Support nested workflows by parsing processes recursively
Merge commit 'refs/pull/39/head' of github.com:apache/incubator-taverna-language into cwlparser
Merges #39
Contributed by @haouech, ICLA on file.
Signed-off-by: Stian Soiland-Reyes <stain@apache.org>
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
index 382208d..63e70d1 100644
--- 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
@@ -35,11 +35,10 @@
public class CWLParser {
private JsonNode cwlFile;
- private YAMLHelper yamlHelper;
+ private YAMLHelper yamlHelper = new YAMLHelper();
public CWLParser(JsonNode cwlFile) {
this.cwlFile = cwlFile;
- this.yamlHelper = new YAMLHelper();
}
public Set<Step> parseSteps() {
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLReader.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLReader.java
new file mode 100644
index 0000000..de9d799
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/CWLReader.java
@@ -0,0 +1,62 @@
+/*
+ * 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 static java.util.Collections.singleton;
+
+import java.io.*;
+import java.util.Set;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleReader;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+
+
+public class CWLReader implements WorkflowBundleReader {
+
+ public static final String CWL_TYPE = "text/cwl";
+
+ @Override
+ public Set<String> getMediaTypes() {
+ return singleton(CWL_TYPE);
+ }
+
+ @Override
+ public WorkflowBundle readBundle(File bundleFile, String mediaType) throws ReaderException, IOException {
+ try (BufferedInputStream is = new BufferedInputStream(
+ new FileInputStream(bundleFile))) {
+ Converter converter = new Converter();
+ return converter.buildWorkflowBundle(new WorkflowProcess(is));
+ }
+ }
+
+ @Override
+ public WorkflowBundle readBundle(InputStream inputStream, String mediaType) throws ReaderException, IOException {
+ Converter converter = new Converter();
+ return converter.buildWorkflowBundle(new WorkflowProcess(inputStream));
+ }
+
+ @Override
+ public String guessMediaTypeForSignature(byte[] firstBytes) {
+ if (new String(firstBytes)
+ .contains("cwlVersion"))
+ return CWL_TYPE;
+ return null;
+ }
+}
\ No newline at end of file
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 eff7ef6..5cfd9ce 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;
@@ -62,17 +63,17 @@
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());
+ Set<InputPort> inputs = step.getInputs();
+ for(InputPort input: inputs) {
+ InputProcessorPort port = new InputProcessorPort(processor, input.getName());
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());
+ Set<OutputPort> outputs = step.getOutputs();
+ for(OutputPort output: outputs) {
+ OutputProcessorPort port = new OutputProcessorPort(processor, output.getName());
processorOutputs.add(port);
}
processor.setOutputPorts(processorOutputs);
@@ -81,10 +82,6 @@
}
public JsonNode convertWorkflowProcessToJsonNode(WorkflowProcess workflow) {
- Map<String, Processor> workflowProcessors = workflow.getWorkflowProcessors();
- Map<String, InputProcessorPort> processorInputs = workflow.getProcessorInputs();
- Map<String, OutputProcessorPort> processorOutputs = workflow.getProcessorOutputs();
-
ObjectNode result = jsonNodeFactory.objectNode();
ObjectNode inputs = convertInputWorkflows(workflow.getWorkflowInputs());
ObjectNode outputs = convertOutputWorkflows(workflow.getWorkflowOutputs());
@@ -162,4 +159,77 @@
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) {
+ Processor processor = new Processor(null, command.getBaseCommand());
+
+ processor.setInputPorts(convertInputProcessPorts(command.getInputPorts()));
+ processor.setOutputPorts(convertOutputProcessPorts(command.getOutputPorts()));
+
+ return processor;
+ }
+
+ public Processor convertReference(Reference reference) {
+ Processor processor = new Processor(null, reference.getSource());
+
+ processor.setInputPorts(convertInputProcessPorts(reference.getInputPorts()));
+ processor.setOutputPorts(convertOutputProcessPorts(reference.getOutputPorts()));
+
+ return processor;
+ }
+
+ public Set<InputProcessorPort> convertInputProcessPorts(Set<InputPort> inputPorts) {
+ Set<InputProcessorPort> processorInputPorts = new HashSet<>();
+
+ for(InputPort port: inputPorts) {
