Examples with OutputDataObjectType org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType used on opensource projects

Example 1 with OutputDataObjectType

use of org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType in project airavata by apache.

the class DataTransferrer method downloadRemoteFiles.

/**
 * This method will download all the remote files specified in the output
 * context of a job.
 */
public void downloadRemoteFiles() throws GFacProviderException {
    String downloadLocation = getDownloadLocation();
    File file = new File(downloadLocation);
    if (!file.exists()) {
        file.mkdirs();
    }
    Map<String, Object> output = jobContext.getOutMessageContext().getParameters();
    Set<String> keys = output.keySet();
    for (String outPrm : keys) {
        OutputDataObjectType actualParameter = (OutputDataObjectType) output.get(outPrm);
        if (DataType.STDERR == actualParameter.getType())
            continue;
        if (DataType.STDOUT == actualParameter.getType())
            continue;
        String value = actualParameter.getValue();
        FileDownloader fileDownloader = new FileDownloader(value, downloadLocation, Mode.overwrite);
        try {
            fileDownloader.perform(storageClient);
            String outputPath = downloadLocation + File.separator + value.substring(value.lastIndexOf('/') + 1);
            actualParameter.setValue(outputPath);
            actualParameter.setType(DataType.URI);
            jobContext.addOutputFile(outputPath);
        } catch (Exception e) {
            throw new GFacProviderException(e.getLocalizedMessage(), e);
        }
    }
    downloadStdOuts();
}

Example 2 with OutputDataObjectType

use of org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType in project airavata by apache.

the class LaunchApplicationWindow method execute.

private void execute() throws AiravataClientConnectException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException {
    List<NodeImpl> nodes = workflow.getGraph().getNodes();
    String gatewayId = engine.getConfiguration().getThriftClientData(ThriftServiceType.API_SERVICE).getGatewayId();
    String appId = null;
    NodeImpl node = null;
    for (int i = 0; i < nodes.size(); i++) {
        node = nodes.get(i);
        String html = node.getComponent().toHTML();
        String nodeType = html.substring(html.indexOf("<h1>") + 4, html.indexOf(":")).trim();
        if (nodeType.equals("Application")) {
            appId = html.substring(html.indexOf("</h2>") + 6, html.indexOf("<br")).trim();
            break;
        }
    }
    String hostId = null;
    String hostName = (String) host.getSelectedItem();
    hostId = hostNames.get(hostName);
    String instanceName = this.instanceNameTextField.getText();
    if (instanceName.trim().equals("")) {
        JOptionPane.showMessageDialog(engine.getGUI().getFrame(), "Experiment name cannot be empty", "Experiment Name", JOptionPane.ERROR_MESSAGE);
        return;
    }
    // previous instance name
    if (!instanceNameTextField.getText().equals("")) {
        this.instanceNameTextField.setText("");
    }
    Project project = new Project();
    project.setName("project1");
    String owner = this.thriftClientData.getUsername();
    if (owner.equals(""))
        owner = "NotKnown";
    project.setOwner(owner);
    project.setProjectID(airavataClient.createProject(gatewayId, project));
    // final List<InputNode> inputNodes = GraphUtil.getInputNodes(this.workflow.getGraph());
    final List<DataPort> inputPorts = node.getInputPorts();
    final Experiment experiment = new Experiment();
    experiment.setApplicationId(appId);
    ComputationalResourceScheduling scheduling = new ComputationalResourceScheduling();
    scheduling.setResourceHostId(hostId);
    if (hostName.trim().equals("trestles.sdsc.xsede.org")) {
        scheduling.setComputationalProjectAccount("sds128");
    } else if (hostName.trim().equals("stampede.tacc.xsede.org")) {
        scheduling.setComputationalProjectAccount("TG-STA110014S");
    }
    scheduling.setNodeCount(1);
    scheduling.setTotalCPUCount(1);
    scheduling.setWallTimeLimit(15);
    scheduling.setQueueName("normal");
    UserConfigurationData userConfigurationData = new UserConfigurationData();
    userConfigurationData.setAiravataAutoSchedule(false);
    userConfigurationData.setOverrideManualScheduledParams(false);
    userConfigurationData.setComputationalResourceScheduling(scheduling);
    experiment.setUserConfigurationData(userConfigurationData);
    experiment.setName(instanceName);
    experiment.setProjectID(project.getProjectID());
    experiment.setUserName(thriftClientData.getUsername());
    for (int i = 0; i < inputPorts.size(); i++) {
        DataPort inputPort = inputPorts.get(i);
        XBayaTextField parameterTextField = this.parameterTextFields.get(i);
        String value = parameterTextField.getText();
        InputDataObjectType elem = new InputDataObjectType();
        elem.setName(inputPort.getName());
        elem.setType(elem.getType());
        elem.setValue(value);
        experiment.addToExperimentInputs(elem);
    }
    final List<DataPort> outputPorts = node.getOutputPorts();
    for (int i = 0; i < outputPorts.size(); i++) {
        DataPort outputPort = outputPorts.get(i);
        OutputDataObjectType elem = new OutputDataObjectType();
        elem.setName(outputPort.getName());
        elem.setType(elem.getType());
        elem.setValue("");
        experiment.addToExperimentOutputs(elem);
    }
    experiment.setExperimentID(airavataClient.createExperiment(gatewayId, experiment));
    airavataClient.launchExperiment(experiment.getExperimentID(), "testToken");
    hide();
    JOptionPane.showMessageDialog(null, "Experiment Launched. You will be alerted on completion.");
    String status = airavataClient.getExperimentStatus(experiment.getExperimentID()).getExperimentState().toString().trim();
    while (!status.equals("COMPLETED") && !status.equals("FAILED")) {
        try {
            Thread.sleep(1000);
            status = airavataClient.getExperimentStatus(experiment.getExperimentID()).getExperimentState().toString().trim();
        } catch (InterruptedException e) {
            logger.error(e.getMessage(), e);
        }
    }
    try {
        Thread.sleep(1000);
    } catch (InterruptedException e) {
        logger.error(e.getMessage(), e);
    }
    if (status.equals("COMPLETED")) {
        String output = "";
        ;
        String fullOutput = "";
        while (output.equals("")) {
            output = "";
            fullOutput = "Experiment Completed Successfully. Output(s) are shown below:\n";
            List<OutputDataObjectType> outputs = airavataClient.getExperimentOutputs(experiment.getExperimentID());
            for (int i1 = 0; i1 < outputs.size(); i1++) {
                output = outputs.get(i1).getValue();
                fullOutput += outputs.get(i1).getName() + ": " + output + "\n";
            }
        }
        JOptionPane.showMessageDialog(null, fullOutput);
    } else {
        JOptionPane.showMessageDialog(null, "Experiment Failed");
        return;
    }
    new Thread() {

