Merge branch 'development' into fix/the-display-of-definitions-and-pa…

…rent-in-properties-tab
ontoportal-lirmm · Nov 27, 2023 · 90ebb3e · 90ebb3e
2 parents 4bec7c0 + dcfc93f
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diff --git a/.github/workflows/docker-image-arm.yml b/.github/workflows/docker-image-arm.yml
@@ -0,0 +1,56 @@
+name: Docker branch Images build - ARM version
+
+on:
+  push:
+    branches:
+      - development
+      - stage
+      - test
+  release:
+    types: [ published ]
+jobs:
+  push_to_registry:
+    name: Push Docker branch image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: | 
+            agroportal/ontologies_api
+            ghcr.io/agroportal/ontoloportal_web_ui
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/arm64
+          build-args: |
+            RUBY_VERSION=2.7
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}-${{ env.BRANCH_NAME }}-arm64
+          labels: ${{ steps.meta.outputs.labels }}
+
diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -8,53 +8,48 @@ on:
       - test
   release:
     types: [ published ]
-
 jobs:
   push_to_registry:
     name: Push Docker branch image to Docker Hub
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        platform: [ linux/amd64, linux/arm64 ]
-
     steps:
       - name: Check out the repo
         uses: actions/checkout@v3
 
-      - name: Cache Docker layers
-        uses: actions/cache@v2
-        with:
-          path: |
-            /tmp/.buildx-cache
-          key: docker-${{ runner.os }}-${{ hashFiles('**/Dockerfile') }}
-          restore-keys: |
-            docker-${{ runner.os }}-
-
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v2
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Extract metadata (tags, labels) for Docker
         id: meta
         uses: docker/metadata-action@v4
         with:
-          images: agroportal/ontoportal_web_ui
+          images: |
+            agroportal/ontoloportal_web_ui
+            ghcr.io/agroportal/ontoloportal_web_ui
 
       - name: Build and push Docker image
         uses: docker/build-push-action@v4
         with:
           context: .
-          platforms: ${{ matrix.platform }}
+          platforms: linux/amd64
           build-args: |
-            RUBY_VERSION=2.7.8
+            RUBY_VERSION=2.7
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/tests-real-data-stageportal.yml b/.github/workflows/tests-real-data-stageportal.yml
@@ -0,0 +1,52 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
+# For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
+name: "Run remote API (stageportal) tests CI"
+
+on:
+  push:
+  pull_request_target:
+    types: [ opened, reopened ]
+env:
+  API_URL: https://data.stageportal.lirmm.fr/ # or ${{ secrets.API_URL }}
+  API_KEY: 1de0a270-29c5-4dda-b043-7c3580628cd5 # public apikey or ${{ secrets.API_KEY }}
+  BIOMIXER_URL: ${{ secrets.BIOMIXER_URL }}
+  FAIRNESS_URL: ${{ secrets.FAIRNESS_URL }}
+  ANNOTATOR_URL: ${{ secrets.ANNOTATOR_URL }}
+  DB_HOST: 127.0.0.1
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      mysql:
+        image: mysql:8.0
+        ports:
+          - "3306:3306"
+        env:
+          MYSQL_ROOT_PASSWORD: root
+      memcached:
+        image: memcached:1.6
+        ports:
+          - 11211:11211
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      # Add or replace dependency steps here
+      - name: Install Ruby and gems
+        uses: ruby/setup-ruby@v1
+        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:setup
+      - name: Set up yarn
+        run: yarn install
+      # Add or replace test runners here
+      - name: Run tests
+        run:  RAILS_ENV=test bin/rails test test/controllers/* -v
diff --git a/.github/workflows/tests-real-data.yml → .../workflows/tests-real-data-testportal.yml b/.github/workflows/tests-real-data.yml → .../workflows/tests-real-data-testportal.yml
@@ -4,15 +4,15 @@
 # documentation.
 # This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
 # For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
-name: "Run remote API tests CI"
+name: "Run remote API (testportal) tests CI"
 
 on:
   push:
   pull_request_target:
     types: [ opened, reopened ]
 env:
-  API_URL: ${{ secrets.API_URL }}
-  API_KEY: ${{ secrets.API_KEY }}
+  API_URL: https://data.testportal.lirmm.fr/ # or ${{ secrets.API_URL }}
+  API_KEY: 1de0a270-29c5-4dda-b043-7c3580628cd5 # public apikey or ${{ secrets.API_KEY }}
   BIOMIXER_URL: ${{ secrets.BIOMIXER_URL }}
   FAIRNESS_URL: ${{ secrets.FAIRNESS_URL }}
   ANNOTATOR_URL: ${{ secrets.ANNOTATOR_URL }}

