Merge branch haouech:cwlparser (#38) into cwlparser
Contributed by Majdi Haouech @haouech
(ASF ICLA on file)
Add structural import for a CWL workflow to Apache Taverna. The current
code parses the cwl file to extract inputs, outputs and steps of a
workflow, and then converts them to a Taverna workflow containing ports,
processors and data links.
This closes #38
diff --git a/taverna-scufl2-cwl/pom.xml b/taverna-scufl2-cwl/pom.xml
new file mode 100644
index 0000000..3b11dff
--- /dev/null
+++ b/taverna-scufl2-cwl/pom.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ 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.
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>apache-taverna-language</artifactId>
+ <version>0.16.0-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-scufl2-cwl</artifactId>
+ <packaging>bundle</packaging>
+ <name>Apache Taverna Scufl 2 CWL parser</name>
+ <description>Parser for .cwl file format</description>
+ <dependencies>
+
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>taverna-scufl2-api</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.yaml</groupId>
+ <artifactId>snakeyaml</artifactId>
+ <version>1.17</version>
+ </dependency>
+
+ </dependencies>
+</project>
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java
new file mode 100644
index 0000000..5a4d6cf
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLParser.java
@@ -0,0 +1,83 @@
+/*
+ * 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.Map;
+import java.util.Set;
+import java.util.HashSet;
+
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.core.Processor;
+
+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 com.fasterxml.jackson.databind.JsonNode;
+
+public class CWLParser {
+
+ private JsonNode cwlFile;
+ private YAMLHelper yamlHelper;
+
+ public CWLParser(JsonNode cwlFile) {
+ this.cwlFile = cwlFile;
+ this.yamlHelper = new YAMLHelper();
+ }
+
+ public Set<Step> parseSteps() {
+ return yamlHelper.processSteps(cwlFile);
+ }
+
+ public Set<PortDetail> parseInputs() {
+ Map<String, PortDetail> inputs = yamlHelper.processInputDetails(cwlFile);
+ Map<String, Integer> inputDepths = yamlHelper.processInputDepths(cwlFile);
+
+ if(inputs == null || inputDepths == null) {
+ return null;
+ }
+ Set<PortDetail> result = new HashSet<PortDetail>();
+ for(String id: inputs.keySet()) {
+ PortDetail port = inputs.get(id);
+ port.setId(id);
+ int depth = inputDepths.get(id);
+ port.setDepth(depth);
+ result.add(port);
+ }
+
+ return result;
+ }
+
+ public Set<PortDetail> parseOutputs() {
+ Map<String, PortDetail> inputs = yamlHelper.processOutputDetails(cwlFile);
+
+ if(inputs == null) {
+ return null;
+ }
+ Set<PortDetail> result = new HashSet<PortDetail>();
+ for(String id: inputs.keySet()) {
+ PortDetail port = inputs.get(id);
+ result.add(port);
+ }
+
+ return result;
+ }
+
+}
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
new file mode 100644
index 0000000..7ddf9de
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Converter.java
@@ -0,0 +1,76 @@
+/*
+ * 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 org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.core.Processor;
+
+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 com.fasterxml.jackson.databind.JsonNode;
+
+public class Converter {
+
+ public Converter() {
+
+ }
+
+ public InputWorkflowPort convertInputWorkflowPort(PortDetail input) {
+ InputWorkflowPort port = new InputWorkflowPort();
+ port.setName(input.getId());
+ port.setDepth(input.getDepth());
+
+ return port;
+ }
+
+ public OutputWorkflowPort convertOutputWorkflowPort(PortDetail input) {
+ OutputWorkflowPort port = new OutputWorkflowPort();
+ port.setName(input.getId());
+
+ return port;
+ }
+
+ public Processor convertStepToProcessor(Step step) {
+ Processor processor = new Processor(null, step.getId());
