diff OPPL/Tool.java @ 8:40adbcb2a7cc

Added merge function and FaCT++ support. Improved OBO render

--- a/OPPL/Tool.java	Sun Sep 18 12:57:22 2011 +0200
+++ b/OPPL/Tool.java	Tue Oct 11 11:09:52 2011 +0200
@@ -17,12 +17,17 @@
 
 package es.upm.fi.dia.oeg.oppl.galaxy;
 
+import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FileNotFoundException;
+//import java.io.PrintWriter;
+//import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
-import java.util.logging.Level;
+//import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import org.coode.oppl.ChangeExtractor;
@@ -30,29 +35,46 @@
 import org.coode.oppl.OPPLScript;
 import org.coode.oppl.ParserFactory;
 import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
-import org.coode.oppl.log.Logging;
+//import org.coode.oppl.log.Logging;
 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
 import org.coode.parsers.ErrorListener;
 import org.coode.parsers.LoggerErrorListener;
+//import org.obolibrary.obo2owl.Owl2Obo;
+//import org.obolibrary.oboformat.model.OBODoc;
+//import org.obolibrary.oboformat.writer.OBOFormatWriter;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
+import org.semanticweb.owlapi.model.AddAxiom;
 import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLAxiomChange;
+import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLLiteral;
+//import org.semanticweb.owlapi.model.OWLObjectProperty;
 import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+//import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory;
 import org.semanticweb.owlapi.reasoner.InferenceType;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
+import org.semanticweb.owlapi.util.OWLEntityRenamer;
+import org.semanticweb.owlapi.util.OWLOntologyMerger;
 import org.semanticweb.owlapi.util.SimpleIRIMapper;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
+
+import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
 
 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
 
@@ -64,18 +86,20 @@
 public class Tool {
 
 	/**
-	 * @throws FileNotFoundException 
 	 * @throws OWLOntologyCreationException 
 	 * @throws OWLOntologyStorageException 
+	 * @throws IOException 
+	 * @throws URISyntaxException 
 	 */
-	public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {		
+	public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException, URISyntaxException {		
 		// Get the arguments from command-line
 		String OWLFilePath = args [0]; 
 		String OPPL_script_file = args [1];
 		String Output_format = args [2]; // OWL|OBO
-		String Add_inferred = args [3]; // Add_inferred|Whatever
-		String imports_file_path = args [4]; // Flat tab delimited file: URI	Document URI
-		String reasoner_type = args [5]; // Pellet|HermiT
+		String Add_inferred = args [3]; // AddInferred|Whatever
+		String imports_file_path = args [4]; // NoImports|Flat tab delimited file: URI	Document URI
+		String reasoner_type = args [5]; // Pellet|FaCTPlusPlus|HermiT
+		String merge_URI = args [6]; // NoMerge|URI for merged ontology
 		
 		// Load the main ontology		
 		File owl_file = new File(OWLFilePath);
@@ -97,21 +121,33 @@
 			}
 			imports_input.close();
 		}
-		OWLDataFactory factory = manager.getOWLDataFactory();
 		OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
 		
 		// Reasoner
 		OWLReasonerFactory reasonerFactory = null;
 		OWLReasoner reasoner = null;
+		
+		// Pellet
 		if(reasoner_type.equals("Pellet")){
 			reasonerFactory = new PelletReasonerFactory(); 
 			reasoner = reasonerFactory.createReasoner(OWL_ontology);
 		}
+		// FaCTPlusPlus
+		else if (reasoner_type.equals("FaCTPlusPlus")){
+			reasonerFactory = new FaCTPlusPlusReasonerFactory();
+			reasoner = reasonerFactory.createReasoner(OWL_ontology);
+		}
+		// HermiT
 		else{
 			reasonerFactory = new Reasoner.ReasonerFactory();
 			reasoner = reasonerFactory.createReasoner(OWL_ontology);
 		}
 		
+		// OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy
+		// I have to change Racer settings and OWLLink settings
+//		OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
+//		reasoner = factory.createReasoner(OWL_ontology);
+		
 		// Load the flat file with script in memory
 		String OPPL_script_source = "";
 		File file = new File(OPPL_script_file);
@@ -136,20 +172,100 @@
 		manager.applyChanges(changes);
 		
 		// Add the inferred axioms as asserted axioms to the original ontology
-		if(Add_inferred.equals("Add_inferred")){
+		if(Add_inferred.equals("AddInferred")){
 			reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
 			List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
 			gens.add(new InferredSubClassAxiomGenerator());
 			InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
 			iog.fillOntology(manager, OWL_ontology);	
 		}
+		
+		// Print the ontology to the standard output so other galaxy tools can operate on it
+		
+		// Do not merge ontologies
+		if(merge_URI.equals("NoMerge")){
+			saveOntology(manager, OWL_ontology, Output_format);
+		}
+		// Merge ontologies
+		else{	
+			OWLOntologyMerger merger = new OWLOntologyMerger(manager);
+			IRI mergedOntologyIRI = IRI.create(merge_URI);
+			OWLOntology merged = merger.createMergedOntology(manager, mergedOntologyIRI);
+			saveOntology(manager, merged, Output_format);
+		}
+	}
+	
+	private static void saveOntology (OWLOntologyManager manager, OWLOntology ontology, String Format) throws OWLOntologyStorageException, IOException, URISyntaxException {
+		
+		// OBO format
+		if(Format.equals("OBO")){
+			
+			// OWL API generates bad OBO but OBOformat doesn't work either so I correct the OWL API problems (More predictable) in a temporary file
+			// Very inefficient but no time for another solution
+			
+			OWLDataFactory factory = manager.getOWLDataFactory();
+			
+			OWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());
+			OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
+			
+			for(OWLClass cls : ontology.getClassesInSignature()){
+				// Remove annotations (OWL API generates bad OBO annotations)
+				
+				// Keep rdfs:label
+				String class_name = null;
+				for (OWLAnnotation annotation : cls.getAnnotations(ontology, label)) {
+	                if (annotation.getValue() instanceof OWLLiteral) {
+	                    OWLLiteral val = (OWLLiteral) annotation.getValue();
+	                    class_name = val.getLiteral();
+	                }
+	            }
+							
+//				I have to remove all the annotations cause I don't know which ones are rendered properly
+				manager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));
+				
+				// Add rdfs:label again
+				OWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(
+				OWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));
+				OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);
+				manager.applyChange(new AddAxiom(ontology, ax));
+				
+				// Rename entities
+				String cls_IRI = cls.getIRI().toString();
+				String cls_proper_IRI = cls_IRI.replace("_", ":");
+				List<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));
+				manager.applyChanges(changes);
+			}
+			
+			File file = new File("tmp.obo");
+			manager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));
+			BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));		
+			Scanner input = new Scanner(file);
+			String buffer = "";
 
-		// Print the ontology to the standard output so other galaxy tools can operate on the output	
-		if(Output_format.equals("OBO")){
-			manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
+			while(input.hasNext()){
+				String nextLine = input.nextLine();
+				if(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){
+					if(buffer.isEmpty()){
+						bw.write(buffer);
+						bw.newLine();
+					}
+				}
+				if(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){
+					if(!nextLine.isEmpty() && !buffer.contains("relationship:")){
+						bw.write(nextLine);
+						bw.newLine();
+					}
+				}
+				buffer = nextLine;
+			}
+			input.close();
+			bw.close();
+			file.delete();
 		}
+		
+		//OWL format
 		else{
-			manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
+			manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
 		}
 	}
 }