Add support for multiple outputs->one input in data structures

Author: Mark Robinson

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

@@ -267,7 +267,7 @@ private CWLElement getDetails(JsonNode inputOutput) {
             } else {
                 details.setLabel(extractLabel(inputOutput));
                 details.setDoc(extractDoc(inputOutput));
-                details.setSourceID(extractOutputSource(inputOutput));
+                details.addSourceID(extractOutputSource(inputOutput));
                 details.setDefaultVal(extractDefault(inputOutput));
 
                 // Type is only for inputs

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

@@ -19,17 +19,24 @@
 
 package org.commonwl.viewer.domain;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
- * Represents the input/output/step of a workflow/tool
+ * Represents the input/output of a workflow/tool
  */
 public class CWLElement {
 
     private String label;
     private String doc;
     private String type;
-    private String sourceID;
+    private List<String> sourceID;
     private String defaultVal;
 
+    public CWLElement() {
+        this.sourceID = new ArrayList<String>();
+    }
+
     public String getLabel() {
         return label;
     }
@@ -54,12 +61,14 @@ public void setType(String type) {
         this.type = type;
     }
 
-    public String getSourceID() {
+    public List<String> getSourceIDs() {
         return sourceID;
     }
 
-    public void setSourceID(String sourceID) {
-        this.sourceID = sourceID;
+    public void addSourceID(String sourceID) {
+        if (sourceID != null) {
+            this.sourceID.add(sourceID);
+        }
     }
 
     public String getDefaultVal() {

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

@@ -160,25 +160,31 @@ private void writeSteps(Workflow workflow) throws IOException {
         // Write the links between nodes
         // Write links between outputs and penultimate steps
         for (Map.Entry<String, CWLElement> output : workflow.getOutputs().entrySet()) {
-            writeLine("  \"" + output.getValue().getSourceID() + "\" -> \"" + output.getKey() + "\";");
+            for (String sourceID : output.getValue().getSourceIDs()) {
+                writeLine("  \"" + sourceID + "\" -> \"" + output.getKey() + "\";");
+            }
         }
 
         // Write links between the remaining steps
         int defaultCount = 0;
         for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
             if (step.getValue().getInputs() != null) {
                 for (Map.Entry<String, CWLElement> input : step.getValue().getInputs().entrySet()) {
-                    String sourceID = input.getValue().getSourceID();
+                    List<String> sourceIDs = input.getValue().getSourceIDs();
+
+                    // Draw the default value on the graph if there are no step inputs (it is a constant)
                     String defaultVal = input.getValue().getDefaultVal();
-                    if (sourceID != null) {
-                        // Regular link from source step to destination step
-                        writeLine("  \"" + sourceID + "\" -> \"" + step.getKey() + "\";");
-                    } else if (defaultVal != null) {
+                    if (sourceIDs.isEmpty() && defaultVal != null) {
                         // New node for a default value to be used as the source
                         defaultCount++;
                         writeLine("  \"default" + defaultCount + "\" [label=\"" + defaultVal + "\", fillcolor=\"#D5AEFC\"]");
                         writeLine("  \"default" + defaultCount + "\" -> \"" + step.getKey() + "\";");
                     }
+
+                    // Otherwise write regular links from source step to destination step
+                    for (String sourceID : sourceIDs) {
+                        writeLine("  \"" + sourceID + "\" -> \"" + step.getKey() + "\";");
+                    }
                 }
             }
         }