handle SBOL exception

Author: dany-fu

src/main/java/knox/spring/data/neo4j/controller/KnoxController.java

@@ -5,11 +5,8 @@
 import java.util.*;
 
 import knox.spring.data.neo4j.domain.DesignSpace;
+import knox.spring.data.neo4j.exception.*;
 import knox.spring.data.neo4j.sample.DesignSampler.EnumerateType;
-import knox.spring.data.neo4j.exception.DesignSpaceBranchesConflictException;
-import knox.spring.data.neo4j.exception.DesignSpaceConflictException;
-import knox.spring.data.neo4j.exception.DesignSpaceNotFoundException;
-import knox.spring.data.neo4j.exception.ParameterEmptyException;
 import knox.spring.data.neo4j.sbol.SBOLConversion;
 import knox.spring.data.neo4j.services.DesignSpaceService;
 
@@ -654,7 +651,7 @@ public ResponseEntity<String> importSBOL(@RequestParam("inputSBOLFiles[]") List<
 
     	try {
 			designSpaceService.importSBOL(sbolDocs, outputSpaceID);
-		} catch (IOException | SBOLValidationException | SBOLConversionException e) {
+		} catch (IOException | SBOLValidationException | SBOLConversionException | SBOLException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}

src/main/java/knox/spring/data/neo4j/exception/SBOLException.java

@@ -0,0 +1,11 @@
+package knox.spring.data.neo4j.exception;
+
+public class SBOLException extends RuntimeException{
+    private static final long serialVersionUID = 462532991641214656L;
+
+    private String message;
+
+    public SBOLException(String message) {
+        this.message = message;
+    }
+}

src/main/java/knox/spring/data/neo4j/sbol/SBOLConversion.java

@@ -15,6 +15,7 @@
 import knox.spring.data.neo4j.operations.JoinOperator;
 import knox.spring.data.neo4j.operations.OROperator;
 import knox.spring.data.neo4j.operations.RepeatOperator;
+import knox.spring.data.neo4j.exception.SBOLException;
 
 public class SBOLConversion {
 
@@ -35,7 +36,7 @@ public void setSbolDoc(List<SBOLDocument> sbolDocs) {
 	 * calls the appropriate SBOL parser by checking for CombinatorialDerivations
 	 * @return
 	 */
-	public List<DesignSpace> convertSBOLsToSpaces(){
+	public List<DesignSpace> convertSBOLsToSpaces() throws SBOLException{
 
 		List<DesignSpace> allOutputSpaces = new ArrayList<>();
 
@@ -56,7 +57,7 @@ public List<DesignSpace> convertSBOLsToSpaces(){
 	 * @param sbolDoc
 	 * @return list of design spaces
 	 */
-	private List<DesignSpace> convertCombinatorialSBOL(SBOLDocument sbolDoc) {
+	private List<DesignSpace> convertCombinatorialSBOL(SBOLDocument sbolDoc) throws SBOLException{
 
 		List<DesignSpace> outputSpaces = new ArrayList<>();
 		Set<CombinatorialDerivation> rootCVs = getRootCombinatorialDerivation(sbolDoc);
@@ -77,7 +78,7 @@ private List<DesignSpace> convertCombinatorialSBOL(SBOLDocument sbolDoc) {
 		return outputSpaces;
 	}
 
-	private List<NodeSpace> recurseVariableComponents(CombinatorialDerivation combinatorialDerivation){
+	private List<NodeSpace> recurseVariableComponents(CombinatorialDerivation combinatorialDerivation) throws SBOLException{
 		ComponentDefinition template = combinatorialDerivation.getTemplate();
 		List<NodeSpace> inputSpace = new LinkedList<>();
 
@@ -161,7 +162,7 @@ private VariableComponent[] sortVariableComponents(CombinatorialDerivation combi
 		return orderedVCs;
 	}
 
-	private NodeSpace createNodeSpaceFromVariableComponent(VariableComponent variableComponent, ComponentDefinition template){
+	private NodeSpace createNodeSpaceFromVariableComponent(VariableComponent variableComponent, ComponentDefinition template) throws SBOLException{
 		ArrayList<String> atomIDs = new ArrayList<>();
 		ArrayList<String> atomRoles = new ArrayList<>();
 
@@ -209,7 +210,7 @@ private Edge.Orientation getOrientation(Component component, ComponentDefinition
 		if(Objects.nonNull(annotation)){
 			// throw error if there is more than one location
 			if(annotation.getLocations().size() > 1){
-				throw new RuntimeException("Cannot parse SBOL with more than one Location in SequenceAnnotation");
+				throw new SBOLException("Cannot parse SBOL with more than one Location in SequenceAnnotation");
 			}
 
 			OrientationType orientation = annotation.getLocations().iterator().next().getOrientation();

src/main/java/knox/spring/data/neo4j/services/DesignSpaceService.java

@@ -7,10 +7,7 @@
 import knox.spring.data.neo4j.domain.Node;
 import knox.spring.data.neo4j.domain.NodeSpace;
 import knox.spring.data.neo4j.domain.Snapshot;
-import knox.spring.data.neo4j.exception.DesignSpaceBranchesConflictException;
-import knox.spring.data.neo4j.exception.DesignSpaceConflictException;
-import knox.spring.data.neo4j.exception.DesignSpaceNotFoundException;
-import knox.spring.data.neo4j.exception.ParameterEmptyException;
+import knox.spring.data.neo4j.exception.*;
 import knox.spring.data.neo4j.operations.ANDOperator;
 import knox.spring.data.neo4j.operations.Concatenation;
 import knox.spring.data.neo4j.operations.JoinOperator;
@@ -601,7 +598,7 @@ public HashMap<String, String> processCSVComponents(BufferedReader csvReader) th
     }
 
     public void importSBOL(List<SBOLDocument> sbolDocs, String outputSpaceID) 
-    		throws SBOLValidationException, IOException, SBOLConversionException {
+    		throws SBOLValidationException, IOException, SBOLConversionException, SBOLException {
     	SBOLConversion sbolConv = new SBOLConversion();
 
     	sbolConv.setSbolDoc(sbolDocs);