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

Example 6 with GFacException

use of org.apache.airavata.gfac.core.GFacException in project airavata by apache.

the class Factory method getSSHSession.

public static synchronized Session getSSHSession(AuthenticationInfo authenticationInfo, ServerInfo serverInfo) throws GFacException {
    if (authenticationInfo == null || serverInfo == null) {
        throw new IllegalArgumentException("Can't create ssh session, argument should be valid (not null)");
    }
    SSHKeyAuthentication authentication;
    if (authenticationInfo instanceof SSHKeyAuthentication) {
        authentication = (SSHKeyAuthentication) authenticationInfo;
    } else {
        throw new GFacException("Support ssh key authentication only");
    }
    String key = buildKey(serverInfo);
    Session session = sessionCache.getIfPresent(key);
    boolean valid = isValidSession(session);
    // FIXME - move following info logs to debug
    if (valid) {
        log.info("SSH Session validation succeeded, key :" + key);
        valid = testChannelCreation(session);
        if (valid) {
            log.info("Channel creation test succeeded, key :" + key);
        } else {
            log.info("Channel creation test failed, key :" + key);
        }
    } else {
        log.info("Session validation failed, key :" + key);
    }
    if (!valid) {
        if (session != null) {
            log.info("Reinitialize a new SSH session for :" + key);
        } else {
            log.info("Initialize a new SSH session for :" + key);
        }
        try {
            JSch jSch = new JSch();
            jSch.addIdentity(UUID.randomUUID().toString(), authentication.getPrivateKey(), authentication.getPublicKey(), authentication.getPassphrase().getBytes());
            session = jSch.getSession(serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
            session.setUserInfo(new DefaultUserInfo(serverInfo.getUserName(), null, authentication.getPassphrase()));
            if (authentication.getStrictHostKeyChecking().equals("yes")) {
                jSch.setKnownHosts(authentication.getKnownHostsFilePath());
            } else {
                session.setConfig("StrictHostKeyChecking", "no");
            }
            // 0 connection timeout
            session.connect();
            sessionCache.put(key, session);
        } catch (JSchException e) {
            throw new GFacException("JSch initialization error ", e);
        }
    } else {
        // FIXME - move following info log to debug
        log.info("Reuse SSH session for :" + key);
    }
    return session;
}

Example 7 with GFacException

use of org.apache.airavata.gfac.core.GFacException in project airavata by apache.

the class GFacEngineImpl method outputDataStaging.

/**
 * @param taskContext
 * @param recovery
 * @return <code>true</code> if process execution interrupted , <code>false</code> otherwise.
 * @throws GFacException
 */
private boolean outputDataStaging(TaskContext taskContext, boolean recovery, boolean isArchive) throws GFacException {
    TaskStatus taskStatus = new TaskStatus(TaskState.EXECUTING);
    taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
    taskContext.setTaskStatus(taskStatus);
    GFacUtils.saveAndPublishTaskStatus(taskContext);
    ProcessContext processContext = taskContext.getParentProcessContext();
    Task dMoveTask = null;
    if (isArchive) {
        dMoveTask = Factory.getArchiveTask();
    } else {
        dMoveTask = Factory.getDataMovementTask(processContext.getDataMovementProtocol());
    }
    if (null == dMoveTask) {
        throw new GFacException("Unsupported security protocol, Airavata doesn't support " + processContext.getDataMovementProtocol() + " protocol yet.");
    }
    taskStatus = executeTask(taskContext, dMoveTask, recovery);
    taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
    taskContext.setTaskStatus(taskStatus);
    GFacUtils.saveAndPublishTaskStatus(taskContext);
    if (taskStatus.getState() == TaskState.FAILED) {
        log.error("expId: {}, processId: {}, taskId: {} type: {},:- output staging failed, " + "reason:" + " {}", taskContext.getParentProcessContext().getExperimentId(), taskContext.getParentProcessContext().getProcessId(), taskContext.getTaskId(), dMoveTask.getType().name(), taskStatus.getReason());
        String errorMsg = new StringBuilder("expId: ").append(processContext.getExperimentId()).append(", processId: ").append(processContext.getProcessId()).append(", taskId: ").append(taskContext.getTaskId()).append(", type: ").append(taskContext.getTaskType().name()).append(" :- Output staging failed. Reason: ").append(taskStatus.getReason()).toString();
        ErrorModel errorModel = new ErrorModel();
        errorModel.setUserFriendlyMessage("Error while staging output data");
        errorModel.setActualErrorMessage(errorMsg);
        GFacUtils.saveTaskError(taskContext, errorModel);
    }
    return false;
}

Example 8 with GFacException

use of org.apache.airavata.gfac.core.GFacException in project airavata by apache.