        @Override
        public void run() {
        }
    }.start();
    hide();
}

Example 3 with OutputDataObjectType

use of org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType in project airavata by apache.

the class WorkflowInterpreterLaunchWindow method execute.

private void execute() throws AiravataClientConnectException, TException {
    String instanceName = this.instanceNameTextField.getText();
    if (instanceName.trim().equals("")) {
        JOptionPane.showMessageDialog(engine.getGUI().getFrame(), "Experiment name cannot be empty", "Experiment Name", JOptionPane.ERROR_MESSAGE);
        return;
    }
    ThriftClientData thriftClientData = engine.getConfiguration().getThriftClientData(ThriftServiceType.API_SERVICE);
    Client airavataClient = XBayaUtil.getAiravataClient(thriftClientData);
    String gatewayId = engine.getConfiguration().getThriftClientData(ThriftServiceType.API_SERVICE).getGatewayId();
    final List<InputNode> inputNodes = GraphUtil.getInputNodes(this.workflow.getGraph());
    List<InputDataObjectType> inputDataTypes = new ArrayList<InputDataObjectType>();
    List<OutputDataObjectType> outputDataTypes = new ArrayList<OutputDataObjectType>();
    InputDataObjectType input = null;
    for (int i = 0; i < inputNodes.size(); i++) {
        InputNode inputNode = inputNodes.get(i);
        XBayaTextField parameterTextField = this.parameterTextFields.get(i);
        inputNode.getID();
        String value = parameterTextField.getText();
        input = new InputDataObjectType();
        // inputNode.setDefaultValue(value);
        input.setName(inputNode.getID());
        input.setType(inputNode.getDataType());
        input.setValue(value);
        input.setApplicationArgument(inputNode.getApplicationArgument());
        input.setInputOrder(inputNode.getInputOrder());
        inputDataTypes.add(input);
    }
    final List<OutputNode> outputNodes = GraphUtil.getOutputNodes(this.workflow.getGraph());
    OutputDataObjectType output = null;
    for (OutputNode outputNode : outputNodes) {
        output = new OutputDataObjectType();
        output.setName(outputNode.getID());
        output.setType(DataType.STRING);
        outputDataTypes.add(output);
    }
    Workflow workflowClone = workflow.clone();
    workflowClone.setName(workflowClone.getName() + UUID.randomUUID().toString());
    org.apache.airavata.model.Workflow workflowModel = new org.apache.airavata.model.Workflow();
    workflowModel.setName(workflowClone.getName());
    workflowModel.setGraph(JSONUtil.jsonElementToString(workflowClone.toJSON()));
    for (InputDataObjectType inputDataType : inputDataTypes) {
        workflowModel.addToWorkflowInputs(inputDataType);
    }
    for (OutputDataObjectType outputDataType : outputDataTypes) {
        workflowModel.addToWorkflowOutputs(outputDataType);
    }
    workflowModel.setTemplateId(airavataClient.registerWorkflow(gatewayId, workflowModel));
    // Use topic as a base of workflow instance ID so that the monitor can
    // find it.
    Project project = new Project();
    project.setName("project1");
    project.setOwner(thriftClientData.getUsername());
    project.setProjectID(airavataClient.createProject(gatewayId, project));
    final Experiment experiment = new Experiment();
    experiment.setApplicationId(workflowModel.getTemplateId());
    experiment.setName(instanceName);
    experiment.setProjectID(project.getProjectID());
    experiment.setUserName(thriftClientData.getUsername());
    for (InputDataObjectType inputDataType : inputDataTypes) {
        experiment.addToExperimentInputs(inputDataType);
    }
    for (OutputDataObjectType outputDataType : outputDataTypes) {
        experiment.addToExperimentOutputs(outputDataType);
    }
    // Add scheduling configurations
    if (host != null && host.getSelectedIndex() >= 0) {
        String selectedHostName = host.getSelectedItem().toString();
