Mercurial > repos > mikel-egana-aranguren > oppl

comparison OPPL/src/OPPLGalaxy.java @ 11:6ca67b155e32

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Imports simplified, new tool for inference added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Fri, 09 Mar 2012 16:15:27 +0100
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children 7e6604a5ee55
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10:3f31c0eb7539 11:6ca67b155e32
1 /**
2 *
3 */
4 package es.upm.fi.dia.oeg.oppl.galaxy;
5
6 import java.io.File;
7 import java.io.IOException;
8 import java.util.List;
9 import java.util.Scanner;
10 import java.util.logging.Logger;
11
12 import org.coode.oppl.ChangeExtractor;
13 import org.coode.oppl.OPPLParser;
14 import org.coode.oppl.OPPLScript;
15 import org.coode.oppl.ParserFactory;
16 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
17 import org.coode.parsers.ErrorListener;
18 import org.coode.parsers.LoggerErrorListener;
19 import org.semanticweb.owlapi.model.OWLAxiomChange;
20 import org.semanticweb.owlapi.model.OWLOntology;
21 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
22 import org.semanticweb.owlapi.model.OWLOntologyManager;
23 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
24 import org.semanticweb.owlapi.reasoner.OWLReasoner;
25
26
27 /**
28 * @author Mikel Egaña Aranguren
29 *
30 */
31 public class OPPLGalaxy {
32
33 /**
34 * @param args
35 * @throws OWLOntologyCreationException
36 * @throws OWLOntologyStorageException
37 * @throws IOException
38 */
39 public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
40 // Get the arguments from command-line
41 String OWLFilePath = args [0];
42 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
43
44 String OPPL_script_file = args [2];
45 String OWL = args [3]; // OWL|OBO
46
47 // Create the manager
48 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
49
50 // Load the main ontology and hope for the imported URIs to be resolvable
51 galaxyowlapi.loadMainOntology(OWLFilePath);
52
53 // Set the reasoner
54
55 // Pellet
56 if(reasoner_type.equals("Pellet")){
57 galaxyowlapi.setReasonerPellet();
58 }
59 // FaCTPlusPlus
60 else if (reasoner_type.equals("FaCTPlusPlus")){
61 galaxyowlapi.setReasonerFaCT();
62 }
63 // HermiT
64 else{
65 galaxyowlapi.setReasonerHermit();
66 }
67
68 // Load the OPPL flat file with script in memory
69 String OPPL_script_source = "";
70 File file = new File(OPPL_script_file);
71 Scanner input = new Scanner(file);
72 while(input.hasNext()) {
73 String nextToken = input.next();
74 OPPL_script_source = OPPL_script_source + " " + nextToken;
75 }
76 input.close();
77
78 OWLOntologyManager manager = galaxyowlapi.getOWLManager();
79 OWLOntology ontology = galaxyowlapi.getMainOntology();
80 OWLReasoner reasoner = galaxyowlapi.getReasoner();
81
82 // Parse the OPPL script
83 ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner);
84 Logger logger = Logger.getLogger(Tool.class.getName());
85 // Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
86 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
87 OPPLParser opplparser = parserFactory.build(errorListener);
88 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
89
90 // Execute the script
91 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
92 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
93 manager.applyChanges(changes);
94
95 // Merge imported ontologies if requested
96 // if(merge.equals("Merge")){
97 // galaxyowlapi.merge();
98 // }
99
100 // Save the ontology
101 if(OWL.equals("OWL")){
102 galaxyowlapi.saveOntology(true);
103 }
104 else{
105 galaxyowlapi.saveOntology(false);
106 }
107 }
108 }