diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 000000000..8cdea307d
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,25 @@
+.git/
+log/*
+!log/.keep
+app/assets/builds/*
+!app/assets/builds/.keep
+node_modules/
+public/assets/
+storage/*
+!storage/.keep
+tmp/*
+!tmp/.keep
+
+.bundle
+.byebug_history
+.dockerignore
+.env*
+!.env.example
+config/master.key
+docker-compose.override.yml
+yarn-error.log
+yarn-debug.log*
+.yarn-integrity
+
+config/credentials/*
+config/credentials.yml.enc
\ No newline at end of file
diff --git a/.env.sample b/.env.sample
new file mode 100644
index 000000000..94f4a336b
--- /dev/null
+++ b/.env.sample
@@ -0,0 +1,43 @@
+##################### UI configuration ####################
+RAILS_ENV=development
+SITE=Testportal
+ORG=LIRMM
+ORG_URL=http://www.lirmm.fr
+
+UI_URL=http://localhost:3000
+API_URL=http://localhost:9393
+API_KEY=
+
+UI_THEME=ontoportal
+
+BIOMIXER_URL=
+BIOMIXER_APIKEY=
+
+ANNOTATOR_URL=
+
+FAIRNESS_DISABLED=false
+FAIRNESS_URL=
+
+NCBO_ANNOTATORPLUS_ENABLED=false
+NCBO_ANNOTATOR_URL=
+NCBO_API_KEY=
+
+SUPPORT_EMAIL=sifrportal-support@lirmm.fr
+RELEASE_VERSION="OntoPortal Appliance 3.0.1"
+
+ANALYTICS_ID=
+USE_RECAPTCHA=false
+#################### Buidling the API for running tests ####################
+## An ontology that will be imported in the starting of the API server
+STARTER_ONTOLOGY=STY
+## API key of a remote API used to download the starter ontology
+OP_API_KEY=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+## API url of the remote API used to download the starter ontology
+OP_API_URL="https://data.bioontology.org"
+
+## Image repositroy from which the ontoportal api will be built
+API_IMAGE_REPOSITORY=agroportal
+## Image tag/version from which the ontoportal api will be built
+API_IMAGE_TAG=master
+
+
diff --git a/.gitignore b/.gitignore
index ab0ea98b5..32214c3fa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,8 +17,9 @@ rerun.txt
pickle-email-*.html
config/bioportal_config*.rb
config/database.yml
-config/secrets.yml
config/deploy/*
+config/locales/en.rb
+config/secrets.yml
**.DS_Store
/public/**/cache/**
/public/umls/*
@@ -28,23 +29,28 @@ nohup.out
# Ignore editor files
.idea
*.swp
+.rbenv-gemsets
.tags
.tags_sorted_by_file
-config/newrelic.yml
-
node_modules
-
-# Ignore keys for decrypting credentials
-/config/credentials/development.key
-/config/credentials/test.key
-/config/credentials/staging.key
-/config/credentials/production.key
-/config/credentials/appliance.key
+.env
+config/site_config.rb
+docker-sync.yml
+.docker-sync/daemon.log
+.docker-sync/daemon.pid
/app/assets/builds/*
!/app/assets/builds/.keep
/node_modules
+
+# Encryption keys
+/config/master.key
+/config/credentials/development.key
+/config/credentials/test.key
+/config/credentials/staging.key
+/config/credentials/production.key
+/config/credentials/appliance.key
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 000000000..2eb0ea3ba
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,53 @@
+# Make sure it matches the Ruby version in .ruby-version and Gemfile
+ARG RUBY_VERSION=3.2.0
+FROM ruby:${RUBY_VERSION}-alpine
+
+# Install libvips for Active Storage preview support
+RUN apk add --no-cache build-base \
+ libxml2-dev \
+ libxslt-dev \
+ mariadb-dev \
+ git \
+ tzdata \
+ nodejs yarn \
+ less \
+ bash \
+ docker \
+ docker-compose \
+ && mkdir /node_modules
+
+# Rails app lives here
+WORKDIR /app
+
+# Set production environment
+ARG RAILS_ENV="production"
+ARG BUNDLE_WITHOUT="development test"
+
+ENV RAILS_LOG_TO_STDOUT="1" \
+ RAILS_SERVE_STATIC_FILES="true" \
+ RAILS_ENV="${RAILS_ENV}" \
+ BUNDLE_PATH=/usr/local/bundle \
+ BUNDLE_WITHOUT="${BUNDLE_WITHOUT}"
+
+RUN gem update --system 3.4.22 # the 3.4.22 can be removed if we support Ruby version > 3.0
+
+COPY . .
+
+RUN bundle install
+RUN yarn install && yarn build
+
+
+
+RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_production.rb
+RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_development.rb
+RUN cp config/database.yml.sample config/database.yml
+
+# Precompile bootsnap code for faster boot times
+RUN bundle exec bootsnap precompile --gemfile app/ lib/
+
+RUN SECRET_KEY_BASE_DUMMY="1" ./bin/rails assets:precompile
+
+ENV BINDING="0.0.0.0"
+EXPOSE 3000
+
+CMD ["bash"]
\ No newline at end of file
diff --git a/Gemfile b/Gemfile
index c423cef31..9e0a86931 100644
--- a/Gemfile
+++ b/Gemfile
@@ -2,93 +2,137 @@
source 'https://rubygems.org'
+# Main Rails gem
# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '7.0.8'
-# The original asset pipeline for Rails [https://github.com/rails/sprockets-rails]
-gem 'sprockets-rails', require: 'sprockets/railtie'
+# JavaScript bundling for Rails
+gem 'jsbundling-rails'
-# Bundle and transpile JavaScript [https://github.com/rails/jsbundling-rails]
-gem 'jsbundling-rails', '~> 1.3'
+# Chart.js integration for Rails
+gem 'chart-js-rails'
-# Hotwire's SPA-like page accelerator [https://turbo.hotwired.dev]
-gem 'turbo-rails'
+gem 'select2-rails'
-# Hotwire's modest JavaScript framework [https://stimulus.hotwired.dev]
-gem 'stimulus-rails'
+# SassC as a replacement for sass-rails
+gem 'sassc-rails' # sass-rails replacement
+
+# Terser JavaScript minifier as a replacement for Uglifier
+gem 'terser' # uglifier replacement
+
+# Bootstrap front-end framework
+gem 'bootstrap', '~> 5.2.3'
+
+# jQuery integration for Rails
+gem 'jquery-rails'
+
+# jQuery UI integration for Rails
+gem 'jquery-ui-rails'
+
+# The original asset pipeline for Rails
+# [https://github.com/rails/sprockets-rails]
+gem 'sprockets-rails'
-# Build JSON APIs with ease [https://github.com/rails/jbuilder]
-# gem 'jbuilder'
+# Use the Puma web server
+# [https://github.com/puma/puma]
+gem 'puma', '~> 5.0'
-# Use Redis for Action Cable
-gem 'redis', '~> 4.0'
+# Use JavaScript with ESM import maps
+# [https://github.com/rails/importmap-rails]
+gem 'importmap-rails'
-# Use Kredis to get higher-level data types in Redis [https://github.com/rails/kredis]
-# gem 'kredis'
+# Hotwire's SPA-like page accelerator
+# [https://turbo.hotwired.dev]
+gem 'turbo-rails'
+
+# Hotwire's modest JavaScript framework
+# [https://stimulus.hotwired.dev]
+gem 'stimulus-rails'
-# Use Active Model has_secure_password [https://guides.rubyonrails.org/active_model_basics.html#securepassword]
-# gem "bcrypt", "~> 3.1.7"
+# Debugging tool
+# See https://guides.rubyonrails.org/debugging_rails_applications.html#debugging-with-the-debug-gem gem 'pry'
+gem 'pry'
-# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+# Time zone info for Windows platforms
gem 'tzinfo-data', platforms: %i[mingw mswin x64_mingw jruby]
# Reduces boot times through caching; required in config/boot.rb
gem 'bootsnap', require: false
-# Use Sass to process CSS
-gem 'sassc-rails'
-
-gem 'bootstrap', '~> 5.2.3'
-gem 'chart-js-rails'
-gem 'jquery-rails'
-gem 'jquery-ui-rails'
-gem 'select2-rails'
-
-gem 'base64', '0.1.0'
-gem 'cube-ruby', require: 'cube'
+# Memcached client for Ruby
gem 'dalli'
-gem 'flamegraph'
+
+# GraphQL client for Ruby
# Version 2.1 breaks graphql-client. See: https://github.com/github/graphql-client/issues/310.
gem 'graphql', '~> 2.0.27'
gem 'graphql-client'
+
+
+# Haml template engine for Ruby on Rails
gem 'haml', '~> 5.1'
+
+# Internationalization (i18n)
gem 'i18n'
-gem 'iso-639', '~> 0.3.6'
+gem 'rails-i18n', '~> 7.0.0'
+
+# MySQL database adapter
+gem 'mysql2'
+
+# JSON parsing libraries
gem 'multi_json'
-gem 'mysql2', '0.5.5'
gem 'oj'
-gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.4.0'
-gem 'open_uri_redirections'
-gem 'pry'
-gem 'psych', '< 4'
-gem 'rack-mini-profiler'
-gem 'rails_autolink'
-gem 'rdoc'
+
+# Google reCAPTCHA integration
gem 'recaptcha', '~> 5.9.0'
+
+# Simple HTTP and REST client for Ruby
gem 'rest-client'
-gem 'rexml', '~> 3'
-gem 'stackprof', require: false
-# pinning strscan to v 3.0.1 to deal with deployment issue. Remove line below when issue is fixed
-gem 'strscan', '3.0.1'
+# View components framework for Rails
+gem 'lookbook', '~> 1.5.5'
+
+gem 'view_component', '~> 2.72'
-gem 'terser'
-gem 'thin'
+# Pagination library for Rails
gem 'will_paginate', '~> 3.0'
-gem 'net-ftp'
-gem 'flag-icons-rails', '~> 3.4'
+
+# Render SVG files in Rails views
gem 'inline_svg'
-group :staging, :production do
- # Application monitoring
+# ISO language codes and flags
+gem 'flag-icons-rails', '~> 3.4'
+gem 'iso-639', '~> 0.3.6'
+
+# Custom API client
+gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'master'
+
+# Ruby 2.7.8 pinned gems (to remove when migrating to Ruby >= 3.0)
+gem 'ffi', '~> 1.16.3'
+gem 'net-ftp', '~> 0.2.0', require: false
+gem 'net-http', '~> 0.3.2'
+
+# Multi-Provider Authentication
+gem 'omniauth'
+gem 'omniauth-rails_csrf_protection'
+gem 'omniauth-github'
+gem 'omniauth-google-oauth2'
+gem 'omniauth-keycloak'
+gem 'omniauth-orcid'
+
+group :staging, :production, :appliance do
+ # Application performance monitoring
gem 'newrelic_rpm'
- # Logs in json format, useful for shipping logs to logstash
+
+ # Error monitoring
+ gem 'bugsnag', '~> 6.26'
+
+ # Logs in JSON format, useful for shipping logs to logstash
# gem 'rackstash', git: 'https://github.com/planio-gmbh/rackstash.git'
# gem 'logstash-logger'
end
group :development do
- # Capistrano deployment
+ # Capistrano Deployment
gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false # https://github.com/miloserdow/capistrano-deploy/issues/42
gem 'capistrano', '~> 3.17', require: false
gem 'capistrano-bundler', require: false
@@ -98,22 +142,47 @@ group :development do
gem 'capistrano-rbenv', require: false
gem 'capistrano-yarn', require: false
gem 'ed25519', '>= 1.2', '< 2.0', require: false # https://github.com/miloserdow/capistrano-deploy/issues/42
- gem 'html2haml'
- gem 'listen'
# Static code analysis
gem 'brakeman', require: false
gem 'rubocop', require: false
- # gem 'i18n-debug'
-end
+ # Haml support for Rails
+ gem 'haml-rails'
+ gem 'html2haml'
-group :development, :test do
- # See https://guides.rubyonrails.org/debugging_rails_applications.html#debugging-with-the-debug-gem
+ # Debugging tools
gem 'debug', platforms: %i[mri mingw x64_mingw]
- gem 'rspec-rails'
+
+ # Use console on exceptions pages
+ # [https://github.com/rails/web-console]
+ gem 'web-console'
+
+ # Internationalization tasks
+ # gem 'i18n-debug'
+ gem 'i18n-tasks'
+ gem 'i18n-tasks-csv', '~> 1.1'
+ gem 'deepl-rb'
+
+ # Email preview in the browser
+ gem 'letter_opener_web', '~> 2.0'
end
group :test do
+ # System testing
+ # [https://guides.rubyonrails.org/testing.html#system-testing]
gem 'capybara'
+
+ # WebDriver for system testing
+ gem 'selenium-webdriver'
+
+ # Code coverage generation
+ gem 'simplecov', require: false
+ gem 'simplecov-cobertura' # for codecov.io
+
+ # Mock HTTP requests in tests
+ gem 'webmock'
+
+ # Testing framework for Rails
+ gem 'rspec-rails'
end
diff --git a/Gemfile.lock b/Gemfile.lock
index 4103dea80..604a4594a 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,18 +1,18 @@
GIT
- remote: https://github.com/ncbo/ontologies_api_ruby_client.git
- revision: f589b13dfbbc133ea67cbae1a8f92b41ea85c14b
- tag: v2.4.0
+ remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
+ revision: 24fb2549f7b69841e052491439bc8375ed5acfd9
+ branch: master
specs:
- ontologies_api_client (2.4.0)
- activesupport (= 7.0.8)
- addressable (~> 2.8)
+ ontologies_api_client (2.2.0)
+ activesupport
excon
faraday
- faraday-excon
+ faraday-excon (~> 2.0.0)
faraday-multipart
lz4-ruby
multi_json
oj
+ spawnling (= 2.1.5)
GEM
remote: https://rubygems.org/
@@ -84,24 +84,26 @@ GEM
tzinfo (~> 2.0)
addressable (2.8.7)
public_suffix (>= 2.0.2, < 7.0)
+ aes_key_wrap (1.1.0)
airbrussh (1.5.3)
sshkit (>= 1.6.1, != 1.7.0)
ast (2.4.2)
autoprefixer-rails (10.4.19.0)
execjs (~> 2)
- base64 (0.1.0)
+ base64 (0.2.0)
bcrypt_pbkdf (1.1.1)
- bcrypt_pbkdf (1.1.1-arm64-darwin)
- bcrypt_pbkdf (1.1.1-x86_64-darwin)
bigdecimal (3.1.8)
+ bindata (2.5.0)
+ bindex (0.8.1)
bootsnap (1.18.4)
msgpack (~> 1.2)
bootstrap (5.2.3)
autoprefixer-rails (>= 9.1.0)
popper_js (>= 2.11.6, < 3)
sassc-rails (>= 2.0.0)
- brakeman (6.2.1)
- racc
+ brakeman (5.4.1)
+ bugsnag (6.27.1)
+ concurrent-ruby (~> 1.0)
builder (3.3.0)
capistrano (3.19.1)
airbrussh (>= 1.0.0)
@@ -122,52 +124,56 @@ GEM
sshkit (~> 1.3)
capistrano-yarn (2.0.2)
capistrano (~> 3.0)
- capybara (3.40.0)
+ capybara (3.39.2)
addressable
matrix
mini_mime (>= 0.1.3)
- nokogiri (~> 1.11)
+ nokogiri (~> 1.8)
rack (>= 1.6.0)
rack-test (>= 0.6.3)
regexp_parser (>= 1.5, < 3.0)
xpath (~> 3.2)
chart-js-rails (0.1.7)
railties (> 3.1)
+ childprocess (5.1.0)
+ logger (~> 1.5)
coderay (1.1.3)
concurrent-ruby (1.3.4)
+ crack (1.0.0)
+ bigdecimal
+ rexml
crass (1.0.6)
- cube-ruby (0.0.3)
- daemons (1.4.1)
+ css_parser (1.17.1)
+ addressable
+ csv (3.3.0)
dalli (3.2.8)
date (3.3.4)
debug (1.9.2)
irb (~> 1.10)
reline (>= 0.3.8)
+ deepl-rb (3.0.2)
diff-lcs (1.5.1)
+ docile (1.4.1)
domain_name (0.6.20240107)
ed25519 (1.3.0)
erubi (1.13.0)
erubis (2.7.0)
- eventmachine (1.2.7)
- excon (0.111.0)
+ excon (0.112.0)
execjs (2.9.1)
- faraday (2.12.0)
- faraday-net_http (>= 2.0, < 3.4)
- json
- logger
- faraday-excon (2.2.0)
- excon (>= 0.109.0)
- faraday (>= 2.11.0, < 3)
+ faraday (2.0.1)
+ faraday-net_http (~> 2.0)
+ ruby2_keywords (>= 0.0.4)
+ faraday-excon (2.0.0)
+ excon (>= 0.27.4)
+ faraday (~> 2.0.0.alpha.pre.2)
+ faraday-follow_redirects (0.3.0)
+ faraday (>= 1, < 3)
faraday-multipart (1.0.4)
multipart-post (~> 2)
- faraday-net_http (3.3.0)
- net-http
- ffi (1.17.0)
- ffi (1.17.0-arm64-darwin)
- ffi (1.17.0-x86_64-darwin)
+ faraday-net_http (2.1.0)
+ ffi (1.16.3)
flag-icons-rails (3.4.6.1)
sass-rails
- flamegraph (0.9.5)
globalid (1.2.1)
activesupport (>= 6.1)
graphql (2.0.31)
@@ -178,24 +184,51 @@ GEM
haml (5.2.2)
temple (>= 0.8.0)
tilt
+ haml-rails (2.1.0)
+ actionpack (>= 5.1)
+ activesupport (>= 5.1)
+ haml (>= 4.0.6)
+ railties (>= 5.1)
+ hashdiff (1.1.1)
+ hashie (5.0.0)
+ highline (2.1.0)
html2haml (2.3.0)
erubis (~> 2.7.0)
haml (>= 4.0)
nokogiri (>= 1.6.0)
ruby_parser (~> 3.5)
+ htmlbeautifier (1.4.3)
+ htmlentities (4.3.4)
http-accept (1.7.0)
http-cookie (1.0.7)
domain_name (~> 0.5)
i18n (1.14.6)
concurrent-ruby (~> 1.0)
+ i18n-tasks (0.9.37)
+ activesupport (>= 4.0.2)
+ ast (>= 2.1.0)
+ erubi
+ highline (>= 2.0.0)
+ i18n
+ parser (>= 2.2.3.0)
+ rails-i18n
+ rainbow (>= 2.2.2, < 4.0)
+ terminal-table (>= 1.5.1)
+ i18n-tasks-csv (1.1)
+ i18n-tasks (~> 0.9)
+ importmap-rails (2.0.3)
+ actionpack (>= 6.0.0)
+ activesupport (>= 6.0.0)
+ railties (>= 6.0.0)
inline_svg (1.10.0)
activesupport (>= 3.0)
nokogiri (>= 1.6)
io-console (0.7.2)
- irb (1.14.0)
+ irb (1.14.1)
rdoc (>= 4.0.0)
reline (>= 0.4.2)
- iso-639 (0.3.6)
+ iso-639 (0.3.8)
+ csv
jquery-rails (4.6.0)
rails-dom-testing (>= 1, < 3)
railties (>= 4.2.0)
@@ -205,7 +238,26 @@ GEM
jsbundling-rails (1.3.1)
railties (>= 6.0.0)
json (2.7.2)
+ json-jwt (1.16.6)
+ activesupport (>= 4.2)
+ aes_key_wrap
+ base64
+ bindata
+ faraday (~> 2.0)
+ faraday-follow_redirects
+ jwt (2.9.3)
+ base64
language_server-protocol (3.17.0.3)
+ launchy (3.0.1)
+ addressable (~> 2.8)
+ childprocess (~> 5.0)
+ letter_opener (1.10.0)
+ launchy (>= 2.2, < 4)
+ letter_opener_web (2.0.0)
+ actionmailer (>= 5.2)
+ letter_opener (~> 1.7)
+ railties (>= 5.2)
+ rexml
listen (3.9.0)
rb-fsevent (~> 0.10, >= 0.10.3)
rb-inotify (~> 0.9, >= 0.9.10)
@@ -213,6 +265,19 @@ GEM
loofah (2.22.0)
crass (~> 1.0.2)
nokogiri (>= 1.12.0)
+ lookbook (1.5.5)
+ actioncable
+ activemodel
+ css_parser
+ htmlbeautifier (~> 1.3)
+ htmlentities (~> 4.3.4)
+ listen (~> 3.0)
+ railties (>= 5.0)
+ redcarpet (~> 3.5)
+ rouge (>= 3.26, < 5.0)
+ view_component (> 2.0, < 4)
+ yard (~> 0.9.25)
+ zeitwerk (~> 2.5)
lz4-ruby (0.3.3)
mail (2.8.1)
mini_mime (>= 0.1.1)
@@ -222,19 +287,21 @@ GEM
marcel (1.0.4)
matrix (0.4.2)
method_source (1.1.0)
- mime-types (3.5.2)
+ mime-types (3.6.0)
+ logger
mime-types-data (~> 3.2015)
- mime-types-data (3.2024.0903)
+ mime-types-data (3.2024.1001)
mini_mime (1.1.5)
minitest (5.25.1)
- msgpack (1.7.2)
+ msgpack (1.7.3)
multi_json (1.15.0)
+ multi_xml (0.6.0)
multipart-post (2.4.1)
- mysql2 (0.5.5)
- net-ftp (0.3.7)
+ mysql2 (0.5.6)
+ net-ftp (0.2.1)
net-protocol
time
- net-http (0.4.1)
+ net-http (0.3.2)
uri
net-imap (0.4.16)
date
@@ -249,20 +316,48 @@ GEM
net-ssh (>= 5.0.0, < 8.0.0)
net-smtp (0.5.0)
net-protocol
- net-ssh (7.2.3)
+ net-ssh (7.3.0)
netrc (0.11.0)
- newrelic_rpm (9.13.0)
+ newrelic_rpm (9.14.0)
nio4r (2.7.3)
- nokogiri (1.16.7-arm64-darwin)
- racc (~> 1.4)
- nokogiri (1.16.7-x86_64-darwin)
- racc (~> 1.4)
- nokogiri (1.16.7-x86_64-linux)
+ nokogiri (1.15.6-x86_64-linux)
racc (~> 1.4)
+ oauth2 (2.0.9)
+ faraday (>= 0.17.3, < 3.0)
+ jwt (>= 1.0, < 3.0)
+ multi_xml (~> 0.5)
+ rack (>= 1.2, < 4)
+ snaky_hash (~> 2.0)
+ version_gem (~> 1.1)
oj (3.16.6)
bigdecimal (>= 3.0)
ostruct (>= 0.2)
- open_uri_redirections (0.2.1)
+ omniauth (2.1.2)
+ hashie (>= 3.4.6)
+ rack (>= 2.2.3)
+ rack-protection
+ omniauth-github (2.0.1)
+ omniauth (~> 2.0)
+ omniauth-oauth2 (~> 1.8)
+ omniauth-google-oauth2 (1.2.0)
+ jwt (>= 2.9)
+ oauth2 (~> 2.0)
+ omniauth (~> 2.0)
+ omniauth-oauth2 (~> 1.8)
+ omniauth-keycloak (1.5.2)
+ faraday
+ json-jwt (> 1.13.0)
+ omniauth (>= 2.0)
+ omniauth-oauth2 (>= 1.7, < 1.9)
+ omniauth-oauth2 (1.8.0)
+ oauth2 (>= 1.4, < 3)
+ omniauth (~> 2.0)
+ omniauth-orcid (2.1.1)
+ omniauth-oauth2 (~> 1.3)
+ ruby_dig (~> 0.0.2)
+ omniauth-rails_csrf_protection (1.0.2)
+ actionpack (>= 4.2)
+ omniauth (~> 2.0)
ostruct (0.6.0)
parallel (1.26.3)
parser (3.3.5.0)
@@ -272,12 +367,16 @@ GEM
pry (0.14.2)
coderay (~> 1.1)
method_source (~> 1.0)
- psych (3.3.4)
- public_suffix (6.0.1)
+ psych (5.1.2)
+ stringio
+ public_suffix (5.1.1)
+ puma (5.6.9)
+ nio4r (~> 2.0)
racc (1.8.1)
rack (2.2.9)
- rack-mini-profiler (3.3.1)
- rack (>= 1.2.0)
+ rack-protection (3.2.0)
+ base64 (>= 0.1.0)
+ rack (~> 2.2, >= 2.2.4)
rack-test (2.1.0)
rack (>= 1.3)
rails (7.0.8)
@@ -301,10 +400,9 @@ GEM
rails-html-sanitizer (1.6.0)
loofah (~> 2.21)
nokogiri (~> 1.14)
- rails_autolink (1.1.8)
- actionview (> 3.1)
- activesupport (> 3.1)
- railties (> 3.1)
+ rails-i18n (7.0.9)
+ i18n (>= 0.7, < 2)
+ railties (>= 6.0.0, < 8)
railties (7.0.8)
actionpack (= 7.0.8)
activesupport (= 7.0.8)
@@ -317,10 +415,11 @@ GEM
rb-fsevent (0.11.2)
rb-inotify (0.11.1)
ffi (~> 1.0)
- rdoc (6.3.4.1)
+ rdoc (6.7.0)
+ psych (>= 4.0.0)
recaptcha (5.9.0)
json
- redis (4.8.1)
+ redcarpet (3.6.0)
regexp_parser (2.9.2)
reline (0.5.10)
io-console (~> 0.5)
@@ -329,13 +428,14 @@ GEM
http-cookie (>= 1.0.2, < 2.0)
mime-types (>= 1.16, < 4.0)
netrc (~> 0.8)
- rexml (3.3.7)
+ rexml (3.3.8)
+ rouge (4.4.0)
rspec-core (3.13.1)
rspec-support (~> 3.13.0)
rspec-expectations (3.13.3)
diff-lcs (>= 1.2.0, < 2.0)
rspec-support (~> 3.13.0)
- rspec-mocks (3.13.1)
+ rspec-mocks (3.13.2)
diff-lcs (>= 1.2.0, < 2.0)
