Small code refactor to reuse replace url prefix

Gemfile

@@ -46,7 +46,7 @@ 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 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pr/fix/get-rest-mapping-with-prefix-url'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
 
 group :development do

Gemfile.lock

@@ -52,9 +52,19 @@ GIT
       redis
 
 GIT
-  remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 8196bf34b45c75f8104bb76dfcba1db0f2c048e4
+  remote: https://github.com/ncbo/sparql-client.git
+  revision: fb4a89b420f8eb6dda5190a126b6c62e32c4c0c9
   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: 4cbb5b3e87a91fdcf073f93db733602726405427
+  branch: pr/fix/get-rest-mapping-with-prefix-url
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -71,16 +81,6 @@ GIT
       rsolr
       rubyzip
 
-GIT
-  remote: https://github.com/ncbo/sparql-client.git
-  revision: fb4a89b420f8eb6dda5190a126b6c62e32c4c0c9
-  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/palexander/rack-post-body-to-params.git
   revision: 0fd30e710386d0cb8a3a6833d9549d7b655d5398
@@ -103,8 +103,8 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.0)
-      public_suffix (>= 2.0.2, < 5.0)
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
     airbrussh (1.4.1)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.23.0)
@@ -131,7 +131,7 @@ GEM
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    faraday (1.10.1)
+    faraday (1.10.2)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
@@ -188,7 +188,7 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.6.2)
-    jwt (2.4.1)
+    jwt (2.5.0)
     kgio (2.11.4)
     libxml-ruby (3.2.3)
     logger (1.5.1)
@@ -213,7 +213,7 @@ GEM
       net-ssh (>= 2.6.5)
     net-ssh (7.0.1)
     netrc (0.11.0)
-    newrelic_rpm (8.9.0)
+    newrelic_rpm (8.10.0)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
@@ -224,7 +224,7 @@ GEM
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (4.0.7)
+    public_suffix (5.0.0)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -246,7 +246,7 @@ GEM
     rdf (1.0.8)
       addressable (>= 2.2)
     redcarpet (3.5.1)
-    redis (4.7.1)
+    redis (4.8.0)
     redis-activesupport (5.3.0)
       activesupport (>= 3, < 8)
       redis-store (>= 1.3, < 2)
@@ -325,6 +325,7 @@ GEM
     webrick (1.7.0)
 
 PLATFORMS
+  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES

helpers/application_helper.rb

@@ -344,8 +344,7 @@ 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)
-        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
+        LinkedData::Models::Base.replace_url_prefix_to_id(id)
       end
 
       def retrieve_latest_submissions(options = {})

helpers/batch_helper.rb

@@ -20,9 +20,8 @@ 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
-          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
+          ont_id = LinkedData::Models::Base.replace_url_prefix_to_id(ont_id_orig.to_s)
+
           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]
@@ -43,10 +42,7 @@ 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 = 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
+              ont_id = LinkedData::Models::Base.replace_url_prefix_to_id(ont_id_orig.to_s)
               if all_latest_by_id[ont_id]
                 cls.submission = all_latest_by_id[ont_id]
                 to_reply << cls