KnowledgeGraph.java | searchcode

/plugins/org.integratedmodelling.thinklab.core/src/org/integratedmodelling/thinklab/graph/KnowledgeGraph.java

https://github.com/fvilla/thinklab
Java | 473 lines | 219 code | 95 blank | 159 comment | 55 complexity | 6495caa7aacb6fbcdc7ff74eeaab3b9b MD5 | raw file

/**

 * KnowledgeGraph.java

 * ----------------------------------------------------------------------------------

 * 

 * Copyright (C) 2008 www.integratedmodelling.org

 * Created: Apr 25, 2008

 *

 * ----------------------------------------------------------------------------------

 * This file is part of Thinklab.

 * 

 * Thinklab is free software; you can redistribute it and/or modify

 * it under the terms of the GNU General Public License as published by

 * the Free Software Foundation; either version 3 of the License, or

 * (at your option) any later version.

 * 

 * Thinklab 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 General Public License for more details.

 * 

 * You should have received a copy of the GNU General Public License

 * along with the software; if not, write to the Free Software

 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA

 * 

 * ----------------------------------------------------------------------------------

 * 

 * @copyright 2008 www.integratedmodelling.org

 * @author    Ferdinando Villa (fvilla@uvm.edu)

 * @date      Apr 25, 2008

 * @license   http://www.gnu.org/licenses/gpl.txt GNU General Public License v3

 * @link      http://www.integratedmodelling.org

 **/

package org.integratedmodelling.thinklab.graph;



import java.io.BufferedReader;

import java.io.BufferedWriter;

import java.io.DataInputStream;

import java.io.File;

import java.io.FileInputStream;

import java.io.IOException;

import java.io.InputStreamReader;

import java.io.OutputStream;

import java.io.OutputStreamWriter;

import java.util.HashSet;

import java.util.Set;



import org.integratedmodelling.thinklab.KnowledgeManager;

import org.integratedmodelling.thinklab.exception.ThinklabException;

import org.integratedmodelling.thinklab.exception.ThinklabIOException;

import org.integratedmodelling.thinklab.exception.ThinklabUserErrorException;

import org.integratedmodelling.thinklab.interfaces.knowledge.IConcept;

import org.integratedmodelling.thinklab.interfaces.knowledge.IInstance;

import org.integratedmodelling.thinklab.interfaces.knowledge.IKnowledgeSubject;

import org.integratedmodelling.thinklab.interfaces.knowledge.IProperty;

import org.integratedmodelling.thinklab.interfaces.knowledge.IRelationship;

import org.jgrapht.graph.DefaultDirectedGraph;



/**

 * A directed graph whose nodes are knowledge objects and whose edges may be

 * tagged by properties. Implement followRelationship to define what gets in and

 * what not.

 * 

 * @author Ferdinando Villa

 * 

 */

public abstract class KnowledgeGraph extends

		DefaultDirectedGraph<Object, Object> {

	

	IKnowledgeSubject root = null;



	private static final long serialVersionUID = 9151878779989532686L;



	/*

	 * if true, do not create further links to objects that are already part of

	 * the graph.

	 */

	boolean forceTreeGeometry = false;



	/*

	 * if false, do not follow concepts or instances that are part of a

	 * different concept space than what we start at.

	 */

	boolean crossConceptSpace = false;



	/*

	 * if true and starting at a class, existing instances are followed and

	 * processed. Not recommended in a multi-user environment at least with the

	 * protege implementation (instances are all visibles).

	 */

	boolean followInstances = false;



	/*

	 * if true, edges between vertexes will only be created once, and their

	 * content set to what given in edgeContent

	 */

	boolean collapseEdges = false;

	Object edgeContent = null;



	/*

	 * when starting at an instance, 0 means that the class is not added, 1

	 * means that it's added but not further followed, and >1 means that the

	 * whole class structure is generated.

	 */

	int followClassLevel = 0;



	/*

	 * remember if we have started the current graph from a concept or an

	 * instance

	 */

	boolean rootIsConcept = false;



	public KnowledgeGraph() {

		super(PropertyEdge.class);

	}



	/**

	 * The graph may or may not have a root. It's up to the implementation to

	 * define it. It's obviously a good thing to have if the graph is a tree.