+ processorInputPorts.add(new InputProcessorPort(null, port.getName()));
+ }
+
+ return processorInputPorts;
+ }
+
+ public Set<OutputProcessorPort> convertOutputProcessPorts(Set<OutputPort> outputPorts) {
+ Set<OutputProcessorPort> processorOutputPorts = new HashSet<>();
+
+ for(OutputPort port: outputPorts) {
+ processorOutputPorts.add(new OutputProcessorPort(null, port.getName()));
+ }
+
+ return processorOutputPorts;
+ }
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Main.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Main.java
deleted file mode 100644
index e5f7159..0000000
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/Main.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * 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 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;
-
-public class Main {
-
- private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
- private static final String WORKFLOW_WITH_COMMAND = "/workflow_with_command.cwl";
- private static JsonNode cwlFile;
-
- public static void main(String[] args) {
-
- Yaml reader = new Yaml();
- ObjectMapper mapper = new ObjectMapper();
- cwlFile = mapper.valueToTree(reader.load(Main.class.getResourceAsStream(WORKFLOW_WITH_COMMAND)));
- System.out.println(cwlFile);
-
- Process workflow = ProcessFactory.createProcess(cwlFile);
- workflow.parse();
- Converter converter = new Converter();
- JsonNode node = converter.convertWorkflowProcessToJsonNode((WorkflowProcess) workflow);
- printAsYaml(node);
- }
-
- private static void printAsYaml(JsonNode node) {
- try {
- String yaml = new YAMLMapper().writeValueAsString(node);
- System.out.println("YAML DATA");
- System.out.println(yaml);
- } catch (JsonProcessingException e) {
- System.err.println("Error writing JsonNode to YAML");
- }
- }
-}
\ 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
index b18dc54..2680bf4 100644
--- 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
@@ -53,38 +53,24 @@
private static final String FILE_NAME = "/hello_world.cwl";
private CWLParser cwlParser;
- private Converter converter;
+ private Converter converter = new 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;
+ 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);
- this.converter = new Converter();
- workflowInputs = new HashMap<>();
- workflowOutputs = new HashMap<>();
- workflowProcessors = new HashMap<>();
- processorInputs = new HashMap<>();
- processorOutputs = new HashMap<>();
- dataLinks = new HashSet<DataLink>();
}
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() {
@@ -92,7 +78,7 @@
parseOutputs();
Set<Step> cwlSteps = cwlParser.parseSteps();
parseProcessors(cwlSteps);
- parseDataLinks(cwlSteps);
+// parseDataLinks(cwlSteps);
Workflow workflow = new Workflow();
Set<InputWorkflowPort> inputs = new HashSet<>(workflowInputs.values());
@@ -151,20 +137,20 @@
Processor processor = converter.convertStepToProcessor(step);
workflowProcessors.put(step.getId(), processor);
- for(StepInput stepInput: step.getInputs()) {
- InputProcessorPort processorPort = new InputProcessorPort(processor, stepInput.getId());
- processorInputs.put(stepInput.getId(), processorPort);
+ for(InputPort stepInput: step.getInputs()) {
+ InputProcessorPort processorPort = new InputProcessorPort(processor, stepInput.getName());
+ processorInputs.put(stepInput.getName(), processorPort);
}
- for(StepOutput stepOutput: step.getOutputs()) {
- OutputProcessorPort processorPort = new OutputProcessorPort(processor, stepOutput.getId());
- processorOutputs.put(stepOutput.getId(), 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(StepInput stepInput: step.getInputs()) {
+ for(InputPort stepInput: step.getInputs()) {
String[] sourcePath = stepInput.getSource().split("/");
String source = sourcePath[sourcePath.length-1];
source = source.replace("#", "");
@@ -177,7 +163,7 @@
if(sender == null) {
throw new NullPointerException("Cannot find sender port with name: " + source);
}
- String receiverId = stepInput.getId();
+ String receiverId = stepInput.getName();
ReceiverPort receiver = workflowOutputs.get(receiverId);
if(receiver == null) {
receiver = processorInputs.get(receiverId);
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
