protected Edit<?> makeInsertNestedWorkflowEdit(Dataflow nestedFlow, String name) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); insertedActivity = new DataflowActivity(); editList.add(edits.getConfigureActivityEdit(insertedActivity, nestedFlow)); Processor p = edits.createProcessor(name); editList.add(edits.getDefaultDispatchStackEdit(p)); editList.add(edits.getAddActivityEdit(p, insertedActivity)); editList.add(edits.getAddProcessorEdit(destinationDataflow, p)); CompoundEdit edit = new CompoundEdit(editList); return edit; }
public Edit<?> getAddAnnotationChainEdit(Annotated<?> annotated, AnnotationBeanSPI annotation) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); AnnotationAssertion<?> annotationAssertion = new AnnotationAssertionImpl(); editList.add(getAddAnnotationBean(annotationAssertion, annotation)); AnnotationChain annotationChain = new AnnotationChainImpl(); editList.add(getAddAnnotationAssertionEdit(annotationChain, annotationAssertion)); editList.add(annotated.getAddAnnotationEdit(annotationChain)); return new CompoundEdit(editList); }
public Edit<?> getAddAnnotationChainEdit(Annotated<?> annotated, AnnotationBeanSPI annotation) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); AnnotationAssertion<?> annotationAssertion = new AnnotationAssertionImpl(); editList.add(getAddAnnotationBean(annotationAssertion, annotation)); AnnotationChain annotationChain = new AnnotationChainImpl(); editList.add(getAddAnnotationAssertionEdit(annotationChain, annotationAssertion)); editList.add(annotated.getAddAnnotationEdit(annotationChain)); return new CompoundEdit(editList); }
public static Edit<?> getMoveDatalinkSinkEdit(Dataflow dataflow, Datalink datalink, EventHandlingInputPort sink, Edits edits) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(edits.getDisconnectDatalinkEdit(datalink)); if (datalink.getSink() instanceof ProcessorInputPort) { editList .add(getRemoveProcessorInputPortEdit((ProcessorInputPort) datalink .getSink(), edits)); } editList.add(getCreateAndConnectDatalinkEdit(dataflow, datalink .getSource(), sink, edits)); return new CompoundEdit(editList); }
@Override protected Edit<?> makeInsertNestedWorkflowEdit(Dataflow nestedFlow, String name) { Edits edits = EditsRegistry.getEdits(); Edit<?> configureActivityEdit = edits.getConfigureActivityEdit(getActivity(), nestedFlow); List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(configureActivityEdit); Processor p = findProcessor(fileManager.getCurrentDataflow(), getActivity()); if (p != null && p.getActivityList().size() == 1) { editList.add(edits.getMapProcessorPortsForActivityEdit(p)); } return new CompoundEdit(editList); }
public static Edit<?> getMoveDatalinkSinkEdit(Dataflow dataflow, Datalink datalink, EventHandlingInputPort sink) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(edits.getDisconnectDatalinkEdit(datalink)); if (datalink.getSink() instanceof ProcessorInputPort) { editList .add(getRemoveProcessorInputPortEdit((ProcessorInputPort) datalink .getSink())); } editList.add(getCreateAndConnectDatalinkEdit(dataflow, datalink .getSource(), sink)); return new CompoundEdit(editList); }
public static Edit<?> getRemoveProcessorOutputPortEdit( ProcessorOutputPort port, Edits edits) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); Processor processor = port.getProcessor(); editList.add(edits.getRemoveProcessorOutputPortEdit( port.getProcessor(), port)); for (Activity<?> activity : processor.getActivityList()) { editList.add(edits.getRemoveActivityOutputPortMappingEdit(activity, port.getName())); } return new CompoundEdit(editList); }
public static Edit<?> getRemoveProcessorOutputPortEdit( ProcessorOutputPort port) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); Processor processor = port.getProcessor(); editList.add(edits.getRemoveProcessorOutputPortEdit( port.getProcessor(), port)); for (Activity<?> activity : processor.getActivityList()) { editList.add(edits.getRemoveActivityOutputPortMappingEdit(activity, port.getName())); } return new CompoundEdit(editList); }
