ontologyanalyzer.java

来自「Semantic Web Ontology Editor」· Java 代码 · 共 904 行 · 第 1/3 页

/*
 * Created on Dec 23, 2005
 *
 * TODO To change the template for this generated file go to
 * Window - Preferences - Java - Code Style - Code Templates
 */
package org.mindswap.swoop.automation;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import java.util.Vector;

import javax.swing.JOptionPane;

import org.mindswap.swoop.SwoopFrame;
import org.mindswap.swoop.SwoopModel;
import org.mindswap.swoop.TermsDisplay;
import org.mindswap.swoop.reasoner.PelletReasoner;
import org.mindswap.swoop.reasoner.SwoopReasoner;
import org.mindswap.swoop.reasoner.SwoopToldReasoner;
import org.mindswap.swoop.renderer.ontology.SwoopOntologyInfo;
import org.mindswap.swoop.utils.SwoopStatistics;
import org.mindswap.swoop.utils.owlapi.CorrectedRDFRenderer;
import org.semanticweb.owl.io.RendererException;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLProperty;


/**
 * @author Dave Wang
 *
 * TODO To change the template for this generated type comment go to
 * Window - Preferences - Java - Code Style - Code Templates
 */
public class OntologyAnalyzer 
{
	
	static class AncestorResult
	{
		public HashSet myResult   = null;
		public boolean myHasCycle = false;
		
		AncestorResult( HashSet set, boolean hasCycle )
		{
			myResult = set;
			myHasCycle = hasCycle;
		}
	}
	
	public static final String LOGICAL_URI = "LOGICALURI";
	public static final String PHYSICAL_URI = "PHYSICALURI";
	public static final String NUM_IMPORTED_CLASSES = "NUMIMPORTEDCLASSES";
	public static final String NUM_DEFINED_CLASSES  = "NUMDEFINEDCLASSES";
	public static final String NUM_IMPORTED_DATA_PROP = "NUMIMPORTEDDATAPROPS";
	public static final String NUM_DEFINED_DATA_PROP  = "NUMDEFINEDDATAPROPS";
	public static final String NUM_IMPORTED_OBJ_PROP  = "NUMIMPORTEDOBJPROPS";
	public static final String NUM_DEFINED_OBJ_PROP   = "NUMDEFINEDOBJPROPS";
	public static final String NUM_IMPORTED_ANNO_PROP = "NUMIMPORTEDANNOPROPS";
	public static final String NUM_DEFINED_ANNO_PROP  = "NUMDEFINEDANNOPROPS";
	public static final String NUM_LINKED_PROP        = "NUMLINKEDPROPS";
	public static final String NUM_IMPORTED_IND       = "NUMIMPORTEDIND";
	public static final String NUM_DEFINED_IND       = "NUMDEFINEDIND";	
	public static final String CONSISTENCY           = "CONSISTENCY";
	public static final String EXPRESSIVITY          = "EXPRESSIVITY";
	public static final String GRAPH_MORPHOLOGY      = "GRAPHMORPHOLOGY";

	// graph morphology categories
	public static final String LIST      = "List";
	public static final String LISTS     = "Lists";
	public static final String TREE      = "Tree";
	public static final String TREES     = "Trees";
	public static final String MULTITREE = "Multitree";
	public static final String DAG       = "DAG";
	public static final String GRAPH     = "Graph";
	public static final String NONE      = "None";
	public static final String INCONSISTENT = "INCONSISTENT";
	
	// individual stats constants
	public static final String NUM_TYPE_ASSERTIONS = "NUMTYPEASSERTIONS";
	public static final String NUM_DPROP_ASSERTIONS = "NUMDPROPASSERTIONS";
	public static final String NUM_OPROP_ASSERTIONS = "NUMOPROPASSERTIONS";
	
	public static final String OWLTHING  = "http://www.w3.org/2002/07/owl#Thing";
	
    public static SwoopFrame theFrame;
        
    public static boolean IS_DEBUG = false;
    public static boolean INFERRED_STATS = false; // whether to get reasoned stats
    
	public Vector analyzeInput(AutomatedSwoopModel model, String[] args) 
	{
		Vector analyses = new Vector();
		for (int i = 0; i < args.length; i++) {
			try 
			{
				OntologyAnalysis oa = analyze( model, new URI(args[i]) );
				SwoopFrame frame = model.getFrame();
				OWLOntology ontology = model.getSelectedOntology();
				model.clearCaches( ontology );             // force clearing!
				model.removeOntStats( ontology );          // force clearing!
				model.removeOntology( ontology.getURI() ); // force removing!
        		frame.termDisplay.removeFromCache(ontology);
				frame.clearWorkspace( false );             // just in case

				//model.getFrame().clearWorkspace( false ); // false for "No popup confirmation"
			} 
			catch (Exception exception) 
			{
				exception.printStackTrace();
				if ( IS_DEBUG )
					System.out.println(" * OntologyAnalyzer: Could not load ontology " + args[i]);
			}
		}
		return analyses;
	}
	
	public Vector analyzeInput(AutomatedSwoopModel model, BufferedReader reader, String outputfile, String logfilename ) 
	{ return analyzeInput(model, reader, outputfile, 1, logfilename); }
	
