Clean up warnings and dependencies.
diff --git a/pom.xml b/pom.xml
index 9b72c52..4fc2733 100644
--- a/pom.xml
+++ b/pom.xml
@@ -30,6 +30,11 @@
<version>${log4j.version}</version>
</dependency>
<dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+ <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
@@ -40,6 +45,26 @@
<artifactId>robundle</artifactId>
<version>0.3.1</version>
</dependency>
+ <dependency>
+ <groupId>uk.org.taverna.databundle</groupId>
+ <artifactId>databundle</artifactId>
+ <version>${taverna.databundle.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.scufl2</groupId>
+ <artifactId>scufl2-api</artifactId>
+ <version>${scufl2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.compendium</artifactId>
+ <version>${osgi.core.version}</version>
+ </dependency>
</dependencies>
</dependencyManagement>
<repositories>
diff --git a/taverna-capability-api/pom.xml b/taverna-capability-api/pom.xml
index b895e17..a32cec2 100644
--- a/taverna-capability-api/pom.xml
+++ b/taverna-capability-api/pom.xml
@@ -19,7 +19,6 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
diff --git a/taverna-capability-impl/pom.xml b/taverna-capability-impl/pom.xml
index 02ea9cd..00431f0 100644
--- a/taverna-capability-impl/pom.xml
+++ b/taverna-capability-impl/pom.xml
@@ -37,7 +37,6 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
@@ -54,7 +53,6 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
diff --git a/taverna-execution-api/pom.xml b/taverna-execution-api/pom.xml
index afabb91..ba7e453 100644
--- a/taverna-execution-api/pom.xml
+++ b/taverna-execution-api/pom.xml
@@ -25,23 +25,21 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
</dependency>
<dependency>
<groupId>org.purl.wf4ever.robundle</groupId>
<artifactId>robundle</artifactId>
</dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
</dependencies>
<repositories>
<repository>
diff --git a/taverna-execution-api/src/main/java/uk/org/taverna/platform/execution/api/ExecutionService.java b/taverna-execution-api/src/main/java/uk/org/taverna/platform/execution/api/ExecutionService.java
index 75955a3..2ae7067 100755
--- a/taverna-execution-api/src/main/java/uk/org/taverna/platform/execution/api/ExecutionService.java
+++ b/taverna-execution-api/src/main/java/uk/org/taverna/platform/execution/api/ExecutionService.java
@@ -64,7 +64,7 @@
*
* @return the ExecutionEnvironments available for this ExecutionService
*/
- public Set<ExecutionEnvironment> getExecutionEnvivonments();
+ public Set<ExecutionEnvironment> getExecutionEnvironments();
/**
* Creates a workflow execution and returns its ID.
diff --git a/taverna-execution-impl/pom.xml b/taverna-execution-impl/pom.xml
index 91b6537..47f5f79 100644
--- a/taverna-execution-impl/pom.xml
+++ b/taverna-execution-impl/pom.xml
@@ -33,12 +33,10 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
</dependency>
</dependencies>
<repositories>
diff --git a/taverna-execution-impl/src/main/java/uk/org/taverna/platform/execution/impl/ExecutionEnvironmentServiceImpl.java b/taverna-execution-impl/src/main/java/uk/org/taverna/platform/execution/impl/ExecutionEnvironmentServiceImpl.java
index 367aec5..13eeec2 100644
--- a/taverna-execution-impl/src/main/java/uk/org/taverna/platform/execution/impl/ExecutionEnvironmentServiceImpl.java
+++ b/taverna-execution-impl/src/main/java/uk/org/taverna/platform/execution/impl/ExecutionEnvironmentServiceImpl.java
@@ -49,18 +49,18 @@
* @author David Withers
*/
public class ExecutionEnvironmentServiceImpl implements ExecutionEnvironmentService {
-
private static final Logger logger = Logger.getLogger(ExecutionEnvironmentServiceImpl.class.getName());
+ @SuppressWarnings("unused")
private final Scufl2Tools scufl2Tools = new Scufl2Tools();
-
private Set<ExecutionService> executionServices;
@Override
public Set<ExecutionEnvironment> getExecutionEnvironments() {
Set<ExecutionEnvironment> executionEnvironments = new HashSet<>();