diff --git a/.github/workflows/tests-system.yml b/.github/workflows/tests-system.yml
@@ -0,0 +1,65 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
+# For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
+name: "Run system tests CI"
+
+on:
+  push:
+  pull_request_target:
+    types: [ opened, reopened ]
+env:
+  API_URL: http://localhost:9393
+  REMOTE_API_KEY: 8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+  REMOTE_API_URL: https://data.bioontology.org
+  BIOMIXER_URL: ${{ secrets.BIOMIXER_URL }}
+  FAIRNESS_URL: ${{ secrets.FAIRNESS_URL }}
+  ANNOTATOR_URL: ${{ secrets.ANNOTATOR_URL }}
+  DB_HOST: 127.0.0.1
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      mysql:
+        image: mysql:8.0
+        ports:
+          - "3306:3306"
+        env:
+          MYSQL_ROOT_PASSWORD: root
+      memcached:
+        image: memcached:1.6
+        ports:
+          - 11211:11211
+      chrome-server:
+        image: selenium/standalone-chrome:112.0-chromedriver-112.0-grid-4.9.0-20230421
+        options: "--shm-size=2g"
+        ports:
+          - "4444:4444"
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      # Add or replace dependency steps here
+      - name: Install Ruby and gems
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 2.7.8
+          bundler-cache: true
+
+      - name: Run OntoPortal API
+        run: bin/run_api -k ${{ env.REMOTE_API_KEY }} -r agroportal -t development -s STY -u ${{ env.REMOTE_API_URL }}
+
+      # 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:setup
+      - name: Set up yarn
+        run: yarn install
+      # Add or replace test runners here
+      - name: Run integration tests
+        run:  |
+          CI=true RAILS_ENV=test bin/rails  assets:precompile
+          CI=true RAILS_ENV=test bin/rails test -v test/system/*
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -43,7 +43,7 @@ jobs:
           bundler-cache: true
 
       - name: Run OntoPortal API
-        run: bin/run_api -k ${{ env.REMOTE_API_KEY }} -r agroportal -t stage -s STY -u ${{ env.REMOTE_API_URL }}
+        run: bin/run_api -k ${{ env.REMOTE_API_KEY }} -r agroportal -t development -s STY -u ${{ env.REMOTE_API_URL }}
 
       # Add or replace database setup steps here
       - name: set up config file
@@ -54,4 +54,9 @@ jobs:
         run: yarn install
       # Add or replace test runners here
       - name: Run tests
-        run:  RAILS_ENV=test bin/rails test -v
+        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/
diff --git a/Gemfile b/Gemfile
@@ -128,7 +128,8 @@ group :test do
   # Use system testing [https://guides.rubyonrails.org/testing.html#system-testing]
   gem 'capybara'
   gem 'selenium-webdriver'
-  gem 'webdrivers'
+  gem 'simplecov', require: false
+  #gem 'webdrivers'
 end
 
 

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -150,6 +150,7 @@ GEM
       reline (>= 0.3.1)
     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)
     ed25519 (1.3.0)
@@ -279,6 +280,7 @@ 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)
@@ -306,6 +308,9 @@ GEM
     newrelic_rpm (9.6.0)
       base64
     nio4r (2.5.9)
+    nokogiri (1.15.4)
+      mini_portile2 (~> 2.8.2)
+      racc (~> 1.4)
     nokogiri (1.15.4-x86_64-darwin)
       racc (~> 1.4)
     nokogiri (1.15.4-x86_64-linux)
@@ -472,6 +477,12 @@ GEM
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
     sexp_processor (4.17.0)
+    simplecov (0.22.0)
+      docile (~> 1.1)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.4)
     smart_properties (1.17.0)
     snaky_hash (2.0.1)
       hashie
@@ -530,10 +541,6 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webdrivers (5.3.1)
-      nokogiri (~> 1.6)
-      rubyzip (>= 1.3.0)
-      selenium-webdriver (~> 4.0, < 4.11)
     websocket (1.2.10)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
@@ -545,6 +552,7 @@ GEM
     zeitwerk (2.6.11)
 
 PLATFORMS
+  ruby
   x86_64-darwin-23
   x86_64-linux
   x86_64-linux-musl
@@ -613,6 +621,7 @@ DEPENDENCIES
   sassc-rails
   select2-rails
   selenium-webdriver
+  simplecov
   sprockets-rails
   stackprof
   stimulus-rails
@@ -623,7 +632,6 @@ DEPENDENCIES
   tzinfo-data
   view_component (~> 2.72)
   web-console
-  webdrivers
   will_paginate (~> 3.0)
 
 BUNDLED WITH

diff --git a/app/components/tab_item_component.rb b/app/components/tab_item_component.rb
@@ -27,7 +27,7 @@ def target_id
 
 
   def id
-    @title || @id
+    @id || @title
   end
 
   def title
-Original file line number
+Diff line change
@@ Expand Up / @@ -27,7 +27,7 @@ def target_id @@
       def id
-        @title || @id
+        @id || @title
       end
       def title
@@ Expand Down @@