From 4e891a8c23a6d3473f294c83c6d054cbb405872c Mon Sep 17 00:00:00 2001 From: Guillaume Alviset Date: Fri, 20 Sep 2024 02:36:05 +0200 Subject: [PATCH] Solved translated keys conflict --- Gemfile | 169 +- Gemfile.lock | 313 +- app/assets/images/icons/slices.svg | 4 + app/assets/javascripts/application.js | 1 - app/assets/javascripts/bp_mappings.js.erb | 145 - app/assets/javascripts/vendor.js | 1 - app/assets/stylesheets/account.scss | 9 + app/assets/stylesheets/agents.scss | 24 + .../stylesheets/application.css.scss.erb | 2 +- app/assets/stylesheets/bioportal.scss | 242 +- .../components/concept_details.scss | 4 + app/assets/stylesheets/components/index.scss | 3 +- .../stylesheets/components/pill_button.scss | 3 + .../stylesheets/components/search_input.scss | 6 + .../stylesheets/components/tree_view.scss | 170 + app/assets/stylesheets/concepts.scss | 8 +- app/assets/stylesheets/fair_assement.scss | 1 + app/assets/stylesheets/home.scss | 74 +- app/assets/stylesheets/login.scss | 2 +- app/assets/stylesheets/mappings.scss | 16 - app/assets/stylesheets/notice.scss | 23 + app/assets/stylesheets/ontologies.scss | 8 +- app/assets/stylesheets/taxonomy.scss | 101 + .../stylesheets/theme-variables.scss.erb | 2 +- .../agent_search_input_component.html.haml | 6 +- app/components/concept_details_component.rb | 2 +- .../concept_details_component.html.haml | 2 +- .../rdf_highlighter_component_controller.js | 5 +- .../display/search_result_component.rb | 2 + .../search_result_component.html.haml | 5 +- .../display/taxonomy_card_component.rb | 10 + .../taxonomy_card_component.html.haml | 29 + app/components/input/text_area_component.rb | 6 +- .../text_area_component.html.haml | 2 +- .../ontology_browse_card_component.html.haml | 4 +- .../ontology_subscribe_button_component.rb | 6 + ...ology_subscribe_button_component.html.haml | 2 +- ...y_subscribe_button_component_controller.js | 8 +- app/components/search_input_component.rb | 7 +- .../search_input_component.html.haml | 5 +- .../search_input_component_controller.js | 23 +- .../submission_status_component.html.haml | 2 +- app/components/tab_item_component.rb | 7 +- app/components/table_component.rb | 6 +- .../table_component/table_component.html.haml | 5 +- .../table_component_controller.js | 9 +- app/components/tree_link_component.rb | 4 +- .../tree_link_component.html.haml | 4 +- app/components/url_resolvability_component.rb | 2 +- .../admin/categories_controller.rb | 3 +- app/controllers/admin/groups_controller.rb | 2 +- app/controllers/agents_controller.rb | 94 +- app/controllers/ajax_proxy_controller.rb | 86 - app/controllers/annotator_controller.rb | 24 +- app/controllers/application_controller.rb | 297 +- app/controllers/collections_controller.rb | 7 +- app/controllers/concepts_controller.rb | 55 +- app/controllers/concerns/ontology_updater.rb | 8 +- app/controllers/concerns/search_aggregator.rb | 36 +- app/controllers/concerns/submission_filter.rb | 4 +- app/controllers/concerns/terms_reuses.rb | 15 + app/controllers/concerns/uri_redirection.rb | 34 +- app/controllers/home_controller.rb | 39 +- app/controllers/instances_controller.rb | 8 +- app/controllers/mappings_controller.rb | 1 + app/controllers/notes_controller.rb | 5 - app/controllers/ontologies_controller.rb | 66 +- .../ontologies_redirection_controller.rb | 84 +- app/controllers/properties_controller.rb | 14 +- app/controllers/schemes_controller.rb | 6 +- app/controllers/search_controller.rb | 8 +- app/controllers/taxonomy_controller.rb | 46 + app/controllers/users_controller.rb | 30 +- app/helpers/agent_helper.rb | 40 +- app/helpers/application_helper.rb | 156 +- app/helpers/check_resolvability_helper.rb | 68 +- app/helpers/collections_helper.rb | 12 +- app/helpers/components_helper.rb | 38 +- app/helpers/concepts_helper.rb | 30 +- app/helpers/fair_score_helper.rb | 14 +- app/helpers/home_helper.rb | 13 +- app/helpers/inputs_helper.rb | 4 +- app/helpers/mappings_helper.rb | 2 +- app/helpers/multi_languages_helper.rb | 7 +- app/helpers/ontologies_helper.rb | 34 +- app/helpers/properties_helper.rb | 11 +- app/helpers/schemes_helper.rb | 6 +- app/helpers/search_helper.rb | 8 +- app/helpers/submission_inputs_helper.rb | 14 +- app/helpers/submissions_helper.rb | 17 +- app/javascript/component_controllers/index.js | 3 +- .../controllers/chosen_controller.js | 68 - .../concepts_json_button_controller.js | 19 + .../controllers/content_finder_controller.js | 105 - .../controllers/history_controller.js | 1 - app/javascript/controllers/index.js | 9 +- .../controllers/label_ajax_controller.js | 40 +- .../mappings_visualization_controller.js | 2 +- .../controllers/simple_tree_controller.js | 21 +- .../skos_collection_colors_controller.js | 22 +- .../controllers/skos_collections_selector.js | 49 + .../controllers/turbo_frame_controller.js | 37 +- app/javascript/mixins/useChosen.js | 8 - app/javascript/mixins/useHistory.js | 6 +- app/models/bpid_resolver.rb | 46 - app/views/admin/categories/_form.html.haml | 5 + app/views/admin/index.html.haml | 6 +- app/views/agents/_agent.html.haml | 2 + app/views/agents/_form.html.haml | 44 +- app/views/agents/index.html.haml | 1 + app/views/annotator/index.html.haml | 1 + app/views/check_resolvability/index.html.haml | 17 +- app/views/collections/_list_view.html.haml | 2 +- app/views/concepts/_list.html.haml | 2 +- app/views/concepts/_show.html.haml | 113 +- app/views/home/cookies.html.haml | 13 + app/views/home/feedback/feedback.html.haml | 3 + app/views/home/index.html.haml | 59 +- app/views/instances/_details.html.haml | 2 +- app/views/layouts/_header.html.erb | 69 +- app/views/layouts/_notices.html.haml | 29 +- app/views/layouts/_topnav.html.haml | 2 + app/views/layouts/appliance.html.haml | 3 +- .../layouts/ontology_viewer/_header.html.haml | 6 +- app/views/login/index.html.haml | 9 +- app/views/mappings/_count.html.haml | 2 +- app/views/mappings/_form.html.haml | 2 +- app/views/mappings/_show_line.html.haml | 4 +- .../ontologies/browser/_ontologies.html.haml | 2 +- app/views/ontologies/browser/browse.html.haml | 6 +- .../_collections_picker.html.haml | 4 +- .../_concepts_tree.html.haml | 2 +- .../_scheme_picker.html.haml | 2 +- .../ontologies/content_serializer.html.haml | 3 +- app/views/ontologies/htaccess.html.haml | 122 +- app/views/ontologies/new.html.haml | 2 +- .../ontologies/sections/_metadata.html.haml | 4 +- .../_ontology_description_section.html.haml | 2 +- app/views/properties/_show.html.haml | 16 +- app/views/recommender/index.html.haml | 2 +- app/views/taxonomy/_taxonomies.html.haml | 10 + app/views/taxonomy/index.html.haml | 24 + app/views/users/_form.html.haml | 4 +- app/views/users/show.html.haml | 42 +- bin/ontoportal | 2 +- bin/run_api | 4 +- config/bioportal_config_env.rb.sample | 9 +- config/bioportal_config_test.rb | 9 +- config/environment.rb | 3 +- config/initializers/cube_reporter.rb | 43 - config/initializers/miniprofiler.rb | 2 - config/locales/en.yml | 56 +- config/locales/fr.yml | 57 +- config/routes.rb | 41 +- docker-compose.yml | 22 +- lib/resolver/acronym_from_virtual.rb | 535 -- lib/resolver/virtual_from_acronym.rb | 533 -- lib/resolver/virtual_from_version.rb | 7144 ----------------- lib/tasks/schema.rake | 14 +- test/application_system_test_case.rb | 25 +- .../controllers/ontologies_controller_test.rb | 65 + test/fixtures/agents.yml | 55 - test/fixtures/annotator.yml | 181 + test/fixtures/ontologies.yml | 84 + test/fixtures/users.yml | 4 + test/helpers/application_test_helpers.rb | 38 +- test/integration/login_flows_test.rb | 2 +- test/system/agent_flows_test.rb | 17 +- test/system/annotator_page_test.rb | 108 + test/system/content_redirection_test.rb | 68 + test/system/login_flows_test.rb | 6 +- test/system/submission_flows_test.rb | 17 +- test/test_helper.rb | 2 + vendor/assets/images/chosen/chosen-sprite.png | Bin 538 -> 0 bytes .../assets/images/chosen/chosen-sprite@2x.png | Bin 738 -> 0 bytes vendor/assets/javascripts/chosen.jquery.js | 1269 --- vendor/assets/stylesheets/chosen.css.scss | 452 -- 177 files changed, 2673 insertions(+), 12213 deletions(-) create mode 100644 app/assets/images/icons/slices.svg delete mode 100644 app/assets/javascripts/bp_mappings.js.erb create mode 100644 app/assets/stylesheets/components/tree_view.scss create mode 100644 app/assets/stylesheets/taxonomy.scss create mode 100644 app/components/display/taxonomy_card_component.rb create mode 100644 app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml delete mode 100644 app/controllers/ajax_proxy_controller.rb create mode 100644 app/controllers/concerns/terms_reuses.rb create mode 100644 app/controllers/taxonomy_controller.rb delete mode 100644 app/javascript/controllers/chosen_controller.js create mode 100644 app/javascript/controllers/concepts_json_button_controller.js delete mode 100644 app/javascript/controllers/content_finder_controller.js create mode 100644 app/javascript/controllers/skos_collections_selector.js delete mode 100644 app/javascript/mixins/useChosen.js delete mode 100644 app/models/bpid_resolver.rb create mode 100644 app/views/home/cookies.html.haml create mode 100644 app/views/taxonomy/_taxonomies.html.haml create mode 100644 app/views/taxonomy/index.html.haml delete mode 100644 config/initializers/cube_reporter.rb delete mode 100644 config/initializers/miniprofiler.rb delete mode 100644 lib/resolver/acronym_from_virtual.rb delete mode 100644 lib/resolver/virtual_from_acronym.rb delete mode 100644 lib/resolver/virtual_from_version.rb create mode 100644 test/fixtures/annotator.yml create mode 100644 test/system/annotator_page_test.rb create mode 100644 test/system/content_redirection_test.rb delete mode 100755 vendor/assets/images/chosen/chosen-sprite.png delete mode 100755 vendor/assets/images/chosen/chosen-sprite@2x.png delete mode 100755 vendor/assets/javascripts/chosen.jquery.js delete mode 100755 vendor/assets/stylesheets/chosen.css.scss diff --git a/Gemfile b/Gemfile index 34aad240b5..c40e3640c5 100644 --- a/Gemfile +++ b/Gemfile @@ -1,93 +1,127 @@ source 'https://rubygems.org' +# Main Rails gem # Bundle edge Rails instead: gem 'rails', github: 'rails/rails' -gem 'rails', '7.0.3' +gem 'rails', '7.0.4' -gem 'chart-js-rails' +# JavaScript bundling for Rails gem 'jsbundling-rails' -gem 'sassc-rails' # sass-rails replacent -gem 'terser' # ugilifer replacent -# See https://github.com/rails/execjs#readme for more supported runtimes -# gem 'therubyracer', platforms: :ruby -# gem 'duktape' +# Chart.js integration for Rails +gem 'chart-js-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', '~> 4.2.0' + +# 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] +# The original asset pipeline for Rails +# [https://github.com/rails/sprockets-rails] gem 'sprockets-rails' -# Use the Puma web server [https://github.com/puma/puma] +# Use the Puma web server +# [https://github.com/puma/puma] gem 'puma', '~> 5.0' -# Use JavaScript with ESM import maps [https://github.com/rails/importmap-rails] +# Use JavaScript with ESM import maps +# [https://github.com/rails/importmap-rails] gem 'importmap-rails' -# Hotwire's SPA-like page accelerator [https://turbo.hotwired.dev] +# Hotwire's SPA-like page accelerator +# [https://turbo.hotwired.dev] gem 'turbo-rails' -# Hotwire's modest JavaScript framework [https://stimulus.hotwired.dev] +# Hotwire's modest JavaScript framework +# [https://stimulus.hotwired.dev] gem 'stimulus-rails' -# Build JSON APIs with ease [https://github.com/rails/jbuilder] -# gem "jbuilder" +# 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] -# To use ActiveModel has_secure_password -# gem 'bcrypt-ruby', '~> 3.0.0' - # Reduces boot times through caching; required in config/boot.rb - gem 'bootsnap', require: false -gem 'cube-ruby', require: 'cube' +# Memcached client for Ruby gem 'dalli' -gem 'ffi', '~> 1.16.3' -gem 'flag-icons-rails', '~> 3.4' -gem 'flamegraph' + +# GraphQL client for Ruby gem 'graphql-client' + +# Haml template engine for Ruby on Rails gem 'haml', '~> 5.1' + +# Internationalization (i18n) gem 'i18n' -gem 'iconv' -gem 'inline_svg' -gem 'iso-639', '~> 0.3.6' -gem 'lookbook', '~> 1.5.5' -gem 'multi_json' +gem 'rails-i18n', '~> 7.0.0' + +# MySQL database adapter gem 'mysql2' + +# JSON parsing libraries +gem 'multi_json' gem 'oj' -gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', - branch: 'development' -gem 'open_uri_redirections' -gem 'pry' -gem 'psych', '< 4' -gem 'rack-mini-profiler' -gem 'rails_autolink' -gem 'rails-i18n', '~> 7.0.0' -gem 'rdoc' + +# Google reCAPTCHA integration gem 'recaptcha', '~> 5.9.0' + +# Simple HTTP and REST client for Ruby gem 'rest-client' -gem 'stackprof', require: false -gem 'thin' -gem 'turnout' + +# View components framework for Rails +gem 'lookbook', '~> 1.5.5' gem 'view_component', '~> 2.72' + +# Pagination library for Rails gem 'will_paginate', '~> 3.0' +# Render SVG files in Rails views +gem 'inline_svg' + +# 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' -gem 'omniauth-rails_csrf_protection' + +# Used to generate colors randomly +gem "color", "~> 1.8" group :staging, :production, :appliance do - # application monitoring - gem 'newrelic_rpm', '< 9.10.0' - # logs in json format, useful for shipping logs to logstash + # Application performance monitoring + gem 'newrelic_rpm' + + # 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 @@ -102,40 +136,47 @@ group :development do gem 'capistrano-rails', '~> 1.4', 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 + + # Static code analysis gem 'brakeman', require: false gem 'rubocop', require: false - # gem 'i18n-debug' - # See https://guides.rubyonrails.org/debugging_rails_applications.html#debugging-with-the-debug-gem + + # Haml support for Rails + gem 'haml-rails' + gem 'html2haml' + + # Debugging tools gem 'debug', platforms: %i[mri mingw x64_mingw] - # Use console on exceptions pages [https://github.com/rails/web-console] - gem 'i18n-tasks' - gem 'i18n-tasks-csv', '~> 1.1' + # 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' - gem 'haml-rails' - gem 'letter_opener_web', '~> 2.0' -end -group :test, :development do - gem 'rspec-rails' + # Email preview in the browser + gem 'letter_opener_web', '~> 2.0' end group :test do - # Use system testing [https://guides.rubyonrails.org/testing.html#system-testing] + # 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 - # gem 'webdrivers' - gem 'webmock' -end -gem 'net-ftp', '~> 0.2.0', require: false -gem 'net-http', '~> 0.3.2' + # Mock HTTP requests in tests + gem 'webmock' -gem 'bugsnag', '~> 6.26' + # Testing framework for Rails + gem 'rspec-rails' +end \ No newline at end of file diff --git a/Gemfile.lock b/Gemfile.lock index 5c78134fd4..51f97081af 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git - revision: abea6c217c0ee93bcfd80c47c2af52747365d491 - branch: development + revision: 24fb2549f7b69841e052491439bc8375ed5acfd9 + branch: master specs: ontologies_api_client (2.2.0) activesupport @@ -17,102 +17,100 @@ GIT GEM remote: https://rubygems.org/ specs: - actioncable (7.0.3) - actionpack (= 7.0.3) - activesupport (= 7.0.3) + actioncable (7.0.4) + actionpack (= 7.0.4) + activesupport (= 7.0.4) nio4r (~> 2.0) websocket-driver (>= 0.6.1) - actionmailbox (7.0.3) - actionpack (= 7.0.3) - activejob (= 7.0.3) - activerecord (= 7.0.3) - activestorage (= 7.0.3) - activesupport (= 7.0.3) + actionmailbox (7.0.4) + actionpack (= 7.0.4) + activejob (= 7.0.4) + activerecord (= 7.0.4) + activestorage (= 7.0.4) + activesupport (= 7.0.4) mail (>= 2.7.1) net-imap net-pop net-smtp - actionmailer (7.0.3) - actionpack (= 7.0.3) - actionview (= 7.0.3) - activejob (= 7.0.3) - activesupport (= 7.0.3) + actionmailer (7.0.4) + actionpack (= 7.0.4) + actionview (= 7.0.4) + activejob (= 7.0.4) + activesupport (= 7.0.4) mail (~> 2.5, >= 2.5.4) net-imap net-pop net-smtp rails-dom-testing (~> 2.0) - actionpack (7.0.3) - actionview (= 7.0.3) - activesupport (= 7.0.3) + actionpack (7.0.4) + actionview (= 7.0.4) + activesupport (= 7.0.4) rack (~> 2.0, >= 2.2.0) rack-test (>= 0.6.3) rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.0, >= 1.2.0) - actiontext (7.0.3) - actionpack (= 7.0.3) - activerecord (= 7.0.3) - activestorage (= 7.0.3) - activesupport (= 7.0.3) + actiontext (7.0.4) + actionpack (= 7.0.4) + activerecord (= 7.0.4) + activestorage (= 7.0.4) + activesupport (= 7.0.4) globalid (>= 0.6.0) nokogiri (>= 1.8.5) - actionview (7.0.3) - activesupport (= 7.0.3) + actionview (7.0.4) + activesupport (= 7.0.4) builder (~> 3.1) erubi (~> 1.4) rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.1, >= 1.2.0) - activejob (7.0.3) - activesupport (= 7.0.3) + activejob (7.0.4) + activesupport (= 7.0.4) globalid (>= 0.3.6) - activemodel (7.0.3) - activesupport (= 7.0.3) - activerecord (7.0.3) - activemodel (= 7.0.3) - activesupport (= 7.0.3) - activestorage (7.0.3) - actionpack (= 7.0.3) - activejob (= 7.0.3) - activerecord (= 7.0.3) - activesupport (= 7.0.3) + activemodel (7.0.4) + activesupport (= 7.0.4) + activerecord (7.0.4) + activemodel (= 7.0.4) + activesupport (= 7.0.4) + activestorage (7.0.4) + actionpack (= 7.0.4) + activejob (= 7.0.4) + activerecord (= 7.0.4) + activesupport (= 7.0.4) marcel (~> 1.0) mini_mime (>= 1.1.0) - activesupport (7.0.3) + activesupport (7.0.4) concurrent-ruby (~> 1.0, >= 1.0.2) i18n (>= 1.6, < 2) minitest (>= 5.1) tzinfo (~> 2.0) - addressable (2.8.6) - public_suffix (>= 2.0.2, < 6.0) + addressable (2.8.7) + public_suffix (>= 2.0.2, < 7.0) aes_key_wrap (1.1.0) - airbrussh (1.5.2) + airbrussh (1.5.3) sshkit (>= 1.6.1, != 1.7.0) ast (2.4.2) - autoprefixer-rails (10.4.16.0) + autoprefixer-rails (10.4.19.0) execjs (~> 2) 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 (1.18.3) + bootsnap (1.18.4) msgpack (~> 1.2) bootstrap (4.2.1) autoprefixer-rails (>= 9.1.0) popper_js (>= 1.14.3, < 2) sassc-rails (>= 2.0.0) brakeman (5.4.1) - bugsnag (6.27.0) + bugsnag (6.27.1) concurrent-ruby (~> 1.0) builder (3.3.0) - capistrano (3.18.1) + capistrano (3.19.1) airbrussh (>= 1.0.0) i18n rake (>= 10.0.0) sshkit (>= 1.9.0) - capistrano-bundler (2.1.0) + capistrano-bundler (2.1.1) capistrano (~> 3.1) capistrano-locally (0.3.0) capistrano (~> 3.0) @@ -134,17 +132,17 @@ GEM xpath (~> 3.2) chart-js-rails (0.1.7) railties (> 3.1) - childprocess (5.0.0) + childprocess (5.1.0) + logger (~> 1.5) coderay (1.1.3) - concurrent-ruby (1.3.2) + color (1.8) + concurrent-ruby (1.3.4) crack (1.0.0) bigdecimal rexml crass (1.0.6) css_parser (1.17.1) addressable - cube-ruby (0.0.3) - daemons (1.4.1) dalli (3.2.8) date (3.3.4) debug (1.9.2) @@ -152,13 +150,12 @@ GEM reline (>= 0.3.8) deepl-rb (2.5.3) diff-lcs (1.5.1) - docile (1.4.0) + docile (1.4.1) domain_name (0.6.20240107) ed25519 (1.3.0) - erubi (1.12.0) + erubi (1.13.0) erubis (2.7.0) - eventmachine (1.2.7) - excon (0.110.0) + excon (0.111.0) execjs (2.9.1) faraday (2.0.1) faraday-net_http (~> 2.0) @@ -172,14 +169,15 @@ GEM multipart-post (~> 2) faraday-net_http (2.1.0) ffi (1.16.3) + fiber-storage (1.0.0) flag-icons-rails (3.4.6.1) sass-rails - flamegraph (0.9.5) globalid (1.2.1) activesupport (>= 6.1) - graphql (2.3.4) + graphql (2.3.14) base64 - graphql-client (0.22.0) + fiber-storage + graphql-client (0.23.0) activesupport (>= 3.0) graphql (>= 1.13.0) haml (5.2.2) @@ -190,7 +188,7 @@ GEM activesupport (>= 5.1) haml (>= 4.0.6) railties (>= 5.1) - hashdiff (1.1.0) + hashdiff (1.1.1) hashie (5.0.0) highline (2.1.0) html2haml (2.3.0) @@ -201,7 +199,7 @@ GEM htmlbeautifier (1.4.3) htmlentities (4.3.4) http-accept (1.7.0) - http-cookie (1.0.6) + http-cookie (1.0.7) domain_name (~> 0.5) i18n (1.14.5) concurrent-ruby (~> 1.0) @@ -217,16 +215,15 @@ GEM terminal-table (>= 1.5.1) i18n-tasks-csv (1.1) i18n-tasks (~> 0.9) - iconv (1.0.8) importmap-rails (2.0.1) actionpack (>= 6.0.0) activesupport (>= 6.0.0) railties (>= 6.0.0) - inline_svg (1.9.0) + inline_svg (1.10.0) activesupport (>= 3.0) nokogiri (>= 1.6) io-console (0.7.2) - irb (1.13.1) + irb (1.14.0) rdoc (>= 4.0.0) reline (>= 0.4.2) iso-639 (0.3.6) @@ -236,7 +233,7 @@ GEM thor (>= 0.14, < 2.0) jquery-ui-rails (7.0.0) railties (>= 3.2.16) - jsbundling-rails (1.3.0) + jsbundling-rails (1.3.1) railties (>= 6.0.0) json (2.7.2) json-jwt (1.16.6) @@ -246,7 +243,7 @@ GEM bindata faraday (~> 2.0) faraday-follow_redirects - jwt (2.8.1) + jwt (2.8.2) base64 language_server-protocol (3.17.0.3) launchy (3.0.1) @@ -262,6 +259,7 @@ GEM listen (3.9.0) rb-fsevent (~> 0.10, >= 0.10.3) rb-inotify (~> 0.9, >= 0.9.10) + logger (1.6.1) loofah (2.22.0) crass (~> 1.0.2) nokogiri (>= 1.12.0) @@ -289,21 +287,20 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0604) + mime-types-data (3.2024.0903) mini_mime (1.1.5) - minitest (5.23.1) + minitest (5.25.1) msgpack (1.7.2) multi_json (1.15.0) multi_xml (0.6.0) multipart-post (2.4.1) - mutex_m (0.2.0) mysql2 (0.5.6) net-ftp (0.2.1) net-protocol time net-http (0.3.2) uri - net-imap (0.4.12) + net-imap (0.4.16) date net-protocol net-pop (0.1.2) @@ -318,18 +315,8 @@ GEM net-protocol net-ssh (7.2.3) netrc (0.11.0) - newrelic_rpm (9.9.0) + newrelic_rpm (9.13.0) nio4r (2.7.3) - nokogiri (1.15.6-aarch64-linux) - racc (~> 1.4) - nokogiri (1.15.6-arm-linux) - racc (~> 1.4) - nokogiri (1.15.6-arm64-darwin) - racc (~> 1.4) - nokogiri (1.15.6-x86-linux) - racc (~> 1.4) - nokogiri (1.15.6-x86_64-darwin) - racc (~> 1.4) nokogiri (1.15.6-x86_64-linux) racc (~> 1.4) oauth2 (2.0.9) @@ -339,8 +326,9 @@ GEM rack (>= 1.2, < 4) snaky_hash (~> 2.0) version_gem (~> 1.1) - oj (3.16.4) + oj (3.16.5) bigdecimal (>= 3.0) + ostruct (>= 0.2) omniauth (2.1.2) hashie (>= 3.4.6) rack (>= 2.2.3) @@ -348,7 +336,7 @@ GEM omniauth-github (2.0.1) omniauth (~> 2.0) omniauth-oauth2 (~> 1.8) - omniauth-google-oauth2 (1.1.2) + omniauth-google-oauth2 (1.1.3) jwt (>= 2.0) oauth2 (~> 2.0) omniauth (~> 2.0) @@ -367,44 +355,41 @@ GEM omniauth-rails_csrf_protection (1.0.2) actionpack (>= 4.2) omniauth (~> 2.0) - open_uri_redirections (0.2.1) - parallel (1.25.1) - parser (3.3.2.0) + ostruct (0.6.0) + parallel (1.26.3) + parser (3.3.5.0) ast (~> 2.4.1) racc popper_js (1.16.1) pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) - psych (3.3.4) - public_suffix (5.0.5) + psych (5.1.2) + stringio + public_suffix (5.1.1) puma (5.6.8) nio4r (~> 2.0) - racc (1.8.0) + racc (1.8.1) rack (2.2.9) - rack-accept (0.4.5) - rack (>= 0.4) - 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 (7.0.3) - actioncable (= 7.0.3) - actionmailbox (= 7.0.3) - actionmailer (= 7.0.3) - actionpack (= 7.0.3) - actiontext (= 7.0.3) - actionview (= 7.0.3) - activejob (= 7.0.3) - activemodel (= 7.0.3) - activerecord (= 7.0.3) - activestorage (= 7.0.3) - activesupport (= 7.0.3) + rails (7.0.4) + actioncable (= 7.0.4) + actionmailbox (= 7.0.4) + actionmailer (= 7.0.4) + actionpack (= 7.0.4) + actiontext (= 7.0.4) + actionview (= 7.0.4) + activejob (= 7.0.4) + activemodel (= 7.0.4) + activerecord (= 7.0.4) + activestorage (= 7.0.4) + activesupport (= 7.0.4) bundler (>= 1.15.0) - railties (= 7.0.3) + railties (= 7.0.4) rails-dom-testing (2.2.0) activesupport (>= 5.0.0) minitest @@ -415,13 +400,9 @@ GEM rails-i18n (7.0.9) i18n (>= 0.7, < 2) railties (>= 6.0.0, < 8) - rails_autolink (1.1.8) - actionview (> 3.1) - activesupport (> 3.1) - railties (> 3.1) - railties (7.0.3) - actionpack (= 7.0.3) - activesupport (= 7.0.3) + railties (7.0.4) + actionpack (= 7.0.4) + activesupport (= 7.0.4) method_source rake (>= 12.2) thor (~> 1.0) @@ -431,55 +412,54 @@ 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 redcarpet (3.6.0) regexp_parser (2.9.2) - reline (0.5.8) + reline (0.5.10) io-console (~> 0.5) rest-client (2.1.0) http-accept (>= 1.7.0, < 2.0) http-cookie (>= 1.0.2, < 2.0) mime-types (>= 1.16, < 4.0) netrc (~> 0.8) - rexml (3.2.8) - strscan (>= 3.0.9) - rouge (4.2.1) - rspec-core (3.13.0) + rexml (3.3.7) + rouge (4.3.0) + rspec-core (3.13.1) rspec-support (~> 3.13.0) - rspec-expectations (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) diff-lcs (>= 1.2.0, < 2.0) rspec-support (~> 3.13.0) - rspec-rails (6.1.2) - actionpack (>= 6.1) - activesupport (>= 6.1) - railties (>= 6.1) + rspec-rails (7.0.1) + actionpack (>= 7.0) + activesupport (>= 7.0) + railties (>= 7.0) rspec-core (~> 3.13) rspec-expectations (~> 3.13) rspec-mocks (~> 3.13) rspec-support (~> 3.13) rspec-support (3.13.1) - rubocop (1.64.1) + rubocop (1.66.1) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) parser (>= 3.3.0.2) rainbow (>= 2.2.2, < 4.0) - regexp_parser (>= 1.8, < 3.0) - rexml (>= 3.2.5, < 4.0) - rubocop-ast (>= 1.31.1, < 2.0) + regexp_parser (>= 2.4, < 3.0) + rubocop-ast (>= 1.32.2, < 2.0) ruby-progressbar (~> 1.7) unicode-display_width (>= 2.4.0, < 3.0) - rubocop-ast (1.31.3) + 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 (3.21.0) + ruby_parser (3.21.1) racc (~> 1.5) sexp_processor (~> 4.16) rubyzip (2.3.2) @@ -497,7 +477,7 @@ GEM rexml (~> 3.2, >= 3.2.5) rubyzip (>= 1.2.2, < 3.0) websocket (~> 1.0) - sexp_processor (4.17.1) + sexp_processor (4.17.2) simplecov (0.22.0) docile (~> 1.1) simplecov-html (~> 0.11) @@ -505,7 +485,7 @@ GEM simplecov-cobertura (2.1.0) rexml simplecov (~> 0.19) - simplecov-html (0.12.3) + simplecov-html (0.13.0) simplecov_json_formatter (0.1.4) snaky_hash (2.0.1) hashie @@ -514,47 +494,37 @@ GEM sprockets (4.2.1) concurrent-ruby (~> 1.0) rack (>= 2.2.4, < 4) - sprockets-rails (3.5.1) + sprockets-rails (3.5.2) actionpack (>= 6.1) activesupport (>= 6.1) sprockets (>= 3.0.0) - sshkit (1.22.2) + sshkit (1.23.1) base64 - mutex_m net-scp (>= 1.1.2) net-sftp (>= 2.1.2) net-ssh (>= 2.8.0) - stackprof (0.2.26) - stimulus-rails (1.3.3) + ostruct + stimulus-rails (1.3.4) railties (>= 6.0.0) - strscan (3.1.0) + stringio (3.1.1) temple (0.10.3) terminal-table (3.0.2) unicode-display_width (>= 1.1.1, < 3) - terser (1.2.2) + terser (1.2.3) 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 (1.3.1) - tilt (2.3.0) - time (0.3.0) + thor (1.3.2) + tilt (2.4.0) + time (0.4.0) date timeout (0.4.1) - turbo-rails (2.0.5) + turbo-rails (2.0.6) actionpack (>= 6.0.0) activejob (>= 6.0.0) railties (>= 6.0.0) - turnout (2.5.0) - i18n (>= 0.7, < 2) - rack (>= 1.3, < 3) - rack-accept (~> 0.4) - tilt (>= 1.4, < 3) tzinfo (2.0.6) concurrent-ruby (~> 1.0) unicode-display_width (2.5.0) - uri (0.13.0) + uri (0.13.1) version_gem (1.1.4) view_component (2.83.0) activesupport (>= 5.2.0, < 8.0) @@ -569,30 +539,18 @@ GEM addressable (>= 2.8.0) crack (>= 0.3.2) hashdiff (>= 0.4.0, < 2.0.0) - websocket (1.2.10) + 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 (0.9.36) - zeitwerk (2.6.15) + yard (0.9.37) + zeitwerk (2.6.18) PLATFORMS - aarch64-linux - aarch64-linux-gnu - aarch64-linux-musl - arm-linux - arm-linux-gnu - arm-linux-musl - arm64-darwin - x86-linux - x86-linux-gnu - x86-linux-musl - x86_64-darwin x86_64-linux - x86_64-linux-gnu x86_64-linux-musl DEPENDENCIES @@ -609,14 +567,13 @@ DEPENDENCIES capistrano-yarn capybara chart-js-rails - cube-ruby + color (~> 1.8) dalli debug deepl-rb ed25519 (>= 1.2, < 2.0) ffi (~> 1.16.3) flag-icons-rails (~> 3.4) - flamegraph graphql-client haml (~> 5.1) haml-rails @@ -624,7 +581,6 @@ DEPENDENCIES i18n i18n-tasks i18n-tasks-csv (~> 1.1) - iconv importmap-rails inline_svg iso-639 (~> 0.3.6) @@ -632,13 +588,12 @@ DEPENDENCIES jquery-ui-rails jsbundling-rails letter_opener_web (~> 2.0) - listen lookbook (~> 1.5.5) multi_json mysql2 net-ftp (~> 0.2.0) net-http (~> 0.3.2) - newrelic_rpm (< 9.10.0) + newrelic_rpm oj omniauth omniauth-github @@ -647,15 +602,10 @@ DEPENDENCIES omniauth-orcid omniauth-rails_csrf_protection ontologies_api_client! - open_uri_redirections pry - psych (< 4) puma (~> 5.0) - rack-mini-profiler - rails (= 7.0.3) + rails (= 7.0.4) rails-i18n (~> 7.0.0) - rails_autolink - rdoc recaptcha (~> 5.9.0) rest-client rspec-rails @@ -665,12 +615,9 @@ DEPENDENCIES simplecov simplecov-cobertura sprockets-rails - stackprof stimulus-rails terser - thin turbo-rails - turnout tzinfo-data view_component (~> 2.72) web-console diff --git a/app/assets/images/icons/slices.svg b/app/assets/images/icons/slices.svg new file mode 100644 index 0000000000..ce6a9a3d98 --- /dev/null +++ b/app/assets/images/icons/slices.svg @@ -0,0 +1,4 @@ + + + + diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js index 3fe97607a4..1a42c65807 100644 --- a/app/assets/javascripts/application.js +++ b/app/assets/javascripts/application.js @@ -15,7 +15,6 @@ //= require bp_ajax_controller //= require bp_notes //= require bp_form_complete -//= require bp_mappings //= require bp_admin //= require concepts //= require projects diff --git a/app/assets/javascripts/bp_mappings.js.erb b/app/assets/javascripts/bp_mappings.js.erb deleted file mode 100644 index c47edb29f9..0000000000 --- a/app/assets/javascripts/bp_mappings.js.erb +++ /dev/null @@ -1,145 +0,0 @@ -"use strict"; - -// The count returned may not match the actual number of mappings -// To get around this, we re-calculate based on the mapping table size - -function updateMappingCount() { - // Go through every tr in the concept mappings tables. Add 1 to the count if the tr is not filled with "currently no mappings" - var rows = jQuery("#concept_mappings_table tbody tr"), mappings_count = 0; - rows.each(function() { - if (this.innerHTML.indexOf("currently no") < 0) { - mappings_count++; - } - }); - if (mappings_count === null) { - mappings_count = rows.length; - } - jQuery("#mapping_count").html(mappings_count); -} - -// Also in bp_create_mappings.js -function updateMappingDeletePermissions() { - var mapping_permission_checkbox = jQuery("#delete_mappings_permission"); - if (mapping_permission_checkbox.length === 0){ - //console.error("Failed to select #delete_mappings_permission"); - jQuery("#delete_mappings_button").hide(); - jQuery(".delete_mappings_column").hide(); - jQuery("input[name='delete_mapping_checkbox']").prop('disabled', true); - } else { - // Ensure the permission checkbox is hidden. - mapping_permission_checkbox.hide(); - if (mapping_permission_checkbox.is(':checked')) { - jQuery("#delete_mappings_button").show(); - jQuery(".delete_mappings_column").show(); - jQuery("input[name='delete_mapping_checkbox']").prop('disabled', false); - } else { - jQuery("#delete_mappings_button").hide(); - jQuery(".delete_mappings_column").hide(); - jQuery("input[name='delete_mapping_checkbox']").prop('disabled', true); - } - } - jQuery("input[name='delete_mapping_checkbox']").prop('checked', false); -} - -function loadMappings(value) { - jQuery('#mappingCount').html(""); - jQuery('#mapping_load').show(); - - jQuery('#mappingCount').load('/mappings/count/' + value, function () { - jQuery('#mapping_load').hide(); - let mappings_table_elem = jQuery("#mapping_count_table"); - mappings_table_elem.effect("highlight", {color: "#F5F5F5"}, 500); - mappings_table_elem.dataTable({ - "paging": false, - "info": false, - "searching": false, - "columns": [ - { - "className": "text-left" - }, - { - "type": "num-fmt", - "orderSequence": ["desc", "asc"], - "className": "text-right" - } - ] - }); - }); -} - -jQuery(document).ready(function(){ - updateMappingCount(); - updateMappingDeletePermissions(); - - // Handle visualization changes - jQuery("#display_options input").on("click", function(e, button){ - var selectedOnt = jQuery("#search_ontologies").val(); - if (selectedOnt !== "") { - loadMappings(selectedOnt); - } - }); - - jQuery("#mappings-help").on("click", bpPopWindow); -}); - -jQuery(document).bind("tree_changed", updateMappingCount); - -// deleteMappings() is a callback that is called by "#delete_mappings_button" created in -// /app/views/mappings/_concept_mappings.html.haml -// The appearance of that button is controlled by updateMappingDeletePermissions(), which -// relies on @delete_mapping_permission in /app/views/mappings/_mapping_table.html.haml; which, -// in turn, is set by /app/controllers/application_controller.check_delete_mapping_permission() -function deleteMappings() { - var mappingsToDelete = [], params; - var ontologyId = jQuery(document).data().bp.ont_viewer.ontology_id; - var conceptId = jQuery(document).data().bp.ont_viewer.concept_id; - - jQuery("#delete_mappings_error").html(""); - jQuery("#delete_mappings_spinner").show(); - - jQuery("input[name='delete_mapping_checkbox']:checked").each(function(){ - mappingsToDelete.push(jQuery(this).val()); - }); - - params = { - mappingids: mappingsToDelete.join(","), - _method: "delete", - ontologyid: ontologyId, - conceptid: conceptId - }; - - jQuery("#delete_mappings_error").html(""); - - jQuery.ajax({ - url: "/mappings/mappingids", // routed to mappings_controller::destroy - type: "POST", - data: params, - - success: function(data){ - jQuery("#delete_mappings_spinner").hide(); - - var i, rowId, len = data.success.length; - for (i=0; i div{ + margin-right: 10px; +} + @media only screen and (max-width: 1200px) { .account-page-first-row { width: 47vw; diff --git a/app/assets/stylesheets/agents.scss b/app/assets/stylesheets/agents.scss index d909878949..bed9b6b147 100644 --- a/app/assets/stylesheets/agents.scss +++ b/app/assets/stylesheets/agents.scss @@ -26,4 +26,28 @@ .agent-chip-name{ color: #8C8E8D; font-size: 15px; +} +.agent-edit-icon{ + display: flex !important; + flex-direction: column; + justify-content: center; +} +.agent-input-with-icon{ + padding: 8px; + margin-bottom: 0px; + border-radius: 5px; + width: 100%; + color: #5f6573; + outline: none; + font-size: 15px; + font-weight: 500; + border: 1px solid #d7d7d7; + padding-left: 45px; +} +.agent-input-icon{ + height: 20px; + width: 20px; + position: absolute; + padding: 11px 17px; + box-sizing: unset; } \ No newline at end of file diff --git a/app/assets/stylesheets/application.css.scss.erb b/app/assets/stylesheets/application.css.scss.erb index 7f4793fcf7..ac5160afc2 100755 --- a/app/assets/stylesheets/application.css.scss.erb +++ b/app/assets/stylesheets/application.css.scss.erb @@ -10,7 +10,6 @@ * *= require jquery-ui *= require alertify - *= require chosen *= require jquery-ui-1.8.1.custom *= require jquery.autocomplete *= require trumbowyg @@ -59,6 +58,7 @@ @import "agent_tooltip"; @import "content_finder"; @import "tools"; +@import "taxonomy"; /* Bootstrap and Font Awesome */ @import "bootstrap"; diff --git a/app/assets/stylesheets/bioportal.scss b/app/assets/stylesheets/bioportal.scss index 1252111f8b..49c4eb3496 100644 --- a/app/assets/stylesheets/bioportal.scss +++ b/app/assets/stylesheets/bioportal.scss @@ -637,209 +637,7 @@ li.ac_over > .obsolete_class { font-style: italic; } -/******************** -## TREE VIEW -*********************/ -div.tree_error { - background: none repeat scroll 0 0 lightYellow; - font-weight: 600; - padding: 5px 10px; -} - -.expansion_error { - color: red; - font-size: x-small; - font-style: oblique; - padding: 0 3px; -} - -#bd ul.simpleTree li{ - margin-left: 0px; - padding: 5px 0 0 10px; -} - -#bd ul.simpleTree{ - margin-left:0px; - margin-bottom:0px; -} - -.simpleTree { - margin:0; - padding:0; - /* - overflow:auto; - width: 250px; - height:350px; - overflow:auto; - border: 1px solid #444444; - */ - a.tree-link { - display: inline-block; - padding: 5px; - word-break: break-all; - text-wrap: wrap; - color: var(--primary-color) !important; - } - a.tree-link.active { - cursor: default; - background-color: var(--light-color); - font-weight: bold; - border-radius: 3px; - padding: 7px 5px; - } - - .tree-border-left{ - border-left: 2px dotted #eee; - margin-left: 2px; - } -} -.simpleTree li { - list-style: none; - margin:0; - padding:0 0 0 22px; - line-height: 14px; -} -.simpleTree li span { - display:inline; - clear: left; - white-space: nowrap; -} -.simpleTree ul { - margin:0; - padding:0; -} -.simpleTree .root ul { - margin:0; -} -.simpleTree .root { - margin-left:-16px; - /*background: url(/images/tree/root.gif) no-repeat 16px 0 #ffffff;*/ -} -.simpleTree .line { - margin:0 0 0 -16px; - padding:0; - line-height: 3px; - height:3px; - font-size:3px; - background: image-url('jquery.simple.tree/line_bg.gif') 0 0 no-repeat transparent; -} -.simpleTree .line-last { - margin:0 0 0 -16px; - padding:0; - line-height: 3px; - height:3px; - font-size:3px; - background: image-url('jquery.simple.tree/spacer.gif') 0 0 no-repeat transparent; -} -.simpleTree .line-over { - margin:0 0 0 -16px; - padding:0; - line-height: 3px; - height:3px; - font-size:3px; - background: image-url('jquery.simple.tree/line_bg_over.gif') 0 0 no-repeat transparent; -} -.simpleTree .line-over-last { - margin:0 0 0 -16px; - padding:0; - line-height: 3px; - height:3px; - font-size:3px; - background: image-url('jquery.simple.tree/line_bg_over_last.gif') 0 0 no-repeat transparent; -} -.simpleTree .folder-open { - margin-left:-16px; - background: image-url('jquery.simple.tree/collapsable.gif') 0 -2px no-repeat #fff; -} -.simpleTree .folder-open-last { - margin-left:-16px; - background: image-url('jquery.simple.tree/collapsable-last.gif') 0 -2px no-repeat #fff; -} -.simpleTree .folder-close { - margin-left:-16px; - background: image-url('jquery.simple.tree/expandable.gif') 0 -2px no-repeat #fff; -} -.simpleTree .folder-close-last { - margin-left:-16px; - background: image-url('jquery.simple.tree/expandable-last.gif') 0 -2px no-repeat #fff; -} -.simpleTree .doc { - margin-left:-16px; - background: image-url('jquery.simple.tree/leaf.gif') 0 -1px no-repeat #fff; -} -.simpleTree .doc-last { - margin-left:-16px; - background: image-url('jquery.simple.tree/leaf-last.gif') 0 -1px no-repeat #fff; -} -.simpleTree .ajax { - background: image-url('jquery.simple.tree/spinner.gif') no-repeat 0 0 #ffffff; - height: 16px; - display:none; -} -.simpleTree .ajax li { - display:none; - margin:0; - padding:0; -} -.simpleTree .trigger { - display:inline; - margin-left:-32px; - width: 28px; - height: 11px; - cursor:pointer; -} -.simpleTree .text { - cursor: default; - padding: 0 2px; -} -.simpleTree .active { - cursor: default; - background-color: #B9D5E4; - font-weight: bold; - padding-top: 0px; - padding-right: 2px; - padding-bottom: 0px; - padding-left: 2px; -} -.simpleTree a, .simpleTree a:hover { - text-decoration: none; - color: black; -} -.simpleTree a:hover { - cursor: pointer; -} -#drag_container { - background:#ffffff; - color:#000; - font: normal 11px arial, tahoma, helvetica, sans-serif; - border: 1px dashed #767676; -} -#drag_container ul { - list-style: none; - padding:0; - margin:0; -} -#drag_container li { - list-style: none; - background-color:#ffffff; - line-height:18px; - white-space: nowrap; - padding:1px 1px 0px 16px; - margin:0; -} -#drag_container li span { - padding:0; -} -#drag_container li.doc, #drag_container li.doc-last { - background: image-url('jquery.simple.tree/leaf.gif') no-repeat -17px 0 #ffffff; -} -#drag_container .folder-close, #drag_container .folder-close-last { - background: image-url('jquery.simple.tree/expandable.gif') no-repeat -17px 0 #ffffff; -} -#drag_container .folder-open, #drag_container .folder-open-last { - background: image-url('jquery.simple.tree/collapsable.gif') no-repeat -17px 0 #ffffff; -} .contextMenu { display:none; } @@ -1245,4 +1043,44 @@ turbo-frame[busy] ~ .show-if-loading { .hide{ display:none; +} + +.cookies-modal { + position: fixed; + height: auto; + top: initial; + left: initial; + bottom: 30px; + right: 30px; + transform: initial; + grid-template-rows: minmax(0, 1fr); + z-index: 99999; + background: white; + border-style: solid; + border-color: #f2f2f2; + border-radius: 8px; + border-width: 0; + padding: 15px 20px; + display: grid; + grid-gap: 10px; + box-shadow: rgba(0, 0, 0, 0.1) 0px 4px 8px, rgba(0, 0, 0, 0.1) 0px 2px 4px; + width: 526px; + grid-row-gap: 10px; + + h4{ + justify-self: center; + font-size: 16px; + color: var(--primary-color); + font-weight: 500; + } + p { + word-wrap: break-word; + font-size: 12px; + margin-bottom: 5px; + } + .cookie-privacy-link { + font-size: 12px; + text-align: center; + text-decoration: underline; + } } \ No newline at end of file diff --git a/app/assets/stylesheets/components/concept_details.scss b/app/assets/stylesheets/components/concept_details.scss index 47b0eb326b..c61a0170a8 100644 --- a/app/assets/stylesheets/components/concept_details.scss +++ b/app/assets/stylesheets/components/concept_details.scss @@ -6,4 +6,8 @@ .concept_details_component table th { width: 220px; +} + +.concept_details_component td, .concept_details_component th{ + max-width: 200px; } \ No newline at end of file diff --git a/app/assets/stylesheets/components/index.scss b/app/assets/stylesheets/components/index.scss index c3d57ff51f..62355eb785 100644 --- a/app/assets/stylesheets/components/index.scss +++ b/app/assets/stylesheets/components/index.scss @@ -33,4 +33,5 @@ @import "range_slider"; @import "ontologies_selector"; @import "loader"; -@import "vertical_tabs"; \ No newline at end of file +@import "vertical_tabs"; +@import "tree_view"; \ No newline at end of file diff --git a/app/assets/stylesheets/components/pill_button.scss b/app/assets/stylesheets/components/pill_button.scss index 13a88c1fb8..c47e4ea27b 100644 --- a/app/assets/stylesheets/components/pill_button.scss +++ b/app/assets/stylesheets/components/pill_button.scss @@ -23,6 +23,9 @@ a { color: white !important; } + div { + color: white !important; + } } .pill-button:hover svg path { diff --git a/app/assets/stylesheets/components/search_input.scss b/app/assets/stylesheets/components/search_input.scss index dd721562ae..883899fbc8 100644 --- a/app/assets/stylesheets/components/search_input.scss +++ b/app/assets/stylesheets/components/search_input.scss @@ -9,6 +9,12 @@ position: absolute; } +.search-container.search-container-scroll{ + max-height: 400px; + overflow-y: auto; +} + + .search-content{ display: flex; flex-wrap: wrap; diff --git a/app/assets/stylesheets/components/tree_view.scss b/app/assets/stylesheets/components/tree_view.scss new file mode 100644 index 0000000000..1582b9c3a3 --- /dev/null +++ b/app/assets/stylesheets/components/tree_view.scss @@ -0,0 +1,170 @@ +.tree-view-reuse-icon{ + display: inline; +} +.tree-view-reuse-icon svg{ + width: 13px; +} + +div.tree_error { + background: none repeat scroll 0 0 lightYellow; + font-weight: 600; + padding: 5px 10px; +} + +.expansion_error { + color: red; + font-size: x-small; + font-style: oblique; + padding: 0 3px; +} + +#bd ul.simpleTree li{ + margin-left: 0px; + padding: 5px 0 0 10px; +} + +#bd ul.simpleTree{ +margin-left:0px; +margin-bottom:0px; +} + +.simpleTree { +margin:0; +padding:0; + +a.tree-link { + display: inline-block; + padding: 5px; + word-break: break-all; + text-wrap: wrap; + color: var(--primary-color) !important; +} + +a.tree-link.active { + cursor: default; + background-color: var(--light-color); + font-weight: bold; + border-radius: 3px; + padding: 7px 5px; +} + +.tree-border-left{ + border-left: 2px dotted #eee; + margin-left: 2px; +} +} +.simpleTree li { +list-style: none; +margin:0; +padding:0 0 0 22px; +line-height: 14px; +} +.simpleTree li span { +display:inline; +clear: left; +white-space: nowrap; +} +.simpleTree ul { +margin:0; +padding:0; +} +.simpleTree .root ul { +margin:0; +} +.simpleTree .root { +margin-left:-16px; +/*background: url(/images/tree/root.gif) no-repeat 16px 0 #ffffff;*/ +} +.simpleTree .line { +margin:0 0 0 -16px; +padding:0; +line-height: 3px; +height:3px; +font-size:3px; +background: image-url('jquery.simple.tree/line_bg.gif') 0 0 no-repeat transparent; +} +.simpleTree .line-last { +margin:0 0 0 -16px; +padding:0; +line-height: 3px; +height:3px; +font-size:3px; +background: image-url('jquery.simple.tree/spacer.gif') 0 0 no-repeat transparent; +} +.simpleTree .line-over { +margin:0 0 0 -16px; +padding:0; +line-height: 3px; +height:3px; +font-size:3px; +background: image-url('jquery.simple.tree/line_bg_over.gif') 0 0 no-repeat transparent; +} +.simpleTree .line-over-last { +margin:0 0 0 -16px; +padding:0; +line-height: 3px; +height:3px; +font-size:3px; +background: image-url('jquery.simple.tree/line_bg_over_last.gif') 0 0 no-repeat transparent; +} +.simpleTree .folder-open { +margin-left:-16px; +background: image-url('jquery.simple.tree/collapsable.gif') 0 -2px no-repeat #fff; +} +.simpleTree .folder-open-last { +margin-left:-16px; +background: image-url('jquery.simple.tree/collapsable-last.gif') 0 -2px no-repeat #fff; +} +.simpleTree .folder-close { +margin-left:-16px; +background: image-url('jquery.simple.tree/expandable.gif') 0 -2px no-repeat #fff; +} +.simpleTree .folder-close-last { +margin-left:-16px; +background: image-url('jquery.simple.tree/expandable-last.gif') 0 -2px no-repeat #fff; +} +.simpleTree .doc { +margin-left:-16px; +background: image-url('jquery.simple.tree/leaf.gif') 0 -1px no-repeat #fff; +} +.simpleTree .doc-last { +margin-left:-16px; +background: image-url('jquery.simple.tree/leaf-last.gif') 0 -1px no-repeat #fff; +} +.simpleTree .ajax { +background: image-url('jquery.simple.tree/spinner.gif') no-repeat 