index c9b10dc..1b016f8 100644
--- 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
@@ -121,7 +121,7 @@
JsonNode runNode = stepNode.get(RUN);
Process run = ProcessFactory.createProcess(runNode);
run.parse(); // Recursively parse nested process
- Set<StepInput> inputs = processStepInput(stepNode.get(INPUTS));
+ Set<InputPort> inputs = processStepInput(stepNode.get(INPUTS));
step.setId(id);
step.setRun(run);
step.setInputs(inputs);
@@ -141,7 +141,7 @@
run.parse();
step.setRun(run);
}
- Set<StepInput> inputs = processStepInput(value.get(INPUTS));
+ Set<InputPort> inputs = processStepInput(value.get(INPUTS));
step.setId(id);
step.setInputs(inputs);
@@ -152,9 +152,9 @@
return result;
}
- private Set<StepInput> processStepInput(JsonNode inputs) {
+ private Set<InputPort> processStepInput(JsonNode inputs) {
- Set<StepInput> result = new HashSet<>();
+ Set<InputPort> result = new HashSet<>();
if(inputs == null) {
return result;
}
@@ -164,7 +164,7 @@
String id = input.get(ID).asText();
String source = input.get(SOURCE).asText();
- result.add(new StepInput(id, source));
+ result.add(new InputPort(id, source));
}
} else if (inputs.isObject()) {
Iterator<Entry<String, JsonNode>> iterator = inputs.fields();
@@ -174,7 +174,7 @@
String id = entry.getKey();
String source = entry.getValue().get(SOURCE).asText();
- result.add(new StepInput(id, source));
+ result.add(new InputPort(id, source));
}
}
return result;
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java
index 450304a..dc5e16d 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/CommandLineTool.java
@@ -28,7 +28,7 @@
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
import org.apache.taverna.scufl2.api.port.OutputProcessorPort;
-public class CommandLineTool implements Process {
+public class CommandLineTool extends Process {
private final static String BASE_COMMAND = "baseCommand";
private final static String ID = "id";
@@ -39,14 +39,12 @@
private JsonNode node;
private String baseCommand = null;
- private Map<String, InputProcessorPort> processorInputs;
- private Map<String, OutputProcessorPort> processorOutputs;
+ private Map<String, InputProcessorPort> processorInputs = new HashMap<>();
+ private Map<String, OutputProcessorPort> processorOutputs = new HashMap<>();
public CommandLineTool(JsonNode node) {
this.node = node;
this.cwlParser = new CWLParser(node);
- this.processorInputs = new HashMap<>();
- this.processorOutputs = new HashMap<>();
this.parse();
}
@@ -57,6 +55,7 @@
}
public void parseInputs() {
+ // TODO: Set the processor port depth from the CWL type
Set<PortDetail> cwlInputs = cwlParser.parseInputs();
for(PortDetail detail: cwlInputs) {
String portId = detail.getId();
@@ -75,4 +74,8 @@
processorOutputs.put(portId, port);
}
}
+
+ public String getBaseCommand() {
+ return baseCommand;
+ }
}
\ 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/InputPort.java
similarity index 76%
rename from taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepInput.java
rename to taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/InputPort.java
index 0432272..1d1522d 100644
--- 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/InputPort.java
@@ -19,36 +19,35 @@
package org.apache.taverna.scufl2.cwl;
-import java.util.*;
+public class InputPort {
-public class StepInput {
+ private String name;
- private String id;
private String source;
- public StepInput() {
- this.id = null;
- this.source = null;
+ public InputPort() {
+ this.name = "";
+ this.source = "";
}
- public StepInput(String id, String source) {
- this.id = id;
+ public InputPort(String name, String source) {
+ this.name = name;
this.source = source;
}
- public void setId(String id) {
- this.id = id;
+ public String getName() {
+ return this.name;
}
- public String getId() {
- return id;
- }
-
- public void setSource(String source) {
- this.source = source;
+ public void setName(String name) {
+ this.name = name;
}
public String getSource() {
return source;
}
+
+ public void setSource(String source) {
+ this.source = source;
+ }
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Main.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Main.java
deleted file mode 100644
index e69de29..0000000
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Main.java