public static Edit<?> getRemoveProcessorInputPortEdit( ProcessorInputPort port) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); Processor processor = port.getProcessor(); editList.add(edits.getRemoveProcessorInputPortEdit(port.getProcessor(), port)); for (Activity<?> activity : processor.getActivityList()) { editList.add(edits.getRemoveActivityInputPortMappingEdit(activity, port.getName())); } return new CompoundEdit(editList); }
public static Edit<?> getRemoveProcessorInputPortEdit( ProcessorInputPort port, Edits edits) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); Processor processor = port.getProcessor(); editList.add(edits.getRemoveProcessorInputPortEdit(port.getProcessor(), port)); for (Activity<?> activity : processor.getActivityList()) { editList.add(edits.getRemoveActivityInputPortMappingEdit(activity, port.getName())); } return new CompoundEdit(editList); }
public static void configureActivityStatic(Dataflow df, Activity a, Object bean) { Edits edits = EditsRegistry.getEdits(); Edit<?> configureActivityEdit = edits.getConfigureActivityEdit(a, bean); try { List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(configureActivityEdit); Processor p = findProcessor(df, a); if (p != null && p.getActivityList().size() == 1) { editList.add(edits.getMapProcessorPortsForActivityEdit(p)); } EditManager.getInstance().doDataflowEdit(df, new CompoundEdit(editList)); } catch (IllegalStateException e) { // TODO Auto-generated catch block logger.error(e); } catch (EditException e) { logger.error(e); } }
public void actionPerformed(ActionEvent e) { try { Set<? extends Datalink> datalinks = port.getInternalOutputPort().getOutgoingLinks(); if (datalinks.isEmpty()) { editManager.doDataflowEdit(dataflow, edits.getRemoveDataflowInputPortEdit(dataflow, port)); } else { List<Edit<?>> editList = new ArrayList<Edit<?>>(); for (Datalink datalink : datalinks) { editList.add(Tools.getDisconnectDatalinkAndRemovePortsEdit(datalink)); } editList.add(edits.getRemoveDataflowInputPortEdit(dataflow, port)); editManager.doDataflowEdit(dataflow, new CompoundEdit(editList)); } dataflowSelectionModel.removeSelection(port); } catch (EditException e1) { logger.debug("Delete workflow input port failed", e1); } }
public static Edit<?> getDisconnectDatalinkAndRemovePortsEdit( Datalink datalink) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(edits.getDisconnectDatalinkEdit(datalink)); if (datalink.getSource() instanceof ProcessorOutputPort) { ProcessorOutputPort processorOutputPort = (ProcessorOutputPort) datalink .getSource(); if (processorOutputPort.getOutgoingLinks().size() == 1) { editList .add(getRemoveProcessorOutputPortEdit(processorOutputPort)); } } if (datalink.getSink() instanceof ProcessorInputPort) { editList .add(getRemoveProcessorInputPortEdit((ProcessorInputPort) datalink .getSink())); } return new CompoundEdit(editList); }
public static Edit<?> getDisconnectDatalinkAndRemovePortsEdit( Datalink datalink, Edits edits) { List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(edits.getDisconnectDatalinkEdit(datalink)); if (datalink.getSource() instanceof ProcessorOutputPort) { ProcessorOutputPort processorOutputPort = (ProcessorOutputPort) datalink .getSource(); if (processorOutputPort.getOutgoingLinks().size() == 1) { editList .add(getRemoveProcessorOutputPortEdit(processorOutputPort, edits)); } } if (datalink.getSink() instanceof ProcessorInputPort) { editList .add(getRemoveProcessorInputPortEdit((ProcessorInputPort) datalink .getSink(), edits)); } return new CompoundEdit(editList); }