the class GFacEngineImpl method executeCancel.

private void executeCancel(TaskContext taskContext, JobSubmissionTask jSTask) throws GFacException {
    try {
        JobStatus oldJobStatus = jSTask.cancel(taskContext);
        // If Job was in Queued state when cancel command runs, then there won't be any email from this job.
        ProcessContext pc = taskContext.getParentProcessContext();
        JobMonitor monitorService = Factory.getMonitorService(pc.getMonitorMode());
        monitorService.canceledJob(pc.getJobModel().getJobId());
    } catch (TaskException e) {
        throw new GFacException("Error while cancelling job");
    } catch (AiravataException e) {
        throw new GFacException("Error wile getting monitoring service");
    }
}

Example 9 with GFacException

use of org.apache.airavata.gfac.core.GFacException in project airavata by apache.

the class GFacEngineImpl method inputDataStaging.

private boolean inputDataStaging(TaskContext taskContext, boolean recover) throws GFacException, TException {
    TaskStatus taskStatus = new TaskStatus(TaskState.EXECUTING);
    taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
    taskContext.setTaskStatus(taskStatus);
    GFacUtils.saveAndPublishTaskStatus(taskContext);
    ProcessContext processContext = taskContext.getParentProcessContext();
    // handle URI_COLLECTION input data type
    Task dMoveTask = Factory.getDataMovementTask(processContext.getDataMovementProtocol());
    if (null == dMoveTask) {
        throw new GFacException("Unsupported security protocol, Airavata doesn't support " + processContext.getDataMovementProtocol() + " protocol yet.");
    }
    if (taskContext.getProcessInput().getType() == DataType.URI_COLLECTION) {
        String values = taskContext.getProcessInput().getValue();
        String[] multiple_inputs = values.split(GFacConstants.MULTIPLE_INPUTS_SPLITTER);
        DataStagingTaskModel subTaskModel = (DataStagingTaskModel) taskContext.getSubTaskModel();
        for (String input : multiple_inputs) {
            taskContext.getProcessInput().setValue(input);
            subTaskModel.setSource(input);
            taskStatus = executeTask(taskContext, dMoveTask, false);
        }
        taskContext.getProcessInput().setValue(values);
    } else {
        taskStatus = executeTask(taskContext, dMoveTask, false);
    }
    taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
    taskContext.setTaskStatus(taskStatus);
    GFacUtils.saveAndPublishTaskStatus(taskContext);
    checkFailures(taskContext, taskStatus, dMoveTask);
    return false;
}

Example 10 with GFacException

use of org.apache.airavata.gfac.core.GFacException in project airavata by apache.

the class GFacEngineImpl method executeTaskListFrom.

