Merge pull request #169 from ncbo/multilingual_preflabels

fix:Multilingual preflabels
ncbo · Oct 21, 2024 · 106143a · 106143a
2 parents ebf586c + d06a9f4
commit 106143a
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Showing 3 changed files with 39 additions and 32 deletions.
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: a27d6ca79d47eb045b1bdfe311531827428aa504
+  branch: multilingual_preflabels
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: b279f9caa9a6a169bad7350890d7015d56e9e9b2
+  revision: 17b2f2b8522e6b36baa1d003b5e27cb536c04a03
   branch: develop
   specs:
     ncbo_cron (0.0.1)
@@ -56,8 +56,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 812dd78f02b77c9c6d579b0febf1c2a42d513022
-  branch: develop
+  revision: e7d2124381003283696ff863de5ed0dc4c18ecda
+  branch: multilingual_preflabels
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -155,7 +155,6 @@ GEM
       faraday (~> 2.0)
     ffi (1.17.0-aarch64-linux-gnu)
     ffi (1.17.0-arm64-darwin)
-    ffi (1.17.0-x86_64-linux-gnu)
     gapic-common (0.22.0)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -180,7 +179,6 @@ GEM
     google-cloud-errors (1.4.0)
     google-protobuf (3.25.5-aarch64-linux)
     google-protobuf (3.25.5-arm64-darwin)
-    google-protobuf (3.25.5-x86_64-linux)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
@@ -194,13 +192,10 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.66.0-aarch64-linux)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.66.0-arm64-darwin)
+    grpc (1.67.0-aarch64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.66.0-x86_64-linux)
+    grpc (1.67.0-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -245,7 +240,7 @@ 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)
@@ -323,7 +318,7 @@ 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)
@@ -367,7 +362,7 @@ 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)
@@ -399,7 +394,6 @@ GEM
 PLATFORMS
   aarch64-linux
   arm64-darwin-22
-  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 5)
@@ -456,4 +450,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.5.20
+   2.5.7
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