Mercurial > repos > mikel-egana-aranguren > oppl

comparison src/OPPLGalaxy.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/OPPLGalaxy.java@d3616fac4ca5
children
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18:d3616fac4ca5 19:cc270db37d33
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.Level;
11 import java.util.logging.Logger;
12
13 //import org.apache.log4j.Level;
14 import org.coode.oppl.ChangeExtractor;
15 import org.coode.oppl.OPPLParser;
16 import org.coode.oppl.OPPLScript;
17 import org.coode.oppl.ParserFactory;
18 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
19 import org.coode.oppl.log.Logging;
20 import org.coode.parsers.ErrorListener;
21 import org.coode.parsers.LoggerErrorListener;
22 import org.semanticweb.owlapi.model.OWLAxiomChange;
23 import org.semanticweb.owlapi.model.OWLOntology;
24 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
25 import org.semanticweb.owlapi.model.OWLOntologyManager;
26 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
27 import org.semanticweb.owlapi.reasoner.OWLReasoner;
28
29
30
31
32 /**
33 * @author Mikel Ega��a Aranguren
34 *
35 */
36 public class OPPLGalaxy {
37
38 /**
39 * @param args
40 * @throws OWLOntologyCreationException
41 * @throws OWLOntologyStorageException
42 * @throws IOException
43 */
44 public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
45 // Get the arguments from command-line
46 String OWLFilePath = args [0];
47 String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|Elk|HermiT
48
49 String OPPL_script_file = args [2];
50 String OWL = args [3]; // OWL|OBO
51
52 // Create the manager
53 GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
54
55 // Load the main ontology and hope for the imported URIs to be resolvable
56 galaxyowlapi.loadMainOntology(OWLFilePath);
57
58 // Set the reasoner
59
60 // Pellet
61 if(reasoner_type.equals("Pellet")){
62 galaxyowlapi.setReasonerPellet();
63 }
64 // FaCTPlusPlus
65 else if (reasoner_type.equals("FaCTPlusPlus")){
66 galaxyowlapi.setReasonerFaCT();
67 }
68 // Elk
69 else if (reasoner_type.equals("Elk")){
70 galaxyowlapi.setReasonerElk();
71 }
72 // HermiT
73 else{
74 galaxyowlapi.setReasonerHermit();
75 }
76
77 // Load the OPPL flat file with script in memory
78 String OPPL_script_source = "";
79 File file = new File(OPPL_script_file);
80 Scanner input = new Scanner(file);
81 while(input.hasNext()) {
82 String nextToken = input.next();
83 OPPL_script_source = OPPL_script_source + " " + nextToken;
84 }
85 input.close();
86
87 OWLOntologyManager manager = galaxyowlapi.getOWLManager();
88 OWLOntology ontology = galaxyowlapi.getMainOntology();
89 OWLReasoner reasoner = galaxyowlapi.getReasoner();
90
91 // Parse the OPPL script
92 ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner);
93 Logger logger = Logger.getLogger(OPPLGalaxy.class.getName());
94 // logger.setLevel(Level.OFF);
95 // Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
96
97 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
98 OPPLParser opplparser = parserFactory.build(errorListener);
99 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
100
101 // Execute the script
102 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
103 List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
104 manager.applyChanges(changes);
105
106 galaxyowlapi.disposeReasoner();
107
108 // Merge imported ontologies if requested
109 // if(merge.equals("Merge")){
110 // galaxyowlapi.merge();
111 // }
112
113 // Save the ontology
114 if(OWL.equals("OWL")){
115 galaxyowlapi.saveOntology(true);
116 }
117 else{
118 galaxyowlapi.saveOntology(false);
119 }
120 }
121 }