public static <V, E> Neo4jTopology loadTopology(Neo4jWorkspaceSettings settings)
throws Exception {
String db = DatabaseConfiguration.readDatabase(settings);
Logger.getLogger(Neo4jWorkspace.class).info("using db " + db);
// Get neo4j stuffs
GraphDatabaseFactory factory = new GraphDatabaseFactory();
GraphDatabaseService database = factory.newEmbeddedDatabase(db);
GlobalGraphOperations operation = GlobalGraphOperations.at(database);
ViewsManager views = new ViewsManager();
views.load(settings);
// Setup graph model
Neo4jGraphModelIO gio = new Neo4jGraphModelIO();
gio.read(SimpleFile.read(settings.getModelPath()));
Neo4jGraphModel typeModel = gio.getGraphModel();
// Build graph
INeo4jGraphReader r = views.getFirst().getFilter();
Graph<IPropertyNode, IPropertyEdge> graph = r.read(operation, typeModel);
Logger.getLogger(Neo4jWorkspace.class)
.info("filtered graph has " + graph.getVertexCount() + " nodes using db " + db);
// Build topology using graph typing model
String topologyName = views.getFirst().getTopologyName();
Neo4jTopologyFactory tfact = new Neo4jTopologyFactory();
Neo4jTopology topology = tfact.newTopology(topologyName, graph, typeModel);
return topology;
}
public void testNoLabels() throws IOException {
String test = "*Vertices 3\n1\n2\n3\n*Edges\n1 2\n2 2";
Reader r = new StringReader(test);
Graph<Number, Number> g = pnr.load(r, undirectedGraphFactory);
assertEquals(g.getVertexCount(), 3);
assertEquals(g.getEdgeCount(), 2);
}
/**
* Build full Neo4jWorkspace involving reading files given by settings:
*
* <ul>
* <li>neo4j database
* <li>view
* <li>graph model
* <li>projection
* </ul>
*
* and build topology & geometrical model according to Neo4j factories
*
* @param settings
* @throws Exception
*/
public Neo4jWorkspace(Neo4jWorkspaceSettings settings) throws Exception {
String db = DatabaseConfiguration.readDatabase(settings);
Logger.getLogger(Neo4jWorkspace.class).info("using db " + db);
// Get neo4j stuffs
GraphDatabaseFactory factory = new GraphDatabaseFactory();
database = factory.newEmbeddedDatabase(db);
operation = GlobalGraphOperations.at(database);
views = new ViewsManager();
views.load(settings);
layoutML = views.getFirst().getLayout();
// Setup graph model
Neo4jGraphModelIO gio = new Neo4jGraphModelIO();
gio.read(SimpleFile.read(settings.getModelPath()));
Neo4jGraphModel typeModel = gio.getGraphModel();
// Build graph
INeo4jGraphReader r = views.getFirst().getFilter();
Graph<IPropertyNode, IPropertyEdge> graph = r.read(operation, typeModel);
Logger.getLogger(Neo4jWorkspace.class)
.info("filtered graph has " + graph.getVertexCount() + " nodes using db " + db);
// Build topology using graph typing model
String topologyName = views.getFirst().getTopologyName();
Neo4jTopologyFactory tfact = new Neo4jTopologyFactory();
topology = tfact.newTopology(topologyName, graph, typeModel);
// Edit topology according to dataprism
Dataprism dp = loadDataprism(settings);
if (dp != null) ((Neo4jTopology) topology).edit().apply(dp);
// Build layout model
modelFactory = new Neo4jModelFactory(gio.getGraphModel());
model = (IHierarchicalNodeModel) modelFactory.getLayoutModel(topology);
edgeModel = model.getEdgeModel();
applyLayoutMLConfiguration(model, layoutML);
// Build layout
layoutFactory = new Neo4jLayoutFactory(typeModel);
if (layoutML != null) {
Map<String, String> mapping = extractModelLayoutMapping(layoutML);
layoutFactory.setModelLayoutMapping(mapping);
}
layout = layoutFactory.getLayout(model);
layout.getEdgeLayout().setEdgePostProcess(null);
// finalize workspace
annotationModel = new AnnotationModel();
metadata = null;
setName(settings.getName());
loadMapIfExist();
this.configuration = new ConfigurationFacade(this);
}
/**
* Tests to see whether these two graphs are structurally equivalent, based on the connectivity of
* the vertices with matching indices in each graph. Assumes a 0-based index.
