Mercurial > repos > mikel-egana-aranguren > oppl

comparison OPPL/Tool.java @ 5:68935f90c2db

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Added OWL imports closure
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 17 Sep 2011 13:41:28 +0200
parents 4f60202c58d9
children 3740505b579c
comparison
equal deleted inserted replaced
4:4f60202c58d9 5:68935f90c2db
45 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; 45 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
46 import org.semanticweb.owlapi.io.SystemOutDocumentTarget; 46 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
47 import org.semanticweb.owlapi.model.IRI; 47 import org.semanticweb.owlapi.model.IRI;
48 import org.semanticweb.owlapi.model.OWLAxiom; 48 import org.semanticweb.owlapi.model.OWLAxiom;
49 import org.semanticweb.owlapi.model.OWLAxiomChange; 49 import org.semanticweb.owlapi.model.OWLAxiomChange;
50 import org.semanticweb.owlapi.model.OWLDataFactory;
50 import org.semanticweb.owlapi.model.OWLOntology; 51 import org.semanticweb.owlapi.model.OWLOntology;
51 import org.semanticweb.owlapi.model.OWLOntologyCreationException; 52 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
53 import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
52 import org.semanticweb.owlapi.model.OWLOntologyManager; 54 import org.semanticweb.owlapi.model.OWLOntologyManager;
53 import org.semanticweb.owlapi.model.OWLOntologyStorageException; 55 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
54 import org.semanticweb.owlapi.reasoner.InferenceType; 56 import org.semanticweb.owlapi.reasoner.InferenceType;
55 import org.semanticweb.owlapi.reasoner.OWLReasoner; 57 import org.semanticweb.owlapi.reasoner.OWLReasoner;
56 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; 58 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
57 import org.semanticweb.owlapi.util.InferredAxiomGenerator; 59 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
58 import org.semanticweb.owlapi.util.InferredOntologyGenerator; 60 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
59 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; 61 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
62 import org.semanticweb.owlapi.util.SimpleIRIMapper;
60 63
61 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; 64 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
62 65
63
64 /** 66 /**
65 * @author Mikel Egaña Aranguren 67 * @author Mikel Egaña Aranguren
66 *
67 */ 68 */
68 public class Tool { 69 public class Tool {
69 70
70 /** 71 /**
71 * @param OWL file
72 * @param OPPL script
73 * @throws FileNotFoundException 72 * @throws FileNotFoundException
74 * @throws OWLOntologyCreationException 73 * @throws OWLOntologyCreationException
75 * @throws OWLOntologyStorageException 74 * @throws OWLOntologyStorageException
76 */ 75 */
77 public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException { 76 public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
78
79 // Get the arguments from command-line 77 // Get the arguments from command-line
80 String OWLFilePath = args [0]; 78 String OWLFilePath = args [0];
81 String OPPL_script_file = args [1]; 79 String OPPL_script_file = args [1];
82 String Output_format = args [2]; 80 String Output_format = args [2]; // OWL|OBO
83 String Add_inferred = args [3]; 81 String Add_inferred = args [3]; // Add_inferred|Whatever
84 String OPPL_script_source = ""; 82 String imports_file_path = args [4]; // Flat tab delimited file: URI Document URI
83
84 // Load the main ontology
85 File owl_file = new File(OWLFilePath);
86 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
87
88 // Load the imports if any
89 if(!imports_file_path.equals("NoImports")){
90 File imports_file = new File(imports_file_path);
91 Scanner imports_input = new Scanner(imports_file);
92 while(imports_input.hasNext()){
93 String nextLine = imports_input.nextLine();
94 if(!nextLine.startsWith("#")){
95 String [] URI_documentURI = nextLine.split("\t");
96 // System.out.println(URI_documentURI[0]);
97 // System.out.println(URI_documentURI[1]);
98 // IRI ontology_IRI = IRI.create("http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology");
99 // IRI document_IRI = IRI.create("file://" + "/home/pik/UPM/OPPL_galaxy/SWAT4LS_2011/GONG/chebi.owl");
100 IRI ontology_IRI = IRI.create(URI_documentURI[0]);
101 IRI document_IRI = IRI.create("file://" + URI_documentURI[1]);
102 OWLOntologyIRIMapper iriMapper = new SimpleIRIMapper(ontology_IRI,document_IRI);
103 manager.addIRIMapper(iriMapper);
104 }
105 }
106 imports_input.close();
107 }
108 OWLDataFactory factory = manager.getOWLDataFactory();
109 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
110
111 // Reasoner
112 OWLReasonerFactory reasonerFactory = new PelletReasonerFactory();
113 OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
114 reasoner.isConsistent();
85 115
86 // Load the flat file with script in memory 116 // Load the flat file with script in memory
117 String OPPL_script_source = "";
87 File file = new File(OPPL_script_file); 118 File file = new File(OPPL_script_file);
88 Scanner input = new Scanner(file); 119 Scanner input = new Scanner(file);
89 while(input.hasNext()) { 120 while(input.hasNext()) {
90 String nextToken = input.next(); 121 String nextToken = input.next();
91 OPPL_script_source = OPPL_script_source + " " + nextToken; 122 OPPL_script_source = OPPL_script_source + " " + nextToken;
92 } 123 }
93 input.close(); 124 input.close();
94
95 // Load the OWL ontology
96 File owl_file = new File(OWLFilePath);
97 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
98 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
99
100 // Sync reasoner and check consistency
101 OWLReasonerFactory reasonerFactory = new PelletReasonerFactory();
102 OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
103 125
104 // Parse the OPPL script 126 // Parse the OPPL script
105 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner); 127 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner);
106 Logger logger = Logger.getLogger(Tool.class.getName()); 128 Logger logger = Logger.getLogger(Tool.class.getName());
107 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy 129 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy