Fixed bug: SemaphoreNeighborInject transformations were implemented a…

…mbiguously (some tools used route-semaphore matches, some used route matches)
ftsrg · Nov 21, 2016 · af2b6f3 · af2b6f3
1 parent 5ee6a14
commit af2b6f3
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Showing 43 changed files with 234 additions and 117 deletions.
diff --git a/...java/hu/bme/mit/trainbenchmark/benchmark/emf/matches/EmfSemaphoreNeighborInjectMatch.java b/...java/hu/bme/mit/trainbenchmark/benchmark/emf/matches/EmfSemaphoreNeighborInjectMatch.java
@@ -13,19 +13,27 @@
 
 import hu.bme.mit.trainbenchmark.benchmark.matches.SemaphoreNeighborInjectMatch;
 import hu.bme.mit.trainbenchmark.railway.Route;
+import hu.bme.mit.trainbenchmark.railway.Semaphore;
 
 public class EmfSemaphoreNeighborInjectMatch extends EmfMatch implements SemaphoreNeighborInjectMatch {
 
 	protected final Route route;
+	protected final Semaphore semaphore;
 
-	public EmfSemaphoreNeighborInjectMatch(final Route route) {
+	public EmfSemaphoreNeighborInjectMatch(final Route route, final Semaphore semaphore) {
 		super();
 		this.route = route;
+		this.semaphore = semaphore;
 	}
 
 	@Override
 	public Route getRoute() {
 		return route;
 	}
 
+	@Override
+	public Semaphore getSemaphore() {
+		return semaphore;
+	}
+
 }
diff --git a/.../trainbenchmark/benchmark/emf/transformation/inject/EmfTransformationInjectPosLength.java b/.../trainbenchmark/benchmark/emf/transformation/inject/EmfTransformationInjectPosLength.java
@@ -30,7 +30,6 @@ public void activate(final Collection<TPosLengthInjectMatch> matches) throws IOE
 		for (final TPosLengthInjectMatch match : matches) {
 			match.getSegment().setLength(0);
 		}
-		System.out.println(matches.size());
 	}
 
 }
diff --git a/...nchmark/benchmark/emf/transformation/inject/EmfTransformationInjectSemaphoreNeighbor.java b/...nchmark/benchmark/emf/transformation/inject/EmfTransformationInjectSemaphoreNeighbor.java
@@ -17,6 +17,8 @@
 import hu.bme.mit.trainbenchmark.benchmark.emf.driver.EmfDriver;
 import hu.bme.mit.trainbenchmark.benchmark.emf.matches.EmfSemaphoreNeighborInjectMatch;
 import hu.bme.mit.trainbenchmark.benchmark.emf.transformation.EmfTransformation;
+import hu.bme.mit.trainbenchmark.railway.Route;
+import hu.bme.mit.trainbenchmark.railway.Semaphore;
 
 public class EmfTransformationInjectSemaphoreNeighbor<TDriver extends EmfDriver, TSemaphoreNeighborInjectMatch extends EmfSemaphoreNeighborInjectMatch>
 		extends EmfTransformation<TSemaphoreNeighborInjectMatch, TDriver> {
@@ -28,7 +30,11 @@ public EmfTransformationInjectSemaphoreNeighbor(final TDriver driver) {
 	@Override
 	public void activate(final Collection<TSemaphoreNeighborInjectMatch> matches) throws IOException {
 		for (final TSemaphoreNeighborInjectMatch match : matches) {
-			match.getRoute().setEntry(null);
+			final Route route = match.getRoute();
+			final Semaphore semaphore = match.getSemaphore();
+			if (route.getEntry().equals(semaphore)) {
+				route.setEntry(null);
+			}
 		}
 	}
 }
diff --git a/...trainbenchmark/benchmark/emf/transformation/query/EmfApiQuerySemaphoreNeighborInject.java b/...trainbenchmark/benchmark/emf/transformation/query/EmfApiQuerySemaphoreNeighborInject.java
@@ -20,6 +20,7 @@
 import hu.bme.mit.trainbenchmark.benchmark.emf.matches.EmfSemaphoreNeighborInjectMatch;
 import hu.bme.mit.trainbenchmark.constants.RailwayQuery;
 import hu.bme.mit.trainbenchmark.railway.Route;
+import hu.bme.mit.trainbenchmark.railway.Semaphore;
 
 public class EmfApiQuerySemaphoreNeighborInject<TDriver extends EmfDriver> extends EmfApiQuery<EmfSemaphoreNeighborInjectMatch, TDriver> {
 