	 * 

	 * @param root

	 */

	public void setRoot(IKnowledgeSubject root) {

		this.root = root;

	}

	

	public IKnowledgeSubject getRoot() {

		return this.root;

	}

	

	protected void buildGraph(IKnowledgeSubject root) throws ThinklabException {

		buildGraph(root, null);

	}



	/*

	 * can be called as many times as you want unless forceTreeGeometry is true.

	 */

	private void buildGraph(IKnowledgeSubject rootConcept, Set<String> refs)

			throws ThinklabException {



		if (refs == null && forceTreeGeometry && this.vertexSet().size() > 0)

			throw new ThinklabUserErrorException(

					"knowledge graph: tree geometry requested, cannot add a new root concept");



		String uri = rootConcept.getURI();



		if (refs == null) {

			refs = new HashSet<String>();

			if (rootConcept instanceof IConcept) {

				rootIsConcept = true;

			}

		} else if (refs.contains(uri)) {

			return;

		}



		refs.add(uri);

		this.addVertex(rootConcept);



		/*

		 * do not follow further if we're graphing an instance and we're not

		 * supposed to graph more than the direct type.

		 */

		if (rootConcept instanceof IConcept && !rootIsConcept

				&& followClassLevel == 0) {

			return;

		}



		if (rootConcept instanceof IConcept) {



			/*

			 * see what edge we want for the children

			 */

			for (IConcept c : ((IConcept) rootConcept).getChildren()) {



				if (followProperty((IConcept) rootConcept, c, null)) {



					buildGraph(c, refs);

					this.addEdge(c, rootConcept);

				}



			}

		} else {



			/*

			 * if we're graphing instances and we want concepts, add the concept

			 */

			if (!rootIsConcept && followClassLevel > 0) {



				if (followRelationship(rootConcept, null,

						((IInstance) rootConcept).getDirectType())) {



					buildGraph(((IInstance) rootConcept).getDirectType(), refs);

					this.addEdge(rootConcept, ((IInstance) rootConcept)

							.getDirectType());

				}



			}

		}



		/*

		 * if it's a concept, we want to follow the range of each direct

		 * property

		 */

		if (rootConcept instanceof IConcept) {



			IConcept source = (IConcept) rootConcept;



			for (IProperty property : source.getProperties()) {



				for (IConcept target : source.getPropertyRange(property)) {



					if (!followProperty(source, target, property))

						continue;



					boolean isThere = refs.contains(target.getURI());



					/*

					 * follow the object if it's not there

					 */

					if (!isThere) {

						buildGraph(target, refs);

					}



					/*

					 * add edge unless we want a tree and it's there already

					 */

					if (!(isThere && forceTreeGeometry)) {

						PropertyEdge edge = (PropertyEdge) this.addEdge(rootConcept, target);



						if (edge != null)

							edge.setProperty(property);

					}



					isThere = refs.contains(target.getURI());

				}



			}

		}



		/**

		 * Follow relationships

		 */

		for (IRelationship r : rootConcept.getRelationships()) {



			boolean doit = followRelationship(rootConcept, r, null);



			if (doit) {



				if (r.isObject()) {



					IInstance inst = r.getValue().asObjectReference()

							.getObject();

					boolean isThere = refs.contains(inst.getURI());



					/*

					 * follow the object if it's not there

					 */

					if (!isThere && (!rootIsConcept || followInstances)) {

						buildGraph(inst, refs);

					}



					/*

					 * add edge unless we want a tree and it's there already

					 */

					if (!(isThere && forceTreeGeometry)) {

						((PropertyEdge) this.addEdge(rootConcept, inst)).setProperty(

								r.getProperty());

					}



					isThere = refs.contains(inst.getURI());



				} else if (r.isClassification()) {



					IConcept conc = r.getValue().getConcept();



					/*

					 * follow concept if we are allowed

					 */

					if (rootIsConcept || followClassLevel > 0) {



						buildGraph(conc, refs);

						this.addEdge(rootConcept, conc);



					}

				}

			}

		}

		

	}



	public void forceTreeGeometry(boolean what) {

		forceTreeGeometry = what;

	}



	public void followInstances(boolean what) {

		followInstances = what;

	}



	public void collapseEdges(boolean collapse, Object content) {

		collapseEdges = collapse;

		edgeContent = content;

	}



	/**

	 * Quick and dirty method to show the graph in a window. Depends on graphviz

	 * installed.