private void executeTaskListFrom(ProcessContext processContext, String startingTaskId) throws GFacException {
    // checkpoint
    if (processContext.isInterrupted() && processContext.getProcessState() != ProcessState.MONITORING) {
        GFacUtils.handleProcessInterrupt(processContext);
        return;
    }
    List<TaskModel> taskList = processContext.getTaskList();
    Map<String, TaskModel> taskMap = processContext.getTaskMap();
    boolean fastForward = true;
    for (String taskId : processContext.getTaskExecutionOrder()) {
        if (fastForward) {
            if (taskId.equalsIgnoreCase(startingTaskId)) {
                fastForward = false;
            } else {
                continue;
            }
        }
        TaskModel taskModel = taskMap.get(taskId);
        processContext.setCurrentExecutingTaskModel(taskModel);
        TaskTypes taskType = taskModel.getTaskType();
        TaskContext taskContext = getTaskContext(processContext);
        taskContext.setTaskModel(taskModel);
        ProcessStatus status = null;
        switch(taskType) {
            case ENV_SETUP:
                status = new ProcessStatus(ProcessState.CONFIGURING_WORKSPACE);
                status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                processContext.setProcessStatus(status);
                GFacUtils.saveAndPublishProcessStatus(processContext);
                // checkpoint
                if (processContext.isInterrupted()) {
                    GFacUtils.handleProcessInterrupt(processContext);
                    return;
                }
                configureWorkspace(taskContext, processContext.isRecovery());
                // checkpoint
                if (processContext.isInterrupted()) {
                    GFacUtils.handleProcessInterrupt(processContext);
                    return;
                }
                break;
            case DATA_STAGING:
                try {
                    // checkpoint
                    if (processContext.isInterrupted()) {
                        GFacUtils.handleProcessInterrupt(processContext);
                        return;
                    }
                    DataStagingTaskModel subTaskModel = (DataStagingTaskModel) taskContext.getSubTaskModel();
                    DataStageType type = subTaskModel.getType();
                    switch(type) {
                        case INPUT:
                            status = new ProcessStatus(ProcessState.INPUT_DATA_STAGING);
                            status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                            processContext.setProcessStatus(status);
                            GFacUtils.saveAndPublishProcessStatus(processContext);
                            taskContext.setProcessInput(subTaskModel.getProcessInput());
                            inputDataStaging(taskContext, processContext.isRecovery());
                            break;
                        case OUPUT:
                            status = new ProcessStatus(ProcessState.OUTPUT_DATA_STAGING);
                            status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                            processContext.setProcessStatus(status);
                            GFacUtils.saveAndPublishProcessStatus(processContext);
                            taskContext.setProcessOutput(subTaskModel.getProcessOutput());
                            outputDataStaging(taskContext, processContext.isRecovery(), false);
                            break;
                        case ARCHIVE_OUTPUT:
                            status = new ProcessStatus(ProcessState.OUTPUT_DATA_STAGING);
                            status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                            processContext.setProcessStatus(status);
                            GFacUtils.saveAndPublishProcessStatus(processContext);
                            outputDataStaging(taskContext, processContext.isRecovery(), true);
                            break;
                    }
                    // checkpoint
                    if (processContext.isInterrupted()) {
                        GFacUtils.handleProcessInterrupt(processContext);
                        return;
                    }
                } catch (TException e) {
                    throw new GFacException(e);
                }
                break;
            case JOB_SUBMISSION:
                // checkpoint
                if (processContext.isInterrupted()) {
                    GFacUtils.handleProcessInterrupt(processContext);
                    return;
                }
                status = new ProcessStatus(ProcessState.EXECUTING);
                status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                processContext.setProcessStatus(status);
                GFacUtils.saveAndPublishProcessStatus(processContext);
                executeJobSubmission(taskContext, processContext.isRecovery());
                // Don't put any checkpoint in between JobSubmission and Monitoring tasks
                JobStatus jobStatus = processContext.getJobModel().getJobStatuses().get(0);
                if (jobStatus != null && (jobStatus.getJobState() == JobState.SUBMITTED || jobStatus.getJobState() == JobState.QUEUED || jobStatus.getJobState() == JobState.ACTIVE)) {
                    List<OutputDataObjectType> processOutputs = processContext.getProcessModel().getProcessOutputs();
                    if (processOutputs != null && !processOutputs.isEmpty()) {
                        for (OutputDataObjectType output : processOutputs) {
                            try {
                                if (output.isOutputStreaming()) {
                                    TaskModel streamingTaskModel = new TaskModel();
                                    streamingTaskModel.setTaskType(TaskTypes.OUTPUT_FETCHING);
                                    streamingTaskModel.setTaskStatuses(Arrays.asList(new TaskStatus(TaskState.CREATED)));
                                    streamingTaskModel.setCreationTime(AiravataUtils.getCurrentTimestamp().getTime());
                                    streamingTaskModel.setParentProcessId(processContext.getProcessId());
                                    TaskContext streamingTaskContext = getTaskContext(processContext);
                                    DataStagingTaskModel submodel = new DataStagingTaskModel();
                                    submodel.setType(DataStageType.OUPUT);
                                    submodel.setProcessOutput(output);
                                    URI source = new URI(processContext.getDataMovementProtocol().name(), processContext.getComputeResourceLoginUserName(), processContext.getComputeResourceDescription().getHostName(), 22, processContext.getWorkingDir() + output.getValue(), null, null);
                                    submodel.setSource(source.getPath());
                                    submodel.setDestination("dummy://temp/file/location");
                                    streamingTaskModel.setSubTaskModel(ThriftUtils.serializeThriftObject(submodel));
                                    String streamTaskId = (String) processContext.getExperimentCatalog().add(ExpCatChildDataType.TASK, streamingTaskModel, processContext.getProcessId());
                                    streamingTaskModel.setTaskId(streamTaskId);
                                    streamingTaskContext.setTaskModel(streamingTaskModel);
                                    executeDataStreaming(streamingTaskContext, processContext.isRecovery());
                                }
                            } catch (URISyntaxException | TException | RegistryException e) {
                                log.error("Error while streaming output " + output.getValue());
                            }
                        }
                    }
                }
                break;
            case MONITORING:
                status = new ProcessStatus(ProcessState.MONITORING);
                status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
                processContext.setProcessStatus(status);
                GFacUtils.saveAndPublishProcessStatus(processContext);
                executeJobMonitoring(taskContext, processContext.isRecovery());
                break;
            case ENV_CLEANUP:
                // TODO implement environment clean up task logic
                break;
            default:
                throw new GFacException("Unsupported Task type");
        }
        if (processContext.isPauseTaskExecution()) {
            // If any task put processContext to wait, the same task must continue processContext execution.
            return;
        }
    }
    processContext.setComplete(true);
}