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annotate src/OWLQueryGalaxy.java @ 22:8d4bbaa99b4a draft

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Minor changes for JBS paper
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sun, 14 Oct 2012 17:21:51 +0200
parents cc270db37d33
children
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1 package es.upm.fi.dia.oeg.oppl.galaxy;
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2
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3 import java.util.Set;
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4
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5 import org.semanticweb.owlapi.expression.ParserException;
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6 import org.semanticweb.owlapi.model.IRI;
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7 import org.semanticweb.owlapi.model.OWLClass;
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8 import org.semanticweb.owlapi.model.OWLClassExpression;
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9 import org.semanticweb.owlapi.model.OWLNamedIndividual;
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10 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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12 public class OWLQueryGalaxy {
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14 /**
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15 * @param args
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16 * @throws OWLOntologyCreationException
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17 * @throws ParserException
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18 */
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19 public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
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20 // Get the arguments from command-line
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21 String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
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22 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk
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24 String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
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25 String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
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26 String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049
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27
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28 // Create the manager
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29 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
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30
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31 // Load the main ontology and hope for the imported URIs to be resolvable
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32 galaxyowlapi.loadMainOntology(OWLFilePath);
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33
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34 // Set the reasoner
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35
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36 // Pellet
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37 if(reasoner_type.equals("Pellet")){
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38 galaxyowlapi.setReasonerPellet();
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39 }
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40 // FaCTPlusPlus
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41 else if (reasoner_type.equals("FaCTPlusPlus")){
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42 galaxyowlapi.setReasonerFaCT();
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43 }
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44 // Elk
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45 else if (reasoner_type.equals("Elk")){
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46 galaxyowlapi.setReasonerElk();
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47 }
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48 // HermiT
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49 else{
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50 galaxyowlapi.setReasonerHermit();
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51 }
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52
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53 // Parse the expression to an OWLexpression
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54 OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query);
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55
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56 // Execute query and print results
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57 if(Answer_type.equals("Individuals")){
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58 Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
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59 galaxyowlapi.disposeReasoner();
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60 for(OWLNamedIndividual ind : inds){
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61 print_result_entity(ind.getIRI(), Answer_render);
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62 }
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63 }
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64 else if (Answer_type.equals("EquivalentClasses")) {
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65 Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
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66 galaxyowlapi.disposeReasoner();
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67 for(OWLClass cls : answer_classes){
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68 print_result_entity(cls.getIRI(), Answer_render);
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69 }
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70 }
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71 else if (Answer_type.equals("DirectSuperClasses")) {
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72 Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
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73 galaxyowlapi.disposeReasoner();
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74 for(OWLClass cls : answer_classes){
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75 print_result_entity(cls.getIRI(), Answer_render);
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76 }
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77 }
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78 else if (Answer_type.equals("Ancestors")) {
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79 Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
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80 galaxyowlapi.disposeReasoner();
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81 for(OWLClass cls : answer_classes){
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82 print_result_entity(cls.getIRI(), Answer_render);
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83 }
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84 }
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85 else if (Answer_type.equals("DirectSubClasses")) {
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86 Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
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87 galaxyowlapi.disposeReasoner();
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88 for(OWLClass cls : answer_classes){
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89 print_result_entity(cls.getIRI(), Answer_render);
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90 }
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91 }
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92 // Descendants
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93 else {
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94 Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
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95 galaxyowlapi.disposeReasoner();
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96 for(OWLClass cls : answer_classes){
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97 print_result_entity(cls.getIRI(), Answer_render);
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98 }
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99 }
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100 }
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101
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102 //URI|URIfragment|URIfragment2OBO
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103 private static void print_result_entity (IRI iri, String Answer_render){
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104 if(Answer_render.equals("URI")){
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105 System.out.println(iri);
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106 }
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107
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108 // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't!
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109 // done manually
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110 else if(Answer_render.equals("URIfragment")){
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111 if(iri.toString().contains("#")){
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112 System.out.println(iri.getFragment());
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113 }
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114 else{
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
115 String [] iri_tokens = iri.toString().split("/");
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
116 System.out.println(iri_tokens[iri_tokens.length-1]);
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
117 }
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
118 }
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
119 else{
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
120 if(iri.toString().contains("#")){
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
121 System.out.println((iri.getFragment()).replace("_", ":"));
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
122 }
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
123 else{
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
124 String [] iri_tokens = iri.toString().split("/");
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
125 System.out.println((iri_tokens[iri_tokens.length-1]).replace("_", ":"));
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
126 }
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
127 }
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
128 }
7e6604a5ee55 New query tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
129 }