| /* |
| * 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.Map; |
| import java.util.HashMap; |
| import java.util.Set; |
| import java.util.HashSet; |
| |
| 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 = new Converter(); |
| |
| private Map<String, InputWorkflowPort> workflowInputs = new HashMap<>(); |
| private Map<String, OutputWorkflowPort> workflowOutputs = new HashMap<>(); |
| private Map<String, Processor> workflowProcessors = new HashMap<>(); |
| private Map<String, InputProcessorPort> processorInputs = new HashMap<>(); |
| private Map<String, OutputProcessorPort> processorOutputs = new HashMap<>(); |
| private Set<DataLink> dataLinks = new HashSet<DataLink>(); |
| |
| 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); |
| } |
| |
| public WorkflowParser(JsonNode cwlFile) { |
| this.cwlParser = new CWLParser(cwlFile); |
| } |
| |
| 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); |
| |
| for(InputPort stepInput: step.getInputs()) { |
| InputProcessorPort processorPort = new InputProcessorPort(processor, stepInput.getName()); |
| processorInputs.put(stepInput.getName(), processorPort); |
| } |
| for(OutputPort stepOutput: step.getOutputs()) { |
| OutputProcessorPort processorPort = new OutputProcessorPort(processor, stepOutput.getName()); |
| processorOutputs.put(stepOutput.getName(), processorPort); |
| } |
| } |
| } |
| |
| public void parseDataLinks(Set<Step> cwlSteps) { |
| for(Step step: cwlSteps) { |
| for(InputPort 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.getName(); |
| 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; |
| } |
| } |