@@ -32,9 +33,14 @@ public Collection<EmfSemaphoreNeighborInjectMatch> evaluate() {
 		final List<EmfSemaphoreNeighborInjectMatch> matches = new ArrayList<>();
 
 		for (final Route route : driver.getContainer().getRoutes()) {
-			matches.add(new EmfSemaphoreNeighborInjectMatch(route));
+			final Semaphore entry = route.getEntry();
+			if (entry == null) {
+				continue;
+			}
+
+			matches.add(new EmfSemaphoreNeighborInjectMatch(route, entry));
 		}
-		
+
 		return matches;
 	}
 

diff --git a/...u/bme/mit/trainbenchmark/benchmark/ingraph/match/IngraphSemaphoreNeighborInjectMatch.java b/...u/bme/mit/trainbenchmark/benchmark/ingraph/match/IngraphSemaphoreNeighborInjectMatch.java
@@ -25,4 +25,9 @@ public Long getRoute() {
 		return (Long) qs.get("route").get();
 	}
 
+	@Override
+	public Object getSemaphore() {
+		return (Long) qs.get("semaphore").get();
+	}
+
 }
diff --git a/...va/hu/bme/mit/trainbenchmark/benchmark/jena/matches/JenaSemaphoreNeighborInjectMatch.java b/...va/hu/bme/mit/trainbenchmark/benchmark/jena/matches/JenaSemaphoreNeighborInjectMatch.java
@@ -12,6 +12,7 @@
 package hu.bme.mit.trainbenchmark.benchmark.jena.matches;
 
 import static hu.bme.mit.trainbenchmark.constants.QueryConstants.VAR_ROUTE;
+import static hu.bme.mit.trainbenchmark.constants.QueryConstants.VAR_SEMAPHORE;
 
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.rdf.model.Resource;
@@ -29,4 +30,9 @@ public Resource getRoute() {
 		return qs.getResource(VAR_ROUTE);
 	}
 
+	@Override
+	public Resource getSemaphore() {
+		return qs.getResource(VAR_SEMAPHORE);
+	}
+
 }
diff --git a/...mark/benchmark/jena/transformations/inject/JenaTransformationInjectConnectedSegments.java b/...mark/benchmark/jena/transformations/inject/JenaTransformationInjectConnectedSegments.java
@@ -44,7 +44,7 @@ public void activate(final Collection<JenaConnectedSegmentsInjectMatch> matches)
 
 		for (final JenaConnectedSegmentsInjectMatch csim : matches) {
 			// create (segment2) node
-			final Long newVertexId = driver.getNewVertexId();
+			final Long newVertexId = driver.generateNewVertexId();
 			final Resource segment2 = model.createResource(BASE_PREFIX + ID_PREFIX + newVertexId);
 			model.add(model.createStatement(segment2, RDF.type, segmentType));
 			model.add(model.createLiteralStatement(segment2, length, TrainBenchmarkConstants.DEFAULT_SEGMENT_LENGTH));

diff --git a/...mark/benchmark/jena/transformations/inject/JenaTransformationInjectSemaphoreNeighbor.java b/...mark/benchmark/jena/transformations/inject/JenaTransformationInjectSemaphoreNeighbor.java
@@ -11,18 +11,17 @@
  *******************************************************************************/
 package hu.bme.mit.trainbenchmark.benchmark.jena.transformations.inject;
 
-import static hu.bme.mit.trainbenchmark.constants.ModelConstants.ENTRY;
-
 import java.io.IOException;
 import java.util.Collection;
-import java.util.List;
-import java.util.stream.Collectors;
 