for (ExecutionService executionService : executionServices)
- executionEnvironments.addAll(executionService.getExecutionEnvivonments());
+ executionEnvironments.addAll(executionService
+ .getExecutionEnvironments());
return executionEnvironments;
}
@@ -98,7 +98,7 @@
executionEnvironment.getName(), activity.getType()));
return false;
}
- Configuration activityConfiguration = scufl2Tools.configurationFor(activity, profile);
+ Configuration activityConfiguration = activity.getConfiguration();
if (!isValidActivityConfiguration(executionEnvironment, activityConfiguration, activity)) {
logger.fine(MessageFormat.format("Invalid activity configuration for {1} in {0}",
executionEnvironment.getName(), activity.getType()));
diff --git a/taverna-execution-local/pom.xml b/taverna-execution-local/pom.xml
index 4b537bf..8b55f45 100644
--- a/taverna-execution-local/pom.xml
+++ b/taverna-execution-local/pom.xml
@@ -75,17 +75,14 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
diff --git a/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionService.java b/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionService.java
index e7de9bf..9038e0f 100644
--- a/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionService.java
+++ b/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionService.java
@@ -47,37 +47,39 @@
*
* @author David Withers
*/
-public class LocalExecutionService extends AbstractExecutionService implements WorkflowCompiler {
-
+public class LocalExecutionService extends AbstractExecutionService implements
+ WorkflowCompiler {
private Edits edits;
-
private ActivityService activityService;
-
private DispatchLayerService dispatchLayerService;
-
private ReferenceService referenceService;
/**
- * Constructs an execution service that executes workflows using the T2 dataflow engine.
+ * Constructs an execution service that executes workflows using the T2
+ * dataflow engine.
*/
public LocalExecutionService() {
- super(LocalExecutionService.class.getName(), "Taverna Local Execution Service",
+ super(
+ LocalExecutionService.class.getName(),
+ "Taverna Local Execution Service",
"Execution Service for executing Taverna workflows using a local Taverna Dataflow Engine");
}
@Override
- public Set<ExecutionEnvironment> getExecutionEnvivonments() {
- Set<ExecutionEnvironment> executionEnvironments = new HashSet<ExecutionEnvironment>();
- executionEnvironments.add(new LocalExecutionEnvironment(this, activityService,
- dispatchLayerService));
+ public Set<ExecutionEnvironment> getExecutionEnvironments() {
+ Set<ExecutionEnvironment> executionEnvironments = new HashSet<>();
+ executionEnvironments.add(new LocalExecutionEnvironment(this,
+ activityService, dispatchLayerService));
return executionEnvironments;
}
@Override
- protected Execution createExecutionImpl(WorkflowBundle workflowBundle, Workflow workflow,
- Profile profile, Bundle dataBundle) throws InvalidWorkflowException {
- return new LocalExecution(workflowBundle, workflow, profile, dataBundle,
- referenceService, edits, activityService, dispatchLayerService);
+ protected Execution createExecutionImpl(WorkflowBundle workflowBundle,
+ Workflow workflow, Profile profile, Bundle dataBundle)
+ throws InvalidWorkflowException {
+ return new LocalExecution(workflowBundle, workflow, profile,
+ dataBundle, referenceService, edits, activityService,
+ dispatchLayerService);
}
/**
diff --git a/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/WorkflowToDataflowMapper.java b/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/WorkflowToDataflowMapper.java
index a8def44..986705a 100644
--- a/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/WorkflowToDataflowMapper.java
+++ b/taverna-execution-local/src/main/java/uk/org/taverna/platform/execution/impl/local/WorkflowToDataflowMapper.java
@@ -87,7 +87,7 @@
/**
* Translates a scufl2 {@link Workflow} into a {@link Dataflow}.
