private Map<String, org.embl.ebi.escience.scufl.InputPort> getInputPortMap( org.embl.ebi.escience.scufl.Processor processor) { Map<String, org.embl.ebi.escience.scufl.InputPort> inputPorts = new HashMap<String, org.embl.ebi.escience.scufl.InputPort>(); for (org.embl.ebi.escience.scufl.InputPort inputPort : processor .getInputPorts()) { inputPorts.put(inputPort.getName(), inputPort); } return inputPorts; }
private Map<String, org.embl.ebi.escience.scufl.InputPort> getInputPortMap( org.embl.ebi.escience.scufl.Processor processor) { Map<String, org.embl.ebi.escience.scufl.InputPort> inputPorts = new HashMap<String, org.embl.ebi.escience.scufl.InputPort>(); for (org.embl.ebi.escience.scufl.InputPort inputPort : processor .getInputPorts()) { inputPorts.put(inputPort.getName(), inputPort); } return inputPorts; }
for (InputPort inputPort : apProcessor.getInputPorts()) { Element inputElement = new Element(INPUT_PORT_TAG, XScufl.XScuflNS); inputElement.setText(inputPort.getName()); inputElement.setAttribute(SYNTACTIC_TYPE_ATTRIBUTE, inputPort .getSyntacticType(), XScufl.XScuflNS);
Element inputElement = new Element("beanshellinput", XScuflNS); inputElement.setText(inputs[i].getName()); if (inputs[i].getSyntacticType() != null) inputElement.setAttribute("syntactictype", inputs[i]
for (int i = 0; i < inputs.length; i++) { Element inputElement = new Element("bsfinput", XScufl.XScuflNS); inputElement.setText(inputs[i].getName()); if (inputs[i].getSyntacticType() != null) inputElement.setAttribute("syntactictype", inputs[i].getSyntacticType(), XScufl.XScuflNS);
for (Iterator it = inputs.iterator(); it.hasNext();) { TypeDescriptor desc = (TypeDescriptor) it.next(); if (desc.getName().equalsIgnoreCase(portToSplit.getName())) { typeDescriptor = desc; break; .getElements().iterator(); iterator.hasNext();) { TypeDescriptor desc = (TypeDescriptor) iterator.next(); if (desc.getName().equals(portToSplit.getName())) { typeDescriptor = desc; if (typeDescriptor instanceof ArrayTypeDescriptor
private void populatePortSymanticTypeDetails(Processor processor, RshellActivityConfigurationBean bean) throws ActivityTranslationException { List<RShellPortSymanticTypeBean> inputDefinitions = new ArrayList<RShellPortSymanticTypeBean>(); List<RShellPortSymanticTypeBean> outputDefinitions = new ArrayList<RShellPortSymanticTypeBean>(); for (InputPort inputPort : processor.getInputPorts()) { RShellPortSymanticTypeBean symanticTypeBean = new RShellPortSymanticTypeBean(); symanticTypeBean.setName(inputPort.getName()); symanticTypeBean.setSymanticType(getSymanticType(inputPort)); inputDefinitions.add(symanticTypeBean); } for (OutputPort outPort : processor.getOutputPorts()) { RShellPortSymanticTypeBean symanticTypeBean = new RShellPortSymanticTypeBean(); symanticTypeBean.setName(outPort.getName()); symanticTypeBean.setSymanticType(getSymanticType(outPort)); outputDefinitions.add(symanticTypeBean); } bean.setInputSymanticTypes(inputDefinitions); bean.setOutputSymanticTypes(outputDefinitions); }
name = inputPort.getName() + "XML";
private void populatePortSymanticTypeDetails(Processor processor, RshellActivityConfigurationBean bean) throws ActivityTranslationException { List<RShellPortSymanticTypeBean> inputDefinitions = new ArrayList<RShellPortSymanticTypeBean>(); List<RShellPortSymanticTypeBean> outputDefinitions = new ArrayList<RShellPortSymanticTypeBean>(); for (InputPort inputPort : processor.getInputPorts()) { RShellPortSymanticTypeBean symanticTypeBean = new RShellPortSymanticTypeBean(); symanticTypeBean.setName(inputPort.getName()); symanticTypeBean.setSymanticType(getSymanticType(inputPort)); inputDefinitions.add(symanticTypeBean); } for (OutputPort outPort : processor.getOutputPorts()) { RShellPortSymanticTypeBean symanticTypeBean = new RShellPortSymanticTypeBean(); symanticTypeBean.setName(outPort.getName()); symanticTypeBean.setSymanticType(getSymanticType(outPort)); outputDefinitions.add(symanticTypeBean); } bean.setInputSymanticTypes(inputDefinitions); bean.setOutputSymanticTypes(outputDefinitions); }
bean.setName(inputPort.getName()); bean.setDepth(determineDepthFromSyntacticType(inputPort .getSyntacticType()));
