Merge pull request #171 from SynBioDex/ArrayListDecodeFix

Fix ArrayList decode error

SBOLCanvasBackend/src/utils/MxToSBOL.java

@@ -119,23 +119,17 @@ public void toSBOL1(InputStream graphStream, OutputStream outputStream) throws I
 		SBOLWriter.setKeepGoing(true);
 		SBOLWriter.write(document, outputStream, SBOLDocument.RDFV1);
 	}
-
+	
 	@SuppressWarnings("unchecked")
 	public SBOLDocument setupDocument(InputStream graphStream) throws IOException, URISyntaxException, SBOLValidationException, TransformerFactoryConfigurationError, TransformerException, SynBioHubException {
 		// read in the mxGraph
 		mxGraph graph = parseGraph(graphStream);
 		mxGraphModel model = (mxGraphModel) graph.getModel();
 		mxCell cell0 = (mxCell) model.getCell("0");
 		ArrayList<Object> dataContainer = (ArrayList<Object>)cell0.getValue();
-		infoDict = (Hashtable<String, Info>) dataContainer.get(INFO_DICT_INDEX);
-		if(dataContainer.get(COMBINATORIAL_DICT_INDEX) instanceof ArrayList) {
-			for(CombinatorialInfo combInfo : (ArrayList<CombinatorialInfo>) dataContainer.get(COMBINATORIAL_DICT_INDEX)) {
-				combinatorialDict.put(combInfo.getFullURI(), combInfo);
-			}
-		}else {
-			combinatorialDict = (Hashtable<String, CombinatorialInfo>) dataContainer.get(COMBINATORIAL_DICT_INDEX);			
-		}
-		interactionDict = (Hashtable<String, InteractionInfo>) dataContainer.get(INTERACTION_DICT_INDEX);
+		infoDict = loadDictionary(dataContainer, INFO_DICT_INDEX);
+		combinatorialDict = loadDictionary(dataContainer, COMBINATORIAL_DICT_INDEX);
+		interactionDict = loadDictionary(dataContainer, INTERACTION_DICT_INDEX);
 
 		// cells may show up in the child array not based on their x location
 		enforceChildOrdering(model, graph);
@@ -931,5 +925,35 @@ private mxGraph parseGraph(InputStream graphStream) throws IOException {
 		codec.decode(document.getDocumentElement(), graph.getModel());
 		return graph;
 	}
+
+	/**
+	 * Dictionaries from the front end sometimes get decoded as array lists.
+	 * This method ensures that we load them as hash tables.
+	 * @param <T>
+	 * @param dataContainer
+	 * @param dictionaryIndex
+	 */
+	@SuppressWarnings("unchecked")
+	private <T extends Info> Hashtable<String, T> loadDictionary(ArrayList<Object> dataContainer, int dictionaryIndex) {
+		if(dataContainer.get(dictionaryIndex) instanceof ArrayList) {
+			// 90% sure it only happens when it's empty meaning that we could just return a empty hash table.
+			Hashtable<String, T> dict = new Hashtable<String, T>();
+			for(T item : (ArrayList<T>) dataContainer.get(dictionaryIndex)) {
+				// nasty instanceof as I couldn't convince the compiler that the abstract method is guaranteed to be implemented
+				if(item instanceof GlyphInfo) {
+					dict.put(((GlyphInfo) item).getFullURI(), item);
+				}else if(item instanceof ModuleInfo) {
+					dict.put(((ModuleInfo) item).getFullURI(), item);
+				}else if(item instanceof CombinatorialInfo) {
+					dict.put(((CombinatorialInfo) item).getFullURI(), item);
+				}else if(item instanceof InteractionInfo) {
+					dict.put(((InteractionInfo) item).getFullURI(), item);
+				}
+			}
+			return dict;
+		}else {
+			return (Hashtable<String, T>) dataContainer.get(dictionaryIndex);
+		}
+	}
 
 }