- *
+ *
* @author David Withers
*/
public class WorkflowToDataflowMapper {
@@ -105,13 +105,15 @@
private final Map<net.sf.taverna.t2.workflowmodel.Processor, Processor> dataflowToWorkflowProcessors;
private final Map<Activity, net.sf.taverna.t2.workflowmodel.processor.activity.Activity<?>> workflowToDataflowActivities;
private final Map<net.sf.taverna.t2.workflowmodel.processor.activity.Activity<?>, Activity> dataflowToWorkflowActivities;
+ @SuppressWarnings("unused")
private final WorkflowBundle workflowBundle;
private final Profile profile;
private final ActivityService activityService;
private final DispatchLayerService dispatchLayerService;
- public WorkflowToDataflowMapper(WorkflowBundle workflowBundle, Profile profile, Edits edits,
- ActivityService activityService, DispatchLayerService dispatchLayerService) {
+ public WorkflowToDataflowMapper(WorkflowBundle workflowBundle,
+ Profile profile, Edits edits, ActivityService activityService,
+ DispatchLayerService dispatchLayerService) {
this.workflowBundle = workflowBundle;
this.profile = profile;
this.edits = edits;
@@ -132,7 +134,8 @@
return dataflowToWorkflow.get(dataflow);
}
- public Dataflow getDataflow(Workflow workflow) throws InvalidWorkflowException {
+ public Dataflow getDataflow(Workflow workflow)
+ throws InvalidWorkflowException {
if (!workflowToDataflow.containsKey(workflow)) {
try {
Dataflow dataflow = createDataflow(workflow);
@@ -175,7 +178,7 @@
// create the dataflow
Dataflow dataflow = edits.createDataflow();
// set the dataflow name
- edits.getUpdateDataflowNameEdit(dataflow, new String(workflow.getName())).doEdit();
+ edits.getUpdateDataflowNameEdit(dataflow, workflow.getName()).doEdit();
addInputPorts(workflow, dataflow);
addOutputPorts(workflow, dataflow);
@@ -186,10 +189,10 @@
return dataflow;
}
- private void addProcessors(Workflow workflow, Dataflow dataflow) throws EditException,
- ActivityNotFoundException, ActivityConfigurationException,
- InvalidWorkflowException, DispatchLayerNotFoundException,
- DispatchLayerConfigurationException {
+ private void addProcessors(Workflow workflow, Dataflow dataflow)
+ throws EditException, ActivityNotFoundException,
+ ActivityConfigurationException, InvalidWorkflowException,
+ DispatchLayerNotFoundException, DispatchLayerConfigurationException {
for (Processor processor : workflow.getProcessors()) {
net.sf.taverna.t2.workflowmodel.Processor dataflowProcessor = edits
.createProcessor(processor.getName());
@@ -198,8 +201,9 @@
workflowToDataflowProcessors.put(processor, dataflowProcessor);
dataflowToWorkflowProcessors.put(dataflowProcessor, processor);
// add input ports
- for (InputProcessorPort inputProcessorPort : processor.getInputPorts()) {
- if (scufl2Tools.datalinksTo(inputProcessorPort).isEmpty())
+ for (InputProcessorPort inputProcessorPort : processor
+ .getInputPorts()) {
+ if (inputProcessorPort.getDatalinksTo().isEmpty())
continue;
ProcessorInputPort processorInputPort = edits
.createProcessorInputPort(dataflowProcessor,
@@ -210,12 +214,15 @@
inputPorts.put(inputProcessorPort, processorInputPort);
}
// add output ports
- for (OutputProcessorPort outputProcessorPort : processor.getOutputPorts()) {
- ProcessorOutputPort processorOutputPort = edits.createProcessorOutputPort(
- dataflowProcessor, outputProcessorPort.getName(),
- outputProcessorPort.getDepth(), outputProcessorPort.getGranularDepth());
- edits.getAddProcessorOutputPortEdit(dataflowProcessor, processorOutputPort)
- .doEdit();
+ for (OutputProcessorPort outputProcessorPort : processor
+ .getOutputPorts()) {
+ ProcessorOutputPort processorOutputPort = edits
+ .createProcessorOutputPort(dataflowProcessor,
+ outputProcessorPort.getName(),
+ outputProcessorPort.getDepth(),
+ outputProcessorPort.getGranularDepth());