+ // Convert input ports
+ Set<InputProcessorPort> processorInputs = new HashSet<>();
+ Set<StepInput> inputs = step.getInputs();
+ for(StepInput input: inputs) {
+ InputProcessorPort port = new InputProcessorPort(processor, input.getId());
+ processorInputs.add(port);
+ }
+ processor.setInputPorts(processorInputs);
+ // Convert output ports
+ Set<OutputProcessorPort> processorOutputs = new HashSet<>();
+ Set<StepOutput> outputs = step.getOutputs();
+ for(StepOutput output: outputs) {
+ OutputProcessorPort port = new OutputProcessorPort(processor, output.getId());
+ processorOutputs.add(port);
+ }
+ processor.setOutputPorts(processorOutputs);
+
+ return processor;
+ }
+}
\ No newline at end of file
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..0b6c095
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/WorkflowParser.java
@@ -0,0 +1,236 @@
+/*
+ * 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;
+
+ 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/YAMLHelper.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/YAMLHelper.java
new file mode 100644
index 0000000..dacdc4f
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/YAMLHelper.java
@@ -0,0 +1,484 @@
+/*
+ * 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.ArrayList;
+import java.util.HashSet;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.databind.node.TextNode;
+
+public class YAMLHelper {
+
+ public static final String ARRAY_SPLIT_BRACKETS = "\\[\\]";
+ public static final String ARRAY_SIGNATURE_BRACKETS = "\\[\\]$";
+ private static final String INPUTS = "inputs";
+ private static final String OUTPUTS = "outputs";
+ private static final String STEPS = "steps";
+ private static final String ID = "id";
+ private static final String TYPE = "type";
+ private static final String ARRAY = "array";
+ private static final String DESCRIPTION = "description";
+ private static final int DEPTH_0 = 0;
+ private static final int DEPTH_1 = 1;
+ private static final int DEPTH_2 = 2;
+
+ private static final String FLOAT = "float";
+ private static final String NULL = "null";
+ private static final String BOOLEAN = "boolean";
+ private static final String INT = "int";
+ private static final String DOUBLE = "double";
+ private static final String STRING = "string";
+ private static final String LABEL = "label";
+ private static final String FILE = "file";
+ private static final String DIRECTORY = "directory";
+ private static final String FORMAT = "format";
+ private static final String RUN = "run";
+ private static final String SOURCE = "source";
+
+ private JsonNode nameSpace;
+
+ public YAMLHelper() {
+ this.nameSpace = null;
+ }
+
+ public JsonNode getNameSpace() {
+ return nameSpace;
+ }
+
+ /**
+ * This method is processing the CWL NameSpace for later use such as
+ * figuring out the Format of a input or output
+ */
+ public void processNameSpace(JsonNode file) {
+
+ if (file != null && file.has("$namespaces")) {
+ nameSpace = file.path("$namespaces");
+ }
+
+ }
+
+ public Map<String, Integer> processInputDepths(JsonNode file) {
+ return process(file.get(INPUTS));
+ }
+
+ public Map<String, Integer> processOutputDepths(JsonNode file) {
+ return process(file.get(OUTPUTS));
+ }
+
+ public Map<String, PortDetail> processInputDetails(JsonNode file) {
+ return processdetails(file.get(INPUTS));
+ }
+
+ public Map<String, PortDetail> processOutputDetails(JsonNode file) {
+ return processdetails(file.get(OUTPUTS));
+ }
+
+ /**
+ *
+ */
+ public Set<Step> processSteps(JsonNode file) {
+ Set<Step> result = new HashSet<>();
+
+ if(file == null) {
+ return result;
+ }
+
+ if(file.has(STEPS)) {
+ JsonNode steps = file.get(STEPS);
+ if(steps.isArray()) {
+ for (JsonNode stepNode : steps) {
+ Step step = new Step();
+ String id = stepNode.get(ID).asText();
+
+ String run = stepNode.get(RUN).asText();
