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Organise Gemfile and update all gems #2161

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Organise Gemfile and update all gems #2161

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a40e23a
Strip versions from Gemfile
fbacall Feb 20, 2025
b72a7e0
Format file
fbacall Feb 20, 2025
dc93569
Point docsplit to original repo now that PR is merged
fbacall Feb 20, 2025
7927237
Remove unused gems
fbacall Feb 20, 2025
e25b2f2
`bundle update`
fbacall Feb 20, 2025
5fb0d58
Revert `i18n-js` to version 3 to keep asset pipeline support
fbacall Feb 20, 2025
d5528b5
Handle markdown rendering in a class
fbacall Feb 20, 2025
dac64f5
Replace `parent` `children` associations
fbacall Feb 20, 2025
b1a2d6a
Drop unused table
fbacall Feb 20, 2025
05c818f
Revert `hardbreaks` to previous behaviour. Update tests to remove tra…
fbacall Feb 20, 2025
93ba1db
Replace missing regex
fbacall Feb 27, 2025
64f5714
Rollback to rack 2 for now
fbacall Mar 5, 2025
565ff4d
Ensure sample attribute types are created with consistent names
fbacall Mar 6, 2025
2b6a474
Fix for pid files not being found
fbacall Mar 7, 2025
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292 changes: 120 additions & 172 deletions Gemfile
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Original file line number Diff line number Diff line change
@@ -1,211 +1,159 @@
source 'https://rubygems.org'
git_source(:github) { |repo| "https://github.com/#{repo}.git" }

gem 'rails', '~> 7.2.2'
gem 'rdoc'

#database adaptors
gem 'mysql2'
gem 'pg'
gem 'sqlite3', '~> 1.4'
gem 'rails', '7.2.2.1'

gem 'abbrev'
gem 'active_model_serializers'
gem 'activerecord-import'
gem 'activerecord-session_store'
gem 'acts-as-taggable-on'
gem 'addressable'
gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b' #necessary for newer hashie dependency, original api_smith is no longer active
gem 'attr_encrypted'
gem 'auto_strip_attributes'
gem 'bibtex-ruby'
gem 'bio'
gem 'bioportal', git: 'https://github.com/SysMO-DB/bioportal.git'
gem 'bives'
gem 'bootsnap', require: false
gem 'bootstrap-sass'
gem 'bundler'
gem 'caxlsx'
gem 'caxlsx_rails'
gem 'cff'
gem 'citeproc-ruby'
gem 'coffee-rails'
gem 'commonmarker'
gem 'country_select'
gem 'csl-styles'
gem 'csv'
gem 'daemons'
gem 'delayed_job_active_record'
gem 'docsplit', git: 'https://github.com/documentcloud/docsplit.git'
gem 'doi_query_tool', git: 'https://github.com/seek4science/DOI-query-tool.git'
gem 'doorkeeper'
gem 'dotenv-rails'
gem 'equivalent-xml'
gem 'exception_notification'
gem 'factory_bot'
gem 'feedjira'
gem 'fleximage', git: 'https://github.com/SysMO-DB/fleximage.git'
gem 'gitlab_omniauth-ldap'
gem 'google-analytics-rails'
gem 'libxml-ruby', '~>5.0', require: 'libxml'
gem 'uuid', '~>2.3'
gem 'RedCloth', '>=4.3.0'
gem 'simple-spreadsheet-extractor', '0.18.2'
gem 'open4'
gem 'sample-template-generator', '~>0.7'
gem 'rmagick', '5.3.0'
gem 'rest-client', '~>2.0'
gem 'factory_bot', '~> 6.2.1'
gem 'bio', '~> 1.5.1'
gem 'sunspot_rails'
gem 'progress_bar'
gem 'savon', '1.1.0'
gem 'delayed_job_active_record'
gem 'daemons','1.1.9'
gem 'linkeddata', '~> 3.2.0'
gem 'handlebars_assets'
gem 'html-pipeline'
gem 'i18n-js', '~> 3.9.2' # Version 4+ does not support the asset pipeline
gem 'indefinite_article'

