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Posted to commits@airavata.apache.org by sh...@apache.org on 2015/03/25 21:24:41 UTC
[4/8] airavata git commit: Renamed simple-workflow module to workflow
and created a new workflow-core module which will keep all the core code
http://git-wip-us.apache.org/repos/asf/airavata/blob/509f2037/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParser.java
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diff --git a/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParser.java b/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParser.java
new file mode 100644
index 0000000..1e1a5c5
--- /dev/null
+++ b/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParser.java
@@ -0,0 +1,291 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.workflow.core.parser;
+
+import org.airavata.appcatalog.cpi.AppCatalogException;
+import org.airavata.appcatalog.cpi.WorkflowCatalog;
+import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
+import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
+import org.apache.airavata.model.workspace.experiment.Experiment;
+import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
+import org.apache.airavata.registry.cpi.Registry;
+import org.apache.airavata.registry.cpi.RegistryException;
+import org.apache.airavata.registry.cpi.RegistryModelType;
+import org.apache.airavata.workflow.core.WorkflowParser;
+import org.apache.airavata.workflow.core.dag.edge.DirectedEdge;
+import org.apache.airavata.workflow.core.dag.edge.Edge;
+import org.apache.airavata.workflow.core.dag.nodes.ApplicationNode;
+import org.apache.airavata.workflow.core.dag.nodes.ApplicationNodeImpl;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowInputNode;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowInputNodeImpl;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowNode;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowOutputNode;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowOutputNodeImpl;
+import org.apache.airavata.workflow.core.dag.port.InPort;
+import org.apache.airavata.workflow.core.dag.port.InputPortIml;
+import org.apache.airavata.workflow.core.dag.port.OutPort;
+import org.apache.airavata.workflow.core.dag.port.OutPortImpl;
+import org.apache.airavata.workflow.model.component.ComponentException;
+import org.apache.airavata.workflow.model.component.system.ConstantComponent;
+import org.apache.airavata.workflow.model.component.system.InputComponent;
+import org.apache.airavata.workflow.model.component.system.S3InputComponent;
+import org.apache.airavata.workflow.model.graph.DataEdge;
+import org.apache.airavata.workflow.model.graph.DataPort;
+import org.apache.airavata.workflow.model.graph.GraphException;
+import org.apache.airavata.workflow.model.graph.Node;
+import org.apache.airavata.workflow.model.graph.impl.NodeImpl;
+import org.apache.airavata.workflow.model.graph.system.OutputNode;
+import org.apache.airavata.workflow.model.graph.system.SystemDataPort;
+import org.apache.airavata.workflow.model.graph.ws.WSNode;
+import org.apache.airavata.workflow.model.graph.ws.WSPort;
+import org.apache.airavata.workflow.model.wf.Workflow;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class AiravataWorkflowParser implements WorkflowParser {
+
+ private String credentialToken ;
+
+ private Experiment experiment;
+ private Map<String, WorkflowNode> wfNodes = new HashMap<String, WorkflowNode>();
+
+
+ public AiravataWorkflowParser(String experimentId, String credentialToken) throws RegistryException {
+ this.experiment = getExperiment(experimentId);
+ this.credentialToken = credentialToken;
+ }
+
+ public AiravataWorkflowParser(Experiment experiment, String credentialToken) {
+ this.credentialToken = credentialToken;
+ this.experiment = experiment;
+ }
+
+ @Override
+ public List<WorkflowInputNode> parse() throws RegistryException, AppCatalogException,
+ ComponentException, GraphException {
+ return parseWorkflow(getWorkflowFromExperiment(experiment));
+ }
+
+ public List<WorkflowInputNode> parseWorkflow(Workflow workflow) {
+ List<Node> gNodes = getInputNodes(workflow);
+ List<WorkflowInputNode> wfInputNodes = new ArrayList<WorkflowInputNode>();
+ List<PortContainer> portContainers = new ArrayList<PortContainer>();
+ List<InputDataObjectType> experimentInputs = experiment.getExperimentInputs();
+ Map<String,InputDataObjectType> inputDataMap=new HashMap<String, InputDataObjectType>();
+ WorkflowInputNode wfInputNode = null;
+ for (InputDataObjectType dataObjectType : experimentInputs) {
+ inputDataMap.put(dataObjectType.getName(), dataObjectType);
+ }
+ for (Node gNode : gNodes) {
+ wfInputNode = new WorkflowInputNodeImpl(gNode.getID(), gNode.getName());
+ wfInputNode.setInputObject(inputDataMap.get(wfInputNode.getId()));
+ if (wfInputNode.getInputObject() == null) {
+ throw new RuntimeException("Workflow Input object is not set, workflow node id: " + wfInputNode.getId());
+ }
+ portContainers.addAll(processOutPorts(gNode, wfInputNode));
+ wfInputNodes.add(wfInputNode);
+ }
+
+ // while port container is not empty iterate graph and build the workflow DAG.