0 0 #ffffff; +height: 16px; +display:none; +} +.simpleTree .ajax li { +display:none; +margin:0; +padding:0; +} +.simpleTree .trigger { +display:inline; +margin-left:-32px; +width: 28px; +height: 11px; +cursor:pointer; +} +.simpleTree .text { +cursor: default; +padding: 0 2px; +} +.simpleTree .active { +cursor: default; +background-color: #B9D5E4; +font-weight: bold; +padding-top: 0px; +padding-right: 2px; +padding-bottom: 0px; +padding-left: 2px; +} +.simpleTree a, .simpleTree a:hover { +text-decoration: none; +color: black; +} +.simpleTree a:hover { +cursor: pointer; +} \ No newline at end of file diff --git a/app/assets/stylesheets/concepts.scss b/app/assets/stylesheets/concepts.scss index e466177edc..330d00eb59 100644 --- a/app/assets/stylesheets/concepts.scss +++ b/app/assets/stylesheets/concepts.scss @@ -160,4 +160,10 @@ div.synonym-change-request button { .concepts-mapping-count .d-flex{ display: inline !important; -} \ No newline at end of file +} + +.concepts_json_button{ + margin-right: 5px; + margin-top: -4px; +} + diff --git a/app/assets/stylesheets/fair_assement.scss b/app/assets/stylesheets/fair_assement.scss index ad757bee9c..4d049d521b 100644 --- a/app/assets/stylesheets/fair_assement.scss +++ b/app/assets/stylesheets/fair_assement.scss @@ -35,6 +35,7 @@ $non_applicable_color : rgba(176, 190, 197, 0.4); animation-duration: .75s; animation-timing-function: linear; animation-iteration-count: infinite; + color: var(--primary-color); } .spinner-border-reverse { diff --git a/app/assets/stylesheets/home.scss b/app/assets/stylesheets/home.scss index 327e0ed070..9965d2bfd5 100644 --- a/app/assets/stylesheets/home.scss +++ b/app/assets/stylesheets/home.scss @@ -150,7 +150,59 @@ i.fa.fa-caret-square-o-down { margin-bottom: 5px; font-weight: 700; } - +.home-section-title{ + display: flex; + flex-direction: column; + align-items: start; +} +.home-section-title .text{ + font-size: 20px; + font-weight: 600; + margin-bottom: 0; +} +.home-slice > a{ + display: flex; + align-items: center; +} +.home-slice-icon{ + display: flex; + flex-direction: column; + align-items: center; +} +.home-slice-icon svg{ + width: 40px; + height: 40px; +} +.home-slices-container{ + display: flex; + flex-wrap: wrap; + margin-top: 20px; +} +.home-section-description{ + color: #888888; +} +.home-slice{ + border: 1px solid var(--primary-color); + border-radius: 8px; + padding: 4px 15px; + margin-right: 20px; + margin-bottom: 20px; +} +.home-ontoportal-instances{ + margin-top: 50px; + background: #FBFBFB; + width: 100%; + display: flex; + justify-content: center; +} +.ontoportal-instances-container{ + padding: 0 50px; + width: 1248px; + padding-bottom: 20px; +} +.home-section-title.ontoportal{ + margin-top: 20px; +} .home-section-line{ width: 60px; margin-top: 3px; @@ -169,17 +221,26 @@ i.fa.fa-caret-square-o-down { } .home-statistics-container > div { display: flex; - align-items: center; + align-items: start; + justify-content: center; flex-wrap: wrap; } .home-agroportal-figures{ margin-bottom: 20px; } - +.home-slice-name{ + font-size: 16px; + font-weight: 400; + margin-left: 10px; +} +.home-slice-ontologies{ + font-size: 18px; + font-weight: 500; + margin-bottom: -18px; +} .home-statistics-container > div > p { font-size: 20px; font-weight: 600; - margin-left: 18px; margin-bottom: 0; } .home-statistics-item{ @@ -414,7 +475,6 @@ i.fa.fa-caret-square-o-down { } .home-support-items{ display: flex; - justify-content: center; flex-wrap: wrap; img{ object-fit: scale-down; @@ -429,8 +489,8 @@ i.fa.fa-caret-square-o-down { border-radius: 50%; display: block; } -.home-support-items > *:not(:first-child){ - margin-left: 40px; +.home-support-items > div, .home-support-items > a { + margin-right: 40px; } .home-support-items a{ margin-bottom: 40px; diff --git a/app/assets/stylesheets/login.scss b/app/assets/stylesheets/login.scss index f832c6ed00..f77d8a6b71 100644 --- a/app/assets/stylesheets/login.scss +++ b/app/assets/stylesheets/login.scss @@ -1,5 +1,5 @@ .login-form{ - margin-top: 30px; + margin-top: 10px; padding: 37px 41px; box-shadow: rgba(0, 0, 0, 0.08) 0px 20px 50px; border-radius: 14px; diff --git a/app/assets/stylesheets/mappings.scss b/app/assets/stylesheets/mappings.scss index c0a494fb07..89a7ebffbe 100644 --- a/app/assets/stylesheets/mappings.scss +++ b/app/assets/stylesheets/mappings.scss @@ -284,25 +284,9 @@ p#display_options { vertical-align: middle; } -div#mapping_load { - padding: 1em 1em 0; - margin-bottom: -1em; - display: none; - img { - vertical-align: text-bottom; - } -} -div#mappingCount { - text-align: center; - overflow: hidden; - padding-top: 10px; -} -#mapping_count_table { - width: 100%; -} /* Create New Mapping dialog */ diff --git a/app/assets/stylesheets/notice.scss b/app/assets/stylesheets/notice.scss index c691896538..93dd13e0ef 100644 --- a/app/assets/stylesheets/notice.scss +++ b/app/assets/stylesheets/notice.scss @@ -14,3 +14,26 @@ div#notice_message { } } +.slice-notice-bar-container{ + background-color: var(--warning-color); + display: flex; + justify-content: center; +} +.slice-notice-bar{ + width: var(--container-max-width); + padding: 10px 40px; + display: flex; + justify-content: space-between; + align-items: center; + color: white; +} +.slice-notice-bar>div{ + display: flex; +} +.slice-notice-bar .slice-name{ + margin-left: 5px; + font-weight: 600; +} +.slice-notice-bar .warning-button.primary-button{ + background-color: #efb300 !important; +} diff --git a/app/assets/stylesheets/ontologies.scss b/app/assets/stylesheets/ontologies.scss index afa87ae7c5..ccaf70d314 100644 --- a/app/assets/stylesheets/ontologies.scss +++ b/app/assets/stylesheets/ontologies.scss @@ -195,7 +195,7 @@ $widget-table-border-color: #EFEFEF; #bd_content .sidebar { overflow-x: auto; white-space: nowrap; - min-width: 35%; + min-width: 29%; } #search_box:focus { @@ -293,8 +293,10 @@ $widget-table-border-color: #EFEFEF; } .metadata-exporter .download-btn { position: absolute; - right: 20px; + right: 0; + top: -50px; z-index: 2; + cursor: pointer; .chip_button_container_clickable { opacity: 0.6; &:hover { @@ -303,7 +305,7 @@ $widget-table-border-color: #EFEFEF; } } -.htacess-code-container{ +.htacess-code-container, .nginx-code-container{ margin-top: 20px; margin-bottom: 30px; text-align: left; diff --git a/app/assets/stylesheets/taxonomy.scss b/app/assets/stylesheets/taxonomy.scss new file mode 100644 index 0000000000..6043973aa8 --- /dev/null +++ b/app/assets/stylesheets/taxonomy.scss @@ -0,0 +1,101 @@ +.taxonomy-page-container { + display: flex; + justify-content: center; + } +.taxonomy-page-subcontainer { + width: 1248px; + padding: 20px 50px; +} +.taxonomy-page-title .text{ + font-size: 25px; + font-weight: 700; +} + +.taxonomy-page-title .line{ + height: 2px; + width: 57px; + background-color: var(--primary-color); + border-radius: 10px; +} +.taxonomy-page-decription{ + color: #888888; + margin: 20px 0; +} +.taxonomy-section{ + display: flex; +} +.taxonomy-section .second-row{ + margin-left: 10px; +} +.taxonomy-card{ + border: 1px solid #DFDFDF; + padding: 15px 20px; + width: 569px; + border-radius: 5px; + margin-top: 10px; +} + +.taxonomy-card .title-bar{ + display: flex; + justify-content: space-between; + align-items: center; +} +.taxonomy-card .title{ + color: var(--primary-color); + font-size: 18px; + font-weight: bold; +} + +.taxonomy-card .ontologies{ + display: flex; + align-items: center; + color: var(--primary-color); + margin: 3px 0; +} +.taxonomy-card .ontologies svg{ + width: 15px; + height: 15px; + margin-right: 10px; +} + +.taxonomy-card .ontologies svg path{ + fill: var(--primary-color); +} +.taxonomy-card .description{ + color: #666666; + padding-bottom: 5px; +} +.taxonomy-slice-svg{ + width: 35px; + height: 35px; + margin-bottom: 2px; +} + +.taxonomy-children-reveal{ + display: flex; + align-items: center; + cursor: pointer; + color: var(--primary-color); +} +.taxonomy-children-reveal svg{ + margin-left: 5px; + margin-top: 3px; +} + +.taxonomy-children .taxonomy-card{ + border: none; + padding: 0px 18px; + width: unset; +} + +.taxonomy-children-container{ + display: flex; + margin-top: 10px +} + +.taxonomy-children-line{ + width: 1px; + background-color: var(--primary-color); +} + + diff --git a/app/assets/stylesheets/theme-variables.scss.erb b/app/assets/stylesheets/theme-variables.scss.erb index cca2fc4080..45e0a63c64 100644 --- a/app/assets/stylesheets/theme-variables.scss.erb +++ b/app/assets/stylesheets/theme-variables.scss.erb @@ -46,7 +46,7 @@ // common variables :root{ --error-color: #EB4335; - --warning-color: #e48c11; + --warning-color: #F2BE22; --gray-color: #888888; --success-color: #2DC54E; --admin-color: #145FF4; diff --git a/app/components/agent_search_input_component/agent_search_input_component.html.haml b/app/components/agent_search_input_component/agent_search_input_component.html.haml index 89f0fdd305..9da8101b53 100644 --- a/app/components/agent_search_input_component/agent_search_input_component.html.haml +++ b/app/components/agent_search_input_component/agent_search_input_component.html.haml @@ -1,11 +1,11 @@ = hidden_field_tag "#{@name_prefix}[#{@id}]" -= render SearchInputComponent.new(id: 'agent' + @id, name:'agent' + @id, ajax_url: "/ajax/agents?agent_type=#{@agent_type}&name=", += render SearchInputComponent.new(id: 'agent' + @id, name:'agent' + @id, ajax_url: "/ajax/agents?query=", display_all: true, item_base_url:"/agents/#{@id}?parent_id=#{@parent_id}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}&deletable=#{@deletable}&agent_id=", id_key: 'id', use_cache: false, actions_links: {create_new_agent: {link: "/agents/new?name=&id=#{@id}&parent_id=#{@parent_id}&type=#{@agent_type}&show_affiliations=#{@show_affiliations}&deletable=#{@deletable}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}[#{@id}]", target:'_self'}}) do |s| - s.template do %a{href: "LINK", class: "search-content", 'data-turbo-frame': '_self'} %p.search-element.home-searched-ontology - NAME (IDENTIFIERS) + NAME ACRONYM IDENTIFIERS %p.home-result-type - TYPE \ No newline at end of file + TYPE diff --git a/app/components/concept_details_component.rb b/app/components/concept_details_component.rb index 663e7e1887..ff275effba 100644 --- a/app/components/concept_details_component.rb +++ b/app/components/concept_details_component.rb @@ -81,7 +81,7 @@ def filter_properties(top_keys, bottom_keys, exclude_keys, concept_properties) private def link_to_format_modal(format, icon) - link_to_modal(nil, "/ontologies/#{@acronym}/#{escape(@concept_id)}/serialize/#{format}", data: {show_modal_title_value: @concept_id, show_modal_size_value: 'modal-xl'}) do + link_to_modal(nil, "/ontologies/#{@acronym}/#{escape(@concept_id)}/serialize/#{format}",{ id: "resource_content_#{format}", data: {show_modal_title_value: @concept_id, show_modal_size_value: 'modal-xl'}}) do inline_svg("icons/#{icon}.svg", width: '50px', height: '50px') end end diff --git a/app/components/concept_details_component/concept_details_component.html.haml b/app/components/concept_details_component/concept_details_component.html.haml index e42cfa8187..e8c341b8c4 100644 --- a/app/components/concept_details_component/concept_details_component.html.haml +++ b/app/components/concept_details_component/concept_details_component.html.haml @@ -26,7 +26,7 @@ - if @concept_id - t.row do |r| - r.td(colspan: 2) do - %div.d-flex.justify-content-center.p-2 + %div.d-flex.justify-content-center.p-2#content_resource_formats - [["json","json-ld-file"], ["xml","rdf-xml-file"] , ["ntriples","ntriples-file"], ["turtle","turtle-file"]].each do |format, icon| %div.mx-4{data: {controller: "tooltip"}, title: "Export in #{format.upcase}"} = link_to_format_modal(format, icon) \ No newline at end of file diff --git a/app/components/display/rdf_highlighter_component/rdf_highlighter_component_controller.js b/app/components/display/rdf_highlighter_component/rdf_highlighter_component_controller.js index 0737369702..86b8ecd3cc 100644 --- a/app/components/display/rdf_highlighter_component/rdf_highlighter_component_controller.js +++ b/app/components/display/rdf_highlighter_component/rdf_highlighter_component_controller.js @@ -103,12 +103,12 @@ export default class extends Controller { downloadJsonLd () { this.#toJSONLD().then((jsonld) => { - this.#generateDownloadFile(JSON.stringify(jsonld, null, ' '), 'nt') + this.#generateDownloadFile(JSON.stringify(jsonld, null, ' '), 'json') }) } downloadXML () { - this.#generateDownloadFile(this.#toXML(this.formatedData, this.submissionValue['context']), 'rdf') + this.#generateDownloadFile(this.#toXML(this.formatedData, this.contextValue), 'rdf') } downloadCSV () { @@ -211,7 +211,6 @@ export default class extends Controller { // TODO: change MIME type? element.setAttribute('href', 'data:application/rdf+json;charset=utf-8,' + encodeURIComponent(content)) element.setAttribute('download', jQuery(document).data().bp.ontology.acronym + '_metadata.' + fileExtension) - element.style.display = 'none' document.body.appendChild(element) element.click() diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb index 3a2505e87d..18d56a288e 100644 --- a/app/components/display/search_result_component.rb +++ b/app/components/display/search_result_component.rb @@ -1,6 +1,8 @@ class Display::SearchResultComponent < ViewComponent::Base include UrlsHelper include ModalHelper + include MultiLanguagesHelper + renders_many :subresults, Display::SearchResultComponent renders_many :reuses, Display::SearchResultComponent def initialize(number: 0,title: nil, ontology_acronym: nil ,uri: nil, definition: nil, link: nil, is_sub_component: false) diff --git a/app/components/display/search_result_component/search_result_component.html.haml b/app/components/display/search_result_component/search_result_component.html.haml index 376fbf473d..9d4d48bc08 100644 --- a/app/components/display/search_result_component/search_result_component.html.haml +++ b/app/components/display/search_result_component/search_result_component.html.haml @@ -5,9 +5,8 @@ .uri = @uri - if @definition - - @definition.each do |definition| - .definition - = definition + + = display_in_multiple_languages(@definition) .actions = details_button = visualize_button diff --git a/app/components/display/taxonomy_card_component.rb b/app/components/display/taxonomy_card_component.rb new file mode 100644 index 0000000000..df896191b6 --- /dev/null +++ b/app/components/display/taxonomy_card_component.rb @@ -0,0 +1,10 @@ +class Display::TaxonomyCardComponent < ViewComponent::Base + def initialize(taxonomy: , ontologies_names: ) + @taxonomy = taxonomy + @ontologies_names = ontologies_names + end + + def reveal_id + @taxonomy.id + end +end diff --git a/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml b/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml new file mode 100644 index 0000000000..ab55aa41de --- /dev/null +++ b/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml @@ -0,0 +1,29 @@ +.taxonomy-card{'data-controller': 'reveal-component'} + .title-bar + .title + = "#{@taxonomy.name} (#{@taxonomy.acronym})" + %a{href: "https://#{@taxonomy.acronym}.#{$UI_URL.sub("https://", "")}"} + = inline_svg_tag('icons/slices.svg', class: "taxonomy-slice-svg #{@taxonomy.is_slice ? '' : 'd-none'}") + %a.ontologies{href: "/ontologies?#{@taxonomy.id.split('/')[-2]}=#{@taxonomy.acronym}"} + = inline_svg_tag('icons/ontology.svg') + .number-of-ontologies + = "#{@taxonomy.ontologies.length} ontologies" + .description + = render TextAreaFieldComponent.new(value: @taxonomy.description) + .ontologies-cards + - @taxonomy.ontologies.each_with_index do |ontology, index| + - if index>10 + = render ChipButtonComponent.new(url: "/ontologies?#{@taxonomy.id.split('/')[-2]}=#{@taxonomy.acronym}", text: "...", tooltip:"See all ontologies ...", type: "clickable") + - break + = render ChipButtonComponent.new(url: "/ontologies/#{ontology.split('/').last}", text: ontology.split('/').last, tooltip: @ontologies_names[ontology], type: "clickable") + + - if @taxonomy.children + .taxonomy-children-reveal{'data-action': "click->reveal-component#toggle", 'data-id': reveal_id} + .text + = t('taxonomy.show_sub_categories') + = inline_svg_tag 'icons/arrow-down.svg' + .taxonomy-children-container + .taxonomy-children-line + .taxonomy-children.d-none{id: reveal_id} + - @taxonomy.children.each do |child| + = render Display::TaxonomyCardComponent.new(taxonomy: child, ontologies_names: @ontologies_names) \ No newline at end of file diff --git a/app/components/input/text_area_component.rb b/app/components/input/text_area_component.rb index 940a8b9352..04f4533376 100644 --- a/app/components/input/text_area_component.rb +++ b/app/components/input/text_area_component.rb @@ -1,8 +1,12 @@ # frozen_string_literal: true class Input::TextAreaComponent < Input::InputFieldComponent - def initialize(label: '', name:, value: nil, placeholder: '', error_message: '', helper_text: '', rows: "5") + def initialize(label: '', name:, value: nil, placeholder: '', error_message: '', helper_text: '', rows: "5", resize: nil) super(label: label, name: name, value: value, placeholder: placeholder, error_message: error_message, helper_text: helper_text) @rows = rows + @resize = resize + end + def resize + @resize ? "resize: vertical;" : "" end end diff --git a/app/components/input/text_area_component/text_area_component.html.haml b/app/components/input/text_area_component/text_area_component.html.haml index d2dd1b5d87..f00c4cffbd 100644 --- a/app/components/input/text_area_component/text_area_component.html.haml +++ b/app/components/input/text_area_component/text_area_component.html.haml @@ -1,3 +1,3 @@ = render Input::InputFieldComponent.new(label: @label, name: @name, value: @value, placeholder: @placeholder, error_message: @error_message, helper_text: @helper_text) do - %textarea.input-field-component{name: @name, rows: @rows, placeholder: @placeholder, style: error_style} + %textarea.input-field-component{name: @name, rows: @rows, placeholder: @placeholder, style: "#{error_style} #{resize}"} = @value \ No newline at end of file diff --git a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml index 61daf0e9cb..aaf97e85fd 100644 --- a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml +++ b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml @@ -16,7 +16,7 @@ = t('components.show_more') - - unless ontology[:fairScore].nil? || ontology[:acronym] == 'AGROVOC' + - unless ontology[:fairScore].nil? || ontology[:fairScore].zero? || ontology[:acronym] == 'AGROVOC' .browse-fair %p.browse-fair-title = t('components.fair_score') @@ -47,7 +47,7 @@ - if ontology[:contact] %span.mx-1= t('components.by') %span.browse-uploaded-date.text-truncate - = ontology[:contact].humanize + = ontology[:contact].titleize - if ontology[:released] - date = render DateTimeFieldComponent.new(value: ontology[:released]) diff --git a/app/components/ontology_subscribe_button_component.rb b/app/components/ontology_subscribe_button_component.rb index 9faec90aba..24edeb4093 100644 --- a/app/components/ontology_subscribe_button_component.rb +++ b/app/components/ontology_subscribe_button_component.rb @@ -15,6 +15,8 @@ def initialize(id: '', ontology_id:, subscribed:, user_id:, count: 0, link: 'jav 'subscribe-notes-ontology-id-value': ontology_id, 'subscribe-notes-is-subbed-value': subscribed.to_s, 'subscribe-notes-user-id-value': user_id, + 'subscribe-notes-watch-value': t('components.watch'), + 'subscribe-notes-unwatch-value': t('components.unwatch'), action: 'click->subscribe-notes#subscribeToNotes', }, title: title @@ -30,4 +32,8 @@ def title t('components.join_the_count', count: @count) end end + + def data_turbo + @link.include?('/login') ? 'false' : 'true' + end end diff --git a/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component.html.haml b/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component.html.haml index 9ec723388a..bf0b2add63 100644 --- a/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component.html.haml +++ b/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component.html.haml @@ -1,6 +1,6 @@ %div{@controller_params, style: 'margin-left: 10px;', id: @id} = render PillButtonComponent.new do - %a.d-flex.align-items-center{href: @link} + %a.d-flex.align-items-center{href: @link, 'data-turbo': data_turbo} = inline_svg_tag "eye.svg" %div %span{'data-subscribe-notes-target': 'text'} diff --git a/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component_controller.js b/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component_controller.js index 49d67275b9..b425c5155d 100644 --- a/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component_controller.js +++ b/app/components/ontology_subscribe_button_component/ontology_subscribe_button_component_controller.js @@ -6,7 +6,9 @@ export default class extends Controller { static values = { ontologyId: String, isSubbed: Boolean, - userId: String + userId: String, + watch: String, + unwatch: String } static targets = ["error", "loader", "text" ,"count"] @@ -39,10 +41,10 @@ export default class extends Controller { let txt = this.textTarget.innerHTML let count = parseInt(this.countTarget.innerHTML) - let newButtonText = txt.match("UnWatch") ? txt.replace("UnWatch", "Watch") : txt.replace("Watch", "UnWatch"); + let newButtonText = txt.match(this.unwatchValue) ? txt.replace(this.unwatchValue, this.watchValue) : txt.replace(this.watchValue, this.unwatchValue); this.element.setAttribute('title', newButtonText + ' this ontology') this.textTarget.innerHTML = newButtonText - this.countTarget.innerHTML = newButtonText.match("UnWatch") ? (count + 1) : (count - 1) + this.countTarget.innerHTML = newButtonText.match(this.unwatchValue) ? (count + 1) : (count - 1) }, error: () => { this.#hideSpinner() diff --git a/app/components/search_input_component.rb b/app/components/search_input_component.rb index 941b03d2ec..9390797d36 100644 --- a/app/components/search_input_component.rb +++ b/app/components/search_input_component.rb @@ -11,7 +11,8 @@ def initialize(id: '', item_base_url:, id_key:, links_target: '_top', - search_icon_type: nil) + search_icon_type: nil, + display_all: false) @id = id @name = name @placeholder = placeholder @@ -23,6 +24,7 @@ def initialize(id: '', @id_key = id_key @links_target = links_target @search_icon_type = search_icon_type + @display_all = display_all end def action_link_info(value) if value.is_a?(Hash) @@ -34,4 +36,7 @@ def action_link_info(value) def nav_icon_class @search_icon_type.eql?('nav') ? 'search-input-nav-icon' : '' end + def display_all_mode_class + @display_all ? 'search-container-scroll' : '' + end end diff --git a/app/components/search_input_component/search_input_component.html.haml b/app/components/search_input_component/search_input_component.html.haml index fb0d79f289..9d5e193840 100644 --- a/app/components/search_input_component/search_input_component.html.haml +++ b/app/components/search_input_component/search_input_component.html.haml @@ -4,7 +4,8 @@ 'data-search-input-id-key-value': @id_key, 'data-search-input-cache-value': @use_cache.to_s, 'data-search-input-scroll-down-value': @scroll_down.to_s, - 'data-search-input-selected-item-value': 0 + 'data-search-input-selected-item-value': 0, + 'data-search-input-display-all-value': @display_all } - if @search_icon_type @@ -21,7 +22,7 @@ = render Input::InputFieldComponent.new(name: @name, placeholder: @placeholder, data: {'action': 'input->search-input#search blur->search-input#blur keydown.down->search-input#arrow_down keydown.up->search-input#arrow_up keydown.enter->search-input#enter_key', 'search-input-target': 'input'}) - .search-container{'data-search-input-target': 'dropDown', 'data-action': 'mousedown->search-input#prevent'} + %div{class: "search-container #{display_all_mode_class}", 'data-search-input-target': 'dropDown', 'data-action': 'mousedown->search-input#prevent'} - @actions_links.each do |key, value| - link, target = action_link_info(value) %a.search-content#search-content{href: link, 'data-turbo-frame': target, 'data-search-input-target': 'actionLink'} diff --git a/app/components/search_input_component/search_input_component_controller.js b/app/components/search_input_component/search_input_component_controller.js index 5c8d07cad8..957dc6f049 100644 --- a/app/components/search_input_component/search_input_component_controller.js +++ b/app/components/search_input_component/search_input_component_controller.js @@ -12,7 +12,8 @@ export default class extends Controller { idKey: String, cache: {type: Boolean, default: true}, selectedItem: Number, - searchEndpoint: {type: String, default: '/search'} + searchEndpoint: {type: String, default: '/search'}, + displayAll: Boolean } connect() { @@ -114,14 +115,14 @@ export default class extends Controller { this.dropDown.innerHTML = "" let breaker = 0 for (let i = 0; i < this.items.length; i++) { - if (breaker === 4) { + if (!this.displayAllValue && breaker === 4) { break; } // Get the current item from the ontologies array const item = this.items[i]; let text = Object.values(item).reduce((acc, value) => acc + value, "") - + // Check if the item contains the substring if (!this.cacheValue || text.toLowerCase().includes(inputValue.toLowerCase())) { results_list.push(item); @@ -149,18 +150,22 @@ export default class extends Controller { #renderLine(item) { let template = this.templateTarget.content - let newElement = template.firstElementChild - let string = newElement.outerHTML - + let newElement = template.firstElementChild.outerHTML Object.entries(item).forEach( ([key, value]) => { key = key.toString().toUpperCase() if (key === 'TYPE'){ value = value.toString().split('/').slice(-1) } + if (key === 'ACRONYM'){ + value = value ? `(${value.toString()})` : '' + } + if (key === 'IDENTIFIERS'){ + value = value ? `- ${value.toString()}` : '' + } const regex = new RegExp('\\b' + key + '\\b', 'gi'); - string = string.replace(regex, value ? value.toString() : "") + newElement = newElement.replace(regex, value ? value.toString() : "") }) - - return new DOMParser().parseFromString(string, "text/html").body.firstElementChild + + return new DOMParser().parseFromString(newElement, "text/html").body.firstElementChild } } diff --git a/app/components/submission_status_component/submission_status_component.html.haml b/app/components/submission_status_component/submission_status_component.html.haml index c45bec11d8..a3cce62c7c 100644 --- a/app/components/submission_status_component/submission_status_component.html.haml +++ b/app/components/submission_status_component/submission_status_component.html.haml @@ -1,4 +1,4 @@ -#submission-status{style: "display: -webkit-inline-box"} +.submission-status{style: "display: -webkit-inline-box"} - if @submission.version.present? %p= submission_link - else diff --git a/app/components/tab_item_component.rb b/app/components/tab_item_component.rb index 7779939e6a..88f11f890a 100644 --- a/app/components/tab_item_component.rb +++ b/app/components/tab_item_component.rb @@ -4,13 +4,14 @@ class TabItemComponent < ViewComponent::Base include ActionView::Helpers::UrlHelper - def initialize(id: nil, title: nil, path: nil, page_name: '', selected: false) + def initialize(id: nil, title: nil, path: nil, page_name: '', selected: false, json_link: nil) super @id = id @title = title @path = path @page_name = page_name @selected = selected + @json_link = json_link end def selected_item? @@ -44,9 +45,9 @@ def page_name def call if title && !title.empty? - link_to(title, @path, id: "#{item_id}_tab", class: "#{active_class} tab-link") + link_to(title, @path, id: "#{item_id}_tab", class: "#{active_class} tab-link", 'data-json-link': @json_link) else - link_to(@path, id: "#{item_id}_tab", class: "#{active_class} tab-link") do + link_to(@path, id: "#{item_id}_tab", class: "#{active_class} tab-link", 'data-json-link': @json_link) do content end end diff --git a/app/components/table_component.rb b/app/components/table_component.rb index 671048038a..16bf2c0966 100644 --- a/app/components/table_component.rb +++ b/app/components/table_component.rb @@ -5,7 +5,10 @@ class TableComponent < ViewComponent::Base renders_one :header, TableRowComponent renders_many :rows, TableRowComponent - def initialize(id: '', stripped: true, borderless: false, custom_class: '', layout_fixed: false, small_text: false, outline: false, sort_column: nil, paging: false, searching: false, no_init_sort: false) + def initialize(id: '', stripped: true, borderless: false, custom_class: '', layout_fixed: false, + small_text: false, outline: false, sort_column: nil, + paging: false, searching: false, search_placeholder: nil, + no_init_sort: false) super @id = id @stripped = stripped @@ -18,6 +21,7 @@ def initialize(id: '', stripped: true, borderless: false, custom_class: '', layo @paging = paging @no_init_sort = no_init_sort @custom_class =custom_class + @search_placeholder = search_placeholder end def stripped_class diff --git a/app/components/table_component/table_component.html.haml b/app/components/table_component/table_component.html.haml index 274e4a1bdc..3bdb112da4 100644 --- a/app/components/table_component/table_component.html.haml +++ b/app/components/table_component/table_component.html.haml @@ -1,4 +1,7 @@ -%div{'data-controller': 'table-component', 'data-table-component-sortcolumn-value': @sort_column, 'data-table-component-paging-value': @paging, 'data-table-component-searching-value': @searching, 'data-table-component-noinitsort-value': @no_init_sort} +%div{'data-controller': 'table-component', + 'data-table-component-sortcolumn-value': @sort_column, 'data-table-component-paging-value': @paging, + 'data-table-component-searching-value': @searching, 'data-table-component-noinitsort-value': @no_init_sort, + 'data-table-component-search-placeholder-value': @search_placeholder} %table.table-content{id: @id ,class: @custom_class + ' ' + stripped_class + ' ' + borderless_class + ' ' + layout_fixed_class + ' ' + mini_class + ' ' + outline_class} %thead = header diff --git a/app/components/table_component/table_component_controller.js b/app/components/table_component/table_component_controller.js index 1e9f4e0d63..2032bf4499 100644 --- a/app/components/table_component/table_component_controller.js +++ b/app/components/table_component/table_component_controller.js @@ -8,7 +8,8 @@ export default class extends Controller { sortcolumn: String, paging: Boolean, searching: Boolean, - noinitsort: Boolean + noinitsort: Boolean, + searchPlaceholder: {type: String, default: 'Filter records'}, } connect(){ const table_component = this.element.querySelector('table') @@ -20,7 +21,11 @@ export default class extends Controller { info: false, searching: this.searchingValue, autoWidth: true, - order: this.noinitsortValue ? [] : [[default_sort_column, 'desc']] + order: this.noinitsortValue ? [] : [[default_sort_column, 'desc']], + language: { + search: '_INPUT_', + searchPlaceholder: this.searchPlaceholderValue + } }); } } diff --git a/app/components/tree_link_component.rb b/app/components/tree_link_component.rb index 91eb8b0540..73da902f20 100644 --- a/app/components/tree_link_component.rb +++ b/app/components/tree_link_component.rb @@ -2,7 +2,7 @@ class TreeLinkComponent < ViewComponent::Base include MultiLanguagesHelper, ModalHelper, ApplicationHelper - def initialize(child:, href:, children_href: , selected: false , data: {}, muted: false, target_frame: nil, open_in_modal: false) + def initialize(child:, href:, children_href: , selected: false , data: {}, muted: false, target_frame: nil, open_in_modal: false, is_reused: nil) @child = child @active_style = selected ? 'active' : '' #@icons = child.relation_icon(node) @@ -28,6 +28,8 @@ def initialize(child:, href:, children_href: , selected: false , data: {}, muted end @open_in_modal = open_in_modal + + @is_reused = is_reused end diff --git a/app/components/tree_link_component/tree_link_component.html.haml b/app/components/tree_link_component/tree_link_component.html.haml index c66ef71313..7317e28345 100644 --- a/app/components/tree_link_component/tree_link_component.html.haml +++ b/app/components/tree_link_component/tree_link_component.html.haml @@ -6,7 +6,9 @@ %a{id: @child.id, data: @data, title: @tooltip, href: @href, class: "tree-link #{@muted_style} #{@active_style} #{border_left} #{open?}"} = @pref_label_html - + - if @is_reused + .tree-view-reuse-icon + = inline_svg_tag 'icons/reuses.svg' - if @child.hasChildren && !@child.expanded? = render TurboFrameComponent.new(id: "#{child_id}_childs") - elsif @child.expanded? diff --git a/app/components/url_resolvability_component.rb b/app/components/url_resolvability_component.rb index 379fe49c32..adbd7bf5e4 100644 --- a/app/components/url_resolvability_component.rb +++ b/app/components/url_resolvability_component.rb @@ -12,7 +12,7 @@ def initialize(url: '', resolvable: false, supported_formats: [], status: nil) end def call - text = check_resolvability_message(@resolvable, @supported_formats, @status, @url) + text = check_resolvability_message(@resolvable, @supported_formats, @status, url: @url) if @resolvable && @supported_formats.size > 1 icon = status_icons(ok: true) elsif @resolvable diff --git a/app/controllers/admin/categories_controller.rb b/app/controllers/admin/categories_controller.rb index ffe23c076b..f2c0d3ea00 100644 --- a/app/controllers/admin/categories_controller.rb +++ b/app/controllers/admin/categories_controller.rb @@ -15,7 +15,6 @@ def index def new @category = LinkedData::Client::Models::Category.new - respond_to do |format| format.html { render "new", :layout => false } end @@ -24,7 +23,7 @@ def new def edit @category = _category @acronyms = @category.ontologies.map { |url| url.match(/\/([^\/]+)$/)[1] } - @ontologies_category = LinkedData::Client::Models::Ontology.all(include: 'acronym').map {|o|[o.acronym, o.id] } + @ontologies_category = LinkedData::Client::Models::Ontology.all(include: 'name,acronym').map {|x| ["#{x.name} (#{x.acronym})", x.id.to_s]} respond_to do |format| format.html { render "edit", :layout => false } end diff --git a/app/controllers/admin/groups_controller.rb b/app/controllers/admin/groups_controller.rb index 3fdbd5ef35..d4ae613520 100644 --- a/app/controllers/admin/groups_controller.rb +++ b/app/controllers/admin/groups_controller.rb @@ -24,7 +24,7 @@ def new def edit @group = LinkedData::Client::Models::Group.find_by_acronym(params[:id]).first @acronyms = @group&.ontologies&.map { |url| url.match(/\/([^\/]+)$/)[1] } - @ontologies_group = LinkedData::Client::Models::Ontology.all(include: 'acronym').map {|o|[o.acronym, o.id] } + @ontologies_group = LinkedData::Client::Models::Ontology.all(include: 'name,acronym').map {|x| ["#{x.name} (#{x.acronym})", x.id.to_s]} respond_to do |format| format.html { render "edit", :layout => false } end diff --git a/app/controllers/agents_controller.rb b/app/controllers/agents_controller.rb index 651c02b102..c058eb130f 100644 --- a/app/controllers/agents_controller.rb +++ b/app/controllers/agents_controller.rb @@ -18,15 +18,15 @@ def show end def ajax_agents - filters = { name: params[:name] } - filters[:agentType] = params[:agent_type] if params[:agent_type] - @agents = LinkedData::Client::Models::Agent.all(filters) - agents_json = @agents.map do |x| + filters = { query: params[:query], qf: "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10"} + @agents = LinkedData::Client::HTTP.get('/search/agents', filters) + agents_json = @agents.collection.map do |x| { - id: x.id, - name: x.name, - type: x.agentType, - identifiers: x.identifiers.map { |i| "#{i.schemaAgency}:#{i.notation}" }.join(', ') + id: x.resource_id, + name: x.name_text, + type: x.agentType_t, + identifiers: x.identifiers_texts&.join(', '), + acronym: x.acronym_text } end @@ -51,7 +51,8 @@ def create alert_id = agent_id_alert_container_id(params[:id], parent_id) deletable = params[:deletable]&.eql?('true') if new_agent.errors - render_turbo_stream alert_error(id: alert_id) { JSON.pretty_generate(response_errors(new_agent)) } + errors = generate_errors(response_errors(new_agent)) + render_turbo_stream alert_error(id: alert_id) { errors.join(', ') } else success_message = t('agents.add_agent') streams = [alert_success(id: alert_id) { success_message }] @@ -95,7 +96,8 @@ def update alert_id = agent_alert_container_id(agent, parent_id) deletable = params[:deletable]&.eql?('true') if response_error?(agent_update) - render_turbo_stream(alert_error(id: alert_id) { JSON.pretty_generate(response_errors(agent_update)) }) + errors = generate_errors(response_errors(agent_update).values.first) + render_turbo_stream alert_error(id: alert_id) { errors.join(', ') } else success_message = t('agents.update_agent') table_line_id = agent_table_line_id(agent_id(agent)) @@ -243,7 +245,7 @@ def update_agent_usages_action(agent, params) end values[attr.to_sym] = current_val.map { |x| x.id } else - values[attr.to_sym] = agent + values[attr.to_sym] = agent.id end end @@ -273,6 +275,17 @@ def agent_params v end end + p[:identifiers] = p[:identifiers].reject{ |key, value| value["notation"].empty? } + identifiers_schemaAgency = params[:agentType].eql?('person') ? 'ORCID' : 'ROR' + p[:identifiers]&.each_value do |identifier| + identifier[:schemaAgency] = identifiers_schemaAgency + if identifier[:schemaAgency].downcase.eql?('orcid') + identifier[:notation] = normalize_orcid(identifier[:notation]) + else + identifier[:notation] = normalize_ror(identifier[:notation]) + end + end + p[:identifiers] = (p[:identifiers] || {}).values p[:affiliations] = (p[:affiliations] || {}).values p[:affiliations].each do |affiliation| @@ -287,4 +300,63 @@ def find_agent_display_all(id = params[:id]) obj.id.to_s.eql?("#{rest_url}/Agents/#{id}") end.first end + + def normalize_orcid(orcid) + case orcid + when /\A\d{16}\z/ + # Case 1: 16 digits, add dashes + orcid = orcid.scan(/.{1,4}/).join('-') + + when /\A\d{4}-\d{4}-\d{4}-\d{4}\z/ + orcid = orcid + + when /\Ahttps:\/\/(www\.)?orcid\.org\/\d{4}-\d{4}-\d{4}-\d{4}\z/ + # Case 3: ORCID URL (with or without "www."), extract the numbers with dashes + orcid = orcid.split('/').last + + when /\Aorcid\.org\/\d{4}-\d{4}-\d{4}-\d{4}\z/ + # Case 4: ORCID without scheme (http/https) + orcid = orcid.split('/').last + + when /\Awww\.orcid\.org\/\d{4}-\d{4}-\d{4}-\d{4}\z/ + # Case 5: ORCID with "www." without scheme + orcid = orcid.split('/').last + end + + return orcid + end + + def normalize_ror(ror) + case ror + when /\A0\w{6}\d{2}\z/ + # Case 1: 9 characters, starting with '0', 6 alphanumeric, ending with 2 digits + ror = ror + + when /\Ahttps:\/\/ror\.org\/(0\w{6}\d{2})\z/ + # Case 2: Full URL with 'https://ror.org/', extract the ROR ID + ror = ror.split('/').last + + when /\Aror\.org\/(0\w{6}\d{2})\z/ + # Case 3: ROR without scheme (http/https), extract the ROR ID + ror = ror.split('/').last + end + + return ror + end + + def generate_errors(response_errors) + errors = [] + response_errors.values.each_with_index do |v, i| + if v[:existence] + errors << "#{response_errors.keys[i].capitalize} #{t('agents.errors.required')}" + elsif v[:unique_identifiers] + errors << t('agents.errors.used_identifier') + elsif v[:no_url] + errors << t('agents.errors.invalid_url') + else + errors << JSON.pretty_generate(response_errors) + end + end + return errors + end end diff --git a/app/controllers/ajax_proxy_controller.rb b/app/controllers/ajax_proxy_controller.rb deleted file mode 100644 index 37de212888..0000000000 --- a/app/controllers/ajax_proxy_controller.rb +++ /dev/null @@ -1,86 +0,0 @@ -require 'open-uri' -require 'net/http' -require 'uri' -require 'cgi' - -class AjaxProxyController < ApplicationController - - - def get - - page = open(params[:url]) - content = page.read - render :text => content - - end - - def jsonp - if params[:apikey].nil? || params[:apikey].empty? - render_json '{ "error": "Must supply apikey" }' - return - end - - if params[:path].nil? || params[:path].empty? - render_json '{ "error": "Must supply path" }' - return - end - - url = URI.parse($LEGACY_REST_URL + params[:path]) - url.port = $REST_PORT.to_i - full_path = (url.query.blank?) ? url.path : "#{url.path}?#{url.query}" - full_path = full_path.include?("?") ? full_path + "&apikey=#{params[:apikey]}&userapikey=#{params[:userapikey]}" : full_path + "?apikey=#{params[:apikey]}&userapikey=#{params[:userapikey]}" - http = Net::HTTP.new(url.host, url.port) - headers = { "Accept" => "application/json" } - res = http.get(full_path, headers) - response = res.code.to_i >= 400 ? { :status => res.code.to_i, :body => res.body }.to_json : res.body - render_json response, {:status => 200} - end - - def json_class - concept_not_found if params[:conceptid].nil? || params[:conceptid].empty? - params[:ontology] ||= params[:ontologyid] - - if params[:ontologyid].to_i > 0 - params_cleanup_new_api() - stop_words = ["controller", "action", "ontologyid"] - redirect_to "#{request.path}#{params_string_for_redirect(params, stop_words: stop_words)}", :status => :moved_permanently - return - end - - @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first - ontology_not_found(params[:ontology]) if @ontology.nil? - - @concept = @ontology.explore.single_class({}, params[:conceptid]) - concept_not_found(params[:conceptid]) if @concept.nil? - - render_json @concept.to_json - end - - - def json_ontology - @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first - ontology_not_found(params[:ontology]) if @ontology.nil? - simple_ontology = simplify_ontology_model(@ontology) # application_controller (cached) - render_json simple_ontology.to_json - end - - - private - - def render_json(json, options={}) - callback, variable = params[:callback], params[:variable] - response = begin - if callback && variable - "var #{variable} = #{json};\n#{callback}(#{variable});" - elsif variable - "var #{variable} = #{json};" - elsif callback - "#{callback}(#{json});" - else - json - end - end - render({plain: response, content_type: "application/json"}.merge(options)) - end - -end diff --git a/app/controllers/annotator_controller.rb b/app/controllers/annotator_controller.rb index 6f1ec810b8..a1a4011d37 100644 --- a/app/controllers/annotator_controller.rb +++ b/app/controllers/annotator_controller.rb @@ -72,8 +72,23 @@ def annotator_results(uri) else @results_table_header.push(t('annotator.score')) end + + # if we are in a slice, pass the ontologies of this slice in the params + + if at_slice? + slice_ontologies_acronyms = @subdomain_filter[:ontologies].map{ |id| link_last_part(id)} + if api_params[:ontologies] + selected_ontolgies = api_params[:ontologies].split(',') + filtred_ontologies = selected_ontolgies.select{ |ontology| slice_ontologies_acronyms.include?(ontology) } + else + filtred_ontologies = slice_ontologies_acronyms + end + api_params[:ontologies] = filtred_ontologies.join(',') + end + annotations = LinkedData::Client::HTTP.get(uri, api_params) - @ontologies = get_simplified_ontologies_hash + @ontologies = LinkedData::Client::Models::Ontology.all({:include_views => true}).map{ |o| [o.id.to_s, o]}.to_h + @semantic_types = get_semantic_types @results = [] annotations.each do |annotation| @@ -161,14 +176,14 @@ def get_semantic_types end def annotation_class_info(cls) - return { + { text: cls.prefLabel, link: url_to_endpoint(cls.links["self"]) } end def annotation_ontology_info(ontology_url) - return { - text: @ontologies[ontology_url][:name], + { + text: @ontologies[ontology_url].name, link: url_to_endpoint(ontology_url) } end @@ -201,6 +216,7 @@ def empty_advanced_options params[:fast_context].nil? && params[:lemmatize].nil? end + def remove_special_chars(input) regex = /^[a-zA-Z0-9\s]*$/ diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index 04215413c9..f75a395b75 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -22,7 +22,7 @@ def self.t(*args) end # Sets the locale based on the locale cookie or the value returned by detect_locale. - def set_locale + def set_locale I18n.locale = cookies[:locale] || detect_locale cookies.permanent[:locale] = I18n.locale if cookies[:locale].nil? logger.debug "* Locale set to '#{I18n.locale}'" @@ -30,7 +30,7 @@ def set_locale end # Returns detedted locale based on the Accept-Language header of the request or the default locale if none is found. - def detect_locale + def detect_locale languages = request.headers['Accept-Language']&.split(',') supported_languages = I18n.available_locales @@ -38,10 +38,10 @@ def detect_locale language_code = language.split(/[-;]/).first.downcase.to_sym return language_code if supported_languages.include?