diff --git a/Gemfile b/Gemfile index fdc0aac6..baadce15 100644 --- a/Gemfile +++ b/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 diff --git a/Gemfile.lock b/Gemfile.lock index 2bea0ca4..b2472041 100644 --- a/Gemfile.lock +++ b/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 diff --git a/helpers/application_helper.rb b/helpers/application_helper.rb index 18163099..4ea6fa03 100644 --- a/helpers/application_helper.rb +++ b/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 = {}) diff --git a/helpers/batch_helper.rb b/helpers/batch_helper.rb index bc4ec0d7..2de90faa 100644 --- a/helpers/batch_helper.rb +++ b/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