multilang fixes for default/non localised annotations

KonradHoeffner · Mar 8, 2022 · 388ac3e · 388ac3e
1 parent 6b26b5e
commit 388ac3e
Show file tree

Hide file tree

Showing 7 changed files with 190 additions and 33 deletions.
diff --git a/apitester/src/main/java/uk/ac/ebi/ols/apitester/OlsApiTester.java b/apitester/src/main/java/uk/ac/ebi/ols/apitester/OlsApiTester.java
@@ -231,7 +231,7 @@ public Pair<JsonElement, JsonElement> check(String filenameToSave, String path)
 		Pair<JsonElement, JsonElement> results = getBoth(path);
 
 		JsonElement result1 = results.getLeft();
-		JsonElement result2 = results.getLeft();
+		JsonElement result2 = results.getRight();
 
 		String result1Json = gson.toJson(result1);
 		String result2Json = gson.toJson(result2);
@@ -240,7 +240,7 @@ public Pair<JsonElement, JsonElement> check(String filenameToSave, String path)
 		save(filenameToSave + "_2.json", result2Json);
 
 		if(!result1Json.equals(result2Json)) {
-			System.out.println("⚠️ Response did not match");
+			System.out.println("❌ Response did not match");
 		} else {
 			System.out.println("✅ Response matched");
 		}
@@ -260,7 +260,11 @@ public Pair<JsonElement, JsonElement> getBoth(String path) throws IOException, M
 
 	public JsonElement get(String baseUrl, String path) throws IOException, MalformedURLException {
 
-		URLConnection conn = new URL(baseUrl + path).openConnection();
+		String finalUrl = baseUrl + path;
+
+		System.out.println("GET " + finalUrl);
+
+		URLConnection conn = new URL(finalUrl).openConnection();
 		InputStream is = conn.getInputStream();
 		Reader reader = new InputStreamReader(is, "UTF-8");
 		JsonElement result = JsonParser.parseReader(reader);

diff --git a/ols-apps/ols-config-importer/src/main/resources/obo-config.yaml b/ols-apps/ols-config-importer/src/main/resources/obo-config.yaml
@@ -67,4 +67,125 @@ ontologies:
     repository: https://github.com/Superraptor/GSSO
     title: Gender, Sex, and Sexual Orientation (GSSO) ontology
     tracker: https://github.com/Superraptor/GSSO/issues
+  - activity_status: active
+    contact:
+      email: [email protected]
+      github: dosumis
+      label: David Osumi-Sutherland
+      orcid: 0000-0002-7073-9172
+    dependencies:
+    - id: pr
+    - id: go
+    - id: uberon
+    - id: ro
+    - id: pato
+    - id: ncbitaxon
+    - id: bfo
+    - id: cl
+    - id: omo
+    - id: nbo
+    - id: chebi
+    - id: so
+    description: Cell types that are provisionally defined by experimental techniques
+      such as single cell or single nucleus transcriptomics rather than a straightforward
+      & coherent set of properties.
+    domain: phenotype
+    homepage: https://github.com/obophenotype/provisional_cell_ontology
+    id: pcl
+    layout: ontology_detail
+    license:
+      label: CC BY 4.0
+      logo: http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png
+      url: http://creativecommons.org/licenses/by/4.0/
+    ontology_purl: http://purl.obolibrary.org/obo/pcl.owl
+    preferredPrefix: PCL
+    products:
+    - id: pcl.owl
+      ontology_purl: http://purl.obolibrary.org/obo/pcl.owl
+    - id: pcl.obo
+      ontology_purl: http://purl.obolibrary.org/obo/pcl.obo
+    - id: pcl.json
+      ontology_purl: http://purl.obolibrary.org/obo/pcl.json
+    - id: pcl-base.owl
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-base.owl
+    - id: pcl-base.obo
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-base.obo
+    - id: pcl-base.json
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-base.json
+    - id: pcl-full.owl
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-full.owl
+    - id: pcl-full.obo
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-full.obo
+    - id: pcl-full.json
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-full.json
+    - id: pcl-simple.owl
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-simple.owl
+    - id: pcl-simple.obo
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-simple.obo
+    - id: pcl-simple.json
+      ontology_purl: http://purl.obolibrary.org/obo/pcl-simple.json
+    repository: https://github.com/obophenotype/provisional_cell_ontology
+    title: Provisional Cell Ontology
+    tracker: https://github.com/obophenotype/provisional_cell_ontology/issues
+  - activity_status: active
+    build:
+      checkout: git clone https://github.com/scdodev/scdo-ontology.git
+      path: .
+      system: git
+    contact:
+      email: [email protected]
+      github: JadeHotchkiss
+      label: Jade Hotchkiss
+      orcid: 0000-0002-2193-0704
+    dependencies:
+    - id: apollo_sv
+    - id: aro
+    - id: chebi
+    - id: chmo
+    - id: cmo
+    - id: doid
+    - id: dron
+    - id: duo
+    - id: envo
+    - id: eupath
+    - id: exo
+    - id: gaz
+    - id: gsso
+    - id: hp
+    - id: hsapdv
+    - id: ico
+    - id: ido
+    - id: idomal
+    - id: mp
+    - id: nbo
+    - id: ncit
+    - id: obi
+    - id: ogms
+    - id: opmi
+    - id: pr
+    - id: sbo
+    - id: stato
+    - id: symp
+    - id: uo
+    - id: vo
+    - id: vt
+    description: An ontology for the standardization of terminology and integration
+      of knowledge about Sickle Cell Disease.
+    domain: disease
+    homepage: https://scdontology.h3abionet.org/
+    id: scdo
+    layout: ontology_detail
+    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
+    preferredPrefix: SCDO
+    products:
+    - id: scdo.owl
+      ontology_purl: http://purl.obolibrary.org/obo/scdo.owl
+    - id: scdo.obo
+      ontology_purl: http://purl.obolibrary.org/obo/scdo.obo
+    repository: https://github.com/scdodev/scdo-ontology
+    title: Sickle Cell Disease Ontology
+    tracker: https://github.com/scdodev/scdo-ontology/issues
 
