Feature: sync with NCBO latest version and support ruby RDF 3.0

.dockerignore

@@ -0,0 +1,13 @@
+.bundle
+.git
+.gitignore
+.github
+.DS_Store
+vendor/bundle
+# Logs
+log/*
+# Temp files
+tmp/*
+# Editor temp files
+*.swp
+*.swo

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

@@ -0,0 +1,45 @@
+name: Ruby Unit Tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        goo-slice: [ '20', '100', '500' ]
+        ruby-version: [ '2.7' ]
+        triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: create config.rb file
+        run: cp config/config.test.rb config/config.rb
+      - name: Set up solr configsets
+        run: ./test/solr/generate_ncbo_configsets.sh
+      - 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

@@ -43,3 +43,5 @@ bin/mallet-deps.jar
 bin/CogPOTerms
 
 create_permissions.log
+
+test/data/dictionary-lem.txt

Dockerfile

@@ -0,0 +1,22 @@
+ARG RUBY_VERSION
+ARG DISTRO_NAME=bullseye
+
+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
+RUN mkdir -p /srv/ontoportal/ncbo_annotator
+COPY *.gemspec Gemfile* /srv/ontoportal/ncbo_annotator/
+
+WORKDIR /srv/ontoportal/ncbo_annotator
+
+# set bundler to v2.4.22 which is the last version supported by ruby 2.7
+RUN gem install bundler -v 2.4.22
+ENV BUNDLE_PATH /bundle
+RUN bundle install
+COPY . /srv/ontoportal/ncbo_annotator
+CMD ["/bin/bash"]

Gemfile

@@ -1,17 +1,24 @@
 source 'https://rubygems.org'
 
+gem 'cube-ruby'
+gem 'faraday', '~> 1.9'
+gem 'ffi'
+gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
 gem 'redis'
-gem 'minitest', '~> 4.0'
-gem 'cube-ruby', require: "cube"
 gem 'ruby-xxHash'
-gem 'ffi', '< 1.9.22'
+gem 'request_store'
+gem 'jwt'
+gem 'addressable', '~> 2.8.0'
 
-# Development
-gem 'pry', group: :development
+group :development do
+  gem 'minitest', '~> 4.0'
+  gem 'pry'
+  gem 'simplecov'
+  gem 'simplecov-cobertura' # for codecov.io
+end
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
 gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
-gem 'ncbo_resource_index', github: 'ncbo/resource_index'