+ buildModel(portContainers);
+
+ return wfInputNodes;
+ }
+
+ private void buildModel(List<PortContainer> portContainerList) {
+ // end condition of recursive call.
+ if (portContainerList == null || portContainerList.isEmpty()) {
+ return ;
+ }
+ DataPort dataPort = null;
+ InPort inPort = null;
+ ApplicationNode wfApplicationNode = null;
+ WorkflowOutputNode wfOutputNode = null;
+ List<PortContainer> nextPortContainerList = new ArrayList<PortContainer>();
+ for (PortContainer portContainer : portContainerList) {
+ dataPort = portContainer.getDataPort();
+ inPort = portContainer.getInPort();
+ Node node = dataPort.getNode();
+ if (node instanceof WSNode) {
+ WSNode wsNode = (WSNode) node;
+ WorkflowNode wfNode = wfNodes.get(wsNode.getID());
+ if (wfNode == null) {
+ wfApplicationNode = createApplicationNode(wsNode);
+ wfNodes.put(wfApplicationNode.getId(), wfApplicationNode);
+ nextPortContainerList.addAll(processOutPorts(wsNode, wfApplicationNode));
+ } else if (wfNode instanceof ApplicationNode) {
+ wfApplicationNode = (ApplicationNode) wfNode;
+ } else {
+ throw new IllegalArgumentException("Only support for ApplicationNode implementation, but found other type for node implementation");
+ }
+ inPort.setNode(wfApplicationNode);
+ wfApplicationNode.addInPort(inPort);
+
+ }else if (node instanceof OutputNode) {
+ OutputNode oNode = (OutputNode) node;
+ wfOutputNode = createWorkflowOutputNode(oNode);
+ wfOutputNode.setInPort(inPort);
+ inPort.setNode(wfOutputNode);
+ wfNodes.put(wfOutputNode.getId(), wfOutputNode);
+ }
+ }
+ buildModel(nextPortContainerList);
+
+ }
+
+ private WorkflowOutputNode createWorkflowOutputNode(OutputNode oNode) {
+ WorkflowOutputNodeImpl workflowOutputNode = new WorkflowOutputNodeImpl(oNode.getID(), oNode.getName());
+ OutputDataObjectType outputDataObjectType = new OutputDataObjectType();
+ outputDataObjectType.setType(oNode.getParameterType());
+ workflowOutputNode.setOutputObject(outputDataObjectType);
+ return workflowOutputNode;
+ }
+
+ private ApplicationNode createApplicationNode(WSNode wsNode) {
+ ApplicationNode applicationNode = new ApplicationNodeImpl(wsNode.getID(),
+ wsNode.getComponent().getApplication().getName(),
+ wsNode.getComponent().getApplication().getApplicationId());
+ return applicationNode;
+ }
+
+ private List<PortContainer> processOutPorts(Node node, WorkflowNode wfNode) {
+ OutPort outPort ;
+ Edge edge;
+ InPort inPort = null;
+ List<PortContainer> portContainers = new ArrayList<PortContainer>();
+ for (DataPort dataPort : node.getOutputPorts()) {
+ outPort = createOutPort(dataPort);
+ for (DataEdge dataEdge : dataPort.getEdges()) {
+ edge = new DirectedEdge();
