED);
                jobStatus.setReason("Successfully Submitted to " + taskContext.getParentProcessContext().getComputeResourceDescription().getHostName());
                jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                jobModel.setJobStatuses(Arrays.asList(jobStatus));
                GFacUtils.saveJobStatus(taskContext.getParentProcessContext(), jobModel);
                taskStatus = new TaskStatus(TaskState.COMPLETED);
                taskStatus.setReason("Submitted job to compute resource");
            }
            if (jobId == null || jobId.isEmpty()) {
                String msg = "expId:" + processContext.getProcessModel().getExperimentId() + " Couldn't find " + "remote jobId for JobName:" + jobModel.getJobName() + ", both submit and verify steps " + "doesn't return a valid JobId. " + "Hence changing experiment state to Failed";
                log.error(msg);
                ErrorModel errorModel = new ErrorModel();
                errorModel.setActualErrorMessage(msg);
                errorModel.setCreationTime(AiravataUtils.getCurrentTimestamp().getTime());
                GFacUtils.saveExperimentError(processContext, errorModel);
                GFacUtils.saveProcessError(processContext, errorModel);
                GFacUtils.saveTaskError(taskContext, errorModel);
                taskStatus.setState(TaskState.FAILED);
                taskStatus.setReason("Couldn't find job id in both submitted and verified steps");
            } else {
                GFacUtils.saveJobModel(processContext, jobModel);
            }
        } else {
            taskStatus.setState(TaskState.FAILED);
            if (jobFile == null) {
                taskStatus.setReason("JobFile is null");
            } else {
                taskStatus.setReason("Job file doesn't exist");
            }
        }
    } catch (ApplicationSettingsException e) {
        String msg = "Error occurred while creating job descriptor";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (AppCatalogException e) {
        String msg = "Error while instantiating app catalog";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (GFacException e) {
        String msg = "Error occurred while submitting the job";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (IOException e) {
        String msg = "Error while reading the content of the job file";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    return taskStatus;
}

Example 9 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class LocalJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus taskStatus = new TaskStatus(TaskState.CREATED);
    try {
        ProcessContext processContext = taskContext.getParentProcessContext();
        JobModel jobModel = processContext.getJobModel();
        jobModel.setTaskId(taskContext.getTaskId());
        RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        String jobId = AiravataUtils.getId("JOB_ID_");
        jobModel.setJobName(groovyMap.get(Script.JOB_NAME).toString());
        jobModel.setJobId(jobId);
        ResourceJobManager resourceJobManager = GFacUtils.getResourceJobManager(processContext);
        JobManagerConfiguration jConfig = null;
        if (resourceJobManager != null) {
            jConfig = Factory.getJobManagerConfiguration(resourceJobManager);
        }
        JobStatus jobStatus = new JobStatus();
        File jobFile = GFacUtils.createJobFile(groovyMap, taskContext, jConfig);
        if (jobFile != null && jobFile.exists()) {
            jobModel.setJobDescription(FileUtils.readFileToString(jobFile));
            GFacUtils.saveJobModel(processContext, jobModel);
            JobSubmissionOutput jobSubmissionOutput = remoteCluster.submitBatchJob(jobFile.getPath(), processContext.getWorkingDir());
            jobStatus.setJobState(JobState.SUBMITTED);
            jobStatus.setReason("Successfully Submitted to " + taskContext.getParentProcessContext().getComputeResourceDescription().getHostName());
            jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
            jobModel.setJobStatuses(Arrays.asList(jobStatus));
            // log job submit status
            GFacUtils.saveJobStatus(taskContext.getParentProcessContext(), jobModel);
            // for local, job gets completed synchronously
            // so changing job status to complete
            jobModel.setExitCode(jobSubmissionOutput.getExitCode());
            jobModel.setStdErr(jobSubmissionOutput.getStdErr());
