/*
* Create the setupModule.
*
*/
setupModule = new Module();
setupContext = new LoniContext();
setupModule.setId("Setup");
setupModule.setRotation(4);
setupModule.setName("Setup");
setupModule.setLocation(ConverterConstants.LOCALHOST_PATH + ConverterConfig.PYTHON_BIN);
//create the String parameter containing the script name for the
//setup module.
LONI.tree.module.Parameter setupScript = new LONI.tree.module.Parameter();
setupScript.setEnabled(true);
setupScript.setFileFormat(new Format());
setupScript.getFileFormat().setCardinality(1);
setupScript.getFileFormat().setType("String");
setupScript.setOrder(0);
setupScript.setName("setupScript");
Value scriptValue = new Value();
scriptValue.setValue("{"+SCRIPT_DIR+"}setup_workflow.py");
setupScript.getValues().addValue(scriptValue);
setupModule.getInputs().add(setupScript);
//Create the String Parameter that contains the Galaxy API Key
//for the setupScript Module.
LONI.tree.module.Parameter setupAPI = new LONI.tree.module.Parameter();
setupAPI.setEnabled(true);
setupAPI.setFileFormat(new Format());
setupAPI.getFileFormat().setCardinality(1);
setupAPI.getFileFormat().setType("String");
setupAPI.setOrder(1);
setupAPI.setName("Galaxy API Key");
setupAPI.setPrefix("-api-key");
setupAPI.setPrefixSpaced(true);
Value apiValue = new Value();
apiValue.setValue("{"+API_KEY+"}");
setupAPI.getValues().addValue(apiValue);
setupModule.getInputs().add(setupAPI);
/*
* Initialize and add the String parameter that contains the Galaxy Root Directory
* to the setup Module. This directory is used to call python scripts inside Galaxy.
*/
LONI.tree.module.Parameter setupGalRootDir = new LONI.tree.module.Parameter();
setupGalRootDir.setEnabled(true);
setupGalRootDir.setFileFormat(new Format());
setupGalRootDir.getFileFormat().setCardinality(1);
setupGalRootDir.getFileFormat().setType("String");
setupGalRootDir.setOrder(1);
setupGalRootDir.setName("Galaxy Root Dir");
setupGalRootDir.setPrefix("-galaxy-root-dir");
setupGalRootDir.setPrefixSpaced(true);
Value setupGalRootDirValue = new Value();
setupGalRootDirValue.setValue("{"+GALAXY_DIR+"}");
setupGalRootDir.getValues().addValue(setupGalRootDirValue);
setupModule.getInputs().add(setupGalRootDir);
/*
* Initialize and add String parameter containing Galaxy server url to setup module.
*/
LONI.tree.module.Parameter setupGalURLDir = new LONI.tree.module.Parameter();
setupGalURLDir.setEnabled(true);
setupGalURLDir.setFileFormat(new Format());
setupGalURLDir.getFileFormat().setCardinality(1);
setupGalURLDir.getFileFormat().setType("String");
setupGalURLDir.setOrder(2);
setupGalURLDir.setPrefixSpaced(true);
setupGalURLDir.setName("Galaxy URL");
setupGalURLDir.setPrefix("-galaxy-url");
Value setupGalaxyURLValue = new Value();
setupGalaxyURLValue.setValue("{"+GALAXY_URL+"}");
setupGalURLDir.getValues().addValue(setupGalaxyURLValue);
setupModule.getInputs().add(setupGalURLDir);
/*
* Initialize and add String cookie parameter containing cookie for website
* to setup module.
*/
LONI.tree.module.Parameter setupCookie = new LONI.tree.module.Parameter();
setupCookie.setEnabled(true);
setupCookie.setFileFormat(new Format());
setupCookie.getFileFormat().setCardinality(1);
setupCookie.getFileFormat().setType("String");
setupCookie.setOrder(2);
setupCookie.setName("Cookie for galaxy site");
setupCookie.setPrefix("-cookie");
setupCookie.setPrefixSpaced(true);
Value setupCookieValue = new Value();
setupCookieValue.setValue("{"+COOKIE+"}");
setupCookie.getValues().addValue(setupCookieValue);
setupModule.getInputs().add(setupCookie);
/*
* Initialize and fill in the run module.
*
*/
runModule = new Module();
runModule.setRotation(4);
runContext = new LoniContext();
runModule.setId("Run");
runModule.setLocation(ConverterConstants.LOCALHOST_PATH + ConverterConfig.PYTHON_BIN);
//Add the String script parameter containing the name of the script to run.
LONI.tree.module.Parameter runScript = new LONI.tree.module.Parameter();
runScript.setEnabled(true);
runScript.setFileFormat(new Format());
runScript.getFileFormat().setCardinality(1);
runScript.getFileFormat().setType("String");
runScript.setOrder(0);
runScript.setName("runScript");
scriptValue = new Value();
scriptValue.setValue("{"+SCRIPT_DIR+"}run_workflow.py");
runScript.getValues().addValue(scriptValue);
runModule.getInputs().add(runScript);
//Create the workflow output to the run module. This output contains
//a functional galaxy workflow that was generated from the loni pipeline
//modules.
LONI.tree.module.Output runWorkflow = new LONI.tree.module.Output();
runWorkflow.setEnabled(true);
runWorkflow.setFormat(new Format());
runWorkflow.getFormat().setCardinality(1);
runWorkflow.getFormat().setType("File");
FileType runFileType = new FileType();
runFileType.setName(GENERIC_DICT_TYPE);
runFileType.setDescription("");
runFileType.setExtension("");
runWorkflow.getFormat().getFileTypes().addFileType(runFileType);
runWorkflow.setOrder(0);
runWorkflow.setPrefix("-workflow");
runWorkflow.setPrefixSpaced(true);
runWorkflow.setName("Workflow Data");
runModule.getOutputs().add(runWorkflow);
//Add the setup and run modules to the setup and run contexts respectively.
setupContext.getPathContext().addContext("Setup");
runContext.getPathContext().addContext("Run");
/*
*VISIT THE STEPS IN THE WORKFLOW
*/
//used to place run, setup modules
int totalY=0; // running sum of y values.
int leftX = -1; //furthest left x position
int rightX = 0; //furthest right y position
int spacing = 200; //spacing between modules.
// TODO Auto-generated method stub
for(Step s : workflow.getSteps()){
//visit each step in the workflow
Pair<GraphObject,LoniEnvironment> step = stepVisitor.visit(s, new LoniContext());
//add the returned environment to the pipeline environment.
le.addEnvironment(step.getElem2());
//add the returned graphobject to the pipeline modulegroup
moduleGroup.getModules().add(step.getElem1());
//add the step's y value to the running sum of y values.