Mercurial > repos > mikel-egana-aranguren > oppl

annotate OPPL/Tool.java @ 3:5255f1333cc4

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Version 1.0.1 Added output choice: OBO or OWL(RDF/XML)
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Wed, 07 Sep 2011 10:46:29 +0200
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children 4f60202c58d9
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3
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1 /**
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2 * Copyright (C) 2011, Mikel Egaña Aranguren
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3 *
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4 * This program is free software: you can redistribute it and/or modify
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5 * it under the terms of the GNU General Public License as published by
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6 * the Free Software Foundation, either version 3 of the License, or
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7 * (at your option) any later version.
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8 *
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9 * This program is distributed in the hope that it will be useful,
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10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 * GNU General Public License for more details.
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13 *
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14 * You should have received a copy of the GNU General Public License
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15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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16 */
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17
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18 package es.upm.fi.dia.oeg.oppl.galaxy;
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19
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20 import java.io.BufferedOutputStream;
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21 import java.io.BufferedWriter;
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22 import java.io.File;
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23 import java.io.FileNotFoundException;
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24 import java.io.FilterOutputStream;
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25 import java.io.OutputStream;
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26 import java.io.PipedOutputStream;
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27 import java.io.PrintStream;
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28 import java.util.List;
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29 import java.util.Scanner;
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30 import java.util.logging.Level;
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31 import java.util.logging.Logger;
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32
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33 import org.coode.oppl.ChangeExtractor;
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34 import org.coode.oppl.OPPLParser;
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35 import org.coode.oppl.OPPLScript;
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36 import org.coode.oppl.ParserFactory;
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37 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
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38 import org.coode.oppl.log.Logging;
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39 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
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40 import org.coode.parsers.ErrorListener;
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41 import org.coode.parsers.LoggerErrorListener;
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42 import org.semanticweb.owlapi.apibinding.OWLManager;
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43 import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
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44 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
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45 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
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46 import org.semanticweb.owlapi.model.IRI;
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47 import org.semanticweb.owlapi.model.OWLAxiomChange;
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48 import org.semanticweb.owlapi.model.OWLOntology;
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49 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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50 import org.semanticweb.owlapi.model.OWLOntologyManager;
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51 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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52 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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53 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
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54
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55 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
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56
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57
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58 /**
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59 * @author Mikel Egaña Aranguren
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60 *
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61 */
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62 public class Tool {
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63
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64 /**
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65 * @param OWL file
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66 * @param OPPL script
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67 * @throws FileNotFoundException
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68 * @throws OWLOntologyCreationException
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69 * @throws OWLOntologyStorageException
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70 */
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71 public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
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72
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73 // Get the arguments from command-line
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74 String OWLFilePath = args [0];
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75 String OPPL_script_file = args [1];
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76 String Output_format = args [2];
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77 String OPPL_script_source = "";
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78
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79 // Load the flat file with script in memory
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80 File file = new File(OPPL_script_file);
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81 Scanner input = new Scanner(file);
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82 while(input.hasNext()) {
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83 String nextToken = input.next();
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84 OPPL_script_source = OPPL_script_source + " " + nextToken;
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85 }
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86 input.close();
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87
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88 // Load the OWL ontology
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89 File owl_file = new File(OWLFilePath);
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90 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
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91 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
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92
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93 // Sync reasoner and check consistency
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94 OWLReasonerFactory reasonerFactory = new PelletReasonerFactory();
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95 OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
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96
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97 // Parse the OPPL script
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98 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner);
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99 Logger logger = Logger.getLogger(Tool.class.getName());
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100 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy
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101 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
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102 OPPLParser opplparser = parserFactory.build(errorListener);
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103 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
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104
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105 // Execute the script
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106 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
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107 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
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108 manager.applyChanges(changes);
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109
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110 // Print the ontology to the standard output so other galaxy tools can operate on the output
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111 OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
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112
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113 if(Output_format.equals("OBO")){
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parents:
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114 manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
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115 }
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parents:
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116 else{
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parents:
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117 manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
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118 }
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parents:
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119
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parents:
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120 }
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parents:
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121 }