+++ /dev/null
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/OutputPort.java
similarity index 75%
rename from taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/StepOutput.java
rename to taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/OutputPort.java
index 145fa2d..c865e9c 100644
--- 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/OutputPort.java
@@ -19,23 +19,23 @@
package org.apache.taverna.scufl2.cwl;
-public class StepOutput {
+public class OutputPort {
- private String id;
+ private String name;
- public StepOutput() {
- this.id = null;
+ public OutputPort() {
+ this.name = "";
}
- public StepOutput(String id) {
- this.id = id;
+ public OutputPort(String name) {
+ this.name = name;
}
- public void setId(String id) {
- this.id = id;
+ public String getName() {
+ return this.name;
}
- public String getId() {
- return id;
+ public void setName(String name) {
+ this.name = name;
}
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java
index 70e3669..991df0a 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Process.java
@@ -19,15 +19,31 @@
package org.apache.taverna.scufl2.cwl;
-import java.util.Map;
-import java.util.HashMap;
-import java.util.Set;
import java.util.HashSet;
-import org.apache.taverna.scufl2.api.port.SenderPort;
-import org.apache.taverna.scufl2.api.port.ReceiverPort;
+import java.util.Set;
-public interface Process {
+public abstract class Process {
- public void parse();
+ private Set<InputPort> inputPorts = new HashSet<>();
+ private Set<OutputPort> outputPorts = new HashSet<>();
+
+
+ public abstract void parse();
+
+ public Set<InputPort> getInputPorts() {
+ return this.inputPorts;
+ }
+
+ public void setInputPorts(Set<InputPort> inputs) {
+ this.inputPorts = inputs;
+ }
+
+ public Set<OutputPort> getOutputPorts() {
+ return this.outputPorts;
+ }
+
+ public void setOutputPorts(Set<OutputPort> outputs) {
+ this.outputPorts = outputs;
+ }
}
\ 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..9d5d0c0 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
@@ -21,7 +21,7 @@
import com.fasterxml.jackson.databind.JsonNode;
-public class Reference implements Process {
+public class Reference extends Process {
private String source;
@@ -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/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
index cdcd46e..80ccf03 100644
--- 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
@@ -30,8 +30,8 @@
private String id;
private Process run;
- private Set<StepInput> inputs;
- private Set<StepOutput> outputs;
+ private Set<InputPort> inputs;
+ private Set<OutputPort> outputs;
public Step() {
inputs = new HashSet<>();
@@ -54,27 +54,27 @@
this.run = run;
}
- public void addInput(String id, String source) {
- inputs.add(new StepInput(id, source));
+ public void addInput(String name, String source) {
+ inputs.add(new InputPort(name, source));
}
- public void setInputs(Set<StepInput> inputs) {
+ public void setInputs(Set<InputPort> inputs) {
this.inputs = inputs;
}
- public Set<StepInput> getInputs() {
+ public Set<InputPort> getInputs() {
return inputs;
}
- public void addOutput(String id) {
- outputs.add(new StepOutput(id));
+ public void addOutput(String name) {
+ outputs.add(new OutputPort(name));
}
- public void setOutputs(Set<StepOutput> outputs) {
+ public void setOutputs(Set<OutputPort> outputs) {
this.outputs = outputs;
}
- public Set<StepOutput> getOutputs() {
+ public Set<OutputPort> getOutputs() {
return outputs;
}
diff --git a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
index b41d054..a8e6607 100644
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
@@ -19,20 +19,19 @@
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 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.container.WorkflowBundle;
-
import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
@@ -40,33 +39,35 @@
import org.apache.taverna.scufl2.api.port.SenderPort;
import org.apache.taverna.scufl2.api.port.ReceiverPort;
-import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
-import org.apache.taverna.scufl2.api.io.WriterException;
-
import com.fasterxml.jackson.databind.JsonNode;
-public class WorkflowProcess implements Process {
