support more complex types

Author: mr-c

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

@@ -815,15 +815,18 @@ private CWLElement getDetails(Object inputOutput) {
 			// Shorthand notation "id: type" - no label/doc/other params
 			if (inputOutput.getClass() == String.class) {
 				details.setType((String) inputOutput);
-			} else {
-				details.setLabel(extractLabel((Map<String, Object>) inputOutput));
-				details.setDoc(extractDoc((Map<String, Object>) inputOutput));
-				extractSource((Map<String, Object>) inputOutput).forEach(details::addSourceID);
-				details.setDefaultVal(extractDefault((Map<String, Object>) inputOutput));
+			} else if (List.class.isAssignableFrom(inputOutput.getClass())) {
+				details.setType(this.extractTypes(inputOutput));
+			} else if (Map.class.isAssignableFrom(inputOutput.getClass())) {
+				Map<String, Object> iOMap = (Map<String, Object>) inputOutput;
+				details.setLabel(extractLabel(iOMap));
+				details.setDoc(extractDoc(iOMap));
+				extractSource(iOMap).forEach(details::addSourceID);
+				details.setDefaultVal(extractDefault(iOMap));
 
 				// Type is only for inputs
-				if (((Map<String, Object>) inputOutput).containsKey(TYPE)) {
-					details.setType(extractTypes(((Map<String, Object>) inputOutput).get(TYPE)));
+				if (iOMap.containsKey(TYPE)) {
+					details.setType(extractTypes(iOMap.get(TYPE)));
 				}
 			}
 
@@ -966,7 +969,7 @@ private String extractTypes(Object typeNode) {
 				// Multiple types, build a string to represent them
 				StringBuilder typeDetails = new StringBuilder();
 				boolean optional = false;
-				for (Object type : (List<String>) typeNode) {
+				for (Object type : (List<Object>) typeNode) {
 					if (type.getClass() == String.class) {
 						// This is a simple type
 						if (((String) type).equals("null")) {
@@ -981,8 +984,13 @@ private String extractTypes(Object typeNode) {
 						// This is a verbose type with sub-fields broken down into type: and other
 						// params
 						if (((Map<String, Object>) type).get(TYPE).equals(ARRAY)) {
-							typeDetails.append((String) ((Map<String, Object>) type).get(ARRAY_ITEMS));
-							typeDetails.append("[], ");
+							Object items = ((Map<String, Object>) type).get(ARRAY_ITEMS);
+							if (items.getClass() == String.class) {
+								typeDetails.append(items);
+								typeDetails.append("[], ");
+							} else {
+								typeDetails.append(type.toString() + ", ");
+							}
 						} else {
 							typeDetails.append((String) ((Map<String, Object>) type).get(TYPE));
 						}

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

@@ -42,6 +42,10 @@
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URL;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
 import java.util.Map;
@@ -134,19 +138,24 @@ public void parseLobSTRv1WorkflowNative() throws Exception {
         testLobSTRWorkflow(lobSTRv1, true);
     }
 
-    /**
-     * Test native loading parsing of optional inline types
-     */
-    @Test
-    public void parseWorkflowInlineOptionalTypesNative() throws Exception {
-        CWLService cwlService = new CWLService(rdfService, new CWLTool(), 5242880);
-        Workflow wkflow = cwlService.parseWorkflowNative(
-                Paths.get("src/test/resources/cwl/oneline_optional_types.cwl"), null);
-        assertEquals(wkflow.getInputs().get("qualified_phred_quality").getType(), "int?");
-        assertEquals(wkflow.getInputs().get("ncrna_tab_file").getType(), "File?");
-        assertEquals(wkflow.getInputs().get("reverse_reads").getType(), "File?");
-        
-    }
+	/**
+	 * Test native loading parsing of optional inline types
+	 */
+	@Test
+	public void parseWorkflowInlineOptionalTypesNative() throws Exception {
+		CWLService cwlService = new CWLService(rdfService, new CWLTool(), 5242880);
+//        URI uri = new URI("https://github.com/emo-bon/pipeline-v5/raw/develop/workflows/gos_wf.cwl");
+//        InputStream is = uri.toURL().openStream();
+//        Workflow wkflow = cwlService.parseWorkflowNative(is, null, uri.toURL().getFile());
+		Workflow wkflow = cwlService.parseWorkflowNative(Paths.get("src/test/resources/cwl/oneline_optional_types.cwl"),
+				null);
+		assertEquals(wkflow.getInputs().get("qualified_phred_quality").getType(), "int?");
+		assertEquals(wkflow.getInputs().get("ncrna_tab_file").getType(), "File?");
+		assertEquals(wkflow.getInputs().get("reverse_reads").getType(), "File?");
+		assertEquals(wkflow.getInputs().get("ssu_tax").getType(), "string, File");
+		assertEquals(wkflow.getInputs().get("rfam_models").getType(), "{type=array, items=[string, File]}");
+
+	}
 
     /**
      * Test parsing of a workflow using cwltool

src/test/resources/cwl/oneline_optional_types.cwl

@@ -5,7 +5,12 @@ inputs:
   ncrna_tab_file: {type: File?}
   reverse_reads: File?
   qualified_phred_quality: { type: int? }
-  
+  ssu_tax: [string, File]
+  rfam_models:
+    type:
+      - type: array
+        items: [string, File]
+
 steps: []
 
 outputs: []