gem 'openseek-api'
# for fancy content escaping in openbis integration
gem 'loofah'
gem 'jbuilder', '~> 2.7'
gem 'jbuilder'
gem 'jbuilder-json_api'
gem 'active_model_serializers', '~> 0.10.13'
gem 'rubyzip'

gem 'equivalent-xml'
# FIXME: Change back to "official" docsplit if this PR is ever merged: https://github.com/documentcloud/docsplit/pull/159
gem 'docsplit', git: 'https://github.com/tuttiq/docsplit.git', ref: '6127e3912b8db94ed84dca6be5622d3d5ec0d879'
gem 'exception_notification'
gem 'fssm'
gem 'acts-as-taggable-on'
gem 'acts_as_list'
gem 'acts_as_tree'
gem 'country_select'
gem 'will_paginate', '~> 3.1'
gem 'yaml_db'
gem 'rails_autolink'
gem 'rfc-822'
gem 'nokogiri', '~> 1.18'
#necessary for newer hashie dependency, original api_smith is no longer active
gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b'
gem 'rdf-virtuoso', '>= 0.2.0'
gem 'terrapin'
gem 'lograge'
gem 'psych'
gem 'validate_url'
gem "attr_encrypted"
gem 'libreconv'

# gem for BiVeS and BudHat
gem 'bives', "~> 2.0"

# Linked to SysMO Git repositories
gem 'my_responds_to_parent', git: 'https://github.com/SysMO-DB/my_responds_to_parent.git'
gem 'bioportal', '>=3.0', git: 'https://github.com/SysMO-DB/bioportal.git'
gem 'doi_query_tool', git: 'https://github.com/seek4science/DOI-query-tool.git'
gem 'fleximage', git: 'https://github.com/SysMO-DB/fleximage.git', ref: 'de03bf816a911dc4f69573fd300d4ff90225cca7'

gem 'jquery-rails', '~> 4.4.0'
gem 'jquery-rails'
gem 'jquery-ui-rails'
gem 'recaptcha', '~> 4.1.0'
gem 'metainspector'
gem 'json-schema'
gem 'libreconv'
gem 'libxml-ruby', require: 'libxml'
gem 'licensee'
gem 'linkeddata'
gem 'lograge'
gem 'loofah'
gem 'mechanize'
gem 'mimemagic','~> 0.3.7'
gem 'auto_strip_attributes'
gem 'coffee-rails', '~> 4.2'
gem 'bootstrap-sass', '>=3.4.1'
gem 'sass-rails', '>= 6'
gem 'sprockets-rails'

gem 'ro-bundle', '~> 0.3.0'
gem 'handlebars_assets'
gem 'zenodo-client', git: 'https://github.com/seek4science/zenodo-client.git'

gem 'unicorn-rails'
gem 'seedbank'

gem 'rspec-rails'

gem 'citeproc-ruby', '~> 2.0.0'
gem 'csl-styles', '~> 2.0.0'
gem 'bibtex-ruby', '~> 6.1.0'

gem 'omniauth', '~> 2.1.0'
gem 'gitlab_omniauth-ldap', '~> 2.2.0'
gem 'omniauth_openid_connect'
gem 'openid_connect','1.3.0'
gem 'omniauth-rails_csrf_protection'
gem 'metainspector'
gem 'mimemagic'
gem 'mutex_m'
gem 'mysql2'
gem 'net-ftp'
gem 'nkf'
gem 'nokogiri'
gem 'observer'
gem 'omniauth'
gem 'omniauth-github'

gem 'terser', '~> 1.1', '>= 1.1.1'


# Rails 4 upgrade
gem 'activerecord-session_store'
gem 'rails-observers'
gem 'responders'

gem 'rack-attack', '~> 6.6.0'

gem 'private_address_check'

