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

Example 31 with GFacException

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

the class SSHUtils method listDirectory.

public static List<String> listDirectory(String path, Session session) throws IOException, JSchException, GFacException {
    // exec 'scp -t rfile' remotely
    String command = "ls " + path;
    Channel channel = session.openChannel("exec");
    StandardOutReader stdOutReader = new StandardOutReader();
    ((ChannelExec) channel).setCommand(command);
    ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
    try {
        channel.connect();
    } catch (JSchException e) {
        channel.disconnect();
        throw new GFacException("Unable to retrieve command output. Command - " + command + " on server - " + session.getHost() + ":" + session.getPort() + " connecting user name - " + session.getUserName(), e);
    }
    stdOutReader.onOutput(channel);
    stdOutReader.getStdOutputString();
    if (stdOutReader.getStdErrorString().contains("ls:")) {
        throw new GFacException(stdOutReader.getStdErrorString());
    }
    channel.disconnect();
    return Arrays.asList(stdOutReader.getStdOutputString().split("\n"));
}

Example 32 with GFacException

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

the class SSHUtils method makeDirectory.

public static void makeDirectory(String path, Session session) throws IOException, JSchException, GFacException {
    // exec 'scp -t rfile' remotely
    String command = "mkdir -p " + path;
    Channel channel = session.openChannel("exec");
    StandardOutReader stdOutReader = new StandardOutReader();
    ((ChannelExec) channel).setCommand(command);
    ((ChannelExec) channel).setErrStream(stdOutReader.getStandardError());
    try {
        channel.connect();
    } catch (JSchException e) {
        channel.disconnect();
        // session.disconnect();
        log.error("Unable to retrieve command output. Command - " + command + " on server - " + session.getHost() + ":" + session.getPort() + " connecting user name - " + session.getUserName());
        throw e;
    }
    stdOutReader.onOutput(channel);
    if (stdOutReader.getStdErrorString().contains("mkdir:")) {
        throw new GFacException(stdOutReader.getStdErrorString());
    }
    channel.disconnect();
}

Example 33 with GFacException

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

the class ArchiveTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    // implement archive logic with jscp
    TaskStatus status = new TaskStatus(TaskState.EXECUTING);
    ProcessContext processContext = taskContext.getParentProcessContext();
    RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
    AuthenticationInfo authenticationInfo = null;
    DataStagingTaskModel subTaskModel = null;
    try {
        subTaskModel = (DataStagingTaskModel) ThriftUtils.getSubTaskModel(taskContext.getTaskModel());
    } catch (TException e) {
        String msg = "Error! Deserialization issue with SubTask 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;
    }
    try {
        StorageResourceDescription storageResource = taskContext.getParentProcessContext().getStorageResource();
        if (storageResource != null) {
            hostName = storageResource.getHostName();
        } else {
            throw new GFacException("Storage Resource is null");
        }
        userName = processContext.getStorageResourceLoginUserName();
        inputPath = processContext.getStorageFileSystemRootLocation();
        inputPath = (inputPath.endsWith(File.separator) ? inputPath : inputPath + File.separator);
        status = new TaskStatus(TaskState.COMPLETED);
        Session srcSession = Factory.getSSHSession(Factory.getComputerResourceSSHKeyAuthentication(processContext), processContext.getComputeResourceServerInfo());
        Session destSession = Factory.getSSHSession(Factory.getStorageSSHKeyAuthentication(processContext), processContext.getStorageResourceServerInfo());
        URI sourceURI = new URI(subTaskModel.getSource());
        URI destinationURI = null;
        String workingDirName = null, path = null;
        if (sourceURI.getPath().endsWith("/")) {
            path = sourceURI.getPath().substring(0, sourceURI.getPath().length() - 1);
        } else {
            path = sourceURI.getPath();
        }
        workingDirName = path.substring(path.lastIndexOf(File.separator) + 1, path.length());
        // tar working dir
        // cd /Users/syodage/Desktop/temp/.. && tar -cvf path/workingDir.tar temp
        String archiveTar = "archive.tar";
        String resourceAbsTarFilePath = path + "/" + archiveTar;
        CommandInfo commandInfo = new RawCommandInfo("cd " + path + " && tar -cvf " + resourceAbsTarFilePath + " ./* ");
        // move tar to storage resource
        remoteCluster.execute(commandInfo);
        destinationURI = TaskUtils.getDestinationURI(taskContext, hostName, inputPath, archiveTar);
        remoteCluster.scpThirdParty(resourceAbsTarFilePath, srcSession, destinationURI.getPath(), destSession, RemoteCluster.DIRECTION.FROM, true);
        // delete tar in remote computer resource
        commandInfo = new RawCommandInfo("rm " + resourceAbsTarFilePath);
        remoteCluster.execute(commandInfo);
        // untar file and delete tar in storage resource
        String destPath = destinationURI.getPath();
        String destParent = destPath.substring(0, destPath.lastIndexOf("/"));
        String storageArchiveDir = "ARCHIVE";
        commandInfo = new RawCommandInfo("cd " + destParent + " && mkdir " + storageArchiveDir + " && tar -xvf " + archiveTar + " -C " + storageArchiveDir + " && rm " + archiveTar + " && chmod 755 -R " + storageArchiveDir + "/*");
        executeCommand(destSession, commandInfo, new StandardOutReader());
    } catch (CredentialStoreException e) {
        String msg = "Storage authentication issue, make sure you are passing valid credential token";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (URISyntaxException | GFacException e) {
        String msg = "Error! Archive task failed";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    return status;
}