*
* @param g1
* @param g2
*/
private void compareIndexedGraphs(Graph<Number, Number> g1, Graph<Number, Number> g2) {
int n1 = g1.getVertexCount();
int n2 = g2.getVertexCount();
assertEquals(n1, n2);
assertEquals(g1.getEdgeCount(), g2.getEdgeCount());
List<Number> id1 = new ArrayList<Number>(g1.getVertices());
List<Number> id2 = new ArrayList<Number>(g2.getVertices());
for (int i = 0; i < n1; i++) {
Number v1 = id1.get(i);
Number v2 = id2.get(i);
assertNotNull(v1);
assertNotNull(v2);
checkSets(g1.getPredecessors(v1), g2.getPredecessors(v2), id1, id2);
checkSets(g1.getSuccessors(v1), g2.getSuccessors(v2), id1, id2);
}
}
protected TitledBorder setUpSliderPanel() {
sliderPanel = new JPanel();
sliderPanel.setPreferredSize(new Dimension(210, 50));
int sliderLimit = 50;
if (graph != null) {
final Graph<CallGraphNode, CallGraphLink> jungGraph = graph.getJungGraph();
sliderLimit = jungGraph.getVertexCount();
}
configureIterationSlider(sliderLimit);
sliderPanel.setOpaque(true);
sliderPanel.add(iterationSlider);
iterationSlider.setValue(0);
String eastSize = sliderLabelBase + iterationSlider.getValue();
TitledBorder sliderBorder = BorderFactory.createTitledBorder(eastSize);
sliderPanel.setBorder(sliderBorder);
return sliderBorder;
}
/**
* Searches the graph and searches for the shortest path from a given start node to the
* destination. Returns {@code null} if there are no vertices, edges, or path to the goal,
* otherwise a list with the order of vertices on the shortest path.
*
* @param graph The graph to search
* @param source The vertex to start the search from
* @param destination The goal vertex
* @return A list with the order of vertices on the shortest path, null if no path exists in the
* graph.
*/
public List<V> search(Graph<V, E> graph, V source, V destination) {
// Check if it is even possible to find a path, return null
// if the graph has no vertices or edges
if (graph.getVertexCount() == 0) {
System.out.println("No nodes in the graph, " + "no shortest path can be found");
return null;
} else if (graph.getEdgeCount() == 0) {
System.out.println("No edges in graph, no path " + "can be found");
return null;
}
// Keep record of distance to each vertex, map each vertex
// in the graph to it's distance
HashMap<V, Number> distanceTable = new HashMap<>();
// Unvisited node queue, uses a pair <Vertex, Double> and ordered
// by the distance to the vertex
PriorityQueue<Pair<V, Number>> queue = new PriorityQueue<>(new QueueComparator());
// Map of nodes on the path, parents is value, key is child
HashMap<V, V> parent = new HashMap<>();
Number maxValue;
E edgeTest = graph.getEdges().iterator().next();
// This is so ugly, I hate Java Numbers
int numberType = 0;
if (edgeTest.getWeight() instanceof Integer) {
numberType = 1;
} else if (edgeTest.getWeight() instanceof Double) {
numberType = 2;
}
// Place each vertex in the map, initialize distances and put
// the pairings into the queue.
for (V vertex : graph.getVertices()) {
if (numberType == 1) {
maxValue = Integer.MAX_VALUE;
if (vertex.equals(source)) {
distanceTable.put(source, 0);
queue.add(new Pair<>(vertex, 0));
} else {
distanceTable.put(vertex, Integer.MAX_VALUE);
queue.add(new Pair<>(vertex, maxValue));
}
} else if (numberType == 2) {
maxValue = Double.MAX_VALUE;
if (vertex.equals(source)) {
distanceTable.put(source, 0.0);
queue.add(new Pair<>(vertex, 0.0));
} else {
distanceTable.put(vertex, Double.MAX_VALUE);
queue.add(new Pair<>(vertex, maxValue));
}
}
}
parent.put(source, null);
while (!queue.isEmpty()) {
Pair<V, Number> topPair = queue.remove();
V vertex = topPair.getLeft();
// Goal test, return the list of nodes on the path
// if we reach the destination
if (vertex.equals(destination)) {
return tracePath(parent, destination);
}
Collection<V> neighbours = graph.getNeighbors(vertex);
for (V neighbour : neighbours) {
E edge = graph.findEdge(vertex, neighbour);
assert (edge != null);
// Test for type of number used for weight, work accordingly
// Did I mention I hate the Java Number class.
