swoopmodel.java

Semantic Web Ontology Editor

//The MIT License
//
// Copyright (c) 2004 Mindswap Research Group, University of Maryland, College Park
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to
// deal in the Software without restriction, including without limitation the
// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
// sell copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
// IN THE SOFTWARE.

package org.mindswap.swoop;

import java.awt.Font;
import java.awt.GridLayout;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Reader;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.URI;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
import java.util.TimeZone;
import java.util.Timer;
import java.util.prefs.Preferences;

import javax.swing.ButtonGroup;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;

import org.mindswap.swoop.annotea.Description;
import org.mindswap.swoop.change.ChangeLog;
import org.mindswap.swoop.change.SwoopChange;
import org.mindswap.swoop.reasoner.PelletReasoner;
import org.mindswap.swoop.reasoner.SwoopReasoner;
import org.mindswap.swoop.reasoner.SwoopToldReasoner;
import org.mindswap.swoop.renderer.entity.AbstractSyntaxEntityRenderer;
import org.mindswap.swoop.renderer.entity.RDFXMLEntityRenderer;
import org.mindswap.swoop.utils.RulesExpressivity;
import org.mindswap.swoop.utils.SwoopCache;
import org.mindswap.swoop.utils.SwoopStatistics;
import org.mindswap.swoop.utils.WSPolicy;
import org.mindswap.swoop.utils.change.BooleanElementChange;
import org.mindswap.swoop.utils.change.EnumElementChange;
import org.mindswap.swoop.utils.change.RevertCheckpointChange;
import org.mindswap.swoop.utils.change.SaveCheckpointChange;
import org.mindswap.swoop.utils.owlapi.CorrectedRDFRenderer;
import org.mindswap.swoop.utils.owlapi.DefaultShortFormProvider;
import org.mindswap.swoop.utils.owlapi.LabelShortFormProvider;
import org.mindswap.swoop.utils.owlapi.OWLDescriptionFinder;
import org.mindswap.swoop.utils.owlapi.OWLEntityRemover;
import org.mindswap.swoop.utils.owlapi.OWLOntBuilder;
import org.mindswap.swoop.utils.owlapi.QNameShortFormProvider;
import org.mindswap.swoop.utils.owlapi.diff.FilteredDiff;
import org.mindswap.swoop.utils.ui.SwingWorker;
import org.semanticweb.owl.impl.model.OWLConnectionImpl;
import org.semanticweb.owl.impl.model.OWLDataFactoryImpl;
import org.semanticweb.owl.impl.model.OWLDataPropertyInstanceImpl;
import org.semanticweb.owl.impl.model.OWLDataPropertyRangeAxiomImpl;
import org.semanticweb.owl.impl.model.OWLFunctionalPropertyAxiomImpl;
import org.semanticweb.owl.impl.model.OWLIndividualTypeAssertionImpl;
import org.semanticweb.owl.impl.model.OWLInverseFunctionalPropertyAxiomImpl;
import org.semanticweb.owl.impl.model.OWLInversePropertyAxiomImpl;
import org.semanticweb.owl.impl.model.OWLObjectPropertyInstanceImpl;
import org.semanticweb.owl.impl.model.OWLObjectPropertyRangeAxiomImpl;
import org.semanticweb.owl.impl.model.OWLPropertyDomainAxiomImpl;
import org.semanticweb.owl.impl.model.OWLSubPropertyAxiomImpl;
import org.semanticweb.owl.impl.model.OWLSymmetricPropertyAxiomImpl;
import org.semanticweb.owl.impl.model.OWLTransitivePropertyAxiomImpl;
import org.semanticweb.owl.io.ShortFormProvider;
import org.semanticweb.owl.io.abstract_syntax.AbstractOWLParser;
import org.semanticweb.owl.io.owl_rdf.OWLRDFErrorHandler;
import org.semanticweb.owl.io.owl_rdf.OWLRDFParser;
import org.semanticweb.owl.model.OWLAnd;
import org.semanticweb.owl.model.OWLAnnotationInstance;
import org.semanticweb.owl.model.OWLBooleanDescription;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLClassAxiom;
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDataProperty;
import org.semanticweb.owl.model.OWLDataRange;
import org.semanticweb.owl.model.OWLDataValue;
import org.semanticweb.owl.model.OWLDescription;
import org.semanticweb.owl.model.OWLDifferentIndividualsAxiom;
import org.semanticweb.owl.model.OWLDisjointClassesAxiom;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLEnumeration;
import org.semanticweb.owl.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLIndividualAxiom;
import org.semanticweb.owl.model.OWLNamedObject;
import org.semanticweb.owl.model.OWLNaryBooleanDescription;
import org.semanticweb.owl.model.OWLNot;
import org.semanticweb.owl.model.OWLObject;
import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLOr;
import org.semanticweb.owl.model.OWLProperty;
import org.semanticweb.owl.model.OWLSameIndividualsAxiom;
import org.semanticweb.owl.model.OWLSubClassAxiom;
import org.semanticweb.owl.model.change.AddAnnotationInstance;
import org.semanticweb.owl.model.change.AddClassAxiom;
import org.semanticweb.owl.model.change.AddDomain;
import org.semanticweb.owl.model.change.AddEntity;
import org.semanticweb.owl.model.change.AddEnumeration;
import org.semanticweb.owl.model.change.AddEquivalentClass;
import org.semanticweb.owl.model.change.AddImport;
import org.semanticweb.owl.model.change.AddIndividualClass;
import org.semanticweb.owl.model.change.AddSuperClass;
import org.semanticweb.owl.model.change.AddSuperProperty;
import org.semanticweb.owl.model.change.ChangeVisitor;
import org.semanticweb.owl.model.change.OntologyChange;
import org.semanticweb.owl.model.change.RemoveClassAxiom;
import org.semanticweb.owl.model.change.RemoveEntity;
import org.semanticweb.owl.model.change.RemoveEnumeration;
import org.semanticweb.owl.model.change.RemoveEquivalentClass;
import org.semanticweb.owl.model.change.RemoveImport;
import org.semanticweb.owl.model.change.SetFunctional;
import org.semanticweb.owl.model.helper.OntologyHelper;
import org.semanticweb.owl.util.OWLConnection;
import org.xml.sax.SAXException;

