Add main parser that parses the structure of a CWL workflow
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/WorkflowParser.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/WorkflowParser.java
new file mode 100644
index 0000000..f0f6b2a
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/WorkflowParser.java
@@ -0,0 +1,232 @@
+/*
+ * 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.*;
+import java.util.*;
+
+import java.lang.NullPointerException;
+
+import org.yaml.snakeyaml.Yaml;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.core.Processor;
+import org.apache.taverna.scufl2.api.core.DataLink;
+
+import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
+import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
+import org.apache.taverna.scufl2.api.port.InputProcessorPort;
+import org.apache.taverna.scufl2.api.port.OutputProcessorPort;
+import org.apache.taverna.scufl2.api.port.SenderPort;
+import org.apache.taverna.scufl2.api.port.ReceiverPort;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+
+public class WorkflowParser {
+
+ private static final String FILE_NAME = "/hello_world.cwl";
+ private CWLParser cwlParser;
+ private Converter converter;
+
+ private Map<String, InputWorkflowPort> workflowInputs;
+ private Map<String, OutputWorkflowPort> workflowOutputs;
+ private Map<String, Processor> workflowProcessors;
+ private Map<String, InputProcessorPort> processorInputs;
+ private Map<String, OutputProcessorPort> processorOutputs;
+ private Set<DataLink> dataLinks;
+
+ public WorkflowParser() {
+ Yaml reader = new Yaml();
+ ObjectMapper mapper = new ObjectMapper();
+ JsonNode cwlFile = mapper.valueToTree(reader.load(WorkflowParser.class.getResourceAsStream(FILE_NAME)));
+ this.cwlParser = new CWLParser(cwlFile);
+ this.converter = new Converter();
+ }
+
+ public WorkflowParser(JsonNode cwlFile) {
+ this.cwlParser = new CWLParser(cwlFile);
+ this.converter = new Converter();
+ workflowInputs = new HashMap<>();
+ workflowOutputs = new HashMap<>();
+ workflowProcessors = new HashMap<>();
+ processorInputs = new HashMap<>();
+ processorOutputs = new HashMap<>();
+ dataLinks = new HashSet<DataLink>();
+ }
+
+ public Workflow buildWorkflow() {
+ parseInputs();
+ parseOutputs();
+ Set<Step> cwlSteps = cwlParser.parseSteps();
+ parseProcessors(cwlSteps);
+ parseDataLinks(cwlSteps);
+
+ Workflow workflow = new Workflow();
+ Set<InputWorkflowPort> inputs = new HashSet<>(workflowInputs.values());
+ Set<OutputWorkflowPort> outputs = new HashSet<>(workflowOutputs.values());
+ Set<Processor> processors = new HashSet<>(workflowProcessors.values());
+
+ workflow.setInputPorts(inputs);
+ workflow.setOutputPorts(outputs);
+ workflow.setProcessors(processors);
+ workflow.setDataLinks(dataLinks);
+
+// writeWorkflowToFile(workflow);
+
+ return workflow;
+ }
+
+ public void writeWorkflowToFile(Workflow workflow) {
+ try {
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ File scufl2File = new File("workflow.wfbundle");
+ WorkflowBundle bundle = io.createBundle();
+ Set<Workflow> workflowSet = new HashSet<>();
+ workflowSet.add(workflow);
+ bundle.setWorkflows(workflowSet);
+ bundle.setMainWorkflow(workflow);
+ io.writeBundle(bundle, scufl2File, "application/vnd.taverna.scufl2.workflow-bundle");
+ } catch(WriterException e) {
+ System.out.println("Exception writing the workflow bundle");
+ } catch(IOException e) {
+ System.out.println("IOException");
+ }
+ }
+
+ public void parseInputs() {
+ Set<PortDetail> cwlInputs = cwlParser.parseInputs();
+ if(cwlInputs != null) {
+ for (PortDetail port : cwlInputs) {
+ String portId = port.getId();
+ InputWorkflowPort workflowPort = converter.convertInputWorkflowPort(port);
+ workflowInputs.put(portId, workflowPort);
+ }
+ }
+ }
+