+ Set<StepInput> inputs = processStepInput(stepNode.get(INPUTS));
+ step.setId(id);
+ step.setRun(run);
+ step.setInputs(inputs);
+ result.add(step);
+ }
+ } else if(steps.isObject()) {
+ Iterator<Entry<String, JsonNode>> iterator = steps.fields();
+ while(iterator.hasNext()) {
+ Entry<String, JsonNode> entry = iterator.next();
+ Step step = new Step();
+
+ String id = entry.getKey();
+ JsonNode value = entry.getValue();
+ if(value.has(RUN)) {
+ String run = entry.getValue().get(RUN).asText();
+ step.setRun(run);
+ }
+ Set<StepInput> inputs = processStepInput(value.get(INPUTS));
+ step.setId(id);
+ step.setInputs(inputs);
+
+ result.add(step);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ private Set<StepInput> processStepInput(JsonNode inputs) {
+
+ Set<StepInput> result = new HashSet<>();
+ if(inputs == null) {
+ return result;
+ }
+ if (inputs.getClass() == ArrayNode.class) {
+
+ for (JsonNode input : inputs) {
+ String id = input.get(ID).asText();
+ String source = input.get(SOURCE).asText();
+
+ result.add(new StepInput(id, source));
+ }
+ } else if (inputs.getClass() == ObjectNode.class) {
+ Iterator<Entry<String, JsonNode>> iterator = inputs.fields();
+ while (iterator.hasNext()) {
+ Entry<String, JsonNode> entry = iterator.next();
+
+ String id = entry.getKey();
+ String source = entry.getValue().get(SOURCE).asText();
+
+ result.add(new StepInput(id, source));
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method will go through CWL tool input or out puts and figure outs
+ * their IDs and the respective depths
+ *
+ * @param inputs
+ * This is JsonNode object which contains the Inputs or outputs
+ * of the respective CWL tool
+ * @return This the respective, ID and the depth of the input or output
+ */
+ public Map<String, Integer> process(JsonNode inputs) {
+
+ Map<String, Integer> result = new HashMap<>();
+
+ if (inputs == null)
+ return result;
+
+ if (inputs.getClass() == ArrayNode.class) {
+ Iterator<JsonNode> iterator = inputs.iterator();
+
+ while (iterator.hasNext()) {
+ JsonNode input = iterator.next();
+ String currentInputId = input.get(ID).asText();
+
+ JsonNode typeConfigurations;
+ try {
+
+ typeConfigurations = input.get(TYPE);
+ // if type :single argument
+ if (typeConfigurations.getClass() == TextNode.class) {
+ // inputs:
+ /// -id: input_1
+ //// type: int[]
+ if (isValidArrayType(typeConfigurations.asText()))
+ result.put(currentInputId, DEPTH_1);
+ // inputs:
+ /// -id: input_1
+ //// type: int or int?
+ else
+ result.put(currentInputId, DEPTH_0);
+ // type : defined as another map which contains type:
+ } else if (typeConfigurations.getClass() == ObjectNode.class) {
+ // inputs:
+ /// -id: input_1
+ //// type:
+ ///// type: array or int[]
+ String inputType = typeConfigurations.get(TYPE).asText();
+ if (inputType.equals(ARRAY) || isValidArrayType(inputType)) {
+ result.put(currentInputId, DEPTH_1);
+
+ }
+ // inputs:
+ // -id: input_1
+ // type:
+ // type: ["null",int]
+ } else if (typeConfigurations.getClass() == ArrayNode.class) {
+ if (isValidDataType(typeConfigurations)) {
+ result.put(currentInputId, DEPTH_0);
+ }
+
+ }
+
+ } catch (ClassCastException e) {
+
+ System.out.println("Class cast exception !!!");
+ }
+
+ }
+ } else if (inputs.getClass() == ObjectNode.class) {
+
+ Iterator<Entry<String, JsonNode>> iterator = inputs.fields();
+
+ while (iterator.hasNext()) {
+ Entry<String, JsonNode> entry = iterator.next();
+ String currentInputId = entry.getKey();
+ JsonNode typeConfigurations = entry.getValue();
+
+ if (typeConfigurations.getClass() == TextNode.class) {
+ if (typeConfigurations.asText().startsWith("$")) {
+ System.out.println("Exception");
+ }
+ // inputs:
+ /// input_1: int[]
+ else if (isValidArrayType(typeConfigurations.asText()))
+ result.put(currentInputId, DEPTH_1);
+ // inputs:
+ /// input_1: int or int?
