Mercurial > repos > mikel-egana-aranguren > oppl
comparison OPPL/Tool.java @ 3:5255f1333cc4
Version 1.0.1
Added output choice: OBO or OWL(RDF/XML)
author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
---|---|
date | Wed, 07 Sep 2011 10:46:29 +0200 |
parents | |
children | 4f60202c58d9 |
comparison
equal
deleted
inserted
replaced
2:0a374d0b7759 | 3:5255f1333cc4 |
---|---|
1 /** | |
2 * Copyright (C) 2011, Mikel Egaña Aranguren | |
3 * | |
4 * This program is free software: you can redistribute it and/or modify | |
5 * it under the terms of the GNU General Public License as published by | |
6 * the Free Software Foundation, either version 3 of the License, or | |
7 * (at your option) any later version. | |
8 * | |
9 * This program is distributed in the hope that it will be useful, | |
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of | |
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
12 * GNU General Public License for more details. | |
13 * | |
14 * You should have received a copy of the GNU General Public License | |
15 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
16 */ | |
17 | |
18 package es.upm.fi.dia.oeg.oppl.galaxy; | |
19 | |
20 import java.io.BufferedOutputStream; | |
21 import java.io.BufferedWriter; | |
22 import java.io.File; | |
23 import java.io.FileNotFoundException; | |
24 import java.io.FilterOutputStream; | |
25 import java.io.OutputStream; | |
26 import java.io.PipedOutputStream; | |
27 import java.io.PrintStream; | |
28 import java.util.List; | |
29 import java.util.Scanner; | |
30 import java.util.logging.Level; | |
31 import java.util.logging.Logger; | |
32 | |
33 import org.coode.oppl.ChangeExtractor; | |
34 import org.coode.oppl.OPPLParser; | |
35 import org.coode.oppl.OPPLScript; | |
36 import org.coode.oppl.ParserFactory; | |
37 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler; | |
38 import org.coode.oppl.log.Logging; | |
39 import org.coode.owlapi.obo.parser.OBOOntologyFormat; | |
40 import org.coode.parsers.ErrorListener; | |
41 import org.coode.parsers.LoggerErrorListener; | |
42 import org.semanticweb.owlapi.apibinding.OWLManager; | |
43 import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget; | |
44 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; | |
45 import org.semanticweb.owlapi.io.SystemOutDocumentTarget; | |
46 import org.semanticweb.owlapi.model.IRI; | |
47 import org.semanticweb.owlapi.model.OWLAxiomChange; | |
48 import org.semanticweb.owlapi.model.OWLOntology; | |
49 import org.semanticweb.owlapi.model.OWLOntologyCreationException; | |
50 import org.semanticweb.owlapi.model.OWLOntologyManager; | |
51 import org.semanticweb.owlapi.model.OWLOntologyStorageException; | |
52 import org.semanticweb.owlapi.reasoner.OWLReasoner; | |
53 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; | |
54 | |
55 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; | |
56 | |
57 | |
58 /** | |
59 * @author Mikel Egaña Aranguren | |
60 * | |
61 */ | |
62 public class Tool { | |
63 | |
64 /** | |
65 * @param OWL file | |
66 * @param OPPL script | |
67 * @throws FileNotFoundException | |
68 * @throws OWLOntologyCreationException | |
69 * @throws OWLOntologyStorageException | |
70 */ | |
71 public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException { | |
72 | |
73 // Get the arguments from command-line | |
74 String OWLFilePath = args [0]; | |
75 String OPPL_script_file = args [1]; | |
76 String Output_format = args [2]; | |
77 String OPPL_script_source = ""; | |
78 | |
79 // Load the flat file with script in memory | |
80 File file = new File(OPPL_script_file); | |
81 Scanner input = new Scanner(file); | |
82 while(input.hasNext()) { | |
83 String nextToken = input.next(); | |
84 OPPL_script_source = OPPL_script_source + " " + nextToken; | |
85 } | |
86 input.close(); | |
87 | |
88 // Load the OWL ontology | |
89 File owl_file = new File(OWLFilePath); | |
90 OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); | |
91 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file); | |
92 | |
93 // Sync reasoner and check consistency | |
94 OWLReasonerFactory reasonerFactory = new PelletReasonerFactory(); | |
95 OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology); | |
96 | |
97 // Parse the OPPL script | |
98 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner); | |
99 Logger logger = Logger.getLogger(Tool.class.getName()); | |
100 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy | |
101 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); | |
102 OPPLParser opplparser = parserFactory.build(errorListener); | |
103 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); | |
104 | |
105 // Execute the script | |
106 ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true); | |
107 List<OWLAxiomChange> changes = extractor.visit(OPPLscript); | |
108 manager.applyChanges(changes); | |
109 | |
110 // Print the ontology to the standard output so other galaxy tools can operate on the output | |
111 OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget(); | |
112 | |
113 if(Output_format.equals("OBO")){ | |
114 manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget()); | |
115 } | |
116 else{ | |
117 manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); | |
118 } | |
119 | |
120 } | |
121 } |