Merge remote-tracking branch 'origin/pr/fix-zipped-sumbission-remote-…

…pull' into pr/fix-zipped-sumbission-remote-pull

.dockerignore

@@ -1,5 +1,6 @@
 # Git
-#.git
+.git
+.github
 .gitignore
 # Logs
 log/*
@@ -8,3 +9,9 @@ tmp/*
 # Editor temp files
 *.swp
 *.swo
+coverage
+create_permissions.log
+# Ignore generated test data
+test/data/dictionary.txt
+test/data/ontology_files/repo/**/*
+test/data/tmp/*

.github/workflows/docker-image.yml

@@ -0,0 +1,42 @@
+name: Docker Image CI
+
+on:
+ release:
+ types: [published]
+
+jobs:
+ push_to_registry:
+ name: Push Docker 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@v2
+ with:
+ username: ${{ secrets.DOCKERHUB_USERNAME }}
+ password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+ - name: Extract metadata (tags, labels) for Docker
+ id: meta
+ uses: docker/metadata-action@v4
+ with:
+ images: bioportal/ncbo_cron
+
+ - 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
+ push: true
+ tags: ${{ steps.meta.outputs.tags }}
+ labels: ${{ steps.meta.outputs.labels }}

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

@@ -6,15 +6,25 @@ on:
 
 jobs:
  test:
+ strategy:
+ fail-fast: false
+ matrix:
+ backend: ['ncbo_cron', 'ncbo_cron-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

@@ -3,6 +3,8 @@
 config/config.rb
 config/config_*.rb
 config/*.p12
+config/*.json
+data/
 projectFilesBackup/
 .ruby-version
 repo*
@@ -11,6 +13,9 @@ repo*
 .DS_Store
 tmp
 
+# Code coverage reports
+coverage*
+
 # Ignore eclipse .project
 .project
 .pmd

Dockerfile

@@ -1,14 +1,25 @@
-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 ["bundle","exec","rackup","-p","9393","--host","0.0.0.0"]
+RUN cp /srv/ontoportal/ncbo_cron/config/config.rb.sample /srv/ontoportal/ncbo_cron/config/config.rb
+
+CMD ["/bin/bash"]

Gemfile

@@ -2,13 +2,11 @@ source 'https://rubygems.org'
 
 gemspec
 
-gem 'faraday', '~> 1.9'
 gem 'ffi'
-gem 'google-api-client', '~> 0.10'
+gem 'google-analytics-data'
 gem 'mail', '2.6.6'
-gem 'minitest', '< 5.0'
 gem 'multi_json'
-gem 'oj', '~> 2.0'
+gem 'oj', '~> 3.0'
 gem 'parseconfig'
 gem 'pony'
 gem 'pry'
@@ -20,16 +18,16 @@ gem 'sys-proctable'
 # Monitoring
 gem 'cube-ruby', require: 'cube'
 
-# NCBO gems (can be from a local dev path or from rubygems/git)
-
+# NCBO
 gem 'goo', github: 'ncbo/goo', branch: 'master'
 gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pl/enhance-zipped-submissions-support'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'master'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
 
-# Testing
 group :test do
  gem 'email_spec'
+ gem 'minitest', '< 5.0'
+ gem 'simplecov'
+ gem 'simplecov-cobertura' # for codecov.io
  gem 'test-unit-minitest'
 end
-