make the api use submission naturalLanguage to choose the default lan…

…guage to display

Gemfile

@@ -46,7 +46,7 @@ gem 'ncbo_annotator', git: 'https://github.com/ncbo/ncbo_annotator.git', branch:
 gem 'ncbo_cron', git: 'https://github.com/ncbo/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'pr/sync-agroportal-bioportal'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
 gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pr/sync-agroportal-ncbo'
 
 group :development do

Gemfile.lock

@@ -1,3 +1,19 @@
+GIT
+  remote: https://github.com/ncbo/goo.git
+  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
+  branch: develop
+  specs:
+    goo (0.0.2)
+      addressable (~> 2.8)
+      pry
+      rdf (= 1.0.8)
+      redis
+      request_store
+      rest-client
+      rsolr
+      sparql-client
+      uuid
+
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
   revision: 63c986880aa88c9384043e6611a682434a14aba7
@@ -11,11 +27,13 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: f239b34230131cd7cfb9eec5b34068ba990b698b
+  revision: 67810ddd2e14876d789c63c427b08af6919f661e
   branch: master
   specs:
     ncbo_cron (0.0.1)
       dante
+      faraday (~> 2)
+      faraday-follow_redirects (~> 0)
       goo
       google-analytics-data
       mlanett-redis-lock
@@ -46,25 +64,9 @@ GIT
       net-http-persistent (= 2.9.4)
       rdf (>= 1.0)
 
-GIT
-  remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: f2751fe9324e48a0a5c2a8b15580ab879fc53a2b
-  branch: pr/sync-agroportal-bioportal
-  specs:
-    goo (0.0.2)
-      addressable (~> 2.8)
-      pry
-      rdf (= 1.0.8)
-      redis
-      request_store
-      rest-client
-      rsolr
-      sparql-client
-      uuid
-
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: fc48343ad7a3f1867821c173be900cf16506b4b7
+  revision: 7c5184fc7d3b25b5c9dd54c25f5ea2b1c4951318
   branch: pr/sync-agroportal-ncbo
   specs:
     ontologies_linked_data (0.0.1)
@@ -143,6 +145,8 @@ GEM
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
+    faraday-follow_redirects (0.3.0)
+      faraday (>= 1, < 3)
     faraday-net_http (3.0.2)
     faraday-retry (2.2.1)
       faraday (~> 2.0)
@@ -223,7 +227,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0507)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -232,7 +236,7 @@ GEM
     multi_json (1.15.0)
     mutex_m (0.2.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.10)
+    net-imap (0.4.11)
       date
       net-protocol
     net-pop (0.1.2)
@@ -295,19 +299,20 @@ GEM
       redis-store (>= 1.6, < 2)
     redis-store (1.10.0)
       redis (>= 4, < 6)
-    regexp_parser (2.9.0)
+    regexp_parser (2.9.2)
     request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.6)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.63.4)
+    rubocop (1.63.5)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -359,6 +364,7 @@ GEM
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
+    strscan (3.1.0)
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.3.0)

helpers/application_helper.rb

@@ -409,6 +409,9 @@ def get_ontology_and_submission
             error 404, "Ontology #{@params["acronym"]} does not have any submissions"
           end
         end
+
+        save_submission_language(submission)
+
         return ont, submission
       end
 
@@ -438,6 +441,22 @@ def naive_expiring_cache_read(key)
         return object[:object]
       end
 
+
+      def save_submission_language(submission, language_property = :naturalLanguage)
+        request_lang = RequestStore.store[:requested_lang]
+
+        return if submission.nil? || !request_lang.blank?
+
+        submission.bring(language_property) if submission.bring?(language_property)
+        collection_natural_language = submission.send(language_property) rescue nil
+        return [] if collection_natural_language.blank?
+
+        collection_natural_language = collection_natural_language.values.flatten if collection_natural_language.is_a?(Hash)
+        submissions_language = collection_natural_language.map { |natural_language| natural_language.to_s.split('/').last[0..1] }.compact.first
+
+        RequestStore.store[:requested_lang] =  submissions_language if submissions_language
+      end
+
     end
   end
 end

test/controllers/test_classes_controller.rb

@@ -8,7 +8,8 @@ def self.before_suite
                submissions_to_process: [1, 2],
                process_submission: true,
                random_submission_count: false,
-               process_options: {process_rdf: true, extract_metadata: false}
+               process_options: {process_rdf: true, extract_metadata: false},
+               file_path: "./test/data/ontology_files/BRO_v3.2.owl",
     }
     return LinkedData::SampleData::Ontology.create_ontologies_and_submissions(options)
   end
@@ -531,4 +532,27 @@ def test_class_page_with_metric_count
     assert page_response["collection"].length == 0
   end
 
+  def test_default_multilingual
+    ont = Ontology.find("TEST-ONT-0").include(:acronym).first
+    sub = ont.latest_submission
+    sub.bring_remaining
+
+    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"]
+
+
+    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"]
+  end
 end

test/data/ontology_files/BRO_v3.2.owl

@@ -645,7 +645,7 @@
     <owl:Class rdf:about="&activity;Biospecimen_Management">
         <rdfs:subClassOf rdf:resource="&activity;Activity"/>
         <desc:definition rdf:datatype="&xsd;string">Activity related to the creation, use, or maintenance of a biorepository (http://en.wikipedia.org/wiki/Biorepository)</desc:definition>
-        <core:prefLabel rdf:datatype="&xsd;string">Biospecimen Management</core:prefLabel>
+        <core:prefLabel xml:lang="fr">Biospecimen Management</core:prefLabel>
     </owl:Class>