+ edits.getAddProcessorOutputPortEdit(dataflowProcessor,
+ processorOutputPort).doEdit();
outputPorts.put(outputProcessorPort, processorOutputPort);
}
@@ -233,14 +240,13 @@
private void addDispatchStack(Processor processor,
net.sf.taverna.t2.workflowmodel.Processor dataflowProcessor)
- throws DispatchLayerNotFoundException, DispatchLayerConfigurationException,
- EditException {
+ throws DispatchLayerNotFoundException,
+ DispatchLayerConfigurationException, EditException {
DispatchStack dispatchStack = dataflowProcessor.getDispatchStack();
JsonNode json = null;
try {
- Configuration configuration = scufl2Tools.configurationFor(processor, profile);
- json = configuration.getJson();
+ json = processor.getConfiguration(profile).getJson();
} catch (IndexOutOfBoundsException e) {
// no configuration for processor
}
@@ -254,49 +260,59 @@
dispatchStack,
URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/ErrorBounce"),
layer++, null);
- addDispatchLayer(dispatchStack,
+ addDispatchLayer(
+ dispatchStack,
URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Failover"),
layer++, null);
- addDispatchLayer(dispatchStack,
+ addDispatchLayer(
+ dispatchStack,
URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Retry"),
layer++, json == null ? null : json.get("retry"));
- addDispatchLayer(dispatchStack,
+ addDispatchLayer(
+ dispatchStack,
URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Stop"),
layer++, null);
- addDispatchLayer(dispatchStack,
+ addDispatchLayer(
+ dispatchStack,
URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Invoke"),
layer++, null);
}
- private void addDispatchLayer(DispatchStack dispatchStack, URI dispatchLayerType, int layer,
- JsonNode json) throws DispatchLayerConfigurationException,
+ private void addDispatchLayer(DispatchStack dispatchStack,
+ URI dispatchLayerType, int layer, JsonNode json)
+ throws DispatchLayerConfigurationException,
DispatchLayerNotFoundException, EditException {
// create the dispatch layer
- DispatchLayer<?> dispatchLayer = dispatchLayerService.createDispatchLayer(
- dispatchLayerType, json);
+ DispatchLayer<?> dispatchLayer = dispatchLayerService
+ .createDispatchLayer(dispatchLayerType, json);
// add the dispatch layer to the dispatch layer stack
- edits.getAddDispatchLayerEdit(dispatchStack, dispatchLayer, layer).doEdit();
+ edits.getAddDispatchLayerEdit(dispatchStack, dispatchLayer, layer)
+ .doEdit();
}
private void addIterationStrategy(Processor processor,
- net.sf.taverna.t2.workflowmodel.Processor dataflowProcessor) throws EditException,
- InvalidWorkflowException {
+ net.sf.taverna.t2.workflowmodel.Processor dataflowProcessor)
+ throws EditException, InvalidWorkflowException {
// get the iteration strategy from the processor
net.sf.taverna.t2.workflowmodel.processor.iteration.IterationStrategyStack dataflowIterationStrategyStack = dataflowProcessor
.getIterationStrategy();
// clear the iteration strategy
- edits.getClearIterationStrategyStackEdit(dataflowIterationStrategyStack).doEdit();
- IterationStrategyStack iterationStrategyStack = processor.getIterationStrategyStack();
+ edits.getClearIterationStrategyStackEdit(dataflowIterationStrategyStack)
+ .doEdit();
+ IterationStrategyStack iterationStrategyStack = processor
+ .getIterationStrategyStack();
for (IterationStrategyTopNode iterationStrategyTopNode : iterationStrategyStack) {
// create iteration strategy
- IterationStrategy dataflowIterationStrategy = edits.createIterationStrategy();
+ IterationStrategy dataflowIterationStrategy = edits
+ .createIterationStrategy();
// add iteration strategy to the stack
edits.getAddIterationStrategyEdit(dataflowIterationStrategyStack,
dataflowIterationStrategy).doEdit();
// add the node to the iteration strategy
