Merge pull request #149 from ontoportal-lirmm/pr/sync-agroportal-biop…

…ortal

Feature: make the api use submission naturalLanguage  to choose the default language to display

Gemfile

@@ -40,13 +40,15 @@ gem 'unicorn-worker-killer'
 gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
-# NCBO
+
+# NCBO gems (can be from a local dev path or from rubygems/git)
+gem 'ncbo_annotator', git: 'https://github.com/ncbo/ncbo_annotator.git', branch: 'master'
+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: 'ncbo/goo', branch: 'develop'
-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 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'feature/multilingual-support-add-search-and-languages-serialization'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pr/sync-agroportal-ncbo'
+
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: a55ef42e92bc02129992c77890278831f8ca5387
+  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
   branch: develop
   specs:
     goo (0.0.2)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 7531e10ad55ac66e925c099d7fc05a5a3ceae67e
-  branch: develop
+  revision: 63c986880aa88c9384043e6611a682434a14aba7
+  branch: master
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -27,8 +27,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 98dc1a9bb8aba4ef41a1687251ca1245edd5de57
-  branch: develop
+  revision: 67810ddd2e14876d789c63c427b08af6919f661e
+  branch: master
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -45,8 +45,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: f92a42f660635522eb8709e618ff2e641aef0d17
-  branch: develop
+  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
+  branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -55,9 +55,19 @@ GIT
       redis
 
 GIT
-  remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 0227d37c6431f52a7fd85bdb597cc3d32e975098
-  branch: feature/multilingual-support-add-search-and-languages-serialization
+  remote: https://github.com/ncbo/sparql-client.git
+  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
+  branch: master
+  specs:
+    sparql-client (1.0.1)
+      json_pure (>= 1.4)
+      net-http-persistent (= 2.9.4)
+      rdf (>= 1.0)
+
+GIT
+  remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
+  revision: 67f9e10c03880431590b15ea5b27d2f1fe1354c4
+  branch: pr/sync-agroportal-ncbo
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -74,16 +84,6 @@ GIT
       rsolr
       rubyzip
 
-GIT
-  remote: https://github.com/ncbo/sparql-client.git
-  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
-  branch: develop
-  specs:
-    sparql-client (1.0.1)
-      json_pure (>= 1.4)
-      net-http-persistent (= 2.9.4)
-      rdf (>= 1.0)
-
 GIT
   remote: https://github.com/palexander/rack-post-body-to-params.git
   revision: 0fd30e710386d0cb8a3a6833d9549d7b655d5398
@@ -114,7 +114,9 @@ GEM
     backports (3.25.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
-    bcrypt_pbkdf (1.1.0)
+    bcrypt_pbkdf (1.1.1)
+    bcrypt_pbkdf (1.1.1-arm64-darwin)
+    bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (1.4.2)
     builder (3.2.4)
     capistrano (3.18.1)
@@ -271,7 +273,7 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.5)
-    racc (1.7.3)
+    racc (1.8.0)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -287,7 +289,7 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rack-timeout (0.6.3)
+    rack-timeout (0.7.0)
     rainbow (3.1.1)
     raindrops (0.20.1)
     rake (10.5.0)
@@ -303,15 +305,16 @@ 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)
@@ -367,6 +370,7 @@ 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

@@ -531,4 +531,27 @@ 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>