Eliminate imports

minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java

@@ -1,5 +1,6 @@
 package org.geneontology.minerva.cli;
 
+
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -76,6 +77,9 @@
 import org.openrdf.rio.RDFParseException;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.formats.TurtleDocumentFormat;
+import org.semanticweb.owlapi.io.IRIDocumentSource;
+import org.semanticweb.owlapi.model.AxiomType;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLAnnotation;
 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
@@ -84,6 +88,8 @@
 import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDocumentFormat;
+import org.semanticweb.owlapi.model.OWLImportsDeclaration;
 import org.semanticweb.owlapi.model.OWLLiteral;
 import org.semanticweb.owlapi.model.OWLNamedIndividual;
 import org.semanticweb.owlapi.model.OWLOntology;
@@ -155,6 +161,13 @@ public static void main(String[] args) {
 				.build();
 		methods.addOption(add_taxon_metadata);
 
+		Option clean_gocams = Option.builder()
+				.longOpt("clean-gocams")
+				.desc("remove import statements, add property declarations, remove json-model annotation")
+				.hasArg(false)
+				.build();
+		methods.addOption(clean_gocams);
+
 		Option sparql = Option.builder()
 				.longOpt("sparql-update")
 				.desc("update the blazegraph journal with the given sparql statement")
@@ -202,6 +215,15 @@ public static void main(String[] args) {
 				String ontojournal = cmd.getOptionValue("ontojournal"); //--folder
 				addTaxonMetaData(journalFilePath, ontojournal);
 			}
+
+			if(cmd.hasOption("clean-gocams")) {
+				Options clean_options = new Options();
+				clean_options.addOption(clean_gocams);
+				clean_options.addOption("i", "input", true, "This is the directory of gocam files to clean.");
+				clean_options.addOption("o", "output", true, "This is the directory of cleaned gocam files that are produced.");
+				cmd = parser.parse(clean_options, args, false);
+				cleanGoCams(cmd.getOptionValue("i"), cmd.getOptionValue("o"));
+			}
 
 			if(cmd.hasOption("import-tbox-ontologies")) {
 				Options import_tbox_options = new Options();
@@ -1161,6 +1183,42 @@ public static void addTaxonMetaData(String go_cam_journal, String go_lego_journa
 		return;
 	}
 
+	public static void cleanGoCams(String input_dir, String output_dir) {
+		OWLOntologyManager m = OWLManager.createOWLOntologyManager();
+		File directory = new File(input_dir);
+		boolean ignore_imports = true;
+		if(directory.isDirectory()) {
+			for(File file : directory.listFiles()) {
+				if(file.getName().endsWith("ttl")) {
+					System.out.println("fixing "+file.getAbsolutePath());
+					final IRI modelFile = IRI.create(file.getAbsoluteFile());
+					OWLOntology o;
+					try {
+						o = CoreMolecularModelManager.loadOntologyDocumentSource(new IRIDocumentSource(modelFile), ignore_imports, m);
+						//in case the reader was confused by the missing import, fix declarations
+						o = CoreMolecularModelManager.fixBrokenObjectPropertiesAndAxioms(o);
+						//clean the model
+						OWLOntology cleaned_ont = CoreMolecularModelManager.removeDeadAnnotationsAndImports(o);						
+						//saved the blessed ontology
+						OWLDocumentFormat owlFormat = new TurtleDocumentFormat();
+						m.setOntologyFormat(cleaned_ont, owlFormat);
+						String cleaned_ont_file = output_dir+file.getName();
+						try {
+							m.saveOntology(cleaned_ont, new FileOutputStream(cleaned_ont_file));
+						} catch (OWLOntologyStorageException | FileNotFoundException e) {
+							// TODO Auto-generated catch block
+							e.printStackTrace();
+						}
+					} catch (OWLOntologyCreationException e1) {
+						// TODO Auto-generated catch block
+						e1.printStackTrace();
+					}
+				}
+			}
+		}
+	}
+
+
 	public static void printVersion() throws Exception {
 		printManifestEntry("git-revision-sha1", "UNKNOWN");
 		printManifestEntry("git-revision-url", "UNKNOWN");

minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java

@@ -159,39 +159,6 @@ private BigdataSailRepository initializeRepository(String pathToJournal) {
 		}
 	}
 
