Mercurial > repos > mikel-egana-aranguren > oppl

annotate src/OPPLGalaxy.java @ 21:ffde1fafa066 draft

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README corrected with proper installation instructions for mercurial (hg pull + hg update)
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 13:10:44 +0200
parents cc270db37d33
children
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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.Level;
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11 import java.util.logging.Logger;
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12
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13 //import org.apache.log4j.Level;
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14 import org.coode.oppl.ChangeExtractor;
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15 import org.coode.oppl.OPPLParser;
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16 import org.coode.oppl.OPPLScript;
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17 import org.coode.oppl.ParserFactory;
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18 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
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19 import org.coode.oppl.log.Logging;
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20 import org.coode.parsers.ErrorListener;
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21 import org.coode.parsers.LoggerErrorListener;
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22 import org.semanticweb.owlapi.model.OWLAxiomChange;
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23 import org.semanticweb.owlapi.model.OWLOntology;
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24 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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25 import org.semanticweb.owlapi.model.OWLOntologyManager;
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26 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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27 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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32 /**
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33 * @author Mikel Ega��a Aranguren
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34 *
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35 */
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36 public class OPPLGalaxy {
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38 /**
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39 * @param args
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40 * @throws OWLOntologyCreationException
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41 * @throws OWLOntologyStorageException
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42 * @throws IOException
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43 */
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44 public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
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45 // Get the arguments from command-line
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46 String OWLFilePath = args [0];
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47 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|Elk|HermiT
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48
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49 String OPPL_script_file = args [2];
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50 String OWL = args [3]; // OWL|OBO
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51
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52 // Create the manager
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53 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
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54
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55 // Load the main ontology and hope for the imported URIs to be resolvable
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56 galaxyowlapi.loadMainOntology(OWLFilePath);
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58 // Set the reasoner
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60 // Pellet
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61 if(reasoner_type.equals("Pellet")){
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62 galaxyowlapi.setReasonerPellet();
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63 }
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64 // FaCTPlusPlus
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65 else if (reasoner_type.equals("FaCTPlusPlus")){
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66 galaxyowlapi.setReasonerFaCT();
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67 }
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68 // Elk
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69 else if (reasoner_type.equals("Elk")){
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70 galaxyowlapi.setReasonerElk();
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71 }
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72 // HermiT
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73 else{
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74 galaxyowlapi.setReasonerHermit();
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75 }
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77 // Load the OPPL flat file with script in memory
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78 String OPPL_script_source = "";
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79 File file = new File(OPPL_script_file);
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80 Scanner input = new Scanner(file);
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81 while(input.hasNext()) {
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82 String nextToken = input.next();
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83 OPPL_script_source = OPPL_script_source + " " + nextToken;
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84 }
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85 input.close();
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86
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87 OWLOntologyManager manager = galaxyowlapi.getOWLManager();
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88 OWLOntology ontology = galaxyowlapi.getMainOntology();
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89 OWLReasoner reasoner = galaxyowlapi.getReasoner();
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90
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91 // Parse the OPPL script
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92 ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner);
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93 Logger logger = Logger.getLogger(OPPLGalaxy.class.getName());
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94 // logger.setLevel(Level.OFF);
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95 // Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
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96
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97 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
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98 OPPLParser opplparser = parserFactory.build(errorListener);
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99 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
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100
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101 // Execute the script
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102 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
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103 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
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104 manager.applyChanges(changes);
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105
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106 galaxyowlapi.disposeReasoner();
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107
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108 // Merge imported ontologies if requested
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109 // if(merge.equals("Merge")){
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110 // galaxyowlapi.merge();
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111 // }
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112
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113 // Save the ontology
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114 if(OWL.equals("OWL")){
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115 galaxyowlapi.saveOntology(true);
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116 }
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117 else{
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118 galaxyowlapi.saveOntology(false);
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119 }
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120 }
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121 }