public Set<Scavenger> getFromModel(ScuflModel model) { Set<Scavenger> result = new HashSet<Scavenger>(); Processor[] processors = model.getProcessorsOfType(RDFGeneratorProcessor.class); if (processors.length>0) { try { result.add(new RDFGeneratorScavenger()); } catch (ScavengerCreationException e) { logger.warn("Error creating RDFGeneratorScavenger", e); } } return result; }
public Set<Scavenger> getFromModel(ScuflModel model) { Set<Scavenger> result = new HashSet<Scavenger>(); List<String> existingLocations = new ArrayList<String>(); Processor[] processors = model.getProcessorsOfType(BiomobyProcessor.class); for (Processor processor : processors) { String loc = ((BiomobyProcessor) processor).getMobyEndpoint(); if (!existingLocations.contains(loc)) { existingLocations.add(loc); try { result.add(new BiomobyScavenger(loc)); } catch (ScavengerCreationException e) { logger.warn("Error creating Biomoby Scavenger", e); } } } return result; }
public Set<Scavenger> getFromModel(ScuflModel model) { Set<Scavenger> result = new HashSet<Scavenger>(); List<String> existingLocations = new ArrayList<String>(); Processor[] processors = model.getProcessorsOfType(BiomobyObjectProcessor.class); for (Processor processor : processors) { String loc = ((BiomobyObjectProcessor) processor).getMobyEndpoint(); if (!existingLocations.contains(loc)) { existingLocations.add(loc); try { result.add(new BiomobyObjectScavenger(loc)); } catch (ScavengerCreationException e) { logger.warn("Error creating BiomobyObjectScavenger", e); } } } return result; }
public Set<Scavenger> getFromModel(ScuflModel model) { Set<Scavenger> result = new HashSet<Scavenger>(); List<String> existingLocations = new ArrayList<String>(); Processor[] processors = model .getProcessorsOfType(WSDLBasedProcessor.class); for (Processor processor : processors) { String loc = ((WSDLBasedProcessor) processor).getWSDLLocation(); if (!existingLocations.contains(loc)) { existingLocations.add(loc); try { result.add(new WSDLBasedScavenger(loc)); } catch (ScavengerCreationException e) { logger.warn("Error creating WSDLBasedScavenger", e); } } } return result; }
public Set<Scavenger> getFromModel(ScuflModel model) { Set<Scavenger> result = new HashSet<Scavenger>(); List<String> existingLocations = new ArrayList<String>(); Processor[] processors = model.getProcessorsOfType(SoaplabProcessor.class); for (Processor processor : processors) { String endpoint = ((SoaplabProcessor) processor).getEndpoint().toString(); if (!existingLocations.contains(endpoint)) { existingLocations.add(endpoint); String[] parts = endpoint.split("/"); String base = ""; for (int j = 0; j < parts.length - 1; j++) { base = base + parts[j] + "/"; } try { result.add(new SoaplabScavenger(base)); } catch (ScavengerCreationException e) { logger.warn("Error creating SoaplabScavenger", e); } } } return result; }
for (Processor p : getModel().getProcessorsOfType( DependencyProcessor.class)) { DependencyProcessor proc = (DependencyProcessor) p;
/** * Recurse over all the processors including any nested-nested-nested etc. * workflows * * @param processorList * @return */ private List<Processor> getAllWorkflowProcessors( List<Processor> processorList) { List<Processor> allProcessors = new ArrayList<Processor>(); for (Processor processor : processorList) { ScuflModel internalModel = ((ScuflWorkflowProcessor) processor) .getInternalModel(); Processor[] processorsOfType = internalModel .getProcessorsOfType(ScuflWorkflowProcessor.class); List<Processor> moreProcessors = new ArrayList<Processor>(); for (Processor proc : processorsOfType) { moreProcessors.add(proc); } List<Processor> allWorkflowProcessors = getAllWorkflowProcessors(moreProcessors); if (!allWorkflowProcessors.isEmpty()) { allProcessors.addAll(allWorkflowProcessors); } allProcessors.add(processor); } return allProcessors; } }
/** * Set the URLs where the nested workflow comes from to null and store the * processor and its original URL in the {@link #processorURL} {@link Map} */ public void makeNestedEmbedded() { Processor[] processorsOfType = this.model .getProcessorsOfType(ScuflWorkflowProcessor.class); List<Processor> processorList = new ArrayList<Processor>(); for (Processor processor : processorsOfType) { processorList.add((Processor) processor); } List<Processor> allWorkflowProcessors = getAllWorkflowProcessors(processorList); for (Processor processor : allWorkflowProcessors) { processorURL.put(processor, ((ScuflWorkflowProcessor) processor) .getDefinitionURL()); ((ScuflWorkflowProcessor) processor).setDefinitionURL(null); } }
public Set<Scavenger> getFromModel(ScuflModel model) { Set<Scavenger> result = new HashSet<Scavenger>(); List<String> existingLocations = new ArrayList<String>(); Processor[] processors = model .getProcessorsOfType(BiomartProcessor.class); for (Processor processor : processors) { String loc = ((BiomartProcessor) processor).getQuery().getMartService().getLocation(); if (!existingLocations.contains(loc)) { existingLocations.add(loc); try { result.add(new BiomartScavenger(loc)); } catch (ScavengerCreationException e) { logger.warn("Error creating BiomartScavenger", e); } } } return result; }
@Test public void testBeanshellActivityTranslator() throws Exception { ScuflModel model = loadScufl("beanshell.xml"); Processor p = model.getProcessorsOfType(BeanshellProcessor.class)[0]; assertEquals("beanshell", p.getName()); ActivityTranslator<?> translator = ActivityTranslatorFactory .getTranslator(p); Activity<?> s = translator.doTranslation(p); assertEquals("net.sf.taverna.t2.activities.beanshell.BeanshellActivity", s.getClass().getName()); }
@Test public void testBeanshellActivityTranslator() throws Exception { ScuflModel model = loadScufl("beanshell.xml"); Processor p = model.getProcessorsOfType(BeanshellProcessor.class)[0]; assertEquals("beanshell", p.getName()); ActivityTranslator<?> translator = ActivityTranslatorFactory .getTranslator(p); Activity<?> s = translator.doTranslation(p); assertEquals("net.sf.taverna.t2.activities.beanshell.BeanshellActivity", s.getClass().getName()); }
@Test public void testBeanshellActivityTranslator() throws Exception { setUpRavenRepository(); ScuflModel model = loadScufl("beanshell.xml"); Processor p = model.getProcessorsOfType(BeanshellProcessor.class)[0]; assertEquals("beanshell", p.getName()); ActivityTranslator<?> translator = ActivityTranslatorFactory .getTranslator(p); Activity<?> s = translator.doTranslation(p); assertEquals("net.sf.taverna.t2.activities.beanshell.BeanshellActivity", s.getClass().getName()); }
assertEquals(1, model.getProcessorsOfType(Processor.class).length); assertEquals(valid_name, model.locateProcessor(valid_name).getName());