Merge branch 'upstream' into pr/align-bioportal-agroportal-part-4

ontoportal · Dec 15, 2024 · affe9da · affe9da
2 parents fa600ee + 6626755
commit affe9da
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diff --git a/Gemfile b/Gemfile
@@ -122,10 +122,12 @@ gem 'net-http'
 # Multi-Provider Authentication
 gem 'omniauth'
 gem 'omniauth-rails_csrf_protection'
-gem 'omniauth-github'
-gem 'omniauth-google-oauth2'
-gem 'omniauth-keycloak'
-gem 'omniauth-orcid'
+
+# Additional authentication providers are not yet implemented
+# gem 'omniauth-github'
+# gem 'omniauth-google-oauth2'
+# gem 'omniauth-keycloak'
+# gem 'omniauth-orcid'
 
 group :staging, :production, :appliance do
   # Application performance monitoring

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -84,7 +84,6 @@ GEM
       tzinfo (~> 2.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
-    aes_key_wrap (1.1.0)
     airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
@@ -93,8 +92,8 @@ GEM
     base64 (0.1.0)
     bcrypt_pbkdf (1.1.1)
     bcrypt_pbkdf (1.1.1-arm64-darwin)
+    bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (3.1.8)
-    bindata (2.5.0)
     bindex (0.8.1)
     bootsnap (1.18.4)
       msgpack (~> 1.2)
@@ -149,34 +148,34 @@ GEM
       addressable
     csv (3.3.0)
     dalli (3.2.8)
-    date (3.4.0)
+    date (3.4.1)
     debug (1.9.2)
       irb (~> 1.10)
       reline (>= 0.3.8)
-    deepl-rb (3.0.2)
+    deepl-rb (3.1.0)
     diff-lcs (1.5.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
     erubi (1.13.0)
     erubis (2.7.0)
-    excon (1.2.0)
+    excon (1.2.2)
     execjs (2.10.0)
-    faraday (2.12.0)
-      faraday-net_http (>= 2.0, < 3.4)
+    faraday (2.12.1)
+      faraday-net_http (>= 2.0, < 3.5)
       json
       logger
     faraday-excon (2.3.0)
       excon (>= 1.0.0)
       faraday (>= 2.11.0, < 3)
-    faraday-follow_redirects (0.3.0)
-      faraday (>= 1, < 3)
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
-    faraday-net_http (3.3.0)
-      net-http
-    ffi (1.17.0)
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
+    ffi (1.17.0-aarch64-linux-gnu)
     ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86_64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
     flag-icons-rails (3.4.6.1)
       sass-rails
     globalid (1.2.1)
@@ -229,7 +228,7 @@ GEM
     inline_svg (1.10.0)
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
-    io-console (0.7.2)
+    io-console (0.8.0)
     irb (1.14.1)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
@@ -243,16 +242,7 @@ GEM
       railties (>= 3.2.16)
     jsbundling-rails (1.3.1)
       railties (>= 6.0.0)
-    json (2.8.1)
-    json-jwt (1.16.7)
-      activesupport (>= 4.2)
-      aes_key_wrap
-      base64
-      bindata
-      faraday (~> 2.0)
-      faraday-follow_redirects
-    jwt (2.9.3)
-      base64
+    json (2.9.0)
     language_server-protocol (3.17.0.3)
     launchy (3.0.1)
       addressable (~> 2.8)
@@ -267,7 +257,7 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    logger (1.6.1)
+    logger (1.6.2)
     loofah (2.23.1)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -296,18 +286,17 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1105)
+    mime-types-data (3.2024.1203)
     mini_mime (1.1.5)
-    minitest (5.25.1)
+    minitest (5.25.3)
     msgpack (1.7.5)
     multi_json (1.15.0)
-    multi_xml (0.6.0)
     multipart-post (2.4.1)
     mysql2 (0.5.6)
     net-ftp (0.3.8)
       net-protocol
       time
-    net-http (0.5.0)
+    net-http (0.6.0)
       uri
     net-imap (0.4.18)
       date
@@ -324,47 +313,23 @@ GEM
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
-    newrelic_rpm (9.15.0)
+    newrelic_rpm (9.16.0)
     nio4r (2.7.4)
-    nokogiri (1.16.7-aarch64-linux)
+    nokogiri (1.16.8-aarch64-linux)
       racc (~> 1.4)
-    nokogiri (1.16.7-arm64-darwin)
+    nokogiri (1.16.8-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-linux)
+    nokogiri (1.16.8-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.8-x86_64-linux)
       racc (~> 1.4)
-    oauth2 (2.0.9)
-      faraday (>= 0.17.3, < 3.0)
-      jwt (>= 1.0, < 3.0)
-      multi_xml (~> 0.5)
-      rack (>= 1.2, < 4)
-      snaky_hash (~> 2.0)
-      version_gem (~> 1.1)
     oj (3.16.7)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omniauth (2.1.2)
       hashie (>= 3.4.6)
       rack (>= 2.2.3)
       rack-protection
-    omniauth-github (2.0.1)
-      omniauth (~> 2.0)
-      omniauth-oauth2 (~> 1.8)
-    omniauth-google-oauth2 (1.2.0)
-      jwt (>= 2.9)
-      oauth2 (~> 2.0)
-      omniauth (~> 2.0)
-      omniauth-oauth2 (~> 1.8)
-    omniauth-keycloak (1.5.2)
-      faraday
-      json-jwt (> 1.13.0)
-      omniauth (>= 2.0)
-      omniauth-oauth2 (>= 1.7, < 1.9)
-    omniauth-oauth2 (1.8.0)
-      oauth2 (>= 1.4, < 3)
-      omniauth (~> 2.0)
-    omniauth-orcid (2.1.1)
-      omniauth-oauth2 (~> 1.3)
-      ruby_dig (~> 0.0.2)
     omniauth-rails_csrf_protection (1.0.2)
       actionpack (>= 4.2)
       omniauth (~> 2.0)
@@ -374,10 +339,11 @@ GEM
       ast (~> 2.4.1)
       racc
     popper_js (2.11.8)
-    pry (0.14.2)
+    pry (0.15.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    psych (5.2.0)
+    psych (5.2.1)
+      date
       stringio
     public_suffix (6.0.1)
     puma (5.6.9)
@@ -407,9 +373,9 @@ GEM
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.6.0)
+    rails-html-sanitizer (1.6.1)
       loofah (~> 2.21)
-      nokogiri (~> 1.14)
+      nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     rails-i18n (7.0.10)
       i18n (>= 0.7, < 2)
       railties (>= 6.0.0, < 8)
@@ -425,13 +391,13 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rdoc (6.7.0)
+    rdoc (6.8.1)
       psych (>= 4.0.0)
     recaptcha (5.9.0)
       json
     redcarpet (3.6.0)
-    regexp_parser (2.9.2)
-    reline (0.5.11)
+    regexp_parser (2.9.3)
+    reline (0.5.12)
       io-console (~> 0.5)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -456,21 +422,20 @@ GEM
       rspec-expectations (~> 3.13)
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
-    rspec-support (3.13.1)
-    rubocop (1.68.0)
+    rspec-support (3.13.2)
+    rubocop (1.69.1)
       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 (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.2, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.36.1)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.36.2)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
-    ruby_dig (0.0.2)
     ruby_parser (3.21.1)
       racc (~> 1.5)
       sexp_processor (~> 4.16)
@@ -500,9 +465,6 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
-    snaky_hash (2.0.1)
-      hashie
-      version_gem (~> 1.1, >= 1.1.1)
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -520,8 +482,7 @@ GEM
       railties (>= 6.0.0)
     stringio (3.1.2)
     temple (0.10.3)
-    terminal-table (3.0.2)
-      unicode-display_width (>= 1.1.1, < 3)
+    terminal-table (1.6.0)
     terser (1.2.4)
       execjs (>= 0.3.0, < 3)
     thor (1.3.2)
@@ -534,9 +495,10 @@ GEM
       railties (>= 6.0.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.6.0)
-    uri (1.0.1)
-    version_gem (1.1.4)
+    unicode-display_width (3.1.2)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
+    uri (1.0.2)
     view_component (2.83.0)
       activesupport (>= 5.2.0, < 8.0)
       concurrent-ruby (~> 1.0)
@@ -562,10 +524,9 @@ GEM
 