-	private void createImports(OWLOntology ont, OWLOntologyID tboxId,
-			METADATA metadata) throws OWLOntologyCreationException {
-		OWLOntologyManager m = ont.getOWLOntologyManager();
-		OWLDataFactory f = m.getOWLDataFactory();
-
-		// import T-Box
-		Optional<IRI> ontologyIRI = tboxId.getOntologyIRI();
-		if (ontologyIRI.isPresent()) {
-			OWLImportsDeclaration tBoxImportDeclaration = f
-					.getOWLImportsDeclaration(ontologyIRI.get());
-			m.applyChange(new AddImport(ont, tBoxImportDeclaration));
-		}
-
-		// import additional ontologies via IRI
-		for (IRI importIRI : additionalImports) {
-			OWLImportsDeclaration importDeclaration = f
-					.getOWLImportsDeclaration(importIRI);
-			// check that the import ontology is available
-			OWLOntology importOntology = m.getOntology(importIRI);
-			if (importOntology == null) {
-				// only try to load it, if it isn't already loaded
-				try {
-					m.loadOntology(importIRI);
-				} catch (OWLOntologyDocumentAlreadyExistsException e) {
-					// ignore
-				} catch (OWLOntologyAlreadyExistsException e) {
-					// ignore
-				}
-			}
-			m.applyChange(new AddImport(ont, importDeclaration));
-		}
-	}
-
 	/**
 	 * Generates a blank model
 	 *
@@ -216,10 +183,6 @@ public ModelContainer generateBlankModel(METADATA metadata)
 		ModelContainer model = null;
 		try {
 			abox = m.createOntology(modelId);
-
-			// add imports to T-Box and additional ontologies via IRI
-			createImports(abox, tbox.getOntologyID(), metadata);
-
 			// generate model
 			model = new ModelContainer(modelId, tbox, abox);
 		} catch (OWLOntologyCreationException exception) {
@@ -579,7 +542,6 @@ protected void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCrea
 				statements.close();
 				abox = postLoadFileFilter(abox);
 				ModelContainer model = addModel(modelId, abox);
-				updateImports(model);
 			} finally {
 				connection.close();
 			}

minerva-core/src/main/java/org/geneontology/minerva/BlazegraphOntologyManager.java

@@ -704,6 +704,36 @@ public String getLabel(String entity) throws IOException {
 		}
 		return label;
 	}
+
+	public boolean exists(String entity) throws IOException {
+		boolean exists = false;
+		String query = "select * "
+				+ "WHERE {" + 
+				"{<"+entity+"> ?p ?o . } " + 
+				"UNION " + 
+				"{?s ?p <"+entity+"> . }" + 
+				"} limit 1";		
+		try {
+			BigdataSailRepositoryConnection connection = go_lego_repo.getReadOnlyConnection();
+			try {
+				TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query);
+				TupleQueryResult result = tupleQuery.evaluate();
+				if (result.hasNext()) {
+					exists = true;
+					return exists;
+				}
+			} catch (MalformedQueryException e) {
+				throw new IOException(e);
+			} catch (QueryEvaluationException e) {
+				throw new IOException(e);
+			} finally {
+				connection.close();
+			}
+		} catch (RepositoryException e) {
+			throw new IOException(e);
+		}
+		return exists;
+	}
 
 	public Map<String, String> getLabels(Set<String> entities) throws IOException {
 		Map<String, String> uri_label = new HashMap<String, String>();

minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java

@@ -71,6 +71,7 @@
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
 import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
 import org.semanticweb.owlapi.model.RemoveAxiom;
+import org.semanticweb.owlapi.model.RemoveImport;
 import org.semanticweb.owlapi.model.RemoveOntologyAnnotation;
 import org.semanticweb.owlapi.model.SetOntologyID;
 import org.semanticweb.owlapi.model.parameters.Imports;
@@ -961,9 +962,6 @@ public ModelContainer importModel(String modelData) throws OWLOntologyCreationEx
 		// add to internal model
 		ModelContainer newModel = addModel(modelId, modelOntology);
 
-		// update imports
-		updateImports(newModel);
-
 		return newModel;
 	}
 
@@ -1324,7 +1322,7 @@ protected OWLOntology loadOntologyDocumentSource(final OWLOntologyDocumentSource
 		return loadOntologyDocumentSource(source, minimal, tbox.getOWLOntologyManager());
 	}
 