-import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Property;
 
 import hu.bme.mit.trainbenchmark.benchmark.jena.driver.JenaDriver;
 import hu.bme.mit.trainbenchmark.benchmark.jena.matches.JenaSemaphoreNeighborInjectMatch;
 import hu.bme.mit.trainbenchmark.benchmark.jena.transformations.JenaTransformation;
+import hu.bme.mit.trainbenchmark.constants.ModelConstants;
+import hu.bme.mit.trainbenchmark.rdf.RdfConstants;
 
 public class JenaTransformationInjectSemaphoreNeighbor extends JenaTransformation<JenaSemaphoreNeighborInjectMatch> {
 
@@ -32,8 +31,11 @@ public JenaTransformationInjectSemaphoreNeighbor(final JenaDriver driver) {
 
 	@Override
 	public void activate(final Collection<JenaSemaphoreNeighborInjectMatch> matches) throws IOException {
-		final List<Resource> routes = matches.stream().map(it -> it.getRoute()).collect(Collectors.toList());
-		driver.deleteOutgoingEdges(routes, ENTRY);
+		final Model model = driver.getModel();
+		final Property entry = model.getProperty(RdfConstants.BASE_PREFIX + ModelConstants.ENTRY);
+		for (JenaSemaphoreNeighborInjectMatch match : matches) {
+			model.remove(match.getRoute(), entry, match.getSemaphore());
+		}
 	}
 
 }
diff --git a/...chmark/benchmark/jena/transformations/repair/JenaTransformationRepairSwitchMonitored.java b/...chmark/benchmark/jena/transformations/repair/JenaTransformationRepairSwitchMonitored.java
@@ -41,7 +41,7 @@ public void activate(final Collection<JenaSwitchMonitoredMatch> matches) throws
 
 		for (final JenaSwitchMonitoredMatch match : matches) {
 			final Resource sw = match.getSw();
-			final Long newVertexId = driver.getNewVertexId();
+			final Long newVertexId = driver.generateNewVertexId();
 			final Resource sensor = model.createResource(BASE_PREFIX + ID_PREFIX + newVertexId);
 
 			model.add(model.createStatement(sw, sensorEdge, sensor));

diff --git a/trainbenchmark-tool-neo4j/README.md b/trainbenchmark-tool-neo4j/README.md
@@ -0,0 +1,5 @@
+# Neo4j implementation
+
+Neo4j cannot assign a specific id to a new node.
+
+This means that if we run multiple transformations (e.g. ConnectedSegmentsInject, which inserts new Segments), we cannot guarantee the precise number of matches.
diff --git a/.../hu/bme/mit/trainbenchmark/benchmark/neo4j/matches/Neo4jSemaphoreNeighborInjectMatch.java b/.../hu/bme/mit/trainbenchmark/benchmark/neo4j/matches/Neo4jSemaphoreNeighborInjectMatch.java
@@ -12,6 +12,7 @@
 package hu.bme.mit.trainbenchmark.benchmark.neo4j.matches;
 
 import static hu.bme.mit.trainbenchmark.constants.QueryConstants.VAR_ROUTE;
+import static hu.bme.mit.trainbenchmark.constants.QueryConstants.VAR_SEMAPHORE;
 
 import java.util.Map;
 
@@ -30,4 +31,9 @@ public Node getRoute() {
 		return (Node) match.get(VAR_ROUTE);
 	}
 
+	@Override
+	public Node getSemaphore() {
+		return (Node) match.get(VAR_SEMAPHORE);
+	}
+
 }
diff --git a/...it/trainbenchmark/benchmark/neo4j/queries/core/Neo4jCoreQuerySemaphoreNeighborInject.java b/...it/trainbenchmark/benchmark/neo4j/queries/core/Neo4jCoreQuerySemaphoreNeighborInject.java
@@ -16,8 +16,10 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import org.neo4j.graphdb.Direction;
 import org.neo4j.graphdb.GraphDatabaseService;
 import org.neo4j.graphdb.Node;
+import org.neo4j.graphdb.Relationship;
 import org.neo4j.graphdb.Transaction;
 
