Import/export fix, Event info fields normalized, linting

README.md

@@ -6,18 +6,20 @@ SBOLCanvas is a web application for creation and editing of genetic constructs u
 ## SynBioSuite Branch
 
 This branch is specifically for SBOLCanvas as embedded in the [SynBioSuite app](https://github.com/MyersResearchGroup/SynBioSuite);
-however, it can still function as a standalone application. 
+however, it can still function as a standalone application.
+
 ## Repository Structure
 
 This is a monorepo containing an Angular app as a frontend (in the frontend directory)
-and a Dockerized Java API (in the backend directory) that handles things like 
+and a Dockerized Java API (in the backend directory) that handles things like
 conversion, communication with SynBioHub, etc.
 
 This differs from the *final* branch, which Dockerizes the frontend and backend
 together, and serves the Angular app from the backend.
 
 The changes made were an optimization to allow the API to be deployed serverlessly
-and the frontend to be deployed as a static web app served from CDNs. 
+and the frontend to be deployed as a static web app served from CDNs.
+
 ## Run Locally
 
 Clone the project
@@ -62,6 +64,7 @@ Start the Angular development server
 ```bash
 npm run dev
 ```
+
 Or, if you plan to develop the frontend, use
 
 ```bash
@@ -75,11 +78,14 @@ Alternatively, you can build both the frontend and backend together on one Docke
 ```bash
 docker build -t sbolcanvas .
 ```
+
 and then
+
 ```bash
 docker run --rm --name canvas --publish 4040:8080 sbolcanvas
 ```
-A local instance will be available on http://localhost:4040/
+
+A local instance will be available on <http://localhost:4040/>
 
 If you plan to contribute to this repository, this is recommended before you open a Pull Request. GitHub Actions will use a similar process to check the Docker build and deployment.
 
@@ -92,6 +98,11 @@ cd SBOLCanvasBackend
 mvn test
 ```
 
+```bash
+# when adding a new test class, run a clean build
+mvn clean test
+```
+
 Frontend:
 
 ```bash
@@ -108,15 +119,14 @@ npm run build
 ```
 
 The built output will be available in frontend/dist and can be deployed anywhere
-a static web app can be deployed. Genetic Logic Lab's weapon of choice is 
+a static web app can be deployed. Genetic Logic Lab's weapon of choice is
 [Azure Static Web Apps](https://azure.microsoft.com/en-us/products/app-service/static/).
 
 To build the backend, from the backend directory, run
+
 ```bash
 docker build -t sbolcanvas .
 ```
 
 The resulting Docker image can be deployed anywhere you can run Docker containers.
 Genetic Logic Lab uses [Azure Container Apps](https://azure.microsoft.com/en-us/products/container-apps/).
-
-

SBOLCanvasBackend/src/main/java/org/sbolcanvas/data/EventInfo.java

@@ -5,6 +5,8 @@
 public class EventInfo extends Info {
 
 	private Hashtable<String, Object> simulationData;
+	private String name;
+	private String description;
 
 	@Override
 	public String getFullURI() {
@@ -23,4 +25,20 @@ public void setSimulationData(Hashtable<String, Object> simulationData) {
 		this.simulationData = simulationData;
 	}
 
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
 }

SBOLCanvasBackend/src/main/java/org/sbolcanvas/servlets/Convert.java

@@ -84,15 +84,17 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response)
 		} catch (SBOLValidationException | IOException | SBOLConversionException | ParserConfigurationException
 				| TransformerException | SAXException | TransformerFactoryConfigurationError | URISyntaxException | SynBioHubException | javax.xml.stream.XMLStreamException e) {
 			ServletOutputStream outputStream = response.getOutputStream();
-			String message = e.getMessage() != null ? e.getMessage() : "Export failed";
+			String action = "/toMxGraph".equals(request.getPathInfo()) ? "Import" : "Export";
+			String message = e.getMessage() != null ? e.getMessage() : action + " failed";
 			InputStream inputStream = new ByteArrayInputStream(message.getBytes());
 			IOUtils.copy(inputStream, outputStream);
 
 			response.setStatus(HttpStatus.SC_INTERNAL_SERVER_ERROR);
 			e.printStackTrace();
 		} catch (RuntimeException e) {
 			// Catch unchecked exceptions from SBML export
-			String message = e.getMessage() != null ? e.getMessage() : "Export failed";
+			String action = "/toMxGraph".equals(request.getPathInfo()) ? "Import" : "Export";
+			String message = e.getMessage() != null ? e.getMessage() : action + " failed";
 			ServletOutputStream outputStream = response.getOutputStream();
 			InputStream inputStream = new ByteArrayInputStream(message.getBytes());
 			IOUtils.copy(inputStream, outputStream);