if (numberType == 1) {
Integer alternateDistance = (Integer) edge.getWeight();
if (alternateDistance < (Integer) distanceTable.get(neighbour)) {
distanceTable.put(neighbour, alternateDistance);
parent.put(neighbour, vertex);
queue.add(new Pair<>(neighbour, alternateDistance));
}
} else if (numberType == 2) {
Double alternateDistance = (Double) edge.getWeight();
if (alternateDistance < (Double) distanceTable.get(neighbour)) {
distanceTable.put(neighbour, alternateDistance);
parent.put(neighbour, vertex);
queue.add(new Pair<>(neighbour, alternateDistance));
}
}
}
}
// Exhausted all possible paths from source, could not find a path
// to the goal.
return null;
}
public void testMixedSaveLoadSave() throws IOException {
Graph<Number, Number> graph1 = new SparseMultigraph<Number, Number>();
for (int i = 0; i < 5; i++) {
graph1.addVertex(i);
}
int j = 0;
List<Number> id = new ArrayList<Number>(graph1.getVertices());
GreekLabels<Number> gl = new GreekLabels<Number>(id);
Number[] edges = {0, 1, 2, 3, 4, 5};
graph1.addEdge(j++, 0, 1, EdgeType.DIRECTED);
graph1.addEdge(j++, 0, 2, EdgeType.DIRECTED);
graph1.addEdge(j++, 1, 2, EdgeType.DIRECTED);
graph1.addEdge(j++, 1, 3);
graph1.addEdge(j++, 1, 4);
graph1.addEdge(j++, 4, 3);
Map<Number, Number> nr = new HashMap<Number, Number>();
for (int i = 0; i < edges.length; i++) {
nr.put(edges[i], new Float(Math.random()));
}
assertEquals(graph1.getEdgeCount(), 6);
// System.err.println(" mixed graph1 = "+graph1);
// for(Number edge : graph1.getEdges()) {
// System.err.println("edge "+edge+" is directed? "+graph1.getEdgeType(edge));
// }
// for(Number v : graph1.getVertices()) {
// System.err.println(v+" outedges are "+graph1.getOutEdges(v));
// System.err.println(v+" inedges are "+graph1.getInEdges(v));
// System.err.println(v+" incidentedges are "+graph1.getIncidentEdges(v));
// }
String testFilename = "mtest.net";
String testFilename2 = testFilename + "2";
// assign arbitrary locations to each vertex
Map<Number, Point2D> locations = new HashMap<Number, Point2D>();
for (Number v : graph1.getVertices()) {
locations.put(v, new Point2D.Double(v.intValue() * v.intValue(), 1 << v.intValue()));
}
Function<Number, Point2D> vld = Functions.forMap(locations);
PajekNetWriter<Number, Number> pnw = new PajekNetWriter<Number, Number>();
pnw.save(graph1, testFilename, gl, Functions.forMap(nr), vld);
Graph<Number, Number> graph2 = pnr.load(testFilename, graphFactory);
Function<Number, String> pl = pnr.getVertexLabeller();
List<Number> id2 = new ArrayList<Number>(graph2.getVertices());
Function<Number, Point2D> vld2 = pnr.getVertexLocationTransformer();
assertEquals(graph1.getVertexCount(), graph2.getVertexCount());
assertEquals(graph1.getEdgeCount(), graph2.getEdgeCount());
// test vertex labels and locations
for (int i = 0; i < graph1.getVertexCount(); i++) {
Number v1 = id.get(i);
Number v2 = id2.get(i);
assertEquals(gl.apply(v1), pl.apply(v2));
assertEquals(vld.apply(v1), vld2.apply(v2));
}
// test edge weights
Function<Number, Number> nr2 = pnr.getEdgeWeightTransformer();
for (Number e2 : graph2.getEdges()) {
Pair<Number> endpoints = graph2.getEndpoints(e2);
Number v1_2 = endpoints.getFirst();
Number v2_2 = endpoints.getSecond();
Number v1_1 = id.get(id2.indexOf(v1_2));
