Extend the test for individual nodes, and fix bug that arose

Author: Balletie

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

@@ -18,8 +18,8 @@
 import org.neo4j.graphdb.Node;
 import org.neo4j.graphdb.Path;
 import org.neo4j.graphdb.PathExpanders;
+import org.neo4j.graphdb.ResourceIterable;
 import org.neo4j.graphdb.traversal.Evaluation;
-import org.neo4j.graphdb.traversal.TraversalDescription;
 import org.neo4j.helpers.collection.IteratorUtil;
 
 import java.util.ArrayList;
@@ -63,7 +63,9 @@ public AllClustersQuery(int minRank, int maxRank, int threshold,
 		this.is = is;
 	}
 
-	private TraversalDescription untilMaxRank(GraphDatabaseService service) {
+	private ResourceIterable<Node> untilMaxRank(GraphDatabaseService service) {
+		Iterable<Node> start = IteratorUtil.loop(service.findNodes(NodeLabels.NODE,
+				SequenceProperties.RANK.name(), minRank));
 		return service.traversalDescription()
 				.breadthFirst()
 				.evaluator(path -> {
@@ -74,23 +76,28 @@ private TraversalDescription untilMaxRank(GraphDatabaseService service) {
 						return Evaluation.EXCLUDE_AND_PRUNE;
 					}
 				})
-				.relationships(RelTypes.NEXT, Direction.OUTGOING);
+				.relationships(RelTypes.NEXT, Direction.OUTGOING)
+				.traverse(start).nodes();
 	}
 
 	@Override
 	public Map<Integer, List<Cluster>> execute(GraphDatabaseService service) {
+		Map<Integer, List<Cluster>> individualNodes = new HashMap<>();
 		Set<Long> bubbleSourcesNested = new HashSet<>();
 		Set<Long> bubbleSourcesToCluster = new HashSet<>();
 		Set<Long> bubbleSourcesToKeepIntact = new HashSet<>();
-		Iterable<Node> start = IteratorUtil.loop(service.findNodes(NodeLabels.NODE,
-				SequenceProperties.RANK.name(), minRank));
-		for (Node n : untilMaxRank(service).traverse(start).nodes()) {
+		for (Node n : untilMaxRank(service)) {
 			if (n.hasLabel(NodeLabels.BUBBLE_SOURCE)) {
 				bubbleSourcesToCluster.add(n.getId());
-				if (((long[]) n.getProperty(BubbleProperties.BUBBLE_SOURCE_IDS.name()))
-						.length > 0) {
+				if (getBubbleIDs(n).length > 0) {
 					bubbleSourcesNested.add(n.getId());
 				}
+			} else {
+				if (getBubbleIDs(n).length == 0) {
+					Cluster individualNode = createSingletonCluster(service, n);
+					individualNodes.put(individualNode.getStartRank(),
+							Collections.singletonList(individualNode));
+				}
 			}
 			int interestingness = is.compute(new Neo4jScoreContainer(n));
 			n.setProperty(SequenceProperties.INTERESTINGNESS.name(), interestingness);
@@ -103,7 +110,12 @@ public Map<Integer, List<Cluster>> execute(GraphDatabaseService service) {
 			}
 		}
 		bubbleSourcesToCluster.removeAll(bubbleSourcesNested);
-		return cluster(service, bubbleSourcesToCluster, bubbleSourcesToKeepIntact);
+		return mergeMaps(Stream.of(individualNodes,
+				cluster(service, bubbleSourcesToCluster, bubbleSourcesToKeepIntact)));
+	}
+
+	private long[] getBubbleIDs(Node n) {
+		return (long[]) n.getProperty(BubbleProperties.BUBBLE_SOURCE_IDS.name());
 	}
 
 	private Map<Integer, List<Cluster>> cluster(GraphDatabaseService service,

dnainator-core/src/test/java/nl/tudelft/dnainator/graph/impl/Neo4jClusterTest.java

@@ -63,21 +63,24 @@ public void test() {
 		// CHECKSTYLE.OFF: MagicNumber
 		Map<Integer, List<Cluster>> clusters = db.getAllClusters(0, Integer.MAX_VALUE, 11);
 
+		// The root node is not associated with a bubble, so it should be a singleton cluster.
+		assertUnorderedIDEquals(Sets.newSet("0"), clusters.get(0).get(0).getNodes());
+
 		// first bubble is not clustered because one node has length greater than 11.
-		assertUnorderedIDEquals(Sets.newSet("1"), clusters.get(0).get(0).getNodes());
+		assertUnorderedIDEquals(Sets.newSet("1"), clusters.get(1).get(0).getNodes());
 
 		// 2 and 3 Expected on rank 1
-		assertUnorderedIDEquals(Sets.newSet("2"), clusters.get(1).get(1).getNodes());
-		assertUnorderedIDEquals(Sets.newSet("3"), clusters.get(1).get(0).getNodes());
+		assertUnorderedIDEquals(Sets.newSet("2"), clusters.get(2).get(1).getNodes());
+		assertUnorderedIDEquals(Sets.newSet("3"), clusters.get(2).get(0).getNodes());
 
 		// Source node is not collapsed.
-		assertUnorderedIDEquals(Sets.newSet("4"), clusters.get(2).get(0).getNodes());
+		assertUnorderedIDEquals(Sets.newSet("4"), clusters.get(3).get(0).getNodes());
 
 		// Collapsed bubble.
-		assertUnorderedIDEquals(Sets.newSet("5", "6", "7"), clusters.get(3).get(0).getNodes());
+		assertUnorderedIDEquals(Sets.newSet("5", "6", "7"), clusters.get(4).get(0).getNodes());
 
 		// Sink node is not collapsed.
-		assertUnorderedIDEquals(Sets.newSet("8"), clusters.get(5).get(0).getNodes());
+		assertUnorderedIDEquals(Sets.newSet("8"), clusters.get(6).get(0).getNodes());
 		// CHECKSTYLE.ON: MagicNumber
 	}
 

dnainator-core/src/test/resources/strains/cluster.edge.graph

@@ -1,3 +1,4 @@
+0 1
 1 2
 1 3
 2 4

dnainator-core/src/test/resources/strains/cluster.node.graph

@@ -1,3 +1,5 @@
+> 0 | LENGTH 20 | 0 | 0
+TATATATATATATATATATA
 > 1 | LENGTH 10 | 0 | 0
 TATATATATA
 > 2 | LENGTH 12 | 0 | 0