@Before public void setUp() throws Exception { System.setProperty("raven.eclipse", "true"); setUpRavenRepository(); ScuflModel model = loadScufl("biomart-workflow-t1.xml"); Processor[] processors = model.getProcessors(); assertEquals(1, processors.length); assertTrue(processors[0] instanceof BiomartProcessor); biomartProcessor = (BiomartProcessor) processors[0]; inputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.InputPort port : biomartProcessor.getInputPorts()) { inputPortNames.add(port.getName()); } outputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.OutputPort port : biomartProcessor.getOutputPorts()) { outputPortNames.add(port.getName()); } translator = new BiomartActivityTranslator(); }
@Before public void setUp() throws Exception { System.setProperty("raven.eclipse", "true"); setUpRavenRepository(); ScuflModel model = loadScufl("biomart-workflow-t1.xml"); Processor[] processors = model.getProcessors(); assertEquals(1, processors.length); assertTrue(processors[0] instanceof BiomartProcessor); biomartProcessor = (BiomartProcessor) processors[0]; inputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.InputPort port : biomartProcessor.getInputPorts()) { inputPortNames.add(port.getName()); } outputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.OutputPort port : biomartProcessor.getOutputPorts()) { outputPortNames.add(port.getName()); } translator = new BiomartActivityTranslator(); }
@Before public void setUp() throws Exception { System.setProperty("raven.eclipse", "true"); setUpRavenRepository(); ScuflModel model = loadScufl("biomart-workflow-t1.xml"); Processor[] processors = model.getProcessors(); assertEquals(1, processors.length); assertTrue(processors[0] instanceof BiomartProcessor); biomartProcessor = (BiomartProcessor) processors[0]; inputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.InputPort port : biomartProcessor.getInputPorts()) { inputPortNames.add(port.getName()); } outputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.OutputPort port : biomartProcessor.getOutputPorts()) { outputPortNames.add(port.getName()); } translator = new BiomartActivityTranslator(); }
@Before public void setUp() throws Exception { System.setProperty("raven.eclipse", "true"); setUpRavenRepository(); ScuflModel model = loadScufl("soaplab-workflow-t1.xml"); Processor[] processors = model.getProcessors(); assertEquals(1, processors.length); assertTrue(processors[0] instanceof SoaplabProcessor); soaplabProcessor = (SoaplabProcessor) processors[0]; inputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.InputPort port : soaplabProcessor .getInputPorts()) { inputPortNames.add(port.getName()); } outputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.OutputPort port : soaplabProcessor .getOutputPorts()) { outputPortNames.add(port.getName()); } translator = new SoaplabActivityTranslator(); }
@Ignore("Integration test") @Before public void setUp() throws Exception { System.setProperty("raven.eclipse", "true"); setUpRavenRepository(); ScuflModel model = loadScufl("soaplab-workflow-t1.xml"); Processor[] processors = model.getProcessors(); assertEquals(1, processors.length); assertTrue(processors[0] instanceof SoaplabProcessor); soaplabProcessor = (SoaplabProcessor) processors[0]; inputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.InputPort port : soaplabProcessor .getInputPorts()) { inputPortNames.add(port.getName()); } outputPortNames = new HashSet<String>(); for (org.embl.ebi.escience.scufl.OutputPort port : soaplabProcessor .getOutputPorts()) { outputPortNames.add(port.getName()); } translator = new SoaplabActivityTranslator(); }
String portName = ip[i].getName(); OutputPort port = new OutputPort(m.getWorkflowSourceProcessor(), portName); m.getWorkflowSourceProcessor().addPort(port);
&& t1InputPort.getDefaultValue() != null) { String processorName = t1Processor.getName() + "_" + sanitiseName(t1InputPort.getName()) + "_defaultValue"; try {
&& t1InputPort.getDefaultValue() != null) { String processorName = t1Processor.getName() + "_" + sanitiseName(t1InputPort.getName()) + "_defaultValue"; try { org.embl.ebi.escience.scufl.Processor stringConstantProcessor = new StringConstantProcessor(