addIterationStrategyNode(dataflowIterationStrategy,
- dataflowIterationStrategy.getTerminalNode(), iterationStrategyTopNode);
+ dataflowIterationStrategy.getTerminalNode(),
+ iterationStrategyTopNode);
}
}
@@ -311,39 +327,45 @@
childDataflowIterationStrategyNode = new net.sf.taverna.t2.workflowmodel.processor.iteration.CrossProduct();
for (IterationStrategyNode iterationStrategyNode2 : crossProduct)
addIterationStrategyNode(dataflowIterationStrategy,
- childDataflowIterationStrategyNode, iterationStrategyNode2);
+ childDataflowIterationStrategyNode,
+ iterationStrategyNode2);
} else if (iterationStrategyNode instanceof DotProduct) {
DotProduct dotProduct = (DotProduct) iterationStrategyNode;
childDataflowIterationStrategyNode = new net.sf.taverna.t2.workflowmodel.processor.iteration.DotProduct();
for (IterationStrategyNode iterationStrategyNode2 : dotProduct)
addIterationStrategyNode(dataflowIterationStrategy,
- childDataflowIterationStrategyNode, iterationStrategyNode2);
+ childDataflowIterationStrategyNode,
+ iterationStrategyNode2);
} else if (iterationStrategyNode instanceof PortNode) {
PortNode portNode = (PortNode) iterationStrategyNode;
Integer desiredDepth = portNode.getDesiredDepth();
if (desiredDepth == null)
desiredDepth = portNode.getInputProcessorPort().getDepth();
- NamedInputPortNode namedInputPortNode = new NamedInputPortNode(portNode
- .getInputProcessorPort().getName(), desiredDepth);
- edits.getAddIterationStrategyInputNodeEdit(dataflowIterationStrategy,
- namedInputPortNode).doEdit();
+ NamedInputPortNode namedInputPortNode = new NamedInputPortNode(
+ portNode.getInputProcessorPort().getName(), desiredDepth);
+ edits.getAddIterationStrategyInputNodeEdit(
+ dataflowIterationStrategy, namedInputPortNode).doEdit();
childDataflowIterationStrategyNode = namedInputPortNode;
} else {
- throw new InvalidWorkflowException("Unknown IterationStrategyNode type : "
- + iterationStrategyNode.getClass().getName());
+ throw new InvalidWorkflowException(
+ "Unknown IterationStrategyNode type : "
+ + iterationStrategyNode.getClass().getName());
}
- childDataflowIterationStrategyNode.setParent(dataflowIterationStrategyNode);
+ childDataflowIterationStrategyNode
+ .setParent(dataflowIterationStrategyNode);
}
- private void addActivity(ProcessorBinding processorBinding) throws EditException,
- ActivityNotFoundException, ActivityConfigurationException, InvalidWorkflowException {
+ private void addActivity(ProcessorBinding processorBinding)
+ throws EditException, ActivityNotFoundException,
+ ActivityConfigurationException, InvalidWorkflowException {
net.sf.taverna.t2.workflowmodel.Processor processor = workflowToDataflowProcessors
.get(processorBinding.getBoundProcessor());
Activity scufl2Activity = processorBinding.getBoundActivity();
URI activityType = scufl2Activity.getType();
if (!activityService.activityExists(activityType))
- throw new ActivityNotFoundException("No activity exists for " + activityType);
- Configuration configuration = scufl2Tools.configurationFor(scufl2Activity, profile);
+ throw new ActivityNotFoundException("No activity exists for "
+ + activityType);
+ Configuration configuration = scufl2Activity.getConfiguration();
// create the activity
net.sf.taverna.t2.workflowmodel.processor.activity.Activity<?> activity = activityService
@@ -351,52 +373,67 @@
// check if we have a nested workflow
if (activityType.equals(NESTED_WORKFLOW_URI)) {
if (activity instanceof NestedDataflow) {
- Workflow nestedWorkflow = scufl2Tools.nestedWorkflowForProcessor(
- processorBinding.getBoundProcessor(), profile);
+ Workflow nestedWorkflow = scufl2Tools
+ .nestedWorkflowForProcessor(
+ processorBinding.getBoundProcessor(), profile);
((NestedDataflow) activity)