Example 34 with GFacException

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

the class AuroraJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    // set to completed.
    TaskStatus taskStatus = new TaskStatus(TaskState.COMPLETED);
    ProcessContext processContext = taskContext.getParentProcessContext();
    JobModel jobModel = processContext.getJobModel();
    jobModel.setTaskId(taskContext.getTaskId());
    String jobIdAndName = "A" + GFacUtils.generateJobName();
    jobModel.setJobName(jobIdAndName);
    JobStatus jobStatus = new JobStatus();
    jobStatus.setJobState(JobState.SUBMITTED);
    try {
        JobKeyBean jobKey = new JobKeyBean(AuroraUtils.ENVIRONMENT, AuroraUtils.ROLE, jobIdAndName);
        IdentityBean owner = new IdentityBean(AuroraUtils.ROLE);
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        groovyMap.add(Script.JOB_SUBMITTER_COMMAND, "sh");
        String templateFileName = GFacUtils.getTemplateFileName(ResourceJobManagerType.CLOUD);
        String script = GFacUtils.generateScript(groovyMap, templateFileName);
        Set<ProcessBean> processes = new LinkedHashSet<>();
        ProcessBean process_1 = new ProcessBean("main_process", script, false);
        processes.add(process_1);
        groovyMap.getStringValue(Script.STANDARD_OUT_FILE).ifPresent(stdout -> {
            ProcessBean stdOutProcess = new ProcessBean("stdout_copy_process", "cp .logs/main_process/0/stdout " + stdout, false);
            processes.add(stdOutProcess);
        });
        groovyMap.getStringValue(Script.STANDARD_ERROR_FILE).ifPresent(stderr -> {
            ProcessBean stdErrProcess = new ProcessBean("stderr_copy_process", "cp .logs/main_process/0/stderr " + stderr, false);
            processes.add(stdErrProcess);
        });
        ResourceBean resources = new ResourceBean(1.5, 512, 512);
        TaskConfigBean taskConfig = new TaskConfigBean("Airavata-Aurora-" + jobIdAndName, processes, resources);
        JobConfigBean jobConfig = new JobConfigBean(jobKey, owner, taskConfig, AuroraUtils.CLUSTER);
        String executorConfigJson = AuroraThriftClientUtil.getExecutorConfigJson(jobConfig);
        log.info("Executor Config for Job {} , {}", jobIdAndName, executorConfigJson);
        AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient();
        ResponseBean response = client.createJob(jobConfig);
        log.info("Response for job {}, {}", jobIdAndName, response);
        jobModel.setJobDescription(resources.toString());
        jobModel.setJobId(jobIdAndName);
        jobStatus.setReason("Successfully Submitted");
        jobModel.setJobStatuses(Arrays.asList(jobStatus));
        jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        taskContext.getParentProcessContext().setJobModel(jobModel);
        GFacUtils.saveJobModel(processContext, jobModel);
        GFacUtils.saveJobStatus(processContext, jobModel);
        taskStatus.setReason("Successfully submitted job to Aurora");
    } catch (Throwable e) {
        String msg = "Error occurred while submitting Aurora job";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    taskContext.setTaskStatus(taskStatus);
    try {
        GFacUtils.saveAndPublishTaskStatus(taskContext);
    } catch (GFacException e) {
        log.error("Error while saving task status", e);
    }
    return taskStatus;
}

Example 35 with GFacException

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

the class SecurityUtils method getSecurityContext.

public static UNICORESecurityContext getSecurityContext(ProcessContext processContext) throws GFacException {
    if (processContext.getJobSubmissionProtocol().equals(JobSubmissionProtocol.UNICORE)) {
        // set by the framework
        String credentialStoreToken = processContext.getTokenId();
        RequestData requestData;
        requestData = new RequestData(processContext.getProcessModel().getUserDn());
        requestData.setTokenId(credentialStoreToken);
        CredentialReader credentialReader = null;
        try {
            credentialReader = GFacUtils.getCredentialReader();
            if (credentialReader == null) {
                throw new GFacException("Credential reader returns null");
            }
        } catch (Exception e) {
            throw new GFacException("Error while initializing credential reader");
        }
        return new UNICORESecurityContext(credentialReader, requestData);
    } else {
        throw new GFacException("Only support UNICORE job submissions, invalid job submission protocol " + processContext.getJobSubmissionProtocol().name());
    }
}