Fix for non-localized annotations not visible when viewing another la…

…nguage

ols-apps/ols-config-importer/src/main/resources/obo-config.yaml

@@ -178,7 +178,7 @@ ontologies:
     license:
       label: GPL-3.0
       url: https://www.gnu.org/licenses/gpl-3.0.en.html
-    ontology_purl: https://github.com/scdodev/scdo-ontology/blob/master/scdo_fr-t-en.owl
+    ontology_purl: https://raw.githubusercontent.com/scdodev/scdo-ontology/master/scdo_fr-t-en.owl
     preferredPrefix: SCDO
     products:
     - id: scdo.owl

ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Individual.java

@@ -210,10 +210,10 @@ public Map<String, Object> getAnnotationByLang(String lang) {
 
         for (String k : localizedAnnotations.keySet()) {
 
-		int n = lang.lastIndexOf('-');
+		int n = k.lastIndexOf('-');
 
 		if(n != -1) {
-			String annoLang = lang.substring(0, n);
+			String annoLang = k.substring(0, n);
 
 			if (annoLang.equalsIgnoreCase(lang)) {
 				res.put(k.substring(n + 1), localizedAnnotations.get(k));

ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Property.java

@@ -209,10 +209,10 @@ public Map<String, Object> getAnnotationByLang(String lang) {
 
         for (String k : localizedAnnotations.keySet()) {
 
-		int n = lang.lastIndexOf('-');
+		int n = k.lastIndexOf('-');
 
 		if(n != -1) {
-			String annoLang = lang.substring(0, n);
+			String annoLang = k.substring(0, n);
 
 			if (annoLang.equalsIgnoreCase(lang)) {
 				res.put(k.substring(n + 1), localizedAnnotations.get(k));

ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Term.java

@@ -292,10 +292,10 @@ public Map<String, Object> getAnnotationByLang(String lang) {
 
         for (String k : localizedAnnotations.keySet()) {
 
-		int n = lang.lastIndexOf('-');
+		int n = k.lastIndexOf('-');
 
 		if(n != -1) {
-			String annoLang = lang.substring(0, n);
+			String annoLang = k.substring(0, n);
 
 			if (annoLang.equalsIgnoreCase(lang)) {
 				res.put(k.substring(n + 1), localizedAnnotations.get(k));

ontology-tools/src/main/java/uk/ac/ebi/spot/ols/loader/AbstractOWLOntologyLoader.java

@@ -1,6 +1,7 @@
 package uk.ac.ebi.spot.ols.loader;
 
 import com.google.common.collect.Multimap;
+import com.google.common.collect.SetMultimap;
 
 import org.mockito.internal.debugging.Localized;
 import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -325,6 +326,27 @@ private void initializeVocabularyToIgnore() throws OntologyLoadingException {
         owlVocabulary.add(factory.getOWLBottomObjectProperty().getIRI());    	
     }
 
+
+    private void populateOntologyLanguages(Collection<OWLEntity> allEntities) {
+
+        for (OWLEntity owlEntity: allEntities) {
+		for (OWLOntology anOntology : getManager().ontologies().collect(Collectors.toSet())){
+			EntitySearcher.getAnnotationAssertionAxioms(owlEntity, anOntology).forEach(annotationAssertionAxiom -> {
+
+				OWLAnnotationValue value = annotationAssertionAxiom.getValue();
+
+				if(value.isLiteral()) {
+					if(((OWLLiteral) value).hasLang()) {
+							ontologyLanguages.add( ((OWLLiteral) value).getLang() );
+					}
+				}
+
+			});
+		}
+	}
+    }
+
+
     @Override
     public String getShortForm(IRI ontologyTermIRI) {
 
@@ -440,6 +462,8 @@ protected OWLOntology loadOntology() throws OWLOntologyCreationException {
             ResourceUsage.logUsage(getLogger(), "#### Monitoring ", getOntologyName() +
                     ":After copying of entities", ":");
 
+	    populateOntologyLanguages(allEntities);
+
             indexTerms(allEntities);
             ResourceUsage.logUsage(getLogger(), "#### Monitoring ", getOntologyName() +
                     ":After index terms", ":");
@@ -1242,11 +1266,18 @@ protected Optional<String> evaluateLabelAnnotationValue(OWLEntity entity, OWLAnn
 
     private boolean isEnglishLabel(OWLAnnotationValue value) {
         return value instanceof OWLLiteral && ((OWLLiteral) value).getLang().equalsIgnoreCase("en");
+    }
+
+    protected void evaluateAnnotationValue(OWLEntity entity, OWLAnnotationProperty annotationProperty, IRI annotationPropertyIRI, OWLAnnotationValue value, String lang) {
+
+
+
     }
 
     protected void evaluateAllAnnotationsValues(OWLEntity owlEntity) {
 
         IRI owlEntityIRI = owlEntity.getIRI();
+
         Set<String> slims = new HashSet<>();
 