 PLATFORMS
   aarch64-linux
-  arm64-darwin-22
-  arm64-darwin-23
+  arm64-darwin
+  x86_64-darwin
   x86_64-linux
-  x86_64-linux-musl
 
 DEPENDENCIES
   base64 (= 0.1.0)
@@ -612,10 +573,6 @@ DEPENDENCIES
   newrelic_rpm
   oj
   omniauth
-  omniauth-github
-  omniauth-google-oauth2
-  omniauth-keycloak
-  omniauth-orcid
   omniauth-rails_csrf_protection
   ontologies_api_client!
   pry

diff --git a/app/assets/stylesheets/bioportal.scss b/app/assets/stylesheets/bioportal.scss
@@ -1,6 +1,10 @@
 .turbo-progress-bar {
-  height: 5px;
-  background-color: var(--admin-color);
+  height: 10px;
+  background-color: #ffffff;
+}
+
+.tabs-container .tab-items > div button{
+  color: var(--primary-color) !important
 }
 
 a{

diff --git a/app/assets/stylesheets/components/tabs_container.scss b/app/assets/stylesheets/components/tabs_container.scss
@@ -31,7 +31,7 @@
   transition: opacity 0.3s ease;
 
   a, button {
-    color: #5e5e5e !important;
+    color: #5e5e5e;
     border: none;
     background: none;
   }

diff --git a/app/assets/stylesheets/theme-variables.scss.erb b/app/assets/stylesheets/theme-variables.scss.erb
@@ -3,13 +3,13 @@
 <% themes = {
   "agroportal"  => { primary: "#3CB371", hover: "#41C67C", secondary: "#ffc107", light: "#F1F6FA" },
   "stageportal" => { primary: "#37AEA0", hover: "#3BBDAE", secondary: "#ffc107", light: "#ECF7F6" },
-  "bioportal"   => { primary: "#76A7CC", hover: "#6B96B7", secondary: "#ffc107", light: "#F0F5F6" },
+  "bioportal"   => { primary: "#234979", hover: "#6B96B7", secondary: "#ffc107", light: "#F0F5F6" },
   "ontoportal"  => { primary: "#5499a4", hover: "#6B96B7", secondary: "#ffc107", light: "#F1F6FA" },
   "testportal"  => { primary: "#5499a4", hover: "#6B96B7", secondary: "#ffc107", light: "#F1F6FA" }
 } %>
 
 <% ui_theme = $UI_THEME.to_s.parameterize %>
-<% selected_theme_key = themes.key?(ui_theme) ? ui_theme : "ontoportal" %>
+<% selected_theme_key = themes.key?(ui_theme) ? ui_theme : 'ontoportal' %>
 <% selected_theme = themes[selected_theme_key] %>
 
 :root {

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
@@ -236,34 +236,6 @@ 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 = "Please provide an ontology id or concept id with an ontology id."
-      return
-    end
-    acronym = BPIDResolver.id_to_acronym(params[:ontology])
-    not_found unless acronym
-    if class_view
-      @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
-      @submission = get_ontology_submission_ready(@ontology)
-      concept = get_class(params, @submission).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] || "?"