+ edge.setFromPort(outPort);
+ outPort.addEdge(edge);
+ inPort = createInPort(dataEdge.getToPort());
+ edge.setToPort(inPort);
+ inPort.addEdge(edge);
+ portContainers.add(new PortContainer(dataEdge.getToPort(), inPort));
+ }
+ outPort.setNode(wfNode);
+ if (wfNode instanceof WorkflowInputNode) {
+ WorkflowInputNode workflowInputNode = (WorkflowInputNode) wfNode;
+ workflowInputNode.setOutPort(outPort);
+ } else if (wfNode instanceof ApplicationNode) {
+ ApplicationNode applicationNode = ((ApplicationNode) wfNode);
+ applicationNode.addOutPort(outPort);
+ }
+ }
+ return portContainers;
+ }
+
+ private OutPort createOutPort(DataPort dataPort) {
+ OutPortImpl outPort = new OutPortImpl(dataPort.getID());
+ OutputDataObjectType outputDataObjectType = new OutputDataObjectType();
+ if (dataPort instanceof WSPort) {
+ WSPort wsPort = (WSPort) dataPort;
+ outputDataObjectType.setName(wsPort.getComponentPort().getName());
+ outputDataObjectType.setType(wsPort.getType());
+ }else if (dataPort instanceof SystemDataPort) {
+ SystemDataPort sysPort = (SystemDataPort) dataPort;
+ outputDataObjectType.setName(sysPort.getFromNode().getName());
+ outputDataObjectType.setType(sysPort.getType());
+ }
+
+ outPort.setOutputObject(outputDataObjectType);
+ return outPort;
+ }
+
+ private InPort createInPort(DataPort toPort) {
+ InPort inPort = new InputPortIml(toPort.getID());
+ InputDataObjectType inputDataObjectType = new InputDataObjectType();
+ if (toPort instanceof WSPort) {
+ WSPort wsPort = (WSPort) toPort;
+ inputDataObjectType.setName(wsPort.getName());
+ inputDataObjectType.setType(wsPort.getType());
+ inputDataObjectType.setApplicationArgument(wsPort.getComponentPort().getApplicationArgument());
+ inputDataObjectType.setIsRequired(!wsPort.getComponentPort().isOptional());
+ inputDataObjectType.setInputOrder(wsPort.getComponentPort().getInputOrder());
+
+ inPort.setDefaultValue(wsPort.getComponentPort().getDefaultValue());
+ }else if (toPort instanceof SystemDataPort) {
+ SystemDataPort sysPort = (SystemDataPort) toPort;
+ inputDataObjectType.setName(sysPort.getName());
+ inputDataObjectType.setType(sysPort.getType());
+ }
+ inPort.setInputObject(inputDataObjectType);
+ return inPort;
+ }
+
+ private InputDataObjectType getInputDataObject(DataPort dataPort) {
+ InputDataObjectType inputDataObject = new InputDataObjectType();
+ inputDataObject.setName(dataPort.getName());
+ if (dataPort instanceof WSPort) {
+ WSPort port = (WSPort) dataPort;
+ inputDataObject.setInputOrder(port.getComponentPort().getInputOrder());
+ inputDataObject.setApplicationArgument(port.getComponentPort().getApplicationArgument() == null ?
