Examples with AuthzToken org.apache.airavata.model.security.AuthzToken used on opensource projects

Example 16 with AuthzToken

use of org.apache.airavata.model.security.AuthzToken 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 17 with AuthzToken

use of org.apache.airavata.model.security.AuthzToken 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();
    }
}

Example 18 with AuthzToken

use of org.apache.airavata.model.security.AuthzToken in project airavata by apache.

the class RegisterSampleApplications method registerGatewayResourceProfile.

public void registerGatewayResourceProfile() {
    try {
        System.out.println("#### Registering Application Deployments on BigRed II #### \n");
        ComputeResourcePreference stampedeResourcePreferences = RegisterSampleApplicationsUtils.createComputeResourcePreference(stampedeResourceId, "TG-STA110014S", false, null, JobSubmissionProtocol.SSH, DataMovementProtocol.SCP, "/scratch/01437/ogce/gta-work-dirs");
        ComputeResourcePreference trestlesResourcePreferences = RegisterSampleApplicationsUtils.createComputeResourcePreference(trestlesResourceId, "sds128", false, null, JobSubmissionProtocol.SSH, DataMovementProtocol.SCP, "/oasis/scratch/trestles/ogce/temp_project/gta-work-dirs");
        ComputeResourcePreference bigRedResourcePreferences = RegisterSampleApplicationsUtils.createComputeResourcePreference(bigredResourceId, "TG-STA110014S", false, null, null, null, "/N/dc2/scratch/cgateway/gta-work-dirs");
        ComputeResourcePreference lsfResourcePreferences = RegisterSampleApplicationsUtils.createComputeResourcePreference(lsfResourceId, "airavata", false, null, null, null, "/home/lg11w/mywork");
        ComputeResourcePreference fsdResourcePreferences = RegisterSampleApplicationsUtils.createComputeResourcePreference(fsdResourceId, null, false, null, JobSubmissionProtocol.UNICORE, DataMovementProtocol.UNICORE_STORAGE_SERVICE, null);
        ComputeResourcePreference alamoResourcePreferences = RegisterSampleApplicationsUtils.createComputeResourcePreference(alamoResourceId, null, false, null, JobSubmissionProtocol.SSH, DataMovementProtocol.SCP, "/home/us3/work/uslims3_cauma3-03896");
        GatewayResourceProfile gatewayResourceProfile = new GatewayResourceProfile();
        gatewayResourceProfile.setGatewayID(DEFAULT_GATEWAY);
        gatewayResourceProfile.addToComputeResourcePreferences(stampedeResourcePreferences);
        gatewayResourceProfile.addToComputeResourcePreferences(trestlesResourcePreferences);
        gatewayResourceProfile.addToComputeResourcePreferences(bigRedResourcePreferences);
        gatewayResourceProfile.addToComputeResourcePreferences(fsdResourcePreferences);
        gatewayResourceProfile.addToComputeResourcePreferences(lsfResourcePreferences);
        String gatewayProfile = airavataClient.registerGatewayResourceProfile(new AuthzToken(""), gatewayResourceProfile);
        System.out.println("Gateway Profile is registered with Id " + gatewayProfile);
    } catch (TException e) {
        e.printStackTrace();
    }
}

Example 19 with AuthzToken

use of org.apache.airavata.model.security.AuthzToken in project airavata by apache.

the class RegisterSampleApplications method registerAutoDockInterface.

public void registerAutoDockInterface() {
    try {
        System.out.println("#### Registering AutoDock Interface #### \n");
        List<String> appModules = new ArrayList<String>();
        appModules.add(autoDockModuleId);
        InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Heat_Restart_File", null, DataType.URI, null, 1, true, true, false, "Heating up the system equilibration stage", null);
        InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Production_Control_File", null, DataType.URI, null, 2, true, true, false, "Constant pressure and temperature for production stage", null);
        InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File", null, DataType.URI, null, 3, true, true, false, "Parameter and Topology coordinates", null);
        List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
        applicationInputs.add(input1);
        applicationInputs.add(input2);
        applicationInputs.add(input3);
        OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("STDOUT", null, DataType.STDOUT, true, true, null);
        OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("STDERR", null, DataType.STDERR, true, true, null);
        List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
        applicationOutputs.add(output1);
        applicationOutputs.add(output2);
        autoDockInterfaceId = airavataClient.registerApplicationInterface(new AuthzToken(""), DEFAULT_GATEWAY, RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(autoDockName, autoDockDescription, appModules, applicationInputs, applicationOutputs));
        System.out.println("AutoDock Application Interface Id " + autoDockInterfaceId);
    } catch (TException e) {
        e.printStackTrace();
    }
}

Example 20 with AuthzToken

use of org.apache.airavata.model.security.AuthzToken in project airavata by apache.

the class RegisterSampleApplications method registerAlamoApps.

public void registerAlamoApps() {
    try {
        System.out.println("#### Registering Application Deployments on Alamo #### \n");
        // Register Ultrascan on Alamo
        List<CommandObject> ultrascanMouldes = new ArrayList();
        ultrascanMouldes.add(new CommandObject("module load intel/2015/64"));
        ultrascanMouldes.add(new CommandObject("module load openmpi/intel/1.8.4"));
        ultrascanMouldes.add(new CommandObject("module load qt4/4.8.6"));
        ultrascanMouldes.add(new CommandObject("module load ultrascan3/3.3"));
        String ultrascanAppDeployId = airavataClient.registerApplicationDeployment(new AuthzToken(""), DEFAULT_GATEWAY, RegisterSampleApplicationsUtils.createApplicationDeployment(ultrascanModuleId, alamoResourceId, "/home/us3/bin/us_mpi_analysis", ApplicationParallelismType.OPENMP, ultrascanDescription, ultrascanMouldes, null, null));
        System.out.println("Ultrascan on alamo deployment Id " + ultrascanAppDeployId);
    } catch (TException e) {
        e.printStackTrace();
    }
}