private void buildOutputPortMap() { outputMap = new HashMap<String, OutputPort>(); for (OutputPort outputPort : getOutputPorts()) { outputMap.put(outputPort.getName(), outputPort); } }
public static OutputPort getActivityOutputPort(Activity<?> activity, String portName) { OutputPort activityOutputPort = null; for (OutputPort outputPort : activity.getOutputPorts()) { if (outputPort.getName().equals(portName)) { activityOutputPort = outputPort; break; } } return activityOutputPort; }
public static OutputPort getActivityOutputPort(Activity<?> activity, String portName) { OutputPort activityOutputPort = null; for (OutputPort outputPort : activity.getOutputPorts()) { if (outputPort.getName().equals(portName)) { activityOutputPort = outputPort; break; } } return activityOutputPort; }
private Integer findPortDepth(final String portName) { final Set<OutputPort> ports = this.activity.getOutputPorts(); for (final OutputPort op : ports) { if (op.getName().equals(portName)) { return op.getDepth(); } } return null; }
private List<String> getActivityOutputPorts() { // TODO: Support multiple activities Activity<?> activity = getFirstProcessorActivity(); if (activity == null) { return new ArrayList<String>(); } List<String> ports = new ArrayList<String>(); for (OutputPort outPort : activity.getOutputPorts()) { if (outPort.getDepth() == 0) { ports.add(outPort.getName()); } } Collections.sort(ports); return ports; }
private XMLInputSplitter createSplitter() { List<String> inputNames = new ArrayList<String>(); List<String> inputTypes = new ArrayList<String>(); List<String> outputNames = new ArrayList<String>(); //FIXME: need to use the definition beans for now to get the mimetype. Need to use the actual InputPort once the mimetype becomes available again. for (ActivityInputPortDefinitionBean defBean : getConfiguration().getInputPortDefinitions()) { inputNames.add(defBean.getName()); inputTypes.add(defBean.getMimeTypes().get(0)); } for (OutputPort outputPorts : getOutputPorts()) { outputNames.add(outputPorts.getName()); } return new XMLInputSplitter(typeDescriptor,inputNames.toArray(new String[]{}),inputTypes.toArray(new String[]{}),outputNames.toArray(new String[]{})); }
private XMLInputSplitter createSplitter() { List<String> inputNames = new ArrayList<String>(); List<String> inputTypes = new ArrayList<String>(); List<String> outputNames = new ArrayList<String>(); //FIXME: need to use the definition beans for now to get the mimetype. Need to use the actual InputPort once the mimetype becomes available again. for (ActivityInputPortDefinitionBean defBean : getConfiguration().getInputPortDefinitions()) { inputNames.add(defBean.getName()); inputTypes.add(defBean.getMimeTypes().get(0)); } for (OutputPort outputPorts : getOutputPorts()) { outputNames.add(outputPorts.getName()); } return new XMLInputSplitter(typeDescriptor,inputNames.toArray(new String[]{}),inputTypes.toArray(new String[]{}),outputNames.toArray(new String[]{})); }
private static ActivityOutputPort getActivityOutputPort( Activity<?> activity, ProcessorPort processorOutputPort) { ProcessorInputPort result = null; for (Entry<String, String> mapEntry : activity.getOutputPortMapping() .entrySet()) { if (mapEntry.getKey().equals(processorOutputPort.getName())) { for (OutputPort activityOutputPort : activity .getOutputPorts()) { if (activityOutputPort.getName().equals(mapEntry.getValue())) { return (ActivityOutputPort) activityOutputPort; } } break; } } return null; }
public static ProcessorOutputPort getProcessorOutputPort( Processor processor, Activity<?> activity, OutputPort activityOutputPort) { ProcessorOutputPort result = null; for (Entry<String, String> mapEntry : activity.getOutputPortMapping() .entrySet()) { if (mapEntry.getValue().equals(activityOutputPort.getName())) { for (ProcessorOutputPort processorOutputPort : processor .getOutputPorts()) { if (processorOutputPort.getName().equals(mapEntry.getKey())) { result = processorOutputPort; break; } } break; } } return result; }
private EventForwardingOutputPort getSourcePort(Processor processor, Activity<?> activity, String portName, List<Edit<?>> editList) { OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools.getActivityOutputPort(activity, portName); //check if processor port exists EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools.getProcessorOutputPort(processor, activity, activityPort); if (output == null) { //port doesn't exist so create a processor port and map it ProcessorOutputPort processorOutputPort = edits.createProcessorOutputPort(processor, activityPort.getName(), activityPort.getDepth(), activityPort.getGranularDepth()); editList.add(edits.getAddProcessorOutputPortEdit(processor, processorOutputPort)); editList.add(edits.getAddActivityOutputPortMappingEdit(activity, activityPort.getName(), activityPort.getName())); output = processorOutputPort; } return output; }
private EventForwardingOutputPort getSourcePort(Processor processor, Activity<?> activity, String portName, List<Edit<?>> editList) { OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools.getActivityOutputPort(activity, portName); //check if processor port exists EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools.getProcessorOutputPort(processor, activity, activityPort); if (output == null) { //port doesn't exist so create a processor port and map it ProcessorOutputPort processorOutputPort = edits.createProcessorOutputPort(processor, activityPort.getName(), activityPort.getDepth(), activityPort.getGranularDepth()); editList.add(edits.getAddProcessorOutputPortEdit(processor, processorOutputPort)); editList.add(edits.getAddActivityOutputPortMappingEdit(activity, activityPort.getName(), activityPort.getName())); output = processorOutputPort; } return output; }
