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ontoportal-lirmm · Nov 2, 2023 · 5e25a2f · 5e25a2f
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -0,0 +1,55 @@
+name: "Ruby on Rails CI"
+
+on:
+  push:
+  pull_request_target:
+    types: [ opened, reopened ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      mysql:
+        image: mysql:8.0
+        ports:
+          - "3306:3306"
+        env:
+          MYSQL_ROOT_PASSWORD: password
+          MYSQL_DATABASE: bioportal_ui_test
+          MYSQL_USER: root
+          MYSQL_PASSWORD: bp_user
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      # Add or replace dependency steps here
+      - name: Install Ruby and gems
+        uses: ruby/setup-ruby@55283cc23133118229fd3f97f9336ee23a179fcf # v1.146.0
+        with:
+          ruby-version: 2.7.8
+          bundler-cache: true
+      # Add or replace database setup steps here
+      - name: set up config file
+        run: cp config/database.yml.sample config/database.yml
+      - name: Set up database schema
+        run: RAILS_ENV=test bin/rails db:schema:load
+      # Add or replace test runners here
+      - name: Run tests
+        run: RAILS_ENV=test bin/rake
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      - name: Install Ruby and gems
+        uses: ruby/setup-ruby@55283cc23133118229fd3f97f9336ee23a179fcf # v1.146.0
+        with:
+          ruby-version: 2.7.8
+          bundler-cache: true
+      # Add or replace any other lints here
+      - name: Security audit dependencies
+        run: bin/bundler-audit --update
+      - name: Security audit application code
+        run: bin/brakeman -q -w2
+      - name: Lint Ruby files
+        run: bin/rubocop --parallel
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ruby:2.7.5-alpine AS app
+FROM ruby:2.7.8-alpine AS app
 
 WORKDIR /app
 
@@ -17,34 +17,26 @@ RUN apk add --no-cache \
     less \
   && addgroup --gid ${GID} ruby \
   && adduser  -u ${UID} -G ruby -D  ruby \
-  && chown ruby:ruby -R /app \
-  && mkdir /node_modules \
-  && chown ruby:ruby -R /node_modules /app
+  && mkdir /node_modules
 
-USER ruby
-
-COPY --chown=ruby:ruby bin/ ./bin
-RUN chmod 0755 bin/*
+COPY --chown=ruby:ruby Gemfile* ./
+COPY --chown=ruby:ruby package.json *yarn* ./
 
-ARG RAILS_ENV="production"
+# Set ownership and permissions
+RUN chown -R ruby:ruby /app
 
-ENV RAILS_ENV="${RAILS_ENV}" \
-    NODE_ENV="${NODE_ENV}" \
-    PATH="${PATH}:/home/ruby/.local/bin:/node_modules/.bin" \
-    USER="ruby" \
-    BUNDLE_PATH=/usr/local/bundle
+USER ruby
 
-COPY --chown=ruby:ruby Gemfile* ./
+# Install dependencies
 RUN bundle install --jobs "$(nproc)"
-RUN gem install rails 
-
-
+RUN gem install rails
+RUN yarn install
 
 RUN echo "--modules-folder /node_modules" > .yarnrc
-COPY --chown=ruby:ruby package.json *yarn* ./
-RUN yarn install
 
+# Copy application code
+COPY --chown=ruby:ruby . .
 
