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/CombinatorialInfo.java

@@ -5,7 +5,6 @@
 public class CombinatorialInfo extends Info {
 
 	private String templateURI;
-	private String version;
 	private String strategy;
 	private String name;
 	private String description;
@@ -19,14 +18,6 @@ public void setTemplateURI(String templateURI) {
 		this.templateURI = templateURI;
 	}
 
-	public String getVersion() {
-		return version;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
 	public String getStrategy() {
 		return strategy;
 	}
@@ -59,12 +50,4 @@ public void setVariableComponents(Hashtable<String, VariableComponentInfo> varia
 		this.variableComponents = variableComponents;
 	}
 
-	public String getFullURI() {
-		String fullURI = this.uriPrefix + '/' + this.displayID;
-		if (this.version != null && this.version.length() > 0) {
-			fullURI += '/' + this.version;
-		}
-		return fullURI;
-	}
-
 }

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

@@ -5,15 +5,8 @@
 public class EventInfo extends Info {
 
 	private Hashtable<String, Object> simulationData;
-
-	@Override
-	public String getFullURI() {
-		if (uriPrefix == null || displayID == null) {
-			throw new IllegalStateException(
-					"EventInfo has null uriPrefix or displayID (uriPrefix=" + uriPrefix + ", displayID=" + displayID + ")");
-		}
-		return uriPrefix + "/" + displayID;
-	}
+	private String name;
+	private String description;
 
 	public Hashtable<String, Object> getSimulationData() {
 		return simulationData;
@@ -23,4 +16,20 @@ 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/data/GlyphInfo.java

@@ -11,7 +11,6 @@ public class GlyphInfo extends Info {
 	private String partRefine;
 	private String name;
 	private String description;
-	private String version;
 	private String sequence;
 	private String sequenceURI;
 	private CanvasAnnotation[] annotations;
@@ -75,14 +74,6 @@ public void setDescription(String description) {
 		this.description = description;
 	}
 
-	public String getVersion() {
-		return version;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
 	public String getSequence() {
 		return this.sequence;
 	}
@@ -130,12 +121,4 @@ public Hashtable<String, Object> getSimulationData() {
 	public void setSimulationData(Hashtable<String, Object> simulationData) {
 		this.simulationData = simulationData;
 	}
-
-	public String getFullURI() {
-		String fullURI = this.uriPrefix + '/' + this.displayID;
-		if(this.version != null && this.version.length() > 0) {
-			fullURI += '/' + this.version;
-		}
-		return fullURI;
-	}
 }

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

@@ -4,9 +4,20 @@ public abstract class Info {
 
 	protected String uriPrefix;
 	protected String displayID;
+	protected String version;
+
+	public String getFullURI() {
+		if (uriPrefix == null || displayID == null) {
+			throw new IllegalStateException(
+					"Info has null uriPrefix or displayID (uriPrefix=" + uriPrefix + ", displayID=" + displayID + ")");
+		}
+		String fullURI = this.uriPrefix + '/' + this.displayID;
+		if (this.version != null && this.version.length() > 0) {
+			fullURI += '/' + this.version;
+		}
+		return fullURI;
+	}
 
-	abstract String getFullURI();
-
 	public String getUriPrefix() {
 		return uriPrefix;
 	}
@@ -22,5 +33,26 @@ public String getDisplayID() {
 	public void setDisplayID(String displayID) {
 		this.displayID = displayID;
 	}
-
+
+	public String getVersion() {
+		return version;
+	}
+
+	public void setVersion(String version) {
+		this.version = version;
+	}
+
+	public String getName() {
+		return null;
+	}
+
+	/** The human-facing label: the name when one is set, else the displayID. */
+	public String getDisplayName() {
+		String name = getName();
+		if (name != null && !name.trim().isEmpty()) {
+			return name;
+		}
+		return displayID;
+	}
+
 }

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

@@ -4,7 +4,6 @@ public class ModuleInfo extends Info {
 
 	private String name;
 	private String description;
-	private String version;
 
 	public String getName() {
 		return name;
@@ -22,20 +21,4 @@ public void setDescription(String description) {
 		this.description = description;
 	}
 
-	public String getVersion() {
-		return version;
-	}
-
-	public void setVersion(String version) {
-		this.version = version;
-	}
-
-	public String getFullURI() {
-		String fullURI = this.uriPrefix + '/' + this.displayID;
-		if(this.version != null && this.version.length() > 0) {
-			fullURI += '/' + this.version;
-		}
-		return fullURI;
-	}
-
 }

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);