+ "" : port.getComponentPort().getApplicationArgument());
+ inputDataObject.setType(dataPort.getType());
+ }
+ return inputDataObject;
+ }
+
+ private OutputDataObjectType getOutputDataObject(InputDataObjectType inputObject) {
+ OutputDataObjectType outputDataObjectType = new OutputDataObjectType();
+ outputDataObjectType.setApplicationArgument(inputObject.getApplicationArgument());
+ outputDataObjectType.setName(inputObject.getName());
+ outputDataObjectType.setType(inputObject.getType());
+ outputDataObjectType.setValue(inputObject.getValue());
+ return outputDataObjectType;
+ }
+
+ private Experiment getExperiment(String experimentId) throws RegistryException {
+ Registry registry = RegistryFactory.getDefaultRegistry();
+ return (Experiment)registry.get(RegistryModelType.EXPERIMENT, experimentId);
+ }
+
+ private Workflow getWorkflowFromExperiment(Experiment experiment) throws RegistryException, AppCatalogException, GraphException, ComponentException {
+ WorkflowCatalog workflowCatalog = getWorkflowCatalog();
+ return new Workflow(workflowCatalog.getWorkflow(experiment.getApplicationId()).getGraph());
+ }
+
+ private WorkflowCatalog getWorkflowCatalog() throws AppCatalogException {
+ return AppCatalogFactory.getAppCatalog().getWorkflowCatalog();
+ }
+
+ private ArrayList<Node> getInputNodes(Workflow wf) {
+ ArrayList<Node> list = new ArrayList<Node>();
+ List<NodeImpl> nodes = wf.getGraph().getNodes();
+ for (Node node : nodes) {
+ String name = node.getComponent().getName();
+ if (InputComponent.NAME.equals(name) || ConstantComponent.NAME.equals(name) || S3InputComponent.NAME.equals(name)) {
+ list.add(node);
+ }
+ }
+ return list;
+ }
+
+ public Map<String, WorkflowNode> getWfNodes() {
+ return wfNodes;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/509f2037/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/PortContainer.java
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diff --git a/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/PortContainer.java b/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/PortContainer.java
new file mode 100644
index 0000000..536199c
--- /dev/null
+++ b/modules/workflow/workflow-core/src/main/java/org/apache/airavata/workflow/core/parser/PortContainer.java
@@ -0,0 +1,53 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.workflow.core.parser;
+
+import org.apache.airavata.workflow.core.dag.port.InPort;
+import org.apache.airavata.workflow.model.graph.DataPort;
+
+
+public class PortContainer {
+ private DataPort dataPort;
+ private InPort inPort;
+
+
+ public PortContainer(DataPort dataPort, InPort inPort) {
+ this.dataPort = dataPort;
+ this.inPort = inPort;
+ }
+
+ public DataPort getDataPort() {
+ return dataPort;
+ }
+
+ public void setDataPort(DataPort dataPort) {
+ this.dataPort = dataPort;
+ }
+
+ public InPort getInPort() {
+ return inPort;
+ }
+
+ public void setInPort(InPort inPort) {
+ this.inPort = inPort;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/509f2037/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/WorkflowDAGTest.java
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diff --git a/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/WorkflowDAGTest.java b/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/WorkflowDAGTest.java
new file mode 100644
index 0000000..09c1416
--- /dev/null
+++ b/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/WorkflowDAGTest.java
@@ -0,0 +1,46 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.workflow.core;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class WorkflowDAGTest {
+
+ @Before
+ public void setUp() throws Exception {
+
+ }
+
+ @After
+ public void tearDown() throws Exception {
+
+ }
+
+ @Test
+ public void testWorkflowDAG() throws Exception {
+
+
+
+ }
+}
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http://git-wip-us.apache.org/repos/asf/airavata/blob/509f2037/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParserTest.java
