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annotate OPPL/Tool.java @ 5:68935f90c2db

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Added OWL imports closure
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 17 Sep 2011 13:41:28 +0200
parents 4f60202c58d9
children 3740505b579c
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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.ArrayList;
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29 import java.util.List;
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30 import java.util.Scanner;
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31 import java.util.logging.Level;
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32 import java.util.logging.Logger;
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33
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34 import org.coode.oppl.ChangeExtractor;
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35 import org.coode.oppl.OPPLParser;
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36 import org.coode.oppl.OPPLScript;
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37 import org.coode.oppl.ParserFactory;
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38 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
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39 import org.coode.oppl.log.Logging;
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40 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
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41 import org.coode.parsers.ErrorListener;
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42 import org.coode.parsers.LoggerErrorListener;
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43 import org.semanticweb.owlapi.apibinding.OWLManager;
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44 import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
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45 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
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46 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
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47 import org.semanticweb.owlapi.model.IRI;
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48 import org.semanticweb.owlapi.model.OWLAxiom;
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49 import org.semanticweb.owlapi.model.OWLAxiomChange;
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50 import org.semanticweb.owlapi.model.OWLDataFactory;
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51 import org.semanticweb.owlapi.model.OWLOntology;
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52 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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53 import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
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54 import org.semanticweb.owlapi.model.OWLOntologyManager;
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55 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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56 import org.semanticweb.owlapi.reasoner.InferenceType;
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57 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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58 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
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59 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
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60 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
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61 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
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62 import org.semanticweb.owlapi.util.SimpleIRIMapper;
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64 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
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65
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66 /**
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67 * @author Mikel Egaña Aranguren
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68 */
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69 public class Tool {
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70
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71 /**
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72 * @throws FileNotFoundException
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73 * @throws OWLOntologyCreationException
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74 * @throws OWLOntologyStorageException
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75 */
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76 public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
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77 // Get the arguments from command-line
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78 String OWLFilePath = args [0];
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79 String OPPL_script_file = args [1];
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80 String Output_format = args [2]; // OWL|OBO
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81 String Add_inferred = args [3]; // Add_inferred|Whatever
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82 String imports_file_path = args [4]; // Flat tab delimited file: URI Document URI
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83
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84 // Load the main ontology
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85 File owl_file = new File(OWLFilePath);
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86 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
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87
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88 // Load the imports if any
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89 if(!imports_file_path.equals("NoImports")){
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90 File imports_file = new File(imports_file_path);
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91 Scanner imports_input = new Scanner(imports_file);
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92 while(imports_input.hasNext()){
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93 String nextLine = imports_input.nextLine();
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94 if(!nextLine.startsWith("#")){
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95 String [] URI_documentURI = nextLine.split("\t");
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96 // System.out.println(URI_documentURI[0]);
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97 // System.out.println(URI_documentURI[1]);
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98 // IRI ontology_IRI = IRI.create("http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology");
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99 // IRI document_IRI = IRI.create("file://" + "/home/pik/UPM/OPPL_galaxy/SWAT4LS_2011/GONG/chebi.owl");
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100 IRI ontology_IRI = IRI.create(URI_documentURI[0]);
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101 IRI document_IRI = IRI.create("file://" + URI_documentURI[1]);
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102 OWLOntologyIRIMapper iriMapper = new SimpleIRIMapper(ontology_IRI,document_IRI);
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103 manager.addIRIMapper(iriMapper);
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104 }
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105 }
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106 imports_input.close();
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107 }
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108 OWLDataFactory factory = manager.getOWLDataFactory();
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109 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
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110
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111 // Reasoner
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112 OWLReasonerFactory reasonerFactory = new PelletReasonerFactory();
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113 OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
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114 reasoner.isConsistent();
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115
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116 // Load the flat file with script in memory
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117 String OPPL_script_source = "";
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118 File file = new File(OPPL_script_file);
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119 Scanner input = new Scanner(file);
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120 while(input.hasNext()) {
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121 String nextToken = input.next();
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122 OPPL_script_source = OPPL_script_source + " " + nextToken;
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123 }
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124 input.close();
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125
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126 // Parse the OPPL script
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127 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner);
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128 Logger logger = Logger.getLogger(Tool.class.getName());
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129 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy
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130 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
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131 OPPLParser opplparser = parserFactory.build(errorListener);
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132 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
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133
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134 // Execute the script
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135 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
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136 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
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137 manager.applyChanges(changes);
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138
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139 // Add the inferred axioms as asserted axioms to the original ontology
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140 if(Add_inferred.equals("Add_inferred")){
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141 reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
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142 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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143 gens.add(new InferredSubClassAxiomGenerator());
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144 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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145 iog.fillOntology(manager, OWL_ontology);
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146 }
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147
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148 // Print the ontology to the standard output so other galaxy tools can operate on the output
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149 OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
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150 if(Output_format.equals("OBO")){
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151 manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
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152 }
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153 else{
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154 manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
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155 }
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156 }
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157 }