Merge pull request #1 from lifewatch-eric/ecoportal-ontoportal-reset

Ontoportal align: Ecoportal ontoportal reset

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

@@ -6,15 +6,26 @@ on:
 
 jobs:
   test:
+    strategy:
+      matrix:
+        backend: ['ruby', 'ruby-agraph'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: copy config.rb file from template
       run:  cp config/config.test.rb config/config.rb
     - name: Build docker-compose
       working-directory: ./test
       run: docker-compose build
     - name: Run unit tests
       working-directory: ./test
-      run: docker-compose run unit-test wait-for-it solr-ut:8983 -- rake test TESTOPTS='-v'
+      run: |
+        ci_env=`bash <(curl -s https://codecov.io/env)`
+        docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} 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)
 

.gitignore

@@ -1,6 +1,8 @@
+.bundle/
 # Ignore RubyMine editor files
 .idea/
 config/config.rb
+config/appliance.rb
 config/config_*.rb
 config/*.p12
 projectFilesBackup/
@@ -11,6 +13,9 @@ repo*
 .DS_Store
 tmp
 
+# Code coverage reports
+coverage*
+
 # Ignore eclipse .project
 .project
 .pmd

Dockerfile

@@ -1,13 +1,23 @@
-FROM ruby:2.6
+ARG RUBY_VERSION
+ARG DISTRO_NAME=bullseye
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends openjdk-11-jre-headless raptor2-utils wait-for-it
+FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+
+RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
+  openjdk-11-jre-headless \
+  raptor2-utils \
+  && rm -rf /var/lib/apt/lists/*
 
-# The Gemfile Caching Trick
-# we install gems before copying the code in its own layer so that gems would not have to get
-# installed every single time code is updated
 RUN mkdir -p /srv/ontoportal/ncbo_cron
+RUN mkdir -p /srv/ontoportal/bundle
 COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_cron/
+
 WORKDIR /srv/ontoportal/ncbo_cron
-RUN gem install bundler -v "$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1)"
+
+RUN gem update --system
+RUN gem install bundler
+ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install
+
 COPY . /srv/ontoportal/ncbo_cron
+CMD ["/bin/bash"]

Gemfile

@@ -3,7 +3,7 @@ source 'https://rubygems.org'
 gemspec
 
 gem 'faraday', '~> 1.9'
-gem 'ffi'
+gem 'ffi', '~> 1.15.5'
 gem "google-apis-analytics_v3"
 gem 'mail', '2.6.6'
 gem 'minitest', '< 5.0'
@@ -20,15 +20,16 @@ gem 'sys-proctable'
 # Monitoring
 gem 'cube-ruby', require: 'cube'
 
-# NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_resource_index', github: 'ncbo/resource_index'
-gem 'ontologies_linked_data', github: 'lifewatch-eric/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
-
+gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'ecoportal'
+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: 'master'
+gem 'ncbo_annotator', github: 'ontoportal-lirmm/ncbo_annotator', branch: 'master'
+# Testing
 group :test do
   gem 'email_spec'
+  gem 'simplecov'
+  gem 'simplecov-cobertura' # for codecov.io
   gem 'test-unit-minitest'
 end
 
+gem "binding_of_caller", "~> 1.0"