changes required to support ncbo/ontologies_linked_data#220

ncbo · Oct 19, 2024 · fd54ad2 · fd54ad2
1 parent 84febcf
commit fd54ad2
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diff --git a/Gemfile b/Gemfile
@@ -47,8 +47,8 @@ gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
 gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
 gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
-gem 'goo', github: 'ncbo/goo', branch: 'develop'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'multilingual_preflabels'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'multilingual_preflabels'
 
 
 group :development do

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 74a012eebb9433d031eb00df5abbe488cb8b4512
-  branch: develop
+  revision: d6b84e12d61317dbddc1b86cb1451acb37915369
+  branch: multilingual_preflabels
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -56,8 +56,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 812dd78f02b77c9c6d579b0febf1c2a42d513022
-  branch: develop
+  revision: dec2e789e808e5edea18ca015ee487ddbe02f288
+  branch: multilingual_preflabels
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -176,7 +176,7 @@ GEM
     google-cloud-core (1.7.1)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-env (2.2.0)
+    google-cloud-env (2.2.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
     google-protobuf (3.25.5-aarch64-linux)
@@ -189,23 +189,23 @@ GEM
       grpc (~> 1.41)
     googleapis-common-protos-types (1.16.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.11.0)
+    googleauth (1.11.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.66.0-aarch64-linux)
+    grpc (1.67.0-aarch64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.66.0-arm64-darwin)
+    grpc (1.67.0-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.66.0-x86_64-darwin)
+    grpc (1.67.0-x86_64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.66.0-x86_64-linux)
+    grpc (1.67.0-x86_64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -221,7 +221,7 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.7.2)
-    jwt (2.9.1)
+    jwt (2.9.3)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.3)
@@ -250,7 +250,7 @@ GEM
     net-http (0.4.1)
       uri
     net-http-persistent (2.9.4)
-    net-imap (0.4.16)
+    net-imap (0.4.17)
       date
       net-protocol
     net-pop (0.1.2)
@@ -328,7 +328,7 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.66.1)
+    rubocop (1.67.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -372,7 +372,7 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.23.1)
+    sshkit (1.23.2)
       base64
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)

diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb
@@ -82,7 +82,6 @@ def test_notation_lookup
     assert response["@id"] == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Ontology_Development_and_Management"
   end
 
-
   def test_all_class_pages
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
 
@@ -99,7 +98,7 @@ def test_all_class_pages
       assert last_response.ok?
       page_response = MultiJson.load(last_response.body)
       page_response["collection"].each do |item|
-        assert_instance_of String, item["prefLabel"]
+        assert_instance_of String, item["prefLabel"], item["@id"]
         assert_instance_of String, item["@id"]
         assert_instance_of Hash, item["@context"]
         assert_instance_of Hash, item["links"]
@@ -131,6 +130,7 @@ def test_single_cls_all
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
     clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction',
             "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ]
+
     clss_ids.each do |cls_id|
       escaped_cls= CGI.escape(cls_id)
       call = "/ontologies/#{ont.acronym}/classes/#{escaped_cls}?include=all"
@@ -149,6 +149,7 @@ def test_single_cls_properties
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
     clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction',
             "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ]
+
     clss_ids.each do |cls_id|
       escaped_cls= CGI.escape(cls_id)
       call = "/ontologies/#{ont.acronym}/classes/#{escaped_cls}?include=properties"
@@ -163,7 +164,6 @@ def test_single_cls_properties
 
   def test_single_cls
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
-
     clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction',
             "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ]
 
@@ -208,7 +208,7 @@ def test_roots_for_cls
     roots = MultiJson.load(last_response.body)
     assert_equal 9, roots.length
     roots.each do |r|
-      assert_instance_of String, r["prefLabel"]
+      assert_instance_of String, r["prefLabel"], r["@id"]
       assert_instance_of String, r["@id"]
       assert r.include?"hasChildren"
       #By definition roots have no parents
@@ -221,7 +221,6 @@ def test_roots_for_cls
   end
 
   def test_classes_for_not_parsed_ontology
-
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
 
     #first submission was not parsed
@@ -232,7 +231,6 @@ def test_classes_for_not_parsed_ontology
   end
 
   def test_tree
-
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
 
     clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction',
@@ -251,7 +249,6 @@ def test_tree
   end
 
   def test_path_to_root_for_cls
-
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
     clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction',
             "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ]
@@ -264,7 +261,6 @@ def test_path_to_root_for_cls
   end
 
   def test_ancestors_for_cls
-
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
     ancestors_data = {}
     ancestors_data['http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction'] =[
@@ -454,7 +450,6 @@ def test_calls_not_found
   end
 
   def test_children_for_cls_round_trip
-
     clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_and_Cellular_Data',
             "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Microscope" ]
 
@@ -511,7 +506,7 @@ def test_class_page_with_metric_count
       assert last_response.ok?
       page_response = MultiJson.load(last_response.body)
       page_response["collection"].each do |item|
-        assert_instance_of String, item["prefLabel"]
+        assert_instance_of String, item["prefLabel"], item["@id"]
         assert_instance_of String, item["@id"]
         assert_instance_of Hash, item["@context"]
         assert_instance_of Hash, item["links"]
@@ -536,22 +531,40 @@ def test_default_multilingual
     sub = ont.latest_submission
     sub.bring_remaining
 
-    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}"
+    # rdfs:label is NOT present and the prefLabel is NOT defined for the ontology or portal language
+    sub.naturalLanguage = ['es']
+    sub.save
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Community_Engagement')}"
     assert last_response.ok?
     page_response = MultiJson.load(last_response.body)
+    # does not contain a value in english show the generated one
+    assert_equal 'Community_Engagement', page_response["prefLabel"]
 
+    # rdfs:label is present but NOT for either the ontology or portal language
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
     # does not contain a value in english show the generated one
     assert_equal 'Biospecimen_Management', page_response["prefLabel"]
 
+    # prefLabel NOT present, rdfs:label is present but NOT for either the ontology or portal language
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Gene_Therapy')}"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
+    # does not contain a value in english show the generated one
+    assert_equal 'Gene_Therapy', page_response["prefLabel"]
 
+    # prefLabel is present in the ontology language
     sub.naturalLanguage = ['fr']
     sub.save
-
     get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}"
     assert last_response.ok?
     page_response = MultiJson.load(last_response.body)
-
     # show french value as specified in submission naturalLanguage
     assert_equal 'Biospecimen Management', page_response["prefLabel"]
+
+    sub.naturalLanguage = []
+    sub.save
   end
+
 end