            jobModel.setStdOut(jobSubmissionOutput.getStdOut());
            jobModel.setJobId(jobId);
            jobStatus.setJobState(JobState.COMPLETE);
            jobStatus.setReason("Successfully Completed " + taskContext.getParentProcessContext().getComputeResourceDescription().getHostName());
            jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
            jobModel.setJobStatuses(Arrays.asList(jobStatus));
            // log job complete status
            GFacUtils.saveJobStatus(taskContext.getParentProcessContext(), jobModel);
            taskStatus = new TaskStatus(TaskState.COMPLETED);
            taskStatus.setReason("Submitted job to compute resource");
        } else {
            taskStatus.setState(TaskState.FAILED);
            if (jobFile == null) {
                taskStatus.setReason("JobFile is null");
            } else {
                taskStatus.setReason("Job file doesn't exist");
            }
        }
    } catch (GFacException | IOException | AppCatalogException | ApplicationSettingsException e) {
        String msg = "Error occurred while submitting a local job";
        log.error(msg, e);
        taskStatus.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
        taskStatus.setState(TaskState.FAILED);
    }
    return taskStatus;
}

Example 10 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class SCPDataStageTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus status = new TaskStatus(TaskState.EXECUTING);
    AuthenticationInfo authenticationInfo = null;
    DataStagingTaskModel subTaskModel = null;
    String localDataDir = null;
    ProcessContext processContext = taskContext.getParentProcessContext();
    ProcessState processState = processContext.getProcessState();
    try {
        subTaskModel = ((DataStagingTaskModel) taskContext.getSubTaskModel());
        if (processState == ProcessState.OUTPUT_DATA_STAGING) {
            OutputDataObjectType processOutput = taskContext.getProcessOutput();
            if (processOutput != null && processOutput.getValue() == null) {
                log.error("expId: {}, processId:{}, taskId: {}:- Couldn't stage file {} , file name shouldn't be null", taskContext.getExperimentId(), taskContext.getProcessId(), taskContext.getTaskId(), processOutput.getName());
                status = new TaskStatus(TaskState.FAILED);
                if (processOutput.isIsRequired()) {
                    status.setReason("File name is null, but this output's isRequired bit is not set");
                } else {
                    status.setReason("File name is null");
                }
                return status;
            }
        } else if (processState == ProcessState.INPUT_DATA_STAGING) {
            InputDataObjectType processInput = taskContext.getProcessInput();
            if (processInput != null && processInput.getValue() == null) {
                log.error("expId: {}, processId:{}, taskId: {}:- Couldn't stage file {} , file name shouldn't be null", taskContext.getExperimentId(), taskContext.getProcessId(), taskContext.getTaskId(), processInput.getName());
                status = new TaskStatus(TaskState.FAILED);
                if (processInput.isIsRequired()) {
                    status.setReason("File name is null, but this input's isRequired bit is not set");
                } else {
                    status.setReason("File name is null");
                }
                return status;
            }
        } else {
            status.setState(TaskState.FAILED);
            status.setReason("Invalid task invocation, Support " + ProcessState.INPUT_DATA_STAGING.name() + " and " + "" + ProcessState.OUTPUT_DATA_STAGING.name() + " process phases. found " + processState.name());
            return status;
        }
        StorageResourceDescription storageResource = processContext.getStorageResource();
        // StoragePreference storagePreference = taskContext.getParentProcessContext().getStoragePreference();
        String hostName = null;
        if (storageResource != null) {
            hostName = storageResource.getHostName();
        } else {
            throw new GFacException("Storage Resource is null");
        }
        String inputPath = processContext.getStorageFileSystemRootLocation();
        inputPath = (inputPath.endsWith(File.separator) ? inputPath : inputPath + File.separator);
        // use rsync instead of scp if source and destination host and user name is same.