.setNestedDataflow(getDataflow(nestedWorkflow));
- } else {
+ } else
throw new ActivityConfigurationException(
"Activity is not an instance of NestedDataflow");
- }
}
// add the activity to the processor
edits.getAddActivityEdit(processor, activity).doEdit();
// add input ports
- for (InputActivityPort inputActivityPort : scufl2Activity.getInputPorts()) {
- ActivityInputPort activityInputPort = edits.createActivityInputPort(
- inputActivityPort.getName(), inputActivityPort.getDepth(), false,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(), String.class);
- edits.getAddActivityInputPortEdit(activity, activityInputPort).doEdit();
+ for (InputActivityPort inputActivityPort : scufl2Activity
+ .getInputPorts()) {
+ ActivityInputPort activityInputPort = edits
+ .createActivityInputPort(
+ inputActivityPort.getName(),
+ inputActivityPort.getDepth(),
+ false,
+ new ArrayList<Class<? extends ExternalReferenceSPI>>(),
+ String.class);
+ edits.getAddActivityInputPortEdit(activity, activityInputPort)
+ .doEdit();
}
// add output ports
- for (OutputActivityPort outputActivityPort : scufl2Activity.getOutputPorts()) {
- ActivityOutputPort activitytOutputPort = edits.createActivityOutputPort(
- outputActivityPort.getName(), outputActivityPort.getDepth(),
- outputActivityPort.getGranularDepth());
- edits.getAddActivityOutputPortEdit(activity, activitytOutputPort).doEdit();
+ for (OutputActivityPort outputActivityPort : scufl2Activity
+ .getOutputPorts()) {
+ ActivityOutputPort activitytOutputPort = edits
+ .createActivityOutputPort(outputActivityPort.getName(),
+ outputActivityPort.getDepth(),
+ outputActivityPort.getGranularDepth());
+ edits.getAddActivityOutputPortEdit(activity, activitytOutputPort)
+ .doEdit();
}
// map input ports
- for (ProcessorInputPortBinding portBinding : processorBinding.getInputPortBindings()) {
- InputProcessorPort processorPort = portBinding.getBoundProcessorPort();
+ for (ProcessorInputPortBinding portBinding : processorBinding
+ .getInputPortBindings()) {
+ InputProcessorPort processorPort = portBinding
+ .getBoundProcessorPort();
InputActivityPort activityPort = portBinding.getBoundActivityPort();
- edits.getAddActivityInputPortMappingEdit(activity, processorPort.getName(),
- activityPort.getName()).doEdit();
+ edits.getAddActivityInputPortMappingEdit(activity,
+ processorPort.getName(), activityPort.getName()).doEdit();
}
// map output ports
- for (ProcessorOutputPortBinding portBinding : processorBinding.getOutputPortBindings()) {
- OutputProcessorPort processorPort = portBinding.getBoundProcessorPort();
- OutputActivityPort activityPort = portBinding.getBoundActivityPort();
- edits.getAddActivityOutputPortMappingEdit(activity, processorPort.getName(),
- activityPort.getName()).doEdit();
+ for (ProcessorOutputPortBinding portBinding : processorBinding
+ .getOutputPortBindings()) {
+ OutputProcessorPort processorPort = portBinding
+ .getBoundProcessorPort();
+ OutputActivityPort activityPort = portBinding
+ .getBoundActivityPort();
+ edits.getAddActivityOutputPortMappingEdit(activity,
+ processorPort.getName(), activityPort.getName()).doEdit();
}
workflowToDataflowActivities.put(scufl2Activity, activity);
dataflowToWorkflowActivities.put(activity, scufl2Activity);
}
- private void addDataLinks(Workflow workflow, Dataflow dataflow) throws EditException {
+ private void addDataLinks(Workflow workflow, Dataflow dataflow)
+ throws EditException {
for (DataLink dataLink : workflow.getDataLinks()) {
ReceiverPort receiverPort = dataLink.getSendsTo();
SenderPort senderPort = dataLink.getReceivesFrom();
@@ -411,33 +448,35 @@
}
Merge merge = merges.get(receiverPort);
// create merge input port
- MergeInputPort mergeInputPort = edits.createMergeInputPort(merge, "input"