+ public void parseOutputs() {
+ Set<PortDetail> cwlOutputs = cwlParser.parseOutputs();
+ for(PortDetail port: cwlOutputs) {
+ String portId = port.getId();
+ OutputWorkflowPort workflowPort = converter.convertOutputWorkflowPort(port);
+ workflowOutputs.put(portId, workflowPort);
+ }
+ }
+
+ public void parseProcessors(Set<Step> cwlSteps) {
+ for(Step step: cwlSteps) {
+ Processor processor = converter.convertStepToProcessor(step);
+ workflowProcessors.put(step.getId(), processor);
+
+ DataLink datalink = new DataLink();
+ for(StepInput stepInput: step.getInputs()) {
+ InputProcessorPort processorPort = new InputProcessorPort(processor, stepInput.getId());
+ processorInputs.put(stepInput.getId(), processorPort);
+ }
+ for(StepOutput stepOutput: step.getOutputs()) {
+ OutputProcessorPort processorPort = new OutputProcessorPort(processor, stepOutput.getId());
+ processorOutputs.put(stepOutput.getId(), processorPort);
+ }
+ }
+ }
+
+ public void parseDataLinks(Set<Step> cwlSteps) {
+ for(Step step: cwlSteps) {
+ for(StepInput stepInput: step.getInputs()) {
+ String[] sourcePath = stepInput.getSource().split("/");
+ String source = sourcePath[sourcePath.length-1];
+ source = source.replace("#", "");
+
+ DataLink dataLink = new DataLink();
+ SenderPort sender = workflowInputs.get(source);
+ if(sender == null) {
+ sender = processorOutputs.get(source);
+ }
+ if(sender == null) {
+ throw new NullPointerException("Cannot find sender port with name: " + source);
+ }
+ String receiverId = stepInput.getId();
+ ReceiverPort receiver = workflowOutputs.get(receiverId);
+ if(receiver == null) {
+ receiver = processorInputs.get(receiverId);
+ }
+ if(receiver == null) {
+ throw new NullPointerException("Cannot find receiver port with name: " + receiverId);
+ }
+ dataLink.setSendsTo(receiver);
+ dataLink.setReceivesFrom(sender);
+ dataLinks.add(dataLink);
+ }
+ }
+ }
+
+ public Map<String, InputWorkflowPort> getWorkflowInputs() {
+ return workflowInputs;
+ }
+
+ public void setWorkflowInputs(Map<String, InputWorkflowPort> workflowInputs) {
+ this.workflowInputs = workflowInputs;
+ }
+
+ public Map<String, OutputWorkflowPort> getWorkflowOutputs() {
+ return workflowOutputs;
+ }
+
+ public void setWorkflowOutputs(Map<String, OutputWorkflowPort> workflowOutputs) {
+ this.workflowOutputs = workflowOutputs;
+ }
+
+ public Map<String, Processor> getWorkflowProcessors() {
+ return workflowProcessors;
+ }
+
+ public void setWorkflowProcessors(Map<String, Processor> workflowProcessors) {
+ this.workflowProcessors = workflowProcessors;
+ }
+
+ public Map<String, InputProcessorPort> getProcessorInputs() {
+ return processorInputs;
+ }
+
+ public void setProcessorInputs(Map<String, InputProcessorPort> processorInputs) {
+ this.processorInputs = processorInputs;
+ }
+
+ public Map<String, OutputProcessorPort> getProcessorOutputs() {
+ return processorOutputs;
+ }
+
+ public void setProcessorOutputs(Map<String, OutputProcessorPort> processorOutputs) {
+ this.processorOutputs = processorOutputs;
+ }
+
+ public Set<DataLink> getDataLinks() {
+ return dataLinks;
+ }
+
+ public void setDataLinks(Set<DataLink> dataLinks) {
+ this.dataLinks = dataLinks;
+ }
+}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/PortDetail.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/PortDetail.java
index 563c76f..53604e7 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/PortDetail.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/PortDetail.java
@@ -25,11 +25,21 @@
public class PortDetail {
- private String label;
+ private String id;
+ private String label;
private int depth;
private String description;
private ArrayList<String> format;
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
public int getDepth() {
return depth;
}