 import hu.bme.mit.trainbenchmark.benchmark.neo4j.driver.Neo4jDriver;
@@ -41,9 +43,16 @@ public Collection<Neo4jSemaphoreNeighborInjectMatch> evaluate() {
 			// (route:Route)
 			final Iterable<Node> routes = () -> graphDb.findNodes(Neo4jConstants.labelRoute);
 			for (final Node route : routes) {
-				final Map<String, Object> match = new HashMap<>();
-				match.put(QueryConstants.VAR_ROUTE, route);
-				matches.add(new Neo4jSemaphoreNeighborInjectMatch(match));
+				Iterable<Relationship> entries = route.getRelationships(Direction.OUTGOING, Neo4jConstants.relationshipTypeEntry);
+
+				for (Relationship entry : entries) {
+					final Node semaphore = entry.getEndNode();
+
+					final Map<String, Object> match = new HashMap<>();
+					match.put(QueryConstants.VAR_ROUTE, route);
+					match.put(QueryConstants.VAR_SEMAPHORE, semaphore);
+					matches.add(new Neo4jSemaphoreNeighborInjectMatch(match));
+				}
 			}
 		}
 

diff --git a/.../mit/trainbenchmark/benchmark/neo4j/queries/core/Neo4jCoreQuerySwitchMonitoredInject.java b/.../mit/trainbenchmark/benchmark/neo4j/queries/core/Neo4jCoreQuerySwitchMonitoredInject.java
@@ -38,7 +38,7 @@ public Collection<Neo4jSwitchMonitoredInjectMatch> evaluate() {
 		final Collection<Neo4jSwitchMonitoredInjectMatch> matches = new ArrayList<>();
 
 		final GraphDatabaseService graphDb = driver.getGraphDb();
-		try (Transaction tx = graphDb.beginTx()) {
+		try (final Transaction tx = graphDb.beginTx()) {
 			// (sw:Switch)
 			final Iterable<Node> sws = () -> graphDb.findNodes(Neo4jConstants.labelSwitch);
 			for (final Node sw : sws) {

diff --git a/...ark/neo4j/transformations/core/inject/Neo4jCoreTransformationInjectSemaphoreNeighbor.java b/...ark/neo4j/transformations/core/inject/Neo4jCoreTransformationInjectSemaphoreNeighbor.java
@@ -31,7 +31,9 @@ public void activate(final Collection<Neo4jSemaphoreNeighborInjectMatch> matches
 		for (final Neo4jSemaphoreNeighborInjectMatch match : matches) {
 			final Iterable<Relationship> entries = match.getRoute().getRelationships(Neo4jConstants.relationshipTypeEntry);
 			for (final Relationship entry : entries) {
-				entry.delete();
+				if (entry.getEndNode().equals(match.getSemaphore())) {
+					entry.delete();
+				}
 			}
 		}
 	}

diff --git a/...hmark/neo4j/transformations/core/inject/Neo4jCoreTransformationInjectSwitchMonitored.java b/...hmark/neo4j/transformations/core/inject/Neo4jCoreTransformationInjectSwitchMonitored.java
@@ -28,10 +28,12 @@ public Neo4jCoreTransformationInjectSwitchMonitored(final Neo4jDriver driver) {
 
 	@Override
 	public void activate(final Collection<Neo4jSwitchMonitoredInjectMatch> matches) {
+		System.out.println(matches.size());
 		for (final Neo4jSwitchMonitoredInjectMatch match : matches) {
-			final Iterable<Relationship> sensors = match.getSw().getRelationships(Neo4jConstants.relationshipTypeMonitoredBy);
-			for (final Relationship sensor : sensors) {
-				sensor.delete();
+			System.out.println(match);
+			final Iterable<Relationship> monitoredBys = match.getSw().getRelationships(Neo4jConstants.relationshipTypeMonitoredBy);
+			for (final Relationship monitoredBy : monitoredBys) {
+				monitoredBy.delete();
 			}
 		}
 	}

diff --git a/...neo4j/transformations/cypher/inject/Neo4jCypherTransformationInjectSemaphoreNeighbor.java b/...neo4j/transformations/cypher/inject/Neo4jCypherTransformationInjectSemaphoreNeighbor.java
@@ -23,17 +23,20 @@
 import hu.bme.mit.trainbenchmark.constants.QueryConstants;
 import hu.bme.mit.trainbenchmark.constants.RailwayOperation;
 
