Merge pull request #170 from ncbo/develop

Develop -> Master merge, Release v5.33.1
ncbo · Oct 22, 2024 · ae2d27d · ae2d27d
2 parents b5422b1 + 8d3d031
commit ae2d27d
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diff --git a/Gemfile b/Gemfile
@@ -41,14 +41,13 @@ gem 'unicorn-worker-killer'
 gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
-
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
+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: 'multilingual_preflabels'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
 
 
 group :development do

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: f943ac33e87c55c88131c32d826ed5d39c89302c
-  branch: master
+  revision: a27d6ca79d47eb045b1bdfe311531827428aa504
+  branch: multilingual_preflabels
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: d46d667ec1b2343fbcdab587f1a70e763b894133
-  branch: master
+  revision: b2731c98bfef0958fecb440c8648b7755a670895
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -27,8 +27,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 25d54ae938e63e9d1a6f4b8eb697e0ec2ff1ef87
-  branch: master
+  revision: 4255106846207d79a41716615bc57a379256212b
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -45,8 +45,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3
-  branch: master
+  revision: 084cfc74a78b1c6334f3b74e228ddbf80d36e30a
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -56,8 +56,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 9ab4be437ed84f5a480e7f0d8799824fcea310ae
-  branch: master
+  revision: a65341b714f2734c6ad5fd1999c9e1bf03a17585
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -76,8 +76,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -456,4 +456,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.5.7
+   2.5.20
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