Fix parsing for default values in CWL V1.0

Author: Mark Robinson

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

@@ -72,6 +72,7 @@ public class CWLCollection {
     private final String DESCRIPTION = "description";
     private final String ARRAY = "array";
     private final String ARRAY_ITEMS = "items";
+    private final String LOCATION = "location";
 
     /**
      * Creates a new collection of CWL files from a Github repository
@@ -275,13 +276,22 @@ private Map<String, CWLElement> getStepInputsOutputs(JsonNode inOut) {
 
         if (inOut.getClass() == ArrayNode.class) {
             // array<WorkflowStepInput>
+            int test = 1;
         } else if (inOut.getClass() == ObjectNode.class) {
             // map<WorkflowStepInput.id, WorkflowStepInput.source>
             Iterator<Map.Entry<String, JsonNode>> iterator = inOut.fields();
             while (iterator.hasNext()) {
                 Map.Entry<String, JsonNode> inOutNode = iterator.next();
                 CWLElement inputOutput = new CWLElement();
-                inputOutput.addSourceID(stepIDFromSource(inOutNode.getValue().asText()));
+                if (inOutNode.getValue().getClass() == ObjectNode.class) {
+                    inputOutput.setDefaultVal(extractDefault(inOutNode.getValue()));
+                } else if (inOutNode.getValue().getClass() == ArrayNode.class) {
+                    for (JsonNode key : inOutNode.getValue()) {
+                        inputOutput.addSourceID(stepIDFromSource(key.asText()));
+                    }
+                } else {
+                    inputOutput.addSourceID(stepIDFromSource(inOutNode.getValue().asText()));
+                }
                 returnMap.put(inOutNode.getKey(), inputOutput);
             }
         }
@@ -379,7 +389,11 @@ private String extractLabel(JsonNode node) {
      */
     private String extractDefault(JsonNode node) {
         if (node != null && node.has(DEFAULT)) {
-            return node.get(DEFAULT).asText();
+            if (node.get(DEFAULT).has(LOCATION)) {
+                return node.get(DEFAULT).get(LOCATION).asText();
+            } else {
+                return node.get(DEFAULT).asText();
+            }
         }
         return null;
     }
@@ -425,7 +439,7 @@ private List<String> extractOutputSource(JsonNode node) {
      * @return The step ID
      */
     private String stepIDFromSource(String source) {
-        if (source != null) {
+        if (source != null && source.length() > 0) {
             // Strip leading # if it exists
             if (source.charAt(0) == '#') {
                 source = source.substring(1);