diff --git a/Gemfile b/Gemfile index f067b2ec..c911b3fc 100644 --- a/Gemfile +++ b/Gemfile @@ -27,9 +27,9 @@ gem 'ffi', '~> 1.16.3' # Monitoring gem 'cube-ruby', require: 'cube' -gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'master' +gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development' gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development' -gem 'ontologies_linked_data', github: 'BiodivPortal/ontologies_linked_data', branch: 'master' +gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development' gem 'ncbo_annotator', github: 'ontoportal-lirmm/ncbo_annotator', branch: 'development' # Testing group :test do diff --git a/Gemfile.lock b/Gemfile.lock index d098acc1..201643cf 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,27 +1,7 @@ -GIT - remote: https://github.com/BiodivPortal/ontologies_linked_data.git - revision: 4bd30687ba5800edd1d349267e1aacbd0cc6d0ca - branch: master - specs: - ontologies_linked_data (0.0.1) - activesupport - bcrypt - goo - json - libxml-ruby - multi_json - oj - omni_logger - pony - rack - rack-test - rsolr - rubyzip - GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: c48a1e4dfe82a2e5c42614a30380f3bdb2044ba9 - branch: master + revision: f8ac7b00e8d8b46d1eea04de014175525c1cdd83 + branch: development specs: goo (0.0.2) addressable (~> 2.8) @@ -47,6 +27,26 @@ GIT redis ruby-xxHash +GIT + remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git + revision: 312ef426eeaa461e88fa23124ea5fd531f4276ba + branch: development + specs: + ontologies_linked_data (0.0.1) + activesupport + bcrypt + goo + json + libxml-ruby + multi_json + oj + omni_logger + pony + rack + rack-test + rsolr + rubyzip + GIT remote: https://github.com/ontoportal-lirmm/sparql-client.git revision: 59251e59346c9a69a67c88552ba55a1244eec602 @@ -74,18 +74,15 @@ PATH GEM remote: https://rubygems.org/ specs: - activesupport (3.2.22.5) - i18n (~> 0.6, >= 0.6.4) + activesupport (3.1.12) multi_json (~> 1.0) addressable (2.8.7) public_suffix (>= 2.0.2, < 7.0) - airbrussh (1.5.2) + airbrussh (1.5.3) sshkit (>= 1.6.1, != 1.7.0) base64 (0.2.0) bcrypt (3.1.20) bcrypt_pbkdf (1.1.1) - bcrypt_pbkdf (1.1.1-arm64-darwin) - bcrypt_pbkdf (1.1.1-x86_64-darwin) bigdecimal (3.1.8) binding_of_caller (1.0.1) debug_inspector (>= 1.2.0) @@ -154,40 +151,20 @@ GEM google-cloud-env (2.1.1) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) - google-protobuf (3.25.3) - google-protobuf (3.25.3-aarch64-linux) - google-protobuf (3.25.3-arm64-darwin) - google-protobuf (3.25.3-x86-linux) - google-protobuf (3.25.3-x86_64-darwin) google-protobuf (3.25.3-x86_64-linux) googleapis-common-protos (1.6.0) google-protobuf (>= 3.18, < 5.a) googleapis-common-protos-types (~> 1.7) grpc (~> 1.41) - googleapis-common-protos-types (1.15.0) + googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) - googleauth (1.11.0) + googleauth (1.11.2) faraday (>= 1.0, < 3.a) google-cloud-env (~> 2.1) jwt (>= 1.4, < 3.0) multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.65.2) - google-protobuf (>= 3.25, < 5.0) - googleapis-common-protos-types (~> 1.0) - grpc (1.65.2-aarch64-linux) - google-protobuf (>= 3.25, < 5.0) - googleapis-common-protos-types (~> 1.0) - grpc (1.65.2-arm64-darwin) - google-protobuf (>= 3.25, < 5.0) - googleapis-common-protos-types (~> 1.0) - grpc (1.65.2-x86-linux) - google-protobuf (>= 3.25, < 5.0) - googleapis-common-protos-types (~> 1.0) - grpc (1.65.2-x86_64-darwin) - google-protobuf (>= 3.25, < 5.0) - googleapis-common-protos-types (~> 1.0) grpc (1.65.2-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) @@ -196,9 +173,9 @@ GEM http-cookie (1.0.7) domain_name (~> 0.5) httpclient (2.8.3) - i18n (0.9.5) + i18n (1.14.6) concurrent-ruby (~> 1.0) - json (2.7.2) + json (2.8.1) json-canonicalization (0.4.0) json-ld (3.2.5) htmlentities (~> 4.3) @@ -207,43 +184,44 @@ GEM multi_json (~> 1.15) rack (>= 2.2, < 4) rdf (~> 3.2, >= 3.2.10) - jwt (2.8.2) + jwt (2.9.3) base64 launchy (2.5.2) addressable (~> 2.8) libxml-ruby (5.0.3) link_header (0.0.8) - logger (1.6.0) + logger (1.6.1) macaddr (1.7.2) systemu (~> 2.6.5) mail (2.6.6) mime-types (>= 1.16, < 4) method_source (1.1.0) - mime-types (3.5.2) + mime-types (3.6.0) + logger mime-types-data (~> 3.2015) - mime-types-data (3.2024.0806) + mime-types-data (3.2024.1105) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) mutex_m (0.2.0) - net-http-persistent (4.0.2) + net-http-persistent (4.0.4) connection_pool (~> 2.2) net-scp (4.0.0) net-ssh (>= 2.6.5, < 8.0.0) net-sftp (4.0.0) net-ssh (>= 5.0.0, < 8.0.0) - net-ssh (7.2.3) + net-ssh (7.3.0) netrc (0.11.0) - oj (3.16.5) + oj (3.16.7) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) logger os (1.1.4) ostruct (0.6.0) - parallel (1.26.2) + parallel (1.26.3) parseconfig (1.1.2) pony (1.13.1) mail (>= 2.0) @@ -251,7 +229,7 @@ GEM coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.1.1) - rack (3.1.7) + rack (3.1.8) rack-test (2.1.0) rack (>= 1.3) rake (13.2.1) @@ -270,7 +248,7 @@ GEM rdf-xsd (3.2.1) rdf (~> 3.2) rexml (~> 3.2) - redis (5.2.0) + redis (5.3.0) redis-client (>= 0.22.0) redis-client (0.22.2) connection_pool @@ -286,8 +264,7 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.5) - strscan + rexml (3.3.9) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) @@ -308,14 +285,14 @@ GEM simplecov-cobertura (2.1.0) rexml simplecov (~> 0.19) - simplecov-html (0.12.3) + simplecov-html (0.13.1) simplecov_json_formatter (0.1.4) - sshkit (1.23.0) + sshkit (1.23.2) base64 net-scp (>= 1.1.2) net-sftp (>= 2.1.2) net-ssh (>= 2.8.0) - strscan (3.1.0) + ostruct sys-proctable (1.3.0) ffi (~> 1.1) systemu (2.6.5) @@ -329,11 +306,6 @@ GEM macaddr (~> 1.0) PLATFORMS - aarch64-linux - arm64-darwin - ruby - x86-linux - x86_64-darwin x86_64-linux DEPENDENCIES diff --git a/rakelib/group_management.rake b/rakelib/group_management.rake index 5586f96a..5fde5b53 100644 --- a/rakelib/group_management.rake +++ b/rakelib/group_management.rake @@ -1,5 +1,6 @@ # rake tasks for group and category management # +=begin desc 'Ontology Group Administration' namespace :group do require 'bundler/setup' @@ -42,3 +43,4 @@ namespace :group do end end end +=end diff --git a/rakelib/purl_management.rake b/rakelib/purl_management.rake index b1ba50f8..396f58c9 100644 --- a/rakelib/purl_management.rake +++ b/rakelib/purl_management.rake @@ -1,3 +1,4 @@ +=begin # Task for updating and adding missing purl for all ontologies # desc 'Purl Utilities' @@ -27,3 +28,4 @@ namespace :purl do end end end +=end diff --git a/rakelib/user_management.rake b/rakelib/user_management.rake index bf43dc6b..ed7c5cc1 100644 --- a/rakelib/user_management.rake +++ b/rakelib/user_management.rake @@ -1,3 +1,4 @@ +=begin # tasks for out of band user management # desc 'User Administration' @@ -153,3 +154,4 @@ namespace :user do puts ("--------------------------------\n") end end +=end