private List<ProcessorOutputPort> determineOutputPortsForRemoval(Processor p,Activity<?>a) { List<ProcessorOutputPort> result = new ArrayList<ProcessorOutputPort>(); for (ProcessorOutputPort pPort : p.getOutputPorts()) { boolean found=false; for (OutputPort aPort : a.getOutputPorts()) { if (aPort.getName().equals(pPort.getName())) { if (pPort.getDepth() == aPort.getDepth() && pPort.getGranularDepth() == aPort.getGranularDepth()) { found=true; } break; } } if (!found) { result.add(pPort); } } return result; }
@Test public void testConfigureSoaplabActivityConfigurationBean() throws Exception { Set<String> expectedOutputs = new HashSet<String>(); expectedOutputs.add("report"); expectedOutputs.add("outfile"); activity.configure(configurationBean); Set<OutputPort> ports = activity.getOutputPorts(); assertEquals(expectedOutputs.size(), ports.size()); for (OutputPort outputPort : ports) { assertTrue("Wrong output : " + outputPort.getName(), expectedOutputs.remove(outputPort.getName())); } }
@Ignore("Integration test") @Test public void testConfigureSoaplabActivityConfigurationBean() throws Exception { Set<String> expectedOutputs = new HashSet<String>(); expectedOutputs.add("report"); expectedOutputs.add("outfile"); activity.configure(configurationBean); Set<OutputPort> ports = activity.getOutputPorts(); assertEquals(expectedOutputs.size(), ports.size()); for (OutputPort outputPort : ports) { assertTrue("Wrong output : " + outputPort.getName(), expectedOutputs.remove(outputPort.getName())); } }
@Test public void testConfigureWSDLActivityConfigurationBean() throws Exception { assertEquals("There should be 1 input ports", 1, activity .getInputPorts().size()); assertEquals("There should be 2 output ports", 2, activity .getOutputPorts().size()); assertEquals("parameters", activity.getInputPorts().iterator().next() .getName()); List<String> expectedOutputNames = new ArrayList<String>(); expectedOutputNames.add("parameters"); expectedOutputNames.add("attachmentList"); for (OutputPort port : activity.getOutputPorts()) { assertTrue("Unexpected output name:"+port.getName(),expectedOutputNames.contains(port.getName())); expectedOutputNames.remove(port.getName()); } assertEquals("Not all of the expected outputs were found, those remainng are:"+expectedOutputNames.toArray(),0,expectedOutputNames.size()); }
@Test public void testConfigureDataflowActivityConfigurationBean() throws Exception { activity.configure(dataflow); assertEquals(dataflow, activity.getConfiguration()); assertEquals(1, activity.getInputPorts().size()); assertEquals("input", activity.getInputPorts().iterator().next() .getName()); assertEquals(1, activity.getOutputPorts().size()); assertEquals("output", activity.getOutputPorts().iterator().next() .getName()); }
@Test public void testConfigureDataflowActivityConfigurationBean() throws Exception { activity.configure(configurationBean); assertEquals(configurationBean, activity.getConfiguration()); assertEquals(1, activity.getInputPorts().size()); assertEquals("input", activity.getInputPorts().iterator().next() .getName()); assertEquals(1, activity.getOutputPorts().size()); assertEquals("output", activity.getOutputPorts().iterator().next() .getName()); }
@Test public void testDoTranslationProcessor() throws Exception { BiomartActivity activity = (BiomartActivity) translator .doTranslation(biomartProcessor); assertEquals(biomartProcessor.getQueryElement(null).toString(), activity.getConfiguration().toString()); assertEquals(inputPortNames.size(), activity.getInputPorts().size()); for (InputPort port : activity.getInputPorts()) { assertTrue(inputPortNames.remove(port.getName())); } assertEquals(outputPortNames.size(), activity.getOutputPorts().size()); for (OutputPort port : activity.getOutputPorts()) { assertTrue(outputPortNames.remove(port.getName())); } }
@Test public void testDoTranslationProcessor() throws Exception { BiomartActivity activity = (BiomartActivity) translator .doTranslation(biomartProcessor); assertEquals(biomartProcessor.getQueryElement(null).toString(), activity.getConfiguration().toString()); assertEquals(inputPortNames.size(), activity.getInputPorts().size()); for (InputPort port : activity.getInputPorts()) { assertTrue(inputPortNames.remove(port.getName())); } assertEquals(outputPortNames.size(), activity.getOutputPorts().size()); for (OutputPort port : activity.getOutputPorts()) { assertTrue(outputPortNames.remove(port.getName())); } }
@Test public void testDoTranslationProcessor() throws Exception { BiomartActivity activity = (BiomartActivity) translator .doTranslation(biomartProcessor); assertEquals(biomartProcessor.getQueryElement(null).toString(), activity.getConfiguration() .getQuery().toString()); assertEquals(inputPortNames.size(), activity.getInputPorts().size()); for (InputPort port : activity.getInputPorts()) { assertTrue(inputPortNames.remove(port.getName())); } assertEquals(outputPortNames.size(), activity.getOutputPorts().size()); for (OutputPort port : activity.getOutputPorts()) { assertTrue(outputPortNames.remove(port.getName())); } }