| /* |
| * 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.util.Set; |
| import java.util.HashSet; |
| import java.util.Map; |
| import java.util.HashMap; |
| import java.io.InputStream; |
| |
| import org.yaml.snakeyaml.Yaml; |
| import com.fasterxml.jackson.databind.ObjectMapper; |
| |
| import org.apache.taverna.scufl2.api.core.Processor; |
| import org.apache.taverna.scufl2.api.core.DataLink; |
| 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.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 com.fasterxml.jackson.databind.JsonNode; |
| |
| public class WorkflowProcess implements Process { |
| |
| private CWLParser cwlParser; |
| |
| 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<>(); |
| |
| private Set<Process> processes = new HashSet<>(); |
| |
| private Converter converter = new Converter(); |
| |
| public WorkflowProcess(InputStream stream) { |
| |
| Yaml reader = new Yaml(); |
| ObjectMapper mapper = new ObjectMapper(); |
| JsonNode node = mapper.valueToTree(reader.load(stream)); |
| |
| cwlParser = new CWLParser(node); |
| this.parse(); |
| } |
| |
| public WorkflowProcess(JsonNode node) { |
| cwlParser = new CWLParser(node); |
| this.parse(); |
| } |
| |
| public void parse() { |
| parseInputs(); |
| parseOutputs(); |
| Set<Step> cwlSteps = cwlParser.parseSteps(); |
| this.processes = parseProcessors(cwlSteps); |
| } |
| |
| public void parseInputs() { |
| Set<PortDetail> cwlInputs = cwlParser.parseInputs(); |
| 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 Set<Process> parseProcessors(Set<Step> cwlSteps) { |
| Set<Process> result = new HashSet<>(); |
| |
| for(Step step: cwlSteps) { |
| Process process = step.getRun(); |
| result.add(process); |
| } |
| |
| return result; |
| } |
| |
| // public void parseProcessors(Set<Step> cwlSteps) { |
| // for(Step step: cwlSteps) { |
| // |
| // Processor processor = converter.convertStepToProcessor(step); |
| // workflowProcessors.put(step.getId(), processor); |
| // |
| // // TODO: Add only receiver and sender ports from the Process interface |
| // 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; |
| } |
| |
| public Set<Process> getProcesses() { |
| return processes; |
| } |
| |
| public void setProcesses(Set<Process> processes) { |
| this.processes = processes; |
| } |
| } |