add codevoc generation

.github/workflows/docker-image-arm.yml

@@ -49,7 +49,7 @@ jobs:
           context: .
           platforms: linux/arm64
           build-args: |
-            RUBY_VERSION=2.7
+            RUBY_VERSION=2.7.8
           push: true
           tags: ${{ steps.meta.outputs.tags }}-${{ env.BRANCH_NAME }}-arm64
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docker-image.yml

@@ -49,7 +49,7 @@ jobs:
           context: .
           platforms: linux/amd64
           build-args: |
-            RUBY_VERSION=2.7
+            RUBY_VERSION=2.7.8
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.github/workflows/tests.yml

@@ -55,8 +55,7 @@ jobs:
       # Add or replace test runners here
       - name: Run tests
         run:  COVERAGE=true RAILS_ENV=test bin/rails test -v
-      - name: Upload Code Coverage
-        uses: actions/upload-artifact@v2
-        with:
-          name: code-coverage
-          path: coverage/
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

Dockerfile

@@ -30,7 +30,7 @@ ENV RAILS_LOG_TO_STDOUT="1" \
     BUNDLE_WITHOUT="${BUNDLE_WITHOUT}"
 
 # fix for ruby v2.7.8 only
-RUN gem install uri -v 0.12.2 --no-document
+RUN gem install uri --no-document
 
 COPY Gemfile* .
 RUN bundle install

Gemfile

@@ -129,10 +129,12 @@ group :test do
   gem 'capybara'
   gem 'selenium-webdriver'
   gem 'simplecov', require: false
+  gem 'simplecov-cobertura' # for codecov.io
   #gem 'webdrivers'
 end
 
 
 gem "net-ftp", "~> 0.2.0", require: false
-gem "net-http"
+gem "net-http", "~> 0.3.2"
+
 

Gemfile.lock

@@ -88,7 +88,7 @@ GEM
     airbrussh (1.5.0)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
-    autoprefixer-rails (10.4.15.0)
+    autoprefixer-rails (10.4.16.0)
       execjs (~> 2)
     base64 (0.2.0)
     bcrypt_pbkdf (1.1.0)
@@ -151,13 +151,12 @@ GEM
     deepl-rb (2.5.3)
     diff-lcs (1.5.0)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     ed25519 (1.3.0)
     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)
@@ -170,7 +169,7 @@ 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)
@@ -198,14 +197,14 @@ 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)
@@ -218,7 +217,7 @@ GEM
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
     io-console (0.6.0)
-    irb (1.9.0)
+    irb (1.9.1)
       rdoc
       reline (>= 0.3.8)
     iso-639 (0.3.6)
@@ -251,7 +250,7 @@ GEM
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.21.4)
+    loofah (2.22.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lookbook (1.5.5)
@@ -280,7 +279,6 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2023.1003)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.5)
     minitest (5.20.0)
     msgpack (1.7.2)
     multi_json (1.15.0)
@@ -290,9 +288,9 @@ GEM
     net-ftp (0.2.0)
       net-protocol
       time
-    net-http (0.4.0)
+    net-http (0.3.2)
       uri
-    net-imap (0.4.4)
+    net-imap (0.4.6)
       date
       net-protocol
     net-pop (0.1.2)
@@ -307,13 +305,10 @@ GEM
     netrc (0.11.0)
     newrelic_rpm (9.6.0)
       base64
-    nio4r (2.5.9)
-    nokogiri (1.15.4)
-      mini_portile2 (~> 2.8.2)
+    nio4r (2.6.1)
+    nokogiri (1.15.5-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.4-x86_64-darwin)
-      racc (~> 1.4)
-    nokogiri (1.15.4-x86_64-linux)
+    nokogiri (1.15.5-x86_64-linux)
       racc (~> 1.4)
     oauth2 (2.0.9)
       faraday (>= 0.17.3, < 3.0)
@@ -358,7 +353,7 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     psych (3.3.4)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     puma (5.6.7)
       nio4r (~> 2.0)
     racc (1.7.3)
@@ -416,15 +411,15 @@ GEM
       json
     redcarpet (3.6.0)
     regexp_parser (2.8.2)
-    reline (0.3.8)
+    reline (0.4.0)
       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)
@@ -433,7 +428,7 @@ GEM
     rspec-mocks (3.12.6)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
-    rspec-rails (6.0.3)
+    rspec-rails (6.1.0)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
@@ -481,6 +476,9 @@ GEM
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
+    simplecov-cobertura (2.1.0)
+      rexml
+      simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
     smart_properties (1.17.0)
@@ -495,22 +493,22 @@ GEM
       actionpack (>= 5.2)
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
-    sshkit (1.21.5)
+    sshkit (1.21.6)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     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 (1.1.20)
       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 (0.3.0)
       date
@@ -526,11 +524,8 @@ GEM
       tilt (>= 1.4, < 3)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.9)
     unicode-display_width (2.5.0)
-    uri (0.12.2)
+    uri (0.13.0)
     version_gem (1.1.3)
     view_component (2.82.0)
       activesupport (>= 5.2.0, < 8.0)
@@ -549,10 +544,9 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.34)
-    zeitwerk (2.6.11)
+    zeitwerk (2.6.12)
 