(language_code) end - - return I18n.default_locale + + return I18n.default_locale end - + helper :all # include all helpers, all the time helper_method :bp_config_json, :current_license, :using_captcha? @@ -53,15 +53,6 @@ def detect_locale # Pull configuration parameters for REST connection. REST_URI = $REST_URL API_KEY = $API_KEY - PROXY_URI = $PROXY_URL - REST_URI_BATCH = REST_URI + '/batch' - - # Rails.cache expiration - EXPIRY_RI_STATS = 60 * 60 * 24 # 24:00 hours - EXPIRY_RI_ONTOLOGIES = 60 * 60 * 24 # 24:00 hours - EXPIRY_SEMANTIC_TYPES = 60 * 60 * 24 # 24:00 hours - EXPIRY_RECENT_MAPPINGS = 60 * 60 # 1:00 hours - EXPIRY_ONTOLOGY_SIMPLIFIED = 60 * 1 # 0:01 minute $DATA_CATALOG_VALUES = {"fairsharing.org/" => "FAIRsharing", @@ -90,13 +81,12 @@ def detect_locale # 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 invalidate_cache? params[:invalidate_cache] && params[:invalidate_cache].to_s.eql?('true') end - def show_image_modal url = params[:url] render turbo_stream: helpers.prepend('application_modal_content') { helpers.image_tag(url, style:'width: 100%') } @@ -133,14 +123,13 @@ def domain_ontology_set @subdomain_filter[:active] = true @subdomain_filter[:name] = slice.name @subdomain_filter[:acronym] = slice.acronym + @subdomain_filter[:ontologies] = slice.ontologies end end Thread.current[:slice] = @subdomain_filter end - - def ontology_not_found(ontology_acronym) not_found(t('application.ontology_not_found',acronym: ontology_acronym)) end @@ -158,14 +147,6 @@ def not_found(message = '') raise ActiveRecord::RecordNotFound.new(message || t('application.not_found_message')) end - NOTIFICATION_TYPES = { :notes => "CREATE_NOTE_NOTIFICATION", :all => "ALL_NOTIFICATION" } - - def to_param(name) # Paramaterizes URLs without encoding - unless name.nil? - name.to_s.gsub(' ',"_") - end - end - def bp_config_json # For config settings, see # config/bioportal_config.rb @@ -191,37 +172,9 @@ def bp_config_json config.to_json end - def rest_url helpers.rest_url end - - def check_http_file(url) - session = Net::HTTP.new(url.host, url.port) - session.use_ssl = true if url.port == 443 - session.start do |http| - response_valid = http.head(url.request_uri).code.to_i < 400 - return response_valid - end - end - - def check_ftp_file(uri) - ftp = Net::FTP.new(uri.host, uri.user, uri.password) - ftp.login - begin - file_exists = ftp.size(uri.path) > 0 - rescue - # Check using another method - path = uri.path.split("/") - filename = path.pop - path = path.join("/") - ftp.chdir(path) - files = ftp.dir - # Dumb check, just see if the filename is somewhere in the list - files.each { |file| return true if file.include?(filename) } - end - file_exists - end def parse_response_body(response) return nil if response.nil? @@ -285,55 +238,6 @@ def redirect_to_home # Redirect to Home Page redirect_to "/" end - - def redirect_new_api(class_view = false) - # Hack to make ontologyid and conceptid work in addition to id and ontology params - params[:ontology] = params[:ontology].nil? ? params[:ontologyid] : params[:ontology] - # Error checking - if params[:ontology].nil? || params[:id] && params[:ontology].nil? - @error = t('application.provide_ontology_or_concept') - return - end - acronym = BpidResolver.id_to_acronym(params[:ontology]) - ontology_not_found(params[:ontology]) unless acronym - if class_view - @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first - concept = get_class(params).first.to_s - redirect_to "/ontologies/#{acronym}?p=classes#{params_string_for_redirect(params, prefix: "&")}", :status => :moved_permanently - else - redirect_to "/ontologies/#{acronym}#{params_string_for_redirect(params)}", :status => :moved_permanently - end - end - - def params_cleanup_new_api - params = @_params - if params[:ontology] && params[:ontology].to_i > 0 - params[:ontology] = BpidResolver.id_to_acronym(params[:ontology]) - end - - params - end - - def params_string_for_redirect(params, options = {}) - prefix = options[:prefix] || "?" - stop_words = options[:stop_words] || ["ontology", "controller", "action", "id", "acronym"] - params_array = [] - params.each do |key,value| - next if stop_words.include?(key.to_s) || value.nil? || value.empty? - params_array << "#{key}=#{CGI.escape(value)}" - end - 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 unless session[:user] @@ -341,7 +245,6 @@ def authorize_and_redirect end end - def authorize_admin admin = session[:user] && session[:user].admin? redirect_to_home unless admin @@ -356,7 +259,6 @@ def ontology_restricted?(acronym) restrict_downloads.include? acronym end - def check_delete_mapping_permission(mappings) # ensure mappings is an Array of mappings (some calls may provide only a single mapping instance) mappings = [mappings] if mappings.instance_of? LinkedData::Client::Models::Mapping @@ -465,7 +367,6 @@ def get_class(params) @concept end - def get_ontology_submission_ready(ontology) # Get the latest 'ready' submission submission = ontology.explore.latest_submission({:include_status => 'ready'}) @@ -474,121 +375,6 @@ def get_ontology_submission_ready(ontology) return submission end - def get_simplified_ontologies_hash() - # Note the simplify_ontology_model will cache individual ontology data. - simple_ontologies = {} - begin - ontology_models = LinkedData::Client::Models::Ontology.all({:include_views => true}) - ontology_models.each {|o| simple_ontologies[o.id] = simplify_ontology_model(o) } - rescue Exception => e - LOG.add :error, e.message - return nil - end - return simple_ontologies - end - - - - def simplify_classes(classes) - # Simplify the classes batch service data for the UI - # It takes a list of class objects (hashes or models) and the - # data structure returned is a hash of class hashes, which will - # contain details for the ontology they belong to. For example: - #{ - # "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12439" => { - # :id => "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12439", - # :ui => "http://ncbo-stg-app-12.stanford.edu/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C12439", - # :uri => "http://stagedata.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C12439", - # :prefLabel => "Brain", - # :ontology => { - # :id => "http://stagedata.bioontology.org/ontologies/NCIT", - # :uri => "http://stagedata.bioontology.org/ontologies/NCIT", - # :acronym => "NCIT", - # :name => "National Cancer Institute Thesaurus", - # :ui => "http://ncbo-stg-app-12.stanford.edu/ontologies/NCIT" - # }, - # }, - #} - @ontologies_hash ||= get_simplified_ontologies_hash - classes_hash = {} - classes.each do |cls| - c = simplify_class_model(cls) - c[:ontology] = @ontologies_hash[ c[:ontology] ] - classes_hash[c[:id]] = c - end - return classes_hash - end - - def simplify_class_model(cls_model) - # Simplify the class required required by the UI. - # No modification of the class ontology here, see simplify_classes. - # Default simple class model - cls = { :id => nil, :ontology => nil, :prefLabel => nil, :uri => nil, :ui => nil, :obsolete => false } - begin - if cls_model.instance_of? Hash - cls = { - :id => cls_model['@id'], - :ui => cls_model['links']['ui'], - :uri => cls_model['links']['self'], # different from id - :ontology => cls_model['links']['ontology'] - } - # Try to carry through a prefLabel and the obsolete attribute, if they exist. - cls[:prefLabel] = cls_model['prefLabel'] - cls[:obsolete] = cls_model['obsolete'] || false - else - # try to work with a struct object or a LinkedData::Client::Models::Class - # if not a struct, then: cls_model.instance_of? LinkedData::Client::Models::Class - cls = { - :id => cls_model.id, - :ui => cls_model.links['ui'], - :uri => cls_model.links['self'], # different from id - :ontology => cls_model.links['ontology'], - } - # Try to carry through a prefLabel and the obsolete attribute, if they exist. - cls[:prefLabel] = cls_model.prefLabel if cls_model.respond_to?('prefLabel') - cls[:obsolete] = cls_model.respond_to?('obsolete') && cls_model.obsolete || false - end - rescue Exception => e - LOG.add :error, e.message - LOG.add :error, t('application.error_simplify_class', cls: cls) - end - return cls - end - - def simplify_ontology_model(ont_model) - id = nil - if ont_model.instance_of? Hash - id = ont_model['@id'] - elsif ont_model.instance_of? LinkedData::Client::Models::Ontology - id = ont_model.id - end - ont = Rails.cache.read(id) - return ont unless ont.nil? - # No cache or it has expired - LOG.add :debug, t('application.no_cache', id: id) - ont = {} - ont[:id] = id - ont[:uri] = id - if ont_model.instance_of? Hash - ont[:acronym] = ont_model['acronym'] - ont[:name] = ont_model['name'] - ont[:ui] = ont_model['links']['ui'] - else - # try to work with a struct object or a LinkedData::Client::Models::Ontology - # if not a struct, then: ont_model.instance_of? LinkedData::Client::Models::Ontology - ont[:acronym] = ont_model.acronym - ont[:name] = ont_model.name - ont[:ui] = ont_model.links['ui'] - end - # Only cache a complete representation of a simplified ontology - if ont[:id].nil? || ont[:uri].nil? || ont[:acronym].nil? || ont[:name].nil? || ont[:ui].nil? - raise t('application.incomplete_simple_ontology', id: id, ont: ont) - else - Rails.cache.write(ont[:id], ont, expires_in: EXPIRY_ONTOLOGY_SIMPLIFIED) - end - return ont - end - def get_apikey() apikey = API_KEY if session[:user] @@ -597,72 +383,9 @@ def get_apikey() return apikey end - def parse_json(uri) - uri = URI.parse(uri) - begin - response = open(uri, "Authorization" => "apikey token=#{get_apikey}").read - rescue Exception => error - @retries ||= 0 - if @retries < 1 # retry once only - @retries += 1 - retry - else - raise error - end - end - JSON.parse(response) - end - - - def get_batch_results(params) - begin - response = RestClient.post REST_URI_BATCH, params.to_json, :content_type => :json, :accept => :json, :authorization => "apikey token=#{get_apikey}" - rescue Exception => error - @retries ||= 0 - if @retries < 1 # retry once only - @retries += 1 - retry - else - LOG.add :error, "\nERROR: batch POST, uri: #{REST_URI_BATCH}" - LOG.add :error, "\nERROR: batch POST, params: #{params.to_json}" - LOG.add :error, "\nERROR: batch POST, error response: #{error.response}" - raise error - end - end - response - end - - # Get the latest manual mappings - # All mapping classes are bidirectional. - # Each class in the list maps to all other classes in the list. - def get_recent_mappings - recent_mappings = { - :mappings => [], - :classes => {} - } - begin - recent_url = "#{REST_URI}/mappings/recent/" - cached_mappings_key = recent_url - cached_mappings = Rails.cache.read(cached_mappings_key) - return cached_mappings unless (cached_mappings.nil? || cached_mappings.empty?) - # No cache or it has expired - class_details = {} - mappings = LinkedData::Client::HTTP.get(recent_url, {size: 20, display: "prefLabel"}) - recent_mappings[:mappings] = mappings - unless mappings.nil? || mappings.empty? - # Only cache a successful retrieval - Rails.cache.write(cached_mappings_key, recent_mappings, expires_in: EXPIRY_RECENT_MAPPINGS) - end - rescue Exception => e - LOG.add :error, e.message - # leave recent mappings empty. - end - return recent_mappings - end - def total_mapping_count total_count = 0 - + begin stats = LinkedData::Client::HTTP.get("#{REST_URI}/mappings/statistics/ontologies") unless stats.blank? @@ -674,7 +397,7 @@ def total_mapping_count rescue LOG.add :error, e.message end - + return total_count end @@ -698,7 +421,7 @@ def init_trial_license $trial_license_initialized = true end end - + # Get the submission metadata from the REST API. def submission_metadata @metadata ||= helpers.submission_metadata diff --git a/app/controllers/collections_controller.rb b/app/controllers/collections_controller.rb index 14f6979025..31b5db7786 100644 --- a/app/controllers/collections_controller.rb +++ b/app/controllers/collections_controller.rb @@ -6,8 +6,7 @@ def index acronym = params[:ontology] @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first ontology_not_found(acronym) if @ontology.nil? - - + @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri') collection_id = params[:collectionid] @collection = get_collection(@ontology, collection_id) if collection_id @@ -31,7 +30,8 @@ def index next_page_url: "/ontologies/#{@ontology.acronym}/collections", child_url: "/ontologies/#{@ontology.acronym}/collections/show", child_turbo_frame: 'collection', child_param: :collectionid, - results: results, next_page: next_page, total_count: total_count + results: results, next_page: next_page, + total_count: total_count ) end end @@ -53,6 +53,7 @@ def show_label def show_members @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id] || params[:ontology]).first + @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri') @collection = get_request_collection page = params[:page] || '1' @auto_click = page.to_s.eql?('1') diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb index 96a5fd0b70..196a61f97d 100644 --- a/app/controllers/concepts_controller.rb +++ b/app/controllers/concepts_controller.rb @@ -4,6 +4,7 @@ class ConceptsController < ApplicationController include MappingsHelper include ConceptsHelper include TurboHelper + include TermsReuses layout 'ontology' @@ -44,9 +45,7 @@ def index @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first @ob_instructions = helpers.ontolobridge_instructions_template(@ontology) - # Get the latest 'ready' submission, or fallback to any latest submission - # TODO: change the logic here if the fallback will crash the visualization - @submission = get_ontology_submission_ready(@ontology) # application_controller + @submission = @ontology.explore.latest_submission(include: 'all') @concept = @ontology.explore.single_class({full: true}, params[:id]) concept_not_found(params[:id]) if @concept.nil? @@ -57,7 +56,7 @@ def index render turbo_stream: [ replace(helpers.child_id(@concept) + '_open_link') { TreeLinkComponent.tree_close_icon }, replace(helpers.child_id(@concept) + '_childs') do - helpers.concepts_tree_component(@concept, @concept, @ontology.acronym, Array(@schemes), request_lang, sub_tree: true) + helpers.concepts_tree_component(@concept, @concept, @ontology.acronym, Array(@schemes), request_lang, sub_tree: true, submission: @submission) end ] end @@ -66,41 +65,24 @@ def show_label cls_id = params[:concept] || params[:id] # cls_id should be a full URI ont_id = params[:ontology] # ont_id could be a full URI or an acronym - if ont_id.to_i > 0 - params_cleanup_new_api() - stop_words = ["controller", "action"] - redirect_to "#{request.path}#{params_string_for_redirect(params, stop_words: stop_words)}", :status => :moved_permanently - return - end - render LabelLinkComponent.inline(cls_id, helpers.main_language_label(concept_label(ont_id, cls_id))) end def show_definition - if params[:ontology].to_i > 0 - params_cleanup_new_api() - stop_words = ["controller", "action"] - redirect_to "#{request.path}#{params_string_for_redirect(params, stop_words: stop_words)}", :status => :moved_permanently - return - end + @ontology = LinkedData::Client::Models::Ontology.find(params[:ontology]) cls = @ontology.explore.single_class(params[:concept]) render :text => cls.definition end def show_tree - if params[:ontology].to_i > 0 - params_cleanup_new_api() - stop_words = ["controller", "action"] - redirect_to "#{request.path}#{params_string_for_redirect(params, stop_words: stop_words)}", :status => :moved_permanently - return - end @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first + @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri') if @ontology.nil? || @ontology.errors ontology_not_found(params[:ontology]) else get_class(params) #application_controller - + not_found(t('concepts.missing_roots')) if @root.nil? render inline: helpers.concepts_tree_component(@root, @concept, @@ -114,6 +96,7 @@ def show_date_sorted_list if @ontology.nil? ontology_not_found(params[:ontology]) else + @submission = @ontology.explore.latest_submission(include: 'uriRegexPattern,preferredNamespaceUri') page = params[:page] @last_date = params[:last_date] auto_click = page.to_s.eql?('1') @@ -139,12 +122,6 @@ def show_date_sorted_list end def property_tree - if params[:ontology].to_i > 0 - params_cleanup_new_api() - stop_words = ["controller", "action"] - redirect_to "#{request.path}#{params_string_for_redirect(params, stop_words: stop_words)}", :status => :moved_permanently - return - end @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first ontology_not_found(params[:ontology]) if @ontology.nil? @root = @ontology.property_tree @@ -153,15 +130,7 @@ def property_tree # Renders a details pane for a given ontology/concept def details - concept_not_found('') if params[:conceptid].nil? || params[:conceptid].empty? - - if params[:ontology].to_i > 0 - orig_id = params[:ontology] - params_cleanup_new_api() - options = {stop_words: ["controller", "action", "id"]} - redirect_to "#{request.path.sub(orig_id, params[:ontology])}#{params_string_for_redirect(params, options)}", :status => :moved_permanently - return - end + concept_not_found(params[:conceptid]) if params[:conceptid].blank? @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first ontology_not_found(params[:ontology]) if @ontology.nil? @@ -169,12 +138,8 @@ def details @concept = @ontology.explore.single_class({full: true}, CGI.unescape(params[:conceptid])) concept_not_found(CGI.unescape(params[:conceptid])) if @concept.nil? || @concept.errors @container_id = params[:modal] ? 'application_modal_content' : 'concept_details' - - if params[:styled].eql?("true") - render :partial => "details", :layout => "partial" - else - render :partial => "details" - end + + render :partial => "details" end diff --git a/app/controllers/concerns/ontology_updater.rb b/app/controllers/concerns/ontology_updater.rb index 71672178cc..e0e9585d59 100644 --- a/app/controllers/concerns/ontology_updater.rb +++ b/app/controllers/concerns/ontology_updater.rb @@ -47,7 +47,8 @@ def show_new_errors(object, redirection = 'ontologies/new') @selected_attributes = (Array(errors_attributes) + Array(params[:submission]&.keys)).uniq @ontology = ontology_from_params if @ontology.nil? - @submission = submission_from_params(params[:submission]) if params[:submission] && @submission.nil? + @submission = submission_from_params(params[:submission]) if params[:submission] && (@submission.nil? || @submission.errors) + reset_agent_attributes if redirection.is_a?(Hash) && redirection[:id] render_turbo_stream replace(redirection[:id], partial: redirection[:partial]) @@ -86,7 +87,10 @@ def update_submission_hash(acronym) def reset_agent_attributes helpers.agent_attributes.each do |attr| current_val = @submission[attr] - new_values = Array(current_val).map { |x| LinkedData::Client::Models::Agent.find(x.split('/').last) } + new_values = Array(current_val).map do |x| + next x if x.is_a?(LinkedData::Client::Models::Agent) + LinkedData::Client::Models::Agent.find(x.split('/').last) + end new_values = new_values.first unless current_val.is_a?(Array) diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb index c18e70ce45..d50d369a8f 100644 --- a/app/controllers/concerns/search_aggregator.rb +++ b/app/controllers/concerns/search_aggregator.rb @@ -1,5 +1,5 @@ module SearchAggregator - include UrlsHelper + include UrlsHelper, MultiLanguagesHelper extend ActiveSupport::Concern BLACKLIST_FIX_STR = [ "https://", @@ -50,33 +50,35 @@ def format_search_result(result, ontologies) private + def search_concept_label(label) + label = language_hash(label) + + if label.is_a?(Hash) + label = label.values.flatten + label = label.select do |pref_lab| + pref_lab.downcase.include?(@search_query.downcase) || @search_query.downcase.include?(pref_lab.downcase) + end.first || label.first + end + + label + end def search_result_elem(class_object, ontology_acronym, title) - label = concept_label(class_object.prefLabel) + + label = search_concept_label(class_object.prefLabel) + { uri: class_object.id.to_s, - title: title.empty? ? label : "#{label} - #{title}", + title: title.nil? || title.empty? ? "#{label} - #{ontology_acronym}" : "#{label} - #{title}", ontology_acronym: ontology_acronym, link: "/ontologies/#{ontology_acronym}?p=classes&conceptid=#{escape(class_object.id)}#{helpers.request_lang&.eql?("ALL") ? '' : "&language="+helpers.request_lang.to_s}", - definition: Array(class_object.definition) + definition: class_object.definition } end - def concept_label(pref_labels_list, obsolete = false, max_length = 60) - # select closest to query - selected = pref_labels_list.select do |pref_lab| - pref_lab.downcase.include?(@search_query.downcase) || @search_query.downcase.include?(pref_lab.downcase) - end.first - - selected ||= (pref_labels_list&.first || '') - - selected = selected[0..max_length] if selected.size > max_length - selected = "#{selected}".html_safe if obsolete - selected - end def ontology_name_acronym(ontologies, selected_acronym) ontology = ontologies.select { |x| x.acronym.eql?(selected_acronym.split('/').last) }.first - "#{ontology.name} (#{ontology.acronym})" + "#{ontology.name} (#{ontology.acronym})" if ontology end def aggregate_by_ontology(results) diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb index 44d4f6e52f..45746e36e2 100644 --- a/app/controllers/concerns/submission_filter.rb +++ b/app/controllers/concerns/submission_filter.rb @@ -61,8 +61,8 @@ def submissions_paginate_filter(params) [@page.collection, @page.totalCount, count, filter_params] end - def ontologies_filter_url(filters, page: 1, count: false) - helpers.ontologies_filter_url(filters, page: page, count: count) + def ontologies_with_filters_url(filters, page: 1, count: false) + helpers.ontologies_with_filters_url(filters, page: page, count: count) end private diff --git a/app/controllers/concerns/terms_reuses.rb b/app/controllers/concerns/terms_reuses.rb new file mode 100644 index 0000000000..82eef51c9d --- /dev/null +++ b/app/controllers/concerns/terms_reuses.rb @@ -0,0 +1,15 @@ +module TermsReuses + extend ActiveSupport::Concern + + def concept_reused?(submission: nil, concept_id: nil) + uri_regex_pattern?(submission, concept_id) || preffered_namespace_uri?(submission, concept_id) + end + + private + def uri_regex_pattern?(submission, concept_id) + !(concept_id =~ Regexp.new(submission&.uriRegexPattern || '')) + end + def preffered_namespace_uri?(submission, concept_id) + !(concept_id.include?(submission&.preferredNamespaceUri || '')) + end +end diff --git a/app/controllers/concerns/uri_redirection.rb b/app/controllers/concerns/uri_redirection.rb index 9ef86fcd4d..f250e5c720 100644 --- a/app/controllers/concerns/uri_redirection.rb +++ b/app/controllers/concerns/uri_redirection.rb @@ -21,11 +21,29 @@ def redirect_to_file? end def redirect_to_file - # when dont have the specified format in the accept header - return not_acceptable("Invalid requested format, valid format are: JSON, XML, HTML and CSV\nto download the original file you can get it from: #{rest_url}/ontologies/#{params[:id]}/download\n") if accept_header.nil? + # check for hasOntologySyntax field for turtle format + ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first + ontology_syntax = ontology.explore.latest_submission(include: 'hasOntologySyntax').hasOntologySyntax + return not_acceptable("Invalid requested format, valid format are: HTML, JSON, XML, CSV.\nNTriples and Turtle format is available for some resources\nYou can download the original file you can get it from: #{rest_url}/ontologies/#{params[:id]}/download\n") if accept_header.nil? || (ontology_syntax != "http://www.w3.org/ns/formats/Turtle" && accept_header== "text/turtle") || (ontology_syntax != "http://www.w3.org/ns/formats/N-Triples" && accept_header== "application/ntriples") + # when the format is different than text/html - redirect_to_download_file if (accept_header != "text/html" && params[:p].nil?) + download_ontology(acronym: params[:id], format: accept_header) if (accept_header != "text/html" && params[:p].nil?) + end + + def download_ontology(params) + redirect_url = "#{rest_url}/ontologies/#{params[:acronym]}" + download_url = "#{redirect_url}/download?apikey=#{get_apikey}" + case params[:format] + when 'text/csv', 'csv' + fetch_and_forward_data("#{download_url}&download_format=csv") + when 'text/xml', 'text/rdf+xml', 'application/rdf+xml', 'application/xml', 'xml' + fetch_and_forward_data("#{download_url}&download_format=rdf") + when 'application/json', 'application/ld+json', 'application/*', 'json' + fetch_and_forward_data("#{redirect_url}?apikey=#{get_apikey}") + else + fetch_and_forward_data(download_url) + end end private @@ -56,8 +74,10 @@ def not_acceptable(message = nil) render plain: message, status: 406 end - def redirect_to_download_file - redirect_to("/ontologies/#{params[:id]}/download?format=#{helpers.escape(accept_header)}", allow_other_host: true) + def fetch_and_forward_data(url) + uri = URI.parse(url) + response = Net::HTTP.get_response(uri) + send_data response.body, type: response.content_type, status: response.code.to_i end @@ -86,8 +106,12 @@ def find_content_type_for_media_range(media_range) 'application/ld+json' when 'text/xml', 'text/rdf+xml', 'application/rdf+xml', 'application/xml' 'application/rdf+xml' + when 'application/ntriples', 'application/n-triples' + 'application/ntriples' when 'text/csv' 'text/csv' + when 'text/turtle' + 'text/turtle' else nil end diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb index 87f9e6e2c3..3f75bdd3f6 100644 --- a/app/controllers/home_controller.rb +++ b/app/controllers/home_controller.rb @@ -7,13 +7,20 @@ class HomeController < ApplicationController include FairScoreHelper def index - @analytics = helpers.ontologies_analytics + @analytics = helpers.ontologies_analytics # Calculate BioPortal summary statistics - @ont_count = @analytics.keys.size + + @ont_count = if @analytics.empty? + LinkedData::Client::Models::Ontology.all.size + else + @analytics.keys.size + end + metrics = LinkedData::Client::Models::Metrics.all metrics = metrics.each_with_object(Hash.new(0)) do |h, sum| h.to_hash.slice(:classes, :properties, :individuals).each { |k, v| sum[k] += v } end + @slices = LinkedData::Client::Models::Slice.all @cls_count = metrics[:classes] @individuals_count = metrics[:individuals] @@ -39,6 +46,11 @@ def index end + def set_cookies + cookies.permanent[:cookies_accepted] = params[:cookies] if params[:cookies] + render 'cookies', layout: nil + end + def tools @tools = { search: { @@ -135,32 +147,11 @@ def site_config render json: bp_config_json end - def account - @title = t('home.account_title') - if session[:user].nil? - redirect_to controller: 'login', action: 'index', redirect: '/account' - return - end - - @user = LinkedData::Client::Models::User.get(session[:user].id, include: 'all') - - @user_ontologies = @user.customOntology - @user_ontologies ||= [] - - onts = LinkedData::Client::Models::Ontology.all(include_views: true); - @admin_ontologies = onts.select { |o| o.administeredBy.include? @user.id } - - projects = LinkedData::Client::Models::Project.all - @user_projects = projects.select { |p| p.creator.include? @user.id } - - render 'users/show' - end - def feedback_complete; end def annotator_recommender_form if params[:submit_button] == "annotator" - redirect_to "/annotator?text=#{helpers.escape(params[:text])}" + redirect_to "/annotator?text=#{helpers.escape(params[:input])}" elsif params[:submit_button] == "recommender" redirect_to "/recommender?input=#{helpers.escape(params[:input])}" end diff --git a/app/controllers/instances_controller.rb b/app/controllers/instances_controller.rb index a980ccc614..70db773446 100644 --- a/app/controllers/instances_controller.rb +++ b/app/controllers/instances_controller.rb @@ -1,5 +1,5 @@ class InstancesController < ApplicationController - include InstancesHelper, SearchContent + include InstancesHelper, SearchContent, TermsReuses def index if params[:type].blank? @@ -10,7 +10,7 @@ def index end get_ontology(params) - + @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri') query, page, page_size = helpers.search_content_params results, _, next_page, total_count = search_ontologies_content(query: query, @@ -25,7 +25,7 @@ def index child_turbo_frame: 'instance_show', child_param: :instanceid, show_count: is_concept_instance, - auto_click: params[:instanceid].blank? && page.eql?(1), + auto_click: false, results: results, next_page: next_page, total_count: total_count) if is_concept_instance && page.eql?(1) @@ -50,4 +50,4 @@ def get_ontology(params) @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology] || params[:acronym] || params[:ontology_id]).first ontology_not_found(params[:ontology]) if @ontology.nil? end -end \ No newline at end of file +end diff --git a/app/controllers/mappings_controller.rb b/app/controllers/mappings_controller.rb index e6c9fabd4b..b1bcfc8c32 100644 --- a/app/controllers/mappings_controller.rb +++ b/app/controllers/mappings_controller.rb @@ -40,6 +40,7 @@ def index end @options[select_text] = ontology_acronym end + @options = @options.sort @options.unshift([]) diff --git a/app/controllers/notes_controller.rb b/app/controllers/notes_controller.rb index e088363927..04cca1e7a1 100644 --- a/app/controllers/notes_controller.rb +++ b/app/controllers/notes_controller.rb @@ -160,11 +160,6 @@ def archive end end - def show_concept_list - params[:p] = "classes" - params[:t] = "notes" - redirect_new_api - end private diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb index caec35f99e..a8c744fe4a 100644 --- a/app/controllers/ontologies_controller.rb +++ b/app/controllers/ontologies_controller.rb @@ -14,6 +14,7 @@ class OntologiesController < ApplicationController include SubmissionFilter include OntologyContentSerializer include UriRedirection + include PropertiesHelper require 'multi_json' require 'cgi' @@ -97,11 +98,12 @@ def classes def properties @acronym = @ontology.acronym @properties = LinkedData::Client::HTTP.get("/ontologies/#{@acronym}/properties/roots", { lang: request_lang }) + @property = get_property(params[:propertyid] || @properties.first.id, @acronym, include: 'all') unless @property || @properties.empty? if request.xhr? - return render 'ontologies/sections/properties', layout: false + render 'ontologies/sections/properties', layout: false else - return render 'ontologies/sections/properties', layout: 'ontology_viewer' + render 'ontologies/sections/properties', layout: 'ontology_viewer' end end @@ -152,6 +154,8 @@ def new @ontology.viewOf = params.dig(:ontology, :viewOf) @submission = LinkedData::Client::Models::OntologySubmission.new @submission.hasOntologyLanguage = 'OWL' + @submission.released = Date.today.to_s + @submission.status = 'production' @ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym', include_views: true, display_links: false, display_context: false) @categories = LinkedData::Client::Models::Category.all @groups = LinkedData::Client::Models::Group.all @@ -174,6 +178,8 @@ def notes def instances + params[:instanceid] = params[:instanceid] || search_first_instance_id + if params[:instanceid] @instance = helpers.get_instance_details_json(@ontology.acronym, params[:instanceid], {include: 'all'}) end @@ -232,22 +238,21 @@ def show else params[:conceptid] = params.delete(:purl_conceptid) end - redirect_to "/ontologies/#{params[:acronym]}?p=classes#{params_string_for_redirect(params, prefix: "&")}", status: :moved_permanently + redirect_to "/ontologies/#{params[:acronym]}?p=classes&conceptid=#{params[:conceptid]}", status: :moved_permanently return end - if params[:ontology].to_i > 0 - acronym = BPIDResolver.id_to_acronym(params[:ontology]) - if acronym - redirect_new_api + @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first + + if @ontology.nil? || @ontology.errors + if ontology_access_denied? + redirect_to "/login?redirect=/ontologies/#{params[:ontology]}", alert: t('login.private_ontology') return + else + ontology_not_found(params[:ontology]) end end - # Note: find_by_acronym includes ontology views - @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first - ontology_not_found(params[:ontology]) if @ontology.nil? || @ontology.errors - # Handle the case where an ontology is converted to summary only. # See: https://github.com/ncbo/bioportal_web_ui/issues/133. data_pages = KNOWN_PAGES - %w[summary notes] @@ -279,9 +284,6 @@ def show # This action is now a router using the 'p' parameter as the page to show case params[:p] - when 'terms' - params[:p] = 'classes' - redirect_to "/ontologies/#{params[:ontology]}#{params_string_for_redirect(params)}", status: :moved_permanently when 'classes' self.classes # rescue self.summary when 'mappings' @@ -328,13 +330,15 @@ def summary @views = get_views(@ontology) @view_decorators = @views.map { |view| ViewDecorator.new(view, view_context) } @ontology_relations_data = ontology_relations_data - - category_attributes = submission_metadata.group_by { |x| x['category'] }.transform_values { |x| x.map { |attr| attr['attribute'] } } @relations_array_display = @relations_array.map do |relation| attr = relation.split(':').last ["#{helpers.attr_label(attr, attr_metadata: helpers.attr_metadata(attr), show_tooltip: false)}(#{relation})", relation] end + @relations_array_display.unshift(['View of (bpm:viewOf)', 'bpm:viewOf']) + + category_attributes = submission_metadata.group_by { |x| x['category'] }.transform_values { |x| x.map { |attr| attr['attribute'] } } + @config_properties = properties_hash_values(category_attributes["object description properties"]) @methodology_properties = properties_hash_values(category_attributes["methodology"]) @agents_properties = properties_hash_values(category_attributes["persons and organizations"]) @@ -344,7 +348,7 @@ def summary @community_properties = properties_hash_values(category_attributes["community"] + [:notes]) @identifiers = properties_hash_values([:URI, :versionIRI, :identifier]) @identifiers["ontology_portal_uri"] = ["#{$UI_URL}/ontologies/#{@ontology.acronym}", "#{portal_name} URI"] - @projects_properties = properties_hash_values(category_attributes["usage"]) + @projects_properties = properties_hash_values(category_attributes["usage"] - ["hasDomain"]) @ontology_icon_links = [%w[summary/download dataDump], %w[summary/homepage homepage], %w[summary/documentation documentation], @@ -370,7 +374,7 @@ def subscriptions ontology_acronym = ontology_id.split('/').last if session[:user].nil? - link = "/login?redirect=#{request.url}" + link = "/login?redirect=/ontologies/#{ontology_acronym}" subscribed = false user_id = nil else @@ -379,21 +383,12 @@ def subscriptions link = "javascript:void(0);" user_id = user.id end - count = helpers.count_subscriptions(params[:ontology_id]) render inline: helpers.turbo_frame_tag('subscribe_button') { render_to_string(OntologySubscribeButtonComponent.new(id: '', ontology_id: ontology_id, subscribed: subscribed, user_id: user_id, count: count, link: link), layout: nil) } end - def virtual - redirect_new_api - end - - def visualize - redirect_new_api(true) - end - def widgets if request.xhr? render partial: 'ontologies/sections/widgets', layout: false @@ -503,7 +498,7 @@ def get_views(ontology) def ontology_relations_data(sub = @submission_latest) ontology_relations_array = [] - @relations_array = ["omv:useImports", "door:isAlignedTo", "door:ontologyRelatedTo", "omv:isBackwardCompatibleWith", "omv:isIncompatibleWith", "door:comesFromTheSameDomain", "door:similarTo", + @relations_array = ["bpm:viewOf", "omv:useImports", "door:isAlignedTo", "door:ontologyRelatedTo", "omv:isBackwardCompatibleWith", "omv:isIncompatibleWith", "door:comesFromTheSameDomain", "door:similarTo", "door:explanationEvolution", "voaf:generalizes", "door:hasDisparateModelling", "dct:hasPart", "voaf:usedBy", "schema:workTranslation", "schema:translationOfWork"] return if sub.nil? @@ -538,6 +533,11 @@ def ontology_relations_data(sub = @submission_latest) end end + if ont.viewOf + target_ont = LinkedData::Client::Models::Ontology.find(ont.viewOf) + ontology_relations_array.push({ source: ont.acronym, target: target_ont.acronym, relation: "bpm:viewOf", targetInPortal: true }) + end + ontology_relations_array end @@ -557,5 +557,15 @@ def determine_layout end end + def search_first_instance_id + query, page, page_size = helpers.search_content_params + results, _, _, _ = search_ontologies_content(query: query, + page: page, + page_size: page_size, + filter_by_ontologies: [@ontology.acronym], + filter_by_types: ["NamedIndividual"]) + results.shift # Remove the ontology entry + return !results.blank? ? results.first[:name] : nil + end end diff --git a/app/controllers/ontologies_redirection_controller.rb b/app/controllers/ontologies_redirection_controller.rb index 43269e7884..582817a908 100644 --- a/app/controllers/ontologies_redirection_controller.rb +++ b/app/controllers/ontologies_redirection_controller.rb @@ -30,64 +30,76 @@ def redirect # GET /ontologies/:acronym/htaccess def generate_htaccess ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:acronym]).first - ontology_uri = ontology.explore.latest_submission(include: 'URI').URI + subminssions_params = ontology.explore.latest_submission(include: 'URI,preferredNamespaceUri') + ontology_uri = subminssions_params.URI + preferred_name_space_uri = subminssions_params.preferredNamespaceUri ontology_portal_url = "#{$UI_URL}/ontologies/#{params[:acronym]}" - @htaccess_content = generate_htaccess_content(ontology_portal_url, ontology_uri) - @nginx_content = generate_nginx_content(ontology_portal_url, ontology_uri) + @htaccess_content = generate_htaccess_content(ontology_portal_url, ontology_uri, preferred_name_space_uri) + @nginx_content = generate_nginx_content(ontology_portal_url, ontology_uri, preferred_name_space_uri) render 'ontologies/htaccess', layout: nil end - + # GET /ontologies/ACRONYM/download?format=FORMAT def redirect_ontology - redirect_url = "#{rest_url}/ontologies/#{params[:acronym]}" - download_url = "#{redirect_url}/download?apikey=#{get_apikey}" - case params[:format] - when 'text/csv', 'csv' - redirect_to("#{download_url}&download_format=csv", allow_other_host: true) - when 'text/xml', 'text/rdf+xml', 'application/rdf+xml', 'application/xml', 'xml' - redirect_to("#{download_url}&download_format=rdf", allow_other_host: true) - when 'application/json', 'application/ld+json', 'application/*', 'json' - # redirect to the api - redirect_to("#{redirect_url}?apikey=#{get_apikey}", allow_other_host: true) - else - # redirect to download the original file - redirect_to("#{download_url}", allow_other_host: true) - end + download_ontology(params) end private - def generate_htaccess_content(ontology_portal_url, ontology_uri) - ontology_rule = nil - if ontology_uri - ontology_uri += '/' unless ontology_uri.end_with?('/') - ontology_rule = "RewriteRule ^#{URI.parse(ontology_uri).path[1..-1]}?$ #{ontology_portal_url} [R=301,L]" - end - + def generate_htaccess_content(ontology_portal_url, ontology_uri, preferred_name_space_uri) + preferred_name_space_path = get_path(preferred_name_space_uri) + ontology_uri_path = get_path(ontology_uri) + + rewrite_condition = if preferred_name_space_path + "RewriteCond %{REQUEST_URI} ^.*#{preferred_name_space_path}.*$" + elsif ontology_uri_path + "RewriteCond %{REQUEST_URI} ^.*#{ontology_uri_path}.*$" + end + + ontology_rule = if ontology_uri_path + ontology_uri_path += '/' unless ontology_uri_path.end_with?('/') + "RewriteRule ^#{ontology_uri_path}?$ #{ontology_portal_url} [R=301,L]" + end + <<-HTACCESS.strip_heredoc - RewriteEngine On - #{ontology_rule if ontology_rule} - RewriteRule ^.*/([^/#]+)$ #{ontology_portal_url}/$1 [R=301,L] + RewriteEngine On + #{ontology_rule if ontology_rule} + #{rewrite_condition if rewrite_condition} + RewriteRule ^.*/([^/#]+)/?$ #{ontology_portal_url}/$1 [R=301,L] HTACCESS end - def generate_nginx_content(ontology_portal_url, ontology_uri) - ontology_rule = nil - if ontology_uri - ontology_uri += '/' unless ontology_uri.end_with?('/') - ontology_rule = "rewrite ^#{URI.parse(ontology_uri).path[1..-1]}?$ #{ontology_portal_url} permanent" - end + def generate_nginx_content(ontology_portal_url, ontology_uri, preferred_name_space_uri) + preferred_name_space_path = get_path(preferred_name_space_uri) + ontology_uri_path = get_path(ontology_uri) + + rewrite_condition = preferred_name_space_path || ontology_uri_path + + ontology_rule = if ontology_uri_path + ontology_uri_path += '/' unless ontology_uri_path.end_with?('/') + ontology_rule = "rewrite ^/#{ontology_uri_path}?$ #{ontology_portal_url} permanent;" + end <<-NGINX.strip_heredoc location / { #{ontology_rule if ontology_rule} - if ($request_uri ~ ^.*/([^/]+)$){ - return 301 #{ontology_portal_url}/$1; + if ($request_uri ~* #{rewrite_condition} ){ + rewrite ^.*/([^/]+)/?$ #{ontology_portal_url}/$1 permanent; } } NGINX end + + def get_path(uri) + begin + parsed_uri = URI.parse(uri) + parsed_uri.path[1..-1] + rescue URI::InvalidURIError + nil + end + end + end \ No newline at end of file diff --git a/app/controllers/properties_controller.rb b/app/controllers/properties_controller.rb index 0ff2a31678..7679a7889f 100644 --- a/app/controllers/properties_controller.rb +++ b/app/controllers/properties_controller.rb @@ -1,9 +1,11 @@ class PropertiesController < ApplicationController - include TurboHelper, SearchContent + include TurboHelper, SearchContent, TermsReuses, PropertiesHelper def index acronym = params[:ontology] @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first + @submission = @ontology.explore.latest_submission(include:'uriRegexPattern,preferredNamespaceUri') + ontology_not_found(acronym) if @ontology.nil? if params[:search].blank? @@ -44,19 +46,20 @@ def show_children @property = get_property(id, acronym) @property.children = property_children(id, acronym) + @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first + @submission = @ontology.explore.latest_submission({include: 'uriRegexPattern,preferredNamespaceUri'}) + + render turbo_stream: [ replace(helpers.child_id(@property) + '_open_link') { TreeLinkComponent.tree_close_icon }, replace(helpers.child_id(@property) + '_childs') do - helpers.property_tree_component(@property, @property, acronym, request_lang, sub_tree: true) + helpers.property_tree_component(@property, @property, acronym, request_lang, sub_tree: true, submission: @submission) end ] end private - def get_property(id, acronym = params[:acronym], lang = request_lang, include: nil) - LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/#{helpers.encode_param(id)}", { lang: lang , include: include}) - end def property_tree(id, acronym = params[:acronym], lang = request_lang) LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/#{helpers.encode_param(id)}/tree", { lang: lang }) @@ -85,7 +88,6 @@ def index_tree(container_id) @property ||= @root.children.first end - render inline: helpers.property_tree_component(@root, @property, @ontology.acronym, request_lang, id: container_id, auto_click: true) diff --git a/app/controllers/schemes_controller.rb b/app/controllers/schemes_controller.rb index bea96a89d4..7fbbcc973e 100644 --- a/app/controllers/schemes_controller.rb +++ b/app/controllers/schemes_controller.rb @@ -6,9 +6,9 @@ def index acronym = params[:ontology] @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first ontology_not_found(acronym) if @ontology.nil? + @submission_latest = @submission = @ontology.explore.latest_submission(include: 'all') if params[:search].blank? - @submission_latest = @ontology.explore.latest_submission(include: 'all', invalidate_cache: invalidate_cache?) rescue @ontology.explore.latest_submission(include: '') @schemes = get_schemes(@ontology) render partial: 'schemes/tree_view' @@ -26,8 +26,8 @@ def index next_page_url: "/ontologies/#{@ontology.acronym}/schemes", child_url: "/ontologies/#{@ontology.acronym}/schemes/show", child_turbo_frame: 'scheme', child_param: :schemeid, - results: results, next_page: next_page, total_count: total_count - ) + results: results, next_page: next_page, total_count: total_count) + end end diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb index eeb510ca33..841f0f948a 100644 --- a/app/controllers/search_controller.rb +++ b/app/controllers/search_controller.rb @@ -47,11 +47,12 @@ def json_search # record_type = format_record_type(result[:recordType], result[:obsolete]) record_type = "" - target_value = result.prefLabel.select{|x| x.include?