	/*
	 * pass in null for logfilename if no logging is desired
	 */
	public Vector analyzeInput(AutomatedSwoopModel model, BufferedReader reader, String outputfile, int startline, String logfilename ) 
	{
		if ( startline < 1 )
			startline = 1;
		
		int count = startline; // keep track of how many ontologies we looked at
		
		Vector analyses = new Vector();
		String line = null;
		
		// setting up log file option
		boolean isToLog = true;
		if ( logfilename == null )
			isToLog = false;
		BufferedWriter logWriter = null;
		
		try 
		{
			// setting up log file
			if ( isToLog )
				logWriter = new BufferedWriter( new FileWriter( logfilename ) );
			
			// setting up output file
			BufferedWriter writer = new BufferedWriter( new FileWriter( outputfile ) );
			StatsPrinter.writeFileHeader( writer );
			
			// skip number of lines given
			for ( int i = 1; i < startline; i++ )
				reader.readLine();
						
			int analyzedOntologies   = 0;
			int exceptionedOntologies = 0;
			int skippedOntologies     = 0;
			
			while ( ( line = reader.readLine() ) != null )
			{
				try
				{
					// if line starts with "*", we skip it
					if ( line.startsWith("*"))
					{
						if ( isToLog )
						{
							logWriter.write( "[" + count + "] Skipping <" + line  + ">... ");
							logWriter.newLine();
							skippedOntologies++;
						}
						continue;
					}

					if ( isToLog )
					{
						logWriter.write( "[" + count + "] Analyzing <" + line  + ">... ");
						logWriter.newLine();
						logWriter.flush();
					}
					
					long startTime = System.currentTimeMillis();
					OntologyAnalysis oa = analyze( model, new URI(line) );
					
					// pelletStats can be null if INFERRED_STATS is set to false;
					if (( oa.getPelletStats() != null ) && ( isRDFS( oa ) ))
					{
						System.out.println(" >>>> IS rdfs, fixing... ");
						if ( isToLog )
						{
							logWriter.write( "  - RDFS vocabulary detected instead of owl.  Attempting to fix and reanalyze...");
							logWriter.newLine();
							logWriter.flush();
						}
						oa = analyze( model, new URI(line), true );
					}
					StatsPrinter.printToFileTabDelim( writer, oa.getBasicStats(), oa.getToldStats(), oa.getPelletStats() );
					long stopTime = System.currentTimeMillis();
					double runTime = (stopTime - startTime)/1000;
					analyzedOntologies++;
					if ( isToLog )
					{
						logWriter.write( "  Successful.  Took " + runTime + " seconds.");
						logWriter.newLine();
					}

				}
				catch ( URISyntaxException e )
				{
					e.printStackTrace();
					String trace = Utils.getExceptionTrace( e );
					exceptionedOntologies++;
					writer.newLine(); // write new line so output lines up with input
					if ( isToLog )
					{
						logWriter.write( trace );
						logWriter.newLine();
					}
				}
				catch ( AnalysisException e )
				{
					e.printStackTrace();
					String trace = Utils.getExceptionTrace( e );
					exceptionedOntologies++;
					writer.newLine(); // write new line so output lines up with input
					if ( isToLog )
					{
						logWriter.write( trace );
						logWriter.newLine();
						logWriter.write( " - Caused by " + e.toString() );
						logWriter.newLine();
					}
				}
				finally
				{
					// clean up workspace
					// increment count
					if (isToLog)
					{
						logWriter.newLine();
						logWriter.flush();
					}
					model.getFrame().clearWorkspace( false ); // false for "No popup confirmation"
					count++;
				}
			}
			
			if ( isToLog )
			{
				logWriter.write("Analyzed Ontologies: " + analyzedOntologies );
				logWriter.newLine();
				logWriter.write("Exceptioned Ontologies: " + exceptionedOntologies );
				logWriter.newLine();
				logWriter.write("Skipped Ontologies: " + skippedOntologies );
				logWriter.newLine();
				logWriter.flush();
			}
		} 
		catch ( IOException e ) 
		{
			e.printStackTrace();
			System.err.println("Unrecoverable IOException... halting. ");
			if ( IS_DEBUG )
				System.out.println(" * OntologyAnalyzer: Could not load ontology " + line );
		}
		return analyses;
	}	
	
	
	public OntologyAnalysis analyze( AutomatedSwoopModel model, URI ontURI ) throws AnalysisException
	{ return analyze( model, ontURI, false); }
	
	public OntologyAnalysis analyze( AutomatedSwoopModel model, URI ontURI, boolean isRDFS ) throws AnalysisException
	{
		TermsDisplay display = model.getFrame().termDisplay;
        OWLOntology ont = null;
		try
		{		
			ont = model.loadOntology( ontURI );
			model.setReasonerWithThreadBlock( new SwoopToldReasoner() );
			model.setSelectedOntology( ont );
			model.setShowImportsWithThreadBlock( true );
			
			if ( isRDFS ) // RDFS, we fix the ont by serializing it to OWL, and reload it to the model
			{