rspec-support (~> 3.13.0)
rspec-rails (7.0.1)
@@ -360,9 +460,12 @@ GEM
rubocop-ast (1.32.3)
parser (>= 3.3.1.0)
ruby-progressbar (1.13.0)
+ ruby2_keywords (0.0.5)
+ ruby_dig (0.0.2)
ruby_parser (3.21.1)
racc (~> 1.5)
sexp_processor (~> 4.16)
+ rubyzip (2.3.2)
sass-rails (6.0.0)
sassc-rails (~> 2.1, >= 2.1.1)
sassc (2.4.0)
@@ -374,7 +477,24 @@ GEM
sprockets-rails
tilt
select2-rails (4.0.13)
+ selenium-webdriver (4.9.0)
+ rexml (~> 3.2, >= 3.2.5)
+ rubyzip (>= 1.2.2, < 3.0)
+ websocket (~> 1.0)
sexp_processor (4.17.2)
+ simplecov (0.22.0)
+ docile (~> 1.1)
+ simplecov-html (~> 0.11)
+ simplecov_json_formatter (~> 0.1)
+ simplecov-cobertura (2.1.0)
+ rexml
+ simplecov (~> 0.19)
+ simplecov-html (0.13.1)
+ simplecov_json_formatter (0.1.4)
+ snaky_hash (2.0.1)
+ hashie
+ version_gem (~> 1.1, >= 1.1.1)
+ spawnling (2.1.5)
sprockets (4.2.1)
concurrent-ruby (~> 1.0)
rack (>= 2.2.4, < 4)
@@ -388,49 +508,59 @@ GEM
net-sftp (>= 2.1.2)
net-ssh (>= 2.8.0)
ostruct
- stackprof (0.2.26)
stimulus-rails (1.3.4)
railties (>= 6.0.0)
- strscan (3.0.1)
+ stringio (3.1.1)
temple (0.10.3)
- terser (1.2.3)
+ terminal-table (3.0.2)
+ unicode-display_width (>= 1.1.1, < 3)
+ terser (1.2.4)
execjs (>= 0.3.0, < 3)
- thin (1.8.2)
- daemons (~> 1.0, >= 1.0.9)
- eventmachine (~> 1.0, >= 1.0.4)
- rack (>= 1, < 3)
thor (1.3.2)
tilt (2.4.0)
time (0.4.0)
date
timeout (0.4.1)
- turbo-rails (2.0.9)
+ turbo-rails (2.0.10)
actionpack (>= 6.0.0)
railties (>= 6.0.0)
tzinfo (2.0.6)
concurrent-ruby (~> 1.0)
unicode-display_width (2.6.0)
uri (0.13.1)
+ version_gem (1.1.4)
+ view_component (2.83.0)
+ activesupport (>= 5.2.0, < 8.0)
+ concurrent-ruby (~> 1.0)
+ method_source (~> 1.0)
+ web-console (4.2.1)
+ actionview (>= 6.0.0)
+ activemodel (>= 6.0.0)
+ bindex (>= 0.4.0)
+ railties (>= 6.0.0)
+ webmock (3.24.0)
+ addressable (>= 2.8.0)
+ crack (>= 0.3.2)
+ hashdiff (>= 0.4.0, < 2.0.0)
+ websocket (1.2.11)
websocket-driver (0.7.6)
websocket-extensions (>= 0.1.0)
websocket-extensions (0.1.5)
will_paginate (3.3.1)
xpath (3.2.0)
nokogiri (~> 1.8)
+ yard (0.9.37)
zeitwerk (2.6.18)
PLATFORMS
- arm64-darwin-22
- arm64-darwin-23
- x86_64-darwin-21
- x86_64-linux
+ x86_64-linux-musl
DEPENDENCIES
- base64 (= 0.1.0)
bcrypt_pbkdf (>= 1.0, < 2.0)
bootsnap
bootstrap (~> 5.2.3)
brakeman
+ bugsnag (~> 6.26)
capistrano (~> 3.17)
capistrano-bundler
capistrano-locally
@@ -440,53 +570,63 @@ DEPENDENCIES
capistrano-yarn
capybara
chart-js-rails
- cube-ruby
dalli
debug
+ deepl-rb
ed25519 (>= 1.2, < 2.0)
+ ffi (~> 1.16.3)
flag-icons-rails (~> 3.4)
- flamegraph
graphql (~> 2.0.27)
graphql-client
haml (~> 5.1)
+ haml-rails
html2haml
i18n
+ i18n-tasks
+ i18n-tasks-csv (~> 1.1)
+ importmap-rails
inline_svg
iso-639 (~> 0.3.6)
jquery-rails
jquery-ui-rails
- jsbundling-rails (~> 1.3)
- listen
+ jsbundling-rails
+ letter_opener_web (~> 2.0)
+ lookbook (~> 1.5.5)
multi_json
- mysql2 (= 0.5.5)
- net-ftp
+ mysql2
+ net-ftp (~> 0.2.0)
+ net-http (~> 0.3.2)
newrelic_rpm
oj
+ omniauth
+ omniauth-github
+ omniauth-google-oauth2
+ omniauth-keycloak
+ omniauth-orcid
+ omniauth-rails_csrf_protection
ontologies_api_client!
- open_uri_redirections
pry
- psych (< 4)
- rack-mini-profiler
+ puma (~> 5.0)
rails (= 7.0.8)
- rails_autolink
- rdoc
+ rails-i18n (~> 7.0.0)
recaptcha (~> 5.9.0)
- redis (~> 4.0)
rest-client
- rexml (~> 3)
rspec-rails
rubocop
sassc-rails
select2-rails
+ selenium-webdriver
+ simplecov
+ simplecov-cobertura
sprockets-rails
- stackprof
stimulus-rails
- strscan (= 3.0.1)
terser
- thin
turbo-rails
tzinfo-data
+ view_component (~> 2.72)
+ web-console
+ webmock
will_paginate (~> 3.0)
BUNDLED WITH
- 2.5.11
+ 2.4.22
diff --git a/Procfile.dev b/Procfile.dev
index b19ff761b..03c54b1d7 100644
--- a/Procfile.dev
+++ b/Procfile.dev
@@ -1,2 +1,2 @@
-web: env RUBY_DEBUG_OPEN=true bin/rails server
+web: bin/rails server -p 3000
js: yarn build --watch
diff --git a/README b/README
deleted file mode 100644
index 0d6affddc..000000000
--- a/README
+++ /dev/null
@@ -1,182 +0,0 @@
-== Welcome to Rails
-
-Rails is a web-application and persistence framework that includes everything
-needed to create database-backed web-applications according to the
-Model-View-Control pattern of separation. This pattern splits the view (also
-called the presentation) into "dumb" templates that are primarily responsible
-for inserting pre-built data in between HTML tags. The model contains the
-"smart" domain objects (such as Account, Product, Person, Post) that holds all
-the business logic and knows how to persist themselves to a database. The
-controller handles the incoming requests (such as Save New Account, Update
-Product, Show Post) by manipulating the model and directing data to the view.
-
-In Rails, the model is handled by what's called an object-relational mapping
-layer entitled Active Record. This layer allows you to present the data from
-database rows as objects and embellish these data objects with business logic
-methods. You can read more about Active Record in
-link:files/vendor/rails/activerecord/README.html.
-
-The controller and view are handled by the Action Pack, which handles both
-layers by its two parts: Action View and Action Controller. These two layers
-are bundled in a single package due to their heavy interdependence. This is
-unlike the relationship between the Active Record and Action Pack that is much
-more separate. Each of these packages can be used independently outside of
-Rails. You can read more about Action Pack in
-link:files/vendor/rails/actionpack/README.html.
-
-
-== Getting started
-
-1. At the command prompt, start a new rails application using the rails command
- and your application name. Ex: rails myapp
- (If you've downloaded rails in a complete tgz or zip, this step is already done)
-2. Change directory into myapp and start the web server: script/server (run with --help for options)
-3. Go to http://localhost:3000/ and get "Welcome aboard: You’re riding the Rails!"
-4. Follow the guidelines to start developing your application
-
-
-== Web Servers
-
-By default, Rails will try to use Mongrel and lighttpd if they are installed, otherwise
-Rails will use the WEBrick, the webserver that ships with Ruby. When you run script/server,
-Rails will check if Mongrel exists, then lighttpd and finally fall back to WEBrick. This ensures
-that you can always get up and running quickly.
-
-Mongrel is a Ruby-based webserver with a C-component (which requires compilation) that is
-suitable for development and deployment of Rails applications. If you have Ruby Gems installed,
-getting up and running with mongrel is as easy as: gem install mongrel .
-More info at: http://mongrel.rubyforge.org
-
-If Mongrel is not installed, Rails will look for lighttpd. It's considerably faster than
-Mongrel and WEBrick and also suited for production use, but requires additional
-installation and currently only works well on OS X/Unix (Windows users are encouraged
-to start with Mongrel). We recommend version 1.4.11 and higher. You can download it from
-http://www.lighttpd.net.
-
-And finally, if neither Mongrel or lighttpd are installed, Rails will use the built-in Ruby
-web server, WEBrick. WEBrick is a small Ruby web server suitable for development, but not
-for production.
-
-But of course its also possible to run Rails on any platform that supports FCGI.
-Apache, LiteSpeed, IIS are just a few. For more information on FCGI,
-please visit: http://wiki.rubyonrails.com/rails/pages/FastCGI
-
-
-== Debugging Rails
-
-Have "tail -f" commands running on the server.log and development.log. Rails will
-automatically display debugging and runtime information to these files. Debugging
-info will also be shown in the browser on requests from 127.0.0.1.
-
-
-== Breakpoints
-
-Breakpoint support is available through the script/breakpointer client. This
-means that you can break out of execution at any point in the code, investigate
-and change the model, AND then resume execution! Example:
-
- class WeblogController < ActionController::Base
- def index
- @posts = Post.find(:all)
- breakpoint "Breaking out from the list"
- end
- end
-
-So the controller will accept the action, run the first line, then present you
-with a IRB prompt in the breakpointer window. Here you can do things like:
-
-Executing breakpoint "Breaking out from the list" at .../webrick_server.rb:16 in 'breakpoint'
-
- >> @posts.inspect
- => "[#nil, \"body\"=>nil, \"id\"=>\"1\"}>,
- #\"Rails you know!\", \"body\"=>\"Only ten..\", \"id\"=>\"2\"}>]"
- >> @posts.first.title = "hello from a breakpoint"
- => "hello from a breakpoint"
-
-...and even better is that you can examine how your runtime objects actually work:
-
- >> f = @posts.first
- => #nil, "body"=>nil, "id"=>"1"}>
- >> f.
- Display all 152 possibilities? (y or n)
-
-Finally, when you're ready to resume execution, you press CTRL-D
-
-
-== Console
-
-You can interact with the domain model by starting the console through script/console .
-Here you'll have all parts of the application configured, just like it is when the
-application is running. You can inspect domain models, change values, and save to the
-database. Starting the script without arguments will launch it in the development environment.
-Passing an argument will specify a different environment, like script/console production .
-
-To reload your controllers and models after launching the console run reload!
-
-To reload your controllers and models after launching the console run reload!
-
-
-
-== Description of contents
-
-app
- Holds all the code that's specific to this particular application.
-
-app/controllers
- Holds controllers that should be named like weblogs_controller.rb for
- automated URL mapping. All controllers should descend from ApplicationController
- which itself descends from ActionController::Base.
-
-app/models
- Holds models that should be named like post.rb.
- Most models will descend from ActiveRecord::Base.
-
-app/views
- Holds the template files for the view that should be named like
- weblogs/index.rhtml for the WeblogsController#index action. All views use eRuby
- syntax.
-
-app/views/layouts
- Holds the template files for layouts to be used with views. This models the common
- header/footer method of wrapping views. In your views, define a layout using the
- layout :default and create a file named default.rhtml. Inside default.rhtml,
- call <% yield %> to render the view using this layout.
-
-app/helpers
- Holds view helpers that should be named like weblogs_helper.rb. These are generated
- for you automatically when using script/generate for controllers. Helpers can be used to
- wrap functionality for your views into methods.
-
-config
- Configuration files for the Rails environment, the routing map, the database, and other dependencies.
-
-components
- Self-contained mini-applications that can bundle together controllers, models, and views.
-
-db
- Contains the database schema in schema.rb. db/migrate contains all
- the sequence of Migrations for your schema.
-
-doc
- This directory is where your application documentation will be stored when generated
- using rake doc:app
-
-lib
- Application specific libraries. Basically, any kind of custom code that doesn't
- belong under controllers, models, or helpers. This directory is in the load path.
-
-public
- The directory available for the web server. Contains subdirectories for images, stylesheets,
- and javascripts. Also contains the dispatchers and the default HTML files. This should be
- set as the DOCUMENT_ROOT of your web server.
-
-script
- Helper scripts for automation and generation.
-
-test
- Unit and functional tests along with fixtures. When using the script/generate scripts, template
- test files will be generated for you and placed in this directory.
-
-vendor
- External libraries that the application depends on. Also includes the plugins subdirectory.
- This directory is in the load path.
diff --git a/README.rdoc b/README.rdoc
deleted file mode 100644
index 3e1c15c81..000000000
--- a/README.rdoc
+++ /dev/null
@@ -1,261 +0,0 @@
-== Welcome to Rails
-
-Rails is a web-application framework that includes everything needed to create
-database-backed web applications according to the Model-View-Control pattern.
-
-This pattern splits the view (also called the presentation) into "dumb"
-templates that are primarily responsible for inserting pre-built data in between
-HTML tags. The model contains the "smart" domain objects (such as Account,
-Product, Person, Post) that holds all the business logic and knows how to
-persist themselves to a database. The controller handles the incoming requests
-(such as Save New Account, Update Product, Show Post) by manipulating the model
-and directing data to the view.
-
-In Rails, the model is handled by what's called an object-relational mapping
-layer entitled Active Record. This layer allows you to present the data from
-database rows as objects and embellish these data objects with business logic
-methods. You can read more about Active Record in
-link:files/vendor/rails/activerecord/README.html.
-
-The controller and view are handled by the Action Pack, which handles both
-layers by its two parts: Action View and Action Controller. These two layers
-are bundled in a single package due to their heavy interdependence. This is
-unlike the relationship between the Active Record and Action Pack that is much
-more separate. Each of these packages can be used independently outside of
-Rails. You can read more about Action Pack in
-link:files/vendor/rails/actionpack/README.html.
-
-
-== Getting Started
-
-1. At the command prompt, create a new Rails application:
- rails new myapp (where myapp is the application name)
-
-2. Change directory to myapp and start the web server:
- cd myapp; rails server (run with --help for options)
-
-3. Go to http://localhost:3000/ and you'll see:
- "Welcome aboard: You're riding Ruby on Rails!"
-
-4. Follow the guidelines to start developing your application. You can find
-the following resources handy:
-
-* The Getting Started Guide: http://guides.rubyonrails.org/getting_started.html
-* Ruby on Rails Tutorial Book: http://www.railstutorial.org/
-
-
-== Debugging Rails
-
-Sometimes your application goes wrong. Fortunately there are a lot of tools that
-will help you debug it and get it back on the rails.
-
-First area to check is the application log files. Have "tail -f" commands
-running on the server.log and development.log. Rails will automatically display
-debugging and runtime information to these files. Debugging info will also be
-shown in the browser on requests from 127.0.0.1.
-
-You can also log your own messages directly into the log file from your code
-using the Ruby logger class from inside your controllers. Example:
-
- class WeblogController < ActionController::Base
- def destroy
- @weblog = Weblog.find(params[:id])
- @weblog.destroy
- logger.info("#{Time.now} Destroyed Weblog ID ##{@weblog.id}!")
- end
- end
-
-The result will be a message in your log file along the lines of:
-
- Mon Oct 08 14:22:29 +1000 2007 Destroyed Weblog ID #1!
-
-More information on how to use the logger is at http://www.ruby-doc.org/core/
-
-Also, Ruby documentation can be found at http://www.ruby-lang.org/. There are
-several books available online as well:
-
-* Programming Ruby: http://www.ruby-doc.org/docs/ProgrammingRuby/ (Pickaxe)
-* Learn to Program: http://pine.fm/LearnToProgram/ (a beginners guide)
-
-These two books will bring you up to speed on the Ruby language and also on
-programming in general.
-
-
-== Debugger
-
-Debugger support is available through the debugger command when you start your
-Mongrel or WEBrick server with --debugger. This means that you can break out of
-execution at any point in the code, investigate and change the model, and then,
-resume execution! You need to install ruby-debug to run the server in debugging
-mode. With gems, use sudo gem install ruby-debug . Example:
-
- class WeblogController < ActionController::Base
- def index
- @posts = Post.all
- debugger
- end
- end
-
-So the controller will accept the action, run the first line, then present you
-with a IRB prompt in the server window. Here you can do things like:
-
- >> @posts.inspect
- => "[#nil, "body"=>nil, "id"=>"1"}>,
- #"Rails", "body"=>"Only ten..", "id"=>"2"}>]"
- >> @posts.first.title = "hello from a debugger"
- => "hello from a debugger"
-
-...and even better, you can examine how your runtime objects actually work:
-
- >> f = @posts.first
- => #nil, "body"=>nil, "id"=>"1"}>
- >> f.
- Display all 152 possibilities? (y or n)
-
-Finally, when you're ready to resume execution, you can enter "cont".
-
-
-== Console
-
-The console is a Ruby shell, which allows you to interact with your
-application's domain model. Here you'll have all parts of the application
-configured, just like it is when the application is running. You can inspect
-domain models, change values, and save to the database. Starting the script
-without arguments will launch it in the development environment.
-
-To start the console, run rails console from the application
-directory.
-
-Options:
-
-* Passing the -s, --sandbox argument will rollback any modifications
- made to the database.
-* Passing an environment name as an argument will load the corresponding
- environment. Example: rails console production .
-
-To reload your controllers and models after launching the console run
-reload!
-
-More information about irb can be found at:
-link:http://www.rubycentral.org/pickaxe/irb.html
-
-
-== dbconsole
-
-You can go to the command line of your database directly through rails
-dbconsole . You would be connected to the database with the credentials
-defined in database.yml. Starting the script without arguments will connect you
-to the development database. Passing an argument will connect you to a different
-database, like rails dbconsole production . Currently works for MySQL,
-PostgreSQL and SQLite 3.
-
-== Description of Contents
-
-The default directory structure of a generated Ruby on Rails application:
-
- |-- app
- | |-- assets
- | | |-- images
- | | |-- javascripts
- | | `-- stylesheets
- | |-- controllers
- | |-- helpers
- | |-- mailers
- | |-- models
- | `-- views
- | `-- layouts
- |-- config
- | |-- environments
- | |-- initializers
- | `-- locales
- |-- db
- |-- doc
- |-- lib
- | |-- assets
- | `-- tasks
- |-- log
- |-- public
- |-- script
- |-- test
- | |-- fixtures
- | |-- functional
- | |-- integration
- | |-- performance
- | `-- unit
- |-- tmp
- | `-- cache
- | `-- assets
- `-- vendor
- |-- assets
- | |-- javascripts
- | `-- stylesheets
- `-- plugins
-
-app
- Holds all the code that's specific to this particular application.
-
-app/assets
- Contains subdirectories for images, stylesheets, and JavaScript files.