( params[:q].delete('*'))}.first || result.prefLabel.first + label = search_concept_label(result.prefLabel) + target_value = label case params[:target] when "name" - target_value = result.prefLabel + target_value = label when "shortid" target_value = result.id when "uri" @@ -132,9 +133,6 @@ def check_params_ontologies(params) else params[:ontologies] = [params[:ontologies]] end - if params[:ontologies].first.to_i > 0 - params[:ontologies].map! {|o| BpidResolver.id_to_acronym(o)} - end params[:ontologies] = params[:ontologies].join(",") end end diff --git a/app/controllers/taxonomy_controller.rb b/app/controllers/taxonomy_controller.rb new file mode 100644 index 0000000000..06832abe8b --- /dev/null +++ b/app/controllers/taxonomy_controller.rb @@ -0,0 +1,46 @@ +class TaxonomyController < ApplicationController + + layout :determine_layout + + def index + initialize_taxonomy + @category_section_active = request.path.eql?('/categories') + end + + private + + def initialize_taxonomy + @groups = LinkedData::Client::Models::Group.all + slices = LinkedData::Client::Models::Slice.all + slices_acronyms = slices.map { |slice| slice.acronym.downcase } + @groups.each do |group| + if slices_acronyms.include?(group.acronym.downcase) + group[:is_slice] = true + end + end + @categories = LinkedData::Client::Models::Category.all(display: 'name,acronym,description,ontologies,parentCategory') + @categories = nest_categories_children(@categories) + ontologies = LinkedData::Client::Models::Ontology.all + @ontologies_names = {} + ontologies.each do |o| + @ontologies_names[o.id] = o.name + end + end + + def nest_categories_children(categories) + category_index = {} + categories.each do |category| + category_index[category[:id]] = category + end + categories.each do |category| + if category.parentCategory + parent = category_index[category.parentCategory] + parent[:children] ||= [] + parent[:children] << category + end + end + categories.reject! { |category| category.parentCategory } + categories + end + +end diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb index da3a017535..a3749d4631 100644 --- a/app/controllers/users_controller.rb +++ b/app/controllers/users_controller.rb @@ -23,19 +23,23 @@ def index # GET /users/1 # GET /users/1.xml def show + @title = t('home.account_title') + if session[:user].nil? + redirect_to controller: 'login', action: 'index', redirect: '/account' + return + end @user = if session[:user].admin? && params.has_key?(:id) find_user(params[:id]) else find_user(session[:user].id) end - - @all_ontologies = LinkedData::Client::Models::Ontology.all(ignore_custom_ontologies: true) + @ontologies = LinkedData::Client::Models::Ontology.all(ignore_custom_ontologies: true); + @all_ontologies_for_select = @ontologies.map {|x| ["#{x.name} (#{x.acronym})", x.acronym]} @user_ontologies = @user.customOntology + @user_ontologies ||= [] - ## Copied from home controller , account action - onts = LinkedData::Client::Models::Ontology.all; - @admin_ontologies = onts.select {|o| o.administeredBy.include? @user.id } + @admin_ontologies = @ontologies.select {|o| o.administeredBy.include? @user.id } projects = LinkedData::Client::Models::Project.all; @user_projects = projects.select {|p| p.creator.include? @user.id } @@ -148,18 +152,15 @@ def destroy def custom_ontologies @user = find_user + custom_ontologies = params[:ontologies] || [] - custom_ontologies = params[:ontology] ? params[:ontology][:ontologyId] : [] - custom_ontologies.reject!(&:blank?) @user.update_from_params(customOntology: custom_ontologies) error_response = !@user.update - if error_response flash[:notice] = t('users.error_saving_custom_ontologies') else - updated_user = LinkedData::Client::Models::User.find(@user.id) - session[:user].update_from_params(customOntology: updated_user.customOntology) - flash[:notice] = if updated_user.customOntology.empty? + session[:user].update_from_params(customOntology: @user.customOntology) + flash[:notice] = if @user.customOntology.empty? t('users.custom_ontologies_cleared') else t('users.custom_ontologies_saved') @@ -168,7 +169,7 @@ def custom_ontologies redirect_to user_path(@user.username) end - + def subscribe @user = find_user deliver "subscribe", SubscribeMailer.register_for_announce_list(@user.email,@user.firstName,@user.lastName) @@ -180,13 +181,12 @@ def un_subscribe deliver "unsubscribe", SubscribeMailer.unregister_for_announce_list(@email) end - + private def find_user(id = params[:id]) id = helpers.unescape(id) - @user = LinkedData::Client::Models::User.find(helpers.escape(id), include: 'all') - @user ||= LinkedData::Client::Models::User.find_by_username(helpers.escape(id), include: 'all').first + @user = LinkedData::Client::Models::User.find(id.split('/').last, {include: 'all'}) not_found("User with id #{id} not found") if @user.nil? diff --git a/app/helpers/agent_helper.rb b/app/helpers/agent_helper.rb index f1a5240e23..c8212752b7 100644 --- a/app/helpers/agent_helper.rb +++ b/app/helpers/agent_helper.rb @@ -47,7 +47,7 @@ def link_to_agent_edit_modal(agent, parent_id = nil) end def link_to_agent_edit(agent, parent_id, name_prefix, deletable: false, show_affiliations: true) - link_to(edit_agent_path(agent_id(agent), name_prefix: name_prefix, deletable: deletable, parent_id: parent_id, show_affiliations: show_affiliations), class: 'btn btn-sm btn-light') do + link_to(edit_agent_path(agent_id(agent), name_prefix: name_prefix, deletable: deletable, parent_id: parent_id, show_affiliations: show_affiliations), class: 'btn btn-sm btn-light agent-edit-icon') do content_tag(:i, '', class: 'far fa-edit') end end @@ -69,7 +69,7 @@ def agent_search_input(id, agent_type, parent_id: , name_prefix:, deletable: fal end - def affiliation?(agent) + def is_organization?(agent) agent.agentType.eql?('organization') end @@ -82,6 +82,24 @@ def identifier_link(link, link_to: true) end + + def agent_identifier_input(index, name_prefix, value = '', is_organization: true) + + content_tag :div, id: index, class: 'd-flex' do + content_tag(:div, class: 'w-100') do + + concat hidden_field_tag(agent_identifier_name(index , :creator, name_prefix), session[:user].id) + if is_organization + concat inline_svg_tag 'icons/ror.svg', class: 'agent-input-icon' + else + concat inline_svg_tag('orcid.svg', class: 'agent-input-icon') + end + concat text_field_tag(agent_identifier_name(index, :notation, name_prefix), value, class: 'agent-input-with-icon') + end + end + end + + def display_identifiers(identifiers, link: true) schemes_urls = { ORCID: 'https://orcid.org/', ISNI: 'https://isni.org/', ROR: 'https://ror.org/', GRID: 'https://www.grid.ac/' } Array(identifiers).map do |i| @@ -162,8 +180,8 @@ def display_agent(agent, link: true) def agent_tooltip(agent) name = agent.name - email = agent.email - type = agent.agentType + email = agent.email unless agent.class.eql?(LinkedData::Client::Models::Agent) + type = agent.agentType identifiers = display_identifiers(agent.identifiers, link: false) identifiers = orcid_number(identifiers) if agent.affiliations && agent.affiliations != [] @@ -203,7 +221,7 @@ def generate_agent_tooltip(agent_icon, name, email = nil, identifiers = nil, aff end end end - + def agent_chip_component(agent) person_icon = inline_svg_tag 'icons/person.svg' , class: 'agent-type-icon' @@ -214,21 +232,21 @@ def agent_chip_component(agent) name = agent title = nil else - name = agent.name + name = agent.agentType.eql?("organization") ? (agent.acronym || agent.name) : agent.name agent_icon = agent.agentType.eql?("organization") ? organization_icon : person_icon title = agent_tooltip(agent) end render_chip_component(title, agent_icon, name) - end + end def render_chip_component(title,agent_icon,name) - render ChipButtonComponent.new(type: "static",'data-controller':' tooltip', title: title , class: 'text-truncate', style: 'max-width: 280px; display:block; line-height: unset') do + render ChipButtonComponent.new(type: "static",'data-controller':' tooltip', title: title , class: 'text-truncate', style: 'max-width: 280px; display:block; line-height: unset') do content_tag(:div, class: 'agent-chip') do content_tag(:div, agent_icon, class: 'agent-chip-circle') + content_tag(:div, name, class: 'agent-chip-name text-truncate') - end - end + end + end end def orcid_number(orcid) @@ -236,5 +254,5 @@ def orcid_number(orcid) end - + end diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index e768f3b952..c9fb873758 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -37,9 +37,14 @@ def search_json_link(link = @json_url, style: '') def resolve_namespaces RESOLVE_NAMESPACE end + def ontologies_analytics - data = LinkedData::Client::Analytics.last_month.onts - data.map{|x| [x[:ont].to_s, x[:views]]}.to_h + begin + data = LinkedData::Client::Analytics.last_month.onts + data.map{|x| [x[:ont].to_s, x[:views]]}.to_h + rescue StandardError + {} + end end def get_apikey @@ -75,43 +80,10 @@ def omniauth_token_provider(strategy) omniauth_provider_info(strategy.to_sym).keys.first end - def isOwner?(id) - unless session[:user].nil? - if session[:user].admin? - return true - elsif session[:user].id.eql?(id) - return true - else - return false - end - end - end - - - def encode_param(string) CGI.escape(string) end - def clean(string) - string = string.gsub("\"",'\'') - return string.gsub("\n",'') - end - - def clean_id(string) - new_string = string.gsub(":","").gsub("-","_").gsub(".","_") - return new_string - end - - def to_param(string) - "#{encode_param(string.gsub(" ","_"))}" - end - - def get_username(user_id) - user = LinkedData::Client::Models::User.find(user_id) - username = user.nil? ? user_id : user.username - username - end def current_user session[:user] @@ -126,27 +98,7 @@ def child_id(child) child.id.to_s.split('/').last end - def loading_spinner(padding = false, include_text = true) - loading_text = include_text ? t('application.loading') : "" - if padding - raw('
' + image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + loading_text + '
') - else - raw(image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + loading_text) - end - end - - - def help_icon(link, html_attribs = {}) - html_attribs["title"] ||= "Help" - attribs = [] - html_attribs.each {|k,v| attribs << "#{k.to_s}='#{v}'"} - return <<-BLOCK - - - - BLOCK - end # Create a popup button with a ? inside to display help when hovered def help_tooltip(content, html_attribs = {}, icon = 'fas fa-question-circle', css_class = nil, text = nil) @@ -199,74 +151,11 @@ def link_last_part(url) end end - def get_categories_data(categories = nil) - @categories_for_select = [] - @categories_map = {} - categories ||= LinkedData::Client::Models::Category.all(include: "name,ontologies") - categories.each do |c| - @categories_for_select << [ c.name, c.id ] - @categories_map[c.id] = ontologies_to_acronyms(c.ontologies) # c.ontologies is a list of URIs - end - @categories_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase } - @categories_for_js = @categories_map.to_json - end - - def get_groups_data(groups = nil) - @groups_map = {} - @groups_for_select = [] - groups ||= LinkedData::Client::Models::Group.all(include: "acronym,name,ontologies") - groups.each do |g| - next if ( g.acronym.nil? or g.acronym.empty? ) - @groups_for_select << [ g.name + " (#{g.acronym})", g.acronym ] - @groups_map[g.acronym] = ontologies_to_acronyms(g.ontologies) # g.ontologies is a list of URIs - end - @groups_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase } - @groups_for_js = @groups_map.to_json - end - - - - - def ontologies_to_acronyms(ontologyIDs) - acronyms = [] - ontologyIDs.each do |id| - acronyms << @onts_uri2acronym_map[id] # hash generated in get_ontologies_data - end - return acronyms.compact # remove nil values from any failures to convert ontology URI to acronym - end - def at_slice? !@subdomain_filter.nil? && !@subdomain_filter[:active].nil? && @subdomain_filter[:active] == true end - # TODO this helper is not used but can be usefully - def truncate_with_more(text, options = {}) - length ||= options[:length] ||= 30 - trailing_text ||= options[:trailing_text] ||= " ... " - link_more ||= options[:link_more] ||= "[more]" - link_less ||= options[:link_less] ||= "[less]" - more_text = " #{link_more}#{text} #{link_less}" - more = text.length > length ? more_text : "" - output = "#{truncate(text, :length => length, :omission => trailing_text)}" + more + "" - end - - def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, &block) - content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do - check_input(id: id, name: name, value: value, label: label, checked: checked, &block) - end - end - - def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, &block) - title ||= object["name"] - value ||= (object["value"] || object["acronym"] || object["id"]) - - chips_component(id: id || value, name: name, label: object["acronym"], - checked: checked, - value: value, tooltip: title, &block) - end - alias :category_chip_component :group_chip_component - def add_comment_button(parent_id, parent_type) if session[:user].nil? link_to t('application.add_comment'), login_index_path(redirect: request.url), class: "secondary-button regular-button slim" @@ -284,7 +173,6 @@ def add_reply_button(parent_id) end end - def add_proposal_button(parent_id, parent_type) if session[:user].nil? link_to t('application.add_proposal'), login_index_path(redirect: request.url), class: "secondary-button regular-button slim" @@ -293,7 +181,7 @@ def add_proposal_button(parent_id, parent_type) class: "secondary-button regular-button slim", data: { show_modal_title_value: t('application.add_new_proposal')} end end - + def link?(str) # Regular expression to match strings starting with "http://" or "https://" @@ -324,10 +212,8 @@ def admin_block(ontology: @ontology, user: session[:user], class_css: "admin-bor end end - def subscribed_to_ontology?(ontology_acronym, user) - user.bring(:subscription) if user.subscription.nil? - # user.subscription is an array of subscriptions like {ontology: ontology_id, notification_type: "NOTES"} + user = LinkedData::Client::Models::User.find(user.username, {include: 'subscription'}) if user.subscription.nil? return false if user.subscription.nil? or user.subscription.empty? user.subscription.each do |sub| #sub = {ontology: ontology_acronym, notification_type: "NOTES"} @@ -375,8 +261,6 @@ def notification_type(flash_key) bootstrap_alert_class[flash_key] end - ###BEGIN ruby equivalent of JS code in bp_ajax_controller. - ###Note: this code is used in concepts/_details partial. def bp_ont_link(ont_acronym) return "/ontologies/#{ont_acronym}" end @@ -428,7 +312,7 @@ def get_link_for_cls_ajax(cls_id, ont_acronym, target = nil) cls_url = "/ontologies/#{ont_acronym}?p=classes&conceptid=#{CGI.escape(cls_id)}" label_ajax_link(link, cls_id, ont_acronym, ajax_url , cls_url ,target) else - content_tag(:div, auto_link(cls_id, :all, target: '_blank')) + content_tag(:div, cls_id) end end @@ -453,7 +337,6 @@ def get_link_for_collection_ajax(collection, ont_acronym, target = '_blank') label_ajax_link(link, collection, ont_acronym, ajax_url, collection_url, target) end - def get_link_for_label_xl_ajax(label_xl, ont_acronym, cls_id, modal: true) link = label_xl ajax_uri = "/ajax/label_xl/label?cls_id=#{CGI.escape(cls_id)}" @@ -469,10 +352,10 @@ def get_link_for_label_xl_ajax(label_xl, ont_acronym, cls_id, modal: true) end - ###END ruby equivalent of JS code in bp_ajax_controller. def ontology_viewer_page_name(ontology_name, concept_label, page) ontology_name + " | " + " #{page.capitalize}" end + def help_path(anchor: nil) "#{Rails.configuration.settings.links[:help]}##{anchor}" end @@ -539,7 +422,6 @@ def navitems ["/landscape", t("layout.header.landscape")]] end - def beta_badge(text = t('application.beta_badge_text'), tooltip: t('application.beta_badge_tooltip')) return unless text content_tag(:span, text, data: { controller: 'tooltip' }, title: tooltip, class: 'badge badge-pill bg-secondary text-white') @@ -581,7 +463,6 @@ def rest_url "#{protocol}://#{cleaned_path}" end - def prefix_property_url(key_string, key = nil) namespace_key, _ = RESOLVE_NAMESPACE.find { |_, value| key_string.include?(value) } @@ -629,10 +510,9 @@ def empty_state(text) end end - - def ontologies_selector(id:, label: nil, name: nil, selected: nil, placeholder: nil, multiple: true) + def ontologies_selector(id:, label: nil, name: nil, selected: nil, placeholder: nil, multiple: true, ontologies: onts_for_select) content_tag(:div) do - render(Input::SelectComponent.new(id: id, label: label, name: name, value: onts_for_select, multiple: multiple, selected: selected, placeholder: placeholder)) + + render(Input::SelectComponent.new(id: id, label: label, name: name, value: ontologies, multiple: multiple, selected: selected, placeholder: placeholder)) + content_tag(:div, class: 'ontologies-selector-button', 'data-controller': 'ontologies-selector', 'data-ontologies-selector-id-value': id) do content_tag(:div, t('ontologies_selector.clear_selection'), class: 'clear-selection', 'data-action': 'click->ontologies-selector#clear') + link_to_modal(t('ontologies_selector.ontologies_advanced_selection'), "/ontologies_selector?id=#{id}", data: { show_modal_title_value: t('ontologies_selector.ontologies_advanced_selection')}) @@ -640,6 +520,10 @@ def ontologies_selector(id:, label: nil, name: nil, selected: nil, placeholder: end end + def link_button_component(href: , value: , id:, size: nil, variant: 'primary') + render Buttons::RegularButtonComponent.new(id:id, value: value, variant: variant, type: 'link', href: href, size: size) + end + def save_button_component(class_name: nil, id: , value:, data: nil, size: nil, type: nil) content_tag(:div, data: data, class: class_name) do render Buttons::RegularButtonComponent.new(id:id, value: value, variant: "primary", state: 'regular', size: size, type: type) do |btn| @@ -659,7 +543,9 @@ def cancel_button_component(class_name: nil, id: , value:, data: nil) end end end - - + def categories_select(id: nil, name: nil, selected: 'None') + categories_for_select = LinkedData::Client::Models::Category.all.map{|x| ["#{x.name} (#{x.acronym})", x.id]}.unshift(["None", '']) + render Input::SelectComponent.new(id: id, name: name, value: categories_for_select, selected: selected) + end end diff --git a/app/helpers/check_resolvability_helper.rb b/app/helpers/check_resolvability_helper.rb index 5775766200..40d74ea2e5 100644 --- a/app/helpers/check_resolvability_helper.rb +++ b/app/helpers/check_resolvability_helper.rb @@ -3,9 +3,9 @@ module CheckResolvabilityHelper def formats_equivalents(format = nil) all = { 'application/json' => ['application/ld+json'], - 'application/rdf+xml' => %w[application/xml application/rdf+xml text/xml application/octet-stream], - 'text/turtle' => ['application/turtle'], - 'text/n3' => ['application/n-triples'], + 'application/rdf+xml' => %w[application/xml text/xml text/rdf+xml application/octet-stream], + 'text/turtle' => %w[application/turtle application/octet-stream], + 'text/n3' => %w[text/rdf+n3 application/rdf+n3 application/n3 application/n-triples text/n-triples application/ntriples text/ntriples], 'text/html' => [] } @@ -26,7 +26,7 @@ def resolvability_max_redirections 10 end - def resolvability_status(status, allowed_format, redirections, result: nil) + def resolvability_status(status, allowed_format, redirections, result: nil, response_time:0) supported_format = Array(allowed_format) unless result @@ -39,7 +39,7 @@ def resolvability_status(status, allowed_format, redirections, result: nil) end end - { result: result, status: status, allowed_format: supported_format, redirections: redirections } + { result: result, status: status, allowed_format: supported_format, response_time: response_time, redirections: redirections } end def follow_redirection(url, format, timeout_seconds, redirect_limit = resolvability_max_redirections) @@ -49,35 +49,37 @@ def follow_redirection(url, format, timeout_seconds, redirect_limit = resolvabil redirect_count = 0 redirections = [uri] - until (!response.nil? && !response.is_a?(Net::HTTPRedirection)) || redirect_count >= redirect_limit - http = Net::HTTP.new(uri.host, uri.port) - http.use_ssl = (uri.scheme == 'https') - http.open_timeout = timeout_seconds - begin - response = Timeout.timeout(timeout_seconds) { http.request_head(uri, 'Accept' => format) } - rescue Timeout::Error, Net::OpenTimeout - return resolvability_status('Timeout', [], redirections, result: 0) - end + total_time = Benchmark.measure do + until (!response.nil? && !response.is_a?(Net::HTTPRedirection)) || redirect_count >= redirect_limit + http = Net::HTTP.new(uri.host, uri.port) + http.use_ssl = (uri.scheme == 'https') + http.open_timeout = timeout_seconds + begin + response = Timeout.timeout(timeout_seconds) { http.request_head(uri, 'Accept' => format) } + rescue Timeout::Error, Net::OpenTimeout + return resolvability_status('Timeout', [], redirections, result: 0, response_time: timeout_seconds) + end - if response.is_a?(Net::HTTPRedirection) && response['location'] - if !uri.to_s.start_with?(response['location']) && uri.to_s.include?(response['location'].chomp('/')) - uri = URI.parse(uri.scheme + '://' + uri.host + '/' + response['location']) - else - uri = URI.parse(response['location']) + if response.is_a?(Net::HTTPRedirection) && response['location'] + uri = URI.join(uri, response['location']) + redirections << uri + redirect_count += 1 end - redirections << uri - redirect_count += 1 end end - if response&.code.to_s.eql?('200') && (response&.content_type.to_s.include?(format) || formats_equivalents(format)&.include?(response&.content_type.to_s)) - result = 2 - elsif response&.code.to_s.eql?('200') - result = 1 + if redirect_count >= redirect_limit + resolvability_status('Too Many Redirections', [], redirections, result: 0, response_time: total_time.real.round(3)) else - result = 0 + if response&.code.to_s.eql?('200') && (response&.content_type.to_s.include?(format) || formats_equivalents(format)&.include?(response&.content_type.to_s)) + result = 2 + elsif response&.code.to_s.eql?('200') + result = 1 + else + result = 0 + end + resolvability_status(response&.code, [response&.content_type], redirections, result: result, response_time: total_time.real.round(3)) end - resolvability_status(response&.code, [response&.content_type], redirections, result: result) end def check_resolvability_helper(url, negotiation_formats = resolvability_formats, timeout_seconds = resolvability_timeout) @@ -85,7 +87,7 @@ def check_resolvability_helper(url, negotiation_formats = resolvability_formats, supported_format = negotiation_formats.find_all do |format| begin redirections[format] = follow_redirection(url, format, timeout_seconds) - redirections[:result].eql?(2) + redirections[format][:result].eql?(2) rescue StandardError => e redirections[format] = resolvability_status(e.message, [], [], result: 0) false @@ -93,13 +95,14 @@ def check_resolvability_helper(url, negotiation_formats = resolvability_formats, end status = redirections.values.map { |v| v[:status] }.uniq.join(', ') + average_response_time = redirections.values.sum { |v| v[:response_time] }.fdiv(redirections.size).round(3) if supported_format.size > 1 - { result: 2, status: status, allowed_format: supported_format, redirections: redirections } + { result: 2, status: status, allowed_format: supported_format, average_response_time: average_response_time, redirections: redirections } elsif status.include?('200') returned_format = redirections.map { |k, v| !v[:result].eql?(0) ? v[:allowed_format] : nil }.flatten.compact.uniq - { result: 1, status: status, allowed_format: returned_format, redirections: redirections } + { result: 1, status: status, allowed_format: returned_format, average_response_time: average_response_time, redirections: redirections } else - { result: 0, status: status, allowed_format: [], redirections: redirections } + { result: 0, status: status, allowed_format: [], average_response_time: average_response_time, redirections: redirections } end end @@ -116,7 +119,7 @@ def check_resolvability_success(result) url_resolvable?(result) || url_content_negotiable?(result) end - def check_resolvability_message(resolvable, allowed_formats, status, url = nil) + def check_resolvability_message(resolvable, allowed_formats, status, url: nil, response_time: nil) supported_format = Array(allowed_formats).compact supported_format = allowed_formats.empty? ? 'Format not specified' : supported_format.join(', ') @@ -130,6 +133,7 @@ def check_resolvability_message(resolvable, allowed_formats, status, url = nil) text = text + link_to(', click to see details', check_resolvability_path(url: url), target: '_blank') if url + text += " (Average response time: #{response_time}s)" if response_time text end end diff --git a/app/helpers/collections_helper.rb b/app/helpers/collections_helper.rb index 595cddabf3..bb81e39cef 100644 --- a/app/helpers/collections_helper.rb +++ b/app/helpers/collections_helper.rb @@ -75,9 +75,19 @@ def link_to_collection(collection, selected_collection_id) private + require 'color' + + def random_color + hue = rand(0..360) + saturation = rand(50..100) # Higher saturation for more vibrant colors + lightness = rand(30..70) # Middle lightness to avoid extremes + + Color::HSL.new(hue, saturation, lightness).html + end + def generate_collections_colors(collections) collections.each do |c| - c.color = format('#%06x', (rand * 0xffffff)) + c.color = random_color end end end diff --git a/app/helpers/components_helper.rb b/app/helpers/components_helper.rb index 03eef072cd..210e4ab57c 100644 --- a/app/helpers/components_helper.rb +++ b/app/helpers/components_helper.rb @@ -1,4 +1,22 @@ module ComponentsHelper + include TermsReuses + + def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, &block) + content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do + check_input(id: id, name: name, value: value, label: label, checked: checked, &block) + end + end + + def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, &block) + title ||= object["name"] + value ||= (object["value"] || object["acronym"] || object["id"]) + + chips_component(id: id || value, name: name, label: object["acronym"], + checked: checked, + value: value, tooltip: title, &block) + end + alias :category_chip_component :group_chip_component + def rdf_highlighter_container(format, content) render Display::RdfHighlighterComponent.new(format: format, text: content) @@ -29,7 +47,7 @@ def search_page_input_component(name:, value: nil, placeholder: , button_icon: ' end end - def paginated_list_component(id:, results:, next_page_url:, child_url:, child_turbo_frame:, child_param:, open_in_modal: false , selected: nil, auto_click: false) + def paginated_list_component(id:, results:, next_page_url:, child_url:, child_turbo_frame:, child_param:, open_in_modal: false , selected: nil, auto_click: false, submission: nil) render(TreeInfiniteScrollComponent.new( id: id, collection: results.collection, @@ -45,7 +63,7 @@ def paginated_list_component(id:, results:, next_page_url:, child_url:, child_tu end end) end - + concepts = c.collection if concepts && !concepts.empty? concepts.each do |concept| @@ -59,7 +77,8 @@ def paginated_list_component(id:, results:, next_page_url:, child_url:, child_tu selected: selected.blank? ? false : concept.id.eql?(selected) , target_frame: child_turbo_frame, data: data, - open_in_modal: open_in_modal + open_in_modal: open_in_modal, + is_reused: concept_reused?(submission: submission, concept_id: concept.id) ))) end end @@ -87,7 +106,7 @@ def copy_link_to_clipboard(url, show_content: false) def generated_link_to_clipboard(url, acronym) url = "#{$UI_URL}/ontologies/#{acronym}/#{link_last_part(url)}" - content_tag(:span, style: 'display: inline-block;') do + content_tag(:span, id: "generate_portal_link", style: 'display: inline-block;') do render ClipboardComponent.new(icon: 'icons/copy_link.svg', title: "#{t("components.copy_portal_uri", portal_name: portal_name)} #{link_to(url)}", message: url, show_content: false) end end @@ -115,13 +134,13 @@ def link_to_with_actions(link_to_tag, acronym: nil, url: nil, copy: true, check_ tag.html_safe end - def tree_component(root, selected, target_frame:, sub_tree: false, id: nil, auto_click: false, &child_data_generator) + def tree_component(root, selected, target_frame:, sub_tree: false, id: nil, auto_click: false, submission: nil, &child_data_generator) root.children.sort! { |a, b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase } - + render TreeViewComponent.new(id: id, sub_tree: sub_tree, auto_click: auto_click) do |tree_child| root.children.each do |child| children_link, data, href = child_data_generator.call(child) - + if children_link.nil? || data.nil? || href.nil? raise ArgumentError, t('components.error_block') end @@ -130,9 +149,9 @@ def tree_component(root, selected, target_frame:, sub_tree: false, id: nil, auto children_href: children_link, selected: child.id.eql?(selected&.id), muted: child.isInActiveScheme&.empty?, target_frame: target_frame, - data: data) do + data: data, is_reused: concept_reused?(submission: submission, concept_id: child.id)) do tree_component(child, selected, target_frame: target_frame, sub_tree: true, - id: id, auto_click: auto_click, &child_data_generator) + id: id, auto_click: auto_click, submission: submission, &child_data_generator) end end end @@ -260,4 +279,5 @@ def form_cancel_button end end + end diff --git a/app/helpers/concepts_helper.rb b/app/helpers/concepts_helper.rb index 06949543e8..3cec8ade6b 100644 --- a/app/helpers/concepts_helper.rb +++ b/app/helpers/concepts_helper.rb @@ -1,6 +1,6 @@ # frozen_string_literal: true module ConceptsHelper - + include TermsReuses def concept_link(acronym, child, language) child.id.eql?('bp_fake_root') ? '#' : "/ontologies/#{acronym}/concepts/show?id=#{CGI.escape(child.id)}&language=#{language}" end @@ -20,8 +20,11 @@ def concept_tree_data(acronym, child, language, concept_schemes) } [children_link, data, href] end - def concepts_tree_component(root, selected_concept, acronym, concept_schemes, language, sub_tree: false, id: nil, auto_click: false) - tree_component(root, selected_concept, target_frame: 'concept_show', sub_tree: sub_tree, id: id, auto_click: auto_click) do |child| + + def concepts_tree_component(root, selected_concept, acronym, concept_schemes, language, sub_tree: false, id: nil, + auto_click: false, submission: @submission) + tree_component(root, selected_concept, target_frame: 'concept_show', sub_tree: sub_tree, id: id, + auto_click: auto_click, submission: submission) do |child| concept_tree_data(acronym, child, language, concept_schemes) end end @@ -105,25 +108,26 @@ def same_period?(year, month, date) year.eql?(date.year) && month.eql?(date.strftime('%B')) end - def concepts_li_list(concepts, auto_click: false) + def concepts_li_list(concepts, auto_click: false, selected_id: nil, submission: nil) out = '' concepts.each do |concept| children_link, data, href = concept_tree_data(@ontology.acronym, concept, request_lang, []) + out += render TreeLinkComponent.new(child: concept, href: href, - children_href: '#', selected: concept.id.eql?(concepts.first.id) && auto_click, - target_frame: 'concept_show', data: data) + children_href: '#', selected: concept.id.eql?(selected_id) && auto_click, + target_frame: 'concept_show', data: data, is_reused: concept_reused?(submission: submission, concept_id: concept.id)) end out end - def render_concepts_by_dates(auto_click: false) + def render_concepts_by_dates(auto_click: false, submission: @submission) return if @concepts_year_month.empty? first_year, first_month_concepts = @concepts_year_month.shift first_month, first_concepts = first_month_concepts.shift out = '' if same_period?(first_year, first_month, @last_date) - out += "
    #{concepts_li_list(first_concepts, auto_click: auto_click)}
" + out += "
    #{concepts_li_list(first_concepts, auto_click: auto_click, submission: submission)}
" else tmp = {} tmp[first_month] = first_concepts @@ -132,15 +136,15 @@ def render_concepts_by_dates(auto_click: false) tmp = {} tmp[first_year] = first_month_concepts @concepts_year_month = tmp.merge(@concepts_year_month) - + selected_id = @concepts.first.id if @page.page.eql?(1) @concepts_year_month.each do |year, month_concepts| month_concepts.each do |month, concepts| out += "
    #{month + ' ' + year.to_s}" - out += concepts_li_list(concepts, auto_click: auto_click) - out += "
" + out += concepts_li_list(concepts, auto_click: auto_click, selected_id: selected_id, + submission: submission) + out += '' end end - raw out end @@ -199,4 +203,4 @@ def synonym_qualifier_select(form) def concept_redirect_path ontology_path(@ontology.acronym, p: 'classes', conceptid: @concept.id) end -end \ No newline at end of file +end diff --git a/app/helpers/fair_score_helper.rb b/app/helpers/fair_score_helper.rb index 7abb76eb66..ef5b81e2df 100644 --- a/app/helpers/fair_score_helper.rb +++ b/app/helpers/fair_score_helper.rb @@ -16,18 +16,22 @@ def get_fairness_json(ontologies_acronyms, apikey = user_apikey) if Rails.cache.exist?("fairness-#{ontologies_acronyms.gsub(',', '-')}-#{apikey}") out = read_large_data("fairness-#{ontologies_acronyms.gsub(',', '-')}-#{apikey}") else - out = "{}" + out = '{}' begin time = Benchmark.realtime do conn = Faraday.new do |conn| conn.options.timeout = 30 end response = conn.get(get_fairness_service_url(apikey) + "&ontologies=#{ontologies_acronyms}&combined") - out = response.body.force_encoding('ISO-8859-1').encode('UTF-8') - cache_large_data("fairness-#{ontologies_acronyms.gsub(',', '-')}-#{apikey}", out) + if response.status.eql?(200) + out = response.body.force_encoding('ISO-8859-1').encode('UTF-8') + unless out.empty? || out.strip.eql?('{}') + cache_large_data("fairness-#{ontologies_acronyms.gsub(',', '-')}-#{apikey}", out) + end + end end puts "Call fairness service for: #{ontologies_acronyms} (#{time}s)" - rescue + rescue StandardError Rails.logger.warn t('fair_score.fairness_unreachable_warning') end end @@ -140,7 +144,7 @@ def print_score(score) def fairness_link(style: '', ontology: nil) custom_style = "font-size: 50px; line-height: 0.5; margin-left: 6px; #{style}".strip ontology = ontology || 'all' - render IconWithTooltipComponent.new(icon: "json.svg",link: "#{get_fairness_service_url}&ontologies=#{ontology}&combined=true", target: '_blank', title: t('fair_score.go_to_api'), size:'small', style: custom_style) + render IconWithTooltipComponent.new(icon: 'json.svg',link: "#{get_fairness_service_url}&ontologies=#{ontology}&combined=true", target: '_blank', title: t('fair_score.go_to_api'), size:'small', style: custom_style) end private diff --git a/app/helpers/home_helper.rb b/app/helpers/home_helper.rb index fe4f084495..5df6609674 100644 --- a/app/helpers/home_helper.rb +++ b/app/helpers/home_helper.rb @@ -1,5 +1,4 @@ require 'open-uri' -require 'open_uri_redirections' require 'nokogiri' module HomeHelper @@ -8,7 +7,7 @@ def render_footer_link(options = {}) link_content = options[:text][I18n.locale] || options[:text][:en] if options[:text] link_content ||= image_tag(options[:img_src]) if options[:img_src] link_content ||= content_tag(:i, '', class: options[:icon]) if options[:icon] - + link_to(link_content, options[:url], target: options[:target], class: options[:css_class].to_s, style: options[:text].blank? ? 'text-decoration: none' : '').html_safe if link_content end @@ -21,7 +20,7 @@ def format_number_abbreviated(number) else number.to_s end - end + end def discover_ontologies_button render Buttons::RegularButtonComponent.new(id: 'discover-ontologies-button', value: t('home.discover_ontologies_button'), variant: "secondary", state: "regular", href: "/ontologies") do |btn| @@ -31,4 +30,10 @@ def discover_ontologies_button end end -end \ No newline at end of file + def home_ontoportal_description + ontoportal_link = link_to("(#{$ONTOPORTAL_WEBSITE_LINK})", $ONTOPORTAL_WEBSITE_LINK, target: '_blank') + github_link = link_to("(#{$ONTOPORTAL_GITHUB_REPO})", $ONTOPORTAL_GITHUB_REPO, target: '_blank') + content_tag(:div, t('home.ontoportal_description', ontoportal_link: ontoportal_link, github_link: github_link).html_safe, style: "margin-bottom: 20px") + end + +end diff --git a/app/helpers/inputs_helper.rb b/app/helpers/inputs_helper.rb index a844ce0d2d..cd4782b6f3 100644 --- a/app/helpers/inputs_helper.rb +++ b/app/helpers/inputs_helper.rb @@ -46,10 +46,10 @@ def url_input(name:, value:, label: nil, help: nil) helper_text: help) end - def text_area_input(name:, value:, label: nil, help: nil) + def text_area_input(name:, value:, label: nil, help: nil, resize: nil) render Input::TextAreaComponent.new(label: input_label(label, name), name: name, value: value, error_message: input_error_message(name), - helper_text: help) + helper_text: help, resize: resize) end def date_input(name:, value:, label: nil, help: nil, max_date: nil) diff --git a/app/helpers/mappings_helper.rb b/app/helpers/mappings_helper.rb index 352b42a20d..afc85907a8 100644 --- a/app/helpers/mappings_helper.rb +++ b/app/helpers/mappings_helper.rb @@ -52,7 +52,7 @@ def ajax_to_inter_portal_cls(cls) def ajax_to_internal_cls(cls) link_to("#{cls.id}".html_safe, - ontology_path(cls.explore.ontology.acronym, p: 'classes', conceptid: cls.id)) + ontology_path(cls.explore.ontology.acronym, p: 'classes', conceptid: cls.id), target: "_blank") end # to get the apikey from the interportal instance of the interportal class. diff --git a/app/helpers/multi_languages_helper.rb b/app/helpers/multi_languages_helper.rb index 17a96bd6b4..d21d41a302 100644 --- a/app/helpers/multi_languages_helper.rb +++ b/app/helpers/multi_languages_helper.rb @@ -72,6 +72,9 @@ def search_language_selector(id: 'search_language', name: 'search_language', sel def content_languages(submission = @submission || @submission_latest) current_lang = request_lang.downcase submission_lang = submission_languages(submission) + + submission_lang = [current_lang.to_s] if submission_lang.empty? + # Transform each language into a select option submission_lang = submission_lang.map do |lang| lang = lang.split('/').last.upcase @@ -96,7 +99,7 @@ def content_language_selector(id: 'content_language', name: 'content_language') languages, selected = content_languages render Input::LanguageSelectorComponent.new(id: id, name: name, enable_all: true, languages: languages, - selected: selected || 'all', + selected: selected || request_lang, 'data-tooltip-interactive-value': true, 'data-select-input-searchable-value': false, title: content_language_help_text) @@ -163,7 +166,7 @@ def display_in_multiple_languages(label) content_tag(:div) do raw(label.map do |key, value| Array(value).map do |v| - content_tag(:div) do + content_tag(:div, class: 'definition') do concat content_tag(:span, v) concat content_tag(:span, key.upcase, class: 'badge badge-secondary ml-1') unless key.to_s.upcase.eql?('NONE') || key.to_s.upcase.eql?('@NONE') end diff --git a/app/helpers/ontologies_helper.rb b/app/helpers/ontologies_helper.rb index 46c5d3a4fb..33adc9efd5 100644 --- a/app/helpers/ontologies_helper.rb +++ b/app/helpers/ontologies_helper.rb @@ -5,6 +5,10 @@ module OntologiesHelper API_KEY = $API_KEY LANGUAGE_FILTERABLE_SECTIONS = %w[classes schemes collections instances properties].freeze + def ontology_access_denied? + @ontology&.errors&.include?('Access denied for this resource') + end + def concept_search_input(placeholder) content_tag(:div, class: 'search-inputs p-1') do text_input(placeholder: placeholder, label: '', name: "search", value: '', data: { action: "input->browse-filters#dispatchInputEvent" }) @@ -100,8 +104,8 @@ def ontologies_browse_skeleton(pagesize = 5) end end - def ontologies_filter_url(filters, page: 1, count: false) - url = 'ontologies_filter?' + def ontologies_with_filters_url(filters, page: 1, count: false) + url = '/ontologies_filter?' url += "page=#{page}" if page url += "count=#{page}" if count if filters @@ -320,11 +324,22 @@ def visibility_link(ontology) "#{link_name}" end - def show_category_name(domain) - return domain unless link?(domain) + def category_name_chip_component(domain) + text = domain.split('/').last.titleize + + + return render(ChipButtonComponent.new(text: text, tooltip: domain, type: "static")) unless link?(domain) + + acronym = domain.split('/').last.upcase.strip category = LinkedData::Client::Models::Category.find(acronym) - category.name ? category.name : acronym.titleize + + if category.name + render ChipButtonComponent.new(text: text, tooltip: category.name, type: "static") + else + render ChipButtonComponent.new(text: text, tooltip: domain, url: domain, type: "clickable", target: '_blank') + end + end @@ -416,7 +431,7 @@ def lazy_load_section(section_title, &block) block.call else render TurboFrameComponent.new(id: section_title, src: "/ontologies/#{@ontology.acronym}?p=#{section_title}", - loading: Rails.env.development? ? "lazy" : "eager", + loading: Rails.env.development? ? "lazy" : "eager", target: '_top', data: { "turbo-frame-target": "frame" }) end end @@ -765,5 +780,12 @@ def id_to_acronym(id) id.split('/').last end + def browse_taxonomy_tooltip(texonomy) + content_tag(:div, class: 'd-flex') do + content_tag(:div, "See more information about #{texonomy} in ", class: 'mr-1') + + content_tag(:a, 'here', href: "/#{texonomy}", target: '_blank') + end + end + end diff --git a/app/helpers/properties_helper.rb b/app/helpers/properties_helper.rb index a485e79e29..9d8b2fdce3 100644 --- a/app/helpers/properties_helper.rb +++ b/app/helpers/properties_helper.rb @@ -17,8 +17,9 @@ def property_tree_data(acronym, child, language) } [children_link, data, href] end - def property_tree_component(root, selected_concept, acronym, language, sub_tree: false, id: nil, auto_click: false) - tree_component(root, selected_concept, target_frame: 'property_show', sub_tree: sub_tree, id: id, auto_click: auto_click) do |child| + + def property_tree_component(root, selected_concept, acronym, language, sub_tree: false, id: nil, auto_click: false, submission: @submission) + tree_component(root, selected_concept, target_frame: 'property_show', sub_tree: sub_tree, id: id, auto_click: false, submission: submission) do |child| property_tree_data(acronym, child, language) end end @@ -32,4 +33,8 @@ def no_properties_alert t('properties.no_properties_alert', acronym: @ontology.acronym) end end -end \ No newline at end of file + + def get_property(id, acronym = params[:acronym], lang = request_lang, include: nil) + LinkedData::Client::HTTP.get("/ontologies/#{acronym}/properties/#{helpers.encode_param(id)}", { lang: lang , include: include}) + end +end diff --git a/app/helpers/schemes_helper.rb b/app/helpers/schemes_helper.rb index 39bc77a73e..9d3019cd36 100644 --- a/app/helpers/schemes_helper.rb +++ b/app/helpers/schemes_helper.rb @@ -77,7 +77,7 @@ def schemes_data [schemes_labels, main_scheme, selected_scheme] end - def schemes_tree(schemes_labels, main_scheme_label, selected_scheme_id) + def schemes_tree(schemes_labels, main_scheme_label, selected_scheme_id, submission: @submission_latest) selected_scheme = nil schemes = sorted_labels(schemes_labels).map do |s| next nil unless main_scheme_label.nil? || s['prefLabel'] != main_scheme_label['prefLabel'] @@ -104,9 +104,7 @@ def schemes_tree(schemes_labels, main_scheme_label, selected_scheme_id) root = OpenStruct.new root.children = children selected_scheme = selected_scheme || main_scheme || root.children.first - - - tree_component(root, selected_scheme, target_frame: 'scheme', auto_click: false) do |child| + tree_component(root, selected_scheme, target_frame: 'scheme', auto_click: false, submission: submission) do |child| href = scheme_path(child['@id'], request_lang) rescue '' data = { schemeid: (child['@id'] rescue '')} ["#", data, href] diff --git a/app/helpers/search_helper.rb b/app/helpers/search_helper.rb index 524cd521ef..ef0a80f654 100644 --- a/app/helpers/search_helper.rb +++ b/app/helpers/search_helper.rb @@ -8,7 +8,7 @@ def search_content_params def render_search_paginated_list(container_id:, next_page_url:, child_url:, child_turbo_frame:, child_param:, show_count: nil, lang: request_lang, - auto_click: false, results: , next_page: ,total_count: ) + auto_click: false, results: , next_page: ,total_count:, submission: @submission ) query, page, _ = search_content_params @results = OpenStruct.new @@ -34,7 +34,7 @@ def render_search_paginated_list(container_id:, next_page_url:, child_url:, chil child_param: child_param, child_turbo_frame: child_turbo_frame, open_in_modal: show_count, - selected: selected)) + selected: selected, submission: submission)) ] else render inline: paginated_list_component(id: container_id, @@ -45,7 +45,7 @@ def render_search_paginated_list(container_id:, next_page_url:, child_url:, chil child_turbo_frame: child_turbo_frame, open_in_modal: show_count, selected: selected, - auto_click: auto_click) + auto_click: auto_click, submission: submission) end end -end \ No newline at end of file +end diff --git a/app/helpers/submission_inputs_helper.rb b/app/helpers/submission_inputs_helper.rb index e79060bf47..06ecee5b39 100644 --- a/app/helpers/submission_inputs_helper.rb +++ b/app/helpers/submission_inputs_helper.rb @@ -35,6 +35,8 @@ def help_text end def label + return attr_key unless @attr_metadata + @label || @attr_metadata['label'] || @attr_metadata['attribute'].humanize end @@ -97,7 +99,7 @@ def attribute_input(attr_key, long_text: false, label: nil, show_tooltip: true, url_input(name: name, label: label, value: @submission.URI) elsif long_text text_area_input(name: name, label: label, - value: attr.values) + value: attr.values, resize: true) else text_input(name: name, label: label, value: attr.values, help: help) @@ -233,7 +235,7 @@ def ontology_view_of_input(ontology = @ontology) end c.container do content_tag(:div) do - render SelectInputComponent.new(id: 'viewOfSelect', values: onts_for_select, name: 'ontology[viewOf]', selected: ontology.viewOf) + render SelectInputComponent.new(id: 'viewOfSelect', values: onts_for_select, name: 'ontology[viewOf]', selected: ontology.viewOf&.split('/')&.last) end end end @@ -420,13 +422,15 @@ def generate_url_input(attr, helper_text: nil) end end - def generate_ontology_select_input(name, label, selected, multiple) + def generate_ontology_select_input(name, label, selected, multiple, reject_ontology: @ontology) unless @ontology_acronyms @ontology_acronyms = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', display_links: false, display_context: false, include_views: true) .map { |x| ["#{x.name} (#{x.acronym})", x.id.to_s] } @ontology_acronyms << ['', ''] end + @ontology_acronyms = @ontology_acronyms.reject { |acronym, id| id == reject_ontology.id } + input = '' input = hidden_field_tag("#{name}[]") if multiple @@ -444,7 +448,7 @@ def generate_list_text_input(attr, helper_text: nil, long_text: false) generate_list_field_input(attr, name, label, values, helper_text: helper_text) do |value, row_name, id| if long_text - text_area_tag(row_name, value, class: 'input-field-component', label: '') + text_area_tag(row_name, value, class: 'input-field-component', label: '', style: 'resize: vertical;') else text_input(label: '', name: row_name, value: value) end @@ -527,4 +531,4 @@ def attribute_help_text(attr) help_text end end -end \ No newline at end of file +end diff --git a/app/helpers/submissions_helper.rb b/app/helpers/submissions_helper.rb index 8610dda0ec..917ce5bc20 100644 --- a/app/helpers/submissions_helper.rb +++ b/app/helpers/submissions_helper.rb @@ -194,16 +194,25 @@ def submission_properties out end + def ontology_properties + ['acronym', 'name', [t('submission_inputs.visibility'), :viewingRestriction], 'viewOf', 'groups', 'categories', + [t('submission_inputs.administrators'), 'administeredBy']] + end def submission_editable_properties - properties = submission_properties - properties.map do |x| + properties = submission_properties.map do |x| if x.is_a? Array - [x[0].to_s.underscore.humanize, x[0]] + [attr_label(x[0], show_tooltip: false), x[0]] else - [x.to_s.underscore.humanize, x] + [attr_label(x, show_tooltip: false), x] end end + + properties += ontology_properties.map do |x| + x.is_a?