        String computeResouceId = hostNames.get(selectedHostName);
        ComputationalResourceScheduling computationalResourceScheduling;
        if (selectedHostName.equals("localhost")) {
            computationalResourceScheduling = ExperimentModelUtil.createComputationResourceScheduling(computeResouceId, 1, 1, 1, "normal", 1, 0, 1, "test");
        } else if (selectedHostName.equals("trestles.sdsc.xsede.org")) {
            computationalResourceScheduling = ExperimentModelUtil.createComputationResourceScheduling(computeResouceId, 1, 1, 1, "normal", 1, 0, 1, "sds128");
        } else if (selectedHostName.equals("stampede.tacc.xsede.org")) {
            computationalResourceScheduling = ExperimentModelUtil.createComputationResourceScheduling(computeResouceId, 2, 32, 1, "development", 90, 0, 1, "TG-STA110014S");
        } else if (selectedHostName.equals("bigred2.uits.iu.edu")) {
            computationalResourceScheduling = ExperimentModelUtil.createComputationResourceScheduling(computeResouceId, 1, 1, 1, "normal", 1, 0, 1, null);
        } else {
            // TODO handle for other computer resources too.
            throw new IllegalArgumentException("Computational resource scheduling is not configured for host :" + computeResouceId);
        }
        UserConfigurationData userConfigurationData = new UserConfigurationData();
        userConfigurationData.setAiravataAutoSchedule(false);
        userConfigurationData.setOverrideManualScheduledParams(false);
        userConfigurationData.setComputationalResourceScheduling(computationalResourceScheduling);
        experiment.setUserConfigurationData(userConfigurationData);
    } else {
        throw new RuntimeException("Resource scheduling failed, target computer resource host name is not defined");
    }
    /*
// code snippet for load test.
        for (int i = 0; i < 20; i++) {
            experiment.setName(instanceName + "_" + i);

            experiment.setExperimentID(airavataClient.createExperiment(experiment));

            try {
                this.engine.getMonitor().subscribe(experiment.getExperimentID());
                this.engine.getMonitor().fireStartMonitoring(workflow.getName());
            } catch (MonitorException e) {
                logger.error("Error while subscribing with experiment Id : " + experiment.getExperimentID(), e);
            }
            airavataClient.launchExperiment(experiment.getExperimentID(), "testToken");

        }*/
    experiment.setExperimentID(airavataClient.createExperiment(gatewayId, experiment));
    try {
        this.engine.getMonitor().subscribe(experiment.getExperimentID());
        this.engine.getMonitor().fireStartMonitoring(workflow.getName());
    } catch (MonitorException e) {
        logger.error("Error while subscribing with experiment Id : " + experiment.getExperimentID(), e);
    }
    airavataClient.launchExperiment(experiment.getExperimentID(), token.getText());
    clean();
    hide();
}

Example 4 with OutputDataObjectType

use of org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType in project airavata by apache.

the class DataTransferrer method extractOutParams.

public List<String> extractOutParams(JobExecutionContext context) {
    List<String> outPrmsList = new ArrayList<String>();
    List<OutputDataObjectType> applicationOutputs = jobContext.getTaskData().getApplicationOutputs();
    if (applicationOutputs != null && !applicationOutputs.isEmpty()) {
        for (OutputDataObjectType output : applicationOutputs) {
            if (output.getType().equals(DataType.STRING)) {
                outPrmsList.add(output.getValue());
            } else if (output.getType().equals(DataType.FLOAT) || output.getType().equals(DataType.INTEGER)) {
                outPrmsList.add(String.valueOf(output.getValue()));
            }
        }
    }
    return outPrmsList;
}