+ else
+ result.put(currentInputId, DEPTH_0);
+
+ } else if (typeConfigurations.getClass() == ObjectNode.class) {
+
+ if (typeConfigurations.has(TYPE)) {
+ JsonNode inputType = typeConfigurations.get(TYPE);
+ // inputs:
+ /// input_1:
+ //// type: [int,"null"]
+ if (inputType.getClass() == ArrayNode.class) {
+ if (isValidDataType(inputType))
+ result.put(currentInputId, DEPTH_0);
+ } else {
+ // inputs:
+ /// input_1:
+ //// type: array or int[]
+ if (inputType.asText().equals(ARRAY) || isValidArrayType(inputType.asText()))
+ result.put(currentInputId, DEPTH_1);
+ // inputs:
+ /// input_1:
+ //// type: int or int?
+ else
+ result.put(currentInputId, DEPTH_0);
+ }
+ }
+ }
+ }
+
+ }
+ return result;
+ }
+
+ /**
+ * This method is used for extracting details of the CWL tool inputs or
+ * outputs. ex:Label, Format, Description
+ *
+ * @param inputs
+ * This is JsonNode object which contains the Inputs or outputs
+ * of the respective CWL tool
+ * @return
+ */
+ private Map<String, PortDetail> processdetails(JsonNode inputs) {
+
+ Map<String, PortDetail> result = new HashMap<>();
+ if(inputs == null) {
+ return result;
+ }
+ if (inputs.getClass() == ArrayNode.class) {
+
+ for (JsonNode input : inputs) {
+ PortDetail detail = new PortDetail();
+ String currentInputId = input.get(ID).asText();
+
+ getParamDetails(result, input, detail, currentInputId);
+
+ }
+ } else if (inputs.getClass() == ObjectNode.class) {
+ Iterator<Entry<String, JsonNode>> iterator = inputs.fields();
+ while (iterator.hasNext()) {
+ PortDetail detail = new PortDetail();
+ Entry<String, JsonNode> entry = iterator.next();
+ getParamDetails(result, entry.getValue(), detail, entry.getKey());
+ }
+ }
+ return result;
+ }
+
+ private void getParamDetails(Map<String, PortDetail> result, JsonNode input, PortDetail detail,
+ String currentInputId) {
+ extractDescription(input, detail);
+
+ extractFormat(input, detail);
+
+ extractLabel(input, detail);
+
+ result.put(currentInputId, detail);
+ }
+
+ /**
+ * This method is used for extracting the Label of a CWL input or Output
+ *
+ * @param input
+ * Single CWL input or output as a JsonNode
+ * @param detail
+ * respective PortDetail Object to hold the extracted Label
+ */
+ public void extractLabel(JsonNode input, PortDetail detail) {
+ if (input != null)
+ if (input.has(LABEL)) {
+ detail.setLabel(input.get(LABEL).asText());
+ } else {
+ detail.setLabel(null);
+ }
+ }
+
+ /**
+ *
+ * @param input
+ * Single CWL input or output as a JsonNode
+ * @param detail
+ * respective PortDetail Object to hold the extracted Label
+ */
+ public void extractDescription(JsonNode input, PortDetail detail) {
+ if (input != null)
+ if (input.has(DESCRIPTION)) {
+ detail.setDescription(input.get(DESCRIPTION).asText());
+ } else {
+ detail.setDescription(null);
+ }
+ }
+
+ /**
+ * This method is used for extracting the Formats of a CWL input or Output
+ * Single argument(Input or Output) can have multiple Formats.
