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annotate OPPL/src/OPPLQueryGalaxy.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 6c25e717c896
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.cbgp.opplquery.oppl.galaxy;
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5
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6 import java.io.File;
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7 import java.io.FileNotFoundException;
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8 import java.util.Iterator;
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9 import java.util.Scanner;
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10 import java.util.Set;
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11 import java.util.logging.Logger;
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12 import java.util.regex.Matcher;
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13 import java.util.regex.Pattern;
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15 import org.semanticweb.owlapi.expression.ParserException;
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16 import org.semanticweb.owlapi.model.IRI;
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17 import org.semanticweb.owlapi.model.OWLObject;
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18 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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20 import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI;
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22 import org.coode.oppl.ChangeExtractor;
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23 import org.coode.oppl.ConstraintSystem;
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24 import org.coode.oppl.OPPLParser;
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25 import org.coode.oppl.OPPLScript;
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26 import org.coode.oppl.ParserFactory;
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27 import org.coode.parsers.ErrorListener;
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28 import org.coode.parsers.LoggerErrorListener;
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29 import org.coode.oppl.bindingtree.Assignment;
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30 import org.coode.oppl.bindingtree.BindingNode;
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31 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
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32 import org.coode.oppl.exceptions.RuntimeExceptionHandler;
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34 public class OPPLQueryGalaxy {
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35
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36 /**
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37 * @param args
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38 * @throws OWLOntologyCreationException
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39 * @throws ParserException
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40 * @throws FileNotFoundException
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41 */
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42 public static void main(String[] args) throws OWLOntologyCreationException, ParserException, FileNotFoundException {
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43 // Get the arguments from command-line
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44 String OWLFilePath = args [0]; // /home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/single/test.owl
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45 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
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46 String Answer_render = args [2]; // URI|URIfragment|URIfragment2OBO
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47 String OPPL_script_source = args [3];
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49 // String OPPL_script_file = args [3];
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50 // File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query.oppl");
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51 // File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl");
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52 // File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl");
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53
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54 // String OPPL_script_source = "";
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55 // Scanner input = new Scanner(OPPL_script_file);
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56 // while(input.hasNext()) {
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57 // String nextToken = input.next();
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58 // OPPL_script_source = OPPL_script_source + " " + nextToken;
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59 // }
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60 // input.close();
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61
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62 // Create the manager
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63 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
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64
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65 // Load the main ontology and hope for the imported URIs to be resolvable
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66 galaxyowlapi.loadMainOntology(OWLFilePath);
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67
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68 // Set the reasoner
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69
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70 // Pellet
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71 if(reasoner_type.equals("Pellet")){
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72 galaxyowlapi.setReasonerPellet();
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73 }
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74 // FaCTPlusPlus
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75 else if (reasoner_type.equals("FaCTPlusPlus")){
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76 galaxyowlapi.setReasonerFaCT();
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77 }
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78 // HermiT
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79 else{
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80 galaxyowlapi.setReasonerHermit();
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81 }
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82
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83 OPPL_script_source = completeOPPLScript(OPPL_script_source);
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84 // System.out.println(OPPL_script_source);
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85
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86 ParserFactory parserFactory = new ParserFactory(galaxyowlapi.getOWLManager(), galaxyowlapi.getMainOntology(), galaxyowlapi.getReasoner());
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87 Logger logger = Logger.getLogger(OPPLQueryGalaxy.class.getName());
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88 ErrorListener errorListener = (ErrorListener) new LoggerErrorListener(logger);
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89 OPPLParser opplparser = parserFactory.build(errorListener);
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90 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
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91 RuntimeExceptionHandler exceptionhandler = new QuickFailRuntimeExceptionHandler();
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92 ChangeExtractor extractor = new ChangeExtractor(exceptionhandler, true);
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93 extractor.visit(OPPLscript);
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94 ConstraintSystem cs = OPPLscript.getConstraintSystem();
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95 Set<BindingNode> nodes = cs.getLeaves();
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96
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97 Iterator NodesIterator = nodes.iterator();
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98 while(NodesIterator.hasNext()){
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99 Set Assignments = ((BindingNode)NodesIterator.next()).getAssignments();
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100 Iterator AssignmentIterator = Assignments.iterator();
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101 while(AssignmentIterator.hasNext()){
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102 Assignment assignment = (Assignment)AssignmentIterator.next();
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103 System.out.print(assignment.getAssignedVariable().toString());
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104 System.out.print("\t");
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105 String OWLObjectString = ((OWLObject)assignment.getAssignment()).toString();
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106 IRI entityIRI = IRI.create(OWLObjectString.substring(1,OWLObjectString.length()-1));
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107 print_result_entity(entityIRI, Answer_render);
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108 System.out.print("\n");
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109 }
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110 }
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111 }
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112
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113 //URI|URIfragment|URIfragment2OBO
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114 private static void print_result_entity (IRI iri, String Answer_render){
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115 if(Answer_render.equals("URI")){
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116 System.out.print(iri);
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117 }
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118
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119 // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't!
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120 // done manually
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121 else if(Answer_render.equals("URIfragment")){
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122 if(iri.toString().contains("#")){
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123 System.out.print(iri.getFragment());
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124 }
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125 else{
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126 String [] iri_tokens = iri.toString().split("/");
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127 System.out.print(iri_tokens[iri_tokens.length-1]);
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128 }
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129 }
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130 else{
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131 if(iri.toString().contains("#")){
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132 System.out.print((iri.getFragment()).replace("_", ":"));
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133 }
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134 else{
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135 String [] iri_tokens = iri.toString().split("/");
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136 System.out.print((iri_tokens[iri_tokens.length-1]).replace("_", ":"));
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137 }
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138 }
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139 }
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140
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141 // Very crappy stuff: complete the query to make a whole OPPL script that can be parsed
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142 private static String completeOPPLScript (String OPPLQuery){
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143
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144 // Get the first variable and add at least an axiom to make a whole script
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145 Pattern p = Pattern.compile("(\\?\\w+):(CLASS|INDIVIDUAL|OBJECTPROPERTY|DATAPROPERTY|ANNOTATIONPROPERTY|CONSTANT)");
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146 Matcher m = p.matcher(OPPLQuery);
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147 m.find();
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148 if (m.group(2).equals("CLASS")){
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149 OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " SubClassOf !A END;";
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150 }
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151 else if (m.group(2).equals("INDIVIDUAL")){
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152 OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " !p !b END;";
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153 }
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154 else if (m.group(2).equals("OBJECTPROPERTY")){
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155 OPPLQuery = OPPLQuery + " BEGIN ADD Transitive ?p END;";
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156 }
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157 // else if (m.group(2).equals("DATAPROPERTY")){
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158 // OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;";
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159 // }
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160 // else if (m.group(2).equals("ANNOTATIONPROPERTY")){
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161 // OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;";
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162 // }
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163 // else if (m.group(2).equals("CONSTANT")){
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164 // OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;";
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165 // }
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166 else{
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167 OPPLQuery = "Malformed OPPL query";
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168 }
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169 return OPPLQuery;
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170 }
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171 }