+public class WorkflowProcess extends Process {
private CWLParser cwlParser;
- 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;
+ 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 Converter converter;
+ 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);
- converter = new Converter();
- workflowInputs = new HashMap<>();
- workflowOutputs = new HashMap<>();
- workflowProcessors = new HashMap<>();
- processorInputs = new HashMap<>();
- processorOutputs = new HashMap<>();
- dataLinks = new HashSet<>();
this.parse();
}
@@ -74,44 +75,7 @@
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);
-
-// System.out.println(workflow);
-// writeWorkflowToFile(workflow);
-//
-// System.out.println("DEBUG WORKFLOW");
-// System.out.println(workflow.getInputPorts());
-// System.out.println(workflow.getOutputPorts());
-// System.out.println(workflow.getProcessors());
-
- }
-
- 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, "text/vnd.taverna.scufl2.structure");
- } catch(WriterException e) {
- System.out.println("Exception writing the workflow bundle");
- } catch(IOException e) {
- System.out.println("IOException");
- }
+ this.processes = parseProcessors(cwlSteps);
}
public void parseInputs() {
@@ -132,27 +96,40 @@
}
}
- public void parseProcessors(Set<Step> cwlSteps) {
+ public Set<Process> parseProcessors(Set<Step> cwlSteps) {
+ Set<Process> result = new HashSet<>();
+
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);
- }
+ Process process = step.getRun();
+ process.setInputPorts(step.getInputs());
+ process.setOutputPorts(step.getOutputs());
+ 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()) {
+ for(InputPort stepInput: step.getInputs()) {
String[] sourcePath = stepInput.getSource().split("/");
String source = sourcePath[sourcePath.length-1];
source = source.replace("#", "");
@@ -165,7 +142,7 @@
if(sender == null) {
throw new NullPointerException("Cannot find sender port with name: " + source);
}
- String receiverId = stepInput.getId();
+ String receiverId = stepInput.getName();
ReceiverPort receiver = workflowOutputs.get(receiverId);
if(receiver == null) {
receiver = processorInputs.get(receiverId);
@@ -227,4 +204,12 @@
public void setDataLinks(Set<DataLink> dataLinks) {
this.dataLinks = dataLinks;
}
+
+ public Set<Process> getProcesses() {
+ return processes;
+ }
+
+ public void setProcesses(Set<Process> processes) {
+ this.processes = processes;
+ }
}
\ No newline at end of file
diff --git a/taverna-scufl2-cwl/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader b/taverna-scufl2-cwl/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader
new file mode 100644
index 0000000..607d8b7
--- /dev/null
+++ b/taverna-scufl2-cwl/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader
@@ -0,0 +1 @@
+org.apache.taverna.scufl2.cwl.CWLReader
\ 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..2b34a3c
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestConverting.java
@@ -0,0 +1,90 @@
+/*
+ * 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 org.junit.Before;
+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 org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.core.Processor;
+
+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() {
+ this.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() {
+ this.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);
+ }
+
+ @Test
+ public void testConvertWorkflowProcessToWorkflow() {
+ this.cwlFile = loadYamlFile(HELLO_WORLD_CWL);
+
+ WorkflowProcess workflowProcess = (WorkflowProcess) ProcessFactory.createProcess(cwlFile);
+ WorkflowBundle bundle = new WorkflowBundle();
+ Converter converter = new Converter();
+ Workflow workflow = converter.convertWorkflowProcess(workflowProcess, bundle);
+ assertEquals(1, workflow.getProcessors().size());
+ assertEquals(1, workflow.getInputPorts().size());
+ assertEquals(1, workflow.getOutputPorts().size());
+
+ Processor processor = workflow.getProcessors().iterator().next();
+ assertEquals(1, processor.getInputPorts().size());
+ assertEquals(0, processor.getOutputPorts().size());
+ }
+}
diff --git a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowNesting.java b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowNesting.java