-	static OWLOntology loadOntologyDocumentSource(final OWLOntologyDocumentSource source, boolean minimal, OWLOntologyManager manager) throws OWLOntologyCreationException {		
+	public static OWLOntology loadOntologyDocumentSource(final OWLOntologyDocumentSource source, boolean minimal, OWLOntologyManager manager) throws OWLOntologyCreationException {		
 		// silence the OBO parser in the OWL-API
 		java.util.logging.Logger.getLogger("org.obolibrary").setLevel(java.util.logging.Level.SEVERE);
 		final Set<OWLParserFactory> originalFactories = removeOBOParserFactories(manager);
@@ -1389,43 +1387,6 @@ private static OWLOntology loadOWLOntologyDocumentSource(final OWLOntologyDocume
 		return ontology;
 	}
 
-	/**
-	 * This method will check the given model and update the import declarations.
-	 * It will add missing IRIs and remove obsolete ones.
-	 * 
-	 * @param model
-	 * @see #additionalImports
-	 * @see #addImports(Iterable)
-	 */
-	public void updateImports(ModelContainer model) {
-		updateImports(model.getAboxOntology(), tboxIRI, additionalImports);
-	}
-
-	static void updateImports(final OWLOntology aboxOntology, IRI tboxIRI, Set<IRI> additionalImports) {
-		List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
-
-		Set<IRI> missingImports = new HashSet<IRI>();
-		missingImports.add(tboxIRI);
-		missingImports.addAll(additionalImports);
-		Set<OWLImportsDeclaration> importsDeclarations = aboxOntology.getImportsDeclarations();
-		for (OWLImportsDeclaration decl : importsDeclarations) {
-			IRI iri = decl.getIRI();
-			missingImports.remove(iri);
-		}
-		final OWLOntologyManager m = aboxOntology.getOWLOntologyManager();
-		if (!missingImports.isEmpty()) {
-			OWLDataFactory f = m.getOWLDataFactory();
-			for(IRI missingImport : missingImports) {
-				OWLImportsDeclaration decl = f.getOWLImportsDeclaration(missingImport);
-				changes.add(new AddImport(aboxOntology, decl));
-			}
-		}
-
-		if (!changes.isEmpty()) {
-			m.applyChanges(changes);
-		}
-	}
-
 	public OWLOntology getTbox() {
 		return tbox;
 	}
@@ -1453,33 +1414,49 @@ public static OWLOntology fixBrokenObjectPropertiesAndAxioms(OWLOntology ont) th
 		OWLAnnotationProperty title_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/title"));
 		OWLDeclarationAxiom title_prop_declaration = df.getOWLDeclarationAxiom(title_prop);
 		newman.addAxiom(frank, title_prop_declaration);
-
 		OWLAnnotationProperty title_prop2 = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/terms/title"));
 		OWLDeclarationAxiom title_prop2_declaration = df.getOWLDeclarationAxiom(title_prop2);
-		newman.addAxiom(frank, title_prop2_declaration);
-
-
+		newman.addAxiom(frank, title_prop2_declaration);				
 		OWLAnnotationProperty skos_note = df.getOWLAnnotationProperty(IRI.create("http://www.w3.org/2004/02/skos/core#note"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(skos_note));
 		OWLAnnotationProperty version_info = df.getOWLAnnotationProperty(IRI.create(OWL.versionInfo.getURI()));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(version_info));
 		OWLAnnotationProperty contributor_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/contributor"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(contributor_prop));
 		OWLAnnotationProperty date_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/date"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(date_prop));
 		OWLAnnotationProperty source_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/source"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(source_prop));
 		OWLAnnotationProperty state_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/modelstate"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(state_prop));
 		OWLAnnotationProperty evidence_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/evidence"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(evidence_prop));
 		OWLAnnotationProperty provided_by_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/pav/providedBy"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(provided_by_prop));
 		OWLAnnotationProperty x_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/hint/layout/x"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(x_prop));
 		OWLAnnotationProperty y_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/hint/layout/y"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(y_prop));
 		OWLAnnotationProperty rdfs_label = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(rdfs_label));
 		OWLAnnotationProperty rdfs_comment = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI());
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(rdfs_comment));
 		OWLAnnotationProperty rdfs_seealso = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_SEE_ALSO.getIRI());
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(rdfs_seealso));
 		OWLAnnotationProperty skos_exact_match = df.getOWLAnnotationProperty(IRI.create("http://www.w3.org/2004/02/skos/core#exactMatch"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(skos_exact_match));
 		OWLAnnotationProperty skos_altlabel = df.getOWLAnnotationProperty(IRI.create("http://www.w3.org/2004/02/skos/core#altLabel"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(skos_altlabel));
 		OWLAnnotationProperty definition = df.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/IAO_0000115"));	
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(definition));
 		OWLAnnotationProperty database_cross_reference = df.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#hasDbXref"));	
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(database_cross_reference));
 		OWLAnnotationProperty canonical_record = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/canonical_record"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(canonical_record));
 		OWLAnnotationProperty iuphar_id = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/iuphar_id"));
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(iuphar_id));
 		OWLAnnotationProperty in_taxon = df.getOWLAnnotationProperty(IRI.create("https://w3id.org/biolink/vocab/in_taxon"));
-
+		newman.addAxiom(frank, df.getOWLDeclarationAxiom(in_taxon));
 