         LocalizedStrings definitions = new LocalizedStrings();
@@ -1261,7 +1292,21 @@ protected void evaluateAllAnnotationsValues(OWLEntity owlEntity) {
         Collection<OBOSynonym> oboSynonyms = new HashSet<>();
         Collection<OBOXref> oboEntityXrefs = new HashSet<>();
 
-        // loop through other annotations in the imports closure
+	Set<IRI> annotationProperties = new HashSet<>();
+
+	// pass 1: populate the set of all annotation properties used
+        for (OWLOntology anOntology : getManager().ontologies().collect(Collectors.toSet())){
+                EntitySearcher.getAnnotationAssertionAxioms(owlEntity, anOntology).forEach(annotationAssertionAxiom -> {
+
+                        OWLAnnotationProperty annotationProperty = annotationAssertionAxiom.getProperty();
+                        IRI annotationPropertyIRI = annotationProperty.getIRI();
+
+			annotationProperties.add(annotationPropertyIRI);
+		});
+	}
+
+
+        // pass 2: read the annotations
         for (OWLOntology anOntology : getManager().ontologies().collect(Collectors.toSet())){
                 EntitySearcher.getAnnotationAssertionAxioms(owlEntity, anOntology).forEach(annotationAssertionAxiom -> {
                         OWLAnnotationProperty annotationProperty = annotationAssertionAxiom.getProperty();
@@ -1275,11 +1320,9 @@ protected void evaluateAllAnnotationsValues(OWLEntity owlEntity) {
                         if(value.isLiteral()) {
                             if(((OWLLiteral) value).hasLang()) {
                                 lang = ((OWLLiteral) value).getLang();
-				ontologyLanguages.add(lang);
                             }
                         }
 
-
                         if (getLabelIRI().equals(annotationPropertyIRI)) {
                             classLabels.addString(lang, evaluateLabelAnnotationValue(
                                     owlEntity, value).get());
@@ -1390,9 +1433,41 @@ else if (annotationPropertyIRI.equals(Namespaces.OWL.createIRI("deprecated"))) {
                             }
                             oboEntityXrefs.add(oboXrefs);
                         }
+
                 });
         }
 
+
+	// cross reference the set of all ontologies properties with the set of
+	// languages in the ontology.  Any missing languages are added with the English strings.
+	// Otherwise, if you switch language in the webapp to a language into which the ontology
+	// is not localised, the annotations will not appear!
+	//
+	if (termAnnotations.containsKey(owlEntityIRI)) {
+
+		Map<IRI, LocalizedStrings> annotations = termAnnotations.get(owlEntityIRI);
+
+		for(IRI annotationPropertyIri : annotations.keySet()) {
+
+			LocalizedStrings annos = annotations.get(annotationPropertyIri);
+
+			for(String ontologyLang : ontologyLanguages) {
+
+				if(!annos.getLanguages().contains(ontologyLang)) {
+					annos.setStrings(ontologyLang, annos.getStrings("", "en", "en-US"));
+				}
+			}
+
+		}
+	}
+
+	for (String ontologyLang : ontologyLanguages) {
+		if (!classLabels.getLanguages().contains(ontologyLang)) {
+			classLabels.setStrings(ontologyLang, classLabels.getStrings("", "en", "en-US"));
+		}
+	}
+
+
 	setClassLabels(owlEntityIRI, classLabels);
 
         if (definitionCitations.size() > 0) {
@@ -1416,6 +1491,7 @@ else if (annotationPropertyIRI.equals(Namespaces.OWL.createIRI("deprecated"))) {
         if (slims.size() >0) {
             setSlims(owlEntityIRI, slims);
         }
+
     }
 
     private OBOXref extractOBOXrefs (OWLAnnotation annotation) {

ontology-tools/src/main/java/uk/ac/ebi/spot/ols/util/LocalizedStrings.java

@@ -102,6 +102,7 @@ public void addDefaultString(String value) {
 
     }
 
+
     public int size() {
         int n = 0;
         for(List<String> values : this.localizations.values()) {
@@ -119,5 +120,11 @@ public void addAll(LocalizedStrings other) {
         }
 
     }
+
+    public void setStrings(String language, List<String> strings) {
+
+	localizations.put(language, new ArrayList<String>(strings));
+
+    }
 
 }