- + mergePosition, sink.getDepth());
+ MergeInputPort mergeInputPort = edits.createMergeInputPort(
+ merge, "input" + mergePosition, sink.getDepth());
// add it to the correct position in the merge
@SuppressWarnings("unchecked")
- List<MergeInputPort> mergeInputPorts = (List<MergeInputPort>) merge.getInputPorts();
- if (mergePosition > mergeInputPorts.size()) {
+ List<MergeInputPort> mergeInputPorts = (List<MergeInputPort>) merge
+ .getInputPorts();
+ if (mergePosition > mergeInputPorts.size())
mergeInputPorts.add(mergeInputPort);
- } else {
+ else
mergeInputPorts.add(mergePosition, mergeInputPort);
- }
// connect a datalink into the merge
- Datalink datalinkIn = edits.createDatalink(source, mergeInputPort);
+ Datalink datalinkIn = edits.createDatalink(source,
+ mergeInputPort);
edits.getConnectDatalinkEdit(datalinkIn).doEdit();
// check if the merge output has been connected
- EventForwardingOutputPort mergeOutputPort = merge.getOutputPort();
- if (mergeOutputPort.getOutgoingLinks().size() == 0) {
- Datalink datalinkOut = edits.createDatalink(merge.getOutputPort(), sink);
+ EventForwardingOutputPort mergeOutputPort = merge
+ .getOutputPort();
+ if (mergeOutputPort.getOutgoingLinks().isEmpty()) {
+ Datalink datalinkOut = edits.createDatalink(
+ merge.getOutputPort(), sink);
edits.getConnectDatalinkEdit(datalinkOut).doEdit();
} else if (mergeOutputPort.getOutgoingLinks().size() == 1) {
- if (mergeOutputPort.getOutgoingLinks().iterator().next().getSink() != sink) {
+ if (mergeOutputPort.getOutgoingLinks().iterator().next()
+ .getSink() != sink)
throw new EditException(
"Cannot add a different sinkPort to a Merge that already has one defined");
- }
- } else {
+ } else
throw new EditException(
"The merge instance cannot have more that 1 outgoing Datalink");
- }
} else {
Datalink datalink = edits.createDatalink(source, sink);
edits.getConnectDatalinkEdit(datalink).doEdit();
@@ -449,31 +488,40 @@
for (ControlLink controlLink : workflow.getControlLinks()) {
if (controlLink instanceof BlockingControlLink) {
BlockingControlLink blockingControlLink = (BlockingControlLink) controlLink;
- Processor untilFinished = blockingControlLink.getUntilFinished();
+ Processor untilFinished = blockingControlLink
+ .getUntilFinished();
Processor block = blockingControlLink.getBlock();
- edits.getCreateConditionEdit(workflowToDataflowProcessors.get(untilFinished),
+ edits.getCreateConditionEdit(
+ workflowToDataflowProcessors.get(untilFinished),
workflowToDataflowProcessors.get(block)).doEdit();
}
}
}
- private void addOutputPorts(Workflow workflow, Dataflow dataflow) throws EditException {
+ private void addOutputPorts(Workflow workflow, Dataflow dataflow)
+ throws EditException {
for (OutputWorkflowPort outputWorkflowPort : workflow.getOutputPorts()) {
- DataflowOutputPort dataflowOutputPort = edits.createDataflowOutputPort(
- outputWorkflowPort.getName(), dataflow);
- edits.getAddDataflowOutputPortEdit(dataflow, dataflowOutputPort).doEdit();
- inputPorts.put(outputWorkflowPort, dataflowOutputPort.getInternalInputPort());
+ DataflowOutputPort dataflowOutputPort = edits
+ .createDataflowOutputPort(outputWorkflowPort.getName(),
+ dataflow);
+ edits.getAddDataflowOutputPortEdit(dataflow, dataflowOutputPort)
+ .doEdit();
+ inputPorts.put(outputWorkflowPort,
+ dataflowOutputPort.getInternalInputPort());
}
}
- private void addInputPorts(Workflow workflow, Dataflow dataflow) throws EditException {
+ private void addInputPorts(Workflow workflow, Dataflow dataflow)
+ throws EditException {
for (InputWorkflowPort inputWorkflowPort : workflow.getInputPorts()) {
- DataflowInputPort dataflowInputPort = edits.createDataflowInputPort(
- inputWorkflowPort.getName(), inputWorkflowPort.getDepth(),
- inputWorkflowPort.getDepth(), dataflow);
