Add different coloured graph steps for workflow elements

Author: Mark Robinson

src/main/java/org/commonwl/viewer/domain/Workflow.java

@@ -81,8 +81,12 @@ public Workflow(String label, String doc, Map<String, CWLElement> inputs,
         this.outputs = outputs;
         this.steps = steps;
         this.dockerLink = dockerLink;
+    }
 
-        // Create a DOT graph for this workflow and store it
+    /**
+     * Create a DOT graph for this workflow and store it
+     */
+    public void generateDOT() {
         StringWriter graphWriter = new StringWriter();
         DotWriter dotWriter = new DotWriter(graphWriter);
         try {

src/main/java/org/commonwl/viewer/domain/cwl/CWLCollection.java

@@ -277,6 +277,7 @@ public Workflow getWorkflow() {
         Workflow workflowModel = new Workflow(label, extractDoc(mainWorkflow), getInputs(mainWorkflow),
                 getOutputs(mainWorkflow), getSteps(mainWorkflow), getDockerLink(mainWorkflow));
         fillStepRunTypes(workflowModel);
+        workflowModel.generateDOT();
         return workflowModel;
     }
 
@@ -298,6 +299,13 @@ private void fillStepRunTypes(Workflow workflow) {
                     if (cwlDocs.containsKey(filePath.toString())) {
                         JsonNode runDoc = cwlDocs.get(filePath.toString());
                         step.setRunType(extractProcess(runDoc));
+                        // Set label/doc from linked document if none exists for step
+                        if (step.getLabel() == null) {
+                            step.setLabel(extractLabel(runDoc));
+                        }
+                        if (step.getDoc() == null) {
+                            step.setDoc(extractDoc(runDoc));
+                        }
                     }
                 }
             }

src/main/java/org/commonwl/viewer/services/DotWriter.java

@@ -21,6 +21,7 @@
 
 import org.commonwl.viewer.domain.Workflow;
 import org.commonwl.viewer.domain.cwl.CWLElement;
+import org.commonwl.viewer.domain.cwl.CWLProcess;
 import org.commonwl.viewer.domain.cwl.CWLStep;
 
 import java.io.IOException;
@@ -152,9 +153,13 @@ private void writeOutputs(Workflow workflow) throws IOException {
      * @throws IOException Any errors in writing which may have occurred
      */
     private void writeSteps(Workflow workflow) throws IOException {
-        // Write each of the steps as a node
+        // Write each of the steps as a node or subgraph if it is a nested workflow
         for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
-            writeLine("  \"" + step.getKey() + "\"");
+            if (step.getValue().getRunType() == CWLProcess.WORKFLOW) {
+                writeLine("  \"" + step.getKey() + "\" [fillcolor=\"#F3CEA1\"];");
+            } else {
+                writeLine("  \"" + step.getKey() + "\";");
+            }
         }
 
         // Write the links between nodes