Mercurial > repos > mikel-egana-aranguren > oppl

comparison src/OWLQueryGalaxy.java @ 19:cc270db37d33 draft

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author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 06 Oct 2012 21:50:39 +0200
parents OPPL/src/OWLQueryGalaxy.java@d3616fac4ca5
children
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18:d3616fac4ca5 19:cc270db37d33
1 package es.upm.fi.dia.oeg.oppl.galaxy;
2
3 import java.util.Set;
4
5 import org.semanticweb.owlapi.expression.ParserException;
6 import org.semanticweb.owlapi.model.IRI;
7 import org.semanticweb.owlapi.model.OWLClass;
8 import org.semanticweb.owlapi.model.OWLClassExpression;
9 import org.semanticweb.owlapi.model.OWLNamedIndividual;
10 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
11
12 public class OWLQueryGalaxy {
13
14 /**
15 * @param args
16 * @throws OWLOntologyCreationException
17 * @throws ParserException
18 */
19 public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
20 // Get the arguments from command-line
21 String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
22 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk
23
24 String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
25 String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
26 String MOS_query = args [4]; // GO_0007049 or part_of some GO_0007049
27
28 // Create the manager
29 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
30
31 // Load the main ontology and hope for the imported URIs to be resolvable
32 galaxyowlapi.loadMainOntology(OWLFilePath);
33
34 // Set the reasoner
35
36 // Pellet
37 if(reasoner_type.equals("Pellet")){
38 galaxyowlapi.setReasonerPellet();
39 }
40 // FaCTPlusPlus
41 else if (reasoner_type.equals("FaCTPlusPlus")){
42 galaxyowlapi.setReasonerFaCT();
43 }
44 // Elk
45 else if (reasoner_type.equals("Elk")){
46 galaxyowlapi.setReasonerElk();
47 }
48 // HermiT
49 else{
50 galaxyowlapi.setReasonerHermit();
51 }
52
53 // Parse the expression to an OWLexpression
54 OWLClassExpression class_expr = galaxyowlapi.parseMOSClassExpression(MOS_query);
55
56 // Execute query and print results
57 if(Answer_type.equals("Individuals")){
58 Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
59 galaxyowlapi.disposeReasoner();
60 for(OWLNamedIndividual ind : inds){
61 print_result_entity(ind.getIRI(), Answer_render);
62 }
63 }
64 else if (Answer_type.equals("EquivalentClasses")) {
65 Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
66 galaxyowlapi.disposeReasoner();
67 for(OWLClass cls : answer_classes){
68 print_result_entity(cls.getIRI(), Answer_render);
69 }
70 }
71 else if (Answer_type.equals("DirectSuperClasses")) {
72 Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
73 galaxyowlapi.disposeReasoner();
74 for(OWLClass cls : answer_classes){
75 print_result_entity(cls.getIRI(), Answer_render);
76 }
77 }
78 else if (Answer_type.equals("Ancestors")) {
79 Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
80 galaxyowlapi.disposeReasoner();
81 for(OWLClass cls : answer_classes){
82 print_result_entity(cls.getIRI(), Answer_render);
83 }
84 }
85 else if (Answer_type.equals("DirectSubClasses")) {
86 Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
87 galaxyowlapi.disposeReasoner();
88 for(OWLClass cls : answer_classes){
89 print_result_entity(cls.getIRI(), Answer_render);
90 }
91 }
92 // Descendants
93 else {
94 Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
95 galaxyowlapi.disposeReasoner();
96 for(OWLClass cls : answer_classes){
97 print_result_entity(cls.getIRI(), Answer_render);
98 }
99 }
100 }
101
102 //URI|URIfragment|URIfragment2OBO
103 private static void print_result_entity (IRI iri, String Answer_render){
104 if(Answer_render.equals("URI")){
105 System.out.println(iri);
106 }
107
108 // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't!
109 // done manually
110 else if(Answer_render.equals("URIfragment")){
111 if(iri.toString().contains("#")){
112 System.out.println(iri.getFragment());
113 }
114 else{
115 String [] iri_tokens = iri.toString().split("/");
116 System.out.println(iri_tokens[iri_tokens.length-1]);
117 }
118 }
119 else{
120 if(iri.toString().contains("#")){
121 System.out.println((iri.getFragment()).replace("_", ":"));
122 }
123 else{
124 String [] iri_tokens = iri.toString().split("/");
125 System.out.println((iri_tokens[iri_tokens.length-1]).replace("_", ":"));
126 }
127 }
128 }
129 }