diff --git a/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/loader/NodeCreator.java b/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/loader/NodeCreator.java
@@ -184,16 +184,19 @@ protected static void addAnnotationPropertiesConditionally(OntologyLoader loader
 		    for (IRI property : annotations.keySet()) {
 		        LocalizedStrings annotationLabels = loader.getTermLabels().get(property);
 		        LocalizedStrings annotationValues = annotations.get(property);
-				List<String> enValues = annotationValues.getStrings("en");
-				if(enValues != null) {
-					String label = annotationLabels.getFirstString("en");
-					String[] values = enValues.toArray(new String[0]);
+				List<String> defaultValues = annotationValues.getStrings("en", "en-US");
+				if(defaultValues != null) {
+					String label = annotationLabels.getFirstString("en", "en-US");
+					String[] values = defaultValues.toArray(new String[0]);
 					nodeProperties.put(ANNOTATION_DESIGNATION + label, values);
 				}
-				for (String language : annotationLabels.getNonEnLanguages()) {
+				for (String language : annotationLabels.getLanguages()) {
+					if(language.equals("")) {
+						continue;
+					}
 					List<String> localizedValues = annotationValues.getStrings(language);
 					if(localizedValues == null || localizedValues.size() == 0) {
-						localizedValues = annotationValues.getStrings("en");
+						localizedValues = annotationValues.getStrings("en", "en-US");
 					}
 					if (localizedValues != null) {
 						String label = annotationLabels.getFirstString(language);

diff --git a/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Individual.java b/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Individual.java
@@ -204,16 +204,24 @@ public Map<String, Object> getAnnotationByLang(String lang) {
 
         Map<String, Object> res = new TreeMap<>();
 
-        if (lang.equals("en") && annotation != null) {
+        if ( (lang.equals("en") || lang.startsWith("en-")) && annotation != null) {
             res.putAll(annotation.asMap());
         }
 
         for (String k : localizedAnnotations.keySet()) {
-            if (k.indexOf(lang + "-") == 0) {
-                res.put(k.substring(lang.length() + 1), localizedAnnotations.get(k));
-            }
+
+		int n = lang.lastIndexOf('-');
+
+		if(n != -1) {
+			String annoLang = lang.substring(0, n);
+
+			if (annoLang.equalsIgnoreCase(lang)) {
+				res.put(k.substring(n + 1), localizedAnnotations.get(k));
+			}
+		}
         }
 
         return res;
     }
+
 }
diff --git a/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Property.java b/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Property.java
@@ -203,14 +203,21 @@ public Map<String, Object> getAnnotationByLang(String lang) {
 
         Map<String, Object> res = new TreeMap<>();
 