(Array) ? x : [x.to_s.underscore.humanize, x] + end + + properties end def attribute_infos(attr_label) diff --git a/app/javascript/component_controllers/index.js b/app/javascript/component_controllers/index.js index eaf1728f09..c0d3bcd20f 100644 --- a/app/javascript/component_controllers/index.js +++ b/app/javascript/component_controllers/index.js @@ -26,7 +26,6 @@ import clipboard_component_controller from '../../components/clipboard_component import range_slider_component_controller from '../../components/input/range_slider_component/range_slider_component_controller' import RDFHighlighter from '../../components/display/rdf_highlighter_component/rdf_highlighter_component_controller' - application.register("rdf-highlighter", RDFHighlighter) application.register('turbo-modal', TurboModalController) application.register('file-input', FileInputLoaderController) @@ -42,4 +41,4 @@ application.register('progress-pages', Progress_pages_component_controller) application.register('reveal-component', Reveal_component_controller) application.register('table-component', Table_component_controller) application.register('clipboard', clipboard_component_controller) -application.register('range-slider', range_slider_component_controller) +application.register('range-slider', range_slider_component_controller) \ No newline at end of file diff --git a/app/javascript/controllers/chosen_controller.js b/app/javascript/controllers/chosen_controller.js deleted file mode 100644 index 2115f93e45..0000000000 --- a/app/javascript/controllers/chosen_controller.js +++ /dev/null @@ -1,68 +0,0 @@ -import {Controller} from "@hotwired/stimulus" -import {useChosen} from "../mixins/useChosen"; - -// Connects to data-controller="chosen" -export default class extends Controller { - // TODO to update to use TomSelect - static values = { - name: String, - enableColors: {type: Boolean, default: false} - } - - connect() { - useChosen(this.element, {width: '100%', allow_single_deselect: true}, this.#onChange.bind(this)) - } - - #onChange(event) { - const selected = Array.from(event.currentTarget.selectedOptions) - - if(this.enableColorsValue){ - this.#setColors(selected) - } - - const key = this.hasNameValue ? this.nameValue : event.currentTarget.name - const newData = { - [key]: selected.map(x => x.value) - } - this.element.dispatchEvent(new CustomEvent('changed', { - detail: { - data: newData - } - })) - } - - #setColors(selected){ - const snakeCase = string => { - return string.replace(/\W+/g, " ") - .split(/ |\B(?=[A-Z])/) - .map(word => word.toLowerCase()) - .join('_'); - } - const allChosenSelected = Array.from(document.querySelectorAll(`#${snakeCase(this.element.id +'_chosen')} .search-choice`)) - selected.forEach((s) => { - let color = s.dataset.color - if (color) { - const chosenSelected = allChosenSelected.filter(x => x.firstElementChild.textContent === s.text).pop() - const chosenText = chosenSelected.firstElementChild - const chosenClose = chosenSelected.lastElementChild - - chosenSelected.style.display = "flex" - chosenSelected.style.padding = "1px" - chosenSelected.style.paddingTop = "2px" - chosenSelected.style.paddingBottom = "2px" - - - chosenText.style.backgroundColor = color - chosenText.style.display = "inline-block" - chosenText.style.padding = "5px" - chosenText.style.borderRadius = "5px" - chosenText.style.color = "#fff" - chosenText.style.marginLeft = "2px" - chosenText.style.marginRight = "2px" - - chosenClose.style.position = "unset" - chosenClose.style.margin = "auto" - } - }) - } -} diff --git a/app/javascript/controllers/concepts_json_button_controller.js b/app/javascript/controllers/concepts_json_button_controller.js new file mode 100644 index 0000000000..01de7199b9 --- /dev/null +++ b/app/javascript/controllers/concepts_json_button_controller.js @@ -0,0 +1,19 @@ +import {Controller} from "@hotwired/stimulus" + +export default class extends Controller { + static targets = ['button'] + + update(){ + setTimeout(() => { + const tabsList = this.element.querySelectorAll('.nav-item'); + const jsonLink = Array.from(tabsList).find(tab => tab.classList.contains('active'))?.querySelector('a').getAttribute('data-json-link'); + const conceptsJsonLink = this.buttonTarget.querySelector('a'); + if (jsonLink) { + conceptsJsonLink.href = jsonLink; + conceptsJsonLink.style.display = 'flex' + } else { + conceptsJsonLink.style.display = 'none' + } + }, 1); + } +} \ No newline at end of file diff --git a/app/javascript/controllers/content_finder_controller.js b/app/javascript/controllers/content_finder_controller.js deleted file mode 100644 index 177b7d0709..0000000000 --- a/app/javascript/controllers/content_finder_controller.js +++ /dev/null @@ -1,105 +0,0 @@ -import { Controller } from '@hotwired/stimulus' -import * as jsonld from 'jsonld' -import hljs from 'highlight.js/lib/core' -import xml from 'highlight.js/lib/languages/xml' -import json from 'highlight.js/lib/languages/json' - -export default class extends Controller { - static targets = ["content"] - static values = { - format: String - } - connect() { - switch (this.formatValue) { - case 'json': - hljs.registerLanguage('json', json) - this.showJSON() - break - case 'xml': - hljs.registerLanguage('xml', xml) - this.showXML() - break - case 'ntriples': - hljs.registerLanguage('ntriples', function (hljs) { - var URL_PATTERN = /<[^>]+>/; // Regex pattern for matching URLs in angle brackets - return { - case_insensitive: true, - contains: [ - { - className: 'subject', - begin: /^<[^>]+>/, - }, - { - className: 'predicate', - begin: /<[^>]+>/, - }, - { - className: 'object', - begin: /\s([^\s]+)\s\./, - }, - hljs.COMMENT('^#', '$') - ] - }; - }); - this.showNTriples() - break - case 'turtle': - hljs.registerLanguage('turtle', function (hljs) { - var URL_PATTERN = /(?:<[^>]*>)|(?:https?:\/\/[^\s]+)/; - - return { - case_insensitive: true, - contains: [ - { - className: 'custom-prefixes', - begin: '@prefix', - relevance: 10 - }, - { - className: 'meta', - begin: /@base/, - end: /[\r\n]|$/, - relevance: 10 - }, - { - className: 'variable', - begin: /\?[\w\d]+/ - }, - { - className: 'custom-symbol', - begin: /@?[A-Za-z_][A-Za-z0-9_]*(?= *:)/, - relevance: 10 - }, - { - className: 'custom-concepts', - begin: /:\s*(\w+)/, - relevance: 10 - }, - { - className: 'string', - begin: URL_PATTERN - } - ] - }; - }); - this.showTURTLE() - break - } - } - - showJSON() { - this.contentTarget.innerHTML = hljs.highlight(JSON.stringify(JSON.parse(this.contentTarget.textContent), null, " "), { language: 'json' }).value - } - - showXML() { - this.contentTarget.innerHTML = hljs.highlight(this.contentTarget.textContent, { language: 'xml' }).value - } - - showNTriples() { - this.contentTarget.innerHTML = hljs.highlight(this.contentTarget.textContent, { language: 'ntriples' }).value - } - - showTURTLE() { - this.contentTarget.innerHTML = hljs.highlight(this.contentTarget.textContent, { language: 'turtle' }).value - } -} diff --git a/app/javascript/controllers/history_controller.js b/app/javascript/controllers/history_controller.js index 62e3c7c69c..48518c64ac 100644 --- a/app/javascript/controllers/history_controller.js +++ b/app/javascript/controllers/history_controller.js @@ -4,7 +4,6 @@ import { HistoryService } from "../mixins/useHistory"; // Connects to data-controller="history" export default class extends Controller { connect() { - console.log('hello world') this.history = new HistoryService() } updateURL(event) { diff --git a/app/javascript/controllers/index.js b/app/javascript/controllers/index.js index e490eb3a17..24f39bf453 100644 --- a/app/javascript/controllers/index.js +++ b/app/javascript/controllers/index.js @@ -7,8 +7,8 @@ import { application } from "./application" import BrowseFiltersController from "./browse_filters_controller" application.register("browse-filters", BrowseFiltersController) -import ChosenController from "./chosen_controller" -application.register("chosen", ChosenController) +import Skos_collections_selector from "./skos_collections_selector" +application.register("skos-collections-selector", Skos_collections_selector) import ClassSearchAutoCompleteController from "./class_search_auto_complete_controller" application.register("class-search-auto-complete", ClassSearchAutoCompleteController) @@ -102,4 +102,7 @@ application.register("ontologies-selector", OntologiesSelector) import MappingsController from "./mappings_visualization_controller" -application.register('mappings', MappingsController) \ No newline at end of file +application.register('mappings', MappingsController) + +import ConceptsJsonButtonController from "./concepts_json_button_controller.js" +application.register('concepts-json', ConceptsJsonButtonController) \ No newline at end of file diff --git a/app/javascript/controllers/label_ajax_controller.js b/app/javascript/controllers/label_ajax_controller.js index cebf898b38..d3cbcfff46 100644 --- a/app/javascript/controllers/label_ajax_controller.js +++ b/app/javascript/controllers/label_ajax_controller.js @@ -11,27 +11,29 @@ export default class extends Controller { } connect() { - this.linkA = jQuery(this.element); - - if (this.linkA.hasClass('ajax-modified-cls')) { - return true - } - - this.cls_id = this.clsIdValue; - this.ont_acronym = this.ontologyAcronymValue; - - let ajax_uri = new URL(this.ajaxUrlValue, document.location.origin) - - ajax_uri.searchParams.set('ontology', this.ont_acronym) - ajax_uri.searchParams.set('id', this.cls_id) + setTimeout(() => { + this.linkA = jQuery(this.element); + if (this.linkA.hasClass('ajax-modified-cls')) { + return true + } - this.request = useAjax({ - url: ajax_uri.pathname + ajax_uri.search, - timeout: ajax_process_timeout * 1000, - success: this.#ajaxSuccess.bind(this), - error: this.#ajaxError.bind(this) - }); + this.cls_id = this.clsIdValue; + this.ont_acronym = this.ontologyAcronymValue; + + let ajax_uri = new URL(this.ajaxUrlValue, document.location.origin) + + ajax_uri.searchParams.set('ontology', this.ont_acronym) + ajax_uri.searchParams.set('id', this.cls_id) + + + this.request = useAjax({ + url: ajax_uri.pathname + ajax_uri.search, + timeout: ajax_process_timeout * 1000, + success: this.#ajaxSuccess.bind(this), + error: this.#ajaxError.bind(this) + }); + },1) } abort() { diff --git a/app/javascript/controllers/mappings_visualization_controller.js b/app/javascript/controllers/mappings_visualization_controller.js index e75813d368..58d74cc601 100644 --- a/app/javascript/controllers/mappings_visualization_controller.js +++ b/app/javascript/controllers/mappings_visualization_controller.js @@ -26,7 +26,7 @@ export default class extends Controller { ontology_name: key.split('/').pop(), ontology_mappings: value, })) - + this.bubblesTarget.innerHTML = '' useMappingsDrawBubbles(data, width, height, margin, this.bubblesTarget, normalization_ratio, logScaleFactor) this.#centerScroll(this.frameTarget) diff --git a/app/javascript/controllers/simple_tree_controller.js b/app/javascript/controllers/simple_tree_controller.js index 2333fe9069..858bfde2c8 100644 --- a/app/javascript/controllers/simple_tree_controller.js +++ b/app/javascript/controllers/simple_tree_controller.js @@ -7,18 +7,17 @@ export default class extends Controller { } connect () { - let activeElem = this.element.querySelector('a.active') - if (activeElem) { - this.element.scrollTo({ - top: activeElem.offsetTop, - behavior: 'smooth' - }); - - if (this.autoClickValue) { - activeElem.click() + setTimeout(() => { + let activeElem = this.element.querySelector('.tree-link.active'); + if (activeElem) { + activeElem.scrollIntoView({ block: 'center' }); + window.scrollTo({top: 0,}); + if (this.autoClickValue) { + activeElem.click(); + } } - } - this.#onClickTooManyChildrenInit() + this.#onClickTooManyChildrenInit(); + }, 0); } select (event) { diff --git a/app/javascript/controllers/skos_collection_colors_controller.js b/app/javascript/controllers/skos_collection_colors_controller.js index 58baddf4d2..833b49205c 100644 --- a/app/javascript/controllers/skos_collection_colors_controller.js +++ b/app/javascript/controllers/skos_collection_colors_controller.js @@ -25,7 +25,7 @@ export default class extends Controller { let activeCollections = this.#getMatchedCollections(collectionElem, collections, this.selected) this.#removeColors(collectionElem) - this.#addColorsTags(collectionElem, this.#getCollectionColors(activeCollections)) + this.#addColorsTags(collectionElem, this.#getCollections(activeCollections)) } collectionTargetConnected (collectionElem) { @@ -48,7 +48,10 @@ export default class extends Controller { if (options) { Array.from(options.options).forEach(s => { if (s.value !== '') { - out[s.value] = s.dataset.color + out[s.value] = { + color: s.dataset.color, + title: s.textContent + } } }) } @@ -60,10 +63,12 @@ export default class extends Controller { return selected.filter(c => collections.includes(c)) } - #getCollectionColors (collectionsIds) { - return Object.entries(this.allCollections).filter(([key]) => collectionsIds.includes(key)).map(x => x[1]) + #getCollections(collectionsIds) { + return Object.entries(this.allCollections).filter(([key]) => collectionsIds.includes(key)) } + + #getElemCollections (elem) { return JSON.parse(elem.dataset.collectionsValue) } @@ -72,20 +77,23 @@ export default class extends Controller { return JSON.parse(elem.dataset.activeCollectionsValue) } - #addColorsTags (elem, colors) { + #addColorsTags (elem, collections) { const colorsContainer = document.createElement('span') - colors.forEach(c => this.#elemAddColorTag(colorsContainer, c)) + collections.forEach(c => this.#elemAddColorTag(colorsContainer, c[1].title, c[1].color)) elem.appendChild(colorsContainer) } - #elemAddColorTag (elem, color) { + #elemAddColorTag (elem, title, color) { const span = document.createElement('span') + span.dataset.controller = 'tooltip' + span.title = title span.style.backgroundColor = color span.style.height = '10px' span.style.width = '10px' span.style.borderRadius = '50%' span.style.display = 'inline-block' span.className += 'mx-1' + elem.appendChild(span) } } diff --git a/app/javascript/controllers/skos_collections_selector.js b/app/javascript/controllers/skos_collections_selector.js new file mode 100644 index 0000000000..f005e7b2d7 --- /dev/null +++ b/app/javascript/controllers/skos_collections_selector.js @@ -0,0 +1,49 @@ +import {Controller} from "@hotwired/stimulus" +import {useTomSelect} from "../mixins/useTomSelect"; + +// Connects to data-controller="skos-collection-selector" +export default class extends Controller { + // TODO to update to use TomSelect + static values = { + name: String, + enableColors: {type: Boolean, default: false} + } + + connect() { + this.select = useTomSelect(this.element, { + width: '100%', + plugins: ['remove_button'], + render: { + item: (data, escape) => { + if(this.enableColorsValue){ + const bgColor = data.color || '#ccc'; + return '
' + escape(data.text) + '
'; + }else { + return '
' + escape(data.text) + '
' + } + + } + } + }, + this.#onChange.bind(this)) + } + + #onChange(event) { + const selected = this.#getSelectedOptions() + const key = this.hasNameValue ? this.nameValue : event.currentTarget.name + const newData = { + [key]: selected.map(x => x.value) + } + this.element.dispatchEvent(new CustomEvent('changed', { + detail: { + data: newData + }, + bubbles: true, + cancelable: true, + })) + } + + #getSelectedOptions() { + return this.select.items.map(item => this.select.options[item]) + } +} diff --git a/app/javascript/controllers/turbo_frame_controller.js b/app/javascript/controllers/turbo_frame_controller.js index 41c67dd5d9..6520acb64a 100644 --- a/app/javascript/controllers/turbo_frame_controller.js +++ b/app/javascript/controllers/turbo_frame_controller.js @@ -24,8 +24,41 @@ export default class extends Controller { this.frame.innerHTML = this.placeHolderValue } else { this.frame.innerHTML = "" - this.urlValue = new HistoryService().getUpdatedURL(this.urlValue, data) - this.frame.src = this.urlValue + + if(this.#isCurrentPage()){ + this.urlValue = this.#currentPageUrl() + } + + this.urlValue = this.#updatedPageUrl(data) + + this.frame.src = this.urlValue + + } + } + + #isCurrentPage(){ + + let currentDisplayedUrl = new URL(this.#currentPageUrl(), document.location.origin) + + let initUrl = new URL(this.urlValue, document.location.origin) + + if (currentDisplayedUrl.toString().includes(this.urlValue)){ + return true + } else if (currentDisplayedUrl.searchParams.get('p') === initUrl.searchParams.get('p')){ + // this is a custom fix for only the ontology viewer page, + // that use the parameter ?p=section to tell which section is displayed + return true } + + return false + } + + + #currentPageUrl(){ + return document.location.pathname + document.location.search + } + + #updatedPageUrl(newUrlParams){ + return new HistoryService().getUpdatedURL(this.urlValue, newUrlParams) } } diff --git a/app/javascript/mixins/useChosen.js b/app/javascript/mixins/useChosen.js deleted file mode 100644 index 5f2c6c5412..0000000000 --- a/app/javascript/mixins/useChosen.js +++ /dev/null @@ -1,8 +0,0 @@ -export function useChosen(element, params, onChange = null) { - const chosen = $(element).chosen(params) - if(onChange){ - chosen.change(onChange) - } - - return chosen; -} \ No newline at end of file diff --git a/app/javascript/mixins/useHistory.js b/app/javascript/mixins/useHistory.js index ce895f1a64..e34b3c908e 100644 --- a/app/javascript/mixins/useHistory.js +++ b/app/javascript/mixins/useHistory.js @@ -59,9 +59,9 @@ export class HistoryService { return newState } - #updateURLFromState(urlParams, state) { - Object.entries(state).forEach(([key, val]) => { - if (key !== 'p'){ + #updateURLFromState(urlParams, oldState) { + Object.entries(oldState).forEach(([key, val]) => { + if (key !== 'p' && !urlParams.has(key)) { urlParams.set(key, val) } }) diff --git a/app/models/bpid_resolver.rb b/app/models/bpid_resolver.rb deleted file mode 100644 index 3f345b39f1..0000000000 --- a/app/models/bpid_resolver.rb +++ /dev/null @@ -1,46 +0,0 @@ -require 'cgi' -require 'ostruct' -require 'json' -require 'open-uri' - -class BpidResolver - require Rails.root + 'lib/resolver/acronym_from_virtual' - require Rails.root + 'lib/resolver/virtual_from_acronym' - require Rails.root + 'lib/resolver/virtual_from_version' - - def self.id_to_acronym(id) - acronym = self.acronym_from_virtual_id(id) - acronym = self.acronym_from_version_id(id) unless acronym - acronym - end - - def self.acronym_to_virtual_id(acronym) - self.virtual_id_from_acronym(acronym) - end - - private - - def self.acronym_from_id(id) - acronym = self.acronym_from_virtual_id(id) - acronym = self.acronym_from_version_id(id) unless acronym - acronym - end - - def self.acronym_from_virtual_id(virtual_id) - ACRONYM_FROM_VIRTUAL["old:acronym_from_virtual:#{virtual_id}"] - end - - def self.acronym_from_version_id(version_id) - virtual = virtual_id_from_version_id(version_id) - acronym_from_virtual_id(virtual) - end - - def self.virtual_id_from_version_id(version_id) - VIRTUAL_FROM_VERSION["old:virtual_from_version:#{version_id}"] - end - - def self.virtual_id_from_acronym(acronym) - VIRTUAL_FROM_ACRONYM["old:virtual_from_acronym:#{acronym}"] - end - -end \ No newline at end of file diff --git a/app/views/admin/categories/_form.html.haml b/app/views/admin/categories/_form.html.haml index a1abde7419..75974b5a3a 100644 --- a/app/views/admin/categories/_form.html.haml +++ b/app/views/admin/categories/_form.html.haml @@ -30,6 +30,11 @@ = t('admin.categories.form.description') %td.top = f.text_area :description, class: "form-control" + %tr + %th + = t('admin.categories.form.parent_category') + %td.top + = categories_select(id: 'category_parent_select', name: 'category[parentCategory]', selected: @category&.parentCategory) - unless new_record %tr %th diff --git a/app/views/admin/index.html.haml b/app/views/admin/index.html.haml index 9891c88f02..da8f0cbdee 100644 --- a/app/views/admin/index.html.haml +++ b/app/views/admin/index.html.haml @@ -15,7 +15,11 @@ - selected = params[:section] || sections.first.downcase = render Layout::VerticalTabsComponent.new(header: t('admin.index.administration_console'), titles: sections, selected: selected, url_parameter: 'section') do |t| - t.item_content do - = render 'analytics' + - if @ontology_visits[:visits].empty? + %div.d-flex.justify-content-center + Google analytics not enabled + - else + = render 'analytics' - t.item_content do = render 'main' - t.item_content do diff --git a/app/views/agents/_agent.html.haml b/app/views/agents/_agent.html.haml index f6c04ce75d..0f55ca7168 100644 --- a/app/views/agents/_agent.html.haml +++ b/app/views/agents/_agent.html.haml @@ -3,6 +3,8 @@ %div{style: 'width: 250px'} %div.text-truncate{title: agent.name} = agent.name + %td + = agent.acronym %td = raw display_identifiers(agent.identifiers) %td diff --git a/app/views/agents/_form.html.haml b/app/views/agents/_form.html.haml index 60b02f33ee..3a688a6caa 100644 --- a/app/views/agents/_form.html.haml +++ b/app/views/agents/_form.html.haml @@ -9,7 +9,7 @@ = hidden_field_tag :deletable, deletable if deletable = hidden_field_tag agent_field_name(:id, name_prefix), agent.id if agent.id - - if affiliation?(agent) && params[:parent_id] + - if params[:show_affiliations].eql?('false') = hidden_field_tag agent_field_name(:agentType, name_prefix), agent.agentType - else %tr @@ -30,19 +30,19 @@ %span.asterik * %td.top = text_field_tag agent_field_name(:name, name_prefix), agent.name, class: "form-control" - %tr{'data-form-options-display-target':"option1", class: affiliation?(agent) && 'd-none'} + %tr{'data-form-options-display-target':"option1", class: is_organization?(agent) && 'd-none'} %th = t("agents.form.email") %span.asterik %td.top = email_field_tag agent_field_name(:email, name_prefix), agent.email, class: "form-control" - %tr{'data-form-options-display-target':"option2", class: !affiliation?(agent) && 'd-none'} + %tr{'data-form-options-display-target':"option2", class: !is_organization?(agent) && 'd-none'} %th = t("agents.form.acronym") %span.asterik %td.top = text_field_tag agent_field_name(:acronym, name_prefix), agent.acronym,class: "form-control" - %tr{'data-form-options-display-target':"option2", class: !affiliation?(agent) && 'd-none'} + %tr{'data-form-options-display-target':"option2", class: !is_organization?(agent) && 'd-none'} %th = t("agents.form.homepage") %td.top @@ -55,30 +55,22 @@ %tr %th = t("agents.form.identifiers") + - identifier = agent&.identifiers&.first %td.top - %div.agents-identifiers - = render NestedFormInputsComponent.new do |c| - - c.template do - %div.d-flex{id: 'NEW_RECORD'} - %div.w-100 - = hidden_field_tag agent_identifier_name('NEW_RECORD' , :creator, name_prefix), session[:user].id - = text_field_tag agent_identifier_name('NEW_RECORD' , :notation, name_prefix), '', class: "form-control" - %div{style:'width: 15%'} - - values = %w[ORCID ROR ISNI GRID] - = render SelectInputComponent.new(id: "agent_identifiers_schemaAgency_NEW_RECORD", name: agent_identifier_name('NEW_RECORD', :schemaAgency, name_prefix), values: values, selected: 'ORCID') - - c.empty_state do - = hidden_field_tag agent_field_name('', name_prefix+"[#{Array(agent.identifiers).size}]") - - Array(agent.identifiers).each_with_index do |identifier, i| - - c.row do - %div.d-flex{id: identifier.id} - %div.w-100 - = hidden_field_tag agent_identifier_name(i.to_s.upcase, :creator, name_prefix), session[:user].id - = text_field_tag agent_identifier_name(i.to_s.upcase, :notation, name_prefix), identifier.notation, class: "form-control" - %div{style:'width: 15%'} - - values = %w[ORCID ROR ISNI GRID] - = render SelectInputComponent.new(id: "#{name_prefix}_identifiers_schemaAgency_#{i.to_s.upcase}", name: agent_identifier_name(i.to_s.upcase, :schemaAgency, name_prefix), values: values, selected: identifier.schemaAgency) + %div.agents-identifiers{'data-form-options-display-target':"option2", class: !is_organization?(agent) && 'd-none'} + - if identifier&.schemaAgency&.eql?('ROR') + = agent_identifier_input('0', name_prefix, identifier.notation) + - else + = agent_identifier_input('0', name_prefix) + + %div.agents-identifiers{'data-form-options-display-target':"option1", class: is_organization?(agent) && 'd-none'} + - if identifier&.schemaAgency&.eql?('ORCID') + = agent_identifier_input('1', name_prefix, identifier.notation, is_organization: false) + - else + = agent_identifier_input('1', name_prefix, is_organization: false) + - if show_affiliations - %tr + %tr{'data-form-options-display-target':"option1", class: is_organization?(agent) && 'd-none'} %th = t("agents.form.affiliations") %td.top.agents-affiliations.agents-inputs diff --git a/app/views/agents/index.html.haml b/app/views/agents/index.html.haml index 8a038c93a7..8864fe749f 100644 --- a/app/views/agents/index.html.haml +++ b/app/views/agents/index.html.haml @@ -13,6 +13,7 @@ = render TableComponent.new(id: 'admin_agents', custom_class: 'border rounded p-1') do |t| - t.header do |h| - h.th {t("agents.index.first_name")} + - h.th {t("agents.index.acronym")} - h.th {t("agents.form.identifiers")} - h.th {t("agents.form.affiliations")} - h.th {t("agents.form.type")} diff --git a/app/views/annotator/index.html.haml b/app/views/annotator/index.html.haml index 4d5636ed6c..8b83bab08c 100644 --- a/app/views/annotator/index.html.haml +++ b/app/views/annotator/index.html.haml @@ -37,6 +37,7 @@ = render Input::SelectComponent.new(label: t('annotator.include_ancestors'), id: 'ancestors_level', name: 'class_hierarchy_max_level', value: @ancestors_levels, selected: params[:class_hierarchy_max_level]) .filters_line - include_score_helper = 'Score annotations following previous NCBO 2009 measure (old) or Score annotations following C-Value measure (cvalue) or Score annotations following C-Value measure with hierarchy expansion (cvalueh).' + = render Input::SelectComponent.new(label: t('annotator.include_score'), id: 'include_score', name: 'score', value: @include_score, tooltip: include_score_helper, selected: params[:score]) = render Input::NumberComponent.new(label: t('annotator.score_threshold'), name: "score_threshold", value: params[:score_threshold] || 0, tooltip: 'Specify minimum score value for annotations.') = render Input::NumberComponent.new(label: t('annotator.confidence_threshold'), name: 'confidence_threshold', value: params[:confidence_threshold] || 0, tooltip: 'Specify the minimum position in the score distribution (between 1 and 100).') diff --git a/app/views/check_resolvability/index.html.haml b/app/views/check_resolvability/index.html.haml index 2a190c022d..fc5c9bfd9a 100644 --- a/app/views/check_resolvability/index.html.haml +++ b/app/views/check_resolvability/index.html.haml @@ -35,7 +35,7 @@ - if @results %div.bg-white.mt-3.border.rounded %div.p-1 - - text = check_resolvability_message(url_resolvable?(@results), @results[:allowed_format], @results[:status]) + - text = check_resolvability_message(url_resolvable?(@results), @results[:allowed_format], @results[:status], response_time: @results[:average_response_time]) - if url_content_negotiable?(@results) = render Display::AlertComponent.new(type:'success') do = text @@ -45,6 +45,7 @@ - else = render Display::AlertComponent.new(type:'danger') do = text + %div.p-1 - count = 0 - @results[:redirections].each do |format, result| @@ -63,16 +64,8 @@ - else - status = result[:status] - color = status.eql?('200') ? '' : 'bg-danger-light text-danger' - - format_badge = render ChipButtonComponent.new(class: "mx-1", text: result[:allowed_format].first.blank? ? t("check_resolvability.format_not_specified"): result[:allowed_format].first) + - format_badge = render ChipButtonComponent.new(class: "mx-1", type: 'clickable', text: result[:allowed_format].first.blank? ? t("check_resolvability.format_not_specified"): result[:allowed_format].first) = render ChipButtonComponent.new(class: "mx-1 #{color}", type: 'clickable', text: status) = format_badge - - - - - - - - - - + - if index.eql?(result[:redirections].length - 1) + = render ChipButtonComponent.new(class: "mx-1", type: 'clickable', text: "Response time: #{result[:response_time]} s") \ No newline at end of file diff --git a/app/views/collections/_list_view.html.haml b/app/views/collections/_list_view.html.haml index f05ee71946..a50abe0ce2 100644 --- a/app/views/collections/_list_view.html.haml +++ b/app/views/collections/_list_view.html.haml @@ -13,4 +13,4 @@ - scheme.id = scheme['@id'] - tree_child.child(child: scheme, href: collection_path(collection['@id'], request_lang), children_href: '#', selected: scheme.id.eql?(selected_collection_id), - target_frame: 'collection', data: {collectionid: collection['@id']}) + target_frame: 'collection', data: {collectionid: collection['@id']}, is_reused: concept_reused?(submission: @submission, concept_id: scheme.id)) diff --git a/app/views/concepts/_list.html.haml b/app/views/concepts/_list.html.haml index e00c5966e7..9c9a28a848 100644 --- a/app/views/concepts/_list.html.haml +++ b/app/views/concepts/_list.html.haml @@ -9,7 +9,7 @@ - children_link, data, href = concept_tree_data(@ontology.acronym, concept, request_lang, []) = render TreeLinkComponent.new(child: concept, href: href, children_href: '#', selected: concept.id.eql?(concepts.first.id) && c.auto_click?, - target_frame: 'concept_show', data: data) + target_frame: 'concept_show', data: data, is_reused: concept_reused?(submission: @submission, concept_id: concept.id)) - c.error do = t('concepts.list_error') diff --git a/app/views/concepts/_show.html.haml b/app/views/concepts/_show.html.haml index fecb7bea9b..a30f061fdf 100644 --- a/app/views/concepts/_show.html.haml +++ b/app/views/concepts/_show.html.haml @@ -3,72 +3,73 @@ = render Display::AlertComponent.new do = t('concepts.use_jump_to') - else - = render TabsContainerComponent.new(type:'outline') do |c| + %div{'data-controller': 'concepts-json', 'data-action': 'click->concepts-json#update'} + = render TabsContainerComponent.new(type:'outline') do |c| + - c.pinned_right do + - if $PURL_ENABLED + %div.mx-1 + = link_to("#classPermalinkModal", class: "class-permalink nav-link", title: t('concepts.permanent_link_class'), aria: {label: t('concepts.permanent_link_class')}, data: {toggle: "modal", current_purl: "#{@current_purl}"}) do + %i{class: "fas fa-link", aria: {hidden: "true"}} + %div{'data-concepts-json-target': 'button'} + .concepts_json_button + = render RoundedButtonComponent.new(link: "#{@ontology.id}/classes/#{escape(@concept.id)}?display=all&apikey=#{get_apikey}", target:'_blank') + - apikey = "apikey=#{get_apikey}" + - baseClassUrl = "#{@ontology.id}/classes/#{escape(@concept.id)}" + - c.item(title: t('concepts.details'), path: '#details', selected: true, json_link: "#{baseClassUrl}?#{apikey}&display=all") - - c.pinned_right do - - if $PURL_ENABLED - %div.mx-1 - = link_to("#classPermalinkModal", class: "class-permalink nav-link", title: t('concepts.permanent_link_class'), aria: {label: t('concepts.permanent_link_class')}, data: {toggle: "modal", current_purl: "#{@current_purl}"}) do - %i{class: "fas fa-link", aria: {hidden: "true"}} - %div - = render RoundedButtonComponent.new(link: "#{@ontology.id}/classes/#{escape(@concept.id)}?display=all&apikey=#{get_apikey}", target:'_blank') + - unless skos? + - c.item(id: 'instances', path: '#instances', json_link: "#{baseClassUrl}/instances?#{apikey}") do + = t('concepts.instances') + ( + %span#concept_instances_sorted_list_count + ) - - c.item(title: t('concepts.details'), path: '#details', selected: true) + - c.item(title: t('concepts.visualization'), path: '#visualization') - - unless skos? - - c.item(id: 'instances', path: '#instances') do - = t('concepts.instances') - ( - %span#concept_instances_sorted_list_count - ) + - c.item(id: 'notes', path: '#notes', json_link: "#{baseClassUrl}/notes?#{apikey}") do + = t('concepts.notes') + %span#note_count_wrapper + ( + %span#note_count= @notes.length + ) + - c.item(id: 'mappings', path: '#mappings', json_link: "#{baseClassUrl}/mappings?#{apikey}") do + .d-flex + #{t('concepts.mappings')} + ( + = concept_mappings_loader(ontology_acronym: @ontology.acronym, concept_id: @concept.id) + ) - - c.item(title: t('concepts.visualization'), path: '#visualization') + - if @enable_ontolobridge + - c.item(title: t('concepts.new_term_requests'), path: '#request_term') - - c.item(id: 'notes', path: '#notes') do - = t('concepts.notes') - %span#note_count_wrapper - ( - %span#note_count= @notes.length - ) - - c.item(id: 'mappings', path: '#mappings') do - .d-flex - #{t('concepts.mappings')} - ( - = concept_mappings_loader(ontology_acronym: @ontology.acronym, concept_id: @concept.id) - ) - - - if @enable_ontolobridge - - c.item(title: t('concepts.new_term_requests'), path: '#request_term') - - - c.item_content do - = render :partial =>'/concepts/details' - - - unless skos? - c.item_content do - = render :partial =>'instances/instances' , locals: {id: "class-instances-data-table"} - - c.item_content do - = render :partial =>'/concepts/biomixer' + = render :partial =>'/concepts/details' - - c.item_content do - = render :partial =>'/notes/list' + - unless skos? + - c.item_content do + = render :partial =>'instances/instances' , locals: {id: "class-instances-data-table"} + - c.item_content do + = render :partial =>'/concepts/biomixer' - - c.item_content do - = render TurboFrameComponent.new(id:'concept_mappings', - src:"/ajax/mappings/get_concept_table?ontologyid=#{@ontology.acronym}&conceptid=#{CGI.escape(@concept.id)}") + - c.item_content do + = render :partial =>'/notes/list' - - if @enable_ontolobridge - c.item_content do - = render :partial =>'/concepts/request_term' + = render TurboFrameComponent.new(id:'concept_mappings', + src:"/ajax/mappings/get_concept_table?ontologyid=#{@ontology.acronym}&conceptid=#{CGI.escape(@concept.id)}") - :javascript - jQuery(document).ready(function(){ + - if @enable_ontolobridge + - c.item_content do + = render :partial =>'/concepts/request_term' - jQuery("#classPermalinkModal").on("shown.bs.modal", function (e) { - var currentPurl = jQuery("a.class-permalink").data("current-purl"); - jQuery("#purl_input").val(currentPurl); - }) + :javascript + jQuery(document).ready(function(){ + jQuery("#classPermalinkModal").on("shown.bs.modal", function (e) { + var currentPurl = jQuery("a.class-permalink").data("current-purl"); + jQuery("#purl_input").val(currentPurl); + }) - jQuery("#purl_input").on("click", function () { - jQuery(this).select(); - }); - }); + jQuery("#purl_input").on("click", function () { + jQuery(this).select(); + }); + }); diff --git a/app/views/home/cookies.html.haml b/app/views/home/cookies.html.haml new file mode 100644 index 0000000000..d02f687a9b --- /dev/null +++ b/app/views/home/cookies.html.haml @@ -0,0 +1,13 @@ += turbo_frame_tag :cookies_modal do + - if cookies[:cookies_accepted].nil? # don't re-render if a true/false selected + %section.cookies-modal + %h4 + = t('cookies_modal.title') + %p + = t('cookies_modal.paragraph1', portal: portal_name) + %p + = t('cookies_modal.paragraph2', portal: portal_name) + %div + = link_button_component(id:'accept-cookie-selector', value: t('cookies_modal.accept_button'), href: cookies_path(cookies: true), size: "slim", variant: 'primary') + %div.cookie-privacy-link + = link_to t('cookies_modal.privacy_link'), $FOOTER_LINKS.dig(:sections, :agreements, :privacy_policy) diff --git a/app/views/home/feedback/feedback.html.haml b/app/views/home/feedback/feedback.html.haml index 7d54a536b3..e23b01fdec 100644 --- a/app/views/home/feedback/feedback.html.haml +++ b/app/views/home/feedback/feedback.html.haml @@ -25,6 +25,9 @@ %p.feedback-email = t("home.feedback.feedback_info_text") %a{:href => "mailto: #{$SUPPORT_EMAIL}"}= $SUPPORT_EMAIL + = t("home.feedback.feedback_info_text_rest") + %a{:href => $GITHUB_ISSUES} + Github issues - if session[:user].nil? %p.feedback-input-title = t("home.feedback.email") diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml index 7a010b73da..83fc781581 100644 --- a/app/views/home/index.html.haml +++ b/app/views/home/index.html.haml @@ -173,24 +173,44 @@ %h4 = format_number_abbreviated(@users_count) %p= t("home.users") - .home-statistics-link.justify-content-end + .home-statistics-link.justify-content-end{style: @analytics.empty? && "visibility: hidden"} = link_to t("home.see_details"),'/statistics', target: "_blank" - .home-section - .home-statistics-container - .home-support-title - %p= t('home.support_and_collaborations') + - if @slices + .home-section + .home-section-title + .text + = "#{portal_name} slices" %hr.home-section-line/ - .home-support-items - - $HOME_PAGE_LOGOS&.each do |logo| - %a{href:logo[:url], target: "_blanc"} - %img{src: asset_path(logo[:img_src])} - - .home-section - .home-statistics-container - .home-support-title - %p= t('home.ontoportal_instances') + .home-section-description + .div + = t('home.slices_description') + .home-slices-container + - @slices.each do |slice, index| + - slice_link = "https://#{slice.acronym}.#{$UI_URL.sub("https://", "")}" + .home-slice{'data-controller': 'tooltip', title: content_tag(:div, slice.description, style: 'max-width: 200px')} + = link_to slice_link do + .home-slice-icon + .home-slice-ontologies + = slice.ontologies.length + = inline_svg 'icons/slices.svg', width: "70", height: "70" + + .home-slice-name + = "#{slice.name} (#{slice.acronym})" + = render Buttons::RegularButtonComponent.new(id:'regular-button', value: t('home.suggest_slice'), variant: "secondary", state: "regular", href: '/feedback') do |btn| + - btn.icon_right do + = inline_svg_tag "icons/plus.svg" + + .home-ontoportal-instances + .ontoportal-instances-container + .home-section-title.ontoportal + .text.mr-2 + = t('home.ontoportal_instances') %hr.home-section-line/ + + .home-section-description + .div + = home_ontoportal_description .home-support-items - $PORTALS_INSTANCES&.each do |portal| %div.text-center @@ -198,7 +218,16 @@ = inline_svg 'logo-white.svg', width: "35", height: "26" %p{style: "color: #{portal[:color]}"} = portal[:portal] - + + .home-section + .home-section-title + .text + = t('home.support_and_collaborations') + %hr.home-section-line/ + .home-support-items + - $HOME_PAGE_LOGOS&.each do |logo| + %a{href:logo[:url], target: "_blanc"} + %img{src: asset_path(logo[:img_src])} :javascript function submitAnnotator(){ diff --git a/app/views/instances/_details.html.haml b/app/views/instances/_details.html.haml index f1ddcb015a..146dcd9464 100644 --- a/app/views/instances/_details.html.haml +++ b/app/views/instances/_details.html.haml @@ -6,7 +6,7 @@ = render ConceptDetailsComponent.new(id:'instance-details', acronym: ontology_acronym, concept_id: @instance["@id"]) do |c| - c.header(stripped: true) do |t| - - t.add_row({th: t("instances.id")}, {td: link_to_with_actions(@instance["@id"]) }) + - t.add_row({th: t("instances.id")}, {td: link_to_with_actions(@instance["@id"], acronym: @ontology.acronym) }) - label = @instance['label'] || @instance['prefLabel'] - unless label.blank? diff --git a/app/views/layouts/_header.html.erb b/app/views/layouts/_header.html.erb index fcf060a9eb..1340bdbb26 100644 --- a/app/views/layouts/_header.html.erb +++ b/app/views/layouts/_header.html.erb @@ -1,25 +1,28 @@ - lang="<%=I18n.locale%>"> + lang="<%= I18n.locale %>"> - <%= render partial: 'ga_tracking' %> - + <%= render partial: 'ga_tracking' %> + - - + + - <% unless Rails.env.appliance? %> + <% unless Rails.env.appliance? %> - + <% end %> - - <%= csrf_meta_tag %> + + <%= csrf_meta_tag %> - <%if @title.nil?%><%=$ORG_SITE%><%else%><%="#{@title} | #{$ORG_SITE}"%><%end%> + + <% if @title.nil? %><%= $ORG_SITE %> + <% else %><%= "#{@title} | #{$ORG_SITE}" %> + <% end %> - - - - + + + + <%= stylesheet_link_tag "https://use.fontawesome.com/releases/v5.2.0/css/all.css", integrity: "sha384-hWVjflwFxL6sNzntih27bfxkr27PmbbK/iSvJ+a4+0owXq79v+lsFkW54bOGbiDQ", crossorigin: "anonymous" %> <%= stylesheet_link_tag "application" %> @@ -27,18 +30,34 @@ <%= javascript_include_tag "vendor" %> - + - <%=render partial: 'layouts/topnav'%> - -
- <%=render partial: 'layouts/notices'%> \ No newline at end of file +<%= render partial: 'layouts/topnav' %> +<%= turbo_frame_tag :cookies_modal, src: cookies_path if cookies[:cookies_accepted].nil? && !(Rails.env.development? || Rails.env.test?) %> + +