+ *
+ * @param input
+ * Single CWL input or output as a JsonNode
+ * @param detail
+ * respective PortDetail Object to hold the extracted Label
+ */
+ public void extractFormat(JsonNode input, PortDetail detail) {
+ if (input != null)
+ if (input.has(FORMAT)) {
+
+ JsonNode formatInfo = input.get(FORMAT);
+
+ ArrayList<String> format = new ArrayList<>();
+ detail.setFormat(format);
+
+ if (formatInfo.getClass() == TextNode.class) {
+
+ figureOutFormats(formatInfo.asText(), detail);
+ } else if (formatInfo.getClass() == ArrayNode.class) {
+ for (JsonNode eachFormat : formatInfo) {
+ figureOutFormats(eachFormat.asText(), detail);
+ }
+ }
+
+ }
+ }
+
+ /**
+ * Re Format the CWL format using the NameSpace in CWL Tool if possible
+ * otherwise it doesn't change the current nameSpace => edam:http://edam.org
+ * format : edam :1245 => http://edamontology.org/1245
+ *
+ * @param formatInfoString
+ * Single Format
+ * @param detail
+ * respective PortDetail Object to hold the extracted Label
+ */
+ public void figureOutFormats(String formatInfoString, PortDetail detail) {
+ if (formatInfoString.startsWith("$")) {
+
+ detail.addFormat(formatInfoString);
+ } else if (formatInfoString.contains(":")) {
+ String format[] = formatInfoString.split(":");
+ String namespaceKey = format[0];
+ String urlAppednd = format[1];
+
+ if (nameSpace.has(namespaceKey))
+ detail.addFormat(nameSpace.get(namespaceKey).asText() + urlAppednd);
+ else
+ // can't figure out the format
+ detail.addFormat(formatInfoString);
+
+ } else {
+ // can't figure out the format
+ detail.addFormat(formatInfoString);
+ }
+ }
+
+ /**
+ * This method is used to check whether the input/output is valid CWL TYPE
+ * when the type is represented as type: ["null","int"]
+ *
+ * @param typeConfigurations
+ * Type of the CWl input or output
+ * @return
+ */
+ public boolean isValidDataType(JsonNode typeConfigurations) {
+ if (typeConfigurations == null)
+ return false;
+ for (JsonNode type : typeConfigurations) {
+ if (!(type.asText().equals(FLOAT) || type.asText().equals(NULL) || type.asText().equals(BOOLEAN)
+ || type.asText().equals(INT) || type.asText().equals(STRING) || type.asText().equals(DOUBLE)
+ || type.asText().equals(FILE)||type.asText().equals(DIRECTORY)))
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ * This method is for figure out whether the parameter is an array or not.
+ * As from CWL document v1.0, array can be defined as "TYPE[]". For Example
+ * : int[] This method will look for "[]" sequence of characters in the end
+ * of the type and is provided type is a valid CWL TYPE or not
+ *
+ * @param type
+ * type of the CWL parameter
+ * @return
+ */
+ public boolean isValidArrayType(String type) {
+ if (type == null)
+ return false;
+ Pattern pattern = Pattern.compile(ARRAY_SIGNATURE_BRACKETS);
+ Matcher matcher = pattern.matcher(type);
+ ObjectMapper mapper = new ObjectMapper();
+ ArrayNode node = mapper.createArrayNode();
+ node.add(type.split(ARRAY_SPLIT_BRACKETS)[0]);
+ if (matcher.find() && isValidDataType(node))
+ return true;
+ else
+ return false;
+ }
+}
\ 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
new file mode 100644
index 0000000..53604e7
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/PortDetail.java
@@ -0,0 +1,72 @@
+/*
+ * 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.ArrayList;
+
+public class PortDetail {
+
+
+
+ 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;
+ }
+ public void setDepth(int depth) {
+ this.depth = depth;
+ }
+ public String getDescription() {
+ return description;
+ }
+ public void setDescription(String description) {
+ this.description = description;
+ }
+ public String getLabel() {
+ return label;
+ }
+ public void setLabel(String label) {
+ this.label = label;
+ }
+ public ArrayList<String> getFormat() {
+ return format;
+ }
+ public void setFormat(ArrayList<String> format) {
+ this.format = format;
+ }
+
+ public void addFormat(String format){
+ this.format.add(format);
+ }
+
