Examples with OutputDataObjectType org.apache.airavata.model.application.io.OutputDataObjectType used on opensource projects

Example 21 with OutputDataObjectType

use of org.apache.airavata.model.application.io.OutputDataObjectType in project airavata by apache.

the class CreateLaunchExperiment method createExperimentESPRESSOStampede.

public static String createExperimentESPRESSOStampede(Airavata.Client client) throws TException {
    try {
        List<InputDataObjectType> exInputs = client.getApplicationInputs(new AuthzToken(""), espressoAppId);
        setESPRESSOInputs(exInputs);
        List<OutputDataObjectType> exOut = client.getApplicationOutputs(new AuthzToken(""), espressoAppId);
        ExperimentModel simpleExperiment = ExperimentModelUtil.createSimpleExperiment(DEFAULT_GATEWAY, "default", "admin", "EspressoExperiment", "Testing", espressoAppId, exInputs);
        simpleExperiment.setExperimentOutputs(exOut);
        Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(new AuthzToken(""), espressoAppId);
        if (computeResources != null && computeResources.size() != 0) {
            for (String id : computeResources.keySet()) {
                String resourceName = computeResources.get(id);
                if (resourceName.equals(stampedeHostName)) {
                    ComputationalResourceSchedulingModel scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 1);
                    UserConfigurationDataModel userConfigurationData = new UserConfigurationDataModel();
                    userConfigurationData.setAiravataAutoSchedule(false);
                    userConfigurationData.setOverrideManualScheduledParams(false);
                    userConfigurationData.setComputationalResourceScheduling(scheduling);
                    simpleExperiment.setUserConfigurationData(userConfigurationData);
                    return client.createExperiment(new AuthzToken(""), DEFAULT_GATEWAY, simpleExperiment);
                }
            }
        }
    } catch (AiravataSystemException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new AiravataSystemException(e);
    } catch (InvalidRequestException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new InvalidRequestException(e);
    } catch (AiravataClientException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new AiravataClientException(e);
    } catch (TException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new TException(e);
    }
    return null;
}

Example 22 with OutputDataObjectType

use of org.apache.airavata.model.application.io.OutputDataObjectType in project airavata by apache.

the class CreateLaunchExperimentUS3 method createUS3ExperimentForTrestles.

public static String createUS3ExperimentForTrestles(Airavata.Client client) throws AiravataSystemException, InvalidRequestException, AiravataClientException, TException {
    try {
        List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
        InputDataObjectType input = new InputDataObjectType();
        input.setName("input");
        input.setType(DataType.URI);
        input.setValue("file:///home/sgg/chathuri/laptop_backup/airavata/ultrascan_input/hpcinput.tar");
        InputDataObjectType input1 = new InputDataObjectType();
        input1.setName("walltime");
        input1.setType(DataType.STRING);
        input1.setValue("-walltime=60");
        InputDataObjectType input2 = new InputDataObjectType();
        input2.setName("mgroupcount");
        input2.setType(DataType.STRING);
        input2.setValue("-mgroupcount=1");
        exInputs.add(input);
        exInputs.add(input1);
        exInputs.add(input2);
        List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
        OutputDataObjectType output = new OutputDataObjectType();
        output.setName("output");
        output.setType(DataType.URI);
        output.setValue("");
        // OutputDataObjectType output1 = new OutputDataObjectType();
        // output1.setName("stdout");
        // output1.setType(DataType.STDOUT);
        // output1.setValue("");
        // OutputDataObjectType output2 = new OutputDataObjectType();
        // output2.setName("stderr");
        // output2.setType(DataType.STDERR);
        // output2.setValue("");
        exOut.add(output);
        // exOut.add(output1);
        // exOut.add(output2);
        Project project = ProjectModelUtil.createProject("ultrascan", "ultrascan", "test project");
        String projectId = client.createProject(new AuthzToken(""), DEFAULT_GATEWAY, project);
        ExperimentModel simpleExperiment = ExperimentModelUtil.createSimpleExperiment(DEFAULT_GATEWAY, projectId, "ultrascan", "US3ExperimentTrestles", "US3AppTrestles", "ultrascan_7ce6cd43-622c-44e0-87c5-fb7a6528c799", exInputs);
        simpleExperiment.setExperimentOutputs(exOut);
        ComputationalResourceSchedulingModel scheduling = ExperimentModelUtil.createComputationResourceScheduling("trestles.sdsc.xsede.org_72b9181b-7156-4975-a386-ed98b4949496", 32, 1, 0, "shared", 30, 0);
        UserConfigurationDataModel userConfigurationData = new UserConfigurationDataModel();
        scheduling.setResourceHostId("trestles.sdsc.xsede.org_72b9181b-7156-4975-a386-ed98b4949496");
        userConfigurationData.setAiravataAutoSchedule(false);
        userConfigurationData.setOverrideManualScheduledParams(false);
        /*          AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling();
            dataHandling.setOutputDataDir("/home/sgg/chathuri/laptop_backup/airavata");
            userConfigurationData.setAdvanceOutputDataHandling(dataHandling);*/
        userConfigurationData.setComputationalResourceScheduling(scheduling);
        simpleExperiment.setUserConfigurationData(userConfigurationData);
        return client.createExperiment(new AuthzToken(""), DEFAULT_GATEWAY, simpleExperiment);
    } catch (AiravataSystemException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new AiravataSystemException(e);
    } catch (InvalidRequestException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new InvalidRequestException(e);
    } catch (AiravataClientException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new AiravataClientException(e);
    } catch (TException e) {
        logger.error("Error occured while creating the experiment...", e.getMessage());
        throw new TException(e);
    }
}