public class SwoopModel implements ShortFormProvider {
    
	final public static int ALL            = 0;
	final public static int INDIVIDUALS    = 1;
	final public static int CLASSES        = 2;
	final public static int PROPERTIES     = 3;
	final public static int DATAPROPERTIES = 4;
	final public static int OBJPROPERTIES  = 5;
	final public static int IMPORTED_ONT  = 6;
	final public static int BASE_ONT  = 7;
	final public static int TRANSCLOSE_ONT  = 8;
	final public static int RDFXML_SER = 9;
	final public static int JAVA_SER = 10;
	//**********************************************
	//Added for Econnections
	//**********************************************
	final public static int FOREIGN_ENT = 11;
	//***********************************************
	final public static int GCI = 12;
	
	private boolean show_imports = true; // show imported ontologies in class/prop tree
    private boolean showQNames = false; // show QNames
    private boolean showDivisions = true; // show divisions in the entity renderer pane
    private boolean showInherited = false; // show inherited properties and individuals   
    private boolean enableAutoSaveChkPts = false; // enable auto-save checkpoints
    private boolean logChanges = true; // log all changes
    private boolean enableChangeLogDisplay = true; // enable change log display
    private boolean enableDebugging = false; // enable ontology debugging (class expressions, pellet)
    private boolean enableAutoRetrieve = false; // enable auto-retrieve of Annotea annotations whenever entity selection changes
    private boolean highlightCode = true; // highlight entity in source code
    private boolean enableRules = false; // enable definition rules
    public static int changeSharingMethod = RDFXML_SER; // change sharing method for Ontology Change sets (RDF/XML or Java objects)
    private String fontSize = "3";
    private String fontFace = "Verdana";
    private String treeThreshold = "200"; // number below this - tree is fully expanded
    private String termListFilter = "Show All";
    private boolean showChangeAnnotBar = false; // show Changes/Annotations sidebar
    private boolean openLastWorkspace = false; // open last workspace when Swoop starts
    private String lastWorkspaceURL = "";
    private boolean saveCheckPtsDisk = false;
    private boolean showCheckPts = true;
    private SwoopReasoner reasoner;
    private String defaultReasonerName;
    private Map ontologies;
    private Map ontologySettings; // key - uri, value - List of settings (imports, qnames, reasoner) in that order
    protected OWLEntity selectedEntity;
    protected OWLOntology selectedOntology;
    public OWLNamedObject selectedOWLObject;
    private List listeners;
    private ShortFormProvider shortForms;
    private List uncommittedChanges, committedChanges;    
    private boolean editorEnabled;
    private Set changedOntologies; // ontologies changed at each check point (gets reset and created during apply changes)
    public List bufferedChanges; // changes in the uncommitted list get saved to this buffer just before uncommitted is emptied (gets reset and created during apply changes)
    private Set annotatedObjectURIs; // set of all OWLNamedObjects URI's that have one or more Annotea annotations on them
    private Hashtable ResourceAnnotHash;
    private boolean showIcons = false; // show Icons in renderer pane
    private URI currentlyLoadingURI = null;
    private boolean lookupAllOnts = false; // search across all ontologies
    private boolean viewOWLVocabularyAsRDF = false;
    private boolean viewRDFVocabularyAsRDF = false;
    private SwoopCache classTreeCache, propTreeCache; // cache for class/property trees for ontologies
    private SwoopCache annotationCache; // cache for Annotea annotations
    private SwoopCache changesCache; // cache for committed ontology changes
    private SwoopCache reasonerCache; // cache for reasoners
    private HashMap reasonerMap; // key - reasoner name, value - SwoopReasoner instance
    private File wkspcFile; // last workspace file used
    private HashMap classExprHash; // hash for class expressions
    private String userName = ""; // used for version control, general provenance info etc
    public HashMap changeMap; // map for ontology changes (used in changelog)
    public HashMap versionRepository; // map with key: repositoryURI, value: array of Description objects, each corresponding to version commit (first being header)
    public String previousTimeStamp = ""; 
    public SwoopFrame myFrame = null; // keeps track of the frame the model resides in.  Use getFrame/setFrame to access the frame.  Required so entityRenderer can have access to TermsDisplay from SwoopFrame. 
    private boolean debugGlass = false, debugBlack = false;
    private HashMap ontStatMap; // hashmap for storing ontology statistics
	private boolean useLabels; // display entities using rdfs:labels
	private String useLanguage = ""; // display entities in this language
	private String proxyHost = ""; // proxy host
	private String proxyPort = ""; // proxy port
	private boolean useHTTPProxy = false; // use HTTP proxy
	public boolean useTableau = false, findAllMUPS = false; // advanced SOS options
	private boolean autoSaveWkspc = false; // option to save workspace automatically
	private float saveWkspcTime = 1; 
	private String saveWkspcFile = "recentWkspc.swp";
	private Timer swoopTimer; // timer to carry out operations at regular intervals
	public boolean repairColor = false; // FOR Repair Purposes
	public HashSet repairSet = new HashSet(); // FOR Repair Purposes
	public RulesExpressivity ruleExpr = null;
	private Preferences preferences;
	
