Examples of LONI.tree.workflow.Variable

    String varName="GALAXY_DIR";
    String varDescription="directory of galaxy installation. Used to find galaxy scripts.";
    boolean secret = false;
    int order = 0;
    boolean required=true;
    mgroup.getVariables().addVariable(new Variable(varName, varDescription, required,
        secret, order, ConverterConfig.GALAXY_INPUT_DIR) );
    
    varName="OUTPUT_FILE_DIR";
    varDescription="directory of galaxy installation. Used to find galaxy scripts.";
    mgroup.getVariables().addVariable(new Variable(varName, varDescription, required,
        secret, order, ConverterConfig.GALAXY_OUTPUT_DIR) );
    
    /* Record environmental variable in context for future use*/
    /*TODO: Migrate these globals to some sort of configuration file*/

    /**
     * Create Pipeline Variables
     */
    
    //location of galaxy web service scripts
    Variable scriptVar = new Variable();
    scriptVar.setName(SCRIPT_DIR);
    scriptVar.setValue(ConverterConfig.GALAXY_SCRIPT_DIR);
    scriptVar.setDescription("Where the galaxy wrapper scripts are");
    moduleGroup.getVariables().addVariable(scriptVar);
    
    //api key for the galaxy server
    Variable apikeyVal = new Variable();
    apikeyVal.setName(API_KEY);
    apikeyVal.setValue(ConverterConfig.GALAXY_API_KEY);
    apikeyVal.setDescription("api key for server");
    moduleGroup.getVariables().addVariable(apikeyVal);
    
    //location of the galaxy root. scripts are used from the galaxy root.
    Variable dirVal = new Variable();
    dirVal.setName(GALAXY_DIR);
    dirVal.setValue(ConverterConfig.GALAXY_INPUT_DIR);
    dirVal.setDescription("Galaxy distribution sirectory Here");
    moduleGroup.getVariables().addVariable(dirVal);
    
    //url of galaxy server.
    Variable urlVal = new Variable();
    urlVal.setName(GALAXY_URL);
    urlVal.setValue(ConverterConfig.GALAXY_URL);
    urlVal.setDescription("server address");
    moduleGroup.getVariables().addVariable(urlVal);
    
    /*Temporary : Until everything migrates to api*/
    //value of cookie from website. This will be phased out
    //when galaxy migrates completely to web api.
    Variable cookieVal = new Variable();
    cookieVal.setName(COOKIE);
    cookieVal.setValue(ConverterConfig.GALAXY_COOKIE);
    cookieVal.setDescription("login cookie for size");
    moduleGroup.getVariables().addVariable(cookieVal);
    
    
    return pipeline;
  }

Examples of LONI.tree.workflow.Variable

Related Classes of LONI.tree.workflow.Variable