Mercurial > repos > mikel-egana-aranguren > oppl

annotate OPPL/src/OPPLGalaxy.java @ 17:c9e01f86b07c draft

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New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 20 Aug 2012 11:39:56 +0200
parents 7e6604a5ee55
children d3616fac4ca5
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1 /**
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2 *
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3 */
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4 package es.upm.fi.dia.oeg.oppl.galaxy;
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5
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6 import java.io.File;
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7 import java.io.IOException;
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8 import java.util.List;
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9 import java.util.Scanner;
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10 import java.util.logging.Logger;
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12 import org.coode.oppl.ChangeExtractor;
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13 import org.coode.oppl.OPPLParser;
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14 import org.coode.oppl.OPPLScript;
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15 import org.coode.oppl.ParserFactory;
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16 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
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17 import org.coode.parsers.ErrorListener;
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18 import org.coode.parsers.LoggerErrorListener;
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19 import org.semanticweb.owlapi.model.OWLAxiomChange;
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20 import org.semanticweb.owlapi.model.OWLOntology;
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21 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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22 import org.semanticweb.owlapi.model.OWLOntologyManager;
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23 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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24 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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28 /**
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29 * @author Mikel Egaña Aranguren
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30 *
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31 */
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32 public class OPPLGalaxy {
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33
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34 /**
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35 * @param args
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36 * @throws OWLOntologyCreationException
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37 * @throws OWLOntologyStorageException
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38 * @throws IOException
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39 */
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40 public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
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41 // Get the arguments from command-line
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42 String OWLFilePath = args [0];
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43 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
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45 String OPPL_script_file = args [2];
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46 String OWL = args [3]; // OWL|OBO
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47
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48 // Create the manager
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49 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
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50
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51 // Load the main ontology and hope for the imported URIs to be resolvable
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52 galaxyowlapi.loadMainOntology(OWLFilePath);
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54 // Set the reasoner
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56 // Pellet
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57 if(reasoner_type.equals("Pellet")){
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58 galaxyowlapi.setReasonerPellet();
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59 }
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60 // FaCTPlusPlus
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61 else if (reasoner_type.equals("FaCTPlusPlus")){
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62 galaxyowlapi.setReasonerFaCT();
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63 }
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64 // HermiT
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65 else{
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66 galaxyowlapi.setReasonerHermit();
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67 }
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69 // Load the OPPL flat file with script in memory
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70 String OPPL_script_source = "";
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71 File file = new File(OPPL_script_file);
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72 Scanner input = new Scanner(file);
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73 while(input.hasNext()) {
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74 String nextToken = input.next();
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75 OPPL_script_source = OPPL_script_source + " " + nextToken;
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76 }
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77 input.close();
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78
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79 OWLOntologyManager manager = galaxyowlapi.getOWLManager();
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80 OWLOntology ontology = galaxyowlapi.getMainOntology();
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81 OWLReasoner reasoner = galaxyowlapi.getReasoner();
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83 // Parse the OPPL script
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84 ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner);
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85 Logger logger = Logger.getLogger(OPPLGalaxy.class.getName());
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86 // Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
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87 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
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88 OPPLParser opplparser = parserFactory.build(errorListener);
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89 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
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91
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93 // Execute the script
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94 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
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95 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
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96 manager.applyChanges(changes);
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97
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98 // Merge imported ontologies if requested
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99 // if(merge.equals("Merge")){
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100 // galaxyowlapi.merge();
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101 // }
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102
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103 // Save the ontology
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104 if(OWL.equals("OWL")){
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105 galaxyowlapi.saveOntology(true);
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106 }
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107 else{
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108 galaxyowlapi.saveOntology(false);
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109 }
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110 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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