Convert WorkflowProcess to WorkflowBundle with nested processes
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Converter.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Converter.java
index 687a278..086d9dd 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Converter.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Converter.java
@@ -25,6 +25,7 @@
import org.apache.taverna.scufl2.api.core.Workflow;
import org.apache.taverna.scufl2.api.core.Processor;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
@@ -158,4 +159,47 @@
return port;
}
+
+ public WorkflowBundle buildWorkflowBundle(Process process) {
+ WorkflowBundle bundle = new WorkflowBundle();
+ if(!(process instanceof WorkflowProcess)) {
+ throw new UnsupportedOperationException("WorkflowBundle is not created without an initial workflow yet");
+ }
+ Workflow workflow = convertWorkflowProcess((WorkflowProcess) process, bundle);
+ workflow.setParent(bundle);
+
+ return bundle;
+ }
+
+ public Workflow convertWorkflowProcess(WorkflowProcess workflowProcess, WorkflowBundle bundle) {
+ Workflow workflow = new Workflow();
+ Set<InputWorkflowPort> inputs = new HashSet<>(workflowProcess.getWorkflowInputs().values());
+ Set<OutputWorkflowPort> outputs = new HashSet<>(workflowProcess.getWorkflowOutputs().values());
+ workflow.setInputPorts(inputs);
+ workflow.setOutputPorts(outputs);
+
+ for(Process process: workflowProcess.getProcesses()) {
+ if(process instanceof WorkflowProcess) {
+ Workflow childWorkflow = convertWorkflowProcess((WorkflowProcess) process, bundle); // TODO: Add nested relationship
+ bundle.getWorkflows().add(childWorkflow);
+ } else if(process instanceof CommandLineTool) {
+ Processor processor = convertCommandLineTool((CommandLineTool) process);
+ workflow.getProcessors().add(processor);
+ } else {
+ assert(process instanceof Reference);
+ Processor processor = convertReference((Reference) process);
+ workflow.getProcessors().add(processor);
+ }
+ }
+
+ return workflow;
+ }
+
+ public Processor convertCommandLineTool(CommandLineTool command) {
+ return new Processor(null, command.getBaseCommand());
+ }
+
+ public Processor convertReference(Reference reference) {
+ return new Processor(null, reference.getSource());
+ }
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Reference.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Reference.java
index 7a25744..193e1a6 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Reference.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Reference.java
@@ -40,4 +40,8 @@
public String toString() {
return source;
}
+
+ public String getSource() {
+ return source;
+ }
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestConverting.java b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestConverting.java
new file mode 100644
index 0000000..b17cc88
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestConverting.java
@@ -0,0 +1,88 @@
+/*
+ * 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.taverna.scufl2.cwl;
+
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.HashMap;
+
+import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+
+import org.yaml.snakeyaml.Yaml;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLMapper;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+
+import org.apache.taverna.scufl2.api.core.Workflow;
+
+import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
+import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
+
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+public class TestConverting {
+ private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
+ private static final String WORKFLOW_WITH_COMMAND = "/workflow_with_command.cwl";
+ private static final String WORKFLOW_WITH_WORKFLOW = "/workflow_with_workflow.cwl";
+
+ private static JsonNode cwlFile;
+
+ public JsonNode loadYamlFile(String filename) {
+
+ Yaml reader = new Yaml();
+ ObjectMapper mapper = new ObjectMapper();
+ JsonNode node = mapper.valueToTree(reader.load(TestWorkflowProcess.class.getResourceAsStream(filename)));
+
+ return node;
+ }
+
+ @Test
+ public void testWorkflowBundleWithOneWorkflow() {
+ JsonNode cwlFile = loadYamlFile(HELLO_WORLD_CWL);
+
+ WorkflowProcess workflow = (WorkflowProcess) ProcessFactory.createProcess(cwlFile);
+ Converter converter = new Converter();
+ WorkflowBundle workflowBundle = converter.buildWorkflowBundle(workflow);
+
+ assertEquals(workflowBundle.getWorkflows().size(), 1);
+ }
+
+ @Test
+ public void testWorkflowBundleWithMultipleWorkflows() {
+ JsonNode cwlFile = loadYamlFile(WORKFLOW_WITH_WORKFLOW);
+
+ WorkflowProcess workflow = (WorkflowProcess) ProcessFactory.createProcess(cwlFile);
+ Converter converter = new Converter();
+ WorkflowBundle workflowBundle = converter.buildWorkflowBundle(workflow);
+
+ assertEquals(workflowBundle.getWorkflows().size(), 2);
+ }
+
+}