-public class Neo4jCypherTransformationInjectSemaphoreNeighbor extends Neo4jCypherTransformation<Neo4jSemaphoreNeighborInjectMatch> {
+public class Neo4jCypherTransformationInjectSemaphoreNeighbor
+		extends Neo4jCypherTransformation<Neo4jSemaphoreNeighborInjectMatch> {
 
-	public Neo4jCypherTransformationInjectSemaphoreNeighbor(final Neo4jDriver driver, final String workspaceDir) throws IOException {
+	public Neo4jCypherTransformationInjectSemaphoreNeighbor(final Neo4jDriver driver, final String workspaceDir)
+			throws IOException {
 		super(driver, workspaceDir, RailwayOperation.SEMAPHORENEIGHBOR_INJECT);
 	}
 
 	@Override
 	public void activate(final Collection<Neo4jSemaphoreNeighborInjectMatch> matches) throws IOException {
 		for (final Neo4jSemaphoreNeighborInjectMatch match : matches) {
 			final Map<String, Object> parameters = ImmutableMap.of( //
-					QueryConstants.VAR_ROUTE, match.getRoute().getId() //
+					QueryConstants.VAR_ROUTE, match.getRoute().getId(), //
+					QueryConstants.VAR_SEMAPHORE, match.getSemaphore().getId() //
 			);
 
 			driver.runTransformation(transformationDefinition, parameters);

diff --git a/...k/neo4j/transformations/cypher/inject/Neo4jCypherTransformationInjectSwitchMonitored.java b/...k/neo4j/transformations/cypher/inject/Neo4jCypherTransformationInjectSwitchMonitored.java
@@ -23,15 +23,19 @@
 import hu.bme.mit.trainbenchmark.constants.QueryConstants;
 import hu.bme.mit.trainbenchmark.constants.RailwayOperation;
 
-public class Neo4jCypherTransformationInjectSwitchMonitored extends Neo4jCypherTransformation<Neo4jSwitchMonitoredInjectMatch> {
+public class Neo4jCypherTransformationInjectSwitchMonitored
+		extends Neo4jCypherTransformation<Neo4jSwitchMonitoredInjectMatch> {
 
-	public Neo4jCypherTransformationInjectSwitchMonitored(final Neo4jDriver driver, final String workspaceDir) throws IOException {
+	public Neo4jCypherTransformationInjectSwitchMonitored(final Neo4jDriver driver, final String workspaceDir)
+			throws IOException {
 		super(driver, workspaceDir, RailwayOperation.SWITCHMONITORED_INJECT);
 	}
 
 	@Override
 	public void activate(final Collection<Neo4jSwitchMonitoredInjectMatch> matches) throws IOException {
+		System.out.println(matches.size());
 		for (final Neo4jSwitchMonitoredInjectMatch match : matches) {
+			System.out.println(match);
 			final Map<String, Object> parameters = ImmutableMap.of( //
 					QueryConstants.VAR_SW, match.getSw().getId() //
 			);

diff --git a/trainbenchmark-tool-neo4j/src/main/resources/queries/SemaphoreNeighborInject.cyp b/trainbenchmark-tool-neo4j/src/main/resources/queries/SemaphoreNeighborInject.cyp
@@ -1,2 +1,2 @@
-MATCH (route:Route)
-RETURN DISTINCT route
+MATCH (route:Route)-[:entry]->(semaphore:Semaphore)
+RETURN DISTINCT route, semaphore
diff --git a/trainbenchmark-tool-neo4j/src/main/resources/transformations/SemaphoreNeighborInjectRhs.cyp b/trainbenchmark-tool-neo4j/src/main/resources/transformations/SemaphoreNeighborInjectRhs.cyp
@@ -1,3 +1,4 @@
-MATCH (route)-[e:entry]->(semaphore:Semaphore)
-WHERE id(route) = { route } 
+MATCH (route)-[e:entry]->(semaphore)
+WHERE id(route) = { route }
+  AND id(semaphore) = { semaphore } 
 DELETE e
diff --git a/trainbenchmark-tool-neo4j/src/main/resources/transformations/SwitchMonitoredInjectRhs.cyp b/trainbenchmark-tool-neo4j/src/main/resources/transformations/SwitchMonitoredInjectRhs.cyp
@@ -1,3 +1,3 @@
-MATCH (sw)-[m:monitoredBy]->(sensor:Sensor)
+MATCH (sw)-[m:monitoredBy]->(:Sensor)
 WHERE id(sw) = { sw } 
 DELETE m
diff --git a/...mark-tool-rdf/src/main/java/hu/bme/mit/trainbenchmark/benchmark/rdf/driver/RdfDriver.java b/...mark-tool-rdf/src/main/java/hu/bme/mit/trainbenchmark/benchmark/rdf/driver/RdfDriver.java
@@ -30,7 +30,7 @@ public RdfDriver(final boolean inferencing) {
 		this.inferencing = inferencing;
 	}
 
