Revert "Merge branch 'pr/refactor/use-replace-url-prefix' of https://…

…github.com/ontoportal-lirmm/ontologies_api"

This reverts commit 38a3b7e, reversing
changes made to 3e72043.

Gemfile

@@ -41,12 +41,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO
-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: 'develop'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'master'
+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 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
+gem 'sparql-client', github: 'ncbo/sparql-client', 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

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 7a897a8e9c01d3a412d9011df8e26d770d58cd7d
-  branch: develop
+  revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: f60341e8426adcad447a6fc3adb5b80207c5987a
-  branch: develop
+  revision: 63c986880aa88c9384043e6611a682434a14aba7
+  branch: master
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 6185e9f59f35fe131bf53624ef82dd8e399e5448
-  branch: develop
+  revision: 46bd8e7eb7cfde6d173bdf55808a8e28d6700f1e
+  branch: master
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -42,8 +42,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 41e61ddccdde09a45961b0f2bf7ad0ddb18b382e
-  branch: develop
+  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
+  branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: c77d0b390e19c394989e9467e447fcc653b53fa5
-  branch: develop
+  revision: ec3236a71ff172579923245646d0ea058844794e
+  branch: master
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -73,8 +73,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
-  branch: develop
+  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
+  branch: master
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)

helpers/application_helper.rb

@@ -346,7 +346,8 @@ def uri_as_needed(id)
       # If the setting is enabled, replace the URL prefix with the proper id prefix
       # EX: http://stagedata.bioontology.org/ontologies/BRO would become http://data.bioontology.org/ontologies/BRO
       def replace_url_prefix(id)
-        LinkedData::Models::Base.replace_url_prefix_to_id(id)
+        id = id.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix) if LinkedData.settings.replace_url_prefix && id.start_with?(LinkedData.settings.rest_url_prefix)
+        id
       end
 
       def retrieve_latest_submissions(options = {})

helpers/batch_helper.rb

@@ -20,8 +20,9 @@ def batch_class_lookup(class_id_by_ontology, goo_include)
         class_id_to_ontology = Hash.new
         class_id_by_ontology.keys.each do |ont_id_orig|
           ont_id = ont_id_orig
-          ont_id = LinkedData::Models::Base.replace_url_prefix_to_id(ont_id_orig.to_s)
-
+          if LinkedData.settings.replace_url_prefix && ont_id_orig.to_s.start_with?(LinkedData.settings.rest_url_prefix)
+            ont_id = ont_id_orig.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix)
+          end
           if all_latest_by_id[ont_id]
             latest_submissions << all_latest_by_id[ont_id]
             all_class_ids << class_id_by_ontology[ont_id_orig]
@@ -42,7 +43,10 @@ def batch_class_lookup(class_id_by_ontology, goo_include)
           ont_classes.each do |cls|
             if class_id_to_ontology[cls.id.to_s]
               ont_id_orig = class_id_to_ontology[cls.id.to_s]
-              ont_id = LinkedData::Models::Base.replace_url_prefix_to_id(ont_id_orig.to_s)
+              ont_id = ont_id_orig
+              if LinkedData.settings.replace_url_prefix && ont_id_orig.to_s.start_with?(LinkedData.settings.rest_url_prefix)
+                ont_id = ont_id_orig.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix)
+              end
               if all_latest_by_id[ont_id]
                 cls.submission = all_latest_by_id[ont_id]
                 to_reply << cls