Java tutorial
/******************************************************************************* * This file is part of the Coporate Semantic Web Project. * * This work has been partially supported by the ``InnoProfile-Corporate Semantic Web" project funded by the German Federal * Ministry of Education and Research (BMBF) and the BMBF Innovation Initiative for the New German Laender - Entrepreneurial Regions. * * http://www.corporate-semantic-web.de/ * * * Freie Universitaet Berlin * Copyright (c) 2007-2013 * * * Institut fuer Informatik * Working Group Coporate Semantic Web * Koenigin-Luise-Strasse 24-26 * 14195 Berlin * * http://www.mi.fu-berlin.de/en/inf/groups/ag-csw/ * * * * This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published * by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. * You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA or see <http://www.gnu.org/licenses/> ******************************************************************************/ package de.fuberlin.agcsw.heraclitus.graph; import java.awt.Color; import java.awt.Paint; import java.awt.Shape; import java.awt.geom.Arc2D; import java.awt.geom.RoundRectangle2D; import java.io.IOException; import java.net.MalformedURLException; import java.net.URI; import java.util.ArrayList; import java.util.List; import org.apache.commons.collections15.Transformer; import org.eclipse.ui.PartInitException; import org.eclipse.ui.PlatformUI; import org.openrdf.model.Literal; import org.openrdf.model.Resource; import org.openrdf.model.Statement; import org.openrdf.model.Value; import org.openrdf.model.ValueFactory; import org.openrdf.repository.Repository; import org.openrdf.repository.RepositoryConnection; import org.openrdf.repository.RepositoryException; import org.openrdf.repository.RepositoryResult; import org.openrdf.repository.sail.SailRepository; import org.openrdf.rio.RDFFormat; import org.openrdf.rio.RDFParseException; import org.openrdf.sail.memory.MemoryStore; import org.semanticweb.owl.model.OWLClass; import org.semanticweb.owl.model.OWLOntology; import de.fuberlin.agcsw.heraclitus.backend.core.OntologyStore; import de.fuberlin.agcsw.heraclitus.backend.core.conceptTree.ConceptTree; import de.fuberlin.agcsw.heraclitus.backend.core.info.OntologyInfo; import de.fuberlin.agcsw.heraclitus.graph.model.JungEdge; import de.fuberlin.agcsw.heraclitus.graph.model.JungVertex; import de.fuberlin.agcsw.heraclitus.graph.ui.ConceptTreeGraphDoubleClickListener; import de.fuberlin.agcsw.heraclitus.graph.ui.FrameComponentListener; import de.fuberlin.agcsw.heraclitus.graph.ui.JungClickOnPickMouseListener; import de.fuberlin.agcsw.heraclitus.graph.ui.graphviewer.GraphViewer; import edu.uci.ics.jung.algorithms.layout.KKLayout; import edu.uci.ics.jung.graph.DirectedSparseMultigraph; import edu.uci.ics.jung.graph.Graph; import edu.uci.ics.jung.visualization.VisualizationViewer; import edu.uci.ics.jung.visualization.control.DefaultModalGraphMouse; import edu.uci.ics.jung.visualization.control.ModalGraphMouse; import edu.uci.ics.jung.visualization.decorators.ToStringLabeller; import edu.uci.ics.jung.visualization.renderers.Renderer.VertexLabel.Position; public class GraphAnalyse { public static OntologyInfo ontologyInfo; public static OntologyStore ontologyStore; public static String[] preferredRootConcepts; /** * SAIL inMemory Repository for the loaded Ontology */ private static Repository rep; public static boolean fullGraph = false; //not using the jface viwer at the moment public static GraphViewer graphViewer; /** * The Jung Viewer for the Graph */ public static VisualizationViewer<JungVertex, JungEdge> vv; // public static Label GraphInfoLabel; public static void init() { System.out.println("Initialising Graph Analyse"); //we have to do this, else the Treeviewer might not been init. bad fix for that problem try { PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage() .showView("de.fuberlin.agcsw.heraclitus.backend.ui.ConceptExplorerView"); } catch (PartInitException e) { // TODO Auto-generated catch block e.printStackTrace(); } ConceptTree.ontologyTreeViewer.addDoubleClickListener(new ConceptTreeGraphDoubleClickListener()); initJungViewer(); } private static void