-	protected Long determineNewVertexId() throws Exception {
+	protected Long determineInitialNewVertexId() throws Exception {
 		Long id = 5000L;
 
 		// safety measure to avoid infinite loop in case of a driver bug
@@ -46,13 +46,14 @@ protected Long determineNewVertexId() throws Exception {
 		if (iterationCount > 20) {
 			throw new IOException("Could not generate new unique id.");
 		}
+		System.out.println(id);
 
 		return id;
 	}
 
-	public Long getNewVertexId() throws Exception {
+	public Long generateNewVertexId() throws Exception {
 		if (newVertexId == null) {
-			newVertexId = determineNewVertexId();
+			newVertexId = determineInitialNewVertexId();
 		}
 		newVertexId++;
 		return newVertexId;

diff --git a/trainbenchmark-tool-rdf/src/main/resources/queries/SemaphoreNeighborInject.sparql b/trainbenchmark-tool-rdf/src/main/resources/queries/SemaphoreNeighborInject.sparql
@@ -1,7 +1,9 @@
 PREFIX base: <http://www.semanticweb.org/ontologies/2015/trainbenchmark#>
 PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 
-SELECT DISTINCT ?route
+SELECT DISTINCT ?route ?semaphore
 WHERE {
 	?route rdf:type base:Route .
+	?route base:entry ?semaphore .
+	?semaphore rdf:type base:Semaphore .
 }
diff --git a/.../hu/bme/mit/trainbenchmark/benchmark/rdf4j/matches/Rdf4jSemaphoreNeighborInjectMatch.java b/.../hu/bme/mit/trainbenchmark/benchmark/rdf4j/matches/Rdf4jSemaphoreNeighborInjectMatch.java
@@ -12,6 +12,7 @@
 package hu.bme.mit.trainbenchmark.benchmark.rdf4j.matches;
 
 import static hu.bme.mit.trainbenchmark.constants.QueryConstants.VAR_ROUTE;
+import static hu.bme.mit.trainbenchmark.constants.QueryConstants.VAR_SEMAPHORE;
 
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.query.BindingSet;
@@ -29,4 +30,9 @@ public IRI getRoute() {
 		return (IRI) bs.getValue(VAR_ROUTE);
 	}
 
+	@Override
+	public IRI getSemaphore() {
+		return (IRI) bs.getValue(VAR_SEMAPHORE);
+	}
+
 }
diff --git a/...rk/benchmark/rdf4j/transformations/inject/Rdf4jTransformationInjectConnectedSegments.java b/...rk/benchmark/rdf4j/transformations/inject/Rdf4jTransformationInjectConnectedSegments.java
@@ -50,7 +50,7 @@ public void activate(final Collection<Rdf4jConnectedSegmentsInjectMatch> matches
 
 		for (final Rdf4jConnectedSegmentsInjectMatch csim : matches) {
 			// create (segment2) node
-			final Long newVertexId = driver.getNewVertexId();
+			final Long newVertexId = driver.generateNewVertexId();
 			final IRI segment2 = vf.createIRI(BASE_PREFIX + ID_PREFIX + newVertexId);
 			connection.add(segment2, RDF.TYPE, segmentType);