new file mode 100644
index 0000000..d0f3e88
--- /dev/null
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowNesting.java
@@ -0,0 +1,95 @@
+/*
+ * 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 TestWorkflowNesting {
+ 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 testWorkflowWithProcessor() {
+ JsonNode cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
+
+ WorkflowProcess workflow = (WorkflowProcess) ProcessFactory.createProcess(cwlFile);
+ Set<Process> processes = workflow.getProcesses();
+ assertEquals(processes.size(), 1);
+ Process child = processes.iterator().next();
+ assert(child instanceof CommandLineTool);
+ assertEquals(((CommandLineTool) child).getBaseCommand(), "echo");
+ }
+
+ @Test
+ public void testWorkflowWithWorkflow() {
+ JsonNode cwlFile = loadYamlFile(WORKFLOW_WITH_WORKFLOW);
+
+ WorkflowProcess workflow = (WorkflowProcess) ProcessFactory.createProcess(cwlFile);
+ Set<Process> processes = workflow.getProcesses();
+ assert(processes.size() == 1);
+ Process child = processes.iterator().next();
+ assert(child instanceof WorkflowProcess);
+ WorkflowProcess childWorkflow = (WorkflowProcess) child;
+ assertEquals(childWorkflow.getProcesses().size(), 1);
+
+ Process reference = childWorkflow.getProcesses().iterator().next();
+
+ assert(reference instanceof Reference);
+ assertEquals(((Reference) reference).toString(), "example.cwl");
+ }
+}
diff --git a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
index 015ded4..4b3bba7 100644
--- a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
@@ -19,32 +19,33 @@
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.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 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.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;
+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 TestWorkflowProcess {
private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
@@ -90,10 +91,49 @@
}
@Test
- public void testWorkflowSteps() {
+ public void testProcessType() {
cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
- WorkflowProcess workflow = new WorkflowProcess(cwlFile);
+ Process workflow = ProcessFactory.createProcess(cwlFile);
+ assert(workflow instanceof WorkflowProcess);
+ }
+
+ @Test
+ public void testConvertWorkflowProcess() {
+ cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
+
+ Process workflow = ProcessFactory.createProcess(cwlFile);
+ workflow.parse();
+ Converter converter = new Converter();
+ JsonNode node = converter.convertWorkflowProcessToJsonNode((WorkflowProcess) workflow);
+ printAsYaml(node);
+ }
+
+ private static void printAsYaml(JsonNode node) {
+ try {
+ String yaml = new YAMLMapper().writeValueAsString(node);
+ System.out.println("YAML DATA");
+ System.out.println(yaml);
+ } catch (JsonProcessingException e) {
+ System.err.println("Error writing JsonNode to YAML");
+ }
+ }
+
+ 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, "text/vnd.taverna.scufl2.structure");
+ } catch(WriterException e) {
+ System.out.println("Exception writing the workflow bundle");
+ } catch(IOException e) {
+ System.out.println("IOException");
+ }
}
}
diff --git a/taverna-scufl2-cwl/src/main/resources/workflow_with_command.cwl b/taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl
similarity index 100%
rename from taverna-scufl2-cwl/src/main/resources/workflow_with_command.cwl
rename to taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl
diff --git a/taverna-scufl2-cwl/src/test/resources/worklflow2.cwl b/taverna-scufl2-cwl/src/test/resources/workflow_with_workflow.cwl
similarity index 81%
rename from taverna-scufl2-cwl/src/test/resources/worklflow2.cwl
rename to taverna-scufl2-cwl/src/test/resources/workflow_with_workflow.cwl
index fc5e846..58323c5 100644
--- a/taverna-scufl2-cwl/src/test/resources/worklflow2.cwl
+++ b/taverna-scufl2-cwl/src/test/resources/workflow_with_workflow.cwl
@@ -30,14 +30,18 @@
steps:
step1:
run:
- class: CommandLineTool
- baseCommand: echo
+ class: Workflow
inputs:
- text:
- type: string
- inputBinding:
- position: 1
- outputs: []
+ name: string
+ outputs:
+ output1: string
+ steps:
+ step2:
+ run: example.cwl
+ inputs:
+ - id: text
+ source: "#x/name"
+ outputs: []
in:
text: message