initJungViewer() { // Create Layout for Visualization Graph<JungVertex, JungEdge> g = new DirectedSparseMultigraph<JungVertex, JungEdge>(); KKLayout<JungVertex, JungEdge> l = new KKLayout<JungVertex, JungEdge>(g); l.setMaxIterations(100); vv = new VisualizationViewer<JungVertex, JungEdge>(l); vv.addComponentListener(new FrameComponentListener()); JungClickOnPickMouseListener lis = new JungClickOnPickMouseListener(); vv.addMouseListener(lis); vv.addMouseMotionListener(lis); vv.setDoubleBuffered(true); //init Mouse Picking DefaultModalGraphMouse gm = new DefaultModalGraphMouse(); gm.setMode(ModalGraphMouse.Mode.PICKING); vv.setGraphMouse(gm); Transformer<JungVertex, Paint> vertexPaint = new Transformer<JungVertex, Paint>() { public Paint transform(JungVertex v) { if (v.getUri() == null) { //this is a literal return Color.GRAY; } if (v.getLabel().startsWith("node")) { //this is a blank node return Color.orange; } return Color.RED; } }; Transformer<JungVertex, Shape> vertexShape = new Transformer<JungVertex, Shape>() { @Override public Shape transform(JungVertex v) { if (v.getLabel().startsWith("node")) { //this is a blank node Arc2D.Double arc = new Arc2D.Double(-15, -15, 30, 30, 0, 360, Arc2D.CHORD); return arc; } RoundRectangle2D.Double rec = new RoundRectangle2D.Double(-65, -12.5, 130, 25, 30, 30); return rec; } }; vv.getRenderContext().setVertexLabelTransformer(new ToStringLabeller<JungVertex>()); vv.getRenderContext().setEdgeLabelTransformer(new ToStringLabeller<JungEdge>()); vv.getRenderContext().setVertexFillPaintTransformer(vertexPaint); vv.getRenderContext().setVertexShapeTransformer(vertexShape); vv.getRenderer().getVertexLabelRenderer().setPosition(Position.CNTR); } public static void initSailRepository(URI physicalURI, URI namespace) { try { rep = new SailRepository(new MemoryStore()); rep.initialize(); RepositoryConnection con = rep.getConnection(); ValueFactory f = rep.getValueFactory(); con.add(physicalURI.toURL(), namespace.toString(), RDFFormat.RDFXML, f.createURI("http://graph.com")); } catch (RepositoryException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (RDFParseException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (MalformedURLException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } public static Graph<JungVertex, JungEdge> extendGraph(Graph<JungVertex, JungEdge> g, JungVertex startVertex) { ValueFactory f = rep.getValueFactory(); try { //find the Subject Direction Resource startRes; if (startVertex.getLabel().startsWith("node")) { //its a blank Node startRes = f.createBNode(startVertex.getLabel()); } else { //test if literal: if (startVertex.getUri() == null) { //looks like a lit // do nothing return g; // startRes = f.createLiteral(startVertex.getLabel())); } else { //normal node startRes = f.createURI(startVertex.getUri().toString()); } } RepositoryResult<Statement> statements = rep.getConnection().getStatements(startRes, null, null, true); while (statements.hasNext()) { Statement st = statements.next(); Resource sub = st.getSubject(); org.openrdf.model.URI pred = st.getPredicate(); Value obj = st.getObject(); // System.out.println("S: "+ sub.stringValue()+ " P: "+pred.stringValue()+" O: "+obj.stringValue()); String strPred = pred.stringValue().substring(pred.stringValue().indexOf("#") + 1); String strObj = obj.stringValue().substring(obj.stringValue().indexOf("#") + 1); System.out.println("String Object (sub direction) : " + strObj); //test of obj is in Graph JungVertex objVer = null; boolean objExists = false; for (JungVertex v : g.getVertices()) { if (v.getLabel().equals(strObj)) { objExists = true; objVer = v; } } if (!objExists) { if (obj instanceof Literal) { objVer = new JungVertex(strObj, null); } else { objVer = new JungVertex(strObj, URI.create(obj.stringValue())); } g.addVertex(objVer); } // g.c //add Edge JungEdge predV = new JungEdge(strPred); //find out if such an edge is in graph boolean edgeInGraph = false; for (JungEdge je : g.getEdges()) { if (g.getSource(je).getUri().equals(URI.create(sub.stringValue()))) { if (strPred.equals(je.toString())) { JungVertex obj2 = g.getDest(je); if (obj2.getUri() != null) { //no literal if (obj2.getUri().equals(URI.create(obj.stringValue()))) { edgeInGraph = true; } } else { //is literal if (obj2.getLabel().equals(obj.stringValue())) { edgeInGraph = true; } } } } } if (!edgeInGraph) { //test if circle (Schlinge) if (strObj.equals(startVertex.getLabel())) { g.addEdge(predV, startVertex, startVertex); } else { g.addEdge(predV, startVertex, objVer); } } } //find the object direction statements = rep.getConnection().getStatements(null, null, startRes, true); while (statements.hasNext()) { Statement st = statements.next(); Resource sub = st.getSubject(); org.openrdf.model.URI pred = st.getPredicate(); Value obj = st.getObject(); // System.out.println("S: "+ sub.stringValue()+ " P: "+pred.stringValue()+" O: "+obj.stringValue()); String strSub = sub.stringValue().substring(sub.stringValue().indexOf("#") + 1); String strPred = pred.stringValue().substring(pred.stringValue().indexOf("#") + 1); //test of obj is in Graph JungVertex subVer = null; boolean subExists = false; for (JungVertex v : g.getVertices()) { if (v.getLabel().equals(strSub)) { subExists = true; subVer = v; } } if (!subExists) { subVer = new JungVertex(strSub, URI.create(sub.stringValue())); g.addVertex(subVer); } JungEdge predV = new JungEdge(strPred); //find out if such an edge is in graph boolean edgeInGraph = false; for (JungEdge je : g.getEdges()) { if (g.getSource(je).getUri().equals(URI.create(sub.stringValue()))) { if (strPred.equals(je.toString())) { JungVertex obj2 = g.getDest(je); if (obj2.getUri() != null) { //no literal if (obj2.getUri().equals(URI.create(obj.stringValue()))) { edgeInGraph = true; } } else { //is literal if (obj2.getLabel().equals(obj.stringValue())) { edgeInGraph = true; } } } } } if (!edgeInGraph) { //test if circle (Schlinge) if (strSub.equals(startVertex.getLabel())) { g.addEdge(predV, startVertex, startVertex); } else { g.addEdge(predV, subVer, startVertex); } } } } catch (RepositoryException e) { // TODO Auto-generated catch block e.printStackTrace(); } return g; } public static Graph<JungVertex, JungEdge> createGraphModel(URI start) { try { Graph<JungVertex, JungEdge> g = new DirectedSparseMultigraph<JungVertex, JungEdge>(); ValueFactory f = rep.getValueFactory(); System.out.println("Start Node Fragment: " + start); if (start == null) { return null; } Resource startRes; if (start.toString().startsWith("node")) { //its a blank Node startRes = f.createBNode(start.toString()); } else { startRes = f.createURI(start.toString()); } //this is the subject direction RepositoryResult<Statement> statements = rep.getConnection().getStatements(startRes, null, null, true); JungVertex subVer = new JungVertex(start.getFragment(), start); while (statements.hasNext()) { Statement st = statements.next(); Resource sub = st.getSubject(); org.openrdf.model.URI pred = st.getPredicate(); Value obj = st.getObject(); System.out.println( "S: " + sub.stringValue() + " P: " + pred.stringValue() + " O: " + obj.stringValue()); String strPred = pred.stringValue().substring(pred.stringValue().indexOf("#") + 1); String strObj = obj.stringValue().substring(obj.stringValue().indexOf("#") + 1); JungVertex objVer = null; if (obj instanceof Literal) { objVer = new JungVertex(strObj, null); } else { objVer = new JungVertex(strObj, URI.create(obj.stringValue())); } JungEdge predV = new JungEdge(strPred); //test if circle (Schlinge) if (strObj.equals(subVer.toString())) { g.addEdge(predV, subVer, subVer); } else { g.addEdge(predV, subVer, objVer); } } //do the object direction statements = rep.getConnection().getStatements(null, null, startRes, true); JungVertex objVer = subVer; while (statements.hasNext()) { Statement st = statements.next(); Resource sub = st.getSubject(); org.openrdf.model.URI pred = st.getPredicate(); Value obj = st.getObject(); System.out.println( "S: " + sub.stringValue() + " P: " + pred.stringValue() + " O: " + obj.stringValue()); String strSub = sub.stringValue().substring(sub.stringValue().indexOf("#") + 1); String strPred = pred.stringValue().substring(pred.stringValue().indexOf("#") + 1); subVer = new JungVertex(strSub, URI.create(sub.stringValue())); g.addVertex(subVer); JungEdge predV = new JungEdge(strPred); //test if circle (Schlinge) if (strSub.equals(objVer.toString())) { // g.addEdge(predV,subVer,subVer); } else { g.addEdge(predV, subVer, objVer); } } return g; } catch (RepositoryException e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; } public static Graph<JungVertex, JungEdge> mapOntologyToGraphModel(URI physicalURI, URI namespace) { System.out.println("Starting mapping full Ontology to full Graph Model"); Graph<JungVertex, JungEdge> g = new DirectedSparseMultigraph<JungVertex, JungEdge>(); try { rep = new SailRepository(new MemoryStore()); rep.initialize(); RepositoryConnection con = rep.getConnection(); ValueFactory f = rep.getValueFactory(); con.add(physicalURI.toURL(), namespace.toString(), RDFFormat.RDFXML, f.createURI("http://graph.com")); // con.getStatements(arg0, arg1, arg2, arg3, arg4) RepositoryResult<Statement> statements = con.getStatements(null, null, null, true); // System.out.println("There are "+statements.asList().size()+" statements in the graph"); while (statements.hasNext()) { Statement st = statements.next(); Resource sub = st.getSubject(); org.openrdf.model.URI pred = st.getPredicate(); Value obj = st.getObject(); System.out.println( "S: " + sub.stringValue() + " P: " + pred.stringValue() + " O: " + obj.stringValue()); // if (pred.stringValue().equals("http://www.w3.org/2000/01/rdf-schema#subClassOf")) { String strSub = sub.stringValue().substring(sub.stringValue().indexOf("#") + 1); String strPred = pred.stringValue().substring(pred.stringValue().indexOf("#") + 1); String strObj = obj.stringValue().substring(obj.stringValue().indexOf("#") + 1); // if (strPred.equals("subClassOf")) { //test of obj is blank node -- continue then // if (strObj.startsWith("node")) continue; //test id Sub Vertex is in graph JungVertex subV = null; JungVertex objV = null; boolean subExists = false; boolean objExists = false; for (JungVertex v : g.getVertices()) { if (v.toString().equals(strSub)) { subExists = true; subV = v; } if (v.toString().equals(strObj)) { objExists = true; objV = v; } } if (!subExists) { subV = new JungVertex(strSub, URI.create(sub.stringValue())); g.addVertex(subV); } if (!objExists) { //findout if obj is literal if (obj instanceof Literal) { objV = new JungVertex(strObj, null); } else objV = new JungVertex(strObj, URI.create(obj.stringValue())); g.addVertex(objV); } // g.getV // // boolean end = false; // Collection<String> edges = g.findEdgeSet(strSub, strObj); // for (String se : edges) { // if (se.equals(strPred)) { // System.out.println("Edge still exists -- dont add it again"); // end = true; // } // } // if (end) continue; JungEdge predV = new JungEdge(strPred); g.addEdge(predV, subV, objV); } // } // Node e1 = m.createNode(strSub,false); // // Node e2 = m.createNode(strObj,(obj instanceof Literal)); // // m.addEdge(new Edge(e1,e2,strPred)); return g; } catch (RepositoryException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (RDFParseException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (MalformedURLException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } return g; } public static URI getStartNode() { OWLOntology ont = ontologyStore.getLoadedOntologie(ontologyInfo.getURI()); URI start; List<URI> niceStartList = new ArrayList<URI>(); // find a nice start node: String[] pref = preferredRootConcepts; //TODO bad workaround to fix NullPointerExcept if (pref == null) { pref = new String[0]; } if (pref.length != 0) { for (int i = 0; i < pref.length; i++) { String prefString = pref[i]; System.out.println("Searching for " + prefString + "concept as start Node"); for (OWLClass o : ont.getReferencedClasses()) { // System.out.println("Fragment: "+o.getURI().getFragment()); if (o.getURI().getFragment().toLowerCase().contains(prefString)) { niceStartList.add(o.getURI()); System.out.println("Found a nice Node to Start:" + o.getURI()); } } } if (niceStartList.isEmpty()) { System.out.println("Nice start is empty"); return ont.getReferencedClasses().iterator().next().getURI(); } else { //get a random node from that list start = niceStartList.get(0); System.out.println("nice start list not empty using the first:"); System.out.println(start); return start; } } else return ont.getReferencedClasses().iterator().next().getURI(); } public static Repository getRep() { return rep; } }