Merge branch 'feature/index-ontology-agent-metadata' into stage

.github/workflows/ruby-unit-tests.yml

@@ -7,25 +7,35 @@ on:
 jobs:
   test:
     strategy:
+      fail-fast: false
       matrix:
-        backend: ['api'] # api runs tests with 4store backend and api-agraph runs with AllegroGraph backend
+        goo-slice: [ '20', '100', '500' ]
+        ruby-version: [ '2.7' ]
+        triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: copy-env-config
-      run: cp .env.sample .env
-    - name: Build docker-compose
-      run: docker-compose --profile 4store build #profile flag is set in order to build all containers in this step
-    - name: Run unit tests
-      # unit tests are run inside a container
-      # http://docs.codecov.io/docs/testing-with-docker
-      run: |
-        ci_env=`bash <(curl -s https://codecov.io/env)`
-        docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} wait-for-it solr-ut:8983 -- bundle install 
-        docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} wait-for-it solr-ut:8983 -- bundle exec rake test TESTOPTS='-v'
-    - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        flags: unittests
-        verbose: true
-        fail_ci_if_error: false # optional (default = false)
+      - uses: actions/checkout@v3
+      - name: Install Dependencies
+        run: sudo apt-get update && sudo apt-get -y install raptor2-utils
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby-version }}
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+      - name: Run unit tests
+        # unit tests are run inside a container
+        # http://docs.codecov.io/docs/testing-with-docker
+        run: |
+          ci_env=`bash <(curl -s https://codecov.io/env)`
+          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          flags: unittests
+          verbose: true
+          fail_ci_if_error: false # optional (default = false)

Dockerfile

@@ -15,7 +15,7 @@ COPY Gemfile* /srv/ontoportal/ontologies_api/
 
 WORKDIR /srv/ontoportal/ontologies_api
 
-RUN gem update --system
+RUN gem update --system 3.4.22 # the 3.4.22 can be removed if we support Ruby version > 3.0
 RUN gem install bundler
 ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install

Gemfile

@@ -14,6 +14,7 @@ gem 'sinatra', '~> 1.0'
 gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
 gem 'request_store'
+gem 'parallel'
 
 # Rack middleware
 gem 'ffi'
@@ -44,11 +45,11 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'development'
-gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
+gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
 
 group :development do
@@ -74,5 +75,5 @@ group :test do
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-  gem 'webmock'
+  gem 'webmock', '~> 3.19.1'
 end