-        if (lang.equals("en") && annotation != null) {
+        if ( (lang.equals("en") || lang.startsWith("en-")) && annotation != null) {
             res.putAll(annotation.asMap());
         }
 
         for (String k : localizedAnnotations.keySet()) {
-            if (k.indexOf(lang + "-") == 0) {
-                res.put(k.substring(lang.length() + 1), localizedAnnotations.get(k));
-            }
+
+		int n = lang.lastIndexOf('-');
+
+		if(n != -1) {
+			String annoLang = lang.substring(0, n);
+
+			if (annoLang.equalsIgnoreCase(lang)) {
+				res.put(k.substring(n + 1), localizedAnnotations.get(k));
+			}
+		}
         }
 
         return res;

diff --git a/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Term.java b/ols-neo4j/src/main/java/uk/ac/ebi/spot/ols/neo4j/model/Term.java
@@ -286,19 +286,27 @@ public Map<String, Object> getAnnotationByLang(String lang) {
 
         Map<String, Object> res = new TreeMap<>();
 
-        if (lang.equals("en") && annotation != null) {
+        if ( (lang.equals("en") || lang.startsWith("en-")) && annotation != null) {
             res.putAll(annotation.asMap());
         }
 
         for (String k : localizedAnnotations.keySet()) {
-            if (k.indexOf(lang + "-") == 0) {
-                res.put(k.substring(lang.length() + 1), localizedAnnotations.get(k));
-            }
+
+		int n = lang.lastIndexOf('-');
+
+		if(n != -1) {
+			String annoLang = lang.substring(0, n);
+
+			if (annoLang.equalsIgnoreCase(lang)) {
+				res.put(k.substring(n + 1), localizedAnnotations.get(k));
+			}
+		}
         }
 
         return res;
     }
 
+
     @JsonProperty(value = IS_DEFINING_ONTOLOGY)
     public boolean isLocal() {
         return isLocal;

diff --git a/ontology-tools/src/main/java/uk/ac/ebi/spot/ols/util/LocalizedStrings.java b/ontology-tools/src/main/java/uk/ac/ebi/spot/ols/util/LocalizedStrings.java
@@ -16,7 +16,7 @@ public LocalizedStrings() {
 
     public LocalizedStrings(Map<String,String> strings) {
         for(String lang : strings.keySet()) {
-            addString(lang, strings.get(lang));
+            addString(lang, strings.get(lang.toLowerCase()));
         }
     }
 
@@ -27,19 +27,22 @@ public Set<String> getLanguages() {
     public Set<String> getNonEnLanguages() {
 	Set<String> langs = new HashSet<>();
 	for(String lang : localizations.keySet()) {
-		if(lang.compareTo("en") != 0 && lang.compareTo("") != 0) {
+		if(lang.compareTo("en") != 0 && (!lang.startsWith("en-")) && lang.compareTo("") != 0) {
 			langs.add(lang);
 		}
 	}
 	return langs;
     }
 
-    public List<String> getStrings(String language) {
+    public List<String> getStrings(String... languages) {
 
-        List<String> strings = localizations.get(language);
+	for(String lang : languages) {
 
-        if(strings != null) {
-            return strings;
+		List<String> strings = localizations.get(lang.toLowerCase());
+
+		if(strings != null) {
+			return strings;
+		}
 	}
 
 	List<String> defaults = localizations.get("");
@@ -59,12 +62,15 @@ public Map<String, List<String>> getStrings() {
         return localizations;
     }
 
-    public String getFirstString(String language) {
+    public String getFirstString(String... languages) {
 
-        List<String> strings = localizations.get(language);
+	for(String lang : languages) {
 
-        if(strings != null && strings.size() > 0) {
-            return strings.get(0);
+		List<String> strings = localizations.get(lang.toLowerCase());
+
+		if(strings != null && strings.size() > 0) {
+			return strings.get(0);
+		}
 	}
 
 	List<String> defaults = localizations.get("");
@@ -78,11 +84,11 @@ public String getFirstString(String language) {
 
     public void addString(String language, String value) {
 
-        List<String> strings = localizations.get(language);
+        List<String> strings = localizations.get(language.toLowerCase());
 
         if(strings == null) {
             strings = new ArrayList<>();
-            localizations.put(language, strings);
+            localizations.put(language.toLowerCase(), strings);
         }
 
         if(!strings.contains(value)) {