+}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Step.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Step.java
new file mode 100644
index 0000000..3f3d653
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Step.java
@@ -0,0 +1,85 @@
+/*
+ * 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.ArrayList;
+import java.util.Set;
+import java.util.HashSet;
+
+public class Step {
+
+
+ private String id;
+ private String run;
+
+ private Set<StepInput> inputs;
+ private Set<StepOutput> outputs;
+
+ public Step() {
+ inputs = new HashSet<>();
+ outputs = new HashSet<>();
+ }
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public String getRun() {
+ return run;
+ }
+
+ public void setRun(String run) {
+ this.run = run;
+ }
+
+ public void addInput(String id, String source) {
+ inputs.add(new StepInput(id, source));
+ }
+
+ public void setInputs(Set<StepInput> inputs) {
+ this.inputs = inputs;
+ }
+
+ public Set<StepInput> getInputs() {
+ return inputs;
+ }
+
+ public void addOutput(String id) {
+ outputs.add(new StepOutput(id));
+ }
+
+ public void setOutputs(Set<StepOutput> outputs) {
+ this.outputs = outputs;
+ }
+
+ public Set<StepOutput> getOutputs() {
+ return outputs;
+ }
+
+ public String toString() {
+ return "Step " + id + ": run = " + run;
+ }
+
+}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepInput.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepInput.java
new file mode 100644
index 0000000..0432272
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepInput.java
@@ -0,0 +1,54 @@
+/*
+ * 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.*;
+
+public class StepInput {
+
+ private String id;
+ private String source;
+
+ public StepInput() {
+ this.id = null;
+ this.source = null;
+ }
+
+ public StepInput(String id, String source) {
+ this.id = id;
+ this.source = source;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public String getId() {
+ return id;
+ }
+
+ public void setSource(String source) {
+ this.source = source;
+ }
+
+ public String getSource() {
+ return source;
+ }
+}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepOutput.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepOutput.java
new file mode 100644
index 0000000..145fa2d
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepOutput.java
@@ -0,0 +1,41 @@
+/*
+ * 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;
+
+public class StepOutput {
+
+ private String id;
+
+ public StepOutput() {
+ this.id = null;
+ }
+
+ public StepOutput(String id) {
+ this.id = id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public String getId() {
+ return id;
+ }
+}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestParser.java b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestParser.java
new file mode 100644
index 0000000..4e3e69e
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestParser.java
@@ -0,0 +1,120 @@
+/*
+ * 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 org.junit.Before;
+import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+
+import org.yaml.snakeyaml.Yaml;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+
+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.common.NamedSet;
+
+import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
+import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
+import org.apache.taverna.scufl2.api.port.InputProcessorPort;
+
+
+public class TestParser {
+ private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
+
+ private static JsonNode cwlFile;
+ private WorkflowParser parser;
+ private Workflow workflow;
+
+ @Before
+ public void initialize() {
+
+ Yaml reader = new Yaml();
+ ObjectMapper mapper = new ObjectMapper();
+ cwlFile = mapper.valueToTree(reader.load(TestParser.class.getResourceAsStream(HELLO_WORLD_CWL)));
+ System.out.println(cwlFile);
+ this.parser = new WorkflowParser(cwlFile);
+
+ this.workflow = parser.buildWorkflow();
+ }
+
+ @Test
+ public void testParseInputs() throws Exception {
+
+ workflow.setParent(null);
+ NamedSet<InputWorkflowPort> workflowInputs = workflow.getInputPorts();
+
