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annotate OPPL/src/OPPLGalaxy.java @ 11:6ca67b155e32

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Imports simplified, new tool for inference added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Fri, 09 Mar 2012 16:15:27 +0100
parents
children 7e6604a5ee55
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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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11
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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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25
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26
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27 /**
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28 * @author Mikel Egaña Aranguren
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29 *
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30 */
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31 public class OPPLGalaxy {
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32
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33 /**
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34 * @param args
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35 * @throws OWLOntologyCreationException
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36 * @throws OWLOntologyStorageException
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37 * @throws IOException
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38 */
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39 public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
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40 // Get the arguments from command-line
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41 String OWLFilePath = args [0];
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42 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
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43
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44 String OPPL_script_file = args [2];
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45 String OWL = args [3]; // OWL|OBO
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46
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47 // Create the manager
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48 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
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49
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50 // Load the main ontology and hope for the imported URIs to be resolvable
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51 galaxyowlapi.loadMainOntology(OWLFilePath);
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52
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53 // Set the reasoner
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54
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55 // Pellet
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56 if(reasoner_type.equals("Pellet")){
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57 galaxyowlapi.setReasonerPellet();
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58 }
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59 // FaCTPlusPlus
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60 else if (reasoner_type.equals("FaCTPlusPlus")){
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61 galaxyowlapi.setReasonerFaCT();
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62 }
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63 // HermiT
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64 else{
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65 galaxyowlapi.setReasonerHermit();
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66 }
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67
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68 // Load the OPPL flat file with script in memory
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69 String OPPL_script_source = "";
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70 File file = new File(OPPL_script_file);
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71 Scanner input = new Scanner(file);
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72 while(input.hasNext()) {
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73 String nextToken = input.next();
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74 OPPL_script_source = OPPL_script_source + " " + nextToken;
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75 }
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76 input.close();
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77
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78 OWLOntologyManager manager = galaxyowlapi.getOWLManager();
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79 OWLOntology ontology = galaxyowlapi.getMainOntology();
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80 OWLReasoner reasoner = galaxyowlapi.getReasoner();
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81
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82 // Parse the OPPL script
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83 ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner);
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84 Logger logger = Logger.getLogger(Tool.class.getName());
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85 // Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
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86 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
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87 OPPLParser opplparser = parserFactory.build(errorListener);
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88 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
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89
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90 // Execute the script
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91 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
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92 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
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93 manager.applyChanges(changes);
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94
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95 // Merge imported ontologies if requested
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96 // if(merge.equals("Merge")){
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97 // galaxyowlapi.merge();
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98 // }
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99
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100 // Save the ontology
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101 if(OWL.equals("OWL")){
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102 galaxyowlapi.saveOntology(true);
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103 }
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104 else{
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105 galaxyowlapi.saveOntology(false);
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106 }
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107 }
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108 }