Examples of InputDataObjectType

org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType
Application Inputs. The paramters describe how inputs are passed to the application. name: Name of the parameter. value: Value of the parameter. A default value could be set during registration. type: Data type of the parameter applicationArguement: The argument flag sent to the application. Such as -p pressure. standardInput: When this value is set, the parameter is sent as standard input rather than a parameter. Typically this is passed using redirection operator ">". userFriendlyDescription: Description to be displayed at the user interface. metaData: Any metadat. This is typically ignore by Airavata and is used by gateways for application configuration.

Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            String wrfModuleId = addAppModule("WRF");
            String amberModuleId = addAppModule("AMBER");
            List<String> modules = new ArrayList<String>();
            modules.add(wrfModuleId);
            modules.add(amberModuleId);
            InputDataObjectType appInput1 = createAppInput("input1", "input1", DataType.STRING);
            InputDataObjectType appInput2 = createAppInput("input2", "input2", DataType.INTEGER);
            List<InputDataObjectType> inputs = new ArrayList<InputDataObjectType>();
            inputs.add(appInput1);
            inputs.add(appInput2);
            OutputDataObjectType output1 = createAppOutput("output1", "", DataType.STRING);
            OutputDataObjectType output2 = createAppOutput("output2", "", DataType.STRING);

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

        }
        return null;
    }


    public InputDataObjectType createAppInput (String inputName, String value, DataType type ){
        InputDataObjectType input = new InputDataObjectType();
        input.setName(inputName);
        input.setValue(value);
        input.setType(type);
        input.setApplicationArgument("test arg");
        return input;
    }

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

        }
        return inputs;
    }


    public static InputDataObjectType getInputDataObjType (ApplicationInputResource input){
        InputDataObjectType inputDataObjectType = new InputDataObjectType();
        inputDataObjectType.setName(input.getInputKey());
        inputDataObjectType.setValue(input.getInputVal());
        inputDataObjectType.setApplicationArgument(input.getAppArgument());
        inputDataObjectType.setMetaData(input.getMetadata());
        inputDataObjectType.setType(DataType.valueOf(input.getDataType()));
        inputDataObjectType.setStandardInput(input.isStandareInput());
        inputDataObjectType.setUserFriendlyDescription(input.getUserFriendlyDesc());
        return inputDataObjectType;
    }

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

    }


    public static InputDataObjectType createAppInput
            (String inputName, String value, DataType type,
             String applicationArgument, boolean stdIn, String description, String metadata) {
        InputDataObjectType input = new InputDataObjectType();
//        input.setIsEmpty(false);
        if (inputName != null) input.setName(inputName);
        if (value != null) input.setValue(value);
        if (type != null) input.setType(type);
        if (applicationArgument != null) input.setApplicationArgument(applicationArgument);
        if (description != null) input.setUserFriendlyDescription(description);
        input.setStandardInput(stdIn);
        if (metadata != null) input.setMetaData(metadata);
        return input;
    }

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            System.out.println("#### Registering Echo Interface #### \n");


            List<String> appModules = new ArrayList<String>();
            appModules.add(echoModuleId);


            InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Input_to_Echo", "Hello World",
                    DataType.STRING, null, false, "A test string to Echo", null);


            List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
            applicationInputs.add(input1);

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            System.out.println("#### Registering Amber Interface #### \n");


            List<String> appModules = new ArrayList<String>();
            appModules.add(amberModuleId);


            InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Heat_Restart_File", null,
                    DataType.URI, null, false, "Heating up the system equilibration stage - 02_Heat.rst", null);


            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Production_Control_File", null,
                    DataType.URI, null, false, "Constant pressure and temperature for production stage - 03_Prod.in", null);


            InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File", null,
                    DataType.URI, null, false, "Parameter and Topology coordinates - prmtop", null);


            List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
            applicationInputs.add(input1);
            applicationInputs.add(input2);

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            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, false, "Heating up the system equilibration stage", null);


            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Production_Control_File", null,
                    DataType.URI, null, false, "Constant pressure and temperature for production stage", null);


            InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File", null,
                    DataType.URI, null, false, "Parameter and Topology coordinates", null);


            List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
            applicationInputs.add(input1);
            applicationInputs.add(input2);

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            System.out.println("#### Registering Espresso Interface #### \n");


            List<String> appModules = new ArrayList<String>();
            appModules.add(espressoModuleId);


            InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("AI_Primitive_Cell", null,
                    DataType.URI, null, false, "AI_Metal_Input_File - Al.sample.in", null);


            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("AI_Pseudopotential_File", null,
                    DataType.URI, null, false, "Constant pressure and temperature for production stage - Al.pz-vbc.UPF", null);


            List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
            applicationInputs.add(input1);
            applicationInputs.add(input2);

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            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, false, "Coordinates velocities, molecular topology and simulation parameters - pdb1y6l-EM-vacuum.tpr", null);


            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("GROMOS_Coordinate_File", null,
                    DataType.URI, null, 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);

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Examples of org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType

            System.out.println("#### Registering LAMMPS Interface #### \n");


            List<String> appModules = new ArrayList<String>();
            appModules.add(lammpsModuleId);


            InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Friction_Simulation_Input", null,
                    DataType.URI, null, false, "Friction Simulation Input - in.friction", null);


            List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
            applicationInputs.add(input1);

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