-
-app/controllers
- Holds controllers that should be named like weblogs_controller.rb for
- automated URL mapping. All controllers should descend from
- ApplicationController which itself descends from ActionController::Base.
-
-app/models
- Holds models that should be named like post.rb. Models descend from
- ActiveRecord::Base by default.
-
-app/views
- Holds the template files for the view that should be named like
- weblogs/index.html.erb for the WeblogsController#index action. All views use
- eRuby syntax by default.
-
-app/views/layouts
- Holds the template files for layouts to be used with views. This models the
- common header/footer method of wrapping views. In your views, define a layout
- using the layout :default and create a file named default.html.erb.
- Inside default.html.erb, call <% yield %> to render the view using this
- layout.
-
-app/helpers
- Holds view helpers that should be named like weblogs_helper.rb. These are
- generated for you automatically when using generators for controllers.
- Helpers can be used to wrap functionality for your views into methods.
-
-config
- Configuration files for the Rails environment, the routing map, the database,
- and other dependencies.
-
-db
- Contains the database schema in schema.rb. db/migrate contains all the
- sequence of Migrations for your schema.
-
-doc
- This directory is where your application documentation will be stored when
- generated using rake doc:app
-
-lib
- Application specific libraries. Basically, any kind of custom code that
- doesn't belong under controllers, models, or helpers. This directory is in
- the load path.
-
-public
- The directory available for the web server. Also contains the dispatchers and the
- default HTML files. This should be set as the DOCUMENT_ROOT of your web
- server.
-
-script
- Helper scripts for automation and generation.
-
-test
- Unit and functional tests along with fixtures. When using the rails generate
- command, template test files will be generated for you and placed in this
- directory.
-
-vendor
- External libraries that the application depends on. Also includes the plugins
- subdirectory. If the app has frozen rails, those gems also go here, under
- vendor/rails/. This directory is in the load path.
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 06cd2e302..7e1b0acbe 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -39,7 +39,7 @@ class ApplicationController < ActionController::Base
# See ActionController::RequestForgeryProtection for details
protect_from_forgery
- before_action :set_global_thread_values, :domain_ontology_set, :authorize_miniprofiler, :clean_empty_strings_from_params_arrays, :init_trial_license
+ before_action :set_global_thread_values, :domain_ontology_set, :clean_empty_strings_from_params_arrays, :init_trial_license
def set_global_thread_values
Thread.current[:session] = session
@@ -271,14 +271,7 @@ def params_string_for_redirect(params, options = {})
params_array.empty? ? "" : "#{prefix}#{params_array.join('&')}"
end
- # rack-mini-profiler authorization
- def authorize_miniprofiler
- if params[:enable_profiler] && params[:enable_profiler].eql?("true") && session[:user] && session[:user].admin?
- Rack::MiniProfiler.authorize_request
- else
- Rack::MiniProfiler.deauthorize_request
- end
- end
+
# Verifies if user is logged in
def authorize_and_redirect
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 12ec47cfe..9d1d87a7d 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -285,7 +285,7 @@ def get_link_for_cls_ajax(cls_id, ont_acronym, target = nil)
data_ont = " data-ont='#{ont_acronym}' "
"#{cls_id} "
else
- auto_link(cls_id, :all, target: '_blank')
+ content_tag(:div, cls_id)
end
end
diff --git a/bin/dev b/bin/dev
index eda330c72..a4e05fa14 100755
--- a/bin/dev
+++ b/bin/dev
@@ -1,6 +1,6 @@
#!/usr/bin/env sh
-if gem list --no-installed --exact --silent foreman; then
+if ! gem list foreman -i --silent; then
echo "Installing foreman..."
gem install foreman
fi
diff --git a/bin/ontoportal b/bin/ontoportal
new file mode 100755
index 000000000..3fa5d2939
--- /dev/null
+++ b/bin/ontoportal
@@ -0,0 +1,213 @@
+#!/usr/bin/env bash
+
+# Function to display script usage information
+show_help() {
+ echo "Usage: $0 {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY]"
+ echo " dev : Start the Ontoportal Web UI development server."
+ echo " Example: $0 dev --api-url http://localhost:9393 --api-key my_api_key"
+ echo " Use --reset-cache to remove volumes: $0 dev --reset-cache"
+ echo " test : Run tests. Specify either a test file:line_number or empty for 'all'."
+ echo " Example: $0 test test/integration/login_flows_test.rb:22 "
+ echo " run : Run a command in the Ontoportal Web UI Docker container."
+ echo " help : Show this help message."
+ echo
+ echo "Description:"
+ echo " This script provides convenient commands for managing an Ontoportal Web UI"
+ echo " application using Docker Compose. It includes options for starting the development server,"
+ echo " running tests, and executing commands within the Ontoportal Web UI Docker container."
+ echo
+ echo "Goals:"
+ echo " - Simplify common tasks related to Ontoportal Web UI development using Docker."
+ echo " - Provide a consistent and easy-to-use interface for common actions."
+}
+# Function to update or create the .env file with API_URL and API_KEY
+update_env_file() {
+ local api_url="$1"
+ local api_key="$2"
+
+ # Update the .env file with the provided values
+ file_content=$(<.env)
+
+ # Make changes to the variable
+ while IFS= read -r line; do
+ if [[ "$line" == "API_URL="* ]]; then
+ echo "API_URL=$api_url"
+ elif [[ "$line" == "API_KEY="* ]]; then
+ echo "API_KEY=$api_key"
+ else
+ echo "$line"
+ fi
+ done <<< "$file_content" > .env
+}
+
+# Function to create configuration files if they don't exist
+create_config_files() {
+ if [ ! -f ".env" ]; then
+ echo "Creating .env file from env.sample"
+ cp .env.sample .env
+ fi
+
+ if [ ! -f "config/bioportal_config_development.rb" ]; then
+ echo "Creating config/bioportal_config_development.rb file from config/bioportal_config_env.rb.sample"
+ cp config/bioportal_config_env.rb.sample config/bioportal_config_development.rb
+ fi
+
+ if [ ! -f "config/database.yml" ]; then
+ echo "Creating config/database.yml file from config/database.yml.sample"
+ cp config/database.yml.sample config/database.yml
+ fi
+}
+
+# Function to handle the "dev" option
+dev() {
+ echo "Starting Ontoportal Web UI development server..."
+
+
+ local reset_cache=false
+ local api_client_path=""
+ local api_url=""
+ local api_key=""
+
+ # Check for command line arguments
+ while [[ "$#" -gt 0 ]]; do
+ case $1 in
+ --api-client-path)
+ api_client_path="$2"
+ shift 2
+ ;;
+ --reset-cache)
+ reset_cache=true
+ shift
+ ;;
+ --api-url)
+ api_url="$2"
+ shift 2
+ ;;
+ --api-key)
+ api_key="$2"
+ shift 2
+ ;;
+ *)
+ echo "Unknown option: $1"
+ show_help
+ exit 1
+ ;;
+ esac
+ done
+
+
+
+ # Check if arguments are provided
+ if [ -n "$api_url" ] && [ -n "$api_key" ]; then
+ # If arguments are provided, update the .env file
+ update_env_file "$api_url" "$api_key"
+ else
+ # If no arguments, fetch values from the .env file
+ source .env
+ api_url="$API_URL"
+ api_key="$API_KEY"
+ fi
+
+ if [ -z "$api_url" ] || [ -z "$api_key" ]; then
+ echo "Error: Missing required arguments. Please provide both --api-url and --api-key or update them in your .env"
+ exit 1
+ fi
+
+ # Check if --reset-cache is present and execute docker compose down --volumes
+ if [ "$reset_cache" = true ]; then
+ echo "Resetting cache. Running: docker compose down --volumes"
+ docker compose down --volumes
+ fi
+
+ local docker_run_cmd="docker compose run --rm -it"
+ local bash_cmd=""
+ # Conditionally add bind mounts only if the paths are not empty
+ for path_var in "api_client_path:ontologies_api_ruby_client" ; do
+ IFS=':' read -r path value <<< "$path_var"
+
+ if [ -n "${!path}" ]; then
+ host_path="$(realpath "$(dirname "${!path}")")/$value"
+ echo "Run: bundle config local.$value ${!path}"
+ container_path="/app/tmp/$value"
+ docker_run_cmd+=" -v $host_path:$container_path"
+ bash_cmd+="(bundle config local.ontologies_api_client $container_path) &&"
+ else
+ bash_cmd+=" (bundle config unset local.ontologies_api_client) &&"
+ fi
+ done
+ bash_cmd+=" (bundle check || bundle install) && bin/rails secret && EDITOR='nano' bin/rails credentials:edit && bin/rails db:prepare && bundle exec rails s -b 0.0.0.0 -p 3000"
+ docker_run_cmd+=" --service-ports dev bash -c \"$bash_cmd\""
+ echo "$docker_run_cmd"
+ echo "Run: bundle exec rails s -b 0.0.0.0 -p 3000"
+ eval "$docker_run_cmd"
+}
+
+# Function to handle the "test" option
+test() {
+
+
+ local api_url=""
+ local api_key=""
+ local test_options=""
+
+ # Check for command line arguments
+ while [ "$#" -gt 0 ]; do
+ case "$1" in
+ --api-url)
+ shift
+ api_url="$1"
+ ;;
+ *)
+
+ if [ -z "$test_options" ]; then
+ test_options="$1"
+ else
+
+ test_options="$test_options $1"
+ fi
+ ;;
+ esac
+ shift
+ done
+
+ if [ -z "$api_url" ]; then
+ api_url=http://localhost:9393
+ echo "Running API..."
+ bin/run_api
+ fi
+
+ echo "Running tests..."
+ echo "Run: API_URL=$api_url bundle exec rails test -v $test_options"
+
+ docker compose run --rm -it test bash -c "bundle config unset local.ontologies_api_client && (bundle check || bundle install) && RAILS_ENV=test bin/rails db:prepare && API_URL=$api_url bundle exec rails test -v $test_options"
+
+ # echo "Stopping API..."
+ # bin/stop_api
+}
+
+# Function to handle the "run" option
+run() {
+ echo "Run: $*"
+ docker compose run --rm -it dev bash -c "$*"
+}
+
+create_config_files
+# Main script logic
+case "$1" in
+ "run")
+ run "${@:2}"
+ ;;
+ "dev")
+ dev "${@:2}"
+ ;;
+ "test")
+ test "${@:2}"
+ ;;
+ "help")
+ show_help
+ ;;
+ *)
+ show_help
+ exit 1
+ ;;
+esac
diff --git a/bin/run_api b/bin/run_api
new file mode 100755
index 000000000..5d1634b2f
--- /dev/null
+++ b/bin/run_api
@@ -0,0 +1,69 @@
+#!/bin/bash
+display_help() {
+ echo "Usage: $0 [options]"
+ echo "Options:"
+ echo " -f Remove tmp/ontoportal_docker"
+ echo " -k API_KEY API key"
+ echo " -r REPOSITORY Image repository"
+ echo " -t TAG Image tag"
+ echo " -s ONTOLOGY Starter ontology"
+ echo " -u URL Remote API URL"
+ echo " -h Display this help message"
+ exit 0
+}
+
+
+env_file_path="$(realpath "$(dirname "$0")")/../.env"
+
+# Read and parse the .env file
+if [ -f "$env_file_path" ]; then
+ while IFS='=' read -r key value; do
+ [[ "$key" =~ ^\s*# ]] && continue # Skip commented lines
+ [[ "$value" ]] || continue # Skip lines without values
+ export "$key"="$value"
+ done < "$env_file_path"
+fi
+
+
+while getopts ":k:r:t:s:u:fh" opt; do
+ case $opt in
+ k) api_key="$OPTARG" ;;
+ r) image_repository="$OPTARG" ;;
+ t) image_tag="$OPTARG" ;;
+ s) starter_ontology="$OPTARG" ;;
+ u) remote_api_url="$OPTARG" ;;
+ f) rm -fr tmp/ontoportal_docker ;;
+ h) display_help ;;
+ \?) echo "Invalid option: -$OPTARG" >&2; exit 1 ;;
+ :) echo "Option -$OPTARG requires an argument." >&2; exit 1 ;;
+ esac
+done
+
+
+
+if [ ! -d "tmp/ontoportal_docker" ]; then
+ git clone --depth=1 -b main https://github.com/ontoportal-lirmm/ontoportal_docker.git tmp/ontoportal_docker
+fi
+
+# If an option is not provided, check and use the corresponding value from the environment variables
+api_key="${api_key:-$OP_API_KEY}"
+image_repository="${image_repository:-$API_IMAGE_REPOSITORY}"
+image_tag="${image_tag:-$API_IMAGE_TAG}"
+starter_ontology="${starter_ontology:-$STARTER_ONTOLOGY}"
+remote_api_url="${remote_api_url:-$OP_API_URL}"
+
+if curl -sSf http://localhost:9393 > /dev/null 2>&1; then
+ echo "API is already running in http://localhost:9393"
+ exit 0
+fi
+
+# Check if the Docker Compose service exists
+docker compose ls -a --filter "name=ontoportal_docker" | grep -q "ontoportal_docker" && no_provision=true || no_provision=false
+(
+ cd tmp/ontoportal_docker || exit 1
+ command="./run -k $api_key -r $image_repository -t $image_tag -s $starter_ontology -u $remote_api_url"
+ [ "$no_provision" = true ] && command="$command"
+ echo "Run: $command"
+ eval "$command"
+)
+
diff --git a/bin/setup b/bin/setup
index 3bf0c5297..ec47b79b3 100755
--- a/bin/setup
+++ b/bin/setup
@@ -2,7 +2,7 @@
require "fileutils"
# path to your application root.
-APP_ROOT = File.expand_path('..', __dir__)
+APP_ROOT = File.expand_path("..", __dir__)
def system!(*args)
system(*args) || abort("\n== Command #{args} failed ==")
@@ -17,9 +17,6 @@ FileUtils.chdir APP_ROOT do
system! "gem install bundler --conservative"
system("bundle check") || system!("bundle install")
- # Install JavaScript dependencies
- system! 'bin/yarn'
-
# puts "\n== Copying sample files =="
# unless File.exist?("config/database.yml")
# FileUtils.cp "config/database.yml.sample", "config/database.yml"
diff --git a/bin/stop_api b/bin/stop_api
new file mode 100755
index 000000000..31308b172
--- /dev/null
+++ b/bin/stop_api
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Check if the directory exists
+if [ -d "tmp/ontoportal_docker" ]; then
+ # Check if the container is running
+ if docker ps --filter "name=ontoportal_docker-api" --format "{{.Names}}" | grep -q "ontoportal_docker-api"; then
+ container_names=$(docker ps --filter "name=ontoportal_docker-api" --format "{{.Names}}")
+ docker stop "$container_names"
+ fi
+
+ cd "tmp/ontoportal_docker" && docker compose down --volumes
+fi
+
diff --git a/config/application.rb b/config/application.rb
index 65e56ea9c..77aa0796f 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -9,13 +9,12 @@
module BioportalWebUi
class Application < Rails::Application
# Initialize configuration defaults for originally generated Rails version.
- config.load_defaults 6.1
- config.active_support.cache_format_version = 6.1
- config.active_support.disable_to_s_conversion = true
- config.active_record.yaml_column_permitted_classes = [
- ActionController::Parameters,
- HashWithIndifferentAccess
- ]
+ config.load_defaults 7.0
+
+ # permitted locales available for the application
+ config.i18n.available_locales = [:en, :fr, :it, :de]
+ config.i18n.default_locale = :en
+
# Configuration for the application, engines, and railties goes here.
#
@@ -27,9 +26,17 @@ class Application < Rails::Application
config.exceptions_app = self.routes
- config.settings = config_for :settings
+ config.autoload_paths += %W[#{config.root}/app/lib/kgcl]
+
+ config.settings = config_for :settings
# Initialize configuration for KGCL change request functionality.
config.change_request = config_for :change_request
+
+ config.generators.template_engine = :haml
+ config.generators.test_framework = nil
+
+ # Set the default layout to app/views/layouts/component_preview.html.erb
+ config.view_component.default_preview_layout = "component_preview"
end
end
diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
index 8ccef8e12..277b97201 100644
--- a/config/bioportal_config_env.rb.sample
+++ b/config/bioportal_config_env.rb.sample
@@ -1,82 +1,136 @@
-# coding: utf-8
-
# Organization info
-$ORG = "NCBO"
-$ORG_URL = "http://www.bioontology.org"
+$ORG = ENV['ORG']
+$ORG_URL = ENV['ORG_URL']
# Site name (required)
-$SITE = "BioPortal"
+$SITE = ENV['SITE']
+
+# Full string for site, EX: "NCBO BioPortal", do not modify
+$ORG_SITE = $ORG.nil? || $ORG.empty? ? $SITE : "#{$ORG} #{$SITE}"
# The URL for the BioPortal Rails UI (this application)
-$UI_URL = "http://bioportal.bioontology.org"
+$UI_URL = ENV['UI_URL']
+
+# If you are running a PURL server to provide URLs for ontologies in your BioPortal instance, enable this option
+$PURL_ENABLED = false
+# The PURL URL is generated using this prefix + the abbreviation for an ontology.
+# The PURL URL generation algorithm can be altered in app/models/ontology_wrapper.rb
+$PURL_PREFIX = 'http://purl.bioontology.org/ontology'
-# Unique string representing the UI's id for use with the BioPortal API
-$API_KEY = ""
+# If your BioPortal installation includes Annotator set this to false
+$ANNOTATOR_DISABLED = false
+# Unique string representing the UI's id for use with the BioPortal Core
+$API_KEY = ENV['API_KEY']
# BioPortal API service address
-$REST_URL = "http://example.org:8080/"
+$REST_URL = ENV['API_URL']
-# Ontolobridge endpoint url
-$ONTOLOBRIDGE_BASE_URL = "https://ontolobridge.ccs.miami.edu/api-test/requests"
+# Annotator REST service address
+# $ANNOTATOR_URL = "http://services.stageportal.lirmm.fr/annotator"
+$ANNOTATOR_URL = $PROXY_URL = ENV['ANNOTATOR_URL']
+# NCBO annotator URL and apikey
+$NCBO_ANNOTATORPLUS_ENABLED = ENV['NCBO_ANNOTATORPLUS_ENABLED']
+$NCBO_ANNOTATOR_URL = ENV['NCBO_ANNOTATOR_URL']
+$NCBO_API_KEY = ENV['NCBO_API_KEY']
+
+# Fairness Assessment.
+$FAIRNESS_DISABLED = ENV['FAIRNESS_DISABLED']
+$FAIRNESS_URL = ENV['FAIRNESS_URL']
+
+
+
+
+# Used to define other bioportal that can be mapped to
+# Example to map to ncbo bioportal : {"ncbo" => {"api" => "http://data.bioontology.org", "ui" => "http://bioportal.bioontology.org", "apikey" => ""}
+# Then create the mapping using the following class in JSON : "http://purl.bioontology.org/ontology/MESH/C585345": "ncbo:MESH"
+# Where "ncbo" is the namespace used as key in the interportal_hash
+$INTERPORTAL_HASH = {}
+$NOT_DOWNLOADABLE = {}
+
+# Bugsnag API key for monitoring exception
+#$BUGSNAG_API_KEY=
+
+# OAuth2 authentication
+$OMNIAUTH_PROVIDERS = {
+ github: {
+ client_id: 'CLIENT_ID',
+ client_secret: 'CLIENT_SECRET',
+ icon: 'github.svg',
+ enable: true
+ },
+ google: {
+ strategy: :google_oauth2,
+ client_id: 'CLIENT_ID',
+ client_secret: 'CLIENT_SECRET',
+ icon: 'google.svg',
+ enable: true
+ },
+ orcid: {
+ client_id: 'CLIENT_SECRET',
+ client_secret: 'CLIENT_SECRET',
+ icon: 'orcid.svg',
+ enable: false
+ },
+ keycloak: {
+ strategy: :keycloak_openid,
+ client_id: 'YOUR_KEYCLOAK_CLIENT_ID',
+ client_secret: 'YOUR_KEYCLOAK_CLIENT_SECRET',
+ client_options: { site: 'KEYCLOAK_SITE', realm: 'KEYCLOAK_REALM' },
+ name: 'keycloak',
+ icon: 'keycloak.svg',
+ enable: false
+ }
+}.freeze
+
+# Don't load and don't display recent mappings if false, in case of too many mappings (take longer to load homepage)
+$DISPLAY_RECENT = false
+
+# If true then the UI will get available recognize at API_URL/annotators/recognizers
+$MULTIPLE_RECOGNIZERS = false
+
+# Remove download for these ontologies. Default:
+# ["CPT","ICD10","ICNP","ICPC2P","MDDB","MEDDRA","MSHFRE","MSHSPA_1","NDDF","NDFRT","NIC","RCD","SCTSPA","SNOMEDCT","WHO-ART"]
+$RESTRICTED_DOWNLOADS = []
+
+# Ontolobridge endpoint url
+$ONTOLOBRIDGE_BASE_URL = 'https://ontolobridge.ccs.miami.edu/api-test/requests'
# Ontolobridge authentication token
-$ONTOLOBRIDGE_AUTHENTICATION_TOKEN = "Token Uq2pae73ktMtmgjUgtnhEOuHxr9sZeuK"
+$ONTOLOBRIDGE_AUTHENTICATION_TOKEN = 'Token Uq2pae73ktMtmgjUgtnhEOuHxr9sZeuK'
# Ontologies for which to enable the new term request (Ontolobridge) tab
$NEW_TERM_REQUEST_ONTOLOGIES = []
-# Max number of children to return when rendering a tree view
-$MAX_CHILDREN = 2500
-
-# Max number of children that it's possible to display (more than this is either too slow or not helpful to users)
-$MAX_POSSIBLE_DISPLAY = 10000
+# Legacy REST core service address (BioPortal v3.x and lower)
+$LEGACY_REST_URL = 'http://example.org:8080/bioportal'
# Release version text (appears in footer of all pages, except 404 and 500 errors)
-$RELEASE_VERSION = ""
+$RELEASE_VERSION = ENV['RELEASE_VERSION']
# Enable Slices, filtering of ontologies based on subdomain and ontology groups
$ENABLE_SLICES = false
# Google Analytics ID (optional)
-$ANALYTICS_ID = ""
-
-# A user id for user 'anonymous' for use when a user is required for an action on the REST service but you don't want to require a user to login
-$ANONYMOUS_USER = 0
-
-# Cube metrics reporting
-$ENABLE_CUBE = false
-$CUBE_HOST = "localhost"
-$CUBE_PORT = 1180
+$ANALYTICS_ID = ENV['ANALYTICS_ID']
# Enable client request caching
$CLIENT_REQUEST_CACHING = true
-# Enable debugging of API Ruby client
-$DEBUG_RUBY_CLIENT = false
-# When DEBUG_RUBY_CLIENT is true, this array can limit the cache keys for which to receive debug output. Empty array means output debugging info for ALL keys
-$DEBUG_RUBY_CLIENT_KEYS = []
-
-# If you don't use Airbrake you can have exceptions emailed to the $ERROR_EMAIL address by setting this to 'true'
