Merge pull request #36 from common-workflow-language/v1-step-parsing

V1 step parsing

Author: MarkRobbo

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
@@ -237,11 +238,11 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
     private Map<String, CWLElement> getInputs(JsonNode cwlDoc) {
         if (cwlDoc != null) {
             if (cwlDoc.has(INPUTS)) {
-                // For workflow
+                // For workflow/draft steps
                 return getInputsOutputs(cwlDoc.get(INPUTS));
             } else if (cwlDoc.has(IN)) {
-                // For steps
-                return getInputsOutputs(cwlDoc.get(IN));
+                // For V1.0 steps
+                return getStepInputsOutputs(cwlDoc.get(IN));
             }
         }
         return null;
@@ -255,16 +256,49 @@ private Map<String, CWLElement> getInputs(JsonNode cwlDoc) {
     private Map<String, CWLElement> getOutputs(JsonNode cwlDoc) {
         if (cwlDoc != null) {
             if (cwlDoc.has(OUTPUTS)) {
-                // For workflow
+                // For workflow/draft steps
                 return getInputsOutputs(cwlDoc.get(OUTPUTS));
             } else if (cwlDoc.has(OUT)) {
-                // For steps
-                return getInputsOutputs(cwlDoc.get(OUT));
+                // For V1.0 steps
+                return getStepInputsOutputs(cwlDoc.get(OUT));
             }
         }
         return null;
     }
 
+    /**
+     * Get inputs or outputs from an in or out node
+     * @param inOut The in or out node
+     * @return A map of input IDs and details related to them
+     */
+    private Map<String, CWLElement> getStepInputsOutputs(JsonNode inOut) {
+        Map<String, CWLElement> returnMap = new HashMap<>();
+
+        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();
+                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);
+            }
+        }
+
+        return returnMap;
+    }
+
     /**
      * Get inputs or outputs from an inputs or outputs node
      * @param inputsOutputs The inputs or outputs node
@@ -355,7 +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;
     }
@@ -401,7 +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);

src/main/resources/static/bower_components/graphviz-d3-renderer/.bower.json

@@ -1,11 +1,11 @@
 {
   "name": "graphviz-d3-renderer",
-  "version": "0.9.21",
+  "version": "0.9.24",
   "dependencies": {
     "requirejs": "2.1.15",
     "d3": "3.5.3",
     "requirejs-web-workers": "~1.0.1",
-    "viz.js": "~1.4.1"
+    "viz.js": "~1.5.1"
   },
   "devDependencies": {
     "rfactory": "1.1.0",
@@ -46,11 +46,11 @@
     "karma.conf.js"
   ],
   "homepage": "https://github.com/mstefaniuk/graph-viz-d3-js",
-  "_release": "0.9.21",
+  "_release": "0.9.24",
   "_resolution": {
     "type": "version",
-    "tag": "0.9.21",
-    "commit": "9cba7e58b832f59e51271f8f98367ab676ef206f"
+    "tag": "0.9.24",
+    "commit": "9588a63ee3d5ff651b00a6168340a8b7477b9845"
   },
   "_source": "https://github.com/mstefaniuk/graph-viz-d3-js.git",
   "_target": "^0.9.18",

src/main/resources/static/bower_components/graphviz-d3-renderer/bower.json

@@ -1,11 +1,11 @@
 {
   "name": "graphviz-d3-renderer",
-  "version": "0.9.18",
+  "version": "0.9.24",
   "dependencies": {
     "requirejs": "2.1.15",
     "d3": "3.5.3",
     "requirejs-web-workers": "~1.0.1",
-    "viz.js": "~1.4.1"
+    "viz.js": "~1.5.1"
   },
   "devDependencies": {
     "rfactory": "1.1.0",