 EXPOSE 3000
 
-CMD ["sh"]
+CMD ["bash"]
diff --git a/Gemfile b/Gemfile
@@ -57,7 +57,7 @@ gem 'i18n'
 gem 'rails-i18n', '~> 7.0.0'
 gem 'iconv'
 gem 'multi_json'
-gem 'mysql2', '0.5.3'
+gem 'mysql2'
 gem 'oj'
 gem 'open_uri_redirections'
 gem 'pry'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -101,7 +101,7 @@ GEM
       smart_properties
     bindata (2.4.15)
     bindex (0.8.1)
-    bootsnap (1.16.0)
+    bootsnap (1.17.0)
       msgpack (~> 1.2)
     bootstrap (4.2.1)
       autoprefixer-rails (>= 9.1.0)
@@ -156,7 +156,7 @@ GEM
     erubi (1.12.0)
     erubis (2.7.0)
     eventmachine (1.2.7)
-    excon (0.103.0)
+    excon (0.104.0)
     execjs (2.9.1)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -169,13 +169,13 @@ GEM
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
     faraday-net_http (2.1.0)
-    ffi (1.16.1)
+    ffi (1.16.3)
     flag-icons-rails (3.4.6.1)
       sass-rails
     flamegraph (0.9.5)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    graphql (2.1.3)
+    graphql (2.1.6)
       racc (~> 1.4)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
@@ -197,20 +197,21 @@ GEM
       domain_name (~> 0.5)
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
-    i18n-tasks (1.0.12)
+    i18n-tasks (1.0.13)
       activesupport (>= 4.0.2)
       ast (>= 2.1.0)
       better_html (>= 1.0, < 3.0)
       erubi
       highline (>= 2.0.0)
       i18n
-      parser (>= 2.2.3.0)
+      parser (>= 3.2.2.1)
       rails-i18n
       rainbow (>= 2.2.2, < 4.0)
       terminal-table (>= 1.5.1)
     iconv (1.0.8)
-    importmap-rails (1.2.1)
+    importmap-rails (1.2.3)
       actionpack (>= 6.0.0)
+      activesupport (>= 6.0.0)
       railties (>= 6.0.0)
     inline_svg (1.9.0)
       activesupport (>= 3.0)
@@ -274,13 +275,13 @@ GEM
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.3.0)
-    mysql2 (0.5.3)
+    mysql2 (0.5.5)
     net-ftp (0.2.0)
       net-protocol
       time
     net-http (0.3.2)
       uri
-    net-imap (0.4.1)
+    net-imap (0.4.3)
       date
       net-protocol
     net-pop (0.1.2)
@@ -293,7 +294,8 @@ GEM
       net-protocol
     net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.5.0)
+    newrelic_rpm (9.6.0)
+      base64
     nio4r (2.5.9)
     nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
@@ -345,7 +347,7 @@ GEM
     public_suffix (5.0.3)
     puma (5.6.7)
       nio4r (~> 2.0)
-    racc (1.7.1)
+    racc (1.7.2)
     rack (2.2.8)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -391,24 +393,24 @@ GEM
       thor (~> 1.0)
       zeitwerk (~> 2.5)
     rainbow (3.1.1)
-    rake (13.0.6)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rdoc (6.3.3)
     recaptcha (5.9.0)
       json
     redcarpet (3.6.0)
-    regexp_parser (2.8.1)
-    reline (0.3.8)
+    regexp_parser (2.8.2)
+    reline (0.3.9)
       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 (3.2.6)
-    rouge (4.1.3)
+    rouge (4.2.0)
     rspec-core (3.12.2)
       rspec-support (~> 3.12.0)
     rspec-expectations (3.12.3)
@@ -426,8 +428,7 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.1)
-    rubocop (1.56.3)
-      base64 (~> 0.1.1)
+    rubocop (1.57.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -438,7 +439,7 @@ GEM
       rubocop-ast (>= 1.28.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.29.0)
+    rubocop-ast (1.30.0)
       parser (>= 3.2.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -480,16 +481,16 @@ GEM
     stackprof (0.2.25)
     stimulus-rails (1.3.0)
       railties (>= 6.0.0)
-    temple (0.10.2)
+    temple (0.10.3)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
-    terser (1.1.18)
+    terser (1.1.19)
       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 (1.2.2)
+    thor (1.3.0)
     tilt (2.3.0)
     time (0.2.2)
       date
@@ -532,7 +533,7 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.34)
-    zeitwerk (2.6.11)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   x86_64-darwin-21
@@ -574,7 +575,7 @@ DEPENDENCIES
   listen
   lookbook (~> 1.5.5)
   multi_json
-  mysql2 (= 0.5.3)
+  mysql2
   net-ftp (~> 0.2.0)
   net-http
   newrelic_rpm

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
@@ -128,10 +128,7 @@ def domain_ontology_set
     Thread.current[:slice] = @subdomain_filter
   end
 
-  def anonymous_user
-    user = DataAccess.getUser($ANONYMOUS_USER)
-    user ||= User.new({"id" => 0})
-  end
+
 
   def ontology_not_found(ontology_acronym)
     not_found("Ontology #{ontology_acronym} not found")

diff --git a/app/controllers/landscape_controller.rb b/app/controllers/landscape_controller.rb
@@ -110,6 +110,7 @@ def index
         # Get hash of natural language use
         if !sub.naturalLanguage.nil? && !sub.naturalLanguage.empty?
           sub.naturalLanguage.each do |sub_lang|
+            next unless  sub_lang.is_a?(String)
             # replace lexvo URI by lexvo prefix
             prefixed_sub_lang = sub_lang
             if sub_lang.start_with?("http://lexvo.org/id/iso639-3/")

diff --git a/app/views/projects/index.html.haml b/app/views/projects/index.html.haml
@@ -5,7 +5,7 @@
   %h1.tab_header= t("projects.self")
   %p.tab_description
     = t("projects.index.intro", site: "#{$SITE}")
-    = link_to(help_path(anchor: "Projects_Tab"), id: "projects-help", aria: {label: t("projects.view_projects_help")}) do
+    = link_to("#{Rails.configuration.settings.links[:help]}#Projects_Tab", id: "projects-help", aria: {label: t("projects.view_projects_help")}) do
       %i.fas.fa-question-circle.fa-lg{aria: {hidden: "true"}, style: "margin-left: .25em"}
 
   %div{:style => "padding:10px;"}