Example 23 with OutputDataObjectType

use of org.apache.airavata.model.application.io.OutputDataObjectType in project airavata by apache.

the class RegisterSampleApplications method registerGromacsInterface.

public void registerGromacsInterface() {
    try {
        System.out.println("#### Registering Gromacs Interface #### \n");
        List<String> appModules = new ArrayList<String>();
        appModules.add(gromacsModuleId);
        InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Portable_Input_Binary_File", null, DataType.URI, null, 1, true, true, false, "Coordinates velocities, molecular topology and simulation parameters - pdb1y6l-EM-vacuum.tpr", null);
        InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("GROMOS_Coordinate_File", null, DataType.URI, null, 2, true, true, false, "Trajectory Coordinates Molecular Structure in Gromos87 format - pdb1y6l-EM-vacuum.gro", null);
        List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
        applicationInputs.add(input1);
        applicationInputs.add(input2);
        OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("GROMACS_Execution_Log", null, DataType.URI, true, true, null);
        OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Full_Precision_Trajectory_file", null, DataType.URI, true, true, null);
        OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("Portable_Energy_file", null, DataType.URI, true, true, null);
        OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT", null, DataType.STDOUT, true, true, null);
        OutputDataObjectType output5 = RegisterSampleApplicationsUtils.createAppOutput("STDERR", null, DataType.STDERR, true, true, null);
        List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
        applicationOutputs.add(output1);
        applicationOutputs.add(output2);
        applicationOutputs.add(output3);
        applicationOutputs.add(output4);
        applicationOutputs.add(output5);
        gromacsInterfaceId = airavataClient.registerApplicationInterface(new AuthzToken(""), DEFAULT_GATEWAY, RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(gromacsName, gromacsDescription, appModules, applicationInputs, applicationOutputs));
        System.out.println("Gromacs Application Interface Id " + gromacsInterfaceId);
    } catch (TException e) {
        e.printStackTrace();
    }
}

Example 24 with OutputDataObjectType

use of org.apache.airavata.model.application.io.OutputDataObjectType in project airavata by apache.

the class RegisterSampleApplications method registerTrinityInterface.

public void registerTrinityInterface() {
    try {
        System.out.println("#### Registering Trinity Interface #### \n");
        List<String> appModules = new ArrayList<String>();
        appModules.add(trinityModuleId);
        InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Left_Input", null, DataType.URI, null, 1, true, true, false, "RNA-Seq Left Library - reads.left.fq", null);
        InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Right_Input", null, DataType.URI, null, 2, true, true, false, "RNA-Seq Right Library - reads.right.fq", null);
        List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
        applicationInputs.add(input1);
        applicationInputs.add(input2);
        OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_Execution_Log", null, DataType.URI, true, true, null);
        OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_FASTA_File", null, DataType.URI, true, true, null);
        OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT", null, DataType.STDOUT, true, true, null);
        OutputDataObjectType output4 = RegisterSampleApplicationsUtils.createAppOutput("STDERR", null, DataType.STDERR, true, true, null);
        List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
        applicationOutputs.add(output1);
        applicationOutputs.add(output2);
        applicationOutputs.add(output3);
        applicationOutputs.add(output4);
        trinityInterfaceId = airavataClient.registerApplicationInterface(new AuthzToken(""), DEFAULT_GATEWAY, RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(trinityName, trinityDescription, appModules, applicationInputs, applicationOutputs));
        System.out.println("Trinity Application Interface Id " + trinityInterfaceId);
    } catch (TException e) {
        e.printStackTrace();
    }
}

Example 25 with OutputDataObjectType

use of org.apache.airavata.model.application.io.OutputDataObjectType in project airavata by apache.

the class RegisterSampleApplications method registerGaussianInterface.

private void registerGaussianInterface() {
    try {
        System.out.println("#### Registering Gaussian Application Interface ####");
        List<String> appModules = new ArrayList<String>();
        appModules.add(gaussianModuleId);
        InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("MainInputFile", null, DataType.URI, null, 1, true, true, false, "Gaussian main input file", null);
        List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
        applicationInputs.add(input1);
        OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("gaussian.out", "", DataType.URI, true, true, null);
        OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT", null, DataType.STDOUT, true, true, null);
        OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("STDERR", null, DataType.STDERR, true, true, null);
        List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
        applicationOutputs.add(output1);
        applicationOutputs.add(output2);
        applicationOutputs.add(output3);
        String addApplicationInterfaceId = airavataClient.registerApplicationInterface(new AuthzToken(""), DEFAULT_GATEWAY, RegisterSampleApplicationsUtils.createApplicationInterfaceDescription("Gaussian", "Gaussian application", appModules, applicationInputs, applicationOutputs));
        System.out.println("Gaussian Application Interface Id " + addApplicationInterfaceId);
    } catch (TException e) {
        e.printStackTrace();
    }
}