Fix: detaching views from ontology (#48)

* add detach a view from an ontology test

* fix populate_from_params help to reset object value to empty

* reset to master branch the api dependecies

Gemfile

@@ -42,12 +42,12 @@ 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 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'development'
+gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'master'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'master'
 
 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/ncbo_ontology_recommender.git
-  revision: d0ac992c88bd417f2f2137ba62934c3c41b6db7c
+  revision: f440ae855a217807fead1d20629a0f187997b973
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -11,8 +11,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: cda6aff2338e2a2831e4e7bf716abdf8fa8483d2
-  branch: development
+  revision: bd7154217438c3b9160e0e9b495c7c718b55fbf8
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: e9b708c40b2b22b935fb48d18ed19de8148fca35
-  branch: development
+  revision: bf682ec9c1baa3e9e7eae2e5d095187b0f900bf7
+  branch: master
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -103,16 +103,16 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.1)
+    addressable (2.8.5)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.4.1)
+    airbrussh (1.5.0)
       sshkit (>= 1.6.1, != 1.7.0)
-    backports (3.23.0)
-    bcrypt (3.1.18)
+    backports (3.24.1)
+    bcrypt (3.1.19)
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.17.1)
+    capistrano (3.17.3)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -125,7 +125,8 @@ GEM
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.2.0)
+    concurrent-ruby (1.2.2)
+    connection_pool (2.4.1)
     cube-ruby (0.0.3)
     dante (0.2.0)
     date (3.3.3)
@@ -157,12 +158,12 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.15.5)
+    ffi (1.16.3)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-apis-analytics_v3 (0.12.0)
-      google-apis-core (>= 0.9.1, < 2.a)
-    google-apis-core (0.11.0)
+    google-apis-analytics_v3 (0.13.0)
+      google-apis-core (>= 0.11.0, < 2.a)
+    google-apis-core (0.11.1)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (>= 0.16.2, < 2.a)
       httpclient (>= 2.8.1, < 3.a)
@@ -171,10 +172,9 @@ GEM
       retriable (>= 2.0, < 4.a)
       rexml
       webrick
-    googleauth (1.3.0)
+    googleauth (1.8.1)
       faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
-      memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
@@ -191,9 +191,9 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.6.3)
-    jwt (2.7.0)
+    jwt (2.7.1)
     kgio (2.11.4)
-    libxml-ruby (4.0.0)
+    libxml-ruby (4.1.1)
     logger (1.5.3)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -202,20 +202,19 @@ GEM
       net-imap
       net-pop
       net-smtp
-    memoist (0.16.2)
     method_source (1.0.0)
-    mime-types (3.4.1)
+    mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2022.0105)
-    mini_mime (1.1.2)
+    mime-types-data (3.2023.1003)
+    mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.4)
+    net-imap (0.4.1)
       date
       net-protocol
     net-pop (0.1.2)
@@ -224,11 +223,11 @@ GEM
       timeout
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
-    net-smtp (0.3.3)
+    net-smtp (0.4.0)
       net-protocol
-    net-ssh (7.0.1)
+    net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (8.16.0)
+    newrelic_rpm (9.5.0)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
@@ -239,37 +238,40 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.1)
+    public_suffix (5.0.3)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-attack (6.6.1)
       rack (>= 1.0, < 3)
-    rack-cache (1.13.0)
+    rack-cache (1.14.0)
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
-    rack-mini-profiler (3.0.0)
+    rack-mini-profiler (3.1.1)
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
-    rack-test (2.0.2)
+    rack-test (2.1.0)
       rack (>= 1.3)
     rack-timeout (0.6.3)
-    raindrops (0.20.0)
+    raindrops (0.20.1)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
     redcarpet (3.6.0)
-    redis (4.8.1)
+    redis (5.0.7)
+      redis-client (>= 0.9.0)
     redis-activesupport (5.3.0)
       activesupport (>= 3, < 8)
       redis-store (>= 1.3, < 2)
+    redis-client (0.17.0)
+      connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
-    redis-store (1.9.1)
-      redis (>= 4, < 5)
+    redis-store (1.10.0)
+      redis (>= 4, < 6)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -280,7 +282,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.2.5)
+    rexml (3.2.6)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -289,7 +291,7 @@ GEM
     rubyzip (2.3.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    signet (0.17.0)
+    signet (0.18.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
@@ -316,13 +318,13 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.21.3)
+    sshkit (1.21.5)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
-    temple (0.10.0)
-    tilt (2.0.11)
-    timeout (0.3.2)
+    temple (0.10.3)
+    tilt (2.3.0)
+    timeout (0.4.0)
     trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
@@ -341,6 +343,7 @@ GEM
     webrick (1.8.1)
 
 PLATFORMS
+  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES

helpers/application_helper.rb

@@ -31,6 +31,7 @@ def populate_from_params(obj, params)
           # Deal with empty strings for String and URI
           empty_string = value.is_a?(String) && value.empty?
           old_string_value_exists = obj.respond_to?(attribute) && (obj.send(attribute).is_a?(String) || obj.send(attribute).is_a?(RDF::URI))
+          old_string_value_exists = old_string_value_exists || (obj.respond_to?(attribute) && obj.send(attribute).is_a?(LinkedData::Models::Base))
           if old_string_value_exists && empty_string
             value = nil
           elsif empty_string
@@ -59,7 +60,7 @@ def populate_from_params(obj, params)
             # Replace the initial value with the object, handling Arrays as appropriate
             if value.is_a?(Array)
               value = value.map {|e| attr_cls.find(uri_as_needed(e)).include(attr_cls.attributes).first}
-            else
+            elsif !value.nil?
               value = attr_cls.find(uri_as_needed(value)).include(attr_cls.attributes).first
             end
           elsif attr_cls

test/controllers/test_ontologies_controller.rb

@@ -254,6 +254,32 @@ def test_download_acl_only
   end
 
 
+  def test_detach_a_view
+    view = Ontology.find(@@view_acronym).include(:viewOf).first
+    ont =  view.viewOf
+    refute_nil view
+    refute_nil ont
+
+    remove_view_of = {viewOf: ''}
+    patch "/ontologies/#{@@view_acronym}", MultiJson.dump(remove_view_of), "CONTENT_TYPE" => "application/json"
+
+    assert last_response.status == 204
+
+    get "/ontologies/#{@@view_acronym}"
+    onto = MultiJson.load(last_response.body)
+    assert_nil onto["viewOf"]
+
+
+    add_view_of = {viewOf: @@acronym}
+    patch "/ontologies/#{@@view_acronym}", MultiJson.dump(add_view_of), "CONTENT_TYPE" => "application/json"
+
+    assert last_response.status == 204
+
+    get "/ontologies/#{@@view_acronym}"
+    onto = MultiJson.load(last_response.body)
+    assert_equal onto["viewOf"], ont.id.to_s
+  end
+
   private
 
   def check400(response)