Number v2_1 = id.get(id2.indexOf(v2_2));
Number e1 = graph1.findEdge(v1_1, v2_1);
assertNotNull(e1);
assertEquals(nr.get(e1).floatValue(), nr2.apply(e2).floatValue(), 0.0001);
}
pnw.save(graph2, testFilename2, pl, nr2, vld2);
compareIndexedGraphs(graph1, graph2);
pnr.setVertexLabeller(null);
Graph<Number, Number> graph3 = pnr.load(testFilename2, graphFactory);
compareIndexedGraphs(graph2, graph3);
File file1 = new File(testFilename);
File file2 = new File(testFilename2);
Assert.assertTrue(file1.length() == file2.length());
file1.delete();
file2.delete();
}
public void testUndirectedSaveLoadSave() throws IOException {
UndirectedGraph<Number, Number> graph1 = undirectedGraphFactory.get();
for (int i = 0; i < 5; i++) {
graph1.addVertex(i);
}
List<Number> id = new ArrayList<Number>(graph1.getVertices());
int j = 0;
GreekLabels<Number> gl = new GreekLabels<Number>(id);
graph1.addEdge(j++, 0, 1);
graph1.addEdge(j++, 0, 2);
graph1.addEdge(j++, 1, 2);
graph1.addEdge(j++, 1, 3);
graph1.addEdge(j++, 1, 4);
graph1.addEdge(j++, 4, 3);
assertEquals(graph1.getEdgeCount(), 6);
// System.err.println("graph1 = "+graph1);
// for(Number edge : graph1.getEdges()) {
// System.err.println("edge "+edge+" is directed? "+graph1.getEdgeType(edge));
// }
// for(Number v : graph1.getVertices()) {
// System.err.println(v+" outedges are "+graph1.getOutEdges(v));
// System.err.println(v+" inedges are "+graph1.getInEdges(v));
// System.err.println(v+" incidentedges are "+graph1.getIncidentEdges(v));
// }
String testFilename = "utest.net";
String testFilename2 = testFilename + "2";
PajekNetWriter<Number, Number> pnw = new PajekNetWriter<Number, Number>();
pnw.save(graph1, testFilename, gl, null, null);
Graph<Number, Number> graph2 = pnr.load(testFilename, undirectedGraphFactory);
// System.err.println("graph2 = "+graph2);
// for(Number edge : graph2.getEdges()) {
// System.err.println("edge "+edge+" is directed? "+graph2.getEdgeType(edge));
// }
// for(Number v : graph2.getVertices()) {
// System.err.println(v+" outedges are "+graph2.getOutEdges(v));
// System.err.println(v+" inedges are "+graph2.getInEdges(v));
// System.err.println(v+" incidentedges are "+graph2.getIncidentEdges(v));
// }
assertEquals(graph1.getVertexCount(), graph2.getVertexCount());
assertEquals(graph1.getEdgeCount(), graph2.getEdgeCount());
pnw.save(graph2, testFilename2, pnr.getVertexLabeller(), null, null);
compareIndexedGraphs(graph1, graph2);
Graph<Number, Number> graph3 = pnr.load(testFilename2, graphFactory);
// System.err.println("graph3 = "+graph3);
// for(Number edge : graph3.getEdges()) {
// System.err.println("edge "+edge+" is directed? "+graph3.getEdgeType(edge));
// }
// for(Number v : graph3.getVertices()) {
// System.err.println(v+" outedges are "+graph3.getOutEdges(v));
// System.err.println(v+" inedges are "+graph3.getInEdges(v));
// System.err.println(v+" incidentedges are "+graph3.getIncidentEdges(v));
// }
compareIndexedGraphs(graph2, graph3);
File file1 = new File(testFilename);
File file2 = new File(testFilename2);
Assert.assertTrue(file1.length() == file2.length());
file1.delete();
file2.delete();
}
public ExactVA(Graph<Integer, Integer> g, int exactSolutionSize) {
this.g = g;
this.numOfVertices = g.getVertexCount();
this.exactSolutionSize = exactSolutionSize;
}