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GraphApi.java
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GraphApi.java
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/**
* Copyright (C) 2014 The SciGraph authors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package io.scigraph.internal;
import static com.google.common.collect.Iterables.isEmpty;
import static com.google.common.collect.Sets.newHashSet;
import io.scigraph.neo4j.DirectedRelationshipType;
import io.scigraph.owlapi.OwlRelationships;
import io.scigraph.owlapi.curies.AddCuries;
import java.util.Collection;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import javax.inject.Inject;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Path;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.Result;
import org.neo4j.graphdb.Transaction;
import org.neo4j.graphdb.traversal.Evaluation;
import org.neo4j.graphdb.traversal.Evaluator;
import org.neo4j.graphdb.traversal.Evaluators;
import org.neo4j.graphdb.traversal.TraversalDescription;
import org.neo4j.graphdb.traversal.Uniqueness;
import com.google.common.base.Optional;
import com.google.common.base.Predicate;
import com.tinkerpop.blueprints.Graph;
import com.tinkerpop.blueprints.impls.tg.TinkerGraph;
public class GraphApi {
private final GraphDatabaseService graphDb;
private final CypherUtil cypherUtil;
@Inject
public GraphApi(GraphDatabaseService graphDb, CypherUtil cypherUtil) {
this.graphDb = graphDb;
this.cypherUtil = cypherUtil;
}
/***
* @param parent
* @param relationship
* @param traverseEquivalentEdges
* @return the entailment
*/
public Collection<Node> getEntailment(Node parent, DirectedRelationshipType relationship, boolean traverseEquivalentEdges) {
Set<Node> entailment = new HashSet<>();
TraversalDescription description = graphDb.traversalDescription().depthFirst()
.relationships(relationship.getType(), relationship.getDirection())
.evaluator(Evaluators.fromDepth(0))
.evaluator(Evaluators.all());
if (traverseEquivalentEdges) {
description = description.relationships(OwlRelationships.OWL_EQUIVALENT_CLASS);
}
for (Path path : description.traverse(parent)) {
entailment.add(path.endNode());
}
return entailment;
}
@AddCuries
public Graph getNeighbors(Set<Node> nodes, int depth, Set<DirectedRelationshipType> types, final Optional<Predicate<Node>> includeNode) {
TraversalDescription description = graphDb.traversalDescription()
.breadthFirst()
.evaluator(Evaluators.toDepth(depth))
.uniqueness(Uniqueness.RELATIONSHIP_RECENT);
for (DirectedRelationshipType type: types) {
description = description.relationships(type.getType(), type.getDirection());
}
if (includeNode.isPresent()) {
description = description.evaluator(new Evaluator() {
@Override
public Evaluation evaluate(Path path) {
if (includeNode.get().apply(path.endNode())) {
return Evaluation.INCLUDE_AND_CONTINUE;
} else {
return Evaluation.EXCLUDE_AND_PRUNE;
}
}
});
}
Graph graph = new TinkerGraph();
for (Path path: description.traverse(nodes)) {
Relationship relationship = path.lastRelationship();
if (null != relationship) {
TinkerGraphUtil.addEdge(graph, relationship);
}
}
if (isEmpty(graph.getEdges())) {
// If nothing was added to the graph add the root nodes
for (Node node: nodes) {
TinkerGraphUtil.addNode(graph, node);
}
}
return graph;
}
public Graph getEdges(RelationshipType type, boolean entail, long skip, long limit) {
String query = "MATCH path = (start)-[r:" + type.name()
+ (entail ? "!" : "")
+ "]->(end) "
+ " RETURN path "
// TODO: This slows down the query dramatically.
// + " ORDER BY ID(r) "
+ " SKIP " + skip
+ " LIMIT " + limit;
Graph graph = new TinkerGraph();
Result result;
try {
result = cypherUtil.execute(query);
while (result.hasNext()) {
Map<String, Object> map = result.next();
Path path = (Path) map.get("path");
TinkerGraphUtil.addPath(graph, path);
}
} catch (ArrayIndexOutOfBoundsException e) {
// Return and empty graph if the limit is too high...
}
return graph;
}
/***
* @return All the {@link RelationshipType}s in the graph.
*/
public Collection<RelationshipType> getAllRelationshipTypes() {
Set<RelationshipType> relationships = new HashSet<>();
try (Transaction tx = graphDb.beginTx()) {
relationships.addAll(newHashSet(graphDb.getAllRelationshipTypes()));
tx.success();
}
return relationships;
}
/***
* @return All the property keys in the graph.
*/
public Collection<String> getAllPropertyKeys() {
Set<String> propertyKeys = new HashSet<>();
try (Transaction tx = graphDb.beginTx()) {
propertyKeys.addAll(newHashSet(graphDb.getAllPropertyKeys()));
tx.success();
}
return propertyKeys;
}
}