accept nested arrays as well

Author: mr-c

src/main/java/org/commonwl/view/cwl/CWLService.java

@@ -412,9 +412,12 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel, Path workflowFile,
 				CWLStep wfStep = new CWLStep();
 
 				IRI workflowPath = iriFactory.construct(url).resolve("./");
-				IRI runPath = iriFactory.construct(step.get("run").asResource().getURI());
-				wfStep.setRun(workflowPath.relativize(runPath).toString());
-				wfStep.setRunType(rdfService.strToRuntype(step.get("runtype").toString()));
+				Object runValue = step.get("run").asResource().toString();
+				if (String.class.isAssignableFrom(runValue.getClass())) {
+					String runPath = (String) runValue;
+					wfStep.setRun(workflowPath.relativize(runPath).toString());
+					wfStep.setRunType(rdfService.strToRuntype(step.get("runtype").toString()));
+				}
 
 				if (step.contains("src")) {
 					CWLElement src = new CWLElement();
@@ -1012,7 +1015,7 @@ private String extractTypes(Object typeNode) {
 			} else if (Map.class.isAssignableFrom(typeNode.getClass())) {
 				// Type: array and items:
 				if (((Map<String, Object>) typeNode).containsKey(ARRAY_ITEMS)) {
-					return ((Map<String, String>) typeNode).get(ARRAY_ITEMS) + "[]";
+					return extractTypes(((Map<String, String>) typeNode).get(ARRAY_ITEMS)) + "[]";
 				}
 			}
 		}
@@ -1025,10 +1028,10 @@ private String extractTypes(Object typeNode) {
 	 * @param step The root node of a step
 	 * @return A string with the run parameter if it exists
 	 */
-	private String extractRun(Map<String, Object> step) {
+	private Object extractRun(Map<String, Object> step) {
 		if (step != null) {
 			if (step.containsKey(RUN)) {
-				return (String) step.get(RUN);
+				return step.get(RUN);
 			}
 		}
 		return null;

src/main/java/org/commonwl/view/cwl/CWLStep.java

@@ -31,14 +31,14 @@ public class CWLStep {
 
     private String label;
     private String doc;
-    private String run;
+    private Object run;
     private CWLProcess runType;
     private Map<String, CWLElement> sources;
 
     public CWLStep() {
     }
 
-    public CWLStep(String label, String doc, String run,
+    public CWLStep(String label, String doc, Object run,
                    Map<String, CWLElement> sources) {
         this.label = label;
         this.doc = doc;
@@ -62,11 +62,11 @@ public void setDoc(String doc) {
         this.doc = doc;
     }
 
-    public String getRun() {
+    public Object getRun() {
         return run;
     }
 
-    public void setRun(String run) {
+    public void setRun(Object run) {
         this.run = run;
     }
 

src/test/java/org/commonwl/view/cwl/CWLServiceTest.java

@@ -157,6 +157,19 @@ public void parseWorkflowInlineOptionalTypesNative() throws Exception {
 
 	}
 
+	/**
+	 * Test native loading parsing of nested array types
+	 */
+	@Test
+	public void parseWorkflowNestedArrayTypes() throws Exception {
+		CWLService cwlService = new CWLService(rdfService, new CWLTool(), 5242880);
+		Workflow wkflow = cwlService.parseWorkflowNative(Paths.get("src/test/resources/cwl/nested_array.cwl"),
+				null);
+		assertEquals(wkflow.getInputs().get("overlap_files").getType(), "File[][]");
+		assertEquals(wkflow.getOutputs().get("freq_files").getType(), "File[][]");
+		assertEquals(true, Map.class.isAssignableFrom(wkflow.getSteps().get("dummy").getRun().getClass()));
+	}
+
     /**
      * Test parsing of a workflow using cwltool
      */
@@ -309,4 +322,4 @@ private void testLobSTRWorkflow(Workflow lobSTR, boolean nativeParsed) throws Ex
         }
     }
 
-}
+}

src/test/resources/cwl/nested_array.cwl

@@ -0,0 +1,43 @@
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  overlap_files:
+    type:
+      type: array
+      items:
+        type: array
+        items: File
+
+outputs:
+  freq_files:
+    type:
+      type: array
+      items:
+        type: array
+        items: File
+    outputSource: dummy/freq_files
+
+steps:
+  dummy:
+    in:
+      nested_array: overlap_files
+    run:
+      class: ExpressionTool
+      inputs:
+        nested_array:
+          type:
+            type: array
+            items:
+              type: array
+              items: File
+      expression: |
+        ${ return {"freq_files": inputs.nested_array }; }
+      outputs:
+        freq_files:
+          type:
+            type: array
+            items:
+              type: array
+              items: File
+    out: [ freq_files ]