- edits.getAddDataflowInputPortEdit(dataflow, dataflowInputPort).doEdit();
- outputPorts.put(inputWorkflowPort, dataflowInputPort.getInternalOutputPort());
+ DataflowInputPort dataflowInputPort = edits
+ .createDataflowInputPort(inputWorkflowPort.getName(),
+ inputWorkflowPort.getDepth(),
+ inputWorkflowPort.getDepth(), dataflow);
+ edits.getAddDataflowInputPortEdit(dataflow, dataflowInputPort)
+ .doEdit();
+ outputPorts.put(inputWorkflowPort,
+ dataflowInputPort.getInternalOutputPort());
}
}
-
}
diff --git a/taverna-execution-local/src/test/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionTest.java b/taverna-execution-local/src/test/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionTest.java
index 3bb5d42..58a667e 100644
--- a/taverna-execution-local/src/test/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionTest.java
+++ b/taverna-execution-local/src/test/java/uk/org/taverna/platform/execution/impl/local/LocalExecutionTest.java
@@ -143,6 +143,7 @@
// System.out.println(report);
// }
+ @SuppressWarnings("unused")
private void waitForResult(Map<String, Object> results, String port, WorkflowReport report)
throws InterruptedException {
int wait = 0;
diff --git a/taverna-execution-remote/pom.xml b/taverna-execution-remote/pom.xml
index 7c1a63f..a3b7aae 100644
--- a/taverna-execution-remote/pom.xml
+++ b/taverna-execution-remote/pom.xml
@@ -39,12 +39,10 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
</dependency>
</dependencies>
<repositories>
diff --git a/taverna-execution-remote/src/main/java/uk/org/taverna/platform/execution/impl/remote/RemoteExecutionService.java b/taverna-execution-remote/src/main/java/uk/org/taverna/platform/execution/impl/remote/RemoteExecutionService.java
index 53e8e9c..6ca8db7 100644
--- a/taverna-execution-remote/src/main/java/uk/org/taverna/platform/execution/impl/remote/RemoteExecutionService.java
+++ b/taverna-execution-remote/src/main/java/uk/org/taverna/platform/execution/impl/remote/RemoteExecutionService.java
@@ -53,7 +53,7 @@
}
@Override
- public Set<ExecutionEnvironment> getExecutionEnvivonments() {
+ public Set<ExecutionEnvironment> getExecutionEnvironments() {
return Collections.<ExecutionEnvironment>emptySet();
}
diff --git a/taverna-report-api/pom.xml b/taverna-report-api/pom.xml
index 40aa0f1..a7b6650 100644
--- a/taverna-report-api/pom.xml
+++ b/taverna-report-api/pom.xml
@@ -14,28 +14,14 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
- <dependency>
- <groupId>uk.org.taverna.scufl2</groupId>
- <artifactId>scufl2-rdfxml</artifactId>
- <version>${scufl2.version}</version>
- </dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.osgi</groupId>
- <artifactId>org.osgi.compendium</artifactId>
- <version>${osgi.core.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
diff --git a/taverna-run-api/pom.xml b/taverna-run-api/pom.xml
index 77c960c..1b1c8f0 100644
--- a/taverna-run-api/pom.xml
+++ b/taverna-run-api/pom.xml
@@ -25,17 +25,14 @@
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
diff --git a/taverna-run-impl/pom.xml b/taverna-run-impl/pom.xml
index 36fd657..cf6a2e7 100644
--- a/taverna-run-impl/pom.xml
+++ b/taverna-run-impl/pom.xml
@@ -42,27 +42,22 @@
<dependency>
<groupId>uk.org.taverna.configuration</groupId>
<artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.scufl2</groupId>
<artifactId>scufl2-api</artifactId>
- <version>${scufl2.version}</version>
</dependency>
<dependency>
<groupId>uk.org.taverna.databundle</groupId>
<artifactId>databundle</artifactId>
- <version>${taverna.databundle.version}</version>
</dependency>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.compendium</artifactId>
- <version>${osgi.core.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