 		//copy over ontology annotations
 		for(OWLAnnotation anno : ont.getAnnotations()) {
@@ -1522,19 +1499,24 @@ public static OWLOntology fixBrokenObjectPropertiesAndAxioms(OWLOntology ont) th
 		return frank;
 	}
 
-	public static boolean hasLegoImport(OWLOntology ont) {
-		Set<OWLOntology> imports = ont.getDirectImports();
-		for(OWLOntology i : imports) {
-			com.google.common.base.Optional<IRI> iri = i.getOntologyID().getOntologyIRI();
-			if(iri.isPresent()) {
-				String s_iri = iri.get().toString();
-				if(s_iri.equals("http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl")||
-						s_iri.equals("http://purl.obolibrary.org/obo/go/extensions/go-lego.owl")) {
-					return true;
-				}
-
+	public static OWLOntology removeDeadAnnotationsAndImports(OWLOntology ont) throws OWLOntologyCreationException {
+		OWLOntologyManager m = OWLManager.createOWLOntologyManager();
+		OWLAnnotationProperty json_model_prop = m.getOWLDataFactory().getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/json-model"));
+		//get rid of all imports
+		Set<OWLImportsDeclaration> imports = ont.getImportsDeclarations();
+		for(OWLImportsDeclaration import_declaration : imports) {
+			m.applyChange(new RemoveImport(ont, import_declaration));
+		}
+		//get rid of the json annotations lurking about
+		for(OWLAnnotation anno : ont.getAnnotations()) {
+			if(anno.getProperty().equals(json_model_prop)) {
+				RemoveOntologyAnnotation rm = new RemoveOntologyAnnotation(ont, anno);
+				m.applyChange(rm);
 			}
 		}
-		return false;
+		//purify of the json annotation property as well
+		OWLDeclarationAxiom json_prop_declaration = m.getOWLDataFactory().getOWLDeclarationAxiom(json_model_prop);
+		m.removeAxiom(ont, json_prop_declaration);
+		return ont;
 	}
 }

minerva-core/src/main/java/org/geneontology/minerva/MinervaOWLGraphWrapper.java

@@ -111,12 +111,10 @@ private static HashMap<String, IRI> initAnnotationPropertyMap() {
 	 */
 	public OWLClass getOWLClass(IRI iri) {
 		OWLClass c = getDataFactory().getOWLClass(iri);
-		for (OWLOntology o : getAllOntologies()) {
-			if (o.getDeclarationAxioms(c).size() > 0) {
-				return c;
-			}
-		}
-		return null;
+		return c;
+		//there used to be a check here to ensure that the class IRI existed in a tbox ontology
+		//as there is no way to create a class using the UI without getting one out of the tbox ontology
+		//I think it is probably safe to remove this check.  To add it, use BlazegraphOntologyManager.exists()  
 	}
 
 

minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java

@@ -603,18 +603,5 @@ public OWLNamedIndividual removeDataProperties(ModelContainer model, OWLNamedInd
 		return i;
 	}
 
-	/**
-	 * This method will check the given model and update the import declarations.
-	 * It will add missing IRIs and remove obsolete ones.
-	 * 
-	 * @param modelId 
-	 * @throws UnknownIdentifierException
-	 * @see #additionalImports
-	 * @see #addImports(Iterable)
-	 */
-	public void updateImports(IRI modelId) throws UnknownIdentifierException {
-		ModelContainer model = checkModelId(modelId);
-		updateImports(model);
-	}
 
 }