Merge branch 'master' into ecoportal-ontoportal-reset

.dockerignore

@@ -9,3 +9,4 @@ tmp/*
 # Editor temp files
 *.swp
 *.swo
+test/solr

.env.sample

@@ -0,0 +1,4 @@
+API_URL=http://localhost:9393
+ONTOLOGIES_LINKED_DATA_PATH=
+GOO_PATH=
+SPARQL_CLIENT_PATH=

.github/workflows/docker-image.yml

@@ -0,0 +1,56 @@
+name: Docker branch Images build
+
+on:
+  push:
+    branches:
+      - master
+      - 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: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: |
+            agroportal/ontologies_api
+            ghcr.io/${{ github.repository }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          build-args: |
+            RUBY_VERSION=2.7.8
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

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

@@ -7,22 +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: 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 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)

.gitignore

@@ -71,3 +71,5 @@ test/data/ontology_files/catalog-v001.xml
 create_permissions.log
 
 ontologies_api.iml
+
+.env

Dockerfile

@@ -7,6 +7,7 @@ RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
   openjdk-11-jre-headless \
   raptor2-utils \
   wait-for-it \
+  libraptor2-dev \
   && rm -rf /var/lib/apt/lists/*
 
 RUN mkdir -p /srv/ontoportal/ontologies_api
@@ -15,12 +16,13 @@ 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
 
 COPY . /srv/ontoportal/ontologies_api
+RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
 
 EXPOSE 9393
 CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]

Gemfile

@@ -1,6 +1,6 @@
 source 'https://rubygems.org'
 
-gem 'activesupport', '~> 3.1'
+gem 'activesupport', '~> 3.2'
 # see https://github.com/ncbo/ontologies_api/issues/69
 gem 'bigdecimal', '1.4.2'
 gem 'faraday', '~> 1.9'
@@ -14,6 +14,9 @@ gem 'sinatra', '~> 1.0'
 gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
 gem 'request_store'
+gem 'parallel'
+gem 'json-ld'
+
 
 # Rack middleware
 gem 'ffi'
@@ -27,9 +30,8 @@ gem 'rack-timeout'
 gem 'redis-rack-cache', '~> 2.0'
 
 # Data access (caching)
-gem 'redis', '~> 4.8.1'
-gem 'redis-activesupport'
-gem 'redis-store', '1.9.1'
+gem 'redis'
+gem 'redis-store', '~>1.10'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
@@ -44,13 +46,12 @@ 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: 'ecoportal'
-gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
-gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
+gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
 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 'ontologies_linked_data', git: 'https://github.com/lifewatch-eric/ontologies_linked_data.git', branch: 'ecoportal-ontoportal-reset'
-gem 'request_store'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
+gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
+gem 'ontologies_linked_data', git: 'https://github.com/lifewatch-eric/ontologies_linked_data.git', branch: 'master'
+gem 'ncbo_cron', git: 'https://github.com/lifewatch-eric/ncbo_cron.git', branch: 'master'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
@@ -64,6 +65,7 @@ group :development do
   gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
 end
 
+
 group :profiling do
   gem 'rack-mini-profiler'
 end
@@ -74,4 +76,5 @@ group :test do
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-end
+  gem 'webmock', '~> 3.19.1'
+end