+<%= render partial: 'layouts/notices' %> \ No newline at end of file diff --git a/app/views/layouts/_notices.html.haml b/app/views/layouts/_notices.html.haml index 7d99b276eb..3700404d4f 100644 --- a/app/views/layouts/_notices.html.haml +++ b/app/views/layouts/_notices.html.haml @@ -1,4 +1,4 @@ -- if Rails.env.appliance? +- if session[:user]&.admin? && Rails.env.appliance? = license_notification(current_license()) - flash.each do |key, message| @@ -6,21 +6,18 @@ - do_not_display_subdomain_info_here = Set.new(["homeall_resources"]) - if at_slice? && !do_not_display_subdomain_info_here.include?("#{controller.controller_name}#{controller.action_name}") - .subdomain_info{:style => "margin: 13px; padding: 5px; border: 1px solid gray; font-size:14px; background-color: #ffffcc;"} - %p{:style => "text-align: left; margin-bottom: 0;"} - - query_string = request.query_string.empty? ? "" : "?#{request.query_string}" - You are viewing the - %b= @subdomain_filter[:name] - %a.pop_window{:href => "help?pop=true#slice_definition", :target => "_blank"} - = $SITE - = t('layout.notices.slice') - = t('layout.notices.at') - = succeed "." do - %b= request.host - = $SITE - = succeed "." do - %a{:href => "#{$UI_URL}#{request.path}#{query_string}"} - = t('layout.notices.visit_the_site') + .slice-notice-bar-container + .slice-notice-bar + %div + .title + = t('home.viewing_slice') + .slice-name + = @subdomain_filter[:name] + .view-full-site-button + - query_string = request.query_string.empty? ? "" : "?#{request.query_string}" + = render Buttons::RegularButtonComponent.new(id:'slices-view-full-site', value: t('home.view_full_site'), variant: "primary", href: "#{$UI_URL}#{request.path}#{query_string}", color: 'warning', size: "slim") do |btn| + = btn.icon_right do + = inline_svg_tag "arrow-right.svg" #site-notice - message_name = "" - unless $SITE_NOTICE.nil? || $SITE_NOTICE.empty? diff --git a/app/views/layouts/_topnav.html.haml b/app/views/layouts/_topnav.html.haml index 4d0a013748..c73008dfeb 100644 --- a/app/views/layouts/_topnav.html.haml +++ b/app/views/layouts/_topnav.html.haml @@ -60,4 +60,6 @@ = link_to(t('layout.header.cite_us'), $FOOTER_LINKS[:sections][:about][:cite_us], target: "_blank") - s.item do = link_to(t('layout.header.release_notes'), $FOOTER_LINKS[:sections][:products][:release_notes], target: "_blank") + - s.item do + = link_to(t('taxonomy.groups_and_categories'), '/groups') diff --git a/app/views/layouts/appliance.html.haml b/app/views/layouts/appliance.html.haml index 817bd30265..3e306068c0 100644 --- a/app/views/layouts/appliance.html.haml +++ b/app/views/layouts/appliance.html.haml @@ -26,7 +26,8 @@ %body{:class => "#{controller_name} #{action_name}"} = render partial: "layouts/topnav" - + = turbo_frame_tag :cookies_modal, src: cookies_path if cookies[:cookies_accepted].nil? + %div.flex-grow-1 = render partial: "layouts/notices" = modal_frame_container diff --git a/app/views/layouts/ontology_viewer/_header.html.haml b/app/views/layouts/ontology_viewer/_header.html.haml index 877e8c4083..291df004d7 100644 --- a/app/views/layouts/ontology_viewer/_header.html.haml +++ b/app/views/layouts/ontology_viewer/_header.html.haml @@ -4,11 +4,13 @@ -# A header of sorts to display ontology name and subset of details. .ontology-details-header-container .ontology-details-path - %a{href: "/ontologies"} ontologies + %a{href: "/ontologies"} Ontologies - if @ontology.viewOf = inline_svg_tag 'arrow-right-outlined.svg' %div - = @ontology.viewOf.split('/').last + - viewOfAcronym = @ontology.viewOf.split('/').last + %a{href: "/ontologies/#{viewOfAcronym}"} + = viewOfAcronym = inline_svg_tag 'arrow-right-outlined.svg' %div = @ontology.acronym diff --git a/app/views/login/index.html.haml b/app/views/login/index.html.haml index 2ab02ae262..0d39f910b2 100644 --- a/app/views/login/index.html.haml +++ b/app/views/login/index.html.haml @@ -1,10 +1,9 @@ - @title = t('login.title') -- unless @errors.nil? - %div{:style => "color:red;"} - = t('login.invalid_login') - %ul +.d-flex.justify-content-center.mt-4 + - unless @errors.nil? + = render Display::AlertComponent.new(type: "danger", closable: false) do - for error in @errors - %li= error + %div=error .d-flex.justify-content-center .login-form = form_for(:user, :url => {:controller => 'login',:action=>'create'}) do |f| diff --git a/app/views/mappings/_count.html.haml b/app/views/mappings/_count.html.haml index e3cd5f9336..987837b6a3 100644 --- a/app/views/mappings/_count.html.haml +++ b/app/views/mappings/_count.html.haml @@ -1,7 +1,7 @@ = turbo_frame_tag "mappings_table" do .summary-mappings-tab .summary-mappings-tab-table - = render TableComponent.new(id: 'summary-mappings-table', borderless: true, outline: true, searching: true, sort_column: '0', no_init_sort: true) do |t| + = render TableComponent.new(id: 'summary-mappings-table', borderless: true, outline: true, searching: true, sort_column: '0', no_init_sort: true, search_placeholder: "Filter by semantic resources") do |t| - t.header do |h| - h.th {t("mappings.count.ontology")} - h.th {t("mappings.count.mappings")} diff --git a/app/views/mappings/_form.html.haml b/app/views/mappings/_form.html.haml index 264b680e70..edbedd7422 100644 --- a/app/views/mappings/_form.html.haml +++ b/app/views/mappings/_form.html.haml @@ -3,7 +3,7 @@ %div %span#create_mapping_spinner.card.p-3.text-center - = loading_spinner + = loader_component = render_alerts_container diff --git a/app/views/mappings/_show_line.html.haml b/app/views/mappings/_show_line.html.haml index c741b3b497..bbfab2b78e 100644 --- a/app/views/mappings/_show_line.html.haml +++ b/app/views/mappings/_show_line.html.haml @@ -14,11 +14,11 @@ - begin - ont = target_concept.explore.ontology - ont_name = ont.acronym - - ont_link = link_to ont_name, ontology_path(ont_name) + - ont_link = link_to ont_name, ontology_path(ont_name), 'data-turbo-frame':'_top' - rescue - ont_name = target_concept.links['ontology'] || target_concept.id - ont_link = ont_name - - cls_link = raw(get_link_for_cls_ajax(target_concept.id, ont_name)) + - cls_link = raw(get_link_for_cls_ajax(target_concept.id, ont_name, '_top')) - type = 'Internal' - else - cls_label = get_label_for_external_cls(target_concept.links["self"]) diff --git a/app/views/ontologies/browser/_ontologies.html.haml b/app/views/ontologies/browser/_ontologies.html.haml index 8e3d8bd304..bd3aed0cf5 100644 --- a/app/views/ontologies/browser/_ontologies.html.haml +++ b/app/views/ontologies/browser/_ontologies.html.haml @@ -1,6 +1,6 @@ = render InfiniteScrollComponent.new(id: 'ontologies_list', collection: @ontologies, - next_url: ontologies_filter_url(@request_params, page: @page.nextPage), + next_url: ontologies_with_filters_url(@request_params, page: @page.nextPage), current_page: @page.page, next_page: @page.nextPage) do |c| - if @page.page.eql?(1) diff --git a/app/views/ontologies/browser/browse.html.haml b/app/views/ontologies/browser/browse.html.haml index 83da56b6c5..d1979fd359 100644 --- a/app/views/ontologies/browser/browse.html.haml +++ b/app/views/ontologies/browser/browse.html.haml @@ -56,7 +56,11 @@ = browse_filter_section_label(key) %span.badge.badge-primary{"data-show-filter-count-target":"countSpan", style: "#{values[2] && values[2].positive? ? '' : 'display: none;'}"} = values[2] - = inline_svg_tag 'arrow-down.svg' + .d-flex.align-items-center + - if key.eql?(:categories) || key.eql?(:groups) + .mr-2 + = render Display::InfoTooltipComponent.new(text: browse_taxonomy_tooltip(key.to_s)) + = inline_svg_tag 'arrow-down.svg' .collapse{id: "browse-#{key}-filter", class: "#{values[2].positive? ? 'show': ''}"} .browse-filter-checks-container - values.first.each do |object| diff --git a/app/views/ontologies/concepts_browsers/_collections_picker.html.haml b/app/views/ontologies/concepts_browsers/_collections_picker.html.haml index 1191df3ac7..638bc9758b 100644 --- a/app/views/ontologies/concepts_browsers/_collections_picker.html.haml +++ b/app/views/ontologies/concepts_browsers/_collections_picker.html.haml @@ -8,5 +8,5 @@ %label{:for => id} Collections %div = select_tag(:collections,options_for_select(collections_labels.map{|s| [s["prefLabel"].last, s["@id"], {'data-color': s['color']}]}, selected_collection.map{|x| x["@id"]}), - { multiple: multiple, id: id, class:"form-control", include_blank: true, - data:{controller:'chosen', 'chosen-name-value': :collectionid}.merge(data)}) \ No newline at end of file + { multiple: multiple, id: id, + data:{controller:'skos-collections-selector', 'skos-collections-selector-name-value': :collectionid}.merge(data)}) \ No newline at end of file diff --git a/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml b/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml index d4affe93f9..1160a7d29f 100644 --- a/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml +++ b/app/views/ontologies/concepts_browsers/_concepts_tree.html.haml @@ -13,7 +13,7 @@ = render partial: 'ontologies/concepts_browsers/collections_picker', locals: {multiple: true, id: 'collection-color-filter', data: {action: 'changed->skos-collection-colors#updateCollectionTags' , - 'chosen-enable-colors-value': 'true'}} + 'skos-collection-colors-enable-colors-value': 'true'}} -# Class tree %div#sd_content.px-1{style: 'overflow-y: scroll; height: 60vh;'} - if skos? && @roots&.empty? diff --git a/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml b/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml index 958807977a..97046b62ca 100644 --- a/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml +++ b/app/views/ontologies/concepts_browsers/_scheme_picker.html.haml @@ -12,6 +12,6 @@ = select_tag(:concept_schemes, options_for_select(schemes_labels.map{|s| [s["prefLabel"].last, s["@id"]]}, selected_scheme.compact.map{|x| x["@id"]} ), {multiple: true, id: "schemes_select", - data:{controller:'chosen', 'chosen-name-value': :concept_schemes, + data:{controller:'skos-collections-selector', 'skos-collections-selector-name-value': :concept_schemes, action: 'changed->history#updateURL changed->turbo-frame#updateFrame'}}) diff --git a/app/views/ontologies/content_serializer.html.haml b/app/views/ontologies/content_serializer.html.haml index beda316957..34045b7b93 100644 --- a/app/views/ontologies/content_serializer.html.haml +++ b/app/views/ontologies/content_serializer.html.haml @@ -1,2 +1,3 @@ = render_in_modal do - = rdf_highlighter_container(@format, @result) if @result + #resource_content_modal + = rdf_highlighter_container(@format, @result) if @result diff --git a/app/views/ontologies/htaccess.html.haml b/app/views/ontologies/htaccess.html.haml index bd59fcbe1b..a48615550d 100644 --- a/app/views/ontologies/htaccess.html.haml +++ b/app/views/ontologies/htaccess.html.haml @@ -1,68 +1,70 @@ = render_in_modal do - %p - = t("ontologies.htaccess_redirection_description") + #redirection_rules_modal + %p + = t("ontologies.htaccess_redirection_description") - %h5 - %strong - = t("ontologies.instructions_servers", server: "Apache") - %ol - %li + %h5 %strong - = t("ontologies.htaccess_redirection.instruction_1") - = t("ontologies.htaccess_redirection.instruction_1_content") - %li - %strong - = t("ontologies.htaccess_redirection.instruction_2") - = t("ontologies.htaccess_redirection.instruction_2_content") - %li - %strong - = t("ontologies.htaccess_redirection.instruction_3") - = t("ontologies.htaccess_redirection.instruction_3_content") - - .htacess-code-container - .clipboard-component-resource-content{style: 'position: absolute; right: 2%; top: 8%;'} - = render ClipboardComponent.new(message: @htaccess_content, show_content: false) - %pre.mb-0 - %code.d-block{style: 'text-wrap: pretty; word-break: break-all; color: white;'} - = @htaccess_content + = t("ontologies.instructions_servers", server: "Apache") + %ol + %li + %strong + = t("ontologies.htaccess_redirection.instruction_1") + = t("ontologies.htaccess_redirection.instruction_1_content") + %li + %strong + = t("ontologies.htaccess_redirection.instruction_2") + = t("ontologies.htaccess_redirection.instruction_2_content") + %li + %strong + = t("ontologies.htaccess_redirection.instruction_3") + = t("ontologies.htaccess_redirection.instruction_3_content") + + .htacess-code-container + .clipboard-component-resource-content{style: 'position: absolute; right: 2%; top: 8%;'} + = render ClipboardComponent.new(message: @htaccess_content, show_content: false) + %pre.mb-0 + %code.d-block{style: 'text-wrap: pretty; word-break: break-all; color: white;'} + = @htaccess_content - %hr + %hr - %h5 - %strong - = t("ontologies.instructions_servers", server: "Nginx") - %ol - %li - %strong - = t("ontologies.nginx_redirection.instruction_1") - = t("ontologies.nginx_redirection.instruction_1_content") - %li - %strong - = t("ontologies.nginx_redirection.instruction_2") - = t("ontologies.nginx_redirection.instruction_2_content") - %li - %strong - = t("ontologies.nginx_redirection.instruction_3") - = t("ontologies.nginx_redirection.instruction_3_content") - %li - %strong - = t("ontologies.nginx_redirection.instruction_4") - = t("ontologies.nginx_redirection.instruction_4_content") - %li + %h5 %strong - = t("ontologies.nginx_redirection.instruction_5") - = t("ontologies.nginx_redirection.instruction_5_content") + = t("ontologies.instructions_servers", server: "Nginx") + %ol + %li + %strong + = t("ontologies.nginx_redirection.instruction_1") + = t("ontologies.nginx_redirection.instruction_1_content") + %li + %strong + = t("ontologies.nginx_redirection.instruction_2") + = t("ontologies.nginx_redirection.instruction_2_content") + %li + %strong + = t("ontologies.nginx_redirection.instruction_3") + = t("ontologies.nginx_redirection.instruction_3_content") + %li + %strong + = t("ontologies.nginx_redirection.instruction_4") + = t("ontologies.nginx_redirection.instruction_4_content") + %li + %strong + = t("ontologies.nginx_redirection.instruction_5") + = t("ontologies.nginx_redirection.instruction_5_content") - .htacess-code-container - .clipboard-component-resource-content{style: 'position: absolute; right: 2%; top: 8%;'} - = render ClipboardComponent.new(message: @nginx_content, show_content: false) - %pre.mb-0 - %code.d-block{style: 'text-wrap: pretty; word-break: break-all; color: white;'} - = @nginx_content - - %h5 - %strong Note - = render Display::AlertComponent.new(message: t("ontologies.redirection_note"), closable: false, type: "warning") + .nginx-code-container + .clipboard-component-resource-content{style: 'position: absolute; right: 2%; top: 8%;'} + = render ClipboardComponent.new(message: @nginx_content, show_content: false) + %pre.mb-0 + %code.d-block{style: 'text-wrap: pretty; word-break: break-all; color: white;'} + = @nginx_content + + #redirection_note + %h5 + %strong Note + = render Display::AlertComponent.new(message: t("ontologies.redirection_note"), closable: false, type: "warning") - .contact-support{style: "width: 100%; display: flex; justify-content: end;"} - = render Buttons::RegularButtonComponent.new(id:'regular-button', value: t("ontologies.contact_support"), variant: "primary", href: "/feedback", target: "_blank", state: "regular") \ No newline at end of file + .contact-support{style: "width: 100%; display: flex; justify-content: end;"} + = render Buttons::RegularButtonComponent.new(id:'regular-button', value: t("ontologies.contact_support"), variant: "primary", href: "/feedback", target: "_blank", state: "regular") diff --git a/app/views/ontologies/new.html.haml b/app/views/ontologies/new.html.haml index 92f88fc21a..67a9163866 100644 --- a/app/views/ontologies/new.html.haml +++ b/app/views/ontologies/new.html.haml @@ -1,7 +1,7 @@ - @title = t("ontologies.submit_new_ontology") %div{:style => "margin:10px;"} - = form_for :ontology, url: {action: "create"}, html: {id: "ontologyForm", multipart: true} do + = form_for :ontology, url: {action: "create"}, html: {id: "ontologyForm", multipart: true, novalidate: true} do .upload-ontology-container %div{style: 'width: 589px'} = error_message_alert diff --git a/app/views/ontologies/sections/_metadata.html.haml b/app/views/ontologies/sections/_metadata.html.haml index 9dd1a07df7..69aadbc570 100755 --- a/app/views/ontologies/sections/_metadata.html.haml +++ b/app/views/ontologies/sections/_metadata.html.haml @@ -36,7 +36,7 @@ document.querySelector("[data-target='#projects_section']")?.click() } = properties_dropdown('methodology',t("ontologies.sections.methodology_and_provenance"), t("ontologies.sections.info_tooltip_properties_dropdown"), @methodology_properties) - = properties_dropdown('community',t("ontologies.sections.community"), t("ontologies.sections.info_tooltip_properties_dropdown"), nil ) do |c| + = properties_dropdown('community',t("ontologies.sections.community"), t("ontologies.sections.info_tooltip_community_dropdown", site: portal_name), nil ) do |c| - properties_list_component(c, @community_properties, truncate: false) - unless Array(@ontology.group).empty? - c.row do @@ -44,7 +44,7 @@ = horizontal_list_container(@ontology.group) do |v| = render ChipButtonComponent.new(text: show_group_name(v), type: "static", tooltip: show_group_name(v)) - = properties_dropdown('content',t("ontologies.sections.content"), t("ontologies.sections.info_tooltip_properties_dropdown"), nil) do |c| + = properties_dropdown('content',t("ontologies.sections.content"), t("ontologies.sections.info_tooltip_properties_dropdown", site: portal_name), nil) do |c| - properties_list_component(c, @content_properties.reject{|k, v| %w[keyClasses metadataVoc].include?(k.to_s)}) - c.row do = render FieldContainerComponent.new(label: attr_label('metadataVoc', attr_metadata: attr_metadata("metadataVoc"), show_tooltip: false)) do diff --git a/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml b/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml index dc0c5221f8..db7525d510 100644 --- a/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml +++ b/app/views/ontologies/sections/metadata/_ontology_description_section.html.haml @@ -54,7 +54,7 @@ - l.row do = render FieldContainerComponent.new(label: t("ontologies.sections.metadata.categories_and_subjects")) do = horizontal_list_container(show_ontology_domains(domains).uniq) do |v| - = render ChipButtonComponent.new(text: show_category_name(v), type: "static") + = category_name_chip_component(v) - if @submission_latest&.pullLocation - l.row do diff --git a/app/views/properties/_show.html.haml b/app/views/properties/_show.html.haml index c034301496..f74964f85e 100644 --- a/app/views/properties/_show.html.haml +++ b/app/views/properties/_show.html.haml @@ -3,14 +3,16 @@ - if @property.errors = render Display::AlertComponent.new(type:'info', message: @property.errors.join) - else + - properties = LinkedData::Client::Models::Property.properties_to_hash(@property).first = render ConceptDetailsComponent.new(id:'property-details', acronym: @acronym, concept_id: @property.id, - properties: OpenStruct.new(LinkedData::Client::Models::Property.properties_to_hash(@property).first), + properties: @property.properties, top_keys: [], - bottom_keys: [], + bottom_keys: properties.keys.map(&:to_s), exclude_keys: []) do |c| - c.header(stripped: true) do |t| - - t.add_row({th: t('properties.id')}, {td: link_to_with_actions(c.concept_properties[:id][:values], acronym: @acronym)}) if c.concept_properties[:id][:values].present? - - t.add_row({th: t('properties.type')}, {td: c.concept_properties[:type][:values] }) if c.concept_properties[:id][:values].present? - - t.add_row({th: t('properties.preferred_name')}, {td: display_in_multiple_languages(c.concept_properties[:label][:values])}) if c.concept_properties[:label][:values].present? - - t.add_row({th: t('properties.definitions')}, {td: display_in_multiple_languages(c.concept_properties[:definition][:values])}) if c.concept_properties[:definition][:values].present? - - t.add_row({th: t('properties.parent')}, {td: display_in_multiple_languages(c.concept_properties[:parents][:values])}) if c.concept_properties[:parents][:values].present? \ No newline at end of file + - t.add_row({th: t('properties.id')}, {td: link_to_with_actions(@property.id, acronym: @acronym)}) + - t.add_row({th: t('properties.type')}, {td: @property.type }) + - t.add_row({th: t('properties.preferred_name')}, {td: display_in_multiple_languages(@property.label)}) unless @property.label.blank? + - t.add_row({th: t('properties.definitions')}, {td: display_in_multiple_languages(@property.definition)}) unless @property.definition.blank? + - t.add_row({th: t('properties.domain')}, {td: get_link_for_cls_ajax(@property.domain, @acronym, '_top')}) unless @property.domain.blank? + - t.add_row({th: t('properties.range')}, {td: get_link_for_cls_ajax(@property.range, @acronym, '_top')}) unless @property.range.blank? diff --git a/app/views/recommender/index.html.haml b/app/views/recommender/index.html.haml index 10a5c83331..5ac33ba53c 100644 --- a/app/views/recommender/index.html.haml +++ b/app/views/recommender/index.html.haml @@ -51,7 +51,7 @@ .title = t('recommender.weights_configuration') .inputs-container - -#binding.pry + .ninput = render Input::RangeSliderComponent.new(label: t('recommender.coverage'), name: "wc", value: params[:wc] || 0.55, min: '0', max: '1', step: '0.01') .ninput diff --git a/app/views/taxonomy/_taxonomies.html.haml b/app/views/taxonomy/_taxonomies.html.haml new file mode 100644 index 0000000000..0dd56f6876 --- /dev/null +++ b/app/views/taxonomy/_taxonomies.html.haml @@ -0,0 +1,10 @@ +.taxonomy-section + - pairs, impairs = taxonomies.each_with_index.partition { |_, index| index.even? } + - taxonomies_first_row = pairs.map(&:first) + - taxonomies_second_row = impairs.map(&:first) + .first-row + - taxonomies_first_row.each do |taxonomy| + = render Display::TaxonomyCardComponent.new(taxonomy: taxonomy, ontologies_names: @ontologies_names) + .second-row + - taxonomies_second_row.each do |taxonomy| + = render Display::TaxonomyCardComponent.new(taxonomy: taxonomy, ontologies_names: @ontologies_names) \ No newline at end of file diff --git a/app/views/taxonomy/index.html.haml b/app/views/taxonomy/index.html.haml new file mode 100644 index 0000000000..967f63d330 --- /dev/null +++ b/app/views/taxonomy/index.html.haml @@ -0,0 +1,24 @@ +.taxonomy-page-container + .taxonomy-page-subcontainer + .taxonomy-page-title + .text + = t('taxonomy.groups_and_categories') + .line + .taxonomy-page-decription + = t('taxonomy.description') + + = render TabsContainerComponent.new do |c| + - c.item(title: 'Groups', selected: !@category_section_active) + - c.item_content do + = render partial: '/taxonomy/taxonomies', locals: { taxonomies: @groups } + + - c.item(title: 'Categories', selected: @category_section_active) + - c.item_content do + = render partial: '/taxonomy/taxonomies', locals: { taxonomies: @categories } +:javascript + document.getElementById('categories_tab').addEventListener('click', function(event) { + window.history.pushState({ path: '/categories' }, '', '/categories'); + }) + document.getElementById('groups_tab').addEventListener('click', function(event) { + window.history.pushState({ path: '/groups' }, '', '/groups'); + }) \ No newline at end of file diff --git a/app/views/users/_form.html.haml b/app/views/users/_form.html.haml index 3a2f38b52c..02fde4988d 100644 --- a/app/views/users/_form.html.haml +++ b/app/views/users/_form.html.haml @@ -27,13 +27,13 @@ ORCID ID %font.register-optional = t('register.optional') - %img.register-input-icon{:src => "#{asset_path("orcid.svg")}"}/ + = inline_svg_tag 'orcid.svg', class: 'register-input-icon' = text_field :user, :orcidId, value: @user.orcidId, class: "register-input-long register-input-with-icon" %p.register-input-title Github ID %font.register-optional = t('register.optional') - %img.register-input-icon{:src => "#{asset_path("github-icon.svg")}"}/ + = inline_svg_tag 'github-icon.svg', class: 'register-input-icon' = text_field :user, :githubId, value: @user.githubId, class: "register-input-long register-input-with-icon" %p.register-input-title = t('register.email') diff --git a/app/views/users/show.html.haml b/app/views/users/show.html.haml index 3c4f285974..cb69ab11a5 100644 --- a/app/views/users/show.html.haml +++ b/app/views/users/show.html.haml @@ -57,10 +57,10 @@ %a{href: "#{$REST_URL}/documentation", target: "_blank"} = t('users.show.api_documentation') = render partial: "shared/svgs/external_link_icon" - .account-page-card + .account-page-card{'data-controller': 'reveal-component'} %h4.account-page-card-title = t('users.show.custom_semantic_resource') - #custom_ontologies.enable-lists + #custom_ontologies.enable-lists{'data-reveal-component-target': "item"} - if at_slice? %p{style: "padding-left: 7px; font-size: 10pt; margin: -3px 0 7px;"} = t('users.show.please') @@ -70,21 +70,20 @@ = t('users.show.customize_portal_display', portal: portal_name) %p %span{style: "font-weight: normal; font-size: 9pt; padding-left: 7px;"} - %a#edit_custom_ontologies{href: "javascript:void(0);"}= t('users.show.select_semantic_resources') - - if @user_ontologies && !@user_ontologies.empty? - %ul - - @user_ontologies.each do |ont| - - ont = LinkedData::Client::Models::Ontology.get(ont) - %li - #{ont.name} (#{ont.acronym}) - - else - %p{style: "padding-left: 7px;"}= t('users.show.no_semantic_resources') + %a#edit_custom_ontologies{'data-action': "click->reveal-component#toggle", 'data-reveal-component-target': "item", style: 'cursor: pointer;'}= t('users.show.select_semantic_resources') + + .account-page-custom-ontologies + - @user_ontologies.each do |ont| + - ont = @ontologies.select{ |o| o.id.eql?(ont) }.first + = render ChipButtonComponent.new(url: "/ontologies/#{ont.acronym}", text: ont.acronym , type: "clickable", tooltip: ont.name) + %p.account-page-card-desc= t('users.show.note_feature_logged_in') - #custom_ontologies_picker{style: "left: -9999px; position: absolute;"} + #custom_ontologies_picker.d-none{'data-reveal-component-target': "item"} = form_tag custom_ontologies_path(url_encode(@user.username)) do - - selected = @user.customOntology.map {|o| LinkedData::Client::Models::Ontology.get(o).acronym} - = ontologies_selector(id:'account_page_ontologies_selector' ,name: 'ontologies', selected: selected) - = submit_tag t('users.show.save_custom_semantic_resources'), class: "link_button" + - selected = @user.customOntology.map {|o| o.split('/').last } + = ontologies_selector(id:'account_page_ontologies_selector' ,name: 'ontologies', selected: selected, ontologies: @all_ontologies_for_select) + .mt-3 + = render Buttons::RegularButtonComponent.new(id: 'submit_custom_set', variant: "secondary", size: "slim", type: 'submit', value: t('users.show.save_custom_semantic_resources')) .account-page-second-row .account-page-card %h4.account-page-card-title= t('users.show.subscriptions') @@ -128,15 +127,4 @@ - else - @user_projects.each do |project| .account-page-submitted-ontology - %a{href: "/projects/#{project.acronym}"}= project.name - -:javascript - jQuery(document).ready(function(){ - jQuery("#edit_custom_ontologies").click(editCustomOntologies); - }); - - - function editCustomOntologies() { - jQuery("#custom_ontologies_picker").css("left", "").css("position", ""); - jQuery("#custom_ontologies").hide(); - } + %a{href: "/projects/#{project.acronym}"}= project.name \ No newline at end of file diff --git a/bin/ontoportal b/bin/ontoportal index a2c030b23a..3fa5d29391 100755 --- a/bin/ontoportal +++ b/bin/ontoportal @@ -135,7 +135,7 @@ dev() { bash_cmd+=" (bundle config unset local.ontologies_api_client) &&" fi done - bash_cmd+=" (bundle check || bundle install) && bin/rails db:prepare && bundle exec rails s -b 0.0.0.0 -p 3000" + 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" diff --git a/bin/run_api b/bin/run_api index 8ed4d11dc0..5d1634b2f8 100755 --- a/bin/run_api +++ b/bin/run_api @@ -52,7 +52,7 @@ 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 +if curl -sSf http://localhost:9393 > /dev/null 2>&1; then echo "API is already running in http://localhost:9393" exit 0 fi @@ -62,7 +62,7 @@ docker compose ls -a --filter "name=ontoportal_docker" | grep -q "ontoportal_doc ( 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="$command --no-provision" + [ "$no_provision" = true ] && command="$command" echo "Run: $command" eval "$command" ) diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample index bf07df798f..277b972015 100644 --- a/config/bioportal_config_env.rb.sample +++ b/config/bioportal_config_env.rb.sample @@ -258,7 +258,10 @@ $PORTALS_INSTANCES = [ link: 'https://biodivportal.gfbio.org/' } ] +$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" }, @@ -274,12 +277,13 @@ $FOOTER_LINKS = { api: "https://data.agroportal.lirmm.fr/", tools: "/tools", sparql: "https://sparql.agroportal.lirmm.fr/test/", - ontoportal: "https://ontoportal.org/" + 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" + 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, @@ -307,3 +311,4 @@ if $HOSTNAME require_relative "bioportal_config_development_#{$HOSTNAME}" end end + diff --git a/config/bioportal_config_test.rb b/config/bioportal_config_test.rb index 44169096be..91ed16b4df 100644 --- a/config/bioportal_config_test.rb +++ b/config/bioportal_config_test.rb @@ -8,7 +8,7 @@ $API_KEY = ENV['API_KEY'] $REST_URL = ENV['API_URL'] $BIOMIXER_URL = ENV['BIOMIXER_URL'] -$ANNOTATOR_URL = $PROXY_URL = ENV['ANNOTATOR_URL'] +$ANNOTATOR_URL = $PROXY_URL = ENV['ANNOTATOR_URL'].blank? ? "https://services.tesportal.lirmm.fr/annotator" : ENV['ANNOTATOR_URL'] $FAIRNESS_URL = ENV['FAIRNESS_URL'] # Resource term @@ -58,8 +58,6 @@ $ENABLE_SLICES = false $ONTOLOGY_SLICES = {} -# Cube metrics reporting -$ENABLE_CUBE = false $NOT_DOWNLOADABLE = {} # Enable client request caching @@ -218,7 +216,4 @@ } ] -$UI_THEME = :stageportal -if File.exist?('config/bioportal_config_development_testportal.lirmm.fr.rb') - require_relative 'bioportal_config_development_testportal.lirmm.fr' # local credentials -end \ No newline at end of file +$UI_THEME = :stageportal \ No newline at end of file diff --git a/config/environment.rb b/config/environment.rb index 99be33ce5c..0c158d03b5 100755 --- a/config/environment.rb +++ b/config/environment.rb @@ -1,5 +1,6 @@ # Load the Rails application. -require_relative "application" +require_relative 'application' + # Remove this after migrating to Rails 7.1 (https://github.com/rails/rails/issues/32947#issuecomment-1356391185) class Rails::Application diff --git a/config/initializers/cube_reporter.rb b/config/initializers/cube_reporter.rb deleted file mode 100644 index 136f509dd5..0000000000 --- a/config/initializers/cube_reporter.rb +++ /dev/null @@ -1,43 +0,0 @@ -require 'cube' - -## -# This enables collection of request statistics for anaylsis via cube. -# A cube server is required. See http://square.github.io/cube/ for more info. -module Rack - class CubeReporter - - def initialize(app = nil, options = {}) - host = options[:cube_host] || "localhost" - port = options[:cube_port] || 1180 - @app = app - @cube = ::Cube::Client.new(host, port) - end - - def call(env) - start = Time.now - data = @app.call(env) - finish = Time.now - user = env["rack.session"] ? env["rack.session"][:user] : nil - apikey = user.apikey if user - username = user.username if user - req_data = { - duration_ms: ((finish - start)*1000).ceil, - path: env["REQUEST_PATH"], - status: data[0], - user: { - apikey: apikey, - username: username, - ip: env["REMOTE_ADDR"], - user_agent: env["HTTP_USER_AGENT"] - } - } - @cube.send "ui_request", DateTime.now, req_data - data - end - - end -end - -if global_variables.include?(:$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/miniprofiler.rb b/config/initializers/miniprofiler.rb deleted file mode 100644 index 05194cebbe..0000000000 --- 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/locales/en.yml b/config/locales/en.yml index e937ed62de..20d3bea716 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -203,6 +203,7 @@ en: description: Description created: Created ontologies: Ontologies + parent_category: Parent category edit: edit_category: Edit category save: Save @@ -390,7 +391,8 @@ en: error_on_form: Errors On Form leave_your_feedback: Leave your feedback feedback_hi_text: Hi - feedback_info_text: you can use the form below or email us directly at + feedback_info_text: You can use the form below, email us directly at + feedback_info_text_rest: or leave us a github issue here email: Email name: Name proposition_url_page: Error/Proposition page URL @@ -405,6 +407,11 @@ en: feedback_complete: title: Feedback sent successfully message: Thank you for taking the time to share your feedback with us. Our support team will review your message and get back to you as soon as possible with a response. We value your opinion and appreciate your help in improving our services. Thank you for your support! + suggest_slice: Suggest a new group/slice + slices_description: Slices allow users to interact (both via API or UI) only with a subset of ontologies in AgroPortal. If browsing the slice, all the portal features will be restricted to the chosen subset, enabling users to focus on their specific use cases. On AgroPortal, slices and groups are synchronized, so every group has a corresponding slice displaying only the ontologies from that group. + ontoportal_description: "The OntoPortal Alliance %{ontoportal_link} is a consortium of research and infrastructure teams dedicated to promoting the development of ontology repositories and semantic artefact catalogues based on the open, collaboratively developed OntoPortal software %{github_link}. Hereafter are the current public and open repositories built with the technology maintained by the Alliance." + viewing_slice: "Viewing the slice:" + view_full_site: View full website landscape: #select_ontologies: Start typing to select ontologies or leave blank to use them all classes: Number of classes @@ -505,6 +512,7 @@ en: wiki: Wiki documentation: Documentation agro_documentation: "%{site} documentation" + issues_and_requests: Issues and Requests agreements: Legal terms: Terms and Conditions privacy_policy: Privacy Policy @@ -533,7 +541,7 @@ en: enter_email: Enter your username enter_password: Enter your password forgot_password: Forgot password? - invalid_login: Errors on the form + private_ontology: This ontology is private. Please login. no_account: Do not have an account? password: Password register: Register @@ -642,6 +650,10 @@ en: actions: Actions see_other_properties: See other properties agents: + errors: + required: is required and cannot be empty + used_identifier: This identifier is already used by another agent + invalid_url: The identifier must be a valid ORCID/ROR URL not_found_agent: Agent with id %{id} add_agent: New Agent added successfully update_agent: Agent successfully updated @@ -670,6 +682,7 @@ en: index: create_new_agent: Create New Agent first_name: First name + acronym: Acronym usages: Usages actions: Actions no_agents: There are currently no agents. @@ -935,7 +948,7 @@ en: synonym: Synonym definition: Definition parent: Parent - save: save + save: Save note_line: alert_text: "Are you sure you want to delete the note ''%{subject}'' created by %{creator}?
This action CAN NOT be undone!!!" delete: Delete @@ -946,8 +959,8 @@ en: reply: about_note_decorator: about %{note_decorator} comment: Comment - save: save - cancel: cancel + save: Save + cancel: Cancel ontolobridge: problem_of_creating_new_term: "Problem creating a new term %{endpoint}: %{class} - %{message}" new_term_instructions_saved: New term request instructions for %{acronym} saved @@ -1073,21 +1086,21 @@ en: close: Close submit: Submit check_resolvability: - check_resolvability_message_1: "The URL is resolvable and support the following formats: %{supported_format}" - check_resolvability_message_2: "The URL resolvable but is not content negotiable, support only: %{supported_format}" - check_resolvability_message_3: The URL is not resolvable and not content negotiable (returns %{status}). + check_resolvability_message_1: "The URI is resolvable and support the following formats: %{supported_format}" + check_resolvability_message_2: "The URI resolvable but is not content negotiable, support only: %{supported_format}" + check_resolvability_message_3: The URI is not resolvable and not content negotiable (returns %{status}). uri_placeholder: Type a URI to test its resolvability show_help: Show help format_not_specified: Format not specified how_it_works: title: How it works content_1: | - The check resolvability tool allows you to test if a given URL is resolvable. It is based on the HTTP HEAD method. - We check the resolvability of a URL by sending a HEAD request to the URL and checking if the response status code is 200 (OK) and + The check resolvability tool allows you to test if a given URI is resolvable. It is based on the HTTP HEAD method. + We check the resolvability of a URI by sending a HEAD request to the URI and checking if the response status code is 200 (OK) and the returned content type is equal to one of the following %{resolvability_formats}. content_2: | - We have a timeout set to %{resolvability_timeout} seconds, so if the URL is not resolvable within that time, the check will fail. - And a max redirections set to %{resolvability_max_redirections}, so if the URL is not resolvable within that number of redirections, the check will fail. + We have a timeout set to %{resolvability_timeout} seconds, so if the URI is not resolvable within that time, the check will fail. + And a max redirections set to %{resolvability_max_redirections}, so if the URI is not resolvable within that number of redirections, the check will fail. resolving_uri: title: Resolving a URI content: | @@ -1260,6 +1273,7 @@ en: community: Community content: Content info_tooltip_properties_dropdown: Metadata properties primarily encompass the design, methods, and actions to create the ontology. This includes elements such as the tools and software employed by the creator of the ontology during its configuration. + info_tooltip_community_dropdown: Metadata properties related to community information such as the code repository and issue tracker, the mailing list or the target audience. This includes also the Groups in %{site}. See more information about Groups and Categories. visits: Visits views: Views of %{acronym} create_new_view: Create new view @@ -1373,7 +1387,7 @@ en: instruction_4_content: "Run the following command to test the redirection configuration `sudo nginx -t`" instruction_5: "Reload Nginx to apply the changes:" instruction_5_content: "Restart the nginx server to apply the redirection using this command `sudo systemctl reload nginx`" - + components: check_resolvability: checking resolvability... error_block: child_data_generator block did not provide all the child arguements @@ -1405,7 +1419,7 @@ en: view: View debug: Debug loading: Loading - unwatch: UnWatch + unwatch: Unwatch watch: Watch resource: "%{sub_text} this resource" notified_of_all_updates: Be the first to watch this resource and be notified of all its updates @@ -1421,6 +1435,8 @@ en: preferred_name: Preferred name definitions: Definitions parent: Parent + domain: Domain + range: Range no_properties_alert: "%{acronym} does not contain properties" visits: ontology_visits: Ontology visits @@ -1467,4 +1483,14 @@ en: email: "Email: %{email}" location: "Location: %{location}" tags: Tags - feedback: Feedback \ No newline at end of file + feedback: Feedback + cookies_modal: + title: "Manage Cookie Consent" + paragraph1: "%{portal} uses cookies to help you navigate efficiently and for audience measurement. You will find detailed information about all cookies in the \"Privacy policy\" link" + paragraph2: "The cookies are functional and non-optional. By staying on %{portal}, you acknowledge the information was delivered to you." + accept_button: "Accept" + privacy_link: "Privacy policy" + taxonomy: + groups_and_categories: Groups and Categories + description: In AgroPortal, ontologies are organized in groups and tagged with categories. Typically, groups associate ontologies from the same project or organization for better identification of the provenance. Whereas categories are about subjects/topics and enable to classify ontologies. As of 2016, AgroPortal's categories were established in cooperation with FAO AIMS. In 2024, we moved to UNESCO nomenclature for fields of science and technology. Groups and categories, along with other metadata, can be used on the “Browse” page of AgroPortal to filter out the list of ontologies. + show_sub_categories: Show sub categories \ No newline at end of file diff --git a/config/locales/fr.yml b/config/locales/fr.yml index 994644fde5..165eecd62d 100644 --- a/config/locales/fr.yml +++ b/config/locales/fr.yml @@ -209,6 +209,7 @@ fr: description: Description created: Créé ontologies: Ontologies + parent_category: Catégorie parent edit: edit_category: Modifier la catégorie save: Sauvegarder @@ -301,9 +302,9 @@ fr: total_results: Résultats totaux insert_sample_text: Insérer un texte d'exemple sample_text: Il y a eu de nombreuses études récentes sur l'utilisation d'antagonistes microbiens pour contrôler les maladies causées par des bactéries phytopathogènes telluriques - et aériennes, dans le but de remplacer les méthodes actuelles de contrôle chimique et d'éviter l'utilisation extensive de fongicides, qui conduisent souvent à une résistance chez les pathogènes des plantes. - En agriculture, les microorganismes promoteurs de croissance des plantes et de biocontrôle ont émergé comme des alternatives sûres aux pesticides chimiques. Les espèces de Streptomyces et leurs - métabolites peuvent avoir un grand potentiel en tant qu'agents excellents pour contrôler divers phytopathogènes fongiques et bactériens. + et aériennes, dans le but de remplacer les méthodes actuelles de contrôle chimique et d'éviter l'utilisation extensive de fongicides, qui conduisent souvent à une résistance chez les pathogènes des plantes. + En agriculture, les microorganismes promoteurs de croissance des plantes et de biocontrôle ont émergé comme des alternatives sûres aux pesticides chimiques. Les espèces de Streptomyces et leurs + métabolites peuvent avoir un grand potentiel en tant qu'agents excellents pour contrôler divers phytopathogènes fongiques et bactériens. concepts: error_valid_concept: "Erreur : Vous devez fournir un identifiant de concept valide" @@ -397,7 +398,8 @@ fr: error_on_form: Erreurs sur le formulaire leave_your_feedback: Laissez votre retour feedback_hi_text: Salut - feedback_info_text: vous pouvez utiliser le formulaire ci-dessous ou nous envoyer un email directement à + feedback_info_text: Vous pouvez utiliser le formulaire ci-dessous, nous envoyer un email directement à + feedback_info_text_rest: ou nous laisser une github issue ici email: Email name: Nom proposition_url_page: URL de la page Erreur/Proposition @@ -412,6 +414,11 @@ fr: feedback_complete: title: Retour envoyé avec succès message: Merci d'avoir pris le temps de partager votre retour avec nous. Notre équipe de support examinera votre message et vous répondra dès que possible. Nous apprécions votre opinion et sommes reconnaissants de votre aide pour améliorer nos services. Merci de votre soutien ! + suggest_slice: Proposer un nouveau groupe/slice + slices_description: Les "slices" permettent aux utilisateurs d'interagir (à la fois via l'API ou l'interface utilisateur) uniquement avec un sous-ensemble d'ontologies dans AgroPortal. Si vous parcourez une slice, toutes les fonctionnalités du portail seront limitées au sous-ensemble choisi; cela permet aux utilisateurs de se concentrer sur leurs cas d'utilisation spécifiques. Sur AgroPortal, les slices et les groupes sont synchronisés, de sorte que chaque groupe a une slice correspondante affichant uniquement les ontologies de ce groupe. + ontoportal_description: "L'OntoPortal Alliance %{ontoportal_link} est un consortium d'équipes de recherche et d'infrastructure dédiées à promouvoir le développement de portails d'ontologies et de catalogues d'artefacts sémantiques basés sur le logiciel OntoPortal %{github_link} ouvert et collaboratif. Ci-dessous se trouvent les portails publics et ouverts actuels construits avec la technologie maintenue par l'Alliance." + viewing_slice: "Affichage de la slice:" + view_full_site: Voir le site complet landscape: #select_ontologies: Commencez à taper pour sélectionner des ontologies ou laissez vide pour les utiliser toutes @@ -514,6 +521,7 @@ fr: wiki: Wiki documentation: Documentation agro_documentation: Documentation d'%{site} + issues_and_requests: Problèmes et demandes agreements: Légal terms: Termes et conditions privacy_policy: Politique de confidentialité @@ -543,7 +551,7 @@ fr: enter_email: Entrez votre nom d'utilisateur enter_password: Entrez votre mot de passe forgot_password: Mot de passe oublié ? - invalid_login: Erreurs sur le formulaire + private_ontology: Cette ontologie est privée. Veuillez vous connecter. no_account: Vous n'avez pas de compte ? password: Mot de passe register: S'inscrire @@ -656,6 +664,10 @@ fr: agents: + errors: + required: est requis et ne peut pas être vide + used_identifier: Cet identifiant est déjà utilisé par un autre agent + invalid_url: L'identifiant doit être une URL ORCID/ROR valide not_found_agent: Agent avec id %{id} add_agent: Nouvel agent ajouté avec succès update_agent: Agent mis à jour avec succès @@ -684,6 +696,7 @@ fr: index: create_new_agent: Créer un nouvel agent first_name: Prénom + acronym: Acronyme usages: Utilisations actions: Actions no_agents: Il n'y a actuellement aucun agent. @@ -956,7 +969,7 @@ fr: synonym: Synonyme definition: Définition parent: Parent - save: sauvegarder + save: Sauvegarder note_line: alert_text: "Êtes-vous sûr de vouloir supprimer la note ''%{subject}'' créée par %{creator}?