# Rails 5 upgrade
gem 'omniauth-rails_csrf_protection'
gem 'omniauth_openid_connect'
gem 'open4'
gem 'openid_connect'
gem 'openseek-api'
gem 'pg'
gem 'private_address_check'# Rails 5 upgrade
gem 'progress_bar'
gem 'psych'
gem 'puma'
gem 'rack', '< 3.0.0' # Rack >= 3 causes errors when running functional tests that call multiple actions in a single test
gem 'rack-attack'
gem 'rack-cors', require: 'rack/cors'
gem 'rails-html-sanitizer'

gem 'bootsnap', '>= 1.4.4', require: false

gem 'activerecord-import'

gem "puma", "~> 5.6"

gem "doorkeeper", ">= 5.2.5"

gem 'rails-observers'
gem 'rails-static-router'
gem 'rails_autolink'
gem 'rdf-virtuoso'
gem 'RedCloth'
gem 'rdoc'
gem 'recaptcha'
gem 'remotipart'
gem 'request_store'

gem 'bundler', '>= 1.8.4'

gem 'ro-crate', '~> 0.5.3'

gem 'responders'
gem 'rest-client'
gem 'rfc-822'
gem 'rmagick'
gem 'ro-bundle'
gem 'ro-crate'
gem 'rspec-rails'
gem 'rubyzip'
gem 'rugged'
gem 'i18n-js'
gem 'whenever', '~> 1.0.0', require: false
gem 'dotenv-rails', '~> 2.7.6'
gem 'commonmarker'

gem 'rack-cors', require: 'rack/cors'

gem 'addressable'

gem 'json-schema'

gem 'cff', '~> 0.9.0'

gem 'remotipart', '~> 1.4.4' # Allows file upload in AJAX forms

gem 'rails-static-router'

gem 'caxlsx', '>= 4.0' # Write content to an xlsx file
gem 'caxlsx_rails', '~> 0.6.2'

gem 'net-ftp'

gem 'licensee'

gem "sitemap_generator", "~> 6.3"

# removed from Standard in Ruby 3.4
gem 'observer'
gem 'abbrev'
gem 'csv'
gem 'nkf'
gem 'mutex_m'
gem 'sample-template-generator'
gem 'sass-rails'
gem 'seedbank'
gem 'simple-spreadsheet-extractor'
gem 'sitemap_generator'
gem 'sprockets-rails'
gem 'sqlite3'
gem 'sunspot_rails'
gem 'terrapin'
gem 'terser'
gem 'uuid'
gem 'validate_url'
gem 'whenever', require: false
gem 'will_paginate'
gem 'yaml_db'
gem 'zenodo-client', git: 'https://github.com/seek4science/zenodo-client.git'

group :production do
gem 'passenger'
end

group :development do
gem 'better_errors'
gem 'binding_of_caller'
gem 'flamegraph'
gem 'gem-licenses'
gem 'listen'
gem 'pry'
gem 'pry-doc'
gem 'pry-remote'
gem 'rack-mini-profiler'
gem 'rails_best_practices'
gem 'request-log-analyzer'
gem 'rubocop', require: false
gem 'rails_best_practices'
gem 'gem-licenses'
gem "better_errors"
gem "binding_of_caller"

gem 'web-console', '>= 4.1.0'
gem 'rack-mini-profiler', '~> 2.0'
gem "flamegraph", "~> 0.9.5"
gem "stackprof", "~> 0.2.25"
gem 'listen', '~> 3.3'
gem 'ruby-prof'
gem 'stackprof'
gem 'web-console'
end

group :test do
gem 'test-prof'
gem 'rails-perftest'
gem 'minitest', '~> 5.14'
gem 'database_cleaner'
gem 'minitest'
gem 'minitest-reporters'
gem 'sunspot_matchers'
gem 'database_cleaner', '~> 1.7.0'
gem 'vcr', '~> 2.9'
gem 'rails-controller-testing'
gem 'rails-perftest'
gem 'simplecov'
gem 'whenever-test'
# Easy installation and use of web drivers to run system tests with browsers
gem 'sunspot_matchers'
gem 'test-prof'
gem 'vcr'
gem 'webdrivers'
gem 'whenever-test'
end

group :test, :development do
gem 'magic_lamp'
gem 'webmock'
gem 'teaspoon'
gem 'teaspoon-mocha'
gem 'webmock'
end
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