-$EMAIL_EXCEPTIONS = true
-
# Email settings
ActionMailer::Base.smtp_settings = {
- :address => "", # smtp server address, ex: smtp.example.org
- :port => 25, # smtp server port
- :domain => "", # fqdn of rails server, ex: rails.example.org
+ address: '', # smtp server address, ex: smtp.example.org
+ port: 25, # smtp server port
+ domain: '' # fqdn of rails server, ex: rails.example.org
}
-
# Announcements mailman mailing list REQUEST address, EX: list-request@lists.example.org
# NOTE: You must use the REQUEST address for the mailing list. ONLY WORKS WITH MAILMAN LISTS.
-$ANNOUNCE_LIST = "bioportal-test-request@lists.stanford.edu"
-
+$ANNOUNCE_LIST = ENV['SUPPORT_EMAIL']
# Email addresses used for sending notifications (errors, feedback, support)
-$SUPPORT_EMAIL = "recipient@example.org"
-$ADMIN_EMAIL = "recipient@example.org"
-$ERROR_EMAIL = "recipient@example.org"
+$SUPPORT_EMAIL = ENV['SUPPORT_EMAIL']
+# Email used to send notifications
+$NOTIFICATION_EMAIL = ENV['SUPPORT_EMAIL']
+
-# Settings for date formatting
-CalendarDateSelect.format = :american
# reCAPTCHA
# In order to use reCAPTCHA on the account creation and feedback submission pages:
@@ -89,32 +143,172 @@ CalendarDateSelect.format = :american
#
# 3. Set the USE_RECAPTCHA option to 'true'
ENV['USE_RECAPTCHA'] = 'false'
-
-# Memcached servers
-ENV['MEMCACHE_SERVERS'] = 'localhost'
-
# Custom BioPortal logging
require 'log'
# URL where BioMixer GWT app is located
-$BIOMIXER_URL = 'http://biomixer.bioontology.org'
+# $BIOMIXER_URL = "http://bioportal-integration.bio-mixer.appspot.com"
+$BIOMIXER_URL = ENV['BIOMIXER_URL']
+$BIOMIXER_APIKEY = ENV['BIOMIXER_APIKEY']
##
# Custom Ontology Details
# Custom details can be added on a per ontology basis using a key/value pair as columns of the details table
#
# Example:
-# $ADDITIONAL_ONTOLOGY_DETAILS = { 1000 => { "Additional Detail" => "Text to be shown in the right-hand column." } }
+# $ADDITIONAL_ONTOLOGY_DETAILS = { "STY" => { "Additional Detail" => "Text to be shown in the right-hand column." } }
##
$ADDITIONAL_ONTOLOGY_DETAILS = {}
-#################################
-## AUTO-GENERATED DO NOT MODIFY
-#################################
+# Front notice appears on the front page only and is closable by the user. It remains closed for seven days (stored in cookie)
+$FRONT_NOTICE = ''
+# Site notice appears on all pages and remains closed indefinitely. Stored below as a hash with a unique key and a string message
+# EX: $SITE_NOTICE = { :unique_key => 'Put your message here (can include html if you use single quotes).' }
+$SITE_NOTICE = {}
+
+$TERMS_AND_CONDITIONS_LINK = 'https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/terms-conditions-naDsDo2Zxq'
+$CITE_ANNOTATOR = 'https://hal.science/hal-00492024'
+$ANNOTATOR_API_DOC = 'https://data.agroportal.lirmm.fr/documentation#nav_annotator'
+$CITE_RECOMMENDER = 'https://doi.org/10.1186/s13326-017-0128-y'
+# Resource term
+$RESOURCE_TERM = ENV['RESOURCE_TERM'] || 'ontology'
+
+$HOME_PAGE_LOGOS = [
+ {
+ img_src: 'logos/supports/numev.png',
+ url: 'http://www.lirmm.fr/numev',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/supports/anr.png',
+ url: 'https://anr.fr/en',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/supports/eu.png',
+ url: 'https://commission.europa.eu/research-and-innovation_en',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/d2kab.png',
+ url: 'http://d2kab.mystrikingly.com',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/lirmm.png',
+ url: 'http://www.lirmm.fr',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/inrae.png',
+ url: 'https://www.inrae.fr/enm',
+ target: '_blank'
+ },
+ {
+ img_src: 'logos/collaboration/stanford.png',
+ url: 'https://www.stanford.edu',
+ target: '_blank'
+ }
+]
+
+$PORTALS_INSTANCES = [
+ {
+ color: '#31b403',
+ portal: 'AgroPortal',
+ link: 'https://agroportal.lirmm.fr/'
+ },
+ {
+ color: '#234979',
+ portal: 'BioPortal',
+ link: 'https://bioportal.bioontology.org/'
+ },
+ {
+ color: '#74a9cb',
+ portal: 'SIFR BioPortal',
+ link: 'https://bioportal.lirmm.fr/'
+ },
+ {
+ color: '#0d508a',
+ portal: 'EcoPortal',
+ link: 'https://ecoportal.lifewatch.eu/'
+ },
+ {
+ color: '#234979',
+ portal: 'MedPortal',
+ link: 'http://medportal.bmicc.cn/'
+ },
+ {
+ color: '#009574',
+ portal: 'MatPortal',
+ link: 'https://matportal.org/'
+ },
+ {
+ color: '#1c0f5d',
+ portal: 'IndustryPortal',
+ link: 'http://industryportal.enit.fr'
+ },
+ {
+ color: '#1e2251',
+ portal: 'EarthPortal',
+ link: 'https://earthportal.eu/'
+ },
+ {
+ color: '#33691B',
+ portal: 'BiodivPortal',
+ link: 'https://biodivportal.gfbio.org/'
+ }
+]
+$ONTOPORTAL_WEBSITE_LINK = "https://ontoportal.org/"
+$ONTOPORTAL_GITHUB_REPO = "https://github.com/ontoportal"
+
+$GITHUB_ISSUES = "https://github.com/agroportal/project-management/issues"
+$FOOTER_LINKS = {
+ social: [
+ { logo: "social/people.svg", link: "https://github.com/orgs/agroportal/people" },
+ { logo: "social/github.svg", link: "https://github.com/agroportal" },
+ { logo: "social/twitter.svg", link: "https://twitter.com/lagroportal" },
+ { logo: "json.svg", link: $REST_URL },
+ { logo: "summary/sparql.svg", link: "#{$SPARQL_URL}"},
+ { logo: "social/email.svg", link: "mailto:#{$ANNOUNCE_LIST}" },
+ ],
+ sections: {
+ products: {
+ release_notes: "https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/release-notes-btKjZk5tU2",
+ api: "https://data.agroportal.lirmm.fr/",
+ tools: "/tools",
+ sparql: "https://sparql.agroportal.lirmm.fr/test/",
+ ontoportal: $ONTOPORTAL_WEBSITE_LINK
+ },
+ support: {
+ contact_us: "https://#{$SITE}.lirmm.fr/feedback",
+ documentation: "https://ontoportal.github.io/documentation/",
+ agro_documentation: "https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/public-documentation-QMpsC9aVBb",
+ issues_and_requests: $GITHUB_ISSUES
+ },
+ agreements: {
+ terms: $TERMS_AND_CONDITIONS_LINK,
+ privacy_policy: "https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/terms-conditions-naDsDo2Zxq#h-privacy-policy",
+ legal_notices: "https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/terms-conditions-naDsDo2Zxq#h-legal-notice"
+ },
+ about: {
+ about_us: "https://github.com/agroportal/project-management",
+ team: "https://github.com/orgs/agroportal/people",
+ cite_us: "https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/publications-and-references-87tEoeoGKy",
+ acknowledgments: "https://doc.jonquetlab.lirmm.fr/share/e6158eda-c109-4385-852c-51a42de9a412/doc/acknowledgments-15GdRXLQdm"
+ }
+ }
+}
+
+
-# Full string for site, EX: "NCBO BioPortal"
-$ORG_SITE = ($ORG.nil? || $ORG.empty?) ? $SITE : "#{$ORG} #{$SITE}"
+$UI_THEME = ENV['UI_THEME'] || 'ontoportal'
+$HOSTNAME = ENV['API_URL']
-# Email address to mail when exceptions are raised
-ExceptionNotifier.exception_recipients = [$ERROR_EMAIL]
+if $HOSTNAME
+ $HOSTNAME = ENV['API_URL'].split('data.').last
+ # add custom stage server configuration if needed (e.g bioportal_config_development_stageportal.lirmm.fr)
+ if File.exist?("config/bioportal_config_development_#{$HOSTNAME}")
+ require_relative "bioportal_config_development_#{$HOSTNAME}"
+ end
+end
diff --git a/config/credentials.yml.enc b/config/credentials.yml.enc
new file mode 100644
index 000000000..a96b8c065
--- /dev/null
+++ b/config/credentials.yml.enc
@@ -0,0 +1 @@
+0NEifnx5oHgE25IXOvUl+r2KJUh+4aPosj5xLB0hqXf7j1bT+60mgdOgU3emx5+PfU9GagfFR7Tb3dT4QbefFrnGujWqesRpYGCvKsiB1TnudiGL+jiOlb212yU5d0WqsnWNZ/0B8/oXmiv00pUMeMyMXchr9C5qJw4n0/+CGEz1NSC09SYO75mPGpizlriYLgh/d77rsMkD87XCA+fO1h27mra7jSGNe3y57r7z+sr1IMBwuWfjN3bGDhyx1SGwhMmlT5Fx4TOP/mYeNVS1EhmPdRQ5ZBSfNgLhXMPy22kX+vPtBPmSfTE7QkMNN2nTzO6V7WCSpQ3OzIZ2Uovuy6BT9jD95IiqcR5s8ZRXulqHX45fZ/ChNWdcZWh66LG7rTSsg84qqQqnim+fQf2SPJEQuyH9zpSpbMSH--Rk1H/tk4KRtT+LhV--iLJN0olR3i0IT5r29QC5Bg==
\ No newline at end of file
diff --git a/config/database.yml.sample b/config/database.yml.sample
index 76884a865..6edf6ed31 100644
--- a/config/database.yml.sample
+++ b/config/database.yml.sample
@@ -12,10 +12,9 @@
default: &default
adapter: mysql2
encoding: utf8mb4
- pool: <%= ENV.fetch("RAILS_MAX_THREADS") { 5 } %>
username: root
- password:
- host: localhost
+ password: root
+ host: <%= ENV["DB_HOST"] %>
development:
<<: *default
diff --git a/config/environment.rb b/config/environment.rb
index cac531577..0c158d03b 100755
--- a/config/environment.rb
+++ b/config/environment.rb
@@ -1,5 +1,19 @@
# Load the Rails application.
-require_relative "application"
+require_relative 'application'
+
+
+# Remove this after migrating to Rails 7.1 (https://github.com/rails/rails/issues/32947#issuecomment-1356391185)
+class Rails::Application
+ def secret_key_base
+ if Rails.env.development? || Rails.env.test? || ENV["SECRET_KEY_BASE_DUMMY"]
+ secrets.secret_key_base ||= generate_development_secret
+ else
+ validate_secret_key_base(
+ ENV["SECRET_KEY_BASE"] || credentials.secret_key_base || secrets.secret_key_base
+ )
+ end
+ end
+end
# Initialize the Rails application.
Rails.application.initialize!
diff --git a/config/environments/appliance.rb b/config/environments/appliance.rb
index dcf7bbadb..ec5f5e79f 100644
--- a/config/environments/appliance.rb
+++ b/config/environments/appliance.rb
@@ -80,13 +80,14 @@
# Use a different cache store in the appliance.
config.cache_store = :mem_cache_store, ENV["MEMCACHE_SERVERS"] || "localhost:11211", { :namespace => 'bioportal_web_ui', :expires_in => 1.day }
+
# Disable serving static files from the `/public` folder by default since
# Apache or NGINX already handles this.
config.public_file_server.enabled = ENV['RAILS_SERVE_STATIC_FILES'].present?
# Add custom data attributes to sanitize allowed list
config.action_view.sanitized_allowed_attributes = ['id', 'class', 'style', 'data-cls', 'data-ont']
-
+ config.view_component.show_previews = true
# TODO: Fix this?
# enable json logging format. Useful for logstash
# require 'rackstash'
diff --git a/config/environments/development.rb b/config/environments/development.rb
index 95f60f9b5..7e0593176 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -2,12 +2,21 @@
Rails.application.configure do
# Settings specified here will take precedence over those in config/application.rb.
-
+ config.assets.debug = true
# In the development environment your application's code is reloaded any time
# it changes. This slows down response time but is perfect for development
# since you don't have to restart the web server when you make code changes.
config.cache_classes = false
+ config.action_mailer.delivery_method = :letter_opener_web
+
+ config.action_mailer.raise_delivery_errors = false
+
+ config.action_mailer.perform_deliveries = true
+ config.action_mailer.default_url_options = { host: '0.0.0:3000' } # Adjust the host/port as needed
+
+ config.action_mailer_letter_opener_location = Rails.root.join('tmp', 'my_mails')
+
# Do not eager load code on boot.
config.eager_load = false
@@ -16,7 +25,9 @@
# Enable server timing
config.server_timing = true
-
+
+ # Allow all hosts in development
+ config.hosts = nil
# Enable/disable caching. By default caching is disabled.
# Run rails dev:cache to toggle caching.
if Rails.root.join("tmp/caching-dev.txt").exist?
@@ -56,22 +67,20 @@
# Highlight code that triggered database queries in logs.
config.active_record.verbose_query_logs = true
- # Debug mode disables concatenation and preprocessing of assets.
- # This option may cause significant delays in view rendering with a large
- # number of complex assets.
- config.assets.debug = true
-
# Suppress logger output for asset requests.
config.assets.quiet = true
# memcache setup
- config.cache_store = ActiveSupport::Cache::MemCacheStore.new('localhost', namespace: 'BioPortal')
+ config.cache_store = ActiveSupport::Cache::MemCacheStore.new('cache:11211', namespace: 'BioPortal')
# Silence cache output
config.cache_store.logger = Logger.new("/dev/null") if config.cache_store.respond_to?(:logger)
# Add custom data attributes to sanitize allowed list
config.action_view.sanitized_allowed_attributes = ['id', 'class', 'style', 'data-cls', 'data-ont']
+ config.view_component.generate.sidecar = true
+
+ config.file_watcher = ActiveSupport::FileUpdateChecker
# Include BioPortal-specific configuration options
require Rails.root.join('config', "bioportal_config_#{Rails.env}.rb")
@@ -82,10 +91,6 @@
# Annotate rendered view with file names.
# config.action_view.annotate_rendered_view_with_filenames = true
- # Use an evented file watcher to asynchronously detect changes in source code,
- # routes, locales, etc. This feature depends on the listen gem.
- config.file_watcher = ActiveSupport::EventedFileUpdateChecker
-
# Uncomment if you wish to allow Action Cable access from any origin.
# config.action_cable.disable_request_forgery_protection = true
-end
+end
\ No newline at end of file
diff --git a/config/environments/production.rb b/config/environments/production.rb
index 89c5c8c7f..1e89497c1 100644
--- a/config/environments/production.rb
+++ b/config/environments/production.rb
@@ -1,4 +1,4 @@
-require "active_support/core_ext/integer/time"
+require 'active_support/core_ext/integer/time'
Rails.application.configure do
# Settings specified here will take precedence over those in config/application.rb.
@@ -18,7 +18,7 @@
# Ensures that a master key has been made available in either ENV["RAILS_MASTER_KEY"]
# or in config/master.key. This key is used to decrypt credentials (and other encrypted files).
- config.require_master_key = true
+ config.require_master_key = ENV['REQUIRE_MASTER_KEY'].present?
# Disable serving static files from the `/public` folder by default since
# Apache or NGINX already handles this.
@@ -53,10 +53,10 @@
# Include generic and useful information about system operation, but avoid logging too much
# information to avoid inadvertent exposure of personally identifiable information (PII).
- config.log_level = :warn
+ config.log_level = :info
# Prepend all log lines with the following tags.
- config.log_tags = [ :request_id ]
+ config.log_tags = [:request_id]
# Use a different cache store in production.
# config.cache_store = :mem_cache_store
@@ -75,8 +75,8 @@
# the I18n.default_locale when a translation cannot be found).
config.i18n.fallbacks = true
- # Send deprecation notices to registered listeners.
- config.active_support.deprecation = :notify
+ # Don't log any deprecations.
+ config.active_support.report_deprecations = false
# Log disallowed deprecations.
config.active_support.disallowed_deprecation = :log
@@ -95,15 +95,18 @@
# config.logger = ActiveSupport::TaggedLogging.new(Syslog::Logger.new "app-name")
# Include the BioPortal-specific configuration options
- require Rails.root.join('config', "bioportal_config_#{Rails.env}.rb")
+ if File.exist?(Rails.root.join('config', "bioportal_config_#{Rails.env}.rb"))
+ require Rails.root.join('config', "bioportal_config_#{Rails.env}.rb")
+ end
# Use a different cache store in production.
- config.cache_store = :mem_cache_store, ENV["MEMCACHE_SERVERS"] || "localhost:11211", { namespace: 'bioportal_web_ui', expires_in: 1.day }
+ config.cache_store = :mem_cache_store, ENV['MEMCACHE_SERVERS'] || 'localhost:11211',
+ { namespace: 'bioportal_web_ui', expires_in: 1.day }
# Add custom data attributes to sanitize allowed list
- config.action_view.sanitized_allowed_attributes = ['id', 'class', 'style', 'data-cls', 'data-ont']
+ config.action_view.sanitized_allowed_attributes = %w[id class style data-cls data-ont]
- if ENV["RAILS_LOG_TO_STDOUT"].present?
+ if ENV['RAILS_LOG_TO_STDOUT'].present?
logger = ActiveSupport::Logger.new(STDOUT)
logger.formatter = config.log_formatter
config.logger = ActiveSupport::TaggedLogging.new(logger)
diff --git a/config/environments/staging.rb b/config/environments/staging.rb
index a52909fae..c24addeaf 100644
--- a/config/environments/staging.rb
+++ b/config/environments/staging.rb
@@ -87,9 +87,6 @@
# Add custom data attributes to sanitize allowed list
config.action_view.sanitized_allowed_attributes = ['id', 'class', 'style', 'data-cls', 'data-ont']
- # TODO: Fix this?
- # enable json logging format. Useful for logstash
- # require 'rackstash'
- # config.rackstash.enabled = true
- # config.rackstash.tags = ['ruby', 'rails2']
+ # Include BioPortal-specific configuration options
+ require Rails.root.join('config', "bioportal_config_staging.rb")
end
diff --git a/config/environments/test.rb b/config/environments/test.rb
index b31dce4a2..d35b8d0f7 100644
--- a/config/environments/test.rb
+++ b/config/environments/test.rb
@@ -1,4 +1,6 @@
-require "active_support/core_ext/integer/time"
+# frozen_string_literal: true
+
+require 'active_support/core_ext/integer/time'
# The test environment is used exclusively to run your application's
# test suite. You never need to work with it otherwise. Remember that
@@ -14,7 +16,7 @@
# Eager loading loads your whole application. When running a single test locally,
# this probably isn't necessary. It's a good idea to do in a continuous integration
# system, or in some way before deploying your code.
- config.eager_load = ENV["CI"].present?
+ config.eager_load = ENV['CI'].present?
# Configure public file server for tests with Cache-Control for performance.
config.public_file_server.enabled = true
@@ -25,7 +27,7 @@
# Show full error reports and disable caching.
config.consider_all_requests_local = true
config.action_controller.perform_caching = false
- config.cache_store = :null_store
+ config.cache_store = ActiveSupport::Cache::MemCacheStore.new('localhost:11211', namespace: 'BioPortal')
# Raise exceptions instead of rendering exception templates.
config.action_dispatch.show_exceptions = false
@@ -53,10 +55,7 @@
config.active_support.disallowed_deprecation_warnings = []
# Raises error for missing translations.
- # config.i18n.raise_on_missing_translations = true
-
- # Annotate rendered view with file names.
- # config.action_view.annotate_rendered_view_with_filenames = true
+ # config.action_view.raise_on_missing_translations = true
# Include the BioPortal-specific configuration options
require Rails.root.join('config', "bioportal_config_#{Rails.env}.rb")
diff --git a/config/i18n-tasks.yml b/config/i18n-tasks.yml
new file mode 100644
index 000000000..6495aad7c
--- /dev/null
+++ b/config/i18n-tasks.yml
@@ -0,0 +1,8 @@
+# config/i18n-tasks.yml
+<% require 'i18n-tasks-csv' %>
+
+csv:
+ export:
+ - "tmp/i18n-export/main.csv"
+ import:
+ - tmp/i18n-export/main.csv
\ No newline at end of file
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index 4b828e80c..15e020265 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -1,11 +1,9 @@
# Be sure to restart your server when you modify this file.
# Version of your assets, change this if you want to expire all your assets.
-Rails.application.config.assets.version = '1.0'
+Rails.application.config.assets.version = "1.0"
# Add additional assets to the asset load path.
-# Rails.application.config.assets.paths << Emoji.images_path
-# Add Yarn node_modules folder to the asset load path.
Rails.application.config.assets.paths << Rails.root.join('node_modules')
# Precompile additional assets.
diff --git a/config/initializers/cube_reporter.rb b/config/initializers/cube_reporter.rb
deleted file mode 100644
index 136f509dd..000000000
--- a/config/initializers/cube_reporter.rb
+++ /dev/null
@@ -1,43 +0,0 @@
-require 'cube'
-
-##
-# This enables collection of request statistics for anaylsis via cube.
-# A cube server is required. See http://square.github.io/cube/ for more info.