        URI sourceURI = new URI(subTaskModel.getSource());
        String fileName = sourceURI.getPath().substring(sourceURI.getPath().lastIndexOf(File.separator) + 1, sourceURI.getPath().length());
        Session remoteSession = Factory.getSSHSession(Factory.getComputerResourceSSHKeyAuthentication(processContext), processContext.getComputeResourceServerInfo());
        Session storageSession = Factory.getSSHSession(Factory.getStorageSSHKeyAuthentication(processContext), processContext.getStorageResourceServerInfo());
        URI destinationURI = null;
        if (subTaskModel.getDestination().startsWith("dummy")) {
            destinationURI = TaskUtils.getDestinationURI(taskContext, hostName, inputPath, fileName);
            subTaskModel.setDestination(destinationURI.toString());
        } else {
            destinationURI = new URI(subTaskModel.getDestination());
        }
        if (sourceURI.getHost().equalsIgnoreCase(destinationURI.getHost()) && sourceURI.getUserInfo().equalsIgnoreCase(destinationURI.getUserInfo())) {
            localDataCopy(taskContext, sourceURI, destinationURI);
            status.setState(TaskState.COMPLETED);
            status.setReason("Locally copied file using 'cp' command ");
            return status;
        }
        status = new TaskStatus(TaskState.COMPLETED);
        // Wildcard for file name. Has to find the correct name.
        if (fileName.contains("*")) {
            String destParentPath = (new File(destinationURI.getPath())).getParentFile().getPath();
            String sourceParentPath = (new File(sourceURI.getPath())).getParentFile().getPath();
            List<String> fileNames = taskContext.getParentProcessContext().getDataMovementRemoteCluster().getFileNameFromExtension(fileName, sourceParentPath, remoteSession);
            ExperimentCatalog experimentCatalog = processContext.getExperimentCatalog();
            String experimentId = processContext.getExperimentId();
            String processId = processContext.getProcessId();
            OutputDataObjectType processOutput = taskContext.getProcessOutput();
            for (int i = 0; i < fileNames.size(); i++) {
                String temp = fileNames.get(i);
                if (temp != null && temp != "") {
                    fileName = temp;
                }
                if (destParentPath.endsWith(File.separator)) {
                    destinationURI = new URI(destParentPath + fileName);
                } else {
                    destinationURI = new URI(destParentPath + File.separator + fileName);
                }
                // Wildcard support is only enabled for output data staging
                if (processState == ProcessState.OUTPUT_DATA_STAGING) {
                    processOutput.setName(fileName);
                    experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_OUTPUT, Arrays.asList(processOutput), experimentId);
                    experimentCatalog.add(ExpCatChildDataType.PROCESS_OUTPUT, Arrays.asList(processOutput), processId);
                    taskContext.setProcessOutput(processOutput);
                    makeDir(taskContext, destinationURI);
                    // TODO - save updated subtask model with new destination
                    outputDataStaging(taskContext, remoteSession, sourceURI, storageSession, destinationURI);
                    status.setReason("Successfully staged output data");
                }
            }
            if (processState == ProcessState.OUTPUT_DATA_STAGING) {
                status.setReason("Successfully staged output data");
            } else {
                status.setReason("Wildcard support is only enabled for output data staging");
            }
        } else {
            if (processState == ProcessState.INPUT_DATA_STAGING) {
                inputDataStaging(taskContext, storageSession, sourceURI, remoteSession, destinationURI);
                status.setReason("Successfully staged input data");
            } else if (processState == ProcessState.OUTPUT_DATA_STAGING) {
                makeDir(taskContext, destinationURI);
                // TODO - save updated subtask model with new destination
                outputDataStaging(taskContext, remoteSession, sourceURI, storageSession, destinationURI);
                status.setReason("Successfully staged output data");
            }
        }
    } catch (TException e) {
        String msg = "Couldn't create subTask model thrift model";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
        return status;
    } catch (ApplicationSettingsException | FileNotFoundException e) {
        String msg = "Failed while reading credentials";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (URISyntaxException e) {
        String msg = "Source or destination uri is not correct source : " + subTaskModel.getSource() + ", " + "destination : " + subTaskModel.getDestination();
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (CredentialStoreException e) {
        String msg = "Storage authentication issue, could be invalid credential token";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (AiravataException e) {
        String msg = "Error while creating ssh session with client";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (JSchException | IOException e) {
        String msg = "Failed to do scp with client";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (RegistryException | GFacException e) {
        String msg = "Data staging failed";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    return status;
}