Cette action NE PEUT PAS être annulée !!!" delete: Supprimer @@ -967,8 +980,8 @@ fr: reply: about_note_decorator: à propos de %{note_decorator} comment: Commentaire - save: sauvegarder - cancel: annuler + save: Sauvegarder + cancel: Annuler ontolobridge: problem_of_creating_new_term: "Problème de création d'un nouveau terme %{endpoint} : %{class} - %{message}" @@ -1098,21 +1111,21 @@ fr: submit: Soumettre check_resolvability: - check_resolvability_message_1: "L'URL est résolvable et supporte les formats suivants : %{supported_format}" - check_resolvability_message_2: "L'URL est résolvable mais n'est pas négociable en contenu, supporte uniquement : %{supported_format}" - check_resolvability_message_3: L'URL n'est pas résolvable et n'est pas négociable en contenu (retourne %{status}). + check_resolvability_message_1: "L'URI est résolvable et supporte les formats suivants : %{supported_format}" + check_resolvability_message_2: "L'URI est résolvable mais n'est pas négociable en contenu, supporte uniquement : %{supported_format}" + check_resolvability_message_3: L'URI n'est pas résolvable et n'est pas négociable en contenu (retourne %{status}). uri_placeholder: Tapez une URI pour tester sa résolvabilité show_help: Afficher l'aide format_not_specified: Format non spécifié how_it_works: title: Comment ça fonctionne content_1: | - L'outil de vérification de la résolvabilité vous permet de tester si une URL donnée est résolvable. Il est basé sur la méthode HTTP HEAD. - Nous vérifions la résolvabilité d'une URL en envoyant une requête HEAD à l'URL et en vérifiant si le code de statut de la réponse est 200 (OK) et + L'outil de vérification de la résolvabilité vous permet de tester si une URI donnée est résolvable. Il est basé sur la méthode HTTP HEAD. + Nous vérifions la résolvabilité d'une URI en envoyant une requête HEAD à l'URI et en vérifiant si le code de statut de la réponse est 200 (OK) et si le type de contenu retourné est égal à l'un des %{resolvability_formats} suivants. content_2: | - Nous avons un délai d'attente fixé à %{resolvability_timeout} secondes, donc si l'URL n'est pas résolvable dans ce délai, la vérification échouera. - Et un nombre maximal de redirections fixé à %{resolvability_max_redirections}, donc si l'URL n'est pas résolvable dans ce nombre de redirections, la vérification échouera. + Nous avons un délai d'attente fixé à %{resolvability_timeout} secondes, donc si l'URI n'est pas résolvable dans ce délai, la vérification échouera. + Et un nombre maximal de redirections fixé à %{resolvability_max_redirections}, donc si l'URI n'est pas résolvable dans ce nombre de redirections, la vérification échouera. resolving_uri: title: Résolution d'une URI content: | @@ -1289,6 +1302,7 @@ fr: community: Communauté content: Contenu info_tooltip_properties_dropdown: Propriétés de métadonnées englobant principalement la conception, les méthodes et les actions pour créer l'ontologie. Cela inclut des éléments tels que les outils et logiciels utilisés par le créateur de l'ontologie lors de sa configuration. + info_tooltip_community_dropdown: Propriétés des métadonnées liées aux informations communautaires telles que le dépôt de code et le suivi des problèmes, la liste de diffusion ou le public cible. Cela inclut également les Groupes dans %{site}. Voir plus d'informations sur les Groupes et les Catégories. visits: Visites views: Vues de %{acronym} create_new_view: Créer une nouvelle vue @@ -1456,6 +1470,8 @@ fr: preferred_name: Nom préféré definitions: Définitions parent: Parent + domain: Domaine + range: Étendue no_properties_alert: "%{acronym} ne contient pas de propriétés" visits: @@ -1509,3 +1525,14 @@ fr: location: "Emplacement: %{location}" tags: Tags feedback: Feedback + + cookies_modal: + title: "Gérer le consentement des cookies" + paragraph1: "%{portal} utilise des cookies pour vous aider à naviguer efficacement et pour mesurer l'audience. Vous trouverez des informations détaillées sur tous les cookies dans le lien \"Vie privé\"" + paragraph2: "Les cookies sont fonctionnels et non facultatifs. En restant sur %{portal}, vous reconnaissez que les informations vous ont été transmises." + accept_button: "Accepter" + privacy_link: "Vie privé" + taxonomy: + groups_and_categories: Groupes et Catégories + description: Dans AgroPortal, les ontologies sont organisées en groupes et étiquetées avec des catégories. Typiquement, les groupes associent des ontologies provenant du même projet ou de la même organisation pour une meilleure identification de la provenance. Tandis que les catégories concernent des sujets/thématiques et permettent de classifier les ontologies. En 2016, les catégories d'AgroPortal ont été établies en coopération avec FAO AIMS. En 2024, nous sommes passés à la nomenclature de l'UNESCO pour les domaines des sciences et des technologies. Les groupes et les catégories, ainsi que d'autres métadonnées, peuvent être utilisés sur la page “Parcourir” d'AgroPortal pour filtrer la liste des ontologies. + show_sub_categories: Afficher les sous-catégories \ No newline at end of file diff --git a/config/routes.rb b/config/routes.rb index de09142b5e..f31620d09a 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -1,4 +1,5 @@ Rails.application.routes.draw do + match 'cookies', to: 'home#set_cookies', via: [:post, :get] root to: 'home#index' mount LetterOpenerWeb::Engine, at: "/letter_opener" if Rails.env.development? @@ -134,7 +135,7 @@ # Top-level pages match '/feedback', to: 'home#feedback', via: [:get, :post] - get '/account' => 'home#account' + get '/account' => 'users#show' get '/site_config' => 'home#site_config' post '/annotator_recommender_form' => 'home#annotator_recommender_form' match '/visits', to: 'visits#index', via: :get @@ -154,7 +155,6 @@ get '/ontologies/:acronym/:id/serialize/:output_format' => 'ontologies#content_serializer', :id => /.+/ get '/ontologies/:acronym/htaccess' => 'ontologies_redirection#generate_htaccess' - get '/ontologies/virtual/:ontology' => 'ontologies#virtual', :as => :ontology_virtual get '/ontologies/success/:id' => 'ontologies#submit_success' match '/ontologies/:acronym' => 'ontologies#update', via: [:get, :post] match '/ontologies/:acronym/submissions/:id' => 'submissions#update', via: [:get, :post] @@ -162,29 +162,23 @@ match '/ontologies/:ontology_id/submissions' => 'submissions#create', :ontology_id => /.+/, via: [:post] match '/ontologies/:ontology_id/submissions' => 'submissions#index', :ontology_id => /.+/, via: [:get] get '/ontologies/:acronym/classes/:purl_conceptid', to: 'ontologies#show', constraints: { purl_conceptid: /[^\/]+/ } - get '/ontologies/:acronym/: f', to: 'ontologies#show', constraints: { purl_conceptid: /[^\/]+/ } match '/ontologies/:acronym/submissions/:id/edit_metadata' => 'submissions#edit_metadata', via: [:get, :post] get '/ontologies_filter', to: 'ontologies#ontologies_filter' get 'ontologies_selector', to: 'ontologies#ontologies_selector' get 'ontologies_selector/results', to: 'ontologies#ontologies_selector_results' + # Notes get 'ontologies/:ontology/notes/:noteid', to: 'notes#virtual_show', as: :note_virtual, noteid: /.+/ get 'ontologies/:ontology/notes', to: 'notes#virtual_show' get '/ontologies/:acronym/:id' => 'ontologies_redirection#redirect', :id => /.+/ - # Ajax - get '/ajax/' => 'ajax_proxy#get', :as => :ajax get '/ajax/class_details' => 'concepts#details' get '/ajax/mappings/get_concept_table' => 'mappings#get_concept_table' - get '/ajax/json_ontology' => 'ajax_proxy#json_ontology' - get '/ajax/json_class' => 'ajax_proxy#json_class' - get '/ajax/jsonp' => 'ajax_proxy#jsonp' get '/ajax/notes/delete' => 'notes#destroy' - get '/ajax/notes/concept_list' => 'notes#show_concept_list' get '/ajax/classes/label' => 'concepts#show_label' get '/ajax/classes/definition' => 'concepts#show_definition' get '/ajax/classes/treeview' => 'concepts#show_tree' @@ -203,6 +197,7 @@ get '/ajax/ontologies', to: "ontologies#ajax_ontologies" get '/ajax/agents', to: "agents#ajax_agents" get '/ajax/images/show' => 'application#show_image_modal' + # User get '/logout' => 'login#destroy', :as => :logout get '/lost_pass' => 'login#lost_password' @@ -212,6 +207,9 @@ get '/login_as/:login_as' => 'login#login_as', constraints: { login_as: /[\d\w\.\-\%\+ ]+/ } post '/login/send_pass', to: 'login#send_pass' + get '/groups' => 'taxonomy#index' + get '/categories' => 'taxonomy#index' + # Search get 'search', to: 'search#index' get 'ajax/search/ontologies/content', to: 'search#json_ontology_content_search' @@ -219,33 +217,8 @@ get 'check_resolvability' => 'check_resolvability#index' get 'check_url_resolvability' => 'check_resolvability#check_resolvability' - ########################################################################################################### # Install the default route as the lowest priority. get '/:controller(/:action(/:id))' - ########################################################################################################### - - ##### - ## OLD ROUTES - ## All of these should redirect to new addresses in the controller method or using the redirect controller - ##### - - # Redirects from old URL locations - get '/annotate' => 'redirect#index', :url => '/annotator' - get '/visconcepts/:ontology/' => 'redirect#index', :url => '/visualize/' - get '/ajax/terms/label' => 'redirect#index', :url => '/ajax/classes/label' - get '/ajax/terms/definition' => 'redirect#index', :url => '/ajax/classes/definition' - get '/ajax/terms/treeview' => 'redirect#index', :url => '/ajax/classes/treeview' - get '/ajax/term_details/:ontology' => 'redirect#index', :url => '/ajax/class_details' - get '/ajax/json_term' => 'redirect#index', :url => '/ajax/json_class' - - # Visualize - get '/visualize/:ontology' => 'ontologies#visualize', :as => :visualize, :constraints => { ontology: /[^\/?]+/ } - get '/visualize/:ontology/:conceptid' => 'ontologies#visualize', :as => :uri, :constraints => { ontology: /[^\/?]+/, conceptid: /[^\/?]+/ } - get '/visualize' => 'ontologies#visualize', :as => :visualize_concept, :constraints => { ontology: /[^\/?]+/, id: /[^\/?]+/, ontologyid: /[^\/?]+/, conceptid: /[^\/?]+/ } - - get '/exhibit/:ontology/:id' => 'concepts#exhibit' - mount Lookbook::Engine, at: "/lookbook" - end diff --git a/docker-compose.yml b/docker-compose.yml index 644e1ca6ed..3c70bbe887 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -17,16 +17,11 @@ x-app: &default-app condition: service_started node: condition: service_started - links: - - db - - cache environment: &env BUNDLE_WITHOUT: "" BUNDLE_PATH: /srv/ontoportal/bundle DB_HOST: db CACHE_HOST: cache - ports: - - "3000:3000" tmpfs: - /tmp - /app/tmp/pids @@ -64,6 +59,11 @@ services: dev: <<: *default-app + ports: + - "3000:3000" + links: + - db + - cache production: <<: *default-app @@ -77,6 +77,11 @@ services: #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 @@ -103,9 +108,10 @@ services: chrome-server: image: selenium/standalone-chrome:112.0-chromedriver-112.0-grid-4.9.0-20230421 shm_size: 2g - ports: - - "4444:4444" - - "7900:7900" + network_mode: 'host' +# ports: +# - "4444:4444" +# - "7900:7900" volumes: mysql-data: diff --git a/lib/resolver/acronym_from_virtual.rb b/lib/resolver/acronym_from_virtual.rb deleted file mode 100644 index 5e753e84e3..0000000000 --- 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 fed4f1607d..0000000000 --- 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, - 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end -end +# namespace :schema do +# desc 'Update GitHub GraphQL schema' +# task :update do +# GraphQL::Client.dump_schema(GitHub::HTTPAdapter, 'data/schema.json') +# end +# end diff --git a/test/application_system_test_case.rb b/test/application_system_test_case.rb index b4457f965e..aaba7ccc84 100644 --- a/test/application_system_test_case.rb +++ b/test/application_system_test_case.rb @@ -104,7 +104,6 @@ def tom_select(selector, values, open_to_add: false) element = find(ts_wrapper_selector) element.click - return unless page.has_selector?("#{ts_wrapper_selector} > .ts-dropdown") if multiple @@ -137,6 +136,7 @@ def date_picker_fill_in(selector, value, index = 0) end def agent_search(name) + sleep 1 within(".search-inputs:last-of-type") do input = find("input[name^='agent']") agent_id = input[:name].split('agent').last @@ -151,11 +151,11 @@ def agent_search(name) end - def agent_fill(agent, parent_id: nil, enable_affiliations: true) - id = agent.id ? "/#{agent.id}": '' + def agent_fill(agent, parent_id: nil, is_affiliation: false) + id = agent.id ? "/#{agent.id}" : '' form = all("form[action=\"/agents#{id}\"]").first - within form do - choose "", option: agent.agentType, allow_label_click: true if enable_affiliations + within form do + choose "", option: agent.agentType, allow_label_click: true unless is_affiliation fill_in 'name', with: agent.name if agent.agentType.eql?('organization') @@ -168,11 +168,17 @@ def agent_fill(agent, parent_id: nil, enable_affiliations: true) fill_in 'email', with: agent.email end - list_inputs ".agents-identifiers", - "[identifiers]", agent.identifiers + identifier = agent.identifiers.first + + if agent.agentType.eql?('organization') + fill_in "_identifiers_0_notation", with: identifier['notation'] + else + fill_in "_identifiers_1_notation", with: identifier['notation'] + end - unless enable_affiliations + if is_affiliation || agent.agentType.eql?('organization') refute_selector ".agents-affiliations" + click_on "Save" if agent.agentType.eql?('organization') return end @@ -184,8 +190,7 @@ def agent_fill(agent, parent_id: nil, enable_affiliations: true) agent_id = agent_search(aff.name) id = parent_id && !parent_id.eql?('NEW_RECORD') ? "#{parent_id}_#{agent_id}" : agent_id within "turbo-frame[id=\"#{id}\"]" do - agent_fill(aff, enable_affiliations: false) - click_on "Save" + agent_fill(aff, is_affiliation: true) sleep 1 end end diff --git a/test/controllers/ontologies_controller_test.rb b/test/controllers/ontologies_controller_test.rb index 054b4eb90d..b286994b0e 100644 --- a/test/controllers/ontologies_controller_test.rb +++ b/test/controllers/ontologies_controller_test.rb @@ -39,4 +39,69 @@ class OntologiesControllerTest < ActionDispatch::IntegrationTest end end + + test 'test get STY in html format' do + get '/ontologies/STY', headers: { 'Accept' => 'text/html' } + assert_response :success + assert_equal 'text/html; charset=utf-8', response.content_type + end + + test 'test get STY in json format' do + get '/ontologies/STY', headers: { 'Accept' => 'application/json' } + assert_response :success + assert_equal 'application/json', response.content_type + + end + + test 'test get STY in xml format' do + get '/ontologies/STY', headers: { 'Accept' => 'application/xml' } + assert_equal 500, response.status # STY has only Turtle + end + + test 'test get STY in csv format' do + get '/ontologies/STY', headers: { 'Accept' => 'text/csv' } + assert_response :success + end + + test 'test get STY in turtle format' do + get '/ontologies/STY', headers: { 'Accept' => 'text/turtle' } + assert_response :success + end + + test 'test get STY in ntriples format' do + get '/ontologies/STY', headers: { 'Accept' => 'application/ntriples' } + assert_response :not_acceptable + end + + + test 'test get STY resource in html format' do + get '/ontologies/STY/T071', headers: { 'Accept' => 'text/html' } + assert_includes ["http://www.example.com/ontologies/STY?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT071&p=classes", "http://www.example.com/ontologies/STY?conceptid=http%3A%2F%2Fpurl.lirmm.fr%2Fontology%2FSTY%2FT071&p=classes"], response.location + assert_response :redirect + assert_equal "text/html; charset=utf-8" , response.content_type + end + + test 'test get STY resource in json format' do + get '/ontologies/STY/T071', headers: { 'Accept' => 'application/json' } + assert_response :success + assert_equal "application/ld+json; charset=utf-8" , response.content_type + end + + test 'test get STY resource in xml format' do + get '/ontologies/STY/T071', headers: { 'Accept' => 'application/xml' } + assert_response :success + assert_equal "application/rdf+xml; charset=utf-8" , response.content_type + end + + test 'test get STY resource in ntriples format' do + get '/ontologies/STY/T071', headers: { 'Accept' => 'application/n-triples' } + assert_response :success + assert_equal "application/n-triples; charset=utf-8" , response.content_type + end + + test 'test get STY resource in turtle format' do + get '/ontologies/STY/T071', headers: { 'Accept' => 'text/turtle' } + assert_response :success + assert_equal "text/turtle; charset=utf-8" , response.content_type + end end diff --git a/test/fixtures/agents.yml b/test/fixtures/agents.yml index ce32845e0b..73554419d2 100644 --- a/test/fixtures/agents.yml +++ b/test/fixtures/agents.yml @@ -4,8 +4,6 @@ agent1: email: "jonh@test.com" identifiers: - notation: "0000-0001-2345-6789" - - notation: "0000-0001-2345-6788" - - notation: "0000-0001-2345-6788" affiliations: - name: "Research Institute X" agentType: "organization" @@ -97,25 +95,6 @@ organization1: agentType: "organization" identifiers: - notation: "1234-5678" - affiliations: - - name: "Research Consortium A" - agentType: "organization" - identifiers: - - notation: "9876-5432" - affiliations: [ ] - email: "contact@researchconsortiumA.com" - acronym: "RCA" - homepage: "https://www.researchconsortiumA.com/" - - - name: "Innovation Hub B" - agentType: "organization" - identifiers: - - notation: "3456-7890" - affiliations: [ ] - email: "info@innovationhubb.com" - acronym: "IHB" - homepage: "https://www.innovationhubb.com/" - email: "info@techsolutionsgroup.com" acronym: "TSG" homepage: "https://www.techsolutionsgroup.com/" @@ -125,23 +104,6 @@ organization2: agentType: "organization" identifiers: - notation: "5678-9012" - affiliations: - - name: "Space Exploration Consortium" - agentType: "organization" - identifiers: - - notation: "1234-1234" - affiliations: [] - email: "contact@spaceconsortium.com" - acronym: "SEC" - homepage: "https://www.spaceconsortium.com/" - - name: "Tech Innovators Guild" - agentType: "organization" - identifiers: - - notation: "7890-1234" - affiliations: [] - email: "info@techinnovatorsguild.com" - acronym: "TIG" - homepage: "https://www.techinnovatorsguild.com/" email: "info@quantumdynamics.com" acronym: "QDS" homepage: "https://www.quantumdynamics.com/" @@ -151,23 +113,6 @@ organization3: agentType: "organization" identifiers: - notation: "2345-6789" - affiliations: - - name: "Health Research Alliance" - agentType: "organization" - identifiers: - - notation: "5678-9012" - affiliations: [] - email: "contact@healthresearchalliance.com" - acronym: "HRA" - homepage: "https://www.healthresearchalliance.com/" - - name: "GreenTech Innovations" - agentType: "organization" - identifiers: - - notation: "8901-2345" - affiliations: [] - email: "info@greentechinnovations.com" - acronym: "GTI" - homepage: "https://www.greentechinnovations.com/" email: "info@biotechsolutions.com" acronym: "BSI" homepage: "https://www.biotechsolutions.com/" diff --git a/test/fixtures/annotator.yml b/test/fixtures/annotator.yml new file mode 100644 index 0000000000..d678eb033a --- /dev/null +++ b/test/fixtures/annotator.yml @@ -0,0 +1,181 @@ +yaml_structure: regular +sample_response: + - annotatedClass: + prefLabel: Melanom + synonym: + - cilt kanseri + "@id": http://aims.fao.org/aos/agrovoc/c_4713 + "@type": http://www.w3.org/2002/07/owl#Class + links: + self: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713 + ontology: http://localhost:9393/ontologies/STY + children: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/children + parents: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/parents + descendants: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/descendants + ancestors: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/ancestors + instances: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/instances + tree: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/tree + notes: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/notes + mappings: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/mappings + ui: http://stageportal.lirmm.fr/ontologies/AGROVOC?p=classes&conceptid=http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713 + "@context": + self: http://www.w3.org/2002/07/owl#Class + ontology: http://localhost:9393/ontologies/STY + children: http://www.w3.org/2002/07/owl#Class + parents: http://www.w3.org/2002/07/owl#Class + descendants: http://www.w3.org/2002/07/owl#Class + ancestors: http://www.w3.org/2002/07/owl#Class + instances: http://data.bioontology.org/metadata/Instance + tree: http://www.w3.org/2002/07/owl#Class + notes: http://data.bioontology.org/metadata/Note + mappings: http://data.bioontology.org/metadata/Mapping + ui: http://www.w3.org/2002/07/owl#Class + "@context": + "@vocab": http://data.bioontology.org/metadata/ + prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel + synonym: http://www.w3.org/2004/02/skos/core#altLabel + "@language": en + hierarchy: [] + annotations: + - from: 1 + to: 8 + matchType: PREF + text: MELANOMA + mappings: [] + - annotatedClass: + prefLabel: Melanom + synonym: + - malignant melanoma + - melanoma patient + - melanocytes + "@id": http://data.europa.eu/8mn/euroscivoc/276b8c99-a318-48df-aa31-1f9f3e0ba910 + "@type": http://www.w3.org/2002/07/owl#Class + links: + self: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910 + ontology: http://localhost:9393/ontologies/STY + children: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/children + parents: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/parents + descendants: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/descendants + ancestors: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/ancestors + instances: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/instances + tree: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/tree + notes: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/notes + mappings: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/mappings + ui: http://stageportal.lirmm.fr/ontologies/EUROSCIVOC?p=classes&conceptid=http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910 + "@context": + self: http://www.w3.org/2002/07/owl#Class + ontology: http://localhost:9393/ontologies/STY + children: http://www.w3.org/2002/07/owl#Class + parents: http://www.w3.org/2002/07/owl#Class + descendants: http://www.w3.org/2002/07/owl#Class + ancestors: http://www.w3.org/2002/07/owl#Class + instances: http://data.bioontology.org/metadata/Instance + tree: http://www.w3.org/2002/07/owl#Class + notes: http://data.bioontology.org/metadata/Note + mappings: http://data.bioontology.org/metadata/Mapping + ui: http://www.w3.org/2002/07/owl#Class + "@context": + "@vocab": http://data.bioontology.org/metadata/ + prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel + synonym: http://www.w3.org/2004/02/skos/core#altLabel + "@language": en + hierarchy: [] + annotations: + - from: 1 + to: 8 + matchType: PREF + text: MELANOMA + - from: 34 + to: 44 + matchType: SYN + text: MELANOCYTES + mappings: [] + - annotatedClass: + definition: + - http://opendata.inrae.fr/thesaurusINRAE/note_f18c0fe1 + prefLabel: mélanome + synonym: + - malignant melanoma + - mélanome malin + "@id": http://opendata.inrae.fr/thesaurusINRAE/c_11970 + "@type": http://www.w3.org/2002/07/owl#Class + links: + self: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970 + ontology: http://localhost:9393/ontologies/STY + children: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/children + parents: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/parents + descendants: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/descendants + ancestors: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/ancestors + instances: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/instances + tree: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/tree + notes: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/notes + mappings: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/mappings + ui: http://stageportal.lirmm.fr/ontologies/INRAETHES?p=classes&conceptid=http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970 + "@context": + self: http://www.w3.org/2002/07/owl#Class + ontology: http://localhost:9393/ontologies/STY + children: http://www.w3.org/2002/07/owl#Class + parents: http://www.w3.org/2002/07/owl#Class + descendants: http://www.w3.org/2002/07/owl#Class + ancestors: http://www.w3.org/2002/07/owl#Class + instances: http://data.bioontology.org/metadata/Instance + tree: http://www.w3.org/2002/07/owl#Class + notes: http://data.bioontology.org/metadata/Note + mappings: http://data.bioontology.org/metadata/Mapping + ui: http://www.w3.org/2002/07/owl#Class + "@context": + "@vocab": http://data.bioontology.org/metadata/ + prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel + synonym: http://www.w3.org/2004/02/skos/core#altLabel + definition: http://www.w3.org/2004/02/skos/core#definition + "@language": en + hierarchy: [] + annotations: + - from: 1 + to: 8 + matchType: PREF + text: MELANOMA + mappings: [] + - annotatedClass: + prefLabel: tumeur + synonym: + - néoplasme + - néoplasie + "@id": http://opendata.inrae.fr/thesaurusINRAE/c_11887 + "@type": http://www.w3.org/2002/07/owl#Class + links: + self: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887 + ontology: http://localhost:9393/ontologies/STY + children: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/children + parents: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/parents + descendants: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/descendants + ancestors: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/ancestors + instances: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/instances + tree: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/tree + notes: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/notes + mappings: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/mappings + ui: http://stageportal.lirmm.fr/ontologies/INRAETHES?p=classes&conceptid=http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887 + "@context": + self: http://www.w3.org/2002/07/owl#Class + ontology: http://localhost:9393/ontologies/STY + children: http://www.w3.org/2002/07/owl#Class + parents: http://www.w3.org/2002/07/owl#Class + descendants: http://www.w3.org/2002/07/owl#Class + ancestors: http://www.w3.org/2002/07/owl#Class + instances: http://data.bioontology.org/metadata/Instance + tree: http://www.w3.org/2002/07/owl#Class + notes: http://data.bioontology.org/metadata/Note + mappings: http://data.bioontology.org/metadata/Mapping + ui: http://www.w3.org/2002/07/owl#Class + "@context": + "@vocab": http://data.bioontology.org/metadata/ + prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel + synonym: http://www.w3.org/2004/02/skos/core#altLabel + "@language": en + hierarchy: [] + annotations: + - from: 25 + to: 29 + matchType: PREF + text: TUMOR + mappings: [] diff --git a/test/fixtures/ontologies.yml b/test/fixtures/ontologies.yml index 28d345e73c..100d00b3a3 100644 --- a/test/fixtures/ontologies.yml +++ b/test/fixtures/ontologies.yml @@ -61,3 +61,87 @@ ontology_view: hasDomain: acl: viewOf: "ONT1" + +resource_content_formats: + json: + "@context": + ns0: "http://purl.bioontology.org/ontology/STY/" + rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + owl: "http://www.w3.org/2002/07/owl#" + rdfs: "http://www.w3.org/2000/01/rdf-schema#" + skos: "http://www.w3.org/2004/02/skos/core#" + metadata_def: "http://data.bioontology.org/metadata/def/" + "@graph": + - "@id": "ns0:T071" + "@type": "owl:Class" + "rdfs:subClassOf": + "@id": "owl:Thing" + "skos:prefLabel": + "@value": "Entity" + "@language": "en" + "skos:notation": "T071" + "metadata_def:mappingSameURI": + "@id": "ns0:T071" + "metadata_def:mappingLoom": "entity" + - "@id": "ns0:T072" + "rdfs:subClassOf": + "@id": "ns0:T071" + - "@id": "ns0:T077" + "rdfs:subClassOf": + "@id": "ns0:T071" + + xml: | + + + + + Entity + T071 + + entity + + + + + + + + + + + + + + ntriples: | + . + . + "Entity"@en . + "T071" . + . + "entity" . + . + . + . + + + turtle: | + @prefix rdf: . + @prefix ns0: . + @prefix owl: . + @prefix rdfs: . + @prefix skos: . + @prefix metadata_def: . + + ns0:T071 + metadata_def:mappingLoom "entity" ; + metadata_def:mappingSameURI ns0:T071 ; + a owl:Class ; + rdfs:subClassOf owl:Thing ; + skos:notation "T071" ; + skos:prefLabel "Entity"@en . + + ns0:T072 + rdfs:subClassOf ns0:T071 . + + ns0:T077 + rdfs:subClassOf ns0:T071 . \ No newline at end of file diff --git a/test/fixtures/users.yml b/test/fixtures/users.yml index eaaf3596e8..4c7e880436 100644 --- a/test/fixtures/users.yml +++ b/test/fixtures/users.yml @@ -1,3 +1,7 @@ +admin: + username: johndoe + email: admin@example.com + password: password john: firstName: John lastName: Doe diff --git a/test/helpers/application_test_helpers.rb b/test/helpers/application_test_helpers.rb index 054a9f7c40..975c220eac 100644 --- a/test/helpers/application_test_helpers.rb +++ b/test/helpers/application_test_helpers.rb @@ -19,25 +19,47 @@ def sign_in_as(username) if logged_in_user && !logged_in_user.errors logged_in_user = create_user(user) end - session[:user] = logged_in_user + logged_in_user end - def create_user(user , admin: false) - unless (existent_user = LinkedData::Client::Models::User.find_by_username(user.username).first) - values = user.to_h - values[:role] = ["ADMINISTRATOR"] if admin - existent_user = LinkedData::Client::Models::User.new(values: values).save + def create_user(user, admin: false) + admin_user = LinkedData::Client::Models::User.authenticate('admin', 'password') if admin + existent_user = LinkedData::Client::Models::User.find_by_username(user.username).first + + existent_user.delete if existent_user + + values = user.to_h + values[:role] = ["ADMINISTRATOR"] if admin + existent_user = LinkedData::Client::Models::User.new(values: values) + + if admin + # Overwrite the normal ".save" to accept creating admin user + conn = Faraday.new(url: LinkedData::Client.settings.rest_url) do |faraday| + faraday.request :url_encoded + faraday.response :logger + faraday.adapter Faraday.default_adapter + faraday.headers = { + "Accept" => "application/json", + "Authorization" => "apikey token=#{admin_user.apikey}", + "User-Agent" => "NCBO API Ruby Client v0.1.0" + } + + end + conn.post(existent_user.class.collection_path, existent_user.to_hash.to_json, 'Content-Type' => 'application/json') + else + existent_user.save end existent_user.password = user.password existent_user end - def delete_users(ontologies = LinkedData::Client::Models::Ontology.all) - Array(ontologies).each do |o| + def delete_users(users = LinkedData::Client::Models::User.all) + Array(users).each do |o| LinkedData::Client::Models::Ontology.find_by_acronym(o.acronym).first&.delete end end + def delete_user(user) LinkedData::Client::Models::User.find_by_username(user.username).first&.delete end diff --git a/test/integration/login_flows_test.rb b/test/integration/login_flows_test.rb index d446a6d6a3..0f1f70b444 100644 --- a/test/integration/login_flows_test.rb +++ b/test/integration/login_flows_test.rb @@ -50,7 +50,7 @@ class LoginFlowsTest < ActionDispatch::IntegrationTest assert_select '.notification', text: 'Account was successfully created' - get account_path + get "/accounts/#{new_user.username}" assert_response :success assert_select '.account-page-title', text: 'My account' diff --git a/test/system/agent_flows_test.rb b/test/system/agent_flows_test.rb index c4272b71fa..5eeb72055d 100644 --- a/test/system/agent_flows_test.rb +++ b/test/system/agent_flows_test.rb @@ -14,7 +14,7 @@ class AgentFlowsTest < ApplicationSystemTestCase def teardown delete_agents - delete_users + delete_user(@logged_user) if @logged_user end test "go admin page and create an agent person and edit it" do @@ -41,7 +41,7 @@ def teardown click_on "Persons & organizations" # Creation test - create_agent_flow(@new_organization, person_count: 0, organization_count: 3) + create_agent_flow(@new_organization, person_count: 0, organization_count: 1) # Edition test @new_organization2 = fixtures(:agents)[:organization2] @@ -50,7 +50,7 @@ def teardown @new_organization2.id = edit_link['href'].split('/')[-2] edit_link.click - edit_agent_flow(@new_organization2, person_count: 0, organization_count: 5) + edit_agent_flow(@new_organization2, person_count: 0, organization_count: 1) end @@ -61,21 +61,21 @@ def create_agent_flow(new_agent, person_count: , organization_count:) # Creation test click_on "Create New Agent" wait_for_text "TYPE" - agent_fill(new_agent) + agent_fill(new_agent, is_affiliation: false) sleep 1 assert_text "New Agent added successfully" find('.close').click within "table#admin_agents" do assert_selector '.human', count: person_count + organization_count # all created agents assert_text new_agent.name - new_agent.identifiers.map{|x| "https://orcid.org/#{x["notation"]}"}.each do |orcid| + new_agent.identifiers.map{|x| "https://#{new_agent.agentType.eql?('organization') ? 'ror' : 'orcid'}.org/#{x["notation"]}"}.each do |orcid| assert_text orcid end assert_text 'person', count: person_count assert_text 'organization', count: organization_count - new_agent.affiliations.map do |aff| + Array(new_agent.affiliations).map do |aff| aff["identifiers"] = aff["identifiers"].each{|x| x["schemaAgency"] = 'ORCID'} assert_text aff['name'] end @@ -87,16 +87,17 @@ def edit_agent_flow(agent, person_count: , organization_count: ) agent_fill(agent, parent_id: agent.id) # assert_text "New Agent added successfully" find('.close').click + sleep 1 within "table#admin_agents" do assert_selector '.human', count: person_count + organization_count # all created agents assert_text agent.name - agent.identifiers.map{|x| "https://orcid.org/#{x["notation"]}"}.each do |orcid| + agent.identifiers.map{|x| "https://#{agent.agentType.eql?('organization') ? 'ror' : 'orcid'}.org/#{x["notation"]}"}.each do |orcid| assert_text orcid end assert_text 'person', count: person_count assert_text 'organization', count: organization_count - agent.affiliations.map do |aff| + Array(agent.affiliations).map do |aff| aff["identifiers"] = aff["identifiers"].each{|x| x["schemaAgency"] = 'ORCID'} assert_text aff['name'] end diff --git a/test/system/annotator_page_test.rb b/test/system/annotator_page_test.rb new file mode 100644 index 0000000000..5956a75f36 --- /dev/null +++ b/test/system/annotator_page_test.rb @@ -0,0 +1,108 @@ +require "application_system_test_case" +require 'webmock/minitest' + +class AnnotatorPageTest < ApplicationSystemTestCase + def setup + WebMock.disable! + @apikey = LinkedData::Client.settings.apikey + @annotator_api = $ANNOTATOR_URL + @host = "#{@annotator_api.split('/')[-2]}:443" + @annotator_text_area = ".annotator-page-text-area > textarea" + @sample_response = fixtures(:annotator)["sample_response"] + end + + def teardown + WebMock.disable! + end + + test "go to annotator page and check if all the inputs and filters are there" do + visit root_url + click_link(href: '/annotator') + assert_selector @annotator_text_area + assert_selector 'div.insert-sample-text-button' + # Check if there are the annotator's options + assert_selector 'label[for="chips-whole_word_only-check"]' + assert_selector 'label[for="chips-longest_only-check"]' + assert_selector 'label[for="chips-expand_mappings-check"]' + assert_selector 'label[for="chips-exclude_numbers-check"]' + assert_selector 'label[for="chips-exclude_synonyms-check"]' + assert_selector 'div.select-ontologies' + + # Open the advanced options + find('div.advanced-options-button').click + + # Check if there are the advanced options + assert_selector 'input#select_umls_semantic_types-ts-control', visible: :all + assert_selector 'input#select_umls_semantic_groups-ts-control', visible: :all + assert_selector 'input#select_ancestors_level-ts-control', visible: :all + assert_selector 'input#select_include_score-ts-control', visible: :all + assert_selector 'input[name="score_threshold"]' + assert_selector 'input[name="confidence_threshold"]' + assert_selector 'label[for="chips-fast_context-check"]' + assert_selector 'label[for="chips-lemmatize-check"]' + end + + test "go to annotator page insert sample text and get annotations" do + visit root_url + click_link(href: '/annotator') + + # Fill the annotator's text area input by a sample text + find(@annotator_text_area).fill_in(with: 'Melanoma is a malignant tumor of melanocytes found mainly') + + # Mock the api call for the annotator with the entered text + WebMock.enable! + stub_request(:get, "#{@annotator_api}?class_hierarchy_max_level=None&confidence_threshold=0&score_threshold=0&text=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20found%20mainly&whole_word_only=true") + .with( + headers: { + 'Accept'=>'application/json', + 'Authorization'=>"apikey token=#{@apikey}", + 'Host'=> @host, + 'User-Agent'=>'NCBO API Ruby Client v0.1.0' + }) + .to_return(status: 200, body: @sample_response.to_json, headers: {}) + + + find(".annotator-page-button #annotator").click + + # Check if we get the table of annotations + assert_selector 'table#annotator-table' + + # Check if the number of annotations is 4 + assert_equal 5, page.all('tr').count + + # Check if we got the correct annotations + assert_selector 'a[href="ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713"]', text: 'Melanom' + assert_selector 'a[href="ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910"]', text: 'Melanom' + assert_selector 'a[href="ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970"]', text: 'mélanome' + assert_selector 'a[href="ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887"]', text: 'tumeur' + + # Check if the action buttons below the table are there (json, rdf, cite us and api doc buttons) + assert_selector '#annotator_json' + assert_selector '#annotator_rdf' + assert_selector '#annotator_cite_us' + assert_selector '#annotator_api_doc' + + # Clear the sample text in the annotator text area + find(@annotator_text_area).native.clear + + # Fill it with a text that will return an empty state + find(@annotator_text_area).fill_in(with: 'mainly') + + # Mock the api call of the annotator to get and return an empty result + stub_request(:get, "#{@annotator_api}?class_hierarchy_max_level=None&confidence_threshold=0&score_threshold=0&text=mainly&whole_word_only=true") + .with( + headers: { + 'Accept'=>'application/json', + 'Authorization'=>"apikey token=#{@apikey}", + 'Host'=> @host, + 'User-Agent'=>'NCBO API Ruby Client v0.1.0' + }) + .to_return(status: 200, body: ([]).to_json, headers: {}) + + find(".annotator-page-button #annotator").click + + # Check if we got the empty state correctly + assert_selector 'div.browse-empty-illustration' + end + +end \ No newline at end of file diff --git a/test/system/content_redirection_test.rb b/test/system/content_redirection_test.rb new file mode 100644 index 0000000000..bf0a35ab66 --- /dev/null +++ b/test/system/content_redirection_test.rb @@ -0,0 +1,68 @@ +require "application_system_test_case" +require 'webmock/minitest' + +class ContentRedirectionTest < ApplicationSystemTestCase + def setup + WebMock.disable! + + @sty_url = root_url + 'ontologies/STY' + @ontology_portal_uri = 'div.field-container p.field-description_text' + @htaccess_button = 'a[data-show-modal-title-value="Rewrite rules for STY ontology"]' + @redirection_modal = 'div#redirection_rules_modal' + @htaccess_code = 'div.htacess-code-container' + @nginx_code = 'div.nginx-code-container' + @contact_support_button = 'div.contact-support' + + @generate_portal_link_button = 'span#generate_portal_link' + @accordion_concept_details = '.dropdown-title-bar[data-target="#accordion-concept-details"]' + + @resource_div_formats = 'div#content_resource_formats' + @json_response = fixtures(:ontologies)["resource_content_formats"].json + @xml_response = fixtures(:ontologies)["resource_content_formats"].xml.strip + @ntriples_response = fixtures(:ontologies)["resource_content_formats"].ntriples.strip + @turtle_response = fixtures(:ontologies)["resource_content_formats"].turtle.strip + end + + test "go to STY ontology page and test the htaccess button" do + visit @sty_url + assert_selector @ontology_portal_uri, text: $SITE + ' URI' + assert_selector @htaccess_button + find(@htaccess_button).click + assert_selector(@redirection_modal, visible: true, wait: 10) + assert_selector @htaccess_code + assert_selector @nginx_code + assert_selector @contact_support_button + find('button[data-action="turbo-modal#hide"]').click + end + + test "go to STY ontology classes page and test the different format of resource" do + visit @sty_url + click_link('Classes') + assert_selector(@generate_portal_link_button, visible: true, wait: 10) + generated_uri = find(@generate_portal_link_button + " .clipboard.d-flex.align-items-center").find('div[data-clipboard-target="content"]', visible: :all).native.attribute('innerHTML').strip + assert_equal "http://localhost:3000/ontologies/STY/T071", generated_uri + find(@generate_portal_link_button, visible: :all).click + assert_selector(@accordion_concept_details, visible: true, wait: 10) + find(@accordion_concept_details, visible: :all).click + assert_selector(@resource_div_formats, visible: true) + + # test formats content + ["json", "xml", "ntriples", "turtle"].each do |format| + find("a#resource_content_#{format}", visible: true).click + assert_selector("div#resource_content_modal", visible: true, wait: 10) + content = find("div#resource_content_modal pre code", visible: true).text.strip + case format + when "json" + assert_equal JSON.parse(content), @json_response + when "xml" + assert_equal content, @xml_response + when "ntriples" + assert_equal content, @ntriples_response + when "turtle" + assert_equal content, @turtle_response + end + find('button.close[data-action="turbo-modal#hide"]').click + end + end + +end \ No newline at end of file diff --git a/test/system/login_flows_test.rb b/test/system/login_flows_test.rb index 5ed014b2c8..d6ff0deb49 100644 --- a/test/system/login_flows_test.rb +++ b/test/system/login_flows_test.rb @@ -5,7 +5,7 @@ class LoginFlowsTest < ApplicationSystemTestCase setup do WebMock.disable! @user_john = fixtures(:users)[:john] - @user_bob = create_user(fixtures(:users)[:bob]) + @user_bob = fixtures(:users)[:bob] end teardown do @@ -40,7 +40,7 @@ class LoginFlowsTest < ApplicationSystemTestCase assert_selector '.notification', text: 'Account was successfully created' - visit root_url + '/account' + visit root_url + "/accounts/#{new_user.username}" assert_selector '.account-page-title', text: 'My account' @@ -77,7 +77,7 @@ class LoginFlowsTest < ApplicationSystemTestCase test "login and reset password" do login_in_as(@user_bob) - visit root_url + '/account' + visit root_url + "/accounts/#{@user_bob.username}" find("a[href=\"#{edit_user_path(@user_bob.username)}\"]").click diff --git a/test/system/submission_flows_test.rb b/test/system/submission_flows_test.rb index 4a11bd1b8f..6045308d04 100644 --- a/test/system/submission_flows_test.rb +++ b/test/system/submission_flows_test.rb @@ -43,7 +43,7 @@ class SubmissionFlowsTest < ApplicationSystemTestCase assert_selector '.alert-message', text: "The ontology is processing." @new_ontology.hasDomain.each do |cat| - assert_text cat.name + assert_text cat.acronym.titleize end @@ -143,12 +143,12 @@ class SubmissionFlowsTest < ApplicationSystemTestCase assert_text "#{ontology_2.name} (#{@new_ontology.acronym})" selected_categories.each do |cat| - assert_text cat.name + assert_text cat.acronym.titleize end assert_text submission_2.URI assert_text submission_2.versionIRI - assert_selector '#submission-status', text: submission_2.version + assert_selector '.submission-status', text: submission_2.version assert_selector ".flag-icon-fr" # todo fix this submission_2.identifier.each do |id| assert_text id @@ -203,12 +203,15 @@ class SubmissionFlowsTest < ApplicationSystemTestCase open_dropdown "#projects_section" usage_properties = [ :coverage, :knownUsage, - :hasDomain, :example + :example ] usage_properties.each do |property| Array(submission_2[property]).each { |v| assert_text v } # check end + has_domain_values = ["Has Domain2.1", "Has Domain2.2", "Has Domain2.3"] + has_domain_values.each { |v| assert_text v } + submission_2.designedForOntologyTask.each do |task| assert_text task.delete(' ') # TODO fix in the UI the disaply of taskes end @@ -329,7 +332,7 @@ class SubmissionFlowsTest < ApplicationSystemTestCase assert_equal existent_submission.pullLocation, find_field('submission[pullLocation]').value click_button 'Next' - + assert_equal Date.parse(existent_submission.modificationDate).to_s, find('[name="submission[modificationDate]"]', visible: false).value assert_equal existent_submission.contact.map(&:values).flatten.sort, all('[name^="submission[contact]"]').map(&:value).sort @@ -349,7 +352,7 @@ class SubmissionFlowsTest < ApplicationSystemTestCase assert_selector '.alert-message', text: "The ontology is processing." ontology_2.hasDomain.each do |cat| - assert_text cat.name + assert_text cat.acronym.titleize end refute_text 'Version IRI' @@ -651,4 +654,4 @@ def fill_ontology(new_ontology, new_submission, add_submission: false) click_button 'Finish' end end -end \ No newline at end of file +end diff --git a/test/test_helper.rb b/test/test_helper.rb index e8f7cf84af..af79730627 100644 --- a/test/test_helper.rb +++ b/test/test_helper.rb @@ -2,6 +2,7 @@ require_relative '../config/environment' require 'rails/test_help' require 'simplecov' +require 'webmock/minitest' SimpleCov.start 'rails' do add_filter '/bin/' @@ -16,6 +17,7 @@ class ActiveSupport::TestCase # Add more helper methods to be used by all tests here... + WebMock.allow_net_connect! Capybara.server_host = "0.0.0.0" Capybara.app_host = "http://#{Socket.gethostname}:#{Capybara.server_port}" diff --git a/vendor/assets/images/chosen/chosen-sprite.png b/vendor/assets/images/chosen/chosen-sprite.png deleted file mode 100755 index c57da70b4b5b1e08a6977ddde182677af0e5e1b8..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 538 zcmV+#0_FXQP)cz2)-WJLkv8J@4bb5L`rsE?Kc|FrXHkKz)ov z76MHYM&Apx%05P7orE!>9=yZ~6O0^V?1%{=1UASqa<2Pgnk7fs!OIs9gh{NCN+@=) z>Gfttd5uq;oeR{%NHjtqV~jEQeY?tDff=(jqx>~SZ_e+iN26HR*`0Q!Re)~HD85p> zbL()Mw}bI^#`7wp0+cv&7*LhrtOmR)?PK>(-BeLm#jL5Jfogv-QS(TBnUb;))Krqm zD}uDDeVLNhm1G*pFB`O?iA=dnWBEpqHk8Yh%Qu45EIG=&F-dDmt|;|nN@|3lOkVZ7>z*~a1?_t?U)c+&|JFJke1`&0-a z#PjhRlg?=$KTo4|rU@NyV_fzDy@>h!lVyKShsO8>V>$xyIXRbHK%H~^Aaz=s$Jz^V zlb?KfaKdZqu3^#m$mintvgJ15@j`sb2Zr%69Sn=xN01Tm5r)NQanT=jhwm7zqj2>O cEB}D~0$b-QdD7|v=>Px#07*qoM6N<$g6AXnUH||9 diff --git a/vendor/assets/images/chosen/chosen-sprite@2x.png b/vendor/assets/images/chosen/chosen-sprite@2x.png deleted file mode 100755 index 6b50545202cb4770039362c55025b0b9824663ad..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 738 zcmV<80v-K{P)oJoIWh{eAG@xkM<0ryd(K3(} zP8JV&;uuIJ4nL%g8!wSG9E$P+3QVMGgj><+00}M5I5kMzaT<~M;uJ`UhLfbp9Ahdsrux5(g+(>Q*+9wU{AuYPH0}W_u4`|q(9c->{ zt>Jn|lbhH<_x5jU6prFi#S}&XMZ=~Y5VyC3+ZN%hXciz8 zPcLpJgbIK#a49e31-%wf2zh2F&&(Nq;AL%4zA(=QJRGq`sx3y3#0_cg9Fim739XTOu1NKKjlWs`52Q+3 Uja*K~(*OVf07*qoM6N<$g3mu-GXMYp diff --git a/vendor/assets/javascripts/chosen.jquery.js b/vendor/assets/javascripts/chosen.jquery.js deleted file mode 100755 index 060c162842..0000000000 --- a/vendor/assets/javascripts/chosen.jquery.js +++ /dev/null @@ -1,1269 +0,0 @@ -/*! -Chosen, a Select Box Enhancer for jQuery and Prototype -by Patrick Filler for Harvest, http://getharvest.com - -Version 1.6.2 -Full source at https://github.com/harvesthq/chosen -Copyright (c) 2011-2016 Harvest http://getharvest.com - -MIT License, https://github.com/harvesthq/chosen/blob/master/LICENSE.md -This file is generated by `grunt build`, do not edit it by hand. -*/ - -(function() { - var $, AbstractChosen, Chosen, SelectParser, _ref, - __hasProp = {}.hasOwnProperty, - __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor(); child.__super__ = parent.prototype; return child; }; - - SelectParser = (function() { - function SelectParser() { - this.options_index = 0; - this.parsed = []; - } - - SelectParser.prototype.add_node = function(child) { - if (child.nodeName.toUpperCase() === "OPTGROUP") { - return this.add_group(child); - } else { - return this.add_option(child); - } - }; - - SelectParser.prototype.add_group = function(group) { - var group_position, option, _i, _len, _ref, _results; - group_position = this.parsed.length; - this.parsed.push({ - array_index: group_position, - group: true, - label: this.escapeExpression(group.label), - title: group.title ? group.title : void 0, - children: 0, - disabled: group.disabled, - classes: group.className - }); - _ref = group.childNodes; - _results = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - option = _ref[_i]; - _results.push(this.add_option(option, group_position, group.disabled)); - } - return _results; - }; - - SelectParser.prototype.add_option = function(option, group_position, group_disabled) { - if (option.nodeName.toUpperCase() === "OPTION") { - if (option.text !== "") { - if (group_position != null) { - this.parsed[group_position].children += 1; - } - this.parsed.push({ - array_index: this.parsed.length, - options_index: this.options_index, - value: option.value, - text: option.text, - html: option.innerHTML, - title: option.title ? option.title : void 0, - selected: option.selected, - disabled: group_disabled === true ? group_disabled : option.disabled, - group_array_index: group_position, - group_label: group_position != null ? this.parsed[group_position].label : null, - classes: option.className, - style: option.style.cssText - }); - } else { - this.parsed.push({ - array_index: this.parsed.length, - options_index: this.options_index, - empty: true - }); - } - return this.options_index += 1; - } - }; - - SelectParser.prototype.escapeExpression = function(text) { - var map, unsafe_chars; - if ((text == null) || text === false) { - return ""; - } - if (!