+ Workflow expectedWorkflow = new Workflow(workflow.getName());
+ NamedSet<InputWorkflowPort> expectedInputs = expectedWorkflow.getInputPorts();
+ expectedInputs.add(new InputWorkflowPort(expectedWorkflow, "name"));
+
+ assertEquals(expectedInputs, workflowInputs);
+ }
+
+ @Test
+ public void testParseOutputs() throws Exception {
+
+ NamedSet<OutputWorkflowPort> workflowOutputs = workflow.getOutputPorts();
+ NamedSet<OutputWorkflowPort> expectedOutputs = new NamedSet<>();
+
+ assertEquals(expectedOutputs, workflowOutputs);
+ }
+
+ @Test
+ public void testParseProcessors() throws Exception {
+
+ workflow.setParent(null);
+ NamedSet<Processor> workflowProcessors = workflow.getProcessors();
+
+ Workflow expectedWorkflow = new Workflow(workflow.getName());
+ NamedSet<Processor> expectedProcessors = expectedWorkflow.getProcessors();
+ expectedProcessors.add(new Processor(expectedWorkflow, "step1"));
+
+ assertEquals(expectedProcessors, workflowProcessors);
+ }
+
+ @Test
+ public void testParseDataLinks() throws Exception {
+
+ Set<DataLink> workflowDataLinks = workflow.getDataLinks();
+ Set<DataLink> expectedDataLinks = new HashSet<>();
+ NamedSet<Processor> processorSet = workflow.getProcessors();
+ // processorSet has one processor
+ Processor processor = processorSet.getByName("step1");
+ expectedDataLinks.add(
+ new DataLink(
+ workflow,
+ new InputWorkflowPort(workflow, "name"),
+ new InputProcessorPort(processor, "text")
+ )
+ );
+
+ assertEquals(1, workflowDataLinks.size());
+ assertEquals(expectedDataLinks, workflowDataLinks);
+ }
+}
diff --git a/taverna-scufl2-cwl/src/test/resources/1st-tool.cwl b/taverna-scufl2-cwl/src/test/resources/1st-tool.cwl
new file mode 100644
index 0000000..be272f2
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/resources/1st-tool.cwl
@@ -0,0 +1,26 @@
+# 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.
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+inputs:
+ message:
+ type: string
+
+ inputBinding:
+ position: 1
+outputs: []
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/test/resources/hello_world.cwl b/taverna-scufl2-cwl/src/test/resources/hello_world.cwl
new file mode 100644
index 0000000..2172578
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/resources/hello_world.cwl
@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+
+# 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.
+
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+ name: string
+
+outputs: []
+
+steps:
+ step1:
+ run: example.cwl
+
+ inputs:
+ - id: text
+ source: "#x/name"
+
+ outputs: []
diff --git a/taverna-scufl2-cwl/src/test/resources/int_input.cwl b/taverna-scufl2-cwl/src/test/resources/int_input.cwl
new file mode 100644
index 0000000..f2041da
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/resources/int_input.cwl
@@ -0,0 +1,22 @@
+# 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.
+inputs:
+ example_int:
+ type: int
+ inputBinding:
+ position: 2
+ prefix: -i
diff --git a/taverna-scufl2-cwl/src/test/resources/simple_string_input.cwl b/taverna-scufl2-cwl/src/test/resources/simple_string_input.cwl
new file mode 100644
index 0000000..059338f
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/resources/simple_string_input.cwl
@@ -0,0 +1,21 @@
+# 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.
+inputs:
+ example_string: string
+steps:
+ step1:
+ run: run1
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/test/resources/worklflow2.cwl b/taverna-scufl2-cwl/src/test/resources/worklflow2.cwl
new file mode 100644
index 0000000..fc5e846
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/resources/worklflow2.cwl
@@ -0,0 +1,44 @@
+#!/usr/bin/env cwl-runner
+
+# 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.
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+ message: string
+
+outputs:
+ download:
+ type: File
+ outputSource: "#step1/curl"
+
+steps:
+ step1:
+ run:
+ class: CommandLineTool
+ baseCommand: echo
+ inputs:
+ text:
+ type: string
+ inputBinding:
+ position: 1
+ outputs: []
+ in:
+ text: message
+
+ out: [curl]