	//Added for Segmentation
	public Map segmentation;//A mapping from each ontology object to its segmentation object.
	//
	
    public SwoopModel() {
        
    	ontologies = new Hashtable();
    	ontologySettings = new HashMap();
    	listeners = new ArrayList();    	
    	reasoner = new SwoopToldReasoner();
    	defaultReasonerName = "No Reasoner";
    	shortForms = new QNameShortFormProvider();
    	uncommittedChanges = new ArrayList();
    	committedChanges = new ArrayList();
    	annotatedObjectURIs = new HashSet();
    	ResourceAnnotHash = new Hashtable();
    	classTreeCache = new SwoopCache();
    	propTreeCache = new SwoopCache();
    	annotationCache = new SwoopCache();
    	changesCache = new SwoopCache();
    	reasonerCache = new SwoopCache();
    	reasonerMap = new HashMap();
    	classExprHash = new HashMap();
    	changeMap = new HashMap();
    	changedOntologies = new HashSet();
    	versionRepository = new HashMap();
    	
    	//Added for Segmentation
    	segmentation = new HashMap();
    	//
    	
    	ontStatMap = new HashMap();  
    	preferences = Preferences.userNodeForPackage(this.getClass());
//    	**************************************
		// Added for rules
		//**************************************
		ruleExpr = new RulesExpressivity(this);
		//Initializing prolog, consulting programs	
//		if (ruleExpr.USE_PROLOG_ENGINE) {
//		//	Query q1 = new Query("consult('~/rules/allog/preallogPP.qlf')");
//
//			Query q1 = new Query("consult('allog/preallogPP.pl')");
//			System.out.println("consult q1 " + (q1.hasSolution() ? "succeeded" : "failed"));
//			q1 = new Query("compile");
//			System.out.println("consult q1 " + (q1.hasSolution() ? "succeeded" : "failed"));
//		}
	}

    
    public Map getSegmentation(){
    	return segmentation;
    }
    
    public void setSegmentation(Map seg){
    	segmentation = seg;
    }
    
    public void addAnnotatedObjectURI(URI annObjURI) {
    	this.annotatedObjectURIs.add(annObjURI);
    }
    
    public Set getAnnotatedObjectURIs() {
    	return this.annotatedObjectURIs;
    }
    
    public void setAnnotatedObjectURIs(Set annotURIs) {
    	this.annotatedObjectURIs = annotURIs;
    }
    
    public boolean getEnableAutoSaveChkPts() {
    	return this.enableAutoSaveChkPts;
    }
    
    public boolean getEnableChangeLogDisplay() {
    	return this.enableChangeLogDisplay;
    }
    
    public boolean getEnableRules() {
		return enableRules;
	}

    
    public boolean getEnableAutoRetrieve() {
    	return this.enableAutoRetrieve;
    }
   
    public void setEnableAutoRetrieve(boolean mode) {
    	this.enableAutoRetrieve = mode;
    	notifyListeners(new ModelChangeEvent(this, ModelChangeEvent.AUTORETRIEVE_CHANGED, null));
    }
    
    public void setEnableAutoSaveChkPts(boolean mode, boolean notify) {
    	
    	this.enableAutoSaveChkPts = mode;
    	if (notify) notifyListeners(new ModelChangeEvent(this, ModelChangeEvent.ENABLED_CHECKPOINT, null));
    }
    
    public void setEnableChangeLogDisplay(boolean mode) {
    	this.enableChangeLogDisplay = mode;
    	notifyListeners(new ModelChangeEvent(this, ModelChangeEvent.ENABLED_CHANGELOG, null));	
    }
    
    public boolean getEditorEnabled() {
    	return editorEnabled;
    }
    
    public boolean getEnableDebugging() {
    	return enableDebugging;
    }