Fix some perfomance issues: get rid of nested transactions, do explicit autoboxing

Author: Balletie

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/Neo4jGraph.java

@@ -284,8 +284,12 @@ public void setInterestingnessStrategy(InterestingnessStrategy is) {
 	 * order, to assign ranks and scores to nodes.
 	 */
 	protected void analyze() {
-		// Rank the graph.
-		execute(e -> new AnalyzeCommand(rootIterator()).execute(e));
+		ResourceIterator<Node> roots;
+		try (Transaction tx = service.beginTx()) {
+			roots = rootIterator();
+			new AnalyzeCommand(roots).execute(service);
+			tx.success();
+		}
 	}
 
 	@Override

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/NodeLabels.java

@@ -12,5 +12,4 @@ public enum NodeLabels implements Label {
 	SOURCE,
 	NODE,
 	BUBBLE_SOURCE,
-	BUBBLE_SINK
 }

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/RelTypes.java

@@ -11,6 +11,5 @@ public enum RelTypes implements RelationshipType {
 	NEXT,
 	SOURCE,
 	MUTATION,
-	BUBBLE_SINK_OF,
 	BUBBLE_SOURCE_OF
 }

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/command/AnalyzeCommand.java

@@ -8,7 +8,6 @@
 import org.neo4j.graphdb.Node;
 import org.neo4j.graphdb.Relationship;
 import org.neo4j.graphdb.ResourceIterator;
-import org.neo4j.graphdb.Transaction;
 import org.neo4j.graphdb.traversal.InitialBranchState;
 import org.neo4j.graphdb.traversal.Uniqueness;
 
@@ -52,13 +51,8 @@ public Iterable<Node> topologicalOrder(GraphDatabaseService service) {
 
 	@Override
 	public void execute(GraphDatabaseService service) {
-		try (
-			Transaction tx = service.beginTx();
-		) {
-			for (Node n : topologicalOrder(service)) {
-				rankDest(n);
-			}
-			tx.success();
+		for (Node n : topologicalOrder(service)) {
+			rankDest(n);
 		}
 	}
 

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/command/TopologicalPathExpander.java

@@ -94,48 +94,48 @@ private Set<Long> getSourcesToPropagate(Node from) {
 		// This function accumulates unclosed bubble sources from a mapping of incoming edge ids.
 		Set<Long> propagatedSources = new HashSet<>();
 		for (Relationship in : ins) {
-			propagatedSources.addAll(relIDtoSourceIDs.remove(in.getId()).stream()
+			propagatedSources.addAll(relIDtoSourceIDs.remove(Long.valueOf(in.getId())).stream()
 					.filter(source -> bubbleSourceIDtoEndIDs.get(source) != null)
 					.collect(Collectors.toList()));
 		}
 		return propagatedSources;
 	}
 
-	private void advanceEnds(long bubbleSource, Node endnode) {
+	private void advanceEnds(Long bubbleSource, Node endnode) {
 		Set<Long> pathEndIDs = bubbleSourceIDtoEndIDs.get(bubbleSource);
 		if (pathEndIDs != null) {
-			pathEndIDs.remove(endnode.getId());
+			pathEndIDs.remove(Long.valueOf(endnode.getId()));
 
 			// FIXME: we add twice here in most cases.
 			endnode.getRelationships(RelTypes.NEXT, Direction.OUTGOING)
-				.forEach(rel -> pathEndIDs.add(rel.getEndNode().getId()));
+				.forEach(rel -> pathEndIDs.add(Long.valueOf(rel.getEndNode().getId())));
 		}
 	}
 
 	private void createBubbleSource(Node n, Set<Long> toPropagate) {
 		int outDegree = n.getDegree(RelTypes.NEXT, Direction.OUTGOING);
 		if (outDegree >= 2) {
 			Set<Long> pathEnds = new HashSet<>(outDegree);
-			toPropagate.add(n.getId());
+			toPropagate.add(Long.valueOf(n.getId()));
 
 			n.addLabel(NodeLabels.BUBBLE_SOURCE);
 			n.getRelationships(RelTypes.NEXT, Direction.OUTGOING)
-				.forEach(rel -> pathEnds.add(rel.getEndNode().getId()));
+				.forEach(rel -> pathEnds.add(Long.valueOf(rel.getEndNode().getId())));
 
-			bubbleSourceIDtoEndIDs.put(n.getId(), pathEnds);
+			bubbleSourceIDtoEndIDs.put(Long.valueOf(n.getId()), pathEnds);
 		}
 	}
 
 	private void propagateSourceIDs(Set<Long> propagatedUnique, Relationship out) {
-		relIDtoSourceIDs.put(out.getId(), propagatedUnique);
+		relIDtoSourceIDs.put(Long.valueOf(out.getId()), propagatedUnique);
 	}
 
 	private void createBubbleSink(Node n) {
 		int degree = n.getDegree(RelTypes.NEXT, Direction.INCOMING);
 		if (degree >= 2) {
 			Set<Long> bubbleSourceID = new HashSet<>();
 			for (Relationship in : n.getRelationships(RelTypes.NEXT, Direction.INCOMING)) {
-				for (long sourceID : relIDtoSourceIDs.get(in.getId())) {
+				for (Long sourceID : relIDtoSourceIDs.get(Long.valueOf(in.getId()))) {
 					if (bubbleSourceIDtoEndIDs.get(sourceID).size() == 1) {
 						bubbleSourceID.add(sourceID);
 					}
@@ -145,13 +145,9 @@ private void createBubbleSink(Node n) {
 				if (bubbleSourceIDtoEndIDs.get(id).size() == 1) {
 					bubbleSourceIDtoEndIDs.remove(id);
 				}
-				Node bubbleSource = n.getGraphDatabase().getNodeById(id);
-				n.createRelationshipTo(bubbleSource, RelTypes.BUBBLE_SINK_OF);
+				Node bubbleSource = n.getGraphDatabase().getNodeById(id.longValue());
 				bubbleSource.createRelationshipTo(n, RelTypes.BUBBLE_SOURCE_OF);
 			});
-			if (bubbleSourceID.size() != 0) {
-				n.addLabel(NodeLabels.BUBBLE_SINK);
-			}
 		}
 	}