	 * 

	 * @throws ThinklabException

	 */

	public void show() throws ThinklabException {

		

		class NPP implements GraphViz.NodePropertiesProvider {



			public int getNodeHeight(Object o) {

				return 0;

			}



			public String getNodeId(Object o) {

				return o.toString().replace(':', '_').replace(' ', '_');

			}



			public int getNodeWidth(Object o) {

				return 0;

			}

			

		}

		

		GraphViz gv = new GraphViz();

		gv.loadGraph(this, new NPP());

		gv.show();

	}



	public void dump(OutputStream o) {



		BufferedWriter w = new BufferedWriter(new OutputStreamWriter(o));



		try {

			for (Object c : this.vertexSet()) {



				w.write(c.toString());



				int edgecount = 0;

				for (Object p : this.outgoingEdgesOf(c)) {



					if (edgecount++ == 0)

						w.write(": --- " + ((PropertyEdge) p).property

								+ " --> (");

					else

						w.write(", ");



					w.write(this.getEdgeTarget(p).toString());



				}

				if (edgecount > 0)

					w.write(")\n");

				else

					w.write("\n");

			}



		} catch (IOException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

	}



	public void dump() {

		dump(System.out);

	}



	/**

	 * Read a graph from a simple text format. Each non-empty line in the file can be

	 * a comment (starting with #) or a set of edges. 

	 * 

	 * If null property edges are desired, the first token (whitespace-separated) should

	 * be the semantic type of the source concept, and the remaining are concepts that

	 * should be linked to it.

	 * 

	 * If the property for the edge is specified, the first token is the semantic type

	 * of the property with a colon appended. The remaining token are concepts, structured

	 * as said above.

	 * 

	 * @param infile

	 * @throws ThinklabException

	 */

	public void read(File infile) throws ThinklabException {



		try {

			FileInputStream fstream = new FileInputStream(infile);

			DataInputStream in = new DataInputStream(fstream);

			BufferedReader br = new BufferedReader(new InputStreamReader(in));



			String strLine;

			while ((strLine = br.readLine()) != null) {



				strLine = strLine.trim();

				

				if (strLine.startsWith("#") || strLine.equals(""))

					continue;

				

				/* tokenize */

				String[] tokens = strLine.split("\\s+");

				

				if (tokens.length < 1)

					continue;

				

				IProperty property = null;

				

				/* see if we have a property as first token, which must have a : at the end */

				int start = 0;

				if (tokens[0].endsWith(":")) {

					start = 1;

					property = 

						KnowledgeManager.get().requireProperty(

								tokens[0].substring(0, tokens[0].length()-2));

				}

				

				/* first remaining token is concept, others (if any) are its dependents */

				IConcept source = KnowledgeManager.get().requireConcept(tokens[start]);

				

				addVertex(source);

				

				/* add any remaining edges and vertices */

				for (int i = start + 1; i < tokens.length; i++) {



					IConcept target = KnowledgeManager.get().requireConcept(tokens[i]);

					addVertex(target);

					PropertyEdge e = (PropertyEdge) addEdge(source, target);

					

					if (e != null)

						e.setProperty(property);

				

				}

			}



			in.close();



		} catch (IOException e) {

			throw new ThinklabIOException(e);

		}

	}



	/**

	 * Called at each relationship found. If it returns an edge, the associated

	 * knowledge is linked and (if unknown) processed. Otherwise the cycle

	 * stops. It's called on literals and classifications as well; of course it

	 * should return null if called on a literal.

	 * 

	 * @param source

	 * @param relationship

	 *            the relationship. If null, type is not null and the

	 *            relationship is direct type

	 * @param type

	 *            the concept that we're linking to. If not null, we're

	 *            processing a direct type and relationship is null.

	 * @return

	 */

	protected abstract boolean followRelationship(IKnowledgeSubject source,

			IRelationship relationship, IConcept type);



	/**

	 * Called at each explicit relationship between concepts, caused by a range

	 * statement or specialized through a restriction. Also called for isa,

	 * passing a null property.

	 * 

	 * @param source

	 * @param target

	 * @param property

	 *            if null, we're processing children or direct types

	 * @return

	 */

	protected abstract boolean followProperty(IConcept source, IConcept target,

			IProperty property);



}