Fix conflicts and merge branch 'cwlparser' into cwl
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/WorkflowParser.java b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/WorkflowParser.java
index b18dc54..b66991c 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() {
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..ca551fa 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
@@ -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();
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..481c93f 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
@@ -32,7 +32,6 @@
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;
@@ -49,24 +48,17 @@
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 Converter converter = new Converter();
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();
}
@@ -85,35 +77,14 @@
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");
- }
- }
-
public void parseInputs() {
Set<PortDetail> cwlInputs = cwlParser.parseInputs();
for (PortDetail port: cwlInputs) {
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..97d944f 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
@@ -18,7 +18,12 @@
*/
package org.apache.taverna.scufl2.cwl;
+<<<<<<< HEAD
+=======
+import java.io.File;
+import java.io.IOException;
+>>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
import java.util.Set;
import java.util.HashSet;
import java.util.Map;
@@ -45,6 +50,14 @@
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
+<<<<<<< HEAD
+=======
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WriterException;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+>>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
public class TestWorkflowProcess {
private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
@@ -92,8 +105,31 @@
@Test
public void testWorkflowSteps() {
cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
+<<<<<<< HEAD
WorkflowProcess workflow = new WorkflowProcess(cwlFile);
+=======
+ Process workflow = ProcessFactory.createProcess(cwlFile);
+
+ assert(workflow instanceof WorkflowProcess);
+ }
+
+ 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");
+ }
+>>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
}
}