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diff --git a/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParserTest.java b/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParserTest.java
new file mode 100644
index 0000000..f7bffa2
--- /dev/null
+++ b/modules/workflow/workflow-core/src/test/java/org/apache/airavata/workflow/core/parser/AiravataWorkflowParserTest.java
@@ -0,0 +1,119 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.workflow.core.parser;
+
+import org.apache.airavata.model.appcatalog.appinterface.DataType;
+import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
+import org.apache.airavata.model.workspace.experiment.Experiment;
+import org.apache.airavata.workflow.core.dag.nodes.ApplicationNode;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowInputNode;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowNode;
+import org.apache.airavata.workflow.core.dag.nodes.WorkflowOutputNode;
+import org.apache.airavata.workflow.model.wf.Workflow;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+public class AiravataWorkflowParserTest {
+
+ @Before
+ public void setUp() throws Exception {
+
+ }
+
+ @After
+ public void tearDown() throws Exception {
+
+ }
+
+ @Test
+ public void testWorkflowParse() throws Exception {
+ Assert.assertNotNull("Test file (ComplexMathWorkflow.awf) is missing", getClass().getResource("/ComplexMathWorkflow.awf"));
+ InputStreamReader isr = new InputStreamReader(this.getClass().getResourceAsStream("/ComplexMathWorkflow.awf"));
+ BufferedReader br = new BufferedReader(isr);
+ StringBuffer sb = new StringBuffer();
+ String nextLine = br.readLine();
+ while (nextLine != null) {
+ sb.append(nextLine);
+ nextLine = br.readLine();
+ }
+ Workflow workflow = new Workflow(sb.toString());
+ Experiment experiment = new Experiment();
+ InputDataObjectType x = new InputDataObjectType();
+ x.setValue("6");
+ x.setType(DataType.STRING);
+ x.setName("x");
+
+ InputDataObjectType y = new InputDataObjectType();
+ y.setValue("8");
+ y.setType(DataType.STRING);
+ y.setName("y");
+
+ InputDataObjectType z = new InputDataObjectType();
+ z.setValue("10");
+ z.setType(DataType.STRING);
+ z.setName("y_2");
+
+ List<InputDataObjectType> inputs = new ArrayList<InputDataObjectType>();
+ inputs.add(x);
+ inputs.add(y);
+ inputs.add(z);
+ experiment.setExperimentInputs(inputs);
+ // create parser
+ AiravataWorkflowParser parser = new AiravataWorkflowParser(experiment, "testCredentialId");
+ List<WorkflowInputNode> workflowInputNodes = parser.parseWorkflow(workflow);
+ Assert.assertNotNull(workflowInputNodes);
+ Assert.assertEquals(3, workflowInputNodes.size());
+ for (WorkflowInputNode workflowInputNode : workflowInputNodes) {
+ Assert.assertNotNull(workflowInputNode.getOutPort());
+ Assert.assertNotNull(workflowInputNode.getInputObject());
+ }
+
+ Map<String, WorkflowNode> wfNodes = parser.getWfNodes();
+ for (String wfId : wfNodes.keySet()) {
+ WorkflowNode wfNode = wfNodes.get(wfId);
+ if (wfNode instanceof ApplicationNode) {
+ ApplicationNode node = (ApplicationNode) wfNode;
+ Assert.assertEquals(2, node.getInputPorts().size());
+ Assert.assertNotNull(node.getInputPorts().get(0).getInputObject());
+ Assert.assertNotNull(node.getInputPorts().get(1).getInputObject());
+ Assert.assertNotNull(node.getInputPorts().get(0).getEdge());
+ Assert.assertNotNull(node.getInputPorts().get(1).getEdge());
+
+ Assert.assertEquals(1, node.getOutputPorts().size());
+ Assert.assertEquals(1, node.getOutputPorts().get(0).getOutEdges().size());
+ Assert.assertNotNull(node.getOutputPorts().get(0).getOutEdges().get(0));
+ } else if (wfNode instanceof WorkflowOutputNode) {
+ WorkflowOutputNode workflowOutputNode = (WorkflowOutputNode) wfNode;
+ Assert.assertNotNull(workflowOutputNode.getInPort());
+ }
+ }
+
+ }
+}
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