-module Rack
- class CubeReporter
-
- def initialize(app = nil, options = {})
- host = options[:cube_host] || "localhost"
- port = options[:cube_port] || 1180
- @app = app
- @cube = ::Cube::Client.new(host, port)
- end
-
- def call(env)
- start = Time.now
- data = @app.call(env)
- finish = Time.now
- user = env["rack.session"] ? env["rack.session"][:user] : nil
- apikey = user.apikey if user
- username = user.username if user
- req_data = {
- duration_ms: ((finish - start)*1000).ceil,
- path: env["REQUEST_PATH"],
- status: data[0],
- user: {
- apikey: apikey,
- username: username,
- ip: env["REMOTE_ADDR"],
- user_agent: env["HTTP_USER_AGENT"]
- }
- }
- @cube.send "ui_request", DateTime.now, req_data
- data
- end
-
- end
-end
-
-if global_variables.include?(:$ENABLE_CUBE) && $ENABLE_CUBE == true
- Rails.configuration.middleware.use(::Rack::CubeReporter, {cube_host: $CUBE_HOST, cube_port: $CUBE_PORT})
-end
\ No newline at end of file
diff --git a/config/initializers/graphql_client.rb b/config/initializers/graphql_client.rb
index 69a909bb9..1f89525b6 100644
--- a/config/initializers/graphql_client.rb
+++ b/config/initializers/graphql_client.rb
@@ -1,12 +1,12 @@
-# frozen_string_literal: true
-
+#frozen_string_literal: true
+#Disable as no used in ontoportal-lirmm branch and causing problems with docker image build
require 'graphql/client'
require 'graphql/client/http'
module GitHub
HTTPAdapter = GraphQL::Client::HTTP.new('https://api.github.com/graphql') do
def headers(_context)
- { 'Authorization': "Bearer #{Rails.application.credentials[:kgcl][:github_access_token]}" }
+ { 'Authorization': "Bearer #{Rails.application.credentials.dig(:kgcl, :github_access_token)}" }
end
end
diff --git a/config/initializers/miniprofiler.rb b/config/initializers/miniprofiler.rb
deleted file mode 100644
index 05194cebb..000000000
--- a/config/initializers/miniprofiler.rb
+++ /dev/null
@@ -1,2 +0,0 @@
-Rack::MiniProfiler.config.authorization_mode = :allow_authorized
-Rack::MiniProfiler.config.position = 'right'
diff --git a/config/initializers/new_framework_defaults_7_0.rb b/config/initializers/new_framework_defaults_7_0.rb
index cf925f131..a579326e2 100644
--- a/config/initializers/new_framework_defaults_7_0.rb
+++ b/config/initializers/new_framework_defaults_7_0.rb
@@ -11,10 +11,10 @@
# `button_to` view helper will render `` element, regardless of whether
# or not the content is passed as the first argument or as a block.
-Rails.application.config.action_view.button_to_generates_button_tag = true
+# Rails.application.config.action_view.button_to_generates_button_tag = true
# `stylesheet_link_tag` view helper will not render the media attribute by default.
-Rails.application.config.action_view.apply_stylesheet_media_default = false
+# Rails.application.config.action_view.apply_stylesheet_media_default = false
# Change the digest class for the key generators to `OpenSSL::Digest::SHA256`.
# Changing this default means invalidate all encrypted messages generated by
@@ -28,116 +28,90 @@
# Change the digest class for ActiveSupport::Digest.
# Changing this default means that for example Etags change and
# various cache keys leading to cache invalidation.
-Rails.application.config.active_support.hash_digest_class = OpenSSL::Digest::SHA256
+# Rails.application.config.active_support.hash_digest_class = OpenSSL::Digest::SHA256
# Don't override ActiveSupport::TimeWithZone.name and use the default Ruby
# implementation.
-Rails.application.config.active_support.remove_deprecated_time_with_zone_name = true
+# Rails.application.config.active_support.remove_deprecated_time_with_zone_name = true
+
+# Change the format of the cache entry.
+# Changing this default means that all new cache entries added to the cache
+# will have a different format that is not supported by Rails 6.1 applications.
+# Only change this value after your application is fully deployed to Rails 7.0
+# and you have no plans to rollback.
+# Rails.application.config.active_support.cache_format_version = 7.0
# Calls `Rails.application.executor.wrap` around test cases.
# This makes test cases behave closer to an actual request or job.
# Several features that are normally disabled in test, such as Active Record query cache
# and asynchronous queries will then be enabled.
-Rails.application.config.active_support.executor_around_test_case = true
+# Rails.application.config.active_support.executor_around_test_case = true
+
+# Define the isolation level of most of Rails internal state.
+# If you use a fiber based server or job processor, you should set it to `:fiber`.
+# Otherwise the default of `:thread` if preferable.
+# Rails.application.config.active_support.isolation_level = :thread
# Set both the `:open_timeout` and `:read_timeout` values for `:smtp` delivery method.
-Rails.application.config.action_mailer.smtp_timeout = 5
+# Rails.application.config.action_mailer.smtp_timeout = 5
# The ActiveStorage video previewer will now use scene change detection to generate
# better preview images (rather than the previous default of using the first frame
# of the video).
-Rails.application.config.active_storage.video_preview_arguments =
- "-vf 'select=eq(n\\,0)+eq(key\\,1)+gt(scene\\,0.015),loop=loop=-1:size=2,trim=start_frame=1' -frames:v 1 -f image2"
+# Rails.application.config.active_storage.video_preview_arguments =
+# "-vf 'select=eq(n\\,0)+eq(key\\,1)+gt(scene\\,0.015),loop=loop=-1:size=2,trim=start_frame=1' -frames:v 1 -f image2"
# Automatically infer `inverse_of` for associations with a scope.
-Rails.application.config.active_record.automatic_scope_inversing = true
+# Rails.application.config.active_record.automatic_scope_inversing = true
# Raise when running tests if fixtures contained foreign key violations
-Rails.application.config.active_record.verify_foreign_keys_for_fixtures = true
+# Rails.application.config.active_record.verify_foreign_keys_for_fixtures = true
# Disable partial inserts.
# This default means that all columns will be referenced in INSERT queries
# regardless of whether they have a default or not.
-Rails.application.config.active_record.partial_inserts = false
-
+# Rails.application.config.active_record.partial_inserts = false
+#
# Protect from open redirect attacks in `redirect_back_or_to` and `redirect_to`.
-Rails.application.config.action_controller.raise_on_open_redirects = true
+# Rails.application.config.action_controller.raise_on_open_redirects = true
# Change the variant processor for Active Storage.
# Changing this default means updating all places in your code that
# generate variants to use image processing macros and ruby-vips
# operations. See the upgrading guide for detail on the changes required.
# The `:mini_magick` option is not deprecated; it's fine to keep using it.
-Rails.application.config.active_storage.variant_processor = :vips
+# Rails.application.config.active_storage.variant_processor = :vips
+
+# If you're upgrading and haven't set `cookies_serializer` previously, your cookie serializer
+# was `:marshal`. Convert all cookies to JSON, using the `:hybrid` formatter.
+#
+# If you're confident all your cookies are JSON formatted, you can switch to the `:json` formatter.
+#
+# Continue to use `:marshal` for backward-compatibility with old cookies.
+#
+# If you have configured the serializer elsewhere, you can remove this.
+#
+# See https://guides.rubyonrails.org/action_controller_overview.html#cookies for more information.
+# Rails.application.config.action_dispatch.cookies_serializer = :hybrid
# Enable parameter wrapping for JSON.
# Previously this was set in an initializer. It's fine to keep using that initializer if you've customized it.
# To disable parameter wrapping entirely, set this config to `false`.
-Rails.application.config.action_controller.wrap_parameters_by_default = true
+# Rails.application.config.action_controller.wrap_parameters_by_default = true
# Specifies whether generated namespaced UUIDs follow the RFC 4122 standard for namespace IDs provided as a
# `String` to `Digest::UUID.uuid_v3` or `Digest::UUID.uuid_v5` method calls.
#
# See https://guides.rubyonrails.org/configuring.html#config-active-support-use-rfc4122-namespaced-uuids for
# more information.
-Rails.application.config.active_support.use_rfc4122_namespaced_uuids = true
+# Rails.application.config.active_support.use_rfc4122_namespaced_uuids = true
# Change the default headers to disable browsers' flawed legacy XSS protection.
-Rails.application.config.action_dispatch.default_headers = {
- "X-Frame-Options" => "SAMEORIGIN",
- "X-XSS-Protection" => "0",
- "X-Content-Type-Options" => "nosniff",
- "X-Download-Options" => "noopen",
- "X-Permitted-Cross-Domain-Policies" => "none",
- "Referrer-Policy" => "strict-origin-when-cross-origin"
-}
-
-
-# ** Please read carefully, this must be configured in config/application.rb **
-# Change the format of the cache entry.
-# Changing this default means that all new cache entries added to the cache
-# will have a different format that is not supported by Rails 6.1 applications.
-# Only change this value after your application is fully deployed to Rails 7.0
-# and you have no plans to rollback.
-# When you're ready to change format, add this to `config/application.rb` (NOT this file):
-# config.active_support.cache_format_version = 7.0
-
-
-# Cookie serializer: 2 options
-#
-# If you're upgrading and haven't set `cookies_serializer` previously, your cookie serializer
-# is `:marshal`. The default for new apps is `:json`.
-#
-# Rails.application.config.action_dispatch.cookies_serializer = :json
-#
-#
-# To migrate an existing application to the `:json` serializer, use the `:hybrid` option.
-#
-# Rails transparently deserializes existing (Marshal-serialized) cookies on read and
-# re-writes them in the JSON format.
-#
-# It is fine to use `:hybrid` long term; you should do that until you're confident *all* your cookies
-# have been converted to JSON. To keep using `:hybrid` long term, move this config to its own
-# initializer or to `config/application.rb`.
-#
-# Rails.application.config.action_dispatch.cookies_serializer = :hybrid
-#
-#
-# If your cookies can't yet be serialized to JSON, keep using `:marshal` for backward-compatibility.
-#
-# If you have configured the serializer elsewhere, you can remove this section of the file.
-#
-# See https://guides.rubyonrails.org/action_controller_overview.html#cookies for more information.
-
-# Change the return value of `ActionDispatch::Request#content_type` to the Content-Type header without modification.
-Rails.application.config.action_dispatch.return_only_request_media_type_on_content_type = false
-
-# Active Storage `has_many_attached` relationships will default to replacing the current collection instead of appending to it.
-# Thus, to support submitting an empty collection, the `file_field` helper will render an hidden field `include_hidden` by default when `multiple_file_field_include_hidden` is set to `true`.
-# See https://guides.rubyonrails.org/configuring.html#config-active-storage-multiple-file-field-include-hidden for more information.
-Rails.application.config.active_storage.multiple_file_field_include_hidden = true
-
-# ** Please read carefully, this must be configured in config/application.rb (NOT this file) **
-# Disables the deprecated #to_s override in some Ruby core classes
-# See https://guides.rubyonrails.org/configuring.html#config-active-support-disable-to-s-conversion for more information.
-# config.active_support.disable_to_s_conversion = true
+# Rails.application.config.action_dispatch.default_headers = {
+# "X-Frame-Options" => "SAMEORIGIN",
+# "X-XSS-Protection" => "0",
+# "X-Content-Type-Options" => "nosniff",
+# "X-Download-Options" => "noopen",
+# "X-Permitted-Cross-Domain-Policies" => "none",
+# "Referrer-Policy" => "strict-origin-when-cross-origin"
+# }
diff --git a/config/initializers/omniauth.rb b/config/initializers/omniauth.rb
new file mode 100644
index 000000000..c7c4027c3
--- /dev/null
+++ b/config/initializers/omniauth.rb
@@ -0,0 +1,5 @@
+Rails.application.config.middleware.use OmniAuth::Builder do
+ Array($OMNIAUTH_PROVIDERS).each do |provider, config|
+ provider config[:strategy] || provider, config[:client_id], config[:client_secret], client_options: {}.merge(config[:client_options].to_h)
+ end
+end
\ No newline at end of file
diff --git a/config/newrelic.yml b/config/newrelic.yml
new file mode 100644
index 000000000..57282d3ec
--- /dev/null
+++ b/config/newrelic.yml
@@ -0,0 +1,51 @@
+# This file configures the New Relic Agent. New Relic monitors Ruby, Java,
+# .NET, PHP, Python, Node, and Go applications with deep visibility and low
+# overhead. For more information, visit www.newrelic.com.
+#
+# Generated December 31, 2022
+#
+# This configuration file is custom generated for NewRelic Administration
+#
+# For full documentation of agent configuration options, please refer to
+# https://docs.newrelic.com/docs/agents/ruby-agent/installation-configuration/ruby-agent-configuration
+
+common: &default_settings
+ # Required license key associated with your New Relic account.
+ license_key: <%= Rails.application.credentials[:newrelic][:license_key] %>
+
+ # Your application name. Renaming here affects where data displays in New
+ # Relic. For more details, see https://docs.newrelic.com/docs/apm/new-relic-apm/maintenance/renaming-applications
+ app_name: <%= Rails.application.credentials[:newrelic][:app_name] %>
+
+ distributed_tracing:
+ enabled: true
+
+ # To disable the agent regardless of other settings, uncomment the following:
+ # agent_enabled: false
+
+ # Logging level for log/newrelic_agent.log
+ log_level: info
+
+ application_logging:
+ # If `true`, all logging-related features for the agent can be enabled or disabled
+ # independently. If `false`, all logging-related features are disabled.
+ enabled: true
+ forwarding:
+ # If `true`, the agent captures log records emitted by this application.
+ enabled: true
+ # Defines the maximum number of log records to buffer in memory at a time.
+ max_samples_stored: 10000
+ metrics:
+ # If `true`, the agent captures metrics related to logging for this application.
+ enabled: true
+ local_decorating:
+ # If `true`, the agent decorates logs with metadata to link to entities, hosts, traces, and spans.
+ # This requires a log forwarder to send your log files to New Relic.
+ # This should not be used when forwarding is enabled.
+ enabled: false
+
+# Environment-specific settings are in this section.
+# RAILS_ENV or RACK_ENV (as appropriate) is used to determine the environment.
+# If your application has other named environments, configure them here.
+appliance:
+ <<: *default_settings
\ No newline at end of file
diff --git a/config/robots/appliance.txt b/config/robots/appliance.txt
index dd4faa671..6a80fe869 100644
--- a/config/robots/appliance.txt
+++ b/config/robots/appliance.txt
@@ -1,9 +1,18 @@
User-agent: *
+# This will match '/mappings', as well - due to path value wildcard [
+# https://developers.google.com/search/reference/robots_txt#url-matching-based-on-path-values ].
Disallow: /*mappings
+Disallow: /projects
+Disallow: /projects/
Disallow: /login
Disallow: /virtual
Disallow: /visualize
-Crawl-delay: 2
+Disallow: /resource_index
+Disallow: /feedback
+Disallow: /ajax
+Disallow: /javascripts
+Disalow: /widgets
+Crawl-delay: 5
User-agent: SemrushBot
Disallow: /
@@ -17,4 +26,14 @@ Disallow: /
User-agent: MJ12bot
Disallow: /
+User-agent: AhrefsBot
+Disallow: /
+
+User-agent: DataForSeoBot
+Disallow: /
+User-agent: BLEXBot
+Disallow: /
+User agent: MTRobot
+Disallow: /
+
diff --git a/config/settings.yml b/config/settings.yml
index 8edc0882c..788106b08 100644
--- a/config/settings.yml
+++ b/config/settings.yml
@@ -22,6 +22,8 @@ shared:
virtual_appliance: 'https://ontoportal.github.io/documentation/administration'
widgets: 'http://www.bioontology.org/wiki/NCBO_Widgets'
wiki: 'https://www.bioontology.org/wiki/'
+ mappings: 'https://www.bioontology.org/wiki/BioPortal_Help#Mappings_Tab'
+ metadata_help: 'https://doc.jonquetlab.lirmm.fr/share/32c082ff-97f5-45f4-bafe-05f41c9a5ce4'
development:
links:
diff --git a/db/schema.rb b/db/schema.rb
index 5d5db5ddc..ec76487f7 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -11,7 +11,7 @@
# It's strongly recommended that you check this file into your version control system.
ActiveRecord::Schema[7.0].define(version: 2023_11_30_210229) do
- create_table "analytics", id: :integer, charset: "utf8", force: :cascade do |t|
+ create_table "analytics", id: :integer, charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
t.string "segment"
t.string "action"
t.string "bp_slice"
@@ -22,13 +22,13 @@
t.datetime "updated_at", precision: nil
end
- create_table "licenses", charset: "utf8", force: :cascade do |t|
+ create_table "licenses", charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
t.text "encrypted_key"
t.datetime "created_at", precision: nil, null: false
t.datetime "updated_at", precision: nil, null: false
end
- create_table "ontologies", charset: "utf8", force: :cascade do |t|
+ create_table "ontologies", charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
t.string "acronym", null: false
t.text "new_term_instructions"
t.text "custom_message"
@@ -37,7 +37,7 @@
t.index ["acronym"], name: "index_ontologies_on_acronym", unique: true
end
- create_table "timeouts", id: :integer, charset: "utf8", force: :cascade do |t|
+ create_table "timeouts", id: :integer, charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
t.string "path"
t.integer "ontology_id"
t.text "concept_id"
@@ -45,7 +45,7 @@
t.timestamp "created"
end
- create_table "virtual_appliance_users", id: :integer, charset: "utf8", force: :cascade do |t|
+ create_table "virtual_appliance_users", id: :integer, charset: "utf8mb4", collation: "utf8mb4_0900_ai_ci", force: :cascade do |t|
t.string "user_id"