SBOLCanvasBackend/src/main/java/org/sbolcanvas/utils/Converter.java

@@ -82,9 +82,9 @@ public class Converter {
 	/**
 	 * mxObjectCodec that decodes to a Hashtable instead of an ArrayList.
 	 *
-	 * @param template    the template object (e.g., new GlyphInfo())
-	 * @param targetType  the expected runtime class of the decoded object
-	 * @param setter      applies the parsed Hashtable to the decoded object
+	 * @param template   the template object (e.g., new GlyphInfo())
+	 * @param targetType the expected runtime class of the decoded object
+	 * @param setter     applies the parsed Hashtable to the decoded object
 	 */
 	private static <T> mxObjectCodec createSimulationDataCodec(
 			Object template, Class<T> targetType,
@@ -177,7 +177,8 @@ public boolean filter(Object arg0) {
 	static Filter containerFilter = new Filter() {
 		@Override
 		public boolean filter(Object arg0) {
-			return (arg0 instanceof mxCell && ((mxCell) arg0).getStyle() != null && (((mxCell) arg0).getStyle().contains(STYLE_CIRCUIT_CONTAINER)) && (((mxCell) arg0).getChildCount() > 1));
+			return (arg0 instanceof mxCell && ((mxCell) arg0).getStyle() != null && (((mxCell) arg0).getStyle().contains(STYLE_CIRCUIT_CONTAINER))
+					&& (((mxCell) arg0).getChildCount() > 1));
 		}
 	};
 
@@ -215,6 +216,16 @@ public boolean filter(Object arg0) {
 		}
 	};
 
+	/**
+	 * Filters mxCells that contain "eventGlyph" in the style string
+	 */
+	static Filter eventFilter = new Filter() {
+		@Override
+		public boolean filter(Object arg0) {
+			return arg0 instanceof mxCell && ((mxCell) arg0).getStyle() != null && ((mxCell) arg0).getStyle().contains(STYLE_EVENT);
+		}
+	};
+
 	protected static URI getParticipantType(boolean source, Set<URI> interactionTypes) {
 		URI interactionType = null;
 		for (URI interactionURI : SBOLData.interactions.values()) {
@@ -246,12 +257,13 @@ static QName createQName(String name) {
 	 * @see MxToSBML#sanitizeId for SBML SId sanitization (different spec, different rules)
 	 */
 	static String sanitizeAnnotationKey(String key) {
-		if (key == null || key.isEmpty()) return key;
+		if (key == null || key.isEmpty())
+			return key;
 		StringBuilder sb = new StringBuilder();
 		for (int i = 0; i < key.length(); i++) {
 			char c = key.charAt(i);
 			if (i == 0 ? (Character.isLetter(c) || c == '_')
-					   : (Character.isLetterOrDigit(c) || c == '.' || c == '-' || c == '_')) {
+					: (Character.isLetterOrDigit(c) || c == '.' || c == '-' || c == '_')) {
 				sb.append(c);
 			} else {
 				sb.append("_x").append(String.format("%04X", (int) c)).append("_");
@@ -264,7 +276,8 @@ static String sanitizeAnnotationKey(String key) {
 	 * Reverse sanitizeAnnotationKey: decode _xHHHH_ sequences back to characters.
 	 */
 	static String desanitizeAnnotationKey(String key) {
-		if (key == null || key.isEmpty()) return key;
+		if (key == null || key.isEmpty())
+			return key;
 		StringBuilder sb = new StringBuilder();
 		int i = 0;
 		while (i < key.length()) {
@@ -317,7 +330,7 @@ protected mxGraph loadGraphAndDictionaries(InputStream graphStream) throws IOExc
 		infoDict = loadDictionary(dataContainer, INFO_DICT_INDEX);
 		combinatorialDict = loadDictionary(dataContainer, COMBINATORIAL_DICT_INDEX);
 		interactionDict = loadDictionary(dataContainer, INTERACTION_DICT_INDEX);
-		loadEventDictOrEmpty(dataContainer);
+		eventDict = loadDictionary(dataContainer, EVENT_DICT_INDEX);
 		return graph;
 	}
 
@@ -331,6 +344,10 @@ protected mxGraph loadGraphAndDictionaries(InputStream graphStream) throws IOExc
 	 */
 	@SuppressWarnings("unchecked")
 	protected <T extends Info> Hashtable<String, T> loadDictionary(ArrayList<Object> dataContainer, int dictionaryIndex) {
+		// Older designs predate this slot; treat an absent slot as an empty dictionary.
+		if (dictionaryIndex >= dataContainer.size()) {
+			return new Hashtable<String, T>();
+		}
 		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.
@@ -366,7 +383,8 @@ protected <T extends Info> Hashtable<String, T> loadDictionary(ArrayList<Object>
 	 */
 	static void writeSimulationAnnotations(Identified parent, Hashtable<String, Object> simulationData,
 			String identityPrefix) throws SBOLValidationException {
-		if (simulationData == null || simulationData.isEmpty()) return;
+		if (simulationData == null || simulationData.isEmpty())
+			return;
 		List<Annotation> annList = new ArrayList<Annotation>();
 		for (String key : new TreeSet<>(simulationData.keySet())) {
 			annList.add(new Annotation(createQName(sanitizeAnnotationKey(key)), simulationData.get(key).toString()));
@@ -395,16 +413,4 @@ static Hashtable<String, Object> readSimulationAnnotations(Identified identified
 		return new Hashtable<>();
 	}
 
-	/**
-	 * Load eventDict from the dataContainer, falling back to an empty Hashtable
-	 * for designs created before events were added.
-	 */
-	protected void loadEventDictOrEmpty(ArrayList<Object> dataContainer) {
-		if (dataContainer.size() > EVENT_DICT_INDEX) {
-			eventDict = loadDictionary(dataContainer, EVENT_DICT_INDEX);
-		} else {
-			eventDict = new Hashtable<>();
-		}
-	}
-
 }