From f8db0d81036479dcdc7356082bb79d5aebb7eca8 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 8 May 2024 10:56:18 -0700 Subject: [PATCH 1/2] use gems from ncbo repo --- Gemfile | 15 +++++----- Gemfile.lock | 84 ++++++++++++++++++++++++++++------------------------ 2 files changed, 53 insertions(+), 46 deletions(-) diff --git a/Gemfile b/Gemfile index d25c7660..894d1651 100644 --- a/Gemfile +++ b/Gemfile @@ -12,7 +12,6 @@ gem 'rake', '~> 10.0' gem 'sinatra', '~> 1.0' gem 'sinatra-advanced-routes' gem 'sinatra-contrib', '~> 1.0' -gem 'request_store' # Rack middleware gem 'ffi' @@ -41,13 +40,13 @@ gem 'unicorn-worker-killer' 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 '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: 'ontoportal-lirmm/goo', branch: 'pr/sync-agroportal-bioportal' -gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pr/sync-agroportal-ncbo' +# 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: 'feature/multilingual-support-add-search-and-languages-serialization' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' 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 diff --git a/Gemfile.lock b/Gemfile.lock index 488c23ca..f65daacd 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,23 @@ +GIT + remote: https://github.com/ncbo/goo.git + revision: a55ef42e92bc02129992c77890278831f8ca5387 + branch: develop + specs: + goo (0.0.2) + addressable (~> 2.8) + pry + rdf (= 1.0.8) + redis + request_store + rest-client + rsolr + sparql-client + uuid + GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 63c986880aa88c9384043e6611a682434a14aba7 - branch: master + revision: 7531e10ad55ac66e925c099d7fc05a5a3ceae67e + branch: develop specs: ncbo_annotator (0.0.1) goo @@ -11,11 +27,13 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: f239b34230131cd7cfb9eec5b34068ba990b698b - branch: master + revision: 98dc1a9bb8aba4ef41a1687251ca1245edd5de57 + branch: develop specs: ncbo_cron (0.0.1) dante + faraday (~> 2) + faraday-follow_redirects (~> 0) goo google-analytics-data mlanett-redis-lock @@ -27,8 +45,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: 013abea4af3b10910ec661dbb358a4b6cae198a4 - branch: master + revision: f92a42f660635522eb8709e618ff2e641aef0d17 + branch: develop specs: ncbo_ontology_recommender (0.0.1) goo @@ -37,35 +55,9 @@ GIT redis GIT - 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/goo.git - revision: f2751fe9324e48a0a5c2a8b15580ab879fc53a2b - branch: pr/sync-agroportal-bioportal - specs: - goo (0.0.2) - addressable (~> 2.8) - pry - rdf (= 1.0.8) - redis - request_store - rest-client - rsolr - sparql-client - uuid - -GIT - remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: fc48343ad7a3f1867821c173be900cf16506b4b7 - branch: pr/sync-agroportal-ncbo + remote: https://github.com/ncbo/ontologies_linked_data.git + revision: ea7b31b70ea9cbc9a08821a89bd8d28761dd4b32 + branch: feature/multilingual-support-add-search-and-languages-serialization specs: ontologies_linked_data (0.0.1) activesupport @@ -82,6 +74,16 @@ 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 @@ -143,6 +145,8 @@ GEM base64 faraday-net_http (>= 2.0, < 3.1) ruby2_keywords (>= 0.0.4) + faraday-follow_redirects (0.3.0) + faraday (>= 1, < 3) faraday-net_http (3.0.2) faraday-retry (2.2.1) faraday (~> 2.0) @@ -169,6 +173,7 @@ GEM google-cloud-env (2.1.1) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) + google-protobuf (3.25.3-aarch64-linux) google-protobuf (3.25.3-arm64-darwin) google-protobuf (3.25.3-x86_64-darwin) google-protobuf (3.25.3-x86_64-linux) @@ -185,6 +190,9 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) + grpc (1.63.0-aarch64-linux) + google-protobuf (~> 3.25) + googleapis-common-protos-types (~> 1.0) grpc (1.63.0-arm64-darwin) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) @@ -223,7 +231,7 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0305) + mime-types-data (3.2024.0507) mini_mime (1.1.5) minitest (4.7.5) minitest-stub_any_instance (1.0.3) @@ -232,7 +240,7 @@ GEM multi_json (1.15.0) mutex_m (0.2.0) net-http-persistent (2.9.4) - net-imap (0.4.10) + net-imap (0.4.11) date net-protocol net-pop (0.1.2) @@ -380,6 +388,7 @@ GEM hashdiff (>= 0.4.0, < 2.0.0) PLATFORMS + aarch64-linux arm64-darwin-22 arm64-darwin-23 x86_64-darwin-18 @@ -424,7 +433,6 @@ DEPENDENCIES redis redis-rack-cache (~> 2.0) redis-store (~> 1.10) - request_store rubocop shotgun! simplecov From 3dc9f9dcc074956e5a37b511aa63b435042caf6f Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Thu, 9 May 2024 13:23:53 -0700 Subject: [PATCH 2/2] Gemfile update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index f65daacd..6bfc719c 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: ea7b31b70ea9cbc9a08821a89bd8d28761dd4b32 + revision: 0227d37c6431f52a7fd85bdb597cc3d32e975098 branch: feature/multilingual-support-add-search-and-languages-serialization specs: ontologies_linked_data (0.0.1) @@ -315,7 +315,7 @@ GEM rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.63.4) + rubocop (1.63.5) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10)