t.datetime "created_at", precision: nil
t.datetime "updated_at", precision: nil
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 000000000..3c70bbe88
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,122 @@
+x-app: &default-app
+ image: agroportal/ontoportal_web_ui:master
+ env_file:
+ - ".env"
+ tty: true
+ volumes:
+ - bundle:/srv/ontoportal/bundle
+ - node:/node_modules
+ - rails_cache:/app/tmp/cache
+ - assets:/app/public/assets
+ - /var/run/docker.sock:/var/run/docker.sock
+ - .:/app
+ depends_on:
+ db:
+ condition: service_healthy
+ cache:
+ condition: service_started
+ node:
+ condition: service_started
+ environment: &env
+ BUNDLE_WITHOUT: ""
+ BUNDLE_PATH: /srv/ontoportal/bundle
+ DB_HOST: db
+ CACHE_HOST: cache
+ tmpfs:
+ - /tmp
+ - /app/tmp/pids
+
+services:
+ db:
+ image: "mysql:8.0"
+ networks:
+ - default
+ volumes:
+ - mysql-data:/var/lib/mysql
+ ports:
+ - "3306:3306"
+ environment:
+ MYSQL_ROOT_PASSWORD: root
+ healthcheck:
+ test: ["CMD", "mysqladmin", "ping", "-h", "localhost"]
+ timeout: 5s
+ retries: 3
+
+ cache:
+ image: memcached:latest
+ restart: unless-stopped
+ command: ["-m", "1024"]
+ networks:
+ - default
+ ports:
+ - "11211:11211"
+ node:
+ <<: *default-app
+ command: "yarn build --watch"
+ depends_on:
+ - cache
+ - db
+
+ dev:
+ <<: *default-app
+ ports:
+ - "3000:3000"
+ links:
+ - db
+ - cache
+
+ production:
+ <<: *default-app
+ command: "bundle exec puma -C config/puma.rb"
+ environment:
+ <<: *env
+ RAILS_ENV: "production"
+ BUNDLE_WITHOUT: "development test"
+ BUNDLE_PATH: "/usr/local/bundle"
+ #SECRET_KEY_BASE: TODO
+ #RAILS_MASTER_KEY: TODO
+ BIOPORTAL_WEB_UI_DATABASE_PASSWORD: root
+ MEMCACHE_SERVERS: "cache:11211"
+ ports:
+ - "3000:3000"
+ links:
+ - db
+ - cache
+ depends_on:
+ db:
+ condition: service_healthy
+ cache:
+ condition: service_started
+ volumes:
+ - node:/node_modules
+ - rails_cache:/app/tmp/cache
+ - assets:/app/public/assets
+ - app_ui:/app
+
+ test:
+ <<: *default-app
+ depends_on:
+ - db
+ - cache
+ - chrome-server
+ network_mode: "host"
+ environment:
+ BUNDLE_WITHOUT: ""
+ DB_HOST: 127.0.0.1
+ CACHE_HOST: 127.0.0.1
+
+ chrome-server:
+ image: selenium/standalone-chrome:112.0-chromedriver-112.0-grid-4.9.0-20230421
+ shm_size: 2g
+ network_mode: 'host'
+# ports:
+# - "4444:4444"
+# - "7900:7900"
+
+volumes:
+ mysql-data:
+ bundle:
+ rails_cache:
+ assets:
+ node:
+ app_ui:
diff --git a/lib/resolver/acronym_from_virtual.rb b/lib/resolver/acronym_from_virtual.rb
deleted file mode 100644
index b78fd61a0..000000000
--- a/lib/resolver/acronym_from_virtual.rb
+++ /dev/null
@@ -1,535 +0,0 @@
-BPIDResolver::ACRONYM_FROM_VIRTUAL = {
- "old:acronym_from_virtual:3013" => "DIAGONT",
- "old:acronym_from_virtual:3245" => "SuicidO",
- "old:acronym_from_virtual:1247" => "GEOSPECIES",
- "old:acronym_from_virtual:1054" => "AMINO-ACID",
- "old:acronym_from_virtual:2012" => "goslim_pir",
- "old:acronym_from_virtual:3015" => "PMR",
- "old:acronym_from_virtual:3212" => "GLYCOPROT",
- "old:acronym_from_virtual:3271" => "BSAO",
- "old:acronym_from_virtual:2099" => "GWAS_EFO_SKOS",
- "old:acronym_from_virtual:1062" => "PR",
- "old:acronym_from_virtual:3004" => "NATPRO",
- "old:acronym_from_virtual:1584" => "MMO",
- "old:acronym_from_virtual:1046" => "SBO",
- "old:acronym_from_virtual:1545" => "CO-WHEAT",
- "old:acronym_from_virtual:1016" => "FB-DV",
- "old:acronym_from_virtual:1059" => "CPRO",
- "old:acronym_from_virtual:3238" => "PDO",
- "old:acronym_from_virtual:1576" => "FDA-MEDDEVICE",
- "old:acronym_from_virtual:1114" => "BILA",
- "old:acronym_from_virtual:1055" => "GALEN",
- "old:acronym_from_virtual:1158" => "CBO",
- "old:acronym_from_virtual:3151" => "GEXO",
- "old:acronym_from_virtual:2109" => "ooevv-vaccine",
- "old:acronym_from_virtual:1488" => "JERM",
- "old:acronym_from_virtual:3234" => "BOF",
- "old:acronym_from_virtual:3047" => "DEMOGRAPH",
- "old:acronym_from_virtual:1613" => "BDO",
- "old:acronym_from_virtual:1142" => "EP",
- "old:acronym_from_virtual:3127" => "IMMDIS",
- "old:acronym_from_virtual:1461" => "TMO",
- "old:acronym_from_virtual:3146" => "CMS",
- "old:acronym_from_virtual:1125" => "HP",
- "old:acronym_from_virtual:2033" => "iceci-instrument_object_substance",
- "old:acronym_from_virtual:1033" => "NMR",
- "old:acronym_from_virtual:1666" => "MFOEM",
- "old:acronym_from_virtual:1615" => "CHEMBIO",
- "old:acronym_from_virtual:3184" => "ZIP3",
- "old:acronym_from_virtual:3150" => "BRIDG",
- "old:acronym_from_virtual:2054" => "NCBI_NMOsp_1_0_0",
- "old:acronym_from_virtual:1370" => "ATO",
- "old:acronym_from_virtual:3268" => "ERNO",
- "old:acronym_from_virtual:3261" => "STNFRDRXDEMO",
- "old:acronym_from_virtual:2032" => "iceci-details_for_place_of_occurrence",
- "old:acronym_from_virtual:1402" => "NIFCELL",
- "old:acronym_from_virtual:1427" => "RCD",
- "old:acronym_from_virtual:1565" => "OMRSE",
- "old:acronym_from_virtual:1517" => "EHDAA2",
- "old:acronym_from_virtual:1347" => "MEDLINEPLUS",
- "old:acronym_from_virtual:3243" => "NHSQI2009",
- "old:acronym_from_virtual:1640" => "PEDTERM",
- "old:acronym_from_virtual:1354" => "WHO-ART",
- "old:acronym_from_virtual:1095" => "XAO",
- "old:acronym_from_virtual:1661" => "UCSFXPLANT",
- "old:acronym_from_virtual:3174" => "IDODEN",
- "old:acronym_from_virtual:1146" => "ECG",
- "old:acronym_from_virtual:1065" => "TADS",
- "old:acronym_from_virtual:3028" => "SOY",
- "old:acronym_from_virtual:1100" => "OGI",
- "old:acronym_from_virtual:2086" => "SMD_NPLSM_BRST",
- "old:acronym_from_virtual:1136" => "EFO",
- "old:acronym_from_virtual:1050" => "ZEA",
- "old:acronym_from_virtual:3124" => "VSO",
- "old:acronym_from_virtual:2085" => "SMD_NPLSM",
- "old:acronym_from_virtual:1047" => "GRO-CPD",
- "old:acronym_from_virtual:1540" => "DDI",
- "old:acronym_from_virtual:2007" => "goslim_generic_1_770",
- "old:acronym_from_virtual:3155" => "ONTOKBCF",
- "old:acronym_from_virtual:2045" => "ICF-d5",
- "old:acronym_from_virtual:1350" => "LOINC",
- "old:acronym_from_virtual:1099" => "ATMO",
- "old:acronym_from_virtual:3231" => "GLYCANONT",
- "old:acronym_from_virtual:3131" => "PROVO",
- "old:acronym_from_virtual:1123" => "OBI",
- "old:acronym_from_virtual:2035" => "iceci-mechanism",
- "old:acronym_from_virtual:1420" => "MSHSPA_1",
- "old:acronym_from_virtual:1304" => "BCGO",
- "old:acronym_from_virtual:1042" => "OBOREL",
- "old:acronym_from_virtual:1049" => "WB-LS",
- "old:acronym_from_virtual:1328" => "HOM",
- "old:acronym_from_virtual:1575" => "EXO",
- "old:acronym_from_virtual:3077" => "ONTODM-KDD",
- "old:acronym_from_virtual:2108" => "ooevv-tractTrace",
- "old:acronym_from_virtual:3191" => "MPO",
- "old:acronym_from_virtual:1349" => "PDQ",
- "old:acronym_from_virtual:3239" => "CSSO",
- "old:acronym_from_virtual:2038" => "iceci-details_for_activity",
- "old:acronym_from_virtual:1522" => "BP",
- "old:acronym_from_virtual:1587" => "PO",
- "old:acronym_from_virtual:1116" => "BHO",
- "old:acronym_from_virtual:3038" => "HOM-TEST",
- "old:acronym_from_virtual:1001" => "GRO-CPGA",
- "old:acronym_from_virtual:2025" => "NIF-RTH",
- "old:acronym_from_virtual:1537" => "IDOBRU",
- "old:acronym_from_virtual:1009" => "DOID",
- "old:acronym_from_virtual:3178" => "CANONT",
- "old:acronym_from_virtual:2036" => "iceci-place_of_occurrence",
- "old:acronym_from_virtual:1112" => "UO",
- "old:acronym_from_virtual:3153" => "NTDO",
- "old:acronym_from_virtual:1010" => "EMAP",
- "old:acronym_from_virtual:1541" => "MCCL",
- "old:acronym_from_virtual:1067" => "WB-PHENOTYPE",
- "old:acronym_from_virtual:1560" => "COGPO",
- "old:acronym_from_virtual:1697" => "UCSFORTHO",
- "old:acronym_from_virtual:1260" => "RID",
- "old:acronym_from_virtual:1091" => "SPD",
- "old:acronym_from_virtual:2103" => "ICPCFRE",
- "old:acronym_from_virtual:1069" => "ENVO",
- "old:acronym_from_virtual:1686" => "NEOMARK4",
- "old:acronym_from_virtual:1527" => "VANDF",
- "old:acronym_from_virtual:1057" => "RADLEX",
- "old:acronym_from_virtual:3258" => "OBR-Scolio",
- "old:acronym_from_virtual:1500" => "RNAO",
- "old:acronym_from_virtual:3042" => "TEO",
- "old:acronym_from_virtual:2114" => "citation",
- "old:acronym_from_virtual:2003" => "BiositemapIM",
- "old:acronym_from_virtual:2029" => "iceci-countermeasures",
- "old:acronym_from_virtual:3264" => "WH",
- "old:acronym_from_virtual:1144" => "DC-CL",
- "old:acronym_from_virtual:1418" => "TOK",
- "old:acronym_from_virtual:1497" => "PMA",
- "old:acronym_from_virtual:2093" => "OBI_IEDB_view",
- "old:acronym_from_virtual:3252" => "SSE",
- "old:acronym_from_virtual:1183" => "LIPRO",
- "old:acronym_from_virtual:1423" => "RXNORM",
- "old:acronym_from_virtual:1026" => "MAO",
- "old:acronym_from_virtual:1555" => "VSAO",
- "old:acronym_from_virtual:3031" => "QUDT",
- "old:acronym_from_virtual:3223" => "GCO",
- "old:acronym_from_virtual:1172" => "VO",
- "old:acronym_from_virtual:1068" => "SAO",
- "old:acronym_from_virtual:1410" => "KISAO",
- "old:acronym_from_virtual:1520" => "LSM",
- "old:acronym_from_virtual:2050" => "ICF-d810-d839",
- "old:acronym_from_virtual:3021" => "ATC",
- "old:acronym_from_virtual:1063" => "CARO",
- "old:acronym_from_virtual:1530" => "ADW",
- "old:acronym_from_virtual:2120" => "provenance",
- "old:acronym_from_virtual:3017" => "GCC",
- "old:acronym_from_virtual:2056" => "NCBI_NMOsp_1_2_2",
- "old:acronym_from_virtual:3206" => "HCPCS-HIMC",
- "old:acronym_from_virtual:1104" => "BRO",
- "old:acronym_from_virtual:1092" => "IDO",
- "old:acronym_from_virtual:1413" => "SWO",
- "old:acronym_from_virtual:3032" => "EPICMEDS",
- "old:acronym_from_virtual:1456" => "MSHFRE",
- "old:acronym_from_virtual:1077" => "MIRO",
- "old:acronym_from_virtual:1051" => "ZFA",
- "old:acronym_from_virtual:2055" => "NCBI_NMOsp_1_2_1",
- "old:acronym_from_virtual:3090" => "ONTOMA",
- "old:acronym_from_virtual:3104" => "USSOC",
- "old:acronym_from_virtual:1573" => "TM-MER",
- "old:acronym_from_virtual:3092" => "CLINIC",
- "old:acronym_from_virtual:1616" => "PHYLONT",
- "old:acronym_from_virtual:2023" => "NCBITaxonOWL",
- "old:acronym_from_virtual:1656" => "PHENOMEBLAST",
- "old:acronym_from_virtual:3219" => "MSTDE",
- "old:acronym_from_virtual:1025" => "MP",
- "old:acronym_from_virtual:1670" => "ICDO3",
- "old:acronym_from_virtual:1089" => "BIRNLEX",
- "old:acronym_from_virtual:3215" => "MIXS",
- "old:acronym_from_virtual:1532" => "SIO",
- "old:acronym_from_virtual:2105" => "SNMD_BDY",
- "old:acronym_from_virtual:3022" => "BIOMODELS",
- "old:acronym_from_virtual:2053" => "ICF-d840-d859%2Fd860-d879",
- "old:acronym_from_virtual:3262" => "BCTEO",
- "old:acronym_from_virtual:1168" => "Amino_Acid-zh_CN",
- "old:acronym_from_virtual:1550" => "PHARE",
- "old:acronym_from_virtual:1398" => "LDA",
- "old:acronym_from_virtual:1428" => "NIC",
- "old:acronym_from_virtual:1567" => "PVONTO",
- "old:acronym_from_virtual:3211" => "TEST-PROD",
- "old:acronym_from_virtual:2124" => "ICD9CM-PROC",
- "old:acronym_from_virtual:3255" => "CHMO",
- "old:acronym_from_virtual:3204" => "PORO",
- "old:acronym_from_virtual:1043" => "REX",
- "old:acronym_from_virtual:1689" => "FYPO",
- "old:acronym_from_virtual:3008" => "CARELEX",
- "old:acronym_from_virtual:1570" => "TM-CONST",
- "old:acronym_from_virtual:2070" => "obi-fged",
- "old:acronym_from_virtual:2002" => "BRO-AreaOfResearch",
- "old:acronym_from_virtual:2020" => "SNOMEDCT-ANAT",
- "old:acronym_from_virtual:2092" => "envo_153",
- "old:acronym_from_virtual:3045" => "ICD9CM-KM",
- "old:acronym_from_virtual:3108" => "CCONT",
- "old:acronym_from_virtual:1438" => "MCBCC",
- "old:acronym_from_virtual:1348" => "OMIM",
- "old:acronym_from_virtual:1515" => "INO",
- "old:acronym_from_virtual:3176" => "XEO",
- "old:acronym_from_virtual:2009" => "goslim_plant",
- "old:acronym_from_virtual:2078" => "H1_NMOABA",
- "old:acronym_from_virtual:3183" => "IFAR",
- "old:acronym_from_virtual:2046" => "ICF-d6",
- "old:acronym_from_virtual:3186" => "I2B2-LOINC",
- "old:acronym_from_virtual:3265" => "BNO",
- "old:acronym_from_virtual:2110" => "DTVPrecision",
- "old:acronym_from_virtual:1581" => "HLTHINDCTRS",
- "old:acronym_from_virtual:3220" => "MSTDE-FRE",
- "old:acronym_from_virtual:3009" => "MEO",
- "old:acronym_from_virtual:1694" => "CPT-KM",
- "old:acronym_from_virtual:1052" => "PRO-ONT",
- "old:acronym_from_virtual:1290" => "ABA-AMB",
- "old:acronym_from_virtual:3000" => "MIXSCV",
- "old:acronym_from_virtual:1038" => "PSDS",
- "old:acronym_from_virtual:1023" => "FBbi",
- "old:acronym_from_virtual:1060" => "CTONT",
- "old:acronym_from_virtual:1249" => "SBRO",
- "old:acronym_from_virtual:1152" => "MAT",
- "old:acronym_from_virtual:2101" => "test1",
- "old:acronym_from_virtual:1083" => "NPO",
- "old:acronym_from_virtual:1013" => "EVOC",
- "old:acronym_from_virtual:1407" => "TEDDY",
- "old:acronym_from_virtual:2113" => "bibliographic",
- "old:acronym_from_virtual:2030" => "iceci-descriptor_for_intent",
- "old:acronym_from_virtual:2084" => "OGMD_OWL",
- "old:acronym_from_virtual:1053" => "FMA",
- "old:acronym_from_virtual:1422" => "MEDDRA",
- "old:acronym_from_virtual:2010" => "goslim_candida",
- "old:acronym_from_virtual:3273" => "HRDO",
- "old:acronym_from_virtual:3152" => "REXO",
- "old:acronym_from_virtual:3222" => "RSA",
- "old:acronym_from_virtual:3207" => "ATOL",
- "old:acronym_from_virtual:1498" => "EDAM",
- "old:acronym_from_virtual:1109" => "SO",
- "old:acronym_from_virtual:1224" => "SYMP",
- "old:acronym_from_virtual:3253" => "OntoVIP",
- "old:acronym_from_virtual:1237" => "SITBAC",
- "old:acronym_from_virtual:2042" => "ICF-d2",
- "old:acronym_from_virtual:3263" => "OntoBioUSP",
- "old:acronym_from_virtual:1649" => "OSHPD",
- "old:acronym_from_virtual:3247" => "EDDA",
- "old:acronym_from_virtual:1671" => "QIBO",
- "old:acronym_from_virtual:1585" => "XCO",
- "old:acronym_from_virtual:1006" => "CL",
- "old:acronym_from_virtual:1424" => "NDDF",
- "old:acronym_from_virtual:3114" => "RPO",
- "old:acronym_from_virtual:1426" => "MDDB",
- "old:acronym_from_virtual:3169" => "GLYCO",
- "old:acronym_from_virtual:2065" => "obi-device",
- "old:acronym_from_virtual:1192" => "CPTAC",
- "old:acronym_from_virtual:1032" => "NCIT",
- "old:acronym_from_virtual:2067" => "RCJI",
- "old:acronym_from_virtual:1017" => "FB-CV",
- "old:acronym_from_virtual:2014" => "goslim_yeast",
- "old:acronym_from_virtual:3251" => "ADO",
- "old:acronym_from_virtual:1081" => "TTO",
- "old:acronym_from_virtual:3162" => "RETO",
- "old:acronym_from_virtual:1362" => "HAO",
- "old:acronym_from_virtual:3240" => "RNPRIO",
- "old:acronym_from_virtual:3272" => "CARD",
- "old:acronym_from_virtual:3217" => "CABRO",
- "old:acronym_from_virtual:2069" => "H1_NMOABA_1_0",
- "old:acronym_from_virtual:3208" => "IDQA",
- "old:acronym_from_virtual:3228" => "ELIG",
- "old:acronym_from_virtual:1651" => "SDO",
- "old:acronym_from_virtual:3126" => "NIFSUBCELL",
- "old:acronym_from_virtual:3157" => "GENETRIAL",
- "old:acronym_from_virtual:1070" => "GO",
- "old:acronym_from_virtual:2088" => "SNMD_BC",
- "old:acronym_from_virtual:1414" => "OGMS",
- "old:acronym_from_virtual:1516" => "ICD10",
- "old:acronym_from_virtual:1429" => "ICPC2P",
- "old:acronym_from_virtual:3241" => "UDEF",
- "old:acronym_from_virtual:2034" => "iceci-intent",
- "old:acronym_from_virtual:2074" => "H1_NMOABA_2_0",
- "old:acronym_from_virtual:1024" => "LHN",
- "old:acronym_from_virtual:3003" => "CNO",
- "old:acronym_from_virtual:2083" => "H1_NMOABA_4_1",
- "old:acronym_from_virtual:1039" => "PROPREO",
- "old:acronym_from_virtual:1638" => "ONTODM-CORE",
- "old:acronym_from_virtual:2008" => "goslim_goa",
- "old:acronym_from_virtual:3250" => "ONL-MR-DA",
- "old:acronym_from_virtual:3136" => "NHDS",
- "old:acronym_from_virtual:1393" => "IAO",
- "old:acronym_from_virtual:1332" => "BFO",
- "old:acronym_from_virtual:3203" => "HINO",
- "old:acronym_from_virtual:2122" => "SciRes",
- "old:acronym_from_virtual:2013" => "goslim_pombe",
- "old:acronym_from_virtual:1627" => "HOMERUN",
- "old:acronym_from_virtual:2117" => "event",
- "old:acronym_from_virtual:1190" => "OPL",
- "old:acronym_from_virtual:3002" => "MF",
- "old:acronym_from_virtual:1417" => "FLU",
- "old:acronym_from_virtual:1314" => "CLO",
- "old:acronym_from_virtual:1101" => "ICD9CM",
- "old:acronym_from_virtual:3029" => "SPTO",
- "old:acronym_from_virtual:1381" => "NIFDYS",
- "old:acronym_from_virtual:1440" => "GFO-BIO",
- "old:acronym_from_virtual:1344" => "ICPC",
- "old:acronym_from_virtual:1351" => "MESH",
- "old:acronym_from_virtual:1094" => "PTRANS",
- "old:acronym_from_virtual:1115" => "YPO",
- "old:acronym_from_virtual:2126" => "CPT-mod",
- "old:acronym_from_virtual:1621" => "NBO",
- "old:acronym_from_virtual:3007" => "UCSFICU",
- "old:acronym_from_virtual:2041" => "ICF-d1",
- "old:acronym_from_virtual:2080" => "H1_NMOABA_4_0",
- "old:acronym_from_virtual:1501" => "NEOMARK3",
- "old:acronym_from_virtual:3158" => "SWEET",
- "old:acronym_from_virtual:1335" => "PEO",
- "old:acronym_from_virtual:1571" => "TM-OTHER-FACTORS",
- "old:acronym_from_virtual:1061" => "SOPHARM",
- "old:acronym_from_virtual:1411" => "ICF",
- "old:acronym_from_virtual:1394" => "SSO",
- "old:acronym_from_virtual:2018" => "SNOMEDCT-CF",
- "old:acronym_from_virtual:1676" => "RCTONT",
- "old:acronym_from_virtual:1086" => "OGDI",
- "old:acronym_from_virtual:1699" => "VIVO",
- "old:acronym_from_virtual:2079" => "ECGT",
- "old:acronym_from_virtual:2082" => "H3_HIPSeptotemporalAxis",
- "old:acronym_from_virtual:1321" => "NEMO",
- "old:acronym_from_virtual:3267" => "DCO",
- "old:acronym_from_virtual:2001" => "BRO-Activity",
- "old:acronym_from_virtual:2072" => "NCBI_NMOsp_1_4_0",
- "old:acronym_from_virtual:1343" => "HL7",
- "old:acronym_from_virtual:1630" => "UCSFEPIC",
- "old:acronym_from_virtual:2119" => "foaf",
- "old:acronym_from_virtual:3094" => "DWC-TEST",
- "old:acronym_from_virtual:3201" => "BCO",
- "old:acronym_from_virtual:1105" => "MS",
- "old:acronym_from_virtual:3199" => "UCSFICD910CM",