/[\&\<\>\"\'\`]/.test(text)) { - return text; - } - map = { - "<": "<", - ">": ">", - '"': """, - "'": "'", - "`": "`" - }; - unsafe_chars = /&(?!\w+;)|[\<\>\"\'\`]/g; - return text.replace(unsafe_chars, function(chr) { - return map[chr] || "&"; - }); - }; - - return SelectParser; - - })(); - - SelectParser.select_to_array = function(select) { - var child, parser, _i, _len, _ref; - parser = new SelectParser(); - _ref = select.childNodes; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - child = _ref[_i]; - parser.add_node(child); - } - return parser.parsed; - }; - - AbstractChosen = (function() { - function AbstractChosen(form_field, options) { - this.form_field = form_field; - this.options = options != null ? options : {}; - if (!AbstractChosen.browser_is_supported()) { - return; - } - this.is_multiple = this.form_field.multiple; - this.set_default_text(); - this.set_default_values(); - this.setup(); - this.set_up_html(); - this.register_observers(); - this.on_ready(); - } - - AbstractChosen.prototype.set_default_values = function() { - var _this = this; - this.click_test_action = function(evt) { - return _this.test_active_click(evt); - }; - this.activate_action = function(evt) { - return _this.activate_field(evt); - }; - this.active_field = false; - this.mouse_on_container = false; - this.results_showing = false; - this.result_highlighted = null; - this.allow_single_deselect = (this.options.allow_single_deselect != null) && (this.form_field.options[0] != null) && this.form_field.options[0].text === "" ? this.options.allow_single_deselect : false; - this.disable_search_threshold = this.options.disable_search_threshold || 0; - this.disable_search = this.options.disable_search || false; - this.enable_split_word_search = this.options.enable_split_word_search != null ? this.options.enable_split_word_search : true; - this.group_search = this.options.group_search != null ? this.options.group_search : true; - this.search_contains = this.options.search_contains || false; - this.single_backstroke_delete = this.options.single_backstroke_delete != null ? this.options.single_backstroke_delete : true; - this.max_selected_options = this.options.max_selected_options || Infinity; - this.inherit_select_classes = this.options.inherit_select_classes || false; - this.display_selected_options = this.options.display_selected_options != null ? this.options.display_selected_options : true; - this.display_disabled_options = this.options.display_disabled_options != null ? this.options.display_disabled_options : true; - this.include_group_label_in_selected = this.options.include_group_label_in_selected || false; - this.max_shown_results = this.options.max_shown_results || Number.POSITIVE_INFINITY; - return this.case_sensitive_search = this.options.case_sensitive_search || false; - }; - - AbstractChosen.prototype.set_default_text = function() { - if (this.form_field.getAttribute("data-placeholder")) { - this.default_text = this.form_field.getAttribute("data-placeholder"); - } else if (this.is_multiple) { - this.default_text = this.options.placeholder_text_multiple || this.options.placeholder_text || AbstractChosen.default_multiple_text; - } else { - this.default_text = this.options.placeholder_text_single || this.options.placeholder_text || AbstractChosen.default_single_text; - } - return this.results_none_found = this.form_field.getAttribute("data-no_results_text") || this.options.no_results_text || AbstractChosen.default_no_result_text; - }; - - AbstractChosen.prototype.choice_label = function(item) { - if (this.include_group_label_in_selected && (item.group_label != null)) { - return "" + item.group_label + "" + item.html; - } else { - return item.html; - } - }; - - AbstractChosen.prototype.mouse_enter = function() { - return this.mouse_on_container = true; - }; - - AbstractChosen.prototype.mouse_leave = function() { - return this.mouse_on_container = false; - }; - - AbstractChosen.prototype.input_focus = function(evt) { - var _this = this; - if (this.is_multiple) { - if (!this.active_field) { - return setTimeout((function() { - return _this.container_mousedown(); - }), 50); - } - } else { - if (!this.active_field) { - return this.activate_field(); - } - } - }; - - AbstractChosen.prototype.input_blur = function(evt) { - var _this = this; - if (!this.mouse_on_container) { - this.active_field = false; - return setTimeout((function() { - return _this.blur_test(); - }), 100); - } - }; - - AbstractChosen.prototype.results_option_build = function(options) { - var content, data, data_content, shown_results, _i, _len, _ref; - content = ''; - shown_results = 0; - _ref = this.results_data; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - data = _ref[_i]; - data_content = ''; - if (data.group) { - data_content = this.result_add_group(data); - } else { - data_content = this.result_add_option(data); - } - if (data_content !== '') { - shown_results++; - content += data_content; - } - if (options != null ? options.first : void 0) { - if (data.selected && this.is_multiple) { - this.choice_build(data); - } else if (data.selected && !this.is_multiple) { - this.single_set_selected_text(this.choice_label(data)); - } - } - if (shown_results >= this.max_shown_results) { - break; - } - } - return content; - }; - - AbstractChosen.prototype.result_add_option = function(option) { - var classes, option_el; - if (!option.search_match) { - return ''; - } - if (!this.include_option_in_results(option)) { - return ''; - } - classes = []; - if (!option.disabled && !(option.selected && this.is_multiple)) { - classes.push("active-result"); - } - if (option.disabled && !(option.selected && this.is_multiple)) { - classes.push("disabled-result"); - } - if (option.selected) { - classes.push("result-selected"); - } - if (option.group_array_index != null) { - classes.push("group-option"); - } - if (option.classes !== "") { - classes.push(option.classes); - } - option_el = document.createElement("li"); - option_el.className = classes.join(" "); - option_el.style.cssText = option.style; - option_el.setAttribute("data-option-array-index", option.array_index); - option_el.innerHTML = option.search_text; - if (option.title) { - option_el.title = option.title; - } - return this.outerHTML(option_el); - }; - - AbstractChosen.prototype.result_add_group = function(group) { - var classes, group_el; - if (!(group.search_match || group.group_match)) { - return ''; - } - if (!(group.active_options > 0)) { - return ''; - } - classes = []; - classes.push("group-result"); - if (group.classes) { - classes.push(group.classes); - } - group_el = document.createElement("li"); - group_el.className = classes.join(" "); - group_el.innerHTML = group.search_text; - if (group.title) { - group_el.title = group.title; - } - return this.outerHTML(group_el); - }; - - AbstractChosen.prototype.results_update_field = function() { - this.set_default_text(); - if (!this.is_multiple) { - this.results_reset_cleanup(); - } - this.result_clear_highlight(); - this.results_build(); - if (this.results_showing) { - return this.winnow_results(); - } - }; - - AbstractChosen.prototype.reset_single_select_options = function() { - var result, _i, _len, _ref, _results; - _ref = this.results_data; - _results = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - result = _ref[_i]; - if (result.selected) { - _results.push(result.selected = false); - } else { - _results.push(void 0); - } - } - return _results; - }; - - AbstractChosen.prototype.results_toggle = function() { - if (this.results_showing) { - return this.results_hide(); - } else { - return this.results_show(); - } - }; - - AbstractChosen.prototype.results_search = function(evt) { - if (this.results_showing) { - return this.winnow_results(); - } else { - return this.results_show(); - } - }; - - AbstractChosen.prototype.winnow_results = function() { - var escapedSearchText, option, regex, results, results_group, searchText, startpos, text, zregex, _i, _len, _ref; - this.no_results_clear(); - results = 0; - searchText = this.get_search_text(); - escapedSearchText = searchText.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&"); - zregex = new RegExp(escapedSearchText, 'i'); - regex = this.get_search_regex(escapedSearchText); - _ref = this.results_data; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - option = _ref[_i]; - option.search_match = false; - results_group = null; - if (this.include_option_in_results(option)) { - if (option.group) { - option.group_match = false; - option.active_options = 0; - } - if ((option.group_array_index != null) && this.results_data[option.group_array_index]) { - results_group = this.results_data[option.group_array_index]; - if (results_group.active_options === 0 && results_group.search_match) { - results += 1; - } - results_group.active_options += 1; - } - option.search_text = option.group ? option.label : option.html; - if (!(option.group && !this.group_search)) { - option.search_match = this.search_string_match(option.search_text, regex); - if (option.search_match && !option.group) { - results += 1; - } - if (option.search_match) { - if (searchText.length) { - startpos = option.search_text.search(zregex); - text = option.search_text.substr(0, startpos + searchText.length) + '' + option.search_text.substr(startpos + searchText.length); - option.search_text = text.substr(0, startpos) + '' + text.substr(startpos); - } - if (results_group != null) { - results_group.group_match = true; - } - } else if ((option.group_array_index != null) && this.results_data[option.group_array_index].search_match) { - option.search_match = true; - } - } - } - } - this.result_clear_highlight(); - if (results < 1 && searchText.length) { - this.update_results_content(""); - return this.no_results(searchText); - } else { - this.update_results_content(this.results_option_build()); - return this.winnow_results_set_highlight(); - } - }; - - AbstractChosen.prototype.get_search_regex = function(escaped_search_string) { - var regex_anchor, regex_flag; - regex_anchor = this.search_contains ? "" : "^"; - regex_flag = this.case_sensitive_search ? "" : "i"; - return new RegExp(regex_anchor + escaped_search_string, regex_flag); - }; - - AbstractChosen.prototype.search_string_match = function(search_string, regex) { - var part, parts, _i, _len; - if (regex.test(search_string)) { - return true; - } else if (this.enable_split_word_search && (search_string.indexOf(" ") >= 0 || search_string.indexOf("[") === 0)) { - parts = search_string.replace(/\[|\]/g, "").split(" "); - if (parts.length) { - for (_i = 0, _len = parts.length; _i < _len; _i++) { - part = parts[_i]; - if (regex.test(part)) { - return true; - } - } - } - } - }; - - AbstractChosen.prototype.choices_count = function() { - var option, _i, _len, _ref; - if (this.selected_option_count != null) { - return this.selected_option_count; - } - this.selected_option_count = 0; - _ref = this.form_field.options; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - option = _ref[_i]; - if (option.selected) { - this.selected_option_count += 1; - } - } - return this.selected_option_count; - }; - - AbstractChosen.prototype.choices_click = function(evt) { - evt.preventDefault(); - if (!(this.results_showing || this.is_disabled)) { - return this.results_show(); - } - }; - - AbstractChosen.prototype.keyup_checker = function(evt) { - var stroke, _ref; - stroke = (_ref = evt.which) != null ? _ref : evt.keyCode; - this.search_field_scale(); - switch (stroke) { - case 8: - if (this.is_multiple && this.backstroke_length < 1 && this.choices_count() > 0) { - return this.keydown_backstroke(); - } else if (!this.pending_backstroke) { - this.result_clear_highlight(); - return this.results_search(); - } - break; - case 13: - evt.preventDefault(); - if (this.results_showing) { - return this.result_select(evt); - } - break; - case 27: - if (this.results_showing) { - this.results_hide(); - } - return true; - case 9: - case 38: - case 40: - case 16: - case 91: - case 17: - case 18: - break; - default: - return this.results_search(); - } - }; - - AbstractChosen.prototype.clipboard_event_checker = function(evt) { - var _this = this; - return setTimeout((function() { - return _this.results_search(); - }), 50); - }; - - AbstractChosen.prototype.container_width = function() { - if (this.options.width != null) { - return this.options.width; - } else { - return "" + this.form_field.offsetWidth + "px"; - } - }; - - AbstractChosen.prototype.include_option_in_results = function(option) { - if (this.is_multiple && (!this.display_selected_options && option.selected)) { - return false; - } - if (!this.display_disabled_options && option.disabled) { - return false; - } - if (option.empty) { - return false; - } - return true; - }; - - AbstractChosen.prototype.search_results_touchstart = function(evt) { - this.touch_started = true; - return this.search_results_mouseover(evt); - }; - - AbstractChosen.prototype.search_results_touchmove = function(evt) { - this.touch_started = false; - return this.search_results_mouseout(evt); - }; - - AbstractChosen.prototype.search_results_touchend = function(evt) { - if (this.touch_started) { - return this.search_results_mouseup(evt); - } - }; - - AbstractChosen.prototype.outerHTML = function(element) { - var tmp; - if (element.outerHTML) { - return element.outerHTML; - } - tmp = document.createElement("div"); - tmp.appendChild(element); - return tmp.innerHTML; - }; - - AbstractChosen.browser_is_supported = function() { - if ("Microsoft Internet Explorer" === window.navigator.appName) { - return document.documentMode >= 8; - } - if (/iP(od|hone)/i.test(window.navigator.userAgent) || /IEMobile/i.test(window.navigator.userAgent) || /Windows Phone/i.test(window.navigator.userAgent) || /BlackBerry/i.test(window.navigator.userAgent) || /BB10/i.test(window.navigator.userAgent) || /Android.*Mobile/i.test(window.navigator.userAgent)) { - return false; - } - return true; - }; - - AbstractChosen.default_multiple_text = "Select Some Options"; - - AbstractChosen.default_single_text = "Select an Option"; - - AbstractChosen.default_no_result_text = "No results match"; - - return AbstractChosen; - - })(); - - $ = jQuery; - - $.fn.extend({ - chosen: function(options) { - if (!AbstractChosen.browser_is_supported()) { - return this; - } - return this.each(function(input_field) { - var $this, chosen; - $this = $(this); - chosen = $this.data('chosen'); - if (options === 'destroy') { - if (chosen instanceof Chosen) { - chosen.destroy(); - } - return; - } - if (!(chosen instanceof Chosen)) { - $this.data('chosen', new Chosen(this, options)); - } - }); - } - }); - - Chosen = (function(_super) { - __extends(Chosen, _super); - - function Chosen() { - _ref = Chosen.__super__.constructor.apply(this, arguments); - return _ref; - } - - Chosen.prototype.setup = function() { - this.form_field_jq = $(this.form_field); - this.current_selectedIndex = this.form_field.selectedIndex; - return this.is_rtl = this.form_field_jq.hasClass("chosen-rtl"); - }; - - Chosen.prototype.set_up_html = function() { - var container_classes, container_props; - container_classes = ["chosen-container"]; - container_classes.push("chosen-container-" + (this.is_multiple ? "multi" : "single")); - if (this.inherit_select_classes && this.form_field.className) { - container_classes.push(this.form_field.className); - } - if (this.is_rtl) { - container_classes.push("chosen-rtl"); - } - container_props = { - 'class': container_classes.join(' '), - 'style': "width: " + (this.container_width()) + ";", - 'title': this.form_field.title - }; - if (this.form_field.id.length) { - container_props.id = this.form_field.id.replace(/[^\w]/g, '_') + "_chosen"; - } - this.container = $("
", container_props); - if (this.is_multiple) { - this.container.html('
    '); - } else { - this.container.html('' + this.default_text + '
      '); - } - this.form_field_jq.hide().after(this.container); - this.dropdown = this.container.find('div.chosen-drop').first(); - this.search_field = this.container.find('input').first(); - this.search_results = this.container.find('ul.chosen-results').first(); - this.search_field_scale(); - this.search_no_results = this.container.find('li.no-results').first(); - if (this.is_multiple) { - this.search_choices = this.container.find('ul.chosen-choices').first(); - this.search_container = this.container.find('li.search-field').first(); - } else { - this.search_container = this.container.find('div.chosen-search').first(); - this.selected_item = this.container.find('.chosen-single').first(); - } - this.results_build(); - this.set_tab_index(); - return this.set_label_behavior(); - }; - - Chosen.prototype.on_ready = function() { - return this.form_field_jq.trigger("chosen:ready", { - chosen: this - }); - }; - - Chosen.prototype.register_observers = function() { - var _this = this; - this.container.bind('touchstart.chosen', function(evt) { - _this.container_mousedown(evt); - return evt.preventDefault(); - }); - this.container.bind('touchend.chosen', function(evt) { - _this.container_mouseup(evt); - return evt.preventDefault(); - }); - this.container.bind('mousedown.chosen', function(evt) { - _this.container_mousedown(evt); - }); - this.container.bind('mouseup.chosen', function(evt) { - _this.container_mouseup(evt); - }); - this.container.bind('mouseenter.chosen', function(evt) { - _this.mouse_enter(evt); - }); - this.container.bind('mouseleave.chosen', function(evt) { - _this.mouse_leave(evt); - }); - this.search_results.bind('mouseup.chosen', function(evt) { - _this.search_results_mouseup(evt); - }); - this.search_results.bind('mouseover.chosen', function(evt) { - _this.search_results_mouseover(evt); - }); - this.search_results.bind('mouseout.chosen', function(evt) { - _this.search_results_mouseout(evt); - }); - this.search_results.bind('mousewheel.chosen DOMMouseScroll.chosen', function(evt) { - _this.search_results_mousewheel(evt); - }); - this.search_results.bind('touchstart.chosen', function(evt) { - _this.search_results_touchstart(evt); - }); - this.search_results.bind('touchmove.chosen', function(evt) { - _this.search_results_touchmove(evt); - }); - this.search_results.bind('touchend.chosen', function(evt) { - _this.search_results_touchend(evt); - }); - this.form_field_jq.bind("chosen:updated.chosen", function(evt) { - _this.results_update_field(evt); - }); - this.form_field_jq.bind("chosen:activate.chosen", function(evt) { - _this.activate_field(evt); - }); - this.form_field_jq.bind("chosen:open.chosen", function(evt) { - _this.container_mousedown(evt); - }); - this.form_field_jq.bind("chosen:close.chosen", function(evt) { - _this.input_blur(evt); - }); - this.search_field.bind('blur.chosen', function(evt) { - _this.input_blur(evt); - }); - this.search_field.bind('keyup.chosen', function(evt) { - _this.keyup_checker(evt); - }); - this.search_field.bind('keydown.chosen', function(evt) { - _this.keydown_checker(evt); - }); - this.search_field.bind('focus.chosen', function(evt) { - _this.input_focus(evt); - }); - this.search_field.bind('cut.chosen', function(evt) { - _this.clipboard_event_checker(evt); - }); - this.search_field.bind('paste.chosen', function(evt) { - _this.clipboard_event_checker(evt); - }); - if (this.is_multiple) { - return this.search_choices.bind('click.chosen', function(evt) { - _this.choices_click(evt); - }); - } else { - return this.container.bind('click.chosen', function(evt) { - evt.preventDefault(); - }); - } - }; - - Chosen.prototype.destroy = function() { - $(this.container[0].ownerDocument).unbind("click.chosen", this.click_test_action); - if (this.search_field[0].tabIndex) { - this.form_field_jq[0].tabIndex = this.search_field[0].tabIndex; - } - this.container.remove(); - this.form_field_jq.removeData('chosen'); - return this.form_field_jq.show(); - }; - - Chosen.prototype.search_field_disabled = function() { - this.is_disabled = this.form_field_jq[0].disabled; - if (this.is_disabled) { - this.container.addClass('chosen-disabled'); - this.search_field[0].disabled = true; - if (!this.is_multiple) { - this.selected_item.unbind("focus.chosen", this.activate_action); - } - return this.close_field(); - } else { - this.container.removeClass('chosen-disabled'); - this.search_field[0].disabled = false; - if (!this.is_multiple) { - return this.selected_item.bind("focus.chosen", this.activate_action); - } - } - }; - - Chosen.prototype.container_mousedown = function(evt) { - if (!this.is_disabled) { - if (evt && evt.type === "mousedown" && !this.results_showing) { - evt.preventDefault(); - } - if (!((evt != null) && ($(evt.target)).hasClass("search-choice-close"))) { - if (!this.active_field) { - if (this.is_multiple) { - this.search_field.val(""); - } - $(this.container[0].ownerDocument).bind('click.chosen', this.click_test_action); - this.results_show(); - } else if (!this.is_multiple && evt && (($(evt.target)[0] === this.selected_item[0]) || $(evt.target).parents("a.chosen-single").length)) { - evt.preventDefault(); - this.results_toggle(); - } - return this.activate_field(); - } - } - }; - - Chosen.prototype.container_mouseup = function(evt) { - if (evt.target.nodeName === "ABBR" && !this.is_disabled) { - return this.results_reset(evt); - } - }; - - Chosen.prototype.search_results_mousewheel = function(evt) { - var delta; - if (evt.originalEvent) { - delta = evt.originalEvent.deltaY || -evt.originalEvent.wheelDelta || evt.originalEvent.detail; - } - if (delta != null) { - evt.preventDefault(); - if (evt.type === 'DOMMouseScroll') { - delta = delta * 40; - } - return this.search_results.scrollTop(delta + this.search_results.scrollTop()); - } - }; - - Chosen.prototype.blur_test = function(evt) { - if (!this.active_field && this.container.hasClass("chosen-container-active")) { - return this.close_field(); - } - }; - - Chosen.prototype.close_field = function() { - $(this.container[0].ownerDocument).unbind("click.chosen", this.click_test_action); - this.active_field = false; - this.results_hide(); - this.container.removeClass("chosen-container-active"); - this.clear_backstroke(); - this.show_search_field_default(); - return this.search_field_scale(); - }; - - Chosen.prototype.activate_field = function() { - this.container.addClass("chosen-container-active"); - this.active_field = true; - this.search_field.val(this.search_field.val()); - return this.search_field.focus(); - }; - - Chosen.prototype.test_active_click = function(evt) { - var active_container; - active_container = $(evt.target).closest('.chosen-container'); - if (active_container.length && this.container[0] === active_container[0]) { - return this.active_field = true; - } else { - return this.close_field(); - } - }; - - Chosen.prototype.results_build = function() { - this.parsing = true; - this.selected_option_count = null; - this.results_data = SelectParser.select_to_array(this.form_field); - if (this.is_multiple) { - this.search_choices.find("li.search-choice").remove(); - } else if (!this.is_multiple) { - this.single_set_selected_text(); - if (this.disable_search || this.form_field.options.length <= this.disable_search_threshold) { - this.search_field[0].readOnly = true; - this.container.addClass("chosen-container-single-nosearch"); - } else { - this.search_field[0].readOnly = false; - this.container.removeClass("chosen-container-single-nosearch"); - } - } - this.update_results_content(this.results_option_build({ - first: true - })); - this.search_field_disabled(); - this.show_search_field_default(); - this.search_field_scale(); - return this.parsing = false; - }; - - Chosen.prototype.result_do_highlight = function(el) { - var high_bottom, high_top, maxHeight, visible_bottom, visible_top; - if (el.length) { - this.result_clear_highlight(); - this.result_highlight = el; - this.result_highlight.addClass("highlighted"); - maxHeight = parseInt(this.search_results.css("maxHeight"), 10); - visible_top = this.search_results.scrollTop(); - visible_bottom = maxHeight + visible_top; - high_top = this.result_highlight.position().top + this.search_results.scrollTop(); - high_bottom = high_top + this.result_highlight.outerHeight(); - if (high_bottom >= visible_bottom) { - return this.search_results.scrollTop((high_bottom - maxHeight) > 0 ? high_bottom - maxHeight : 0); - } else if (high_top < visible_top) { - return this.search_results.scrollTop(high_top); - } - } - }; - - Chosen.prototype.result_clear_highlight = function() { - if (this.result_highlight) { - this.result_highlight.removeClass("highlighted"); - } - return this.result_highlight = null; - }; - - Chosen.prototype.results_show = function() { - if (this.is_multiple && this.max_selected_options <= this.choices_count()) { - this.form_field_jq.trigger("chosen:maxselected", { - chosen: this - }); - return false; - } - this.container.addClass("chosen-with-drop"); - this.results_showing = true; - this.search_field.focus(); - this.search_field.val(this.search_field.val()); - this.winnow_results(); - return this.form_field_jq.trigger("chosen:showing_dropdown", { - chosen: this - }); - }; - - Chosen.prototype.update_results_content = function(content) { - return this.search_results.html(content); - }; - - Chosen.prototype.results_hide = function() { - if (this.results_showing) { - this.result_clear_highlight(); - this.container.removeClass("chosen-with-drop"); - this.form_field_jq.trigger("chosen:hiding_dropdown", { - chosen: this - }); - } - return this.results_showing = false; - }; - - Chosen.prototype.set_tab_index = function(el) { - var ti; - if (this.form_field.tabIndex) { - ti = this.form_field.tabIndex; - this.form_field.tabIndex = -1; - return this.search_field[0].tabIndex = ti; - } - }; - - Chosen.prototype.set_label_behavior = function() { - var _this = this; - this.form_field_label = this.form_field_jq.parents("label"); - if (!this.form_field_label.length && this.form_field.id.length) { - this.form_field_label = $("label[for='" + this.form_field.id + "']"); - } - if (this.form_field_label.length > 0) { - return this.form_field_label.bind('click.chosen', function(evt) { - if (_this.is_multiple) { - return _this.container_mousedown(evt); - } else { - return _this.activate_field(); - } - }); - } - }; - - Chosen.prototype.show_search_field_default = function() { - if (this.is_multiple && this.choices_count() < 1 && !this.active_field) { - this.search_field.val(this.default_text); - return this.search_field.addClass("default"); - } else { - this.search_field.val(""); - return this.search_field.removeClass("default"); - } - }; - - Chosen.prototype.search_results_mouseup = function(evt) { - var target; - target = $(evt.target).hasClass("active-result") ? $(evt.target) : $(evt.target).parents(".active-result").first(); - if (target.length) { - this.result_highlight = target; - this.result_select(evt); - return this.search_field.focus(); - } - }; - - Chosen.prototype.search_results_mouseover = function(evt) { - var target; - target = $(evt.target).hasClass("active-result") ? $(evt.target) : $(evt.target).parents(".active-result").first(); - if (target) { - return this.result_do_highlight(target); - } - }; - - Chosen.prototype.search_results_mouseout = function(evt) { - if ($(evt.target).hasClass("active-result" || $(evt.target).parents('.active-result').first())) { - return this.result_clear_highlight(); - } - }; - - Chosen.prototype.choice_build = function(item) { - var choice, close_link, - _this = this; - choice = $('
    • ', { - "class": "search-choice" - }).html("" + (this.choice_label(item)) + ""); - if (item.disabled) { - choice.addClass('search-choice-disabled'); - } else { - close_link = $('', { - "class": 'search-choice-close', - 'data-option-array-index': item.array_index - }); - close_link.bind('click.chosen', function(evt) { - return _this.choice_destroy_link_click(evt); - }); - choice.append(close_link); - } - return this.search_container.before(choice); - }; - - Chosen.prototype.choice_destroy_link_click = function(evt) { - evt.preventDefault(); - evt.stopPropagation(); - if (!this.is_disabled) { - return this.choice_destroy($(evt.target)); - } - }; - - Chosen.prototype.choice_destroy = function(link) { - if (this.result_deselect(link[0].getAttribute("data-option-array-index"))) { - this.show_search_field_default(); - if (this.is_multiple && this.choices_count() > 0 && this.search_field.val().length < 1) { - this.results_hide(); - } - link.parents('li').first().remove(); - return this.search_field_scale(); - } - }; - - Chosen.prototype.results_reset = function() { - this.reset_single_select_options(); - this.form_field.options[0].selected = true; - this.single_set_selected_text(); - this.show_search_field_default(); - this.results_reset_cleanup(); - this.form_field_jq.trigger("change"); - if (this.active_field) { - return this.results_hide(); - } - }; - - Chosen.prototype.results_reset_cleanup = function() { - this.current_selectedIndex = this.form_field.selectedIndex; - return this.selected_item.find("abbr").remove(); - }; - - Chosen.prototype.result_select = function(evt) { - var high, item; - if (this.result_highlight) { - high = this.result_highlight; - this.result_clear_highlight(); - if (this.is_multiple && this.max_selected_options <= this.choices_count()) { - this.form_field_jq.trigger("chosen:maxselected", { - chosen: this - }); - return false; - } - if (this.is_multiple) { - high.removeClass("active-result"); - } else { - this.reset_single_select_options(); - } - high.addClass("result-selected"); - item = this.results_data[high[0].getAttribute("data-option-array-index")]; - item.selected = true; - this.form_field.options[item.options_index].selected = true; - this.selected_option_count = null; - if (this.is_multiple) { - this.choice_build(item); - } else { - this.single_set_selected_text(this.choice_label(item)); - } - if (!((evt.metaKey || evt.ctrlKey) && this.is_multiple)) { - this.results_hide(); - } - this.show_search_field_default(); - if (this.is_multiple || this.form_field.selectedIndex !== this.current_selectedIndex) { - this.form_field_jq.trigger("change", { - 'selected': this.form_field.options[item.options_index].value - }); - } - this.current_selectedIndex = this.form_field.selectedIndex; - evt.preventDefault(); - return this.search_field_scale(); - } - }; - - Chosen.prototype.single_set_selected_text = function(text) { - if (text == null) { - text = this.default_text; - } - if (text === this.default_text) { - this.selected_item.addClass("chosen-default"); - } else { - this.single_deselect_control_build(); - this.selected_item.removeClass("chosen-default"); - } - return this.selected_item.find("span").html(text); - }; - - Chosen.prototype.result_deselect = function(pos) { - var result_data; - result_data = this.results_data[pos]; - if (!this.form_field.options[result_data.options_index].disabled) { - result_data.selected = false; - this.form_field.options[result_data.options_index].selected = false; - this.selected_option_count = null; - this.result_clear_highlight(); - if (this.results_showing) { - this.winnow_results(); - } - this.form_field_jq.trigger("change", { - deselected: this.form_field.options[result_data.options_index].value - }); - this.search_field_scale(); - return true; - } else { - return false; - } - }; - - Chosen.prototype.single_deselect_control_build = function() { - if (!this.allow_single_deselect) { - return; - } - if (!this.selected_item.find("abbr").length) { - this.selected_item.find("span").first().after(""); - } - return this.selected_item.addClass("chosen-single-with-deselect"); - }; - - Chosen.prototype.get_search_text = function() { - return $('
      ').text($.trim(this.search_field.val())).html(); - }; - - Chosen.prototype.winnow_results_set_highlight = function() { - var do_high, selected_results; - selected_results = !this.is_multiple ? this.search_results.find(".result-selected.active-result") : []; - do_high = selected_results.length ? selected_results.first() : this.search_results.find(".active-result").first(); - if (do_high != null) { - return this.result_do_highlight(do_high); - } - }; - - Chosen.prototype.no_results = function(terms) { - var no_results_html; - no_results_html = $('
    • ' + this.results_none_found + ' ""
      • '); - no_results_html.find("span").first().html(terms); - this.search_results.append(no_results_html); - return this.form_field_jq.trigger("chosen:no_results", { - chosen: this - }); - }; - - Chosen.prototype.no_results_clear = function() { - return this.search_results.find(".no-results").remove(); - }; - - Chosen.prototype.keydown_arrow = function() { - var next_sib; - if (this.results_showing && this.result_highlight) { - next_sib = this.result_highlight.nextAll("li.active-result").first(); - if (next_sib) { - return this.result_do_highlight(next_sib); - } - } else { - return this.results_show(); - } - }; - - Chosen.prototype.keyup_arrow = function() { - var prev_sibs; - if (!this.results_showing && !this.is_multiple) { - return this.results_show(); - } else if (this.result_highlight) { - prev_sibs = this.result_highlight.prevAll("li.active-result"); - if (prev_sibs.length) { - return this.result_do_highlight(prev_sibs.first()); - } else { - if (this.choices_count() > 0) { - this.results_hide(); - } - return this.result_clear_highlight(); - } - } - }; - - Chosen.prototype.keydown_backstroke = function() { - var next_available_destroy; - if (this.pending_backstroke) { - this.choice_destroy(this.pending_backstroke.find("a").first()); - return this.clear_backstroke(); - } else { - next_available_destroy = this.search_container.siblings("li.search-choice").last(); - if (next_available_destroy.length && !next_available_destroy.hasClass("search-choice-disabled")) { - this.pending_backstroke = next_available_destroy; - if (this.single_backstroke_delete) { - return this.keydown_backstroke(); - } else { - return this.pending_backstroke.addClass("search-choice-focus"); - } - } - } - }; - - Chosen.prototype.clear_backstroke = function() { - if (this.pending_backstroke) { - this.pending_backstroke.removeClass("search-choice-focus"); - } - return this.pending_backstroke = null; - }; - - Chosen.prototype.keydown_checker = function(evt) { - var stroke, _ref1; - stroke = (_ref1 = evt.which) != null ? _ref1 : evt.keyCode; - this.search_field_scale(); - if (stroke !== 8 && this.pending_backstroke) { - this.clear_backstroke(); - } - switch (stroke) { - case 8: - this.backstroke_length = this.search_field.val().length; - break; - case 9: - if (this.results_showing && !this.is_multiple) { - this.result_select(evt); - } - this.mouse_on_container = false; - break; - case 13: - if (this.results_showing) { - evt.preventDefault(); - } - break; - case 32: - if (this.disable_search) { - evt.preventDefault(); - } - break; - case 38: - evt.preventDefault(); - this.keyup_arrow(); - break; - case 40: - evt.preventDefault(); - this.keydown_arrow(); - break; - } - }; - - Chosen.prototype.search_field_scale = function() { - var div, f_width, h, style, style_block, styles, w, _i, _len; - if (this.is_multiple) { - h = 0; - w = 0; - style_block = "position:absolute; left: -1000px; top: -1000px; display:none;"; - styles = ['font-size', 'font-style', 'font-weight', 'font-family', 'line-height', 'text-transform', 'letter-spacing']; - for (_i = 0, _len = styles.length; _i < _len; _i++) { - style = styles[_i]; - style_block += style + ":" + this.search_field.css(style) + ";"; - } - div = $('
      ', { - 'style': style_block - }); - div.text(this.search_field.val()); - $('body').append(div); - w = div.width() + 25; - div.remove(); - f_width = this.container.outerWidth(); - if (w > f_width - 10) { - w = f_width - 10; - } - return this.search_field.css({ - 'width': w + 'px' - }); - } - }; - - return Chosen; - - })(AbstractChosen); - -}).call(this); diff --git a/vendor/assets/stylesheets/chosen.css.scss b/vendor/assets/stylesheets/chosen.css.scss deleted file mode 100755 index 5627b3578b..0000000000 --- a/vendor/assets/stylesheets/chosen.css.scss +++ /dev/null @@ -1,452 +0,0 @@ -/*! -Chosen, a Select Box Enhancer for jQuery and Prototype -by Patrick Filler for Harvest, http://getharvest.com - -Version 1.6.2 -Full source at https://github.com/harvesthq/chosen -Copyright (c) 2011-2016 Harvest http://getharvest.com - -MIT License, https://github.com/harvesthq/chosen/blob/master/LICENSE.md -This file is generated by `grunt build`, do not edit it by hand. -*/ - -/* @group Base */ -.chosen-container { - position: relative; - display: inline-block; - vertical-align: middle; - -webkit-user-select: none; - -moz-user-select: none; - user-select: none; - width: 100%; - /* height: calc(2.25rem + 2px); */ - padding: 0.375rem 0.75rem; - font-size: 1rem; - line-height: 1.5; - color: #495057; - background-color: #fff; - background-clip: padding-box; - border: 1px solid #ced4da; - border-radius: 0.25rem; - transition: border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out; -} -.chosen-container * { - -webkit-box-sizing: border-box; - -moz-box-sizing: border-box; - box-sizing: border-box; -} -.chosen-container .chosen-drop { - position: absolute; - top: 100%; - left: -9999px; - z-index: 1010; - width: 100%; - border: 1px solid #aaa; - border-top: 0; - background: #fff; - box-shadow: 0 4px 5px rgba(0, 0, 0, 0.15); -} -.chosen-container.chosen-with-drop .chosen-drop { - left: 0; -} -.chosen-container a { - cursor: pointer; -} -.chosen-container .search-choice .group-name, .chosen-container .chosen-single .group-name { - margin-right: 4px; - overflow: hidden; - white-space: nowrap; - text-overflow: ellipsis; - font-weight: normal; - color: #999999; -} -.chosen-container .search-choice .group-name:after, .chosen-container .chosen-single .group-name:after { - content: ":"; - padding-left: 2px; - vertical-align: top; -} - -/* @end */ -/* @group Single Chosen */ -.chosen-container-single .chosen-single { - position: relative; - display: block; - overflow: hidden; - padding: 0 0 0 8px; - height: 25px; - border: 1px solid #aaa; - border-radius: 5px; - background-color: #fff; - background: -webkit-gradient(linear, 50% 0%, 50% 100%, color-stop(20%, #ffffff), color-stop(50%, #f6f6f6), color-stop(52%, #eeeeee), color-stop(100%, #f4f4f4)); - background: -webkit-linear-gradient(#ffffff 20%, #f6f6f6 50%, #eeeeee 52%, #f4f4f4 100%); - background: -moz-linear-gradient(#ffffff 20%, #f6f6f6 50%, #eeeeee 52%, #f4f4f4 100%); - background: -o-linear-gradient(#ffffff 20%, #f6f6f6 50%, #eeeeee 52%, #f4f4f4 100%); - background: linear-gradient(#ffffff 20%, #f6f6f6 50%, #eeeeee 52%, #f4f4f4 100%); - background-clip: padding-box; - box-shadow: 0 0 3px white inset, 0 1px 1px rgba(0, 0, 0, 0.1); - color: #444; - text-decoration: none; - white-space: nowrap; - line-height: 24px; -} -.chosen-container-single .chosen-default { - color: #999; -} -.chosen-container-single .chosen-single span { - display: block; - overflow: hidden; - margin-right: 26px; - text-overflow: ellipsis; - white-space: nowrap; -} -.chosen-container-single .chosen-single-with-deselect span { - margin-right: 38px; -} -.chosen-container-single .chosen-single abbr { - position: absolute; - top: 6px; - right: 26px; - display: block; - width: 12px; - height: 12px; - background: image-url('chosen/chosen-sprite.png') -42px 1px no-repeat; - font-size: 1px; -} -.chosen-container-single .chosen-single abbr:hover { - background-position: -42px -10px; -} -.chosen-container-single.chosen-disabled .chosen-single abbr:hover { - background-position: -42px -10px; -} -.chosen-container-single .chosen-single div { - position: absolute; - top: 0; - right: 0; - display: block; - width: 18px; - height: 100%; -} -.chosen-container-single .chosen-single div b { - display: block; - width: 100%; - height: 100%; - background: image-url('chosen/chosen-sprite.png') no-repeat 0px 2px; -} -.chosen-container-single .chosen-search { - position: relative; - z-index: 1010; - margin: 0; - padding: 3px 4px; - white-space: nowrap; -} -.chosen-container-single .chosen-search input[type="text"] { - margin: 1px 0; - padding: 4px 20px 4px 5px; - width: 100%; - height: auto; - outline: 0; - border: 1px solid #aaa; - background: white image-url('chosen/chosen-sprite.png') no-repeat 100% -20px; - background: image-url('chosen/chosen-sprite.png') no-repeat 100% -20px; - font-size: 1em; - font-family: sans-serif; - line-height: normal; - border-radius: 0; -} -.chosen-container-single .chosen-drop { - margin-top: -1px; - border-radius: 0 0 4px 4px; - background-clip: padding-box; -} -.chosen-container-single.chosen-container-single-nosearch .chosen-search { - position: absolute; - left: -9999px; -} - -/* @end */ -/* @group Results */ -.chosen-container .chosen-results { - color: #444; - position: relative; - overflow-x: hidden; - overflow-y: auto; - margin: 0 4px 4px 0; - padding: 0 0 0 4px; - max-height: 240px; - -webkit-overflow-scrolling: touch; -} -.chosen-container .chosen-results li { - display: none; - margin: 0; - padding: 5px 6px; - list-style: none; - line-height: 15px; - word-wrap: break-word; - -webkit-touch-callout: none; -} -.chosen-container .chosen-results li.active-result { - display: list-item; - cursor: pointer; -} -.chosen-container .chosen-results li.disabled-result { - display: list-item; - color: #ccc; - cursor: default; -} -.chosen-container .chosen-results li.highlighted { - background-color: #3875d7; - background-image: -webkit-gradient(linear, 50% 0%, 50% 100%, color-stop(20%, #3875d7), color-stop(90%, #2a62bc)); - background-image: -webkit-linear-gradient(#3875d7 20%, #2a62bc 90%); - background-image: -moz-linear-gradient(#3875d7 20%, #2a62bc 90%); - background-image: -o-linear-gradient(#3875d7 20%, #2a62bc 90%); - background-image: linear-gradient(#3875d7 20%, #2a62bc 90%); - color: #fff; -} -.chosen-container .chosen-results li.no-results { - color: #777; - display: list-item; - background: #f4f4f4; -} -.chosen-container .chosen-results li.group-result { - display: list-item; - font-weight: bold; - cursor: default; -} -.chosen-container .chosen-results li.group-option { - padding-left: 15px; -} -.chosen-container .chosen-results li em { - font-style: normal; - text-decoration: underline; -} - -/* @end */ -/* @group Multi Chosen */ -.chosen-container-multi .chosen-choices { - position: relative; - overflow: hidden; - margin: 0; - padding: 0 5px; - width: 100%; - height: auto; - cursor: text; - -} -.chosen-container-multi .chosen-choices li { - float: left; - list-style: none; -} -.chosen-container-multi .chosen-choices li.search-field { - margin: 0; - padding: 0; - white-space: nowrap; - display: contents; -} -.chosen-container-multi .chosen-choices li.search-field input[type="text"] { - margin: 1px 0; - padding: 0; - height: 25px; - outline: 0; - border: 0 !important; - background: transparent !important; - box-shadow: none; - color: #999; - font-size: 100%; - font-family: sans-serif; - line-height: normal; - border-radius: 0; -} -.chosen-container-multi .chosen-choices li.search-choice { - position: relative; - margin: 3px 5px 3px 0; - padding: 3px 20px 3px 5px; - border: 1px solid #aaa; - max-width: 100%; - border-radius: 3px; - background-color: #eeeeee; - background-image: -webkit-gradient(linear, 50% 0%, 50% 100%, color-stop(20%, #f4f4f4), color-stop(50%, #f0f0f0), color-stop(52%, #e8e8e8), color-stop(100%, #eeeeee)); - background-image: -webkit-linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-image: -moz-linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-image: -o-linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-image: linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-size: 100% 19px; - background-repeat: repeat-x; - background-clip: padding-box; - box-shadow: 0 0 2px white inset, 0 1px 0 rgba(0, 0, 0, 0.05); - color: #333; - line-height: 13px; - cursor: default; -} -.chosen-container-multi .chosen-choices li.search-choice span { - word-wrap: break-word; -} -.chosen-container-multi .chosen-choices li.search-choice .search-choice-close { - position: absolute; - top: 4px; - right: 3px; - display: block; - width: 12px; - height: 12px; - background: image-url('chosen/chosen-sprite.png') -42px 1px no-repeat; - font-size: 1px; -} -.chosen-container-multi .chosen-choices li.search-choice .search-choice-close:hover { - background-position: -42px -10px; -} -.chosen-container-multi .chosen-choices li.search-choice-disabled { - padding-right: 5px; - border: 1px solid #ccc; - background-color: #e4e4e4; - background-image: -webkit-gradient(linear, 50% 0%, 50% 100%, color-stop(20%, #f4f4f4), color-stop(50%, #f0f0f0), color-stop(52%, #e8e8e8), color-stop(100%, #eeeeee)); - background-image: -webkit-linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-image: -moz-linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-image: -o-linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - background-image: linear-gradient(#f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%); - color: #666; -} -.chosen-container-multi .chosen-choices li.search-choice-focus { - background: #d4d4d4; -} -.chosen-container-multi .chosen-choices li.search-choice-focus .search-choice-close { - background-position: -42px -10px; -} -.chosen-container-multi .chosen-results { - margin: 0; - padding: 0; -} -.chosen-container-multi .chosen-drop .result-selected { - display: list-item; - color: #ccc; - cursor: default; -} - -/* @end */ -/* @group Active */ -.chosen-container-active .chosen-single { - border: 1px solid #5897fb; - box-shadow: 0 0 5px rgba(0, 0, 0, 0.3); -} -.chosen-container-active.chosen-with-drop .chosen-single { - border: 1px solid #aaa; - -moz-border-radius-bottomright: 0; - border-bottom-right-radius: 0; - -moz-border-radius-bottomleft: 0; - border-bottom-left-radius: 0; - background-image: -webkit-gradient(linear, 50% 0%, 50% 100%, color-stop(20%, #eeeeee), color-stop(80%, #ffffff)); - background-image: -webkit-linear-gradient(#eeeeee 20%, #ffffff 80%); - background-image: -moz-linear-gradient(#eeeeee 20%, #ffffff 80%); - background-image: -o-linear-gradient(#eeeeee 20%, #ffffff 80%); - background-image: linear-gradient(#eeeeee 20%, #ffffff 80%); - box-shadow: 0 1px 0 #fff inset; -} -.chosen-container-active.chosen-with-drop .chosen-single div { - border-left: none; - background: transparent; -} -.chosen-container-active.chosen-with-drop .chosen-single div b { - background-position: -18px 2px; -} -.chosen-container-active .chosen-choices { - border: 1px solid #5897fb; - box-shadow: 0 0 5px rgba(0, 0, 0, 0.3); -} -.chosen-container-active .chosen-choices li.search-field input[type="text"] { - color: #222 !important; -} - -/* @end */ -/* @group Disabled Support */ -.chosen-disabled { - opacity: 0.5 !important; - cursor: default; -} -.chosen-disabled .chosen-single { - cursor: default; -} -.chosen-disabled .chosen-choices .search-choice .search-choice-close { - cursor: default; -} - -/* @end */ -/* @group Right to Left */ -.chosen-rtl { - text-align: right; -} -.chosen-rtl .chosen-single { - overflow: visible; - padding: 0 8px 0 0; -} -.chosen-rtl .chosen-single span { - margin-right: 0; - margin-left: 26px; - direction: rtl; -} -.chosen-rtl .chosen-single-with-deselect span { - margin-left: 38px; -} -.chosen-rtl .chosen-single div { - right: auto; - left: 3px; -} -.chosen-rtl .chosen-single abbr { - right: auto; - left: 26px; -} -.chosen-rtl .chosen-choices li { - float: right; -} -.chosen-rtl .chosen-choices li.search-field input[type="text"] { - direction: rtl; -} -.chosen-rtl .chosen-choices li.search-choice { - margin: 3px 5px 3px 0; - padding: 3px 5px 3px 19px; -} -.chosen-rtl .chosen-choices li.search-choice .search-choice-close { - right: auto; - left: 4px; -} -.chosen-rtl.chosen-container-single-nosearch .chosen-search, -.chosen-rtl .chosen-drop { - left: 9999px; -} -.chosen-rtl.chosen-container-single .chosen-results { - margin: 0 0 4px 4px; - padding: 0 4px 0 0; -} -.chosen-rtl .chosen-results li.group-option { - padding-right: 15px; - padding-left: 0; -} -.chosen-rtl.chosen-container-active.chosen-with-drop .chosen-single div { - border-right: none; -} -.chosen-rtl .chosen-search input[type="text"] { - padding: 4px 5px 4px 20px; - background: white image-url('chosen/chosen-sprite.png') no-repeat -30px -20px; - background: image-url('chosen/chosen-sprite.png') no-repeat -30px -20px; - direction: rtl; -} -.chosen-rtl.chosen-container-single .chosen-single div b { - background-position: 6px 2px; -} -.chosen-rtl.chosen-container-single.chosen-with-drop .chosen-single div b { - background-position: -12px 2px; -} - -/* @end */ -/* @group Retina compatibility */ -@media only screen and (-webkit-min-device-pixel-ratio: 1.5), only screen and (min-resolution: 144dpi), only screen and (min-resolution: 1.5dppx) { - .chosen-rtl .chosen-search input[type="text"], - .chosen-container-single .chosen-single abbr, - .chosen-container-single .chosen-single div b, - .chosen-container-single .chosen-search input[type="text"], - .chosen-container-multi .chosen-choices .search-choice .search-choice-close, - .chosen-container .chosen-results-scroll-down span, - .chosen-container .chosen-results-scroll-up span { - background-image: image-url('chosen/chosen-sprite@2x.png') !important; - background-size: 52px 37px !important; - background-repeat: no-repeat !important; - } -} -/* @end */