Merge pull request #19 from SynBioDex/14-return_terms_in_english

14 return terms in english
SynBioDex · Apr 19, 2021 · 7bb61ac · 7bb61ac
2 parents ef099e3 + 8ed60d2
commit 7bb61ac
Show file tree

Hide file tree

Showing 2 changed files with 43 additions and 10 deletions.
diff --git a/test/test_ontology.py b/test/test_ontology.py
@@ -48,5 +48,13 @@ def test_dynamic_ontology_attributes(self):
     def test_NCIT(self):
         self.assertEqual(NCIT.Growth_Medium, 'https://identifiers.org/ncit:C85504')
 
+    def test_OM(self):
+        self.assertEqual(OM.molar, OM.molair)
+        self.assertEqual(OM.liter, OM.liter)
+        self.assertEqual(OM.meter, OM.metre)
+        self.assertEqual(OM.get_term_by_uri('http://www.ontology-of-units-of-measure.org/resource/om-2/hour'),
+                         'hour')
+
+
 if __name__ == '__main__':
     unittest.main()
diff --git a/tyto/owlet.py b/tyto/owlet.py
@@ -87,7 +87,8 @@ def _convert_ontobee_response(response):
             response = response.convert()  # Convert http response to JSON
             for var, binding in zip(response['head']['vars'],
                                     response['results']['bindings']):
-                converted_response.append(binding[var]['value'])
+                if var in binding:
+                    converted_response.append(binding[var]['value'])
         return converted_response
 
     def _convert_rdflib_response(response):
@@ -107,12 +108,20 @@ def get_term_by_uri(self, uri):
             SELECT distinct ?label
             WHERE
             {{{{
-                <{uri}> rdfs:label ?label .
+                optional
+                {{{{
+                    <{uri}> rdfs:label ?label .
+                     filter langMatches(lang(?label), "en")
+                }}}}
+                optional
+                {{{{
+                    <{uri}> rdfs:label ?label .
+                }}}}
             }}}}
             '''.format(uri=uri)
         error_msg = '{} not found'.format(uri)
         response = self._query(query, error_msg)
-        return response[0]
+        return self._reverse_sanitize_term(response[0])
 
     def get_uri_by_term(self, term):
         '''
@@ -127,19 +136,25 @@ def get_uri_by_term(self, term):
         # than underscores. This creates a problem when looking up terms by
         # an attribute, e.g., SBO.systems_biology_representation
         sanitized_term=self._sanitize_term(term)
-
         query = '''
             SELECT distinct ?uri
             {{from_clause}}
             WHERE
             {{{{
-                {{{{?uri rdfs:label "{sanitized_term}"}}}} UNION
-                {{{{?uri rdfs:label "{sanitized_term}"^^xsd:string}}}} UNION
-                {{{{?uri rdfs:label "{sanitized_term}"@en}}}} UNION
-                {{{{?uri rdfs:label "{sanitized_term}"@nl}}}}
+                optional 
+                {{{{
+                    ?uri rdfs:label "{sanitized_term}"@en
+                }}}}
+                optional
+                {{{{ 
+                    ?uri rdfs:label "{sanitized_term}"
+                }}}}
+                optional
+                {{{{ 
+                    ?uri rdfs:label "{sanitized_term}"^^xsd:string
+                }}}}
             }}}}
             '''.format(sanitized_term=sanitized_term)
-
         error_msg = '{} not a valid ontology term'.format(term)
         response = self._query(query, error_msg)[0]
         return self._to_user(response)
@@ -160,6 +175,12 @@ def _sanitize_term(self, term):
         # or changing camel-case to snake-case
         return term
 
+    def _reverse_sanitize_term(self, term):
+        # Some Ontology instances may override this method to perform string
+        # manipulation of an ontology terms, for example, replacing spaces
+        # or changing camel-case to snake-case
+        return term
+
     def get_ontology(self):
         query = '''
             SELECT distinct ?ontology_uri
@@ -199,6 +220,9 @@ def multi_replace(target_uri, old_namespaces, new_namespace):
                                            'http://identifiers.org/so/SO:'],
                                            'http://purl.obolibrary.org/obo/SO_')
 
+SBO = Ontology(path=installation_path('ontologies/SBO_OWL.owl'),
+               endpoint='http://sparql.hegroup.org/sparql/',
+               uri='http://purl.obolibrary.org/obo/sbo.owl')
 SBO = Ontology(path=installation_path('ontologies/SBO_OWL.owl'),
                endpoint='http://sparql.hegroup.org/sparql/',
                uri='http://purl.obolibrary.org/obo/sbo.owl')
@@ -225,7 +249,8 @@ def multi_replace(target_uri, old_namespaces, new_namespace):
 
 OM = Ontology(path=installation_path('ontologies/om-2.0.rdf'),
               endpoint=None)
-
+OM._sanitize_term = lambda term: term.replace('liter', 'litre').replace('meter', 'metre').replace('molar', 'molair')
+OM._reverse_sanitize_term = lambda term: term.replace('litre', 'liter').replace('metre', 'meter').replace('molair', 'molar')
 '''
 'http://purl.obolibrary.org/obo/SO_0000167'
 'http://biomodels.net/SBO/SBO_0000241'