- "old:acronym_from_virtual:1085" => "OGMD",
- "old:acronym_from_virtual:1494" => "TMA",
- "old:acronym_from_virtual:1484" => "ICECI",
- "old:acronym_from_virtual:3259" => "InterNano",
- "old:acronym_from_virtual:1444" => "CHEMINF",
- "old:acronym_from_virtual:2048" => "ICF-d8",
- "old:acronym_from_virtual:2051" => "ICF-d840-d859",
- "old:acronym_from_virtual:3226" => "SBOL",
- "old:acronym_from_virtual:2063" => "UCare_Demographics",
- "old:acronym_from_virtual:1134" => "BT",
- "old:acronym_from_virtual:1430" => "AI-RHEUM",
- "old:acronym_from_virtual:1528" => "HUGO",
- "old:acronym_from_virtual:3025" => "CTX",
- "old:acronym_from_virtual:1131" => "MO",
- "old:acronym_from_virtual:1404" => "UBERON",
- "old:acronym_from_virtual:3194" => "PHENOSCAPE-EXT",
- "old:acronym_from_virtual:1526" => "CRISP",
- "old:acronym_from_virtual:2116" => "dcterms",
- "old:acronym_from_virtual:3233" => "CHD",
- "old:acronym_from_virtual:2058" => "SNOMEDCT-MAS",
- "old:acronym_from_virtual:3270" => "suicideo",
- "old:acronym_from_virtual:1037" => "PTO",
- "old:acronym_from_virtual:3269" => "BICSO",
- "old:acronym_from_virtual:1110" => "TAO",
- "old:acronym_from_virtual:1011" => "IEV",
- "old:acronym_from_virtual:1341" => "COSTART",
- "old:acronym_from_virtual:2019" => "SNOMEDCT-TF",
- "old:acronym_from_virtual:3043" => "MEDABBS",
- "old:acronym_from_virtual:2091" => "NDF-RT",
- "old:acronym_from_virtual:1583" => "CMO",
- "old:acronym_from_virtual:1539" => "NIGO",
- "old:acronym_from_virtual:3016" => "ERO",
- "old:acronym_from_virtual:2031" => "iceci-details_for_mechanism",
- "old:acronym_from_virtual:1507" => "CCO",
- "old:acronym_from_virtual:1076" => "OCRE",
- "old:acronym_from_virtual:1078" => "BSPO",
- "old:acronym_from_virtual:3218" => "TRON",
- "old:acronym_from_virtual:1135" => "pseudo",
- "old:acronym_from_virtual:1544" => "CO",
- "old:acronym_from_virtual:3246" => "ONL-MSA",
- "old:acronym_from_virtual:2017" => "BRO-Chinese",
- "old:acronym_from_virtual:1439" => "GFO",
- "old:acronym_from_virtual:1015" => "FB-BT",
- "old:acronym_from_virtual:1041" => "PSIMOD",
- "old:acronym_from_virtual:3232" => "SNMI",
- "old:acronym_from_virtual:1064" => "FB-SP",
- "old:acronym_from_virtual:1655" => "PHARMGKB",
- "old:acronym_from_virtual:2111" => "documentStatus",
- "old:acronym_from_virtual:1014" => "FIX",
- "old:acronym_from_virtual:1521" => "NEUMORE",
- "old:acronym_from_virtual:3181" => "ONTOPNEUMO",
- "old:acronym_from_virtual:2040" => "SNOMEDCT-CORE",
- "old:acronym_from_virtual:1632" => "WSIO",
- "old:acronym_from_virtual:2127" => "NIAID-GSC-BRC",
- "old:acronym_from_virtual:1639" => "EPILONT",
- "old:acronym_from_virtual:3205" => "ICD0",
- "old:acronym_from_virtual:3236" => "VTO",
- "old:acronym_from_virtual:2047" => "ICF-d7",
- "old:acronym_from_virtual:1489" => "OAE",
- "old:acronym_from_virtual:2115" => "dcelements",
- "old:acronym_from_virtual:1588" => "ONTODT",
- "old:acronym_from_virtual:3242" => "NHSQI",
- "old:acronym_from_virtual:3197" => "HIMC-CPT",
- "old:acronym_from_virtual:1027" => "MFO",
- "old:acronym_from_virtual:1311" => "IDOMAL",
- "old:acronym_from_virtual:3224" => "UCSFI9I10CMPCS",
- "old:acronym_from_virtual:1149" => "DERMLEX",
- "old:acronym_from_virtual:1012" => "ECO",
- "old:acronym_from_virtual:2026" => "NCIt-Activity",
- "old:acronym_from_virtual:1035" => "PW",
- "old:acronym_from_virtual:1108" => "PAE",
- "old:acronym_from_virtual:2138" => "Radlex3.9.1",
- "old:acronym_from_virtual:2136" => "DILIo",
- "old:acronym_from_virtual:1572" => "TM-SIGNS-AND-SYMPTS",
- "old:acronym_from_virtual:3230" => "EPSO",
- "old:acronym_from_virtual:1510" => "CPTH",
- "old:acronym_from_virtual:2052" => "ICF-d860-d879",
- "old:acronym_from_virtual:1107" => "PATO",
- "old:acronym_from_virtual:1005" => "BTO",
- "old:acronym_from_virtual:1580" => "AERO",
- "old:acronym_from_virtual:3159" => "VARIO",
- "old:acronym_from_virtual:2062" => "HOM-UCSF_UCareDispostion",
- "old:acronym_from_virtual:1574" => "VHOG",
- "old:acronym_from_virtual:1031" => "MPATH",
- "old:acronym_from_virtual:1529" => "HCPCS",
- "old:acronym_from_virtual:3058" => "DWC",
- "old:acronym_from_virtual:1569" => "HPIO",
- "old:acronym_from_virtual:2100" => "HSDB_OCRe",
- "old:acronym_from_virtual:1491" => "IMGT-ONTOLOGY",
- "old:acronym_from_virtual:2125" => "HCPCS-mod",
- "old:acronym_from_virtual:3120" => "PCO",
- "old:acronym_from_virtual:1019" => "FAO",
- "old:acronym_from_virtual:2043" => "ICF-d3",
- "old:acronym_from_virtual:2049" => "ICF-d9",
- "old:acronym_from_virtual:3139" => "MIRNAO",
- "old:acronym_from_virtual:1352" => "NDFRT",
- "old:acronym_from_virtual:1044" => "SEP",
- "old:acronym_from_virtual:1130" => "ACGT-MO",
- "old:acronym_from_virtual:3214" => "OGSF",
- "old:acronym_from_virtual:3179" => "GENE-CDS",
- "old:acronym_from_virtual:1425" => "ICD10PCS",
- "old:acronym_from_virtual:1090" => "AAO",
- "old:acronym_from_virtual:1030" => "TGMA",
- "old:acronym_from_virtual:1007" => "CHEBI",
- "old:acronym_from_virtual:1087" => "OGR",
- "old:acronym_from_virtual:3019" => "RH-MESH",
- "old:acronym_from_virtual:2037" => "iceci-substance_use",
- "old:acronym_from_virtual:3137" => "ONSTR",
- "old:acronym_from_virtual:3216" => "BAO-GPCR",
- "old:acronym_from_virtual:2064" => "LOINC",
- "old:acronym_from_virtual:3198" => "SEMPHYSKB-HUMAN",
- "old:acronym_from_virtual:1586" => "OntoOrpha",
- "old:acronym_from_virtual:3192" => "MCCV",
- "old:acronym_from_virtual:2104" => "MDRFRE",
- "old:acronym_from_virtual:3078" => "PHENX",
- "old:acronym_from_virtual:3020" => "CPO",
- "old:acronym_from_virtual:1148" => "BP-METADATA",
- "old:acronym_from_virtual:1021" => "EHDAA",
- "old:acronym_from_virtual:3221" => "DERMO",
- "old:acronym_from_virtual:3012" => "NONRCTO",
- "old:acronym_from_virtual:1222" => "APO",
- "old:acronym_from_virtual:1126" => "FHHO",
- "old:acronym_from_virtual:1552" => "REPO",
- "old:acronym_from_virtual:2066" => "RXNORM",
- "old:acronym_from_virtual:3200" => "ZIP5",
- "old:acronym_from_virtual:3249" => "ONL-DP",
- "old:acronym_from_virtual:3190" => "PATHLEX",
- "old:acronym_from_virtual:1672" => "DIKB",
- "old:acronym_from_virtual:3210" => "TRAK",
- "old:acronym_from_virtual:3266" => "OBI_BCGO",
- "old:acronym_from_virtual:3244" => "SEDI",
- "old:acronym_from_virtual:1369" => "PHYFIELD",
- "old:acronym_from_virtual:3189" => "TOP-MENELAS",
- "old:acronym_from_virtual:2106" => "ICF-NoCodeLabel",
- "old:acronym_from_virtual:2112" => "geopolitical",
- "old:acronym_from_virtual:2121" => "skos",
- "old:acronym_from_virtual:1257" => "MEGO",
- "old:acronym_from_virtual:1397" => "GAZ",
- "old:acronym_from_virtual:3062" => "I2B2-PATVISDIM",
- "old:acronym_from_virtual:1568" => "AEO",
- "old:acronym_from_virtual:2022" => "BRO-Resource",
- "old:acronym_from_virtual:1650" => "UNITSONT",
- "old:acronym_from_virtual:3119" => "OBIWS",
- "old:acronym_from_virtual:1578" => "ELIXHAUSER",
- "old:acronym_from_virtual:1082" => "GRO",
- "old:acronym_from_virtual:1490" => "PLATSTG",
- "old:acronym_from_virtual:2006" => "FMA-SUBSET",
- "old:acronym_from_virtual:1122" => "SPO",
- "old:acronym_from_virtual:1504" => "CPT",
- "old:acronym_from_virtual:1128" => "CDAO",
- "old:acronym_from_virtual:1533" => "BAO",
- "old:acronym_from_virtual:3237" => "VBCV",
- "old:acronym_from_virtual:3209" => "OPE",
- "old:acronym_from_virtual:1000" => "MA",
- "old:acronym_from_virtual:2015" => "SOFA",
- "old:acronym_from_virtual:2000" => "BRO-Core",
- "old:acronym_from_virtual:1416" => "SCTSPA",
- "old:acronym_from_virtual:2073" => "ECGF",
- "old:acronym_from_virtual:2021" => "SNOMEDCT-ORG",
- "old:acronym_from_virtual:1506" => "GO-EXT",
- "old:acronym_from_virtual:1401" => "ICNP",
- "old:acronym_from_virtual:2059" => "HOM-ICD9",
- "old:acronym_from_virtual:1696" => "SYN",
- "old:acronym_from_virtual:1058" => "SNPO",
- "old:acronym_from_virtual:3195" => "ICD09",
- "old:acronym_from_virtual:2027" => "3.0_OWL",
- "old:acronym_from_virtual:1582" => "CAO",
- "old:acronym_from_virtual:1048" => "WB-BT",
- "old:acronym_from_virtual:1415" => "CTCAE",
- "old:acronym_from_virtual:1523" => "OBOE-SBC",
- "old:acronym_from_virtual:3185" => "GPI",
- "old:acronym_from_virtual:2004" => "NeuroFMA",
- "old:acronym_from_virtual:1022" => "EHDA",
- "old:acronym_from_virtual:1419" => "TAXRANK",
- "old:acronym_from_virtual:2024" => "RadLex_OWL",
- "old:acronym_from_virtual:2139" => "PROV",
- "old:acronym_from_virtual:3274" => "MSV",
- "old:acronym_from_virtual:1509" => "ICPS",
- "old:acronym_from_virtual:1626" => "EMO",
- "old:acronym_from_virtual:1036" => "PECO",
- "old:acronym_from_virtual:1614" => "IXNO",
- "old:acronym_from_virtual:3030" => "CANCO",
- "old:acronym_from_virtual:2118" => "FaBiO",
- "old:acronym_from_virtual:1487" => "ICD11-BODYSYSTEM",
- "old:acronym_from_virtual:1665" => "SHR",
- "old:acronym_from_virtual:1084" => "NIFSTD",
- "old:acronym_from_virtual:2057" => "SNOMED-Ethnic-Group",
- "old:acronym_from_virtual:1141" => "OPB",
- "old:acronym_from_virtual:3227" => "OVAE",
- "old:acronym_from_virtual:1029" => "IMR",
- "old:acronym_from_virtual:1353" => "SNOMEDCT",
- "old:acronym_from_virtual:2102" => "WHOFRE",
- "old:acronym_from_virtual:1132" => "NCBITAXON",
- "old:acronym_from_virtual:2028" => "iceci-activity",
- "old:acronym_from_virtual:1538" => "ROLEO",
- "old:acronym_from_virtual:2044" => "ICF-d4",
- "old:acronym_from_virtual:1088" => "MHC",
- "old:acronym_from_virtual:3167" => "GLOB",
- "old:acronym_from_virtual:2081" => "H2_HIPClassicRegions",
- "old:acronym_from_virtual:3147" => "CLIN-EVAL",
- "old:acronym_from_virtual:3006" => "OOEVV",
- "old:acronym_from_virtual:3180" => "MEDO",
- "old:acronym_from_virtual:1505" => "OMIT",
- "old:acronym_from_virtual:1553" => "ICD10CM",
- "old:acronym_from_virtual:2107" => "BIOA3v",
- "old:acronym_from_virtual:3046" => "MDCDRG",
- "old:acronym_from_virtual:1633" => "COGAT",
- "old:acronym_from_virtual:1659" => "VT",
- "old:acronym_from_virtual:1040" => "PPIO",
- "old:acronym_from_virtual:3129" => "CONSENT-ONT",
- "old:acronym_from_virtual:1008" => "DDANAT",
- "old:acronym_from_virtual:1020" => "HC",
- "old:acronym_from_virtual:1150" => "RS"
-}
\ No newline at end of file
diff --git a/lib/resolver/virtual_from_acronym.rb b/lib/resolver/virtual_from_acronym.rb
deleted file mode 100644
index 2928be208..000000000
--- a/lib/resolver/virtual_from_acronym.rb
+++ /dev/null
@@ -1,533 +0,0 @@
-BPIDResolver::VIRTUAL_FROM_ACRONYM = {
- "JERM" => 1488,
- "OGSF" => 3214,
- "NATPRO" => 3004,
- "citation" => 2114,
- "ATC" => 3021,
- "SNMD_BC" => 2088,
- "WHO-ART" => 1354,
- "ICD9CM-PROC" => 2124,
- "OGR" => 1087,
- "BAO" => 1533,
- "ATMO" => 1099,
- "goslim_candida" => 2010,
- "CHEBI" => 1007,
- "SNPO" => 1058,
- "provenance" => 2120,
- "WHOFRE" => 2102,
- "EMAP" => 1010,
- "CPT-mod" => 2126,
- "CTONT" => 1060,
- "BICSO" => 3269,
- "NMR" => 1033,
- "NPO" => 1083,
- "NEOMARK4" => 1686,
- "BRO" => 1104,
- "TMA" => 1494,
- "GLYCANONT" => 3231,
- "ICF-d5" => 2045,
- "GLOB" => 3167,
- "SNOMED-Ethnic-Group" => 2057,
- "SBRO" => 1249,
- "YPO" => 1115,
- "PO" => 1587,
- "CPT" => 1504,
- "EXO" => 1575,
- "geopolitical" => 2112,
- "NIC" => 1428,
- "CCONT" => 3108,
- "CLIN-EVAL" => 3147,
- "MMO" => 1584,
- "AMINO-ACID" => 1054,
- "OBOREL" => 1042,
- "IDOBRU" => 1537,
- "ICF-d860-d879" => 2052,
- "BP-METADATA" => 1148,
- "QUDT" => 3031,
- "HOM-UCSF_UCareDispostion" => 2062,
- "MSTDE-FRE" => 3220,
- "SNOMEDCT-ORG" => 2021,
- "NCBI_NMOsp_1_4_0" => 2072,
- "HP" => 1125,
- "BTO" => 1005,
- "UO" => 1112,
- "SWEET" => 3158,
- "OGMD" => 1085,
- "VSAO" => 1555,
- "ICF-d6" => 2046,
- "RPO" => 3114,
- "ECO" => 1012,
- "HCPCS" => 1529,
- "MIRO" => 1077,
- "BSAO" => 3271,
- "BiositemapIM" => 2003,
- "ooevv-vaccine" => 2109,
- "COGPO" => 1560,
- "CMS" => 3146,
- "CCO" => 1507,
- "NHDS" => 3136,
- "pseudo" => 1135,
- "TGMA" => 1030,
- "RID" => 1260,
- "TM-SIGNS-AND-SYMPTS" => 1572,
- "HAO" => 1362,
- "VIVO" => 1699,
- "EPSO" => 3230,
- "OntoBioUSP" => 3263,
- "suicideo" => 3270,
- "SDO" => 1651,
- "ABA-AMB" => 1290,
- "HPIO" => 1569,
- "AAO" => 1090,
- "MCCL" => 1541,
- "HOM-TEST" => 3038,
- "HIMC-CPT" => 3197,
- "ACGT-MO" => 1130,
- "REX" => 1043,
- "TM-MER" => 1573,
- "PHENOSCAPE-EXT" => 3194,
- "IEV" => 1011,
- "EHDA" => 1022,
- "FBbi" => 1023,
- "CHEMBIO" => 1615,
- "ICD10" => 1516,
- "ROLEO" => 1538,
- "GFO" => 1439,
- "MF" => 3002,
- "IMMDIS" => 3127,
- "dcelements" => 2115,
- "ADW" => 1530,
- "BOF" => 3234,
- "iceci-countermeasures" => 2029,
- "GALEN" => 1055,
- "PAE" => 1108,
- "OBI" => 1123,
- "HOM" => 1328,
- "HOMERUN" => 1627,
- "CABRO" => 3217,
- "ICD9CM" => 1101,
- "SNOMEDCT-MAS" => 2058,
- "ICF" => 1411,
- "WH" => 3264,
- "CHMO" => 3255,
- "H1_NMOABA_1_0" => 2069,
- "BSPO" => 1078,
- "MDRFRE" => 2104,
- "ICF-NoCodeLabel" => 2106,
- "GRO" => 1082,
- "NCIT" => 1032,
- "UCSFICD910CM" => 3199,
- "ADO" => 3251,
- "BDO" => 1613,
- "NeuroFMA" => 2004,
- "MCBCC" => 1438,
- "ICD09" => 3195,
- "ICF-d840-d859%2Fd860-d879" => 2053,
- "RCTONT" => 1676,
- "ERNO" => 3268,
- "ONTODM-KDD" => 3077,
- "IXNO" => 1614,
- "ICNP" => 1401,
- "KISAO" => 1410,
- "EDDA" => 3247,
- "GFO-BIO" => 1440,
- "FaBiO" => 2118,
- "UCare_Demographics" => 2063,
- "OGMS" => 1414,
- "Radlex3.9.1" => 2138,
- "MEO" => 3009,
- "SPTO" => 3029,
- "CHEMINF" => 1444,
- "CANONT" => 3178,
- "HC" => 1020,
- "PPIO" => 1040,
- "H1_NMOABA" => 2078,
- "EHDAA" => 1021,
- "VSO" => 3124,
- "NIGO" => 1539,
- "SPO" => 1122,
- "VTO" => 3236,
- "MP" => 1025,
- "GCC" => 3017,
- "BILA" => 1114,
- "iceci-descriptor_for_intent" => 2030,
- "obi-device" => 2065,
- "CL" => 1006,
- "RH-MESH" => 3019,
- "ICD10CM" => 1553,
- "BRIDG" => 3150,
- "UCSFI9I10CMPCS" => 3224,
- "MIXS" => 3215,
- "SNOMEDCT-CF" => 2018,
- "FMA-SUBSET" => 2006,
- "PTO" => 1037,
- "CMO" => 1583,
- "FB-SP" => 1064,
- "EP" => 1142,
- "SIO" => 1532,
- "InterNano" => 3259,
- "ICF-d1" => 2041,
- "REPO" => 1552,
- "PHARE" => 1550,
- "UNITSONT" => 1650,
- "REXO" => 3152,
- "DOID" => 1009,
- "ICDO3" => 1670,
- "DIAGONT" => 3013,
- "I2B2-PATVISDIM" => 3062,
- "NCBI_NMOsp_1_2_1" => 2055,
- "MDDB" => 1426,
- "PROV" => 2139,
- "ICF-d810-d839" => 2050,
- "FLU" => 1417,
- "DC-CL" => 1144,
- "LIPRO" => 1183,
- "UCSFICU" => 3007,
- "SNOMEDCT-CORE" => 2040,
- "NCIt-Activity" => 2026,
- "CARO" => 1063,
- "CPT-KM" => 1694,
- "MFO" => 1027,
- "GRO-CPGA" => 1001,
- "RETO" => 3162,
- "PATHLEX" => 3190,
- "GEOSPECIES" => 1247,
- "OAE" => 1489,
- "EMO" => 1626,
- "MPO" => 3191,
- "OMIM" => 1348,
- "CTX" => 3025,
- "FAO" => 1019,
- "goslim_plant" => 2009,
- "NIFSTD" => 1084,
- "iceci-substance_use" => 2037,
- "BIOA3v" => 2107,
- "QIBO" => 1671,
- "iceci-details_for_activity" => 2038,
- "BCTEO" => 3262,
- "CANCO" => 3030,
- "PDQ" => 1349,
- "NDDF" => 1424,
- "VO" => 1172,
- "H1_NMOABA_4_1" => 2083,
- "iceci-intent" => 2034,
- "IAO" => 1393,
- "RS" => 1150,
- "ONL-DP" => 3249,
- "SciRes" => 2122,
- "CARD" => 3272,
- "goslim_generic_1_770" => 2007,
- "EVOC" => 1013,
- "MSHSPA_1" => 1420,
- "SNOMEDCT-TF" => 2019,
- "MAT" => 1152,
- "GRO-CPD" => 1047,
- "GLYCO" => 3169,
- "UCSFORTHO" => 1697,
- "PCO" => 3120,
- "CRISP" => 1526,
- "IDODEN" => 3174,
- "iceci-details_for_place_of_occurrence" => 2032,
- "ICD0" => 3205,
- "PVONTO" => 1567,
- "GEXO" => 3151,
- "DIKB" => 1672,
- "FB-CV" => 1017,
- "SBO" => 1046,
- "PEO" => 1335,
- "Amino_Acid-zh_CN" => 1168,
- "RNAO" => 1500,
- "PHYLONT" => 1616,
- "GO-EXT" => 1506,
- "ICF-d9" => 2049,
- "ONL-MSA" => 3246,
- "NIFSUBCELL" => 3126,
- "PR" => 1062,
- "CAO" => 1582,
- "VBCV" => 3237,
- "ICD9CM-KM" => 3045,
- "FIX" => 1014,
- "ICECI" => 1484,
- "NEUMORE" => 1521,
- "WSIO" => 1632,
- "goslim_goa" => 2008,
- "ICF-d3" => 2043,
- "MDCDRG" => 3046,
- "DWC-TEST" => 3094,
- "BT" => 1134,
- "H3_HIPSeptotemporalAxis" => 2082,
- "MSV" => 3274,
- "DILIo" => 2136,
- "ICF-d840-d859" => 2051,
- "MCCV" => 3192,
- "HL7" => 1343,
- "XCO" => 1585,
- "ICF-d7" => 2047,
- "ZIP5" => 3200,
- "SSO" => 1394,
- "RXNORM" => 2066,
- "DERMO" => 3221,
- "obi-fged" => 2070,
- "RadLex_OWL" => 2024,
- "H1_NMOABA_2_0" => 2074,
- "MEDDRA" => 1422,
- "BRO-Resource" => 2022,
- "TMO" => 1461,
- "LHN" => 1024,
- "PROPREO" => 1039,
- "CO-WHEAT" => 1545,
- "CARELEX" => 3008,
- "NDFRT" => 1352,
- "iceci-instrument_object_substance" => 2033,
- "PRO-ONT" => 1052,
- "TADS" => 1065,
- "HLTHINDCTRS" => 1581,
- "WB-PHENOTYPE" => 1067,
- "OGDI" => 1086,
- "TEO" => 3042,
- "PHYFIELD" => 1369,
- "NEMO" => 1321,
- "CBO" => 1158,
- "CPO" => 3020,
- "SNOMEDCT" => 1353,
- "DWC" => 3058,
- "foaf" => 2119,
- "LDA" => 1398,
- "HUGO" => 1528,
- "AI-RHEUM" => 1430,
- "MHC" => 1088,
- "XAO" => 1095,
- "UDEF" => 3241,
- "ICF-d8" => 2048,
- "H1_NMOABA_4_0" => 2080,
- "test1" => 2101,
- "TM-CONST" => 1570,
- "FB-DV" => 1016,
- "PORO" => 3204,
- "TTO" => 1081,
- "ECGF" => 2073,
- "EHDAA2" => 1517,
- "BCGO" => 1304,
- "DERMLEX" => 1149,
- "CO" => 1544,
- "ICPCFRE" => 2103,
- "TOP-MENELAS" => 3189,
- "SMD_NPLSM_BRST" => 2086,
- "OntoOrpha" => 1586,
- "GAZ" => 1397,
- "ELIXHAUSER" => 1578,
- "CPTAC" => 1192,
- "ONTOKBCF" => 3155,
- "TAO" => 1110,
- "UCSFXPLANT" => 1661,
- "OBI_BCGO" => 3266,
- "MEGO" => 1257,
- "VARIO" => 3159,
- "VT" => 1659,
- "SYMP" => 1224,
- "BRO-Activity" => 2001,
- "SOY" => 3028,
- "FHHO" => 1126,
- "OPL" => 1190,
- "iceci-mechanism" => 2035,
- "IFAR" => 3183,
- "NHSQI" => 3242,
- "LOINC" => 2064,
- "IDO" => 1092,
- "OBIWS" => 3119,
- "EFO" => 1136,
- "ONTODT" => 1588,
- "ONTOMA" => 3090,
- "ICD10PCS" => 1425,
- "SEDI" => 3244,
- "RSA" => 3222,
- "GENETRIAL" => 3157,
- "SCTSPA" => 1416,
- "iceci-details_for_mechanism" => 2031,
- "SAO" => 1068,
- "NIFDYS" => 1381,
- "ENVO" => 1069,
- "INO" => 1515,
- "MA" => 1000,
- "MFOEM" => 1666,
- "BRO-Chinese" => 2017,
- "NCBITAXON" => 1132,
- "HCPCS-mod" => 2125,
- "dcterms" => 2116,
- "I2B2-LOINC" => 3186,
- "EPICMEDS" => 3032,
- "BRO-Core" => 2000,
- "CDAO" => 1128,
- "ICF-d4" => 2044,
- "TEST-PROD" => 3211,
- "BAO-GPCR" => 3216,
- "ooevv-tractTrace" => 2108,
- "PATO" => 1107,
