Merge pull request #160 from ncbo/develop

Develop to master merge, release v5.32.0

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

@@ -14,13 +14,13 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Build docker-compose
-      run: docker-compose --profile 4store build #profile flag is set in order to build all containers in this step
+      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 }} bundle exec rake test TESTOPTS='-v'
+        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@v4
       with:

.ruby-version

@@ -1 +1 @@
-2.7.8
+3.0.6

Dockerfile

@@ -1,4 +1,4 @@
-ARG RUBY_VERSION
+ARG RUBY_VERSION=3.0
 ARG DISTRO_NAME=bullseye
 
 FROM ruby:$RUBY_VERSION-$DISTRO_NAME
@@ -14,10 +14,7 @@ COPY Gemfile* /srv/ontoportal/ontologies_api/
 
 WORKDIR /srv/ontoportal/ontologies_api
 
-# set rubygem and bundler to the last version supported by ruby 2.7
-# remove version after ruby v3 upgrade
-RUN gem update --system '3.4.22'
-RUN gem install bundler -v 2.4.22
+RUN gem update --system
 RUN gem install bundler
 ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install

Gemfile

@@ -9,6 +9,7 @@ gem 'oj', '~> 3.0'
 gem 'parseconfig'
 gem 'rack'
 gem 'rake', '~> 10.0'
+gem 'rexml' # Investigate why unicorn fails to start under ruby 3 without adding rexml gem to the Gemfile
 gem 'sinatra', '~> 1.0'
 gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
@@ -77,4 +78,5 @@ group :test do
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
   gem 'webmock', '~> 3.19.1'
+  gem 'webrick'
 end