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comparison OPPL/Tool.java @ 6:3740505b579c

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Added reasoner option: Pellet or HermiT
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sun, 18 Sep 2011 12:35:18 +0200
parents 68935f90c2db
children 756f1f5798bf
comparison
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5:68935f90c2db 6:3740505b579c
15 * along with this program. If not, see <http://www.gnu.org/licenses/>. 15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
16 */ 16 */
17 17
18 package es.upm.fi.dia.oeg.oppl.galaxy; 18 package es.upm.fi.dia.oeg.oppl.galaxy;
19 19
20 import java.io.BufferedOutputStream;
21 import java.io.BufferedWriter;
22 import java.io.File; 20 import java.io.File;
23 import java.io.FileNotFoundException; 21 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.ArrayList; 22 import java.util.ArrayList;
29 import java.util.List; 23 import java.util.List;
30 import java.util.Scanner; 24 import java.util.Scanner;
31 import java.util.logging.Level; 25 import java.util.logging.Level;
32 import java.util.logging.Logger; 26 import java.util.logging.Logger;
39 import org.coode.oppl.log.Logging; 33 import org.coode.oppl.log.Logging;
40 import org.coode.owlapi.obo.parser.OBOOntologyFormat; 34 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
41 import org.coode.parsers.ErrorListener; 35 import org.coode.parsers.ErrorListener;
42 import org.coode.parsers.LoggerErrorListener; 36 import org.coode.parsers.LoggerErrorListener;
43 import org.semanticweb.owlapi.apibinding.OWLManager; 37 import org.semanticweb.owlapi.apibinding.OWLManager;
44 import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
45 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat; 38 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
46 import org.semanticweb.owlapi.io.SystemOutDocumentTarget; 39 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
47 import org.semanticweb.owlapi.model.IRI; 40 import org.semanticweb.owlapi.model.IRI;
48 import org.semanticweb.owlapi.model.OWLAxiom; 41 import org.semanticweb.owlapi.model.OWLAxiom;
49 import org.semanticweb.owlapi.model.OWLAxiomChange; 42 import org.semanticweb.owlapi.model.OWLAxiomChange;
61 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; 54 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
62 import org.semanticweb.owlapi.util.SimpleIRIMapper; 55 import org.semanticweb.owlapi.util.SimpleIRIMapper;
63 56
64 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; 57 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
65 58
59 import org.semanticweb.HermiT.Reasoner;
60
66 /** 61 /**
67 * @author Mikel Egaña Aranguren 62 * @author Mikel Egaña Aranguren
68 */ 63 */
69 public class Tool { 64 public class Tool {
70 65
78 String OWLFilePath = args [0]; 73 String OWLFilePath = args [0];
79 String OPPL_script_file = args [1]; 74 String OPPL_script_file = args [1];
80 String Output_format = args [2]; // OWL|OBO 75 String Output_format = args [2]; // OWL|OBO
81 String Add_inferred = args [3]; // Add_inferred|Whatever 76 String Add_inferred = args [3]; // Add_inferred|Whatever
82 String imports_file_path = args [4]; // Flat tab delimited file: URI Document URI 77 String imports_file_path = args [4]; // Flat tab delimited file: URI Document URI
78 String reasoner_type = args [5]; // Pellet|HermiT
83 79
84 // Load the main ontology 80 // Load the main ontology
85 File owl_file = new File(OWLFilePath); 81 File owl_file = new File(OWLFilePath);
86 OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 82 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
87 83
90 File imports_file = new File(imports_file_path); 86 File imports_file = new File(imports_file_path);
91 Scanner imports_input = new Scanner(imports_file); 87 Scanner imports_input = new Scanner(imports_file);
92 while(imports_input.hasNext()){ 88 while(imports_input.hasNext()){
93 String nextLine = imports_input.nextLine(); 89 String nextLine = imports_input.nextLine();
94 if(!nextLine.startsWith("#")){ 90 if(!nextLine.startsWith("#")){
95 String [] URI_documentURI = nextLine.split("\t"); 91 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]); 92 IRI ontology_IRI = IRI.create(URI_documentURI[0]);
101 IRI document_IRI = IRI.create("file://" + URI_documentURI[1]); 93 IRI document_IRI = IRI.create("file://" + URI_documentURI[1]);
102 OWLOntologyIRIMapper iriMapper = new SimpleIRIMapper(ontology_IRI,document_IRI); 94 OWLOntologyIRIMapper iriMapper = new SimpleIRIMapper(ontology_IRI,document_IRI);
103 manager.addIRIMapper(iriMapper); 95 manager.addIRIMapper(iriMapper);
104 } 96 }
107 } 99 }
108 OWLDataFactory factory = manager.getOWLDataFactory(); 100 OWLDataFactory factory = manager.getOWLDataFactory();
109 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file); 101 OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
110 102
111 // Reasoner 103 // Reasoner
112 OWLReasonerFactory reasonerFactory = new PelletReasonerFactory(); 104 OWLReasonerFactory reasonerFactory = null;
113 OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology); 105 OWLReasoner reasoner = null;
114 reasoner.isConsistent(); 106 if(reasoner_type.equals("Pellet")){
107 reasonerFactory = new PelletReasonerFactory();
108 reasoner = reasonerFactory.createReasoner(OWL_ontology);
109 }
110 else{
111 reasonerFactory = new Reasoner.ReasonerFactory();
112 reasoner = reasonerFactory.createReasoner(OWL_ontology);
113 }
115 114
116 // Load the flat file with script in memory 115 // Load the flat file with script in memory
117 String OPPL_script_source = ""; 116 String OPPL_script_source = "";
118 File file = new File(OPPL_script_file); 117 File file = new File(OPPL_script_file);
119 Scanner input = new Scanner(file); 118 Scanner input = new Scanner(file);
124 input.close(); 123 input.close();
125 124
126 // Parse the OPPL script 125 // Parse the OPPL script
127 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner); 126 ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner);
128 Logger logger = Logger.getLogger(Tool.class.getName()); 127 Logger logger = Logger.getLogger(Tool.class.getName());
129 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy 128 Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
130 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); 129 ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
131 OPPLParser opplparser = parserFactory.build(errorListener); 130 OPPLParser opplparser = parserFactory.build(errorListener);
132 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); 131 OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
133 132
134 // Execute the script 133 // Execute the script
140 if(Add_inferred.equals("Add_inferred")){ 139 if(Add_inferred.equals("Add_inferred")){
141 reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY); 140 reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
142 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>(); 141 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
143 gens.add(new InferredSubClassAxiomGenerator()); 142 gens.add(new InferredSubClassAxiomGenerator());
144 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens); 143 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
145 iog.fillOntology(manager, OWL_ontology); 144 iog.fillOntology(manager, OWL_ontology);
146 } 145 }
147 146
148 // Print the ontology to the standard output so other galaxy tools can operate on the output 147 // Print the ontology to the standard output so other galaxy tools can operate on the output
149 OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
150 if(Output_format.equals("OBO")){ 148 if(Output_format.equals("OBO")){
151 manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget()); 149 manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
152 } 150 }
153 else{ 151 else{
154 manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); 152 manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());