public void actionPerformed(ActionEvent e) { try { Datalink datalink = port.getInternalInputPort().getIncomingLink(); if (datalink == null) { editManager.doDataflowEdit(dataflow, edits.getRemoveDataflowOutputPortEdit(dataflow, port)); } else { List<Edit<?>> editList = new ArrayList<Edit<?>>(); editList.add(Tools.getDisconnectDatalinkAndRemovePortsEdit(datalink)); editList.add(edits.getRemoveDataflowOutputPortEdit(dataflow, port)); editManager.doDataflowEdit(dataflow, new CompoundEdit(editList)); } dataflowSelectionModel.removeSelection(port); } catch (EditException e1) { logger.debug("Delete workflow output port failed", e1); } }
@Override protected String doInBackground() throws Exception { ReportManager rm = ReportManager.getInstance(); rm.updateObjectReport(df, p); List<Edit<?>> editList = new ArrayList<Edit<?>>(); try { if (ValidateSwingWorker.checkProcessorDisability(p, rm.getReports(df).get(p), editList)) { EditManager.getInstance().doDataflowEdit(df, new CompoundEdit(editList)); ReportManager.getInstance().updateObjectReport(df, p); } } catch (EditException ex) { logger.error("Enabled of disabled activity failed", ex); } return "done"; }
public void actionPerformed(ActionEvent e) { try { List<? extends MergeInputPort> inputPorts = merge.getInputPorts(); EventForwardingOutputPort outputPort = merge.getOutputPort(); List<Edit<?>> editList = new ArrayList<Edit<?>>(); for (MergeInputPort inputPort : inputPorts) { Datalink datalink = inputPort.getIncomingLink(); if (datalink != null) { editList.add(Tools.getDisconnectDatalinkAndRemovePortsEdit(datalink)); } } for (Datalink datalink : outputPort.getOutgoingLinks()) { editList.add(Tools.getDisconnectDatalinkAndRemovePortsEdit(datalink)); } if (editList.isEmpty()) { editManager.doDataflowEdit(dataflow, edits.getRemoveMergeEdit(dataflow, merge)); } else { editList.add(edits.getRemoveMergeEdit(dataflow, merge)); editManager.doDataflowEdit(dataflow, new CompoundEdit(editList)); } dataflowSelectionModel.removeSelection(merge); } catch (EditException e1) { logger.debug("Delete merge failed", e1); } }
public DefaultDispatchStackEdit(Processor processor) { super(processor); DispatchStackImpl stack = ((ProcessorImpl)processor).getDispatchStack(); // Top level parallelise layer int layer = 0; List<Edit<?>> edits = new ArrayList<Edit<?>>(); edits.add(new AddDispatchLayerEdit(stack, new Parallelize(MAX_JOBS), layer++)); edits.add(new AddDispatchLayerEdit(stack, new ErrorBounce(), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Failover(), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Retry(MAX_RETRIES, INITIAL_DELAY, MAX_DELAY, BACKOFF_FACTOR), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Invoke(), layer++)); compoundEdit=new CompoundEdit(edits); }
public DefaultDispatchStackEdit(Processor processor) { super(processor); DispatchStackImpl stack = ((ProcessorImpl)processor).getDispatchStack(); // Top level parallelise layer int layer = 0; List<Edit<?>> edits = new ArrayList<Edit<?>>(); edits.add(new AddDispatchLayerEdit(stack, new Parallelize(MAX_JOBS), layer++)); edits.add(new AddDispatchLayerEdit(stack, new ErrorBounce(), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Failover(), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Retry(), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Stop(), layer++)); edits.add(new AddDispatchLayerEdit(stack, new Invoke(), layer++)); compoundEdit=new CompoundEdit(edits); }
@Override public void configure(BiomartActivityConfigurationBean configurationBean) throws ActivityConfigurationException { this.configurationBean = configurationBean; biomartQuery = MartServiceXMLHandler.elementToMartQuery(configurationBean.getMartQuery(), null); String location = biomartQuery.getMartService().getLocation(); List<Edit<?>> editList = new ArrayList<Edit<?>>(); buildInputPorts(editList); buildOutputPorts(editList); try { new CompoundEdit(editList).doEdit(); } catch (EditException e) { throw new ActivityConfigurationException(e); } }