 PLATFORMS
-  ruby
   x86_64-darwin-23
   x86_64-linux
   x86_64-linux-musl
@@ -595,7 +589,7 @@ DEPENDENCIES
   multi_json
   mysql2
   net-ftp (~> 0.2.0)
-  net-http
+  net-http (~> 0.3.2)
   newrelic_rpm
   oj
   omniauth
@@ -622,6 +616,7 @@ DEPENDENCIES
   select2-rails
   selenium-webdriver
   simplecov
+  simplecov-cobertura
   sprockets-rails
   stackprof
   stimulus-rails

README.md

@@ -1,14 +1,39 @@
-### Configuration
+# Run ontologies_web_ui
+
+## Using OntoPortal UI utilities script
+### See help
+
+```bash 
+bin/ontoportal help
+```
+
 ```
-cp .env.sample .env 
+Usage: bin/ontoportal {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY]
+  dev            : Start the Ontoportal Web UI development server.
+                  Example: bin/ontoportal dev --api-url http://localhost:9393 --api-key my_api_key
+                  Use --reset-cache to remove volumes: bin/ontoportal dev --reset-cache
+  test           : Run tests. Specify either a test file:line_number or  empty for 'all'.
+                  Example: $0 test test/integration/login_flows_test.rb:22
+  run            : Run a command in the Ontoportal Web UI Docker container.
+  help           : Show this help message.
+
+Description:
+  This script provides convenient commands for managing an Ontoportal Web UI
+  application using Docker Compose. It includes options for starting the development server,
+  running tests, and executing commands within the Ontoportal Web UI Docker container.
+
+Goals:
+  - Simplify common tasks related to Ontoportal Web UI development using Docker.
+  - Provide a consistent and easy-to-use interface for common actions.
 ```
 
+
 ### Run dev
 ```bash 
-bin/ontoportal dev 
+bin/ontoportal dev --api-url <an ontoportal api url> --api-key <my_api_key>
 ```
 
-### Run test with a local OntoPortal API  
+### Run test with a local OntoPortal API
 ```bash 
 bin/ontoportal test 
 ```

bin/ontoportal

@@ -6,7 +6,8 @@ show_help() {
   echo "  dev            : Start the Ontoportal Web UI development server."
   echo "                  Example: $0 dev --api-url http://localhost:9393 --api-key my_api_key"
   echo "                  Use --reset-cache to remove volumes: $0 dev --reset-cache"
-  echo "  test           : Run tests."
+  echo "  test           : Run tests. Specify either a test file:line_number or  empty for 'all'."
+  echo "                   Example: $0 test test/integration/login_flows_test.rb:22 "
   echo "  run            : Run a command in the Ontoportal Web UI Docker container."
   echo "  help           : Show this help message."
   echo