- "OBOE-SBC" => 1523,
- "BP" => 1522,
- "OCRE" => 1076,
- "skos" => 2121,
- "MIXSCV" => 3000,
- "SPD" => 1091,
- "BHO" => 1116,
- "STNFRDRXDEMO" => 3261,
- "FB-BT" => 1015,
- "NCBI_NMOsp_1_2_2" => 2056,
- "WB-LS" => 1049,
- "SNOMEDCT-ANAT" => 2020,
- "TRAK" => 3210,
- "IDOMAL" => 1311,
- "SMD_NPLSM" => 2085,
- "goslim_pombe" => 2013,
- "SSE" => 3252,
- "CONSENT-ONT" => 3129,
- "BCO" => 3201,
- "RCD" => 1427,
- "AEO" => 1568,
- "TAXRANK" => 1419,
- "PHENX" => 3078,
- "goslim_pir" => 2012,
- "MO" => 1131,
- "PSDS" => 1038,
- "ONTODM-CORE" => 1638,
- "CHD" => 3233,
- "PHARMGKB" => 1655,
- "NIF-RTH" => 2025,
- "OPB" => 1141,
- "MSHFRE" => 1456,
- "ZEA" => 1050,
- "MEDLINEPLUS" => 1347,
- "SO" => 1109,
- "OBI_IEDB_view" => 2093,
- "PSIMOD" => 1041,
- "GPI" => 3185,
- "IMGT-ONTOLOGY" => 1491,
- "ONL-MR-DA" => 3250,
- "SHR" => 1665,
- "NHSQI2009" => 3243,
- "FDA-MEDDEVICE" => 1576,
- "OVAE" => 3227,
- "NDF-RT" => 2091,
- "CPRO" => 1059,
- "CSSO" => 3239,
- "event" => 2117,
- "CLO" => 1314,
- "ECG" => 1146,
- "PMR" => 3015,
- "IDQA" => 3208,
- "OntoVIP" => 3253,
- "ZFA" => 1051,
- "HCPCS-HIMC" => 3206,
- "OSHPD" => 1649,
- "ICF-d2" => 2042,
- "BIOMODELS" => 3022,
- "PHENOMEBLAST" => 1656,
- "OMIT" => 1505,
- "SITBAC" => 1237,
- "NIAID-GSC-BRC" => 2127,
- "SNMI" => 3232,
- "SOPHARM" => 1061,
- "BNO" => 3265,
- "DTVPrecision" => 2110,
- "VANDF" => 1527,
- "OOEVV" => 3006,
- "HSDB_OCRe" => 2100,
- "LSM" => 1520,
- "BRO-AreaOfResearch" => 2002,
- "WB-BT" => 1048,
- "H2_HIPClassicRegions" => 2081,
- "ERO" => 3016,
- "EDAM" => 1498,
- "HRDO" => 3273,
- "OPE" => 3209,
- "IMR" => 1029,
- "SYN" => 1696,
- "NONRCTO" => 3012,
- "GCO" => 3223,
- "RCJI" => 2067,
- "GO" => 1070,
- "OMRSE" => 1565,
- "ONSTR" => 3137,
- "SNMD_BDY" => 2105,
- "BIRNLEX" => 1089,
- "APO" => 1222,
- "DDANAT" => 1008,
- "ONTOPNEUMO" => 3181,
- "NIFCELL" => 1402,
- "SOFA" => 2015,
- "ATO" => 1370,
- "CLINIC" => 3092,
- "PROVO" => 3131,
- "NTDO" => 3153,
- "RADLEX" => 1057,
- "FYPO" => 1689,
- "MAO" => 1026,
- "MS" => 1105,
- "VHOG" => 1574,
- "PDO" => 3238,
- "DDI" => 1540,
- "PECO" => 1036,
- "MESH" => 1351,
- "COGAT" => 1633,
- "CPTH" => 1510,
- "MIRNAO" => 3139,
- "goslim_yeast" => 2014,
- "iceci-place_of_occurrence" => 2036,
- "DCO" => 3267,
- "FMA" => 1053,
- "MPATH" => 1031,
- "PTRANS" => 1094,
- "ECGT" => 2079,
- "bibliographic" => 2113,
- "ATOL" => 3207,
- "ELIG" => 3228,
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- "SEP" => 1044,
- "PW" => 1035,
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- "envo_153" => 2092,
- "TOK" => 1418,
- "COSTART" => 1341,
- "ICPS" => 1509,
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- "EPILONT" => 1639,
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- "XEO" => 3176,
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- "SuicidO" => 3245,
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- "documentStatus" => 2111,
- "ICPC" => 1344,
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- "DEMOGRAPH" => 3047,
- "TM-OTHER-FACTORS" => 1571,
- "RNPRIO" => 3240,
- "MSTDE" => 3219,
- "NBO" => 1621
-}
\ No newline at end of file
diff --git a/lib/resolver/virtual_from_version.rb b/lib/resolver/virtual_from_version.rb
deleted file mode 100644
index 06ce01e9a..000000000
--- a/lib/resolver/virtual_from_version.rb
+++ /dev/null
@@ -1,7144 +0,0 @@
-BPIDResolver::VIRTUAL_FROM_VERSION = {
- "old:virtual_from_version:40876" => 1048,
- "old:virtual_from_version:44059" => 1125,
- "old:virtual_from_version:46266" => 1172,
- "old:virtual_from_version:44870" => 1077,
- "old:virtual_from_version:40446" => 1009,
- "old:virtual_from_version:42230" => 1083,
- "old:virtual_from_version:44261" => 1070,
- "old:virtual_from_version:44863" => 1009,
- "old:virtual_from_version:44231" => 1107,
- "old:virtual_from_version:47370" => 1077,
- "old:virtual_from_version:49429" => 1580,
- "old:virtual_from_version:42156" => 1037,
- "old:virtual_from_version:44222" => 1009,
- "old:virtual_from_version:42381" => 1070,
- "old:virtual_from_version:50050" => 3131,
- "old:virtual_from_version:47704" => 1689,
- "old:virtual_from_version:40625" => 1070,
- "old:virtual_from_version:40934" => 1070,
- "old:virtual_from_version:43002" => 2018,
- "old:virtual_from_version:40941" => 1070,
- "old:virtual_from_version:39314" => 1125,
- "old:virtual_from_version:46950" => 1070,
- "old:virtual_from_version:46093" => 1649,
- "old:virtual_from_version:49425" => 1025,
- "old:virtual_from_version:42731" => 1077,
- "old:virtual_from_version:47095" => 1077,
- "old:virtual_from_version:49684" => 1125,
- "old:virtual_from_version:49229" => 1689,
- "old:virtual_from_version:47012" => 3016,
- "old:virtual_from_version:45228" => 1414,
- "old:virtual_from_version:45287" => 1517,
- "old:virtual_from_version:45569" => 1136,
- "old:virtual_from_version:42525" => 1017,
- "old:virtual_from_version:38363" => 1081,
- "old:virtual_from_version:40404" => 1354,
- "old:virtual_from_version:47677" => 1689,
- "old:virtual_from_version:47916" => 1081,
- "old:virtual_from_version:42239" => 1077,
- "old:virtual_from_version:46908" => 1070,
- "old:virtual_from_version:50341" => 3131,
- "old:virtual_from_version:44232" => 1070,
- "old:virtual_from_version:44622" => 1009,
- "old:virtual_from_version:40556" => 1067,
- "old:virtual_from_version:46102" => 1070,
- "old:virtual_from_version:49057" => 1077,
- "old:virtual_from_version:45091" => 1025,
- "old:virtual_from_version:44599" => 1141,
- "old:virtual_from_version:39208" => 1148,
- "old:virtual_from_version:44055" => 1077,
- "old:virtual_from_version:39055" => 1110,
- "old:virtual_from_version:44779" => 1545,
- "old:virtual_from_version:43073" => 2072,
- "old:virtual_from_version:45955" => 1105,
- "old:virtual_from_version:46215" => 1070,
- "old:virtual_from_version:46917" => 1109,
- "old:virtual_from_version:50608" => 1136,
- "old:virtual_from_version:29952" => 1078,
- "old:virtual_from_version:42084" => 1070,
- "old:virtual_from_version:45919" => 1035,
- "old:virtual_from_version:40589" => 1077,
- "old:virtual_from_version:44604" => 1009,
- "old:virtual_from_version:50267" => 3131,
- "old:virtual_from_version:50174" => 1172,
- "old:virtual_from_version:40681" => 1081,
- "old:virtual_from_version:44915" => 1077,
- "old:virtual_from_version:42810" => 1500,
- "old:virtual_from_version:46938" => 3009,
- "old:virtual_from_version:42177" => 1172,
- "old:virtual_from_version:40398" => 1348,
- "old:virtual_from_version:49002" => 1070,
- "old:virtual_from_version:45570" => 1070,
- "old:virtual_from_version:42980" => 1009,
- "old:virtual_from_version:42557" => 1037,
- "old:virtual_from_version:42070" => 1107,
- "old:virtual_from_version:40634" => 1070,
- "old:virtual_from_version:40441" => 1083,
- "old:virtual_from_version:39905" => 1081,
- "old:virtual_from_version:45020" => 1070,
- "old:virtual_from_version:47294" => 1077,
- "old:virtual_from_version:44738" => 1070,
- "old:virtual_from_version:49659" => 3155,
- "old:virtual_from_version:44158" => 1107,
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- "old:virtual_from_version:47658" => 1070,
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- "old:virtual_from_version:50316" => 1311,
- "old:virtual_from_version:45554" => 1172,
- "old:virtual_from_version:46320" => 1115,
- "old:virtual_from_version:46790" => 1077,
- "old:virtual_from_version:45799" => 1067,
- "old:virtual_from_version:49263" => 1532,
- "old:virtual_from_version:45033" => 1016,
- "old:virtual_from_version:45005" => 1006,
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- "old:virtual_from_version:44878" => 1125,
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- "old:virtual_from_version:44050" => 1125,
- "old:virtual_from_version:50616" => 1025,
- "old:virtual_from_version:50308" => 1224,
- "old:virtual_from_version:45330" => 1588,
- "old:virtual_from_version:45783" => 1007,
- "old:virtual_from_version:42948" => 1148,
- "old:virtual_from_version:42159" => 1077,
- "old:virtual_from_version:39932" => 1110,
- "old:virtual_from_version:42828" => 1078,
- "old:virtual_from_version:39175" => 1146,
- "old:virtual_from_version:47474" => 1070,
- "old:virtual_from_version:44796" => 1077,
- "old:virtual_from_version:45353" => 1107,
- "old:virtual_from_version:42081" => 1009,
- "old:virtual_from_version:45491" => 1009,
- "old:virtual_from_version:44302" => 1013,
- "old:virtual_from_version:40848" => 1407,
- "old:virtual_from_version:45954" => 1070,
- "old:virtual_from_version:50612" => 1689,
- "old:virtual_from_version:38407" => 1104,
- "old:virtual_from_version:48010" => 2110,
- "old:virtual_from_version:39483" => 1007,
- "old:virtual_from_version:41000" => 2012,
- "old:virtual_from_version:46948" => 1659,
- "old:virtual_from_version:44362" => 1063,
- "old:virtual_from_version:45446" => 1125,
- "old:virtual_from_version:42256" => 1009,
- "old:virtual_from_version:47113" => 3020,
- "old:virtual_from_version:42442" => 1009,
- "old:virtual_from_version:46735" => 1689,
- "old:virtual_from_version:43021" => 2046,
- "old:virtual_from_version:49586" => 1067,
- "old:virtual_from_version:44579" => 1070,
- "old:virtual_from_version:40892" => 1108,
- "old:virtual_from_version:44692" => 1109,
- "old:virtual_from_version:50607" => 1070,
- "old:virtual_from_version:50177" => 1070,
- "old:virtual_from_version:38801" => 1131,
- "old:virtual_from_version:39897" => 1183,
- "old:virtual_from_version:45015" => 1125,
- "old:virtual_from_version:47406" => 1125,
- "old:virtual_from_version:46305" => 1070,
- "old:virtual_from_version:45506" => 1584,
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- "old:virtual_from_version:47427" => 1136,
- "old:virtual_from_version:43086" => 2083,
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- "old:virtual_from_version:50200" => 1311,
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- "old:virtual_from_version:50668" => 3208,
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- "old:virtual_from_version:49324" => 1070,
- "old:virtual_from_version:47473" => 1616,
- "old:virtual_from_version:49225" => 1125,
- "old:virtual_from_version:50763" => 1417,
- "old:virtual_from_version:45121" => 1077,
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- "old:virtual_from_version:46356" => 1670,
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- "old:virtual_from_version:46452" => 1105,
- "old:virtual_from_version:49589" => 1077,
- "old:virtual_from_version:45476" => 1105,
- "old:virtual_from_version:49352" => 1136,
- "old:virtual_from_version:40828" => 1006,
- "old:virtual_from_version:40651" => 1397,
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- "old:virtual_from_version:49979" => 1062,
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-}
\ No newline at end of file
diff --git a/lib/tasks/generate_component_previews.rake b/lib/tasks/generate_component_previews.rake
new file mode 100644
index 000000000..2bc61c28b
--- /dev/null
+++ b/lib/tasks/generate_component_previews.rake
@@ -0,0 +1,34 @@
+# lib/tasks/generate_component_previews.rake
+
+namespace :component_previews do
+ desc "Generate previews for all components"
+ task generate: :environment do
+ components_path = Rails.root.join("app/components")
+ components = Dir.glob("#{components_path}/**/*_component.rb")
+
+ components.each do |component_path|
+ component_name = File.basename(component_path, "_component.rb")
+ preview_path = Rails.root.join("test/components/previews/#{component_name}_preview.rb")
+
+ # Skip if the preview already exists
+ next if File.exist?(preview_path)
+
+ File.open(preview_path, "w") do |file|
+ file.puts("class #{component_name.camelize}Preview < ViewComponent::Preview")
+ file.puts(" def default")
+ file.puts(" # Initialize the component with any necessary data")
+ file.puts(" component = #{component_name.camelize}Component.new")
+
+ file.puts(" # Add any necessary data or context to the component")
+ file.puts(" # component.some_data = some_value")
+
+ file.puts(" # Render the component")
+ file.puts(" render(component)")
+ file.puts(" end")
+ file.puts("end")
+ end
+
+ puts "Generated preview for #{component_name}"
+ end
+ end
+end
diff --git a/package.json b/package.json
index 7689074db..4e7c6a6a3 100644
--- a/package.json
+++ b/package.json
@@ -1,12 +1,16 @@
{
"name": "app",
- "private": true,
+ "private": "true",
"dependencies": {
- "@hotwired/stimulus": "^3.2.2",
- "@hotwired/turbo-rails": "^8.0.3",
- "esbuild": "^0.20.0"
+ "@hotwired/stimulus": "^3.0.1",
+ "@hotwired/turbo-rails": "^7.1.1",
+ "chart.js": "^4.4.1",
+ "datatables.net-dt": "^1.13.8",
+ "debounce": "^1.2.1",
+ "esbuild": "^0.14.41",
+ "split.js": "^1.6.5"
},
"scripts": {
- "build": "esbuild app/javascript/*.* --bundle --sourcemap --format=esm --outdir=app/assets/builds --public-path=/assets"
+ "build": "esbuild app/javascript/*.* --bundle --sourcemap --outdir=app/assets/builds"
}
}
diff --git a/yarn.lock b/yarn.lock
index 7da15e91d..7b5b8c2f3 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -2,169 +2,199 @@
# yarn lockfile v1
-"@esbuild/aix-ppc64@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/aix-ppc64/-/aix-ppc64-0.20.2.tgz#a70f4ac11c6a1dfc18b8bbb13284155d933b9537"
- integrity sha512-D+EBOJHXdNZcLJRBkhENNG8Wji2kgc9AZ9KiPr1JuZjsNtyHzrsfLRrY0tk2H2aoFu6RANO1y1iPPUCDYWkb5g==
-
-"@esbuild/android-arm64@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/android-arm64/-/android-arm64-0.20.2.tgz#db1c9202a5bc92ea04c7b6840f1bbe09ebf9e6b9"
- integrity sha512-mRzjLacRtl/tWU0SvD8lUEwb61yP9cqQo6noDZP/O8VkwafSYwZ4yWy24kan8jE/IMERpYncRt2dw438LP3Xmg==
-
-"@esbuild/android-arm@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/android-arm/-/android-arm-0.20.2.tgz#3b488c49aee9d491c2c8f98a909b785870d6e995"
- integrity sha512-t98Ra6pw2VaDhqNWO2Oph2LXbz/EJcnLmKLGBJwEwXX/JAN83Fym1rU8l0JUWK6HkIbWONCSSatf4sf2NBRx/w==
-
-"@esbuild/android-x64@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/android-x64/-/android-x64-0.20.2.tgz#3b1628029e5576249d2b2d766696e50768449f98"
- integrity sha512-btzExgV+/lMGDDa194CcUQm53ncxzeBrWJcncOBxuC6ndBkKxnHdFJn86mCIgTELsooUmwUm9FkhSp5HYu00Rg==
-
-"@esbuild/darwin-arm64@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/darwin-arm64/-/darwin-arm64-0.20.2.tgz#6e8517a045ddd86ae30c6608c8475ebc0c4000bb"
- integrity sha512-4J6IRT+10J3aJH3l1yzEg9y3wkTDgDk7TSDFX+wKFiWjqWp/iCfLIYzGyasx9l0SAFPT1HwSCR+0w/h1ES/MjA==
-
-"@esbuild/darwin-x64@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/darwin-x64/-/darwin-x64-0.20.2.tgz#90ed098e1f9dd8a9381695b207e1cff45540a0d0"
- integrity sha512-tBcXp9KNphnNH0dfhv8KYkZhjc+H3XBkF5DKtswJblV7KlT9EI2+jeA8DgBjp908WEuYll6pF+UStUCfEpdysA==
-
-"@esbuild/freebsd-arm64@0.20.2":
- version "0.20.2"
- resolved "https://registry.yarnpkg.com/@esbuild/freebsd-arm64/-/freebsd-arm64-0.20.2.tgz#d71502d1ee89a1130327e890364666c760a2a911"
- integrity sha512-d3qI41G4SuLiCGCFGUrKsSeTXyWG6yem1KcGZVS+3FYlYhtNoNgYrWcvkOoaqMhwXSMrZRl69ArHsGJ9mYdbbw==
-
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+ integrity sha512-T+rdZW19ql9MjS7pixmZYVObd9G7kcaZo+sETqNH4RCkuuYSuv9AGHUVnPoP9hhuE1WM1ZimHz1CIBHBboLU7w==
+
+esbuild-windows-64@0.14.54:
+ version "0.14.54"
+ resolved "https://registry.yarnpkg.com/esbuild-windows-64/-/esbuild-windows-64-0.14.54.tgz#bf54b51bd3e9b0f1886ffdb224a4176031ea0af4"
+ integrity sha512-AoHTRBUuYwXtZhjXZbA1pGfTo8cJo3vZIcWGLiUcTNgHpJJMC1rVA44ZereBHMJtotyN71S8Qw0npiCIkW96cQ==
+
+esbuild-windows-arm64@0.14.54:
+ version "0.14.54"
+ resolved "https://registry.yarnpkg.com/esbuild-windows-arm64/-/esbuild-windows-arm64-0.14.54.tgz#937d15675a15e4b0e4fafdbaa3a01a776a2be982"
+ integrity sha512-M0kuUvXhot1zOISQGXwWn6YtS+Y/1RT9WrVIOywZnJHo3jCDyewAc79aKNQWFCQm+xNHVTq9h8dZKvygoXQQRg==
+
+esbuild@^0.14.41:
+ version "0.14.54"
+ resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.14.54.tgz#8b44dcf2b0f1a66fc22459943dccf477535e9aa2"
+ integrity sha512-Cy9llcy8DvET5uznocPyqL3BFRrFXSVqbgpMJ9Wz8oVjZlh/zUSNbPRbov0VX7VxN2JH1Oa0uNxZ7eLRb62pJA==
optionalDependencies:
- "@esbuild/aix-ppc64" "0.20.2"
- "@esbuild/android-arm" "0.20.2"
- "@esbuild/android-arm64" "0.20.2"
- "@esbuild/android-x64" "0.20.2"
- "@esbuild/darwin-arm64" "0.20.2"
- "@esbuild/darwin-x64" "0.20.2"
- "@esbuild/freebsd-arm64" "0.20.2"
- "@esbuild/freebsd-x64" "0.20.2"
- "@esbuild/linux-arm" "0.20.2"
- "@esbuild/linux-arm64" "0.20.2"
- "@esbuild/linux-ia32" "0.20.2"
- "@esbuild/linux-loong64" "0.20.2"
- "@esbuild/linux-mips64el" "0.20.2"
- "@esbuild/linux-ppc64" "0.20.2"
- "@esbuild/linux-riscv64" "0.20.2"
- "@esbuild/linux-s390x" "0.20.2"
- "@esbuild/linux-x64" "0.20.2"
- "@esbuild/netbsd-x64" "0.20.2"
- "@esbuild/openbsd-x64" "0.20.2"
- "@esbuild/sunos-x64" "0.20.2"
- "@esbuild/win32-arm64" "0.20.2"
- "@esbuild/win32-ia32" "0.20.2"
- "@esbuild/win32-x64" "0.20.2"
+ "@esbuild/linux-loong64" "0.14.54"
+ esbuild-android-64 "0.14.54"
+ esbuild-android-arm64 "0.14.54"
+ esbuild-darwin-64 "0.14.54"
+ esbuild-darwin-arm64 "0.14.54"
+ esbuild-freebsd-64 "0.14.54"
+ esbuild-freebsd-arm64 "0.14.54"
+ esbuild-linux-32 "0.14.54"
+ esbuild-linux-64 "0.14.54"
+ esbuild-linux-arm "0.14.54"
+ esbuild-linux-arm64 "0.14.54"
+ esbuild-linux-mips64le "0.14.54"
+ esbuild-linux-ppc64le "0.14.54"
+ esbuild-linux-riscv64 "0.14.54"
+ esbuild-linux-s390x "0.14.54"
+ esbuild-netbsd-64 "0.14.54"
+ esbuild-openbsd-64 "0.14.54"
+ esbuild-sunos-64 "0.14.54"
+ esbuild-windows-32 "0.14.54"
+ esbuild-windows-64 "0.14.54"
+ esbuild-windows-arm64 "0.14.54"
+
+jquery@>=1.7:
+ version "3.7.1"
+ resolved "https://registry.yarnpkg.com/jquery/-/jquery-3.7.1.tgz#083ef98927c9a6a74d05a6af02806566d16274de"
+ integrity sha512-m4avr8yL8kmFN8psrbFFFmB/If14iN5o9nw/NgnnM+kybDJpRsAynV2BsfpTYrTRysYUdADVD7CkUUizgkpLfg==
+
+split.js@^1.6.5:
+ version "1.6.5"
+ resolved "https://registry.yarnpkg.com/split.js/-/split.js-1.6.5.tgz#f7f61da1044c9984cb42947df4de4fadb5a3f300"
+ integrity sha512-mPTnGCiS/RiuTNsVhCm9De9cCAUsrNFFviRbADdKiiV+Kk8HKp/0fWu7Kr8pi3/yBmsqLFHuXGT9UUZ+CNLwFw==