Sync: BioPortal v5.33.0 release

.env

@@ -0,0 +1,6 @@
+API_URL=http://localhost:9393
+ONTOLOGIES_LINKED_DATA_PATH=
+GOO_PATH=
+SPARQL_CLIENT_PATH=
+ONTOPORTAL_KB=ontoportal_kb
+REDIS_HOST=redis-ut

.github/workflows/docker-image.yml

@@ -35,8 +35,8 @@ jobs:
         with:
           context: .
           platforms: linux/amd64,linux/arm64
-          build-args: |
-            RUBY_VERSION=2.7
+          # build-args: |
+          #   RUBY_VERSION=2.7
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

.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

@@ -1,14 +1,15 @@
 source 'https://rubygems.org'
-
-gem 'activesupport', '~> 3.2'
+gem 'activesupport', '~> 5'
 # see https://github.com/ncbo/ontologies_api/issues/69
-gem 'bigdecimal', '1.4.2'
+gem 'bigdecimal'
+# gem 'faraday', '~> 1.9'
 gem 'json-schema', '~> 2.0'
-gem 'multi_json', '~> 1.0'
-gem 'oj', '~> 3.0'
+gem 'multi_json'
+gem 'oj'
 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'
@@ -40,13 +41,15 @@ gem 'unicorn-worker-killer'
 gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
-# NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
+
+# NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
 gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
 gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'master'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', 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
@@ -69,9 +72,13 @@ group :profiling do
 end
 
 group :test do
-  gem 'minitest', '~> 4.0'
+  gem 'crack', '0.4.5'
+  gem 'minitest', '~> 5.0'
+  gem 'minitest-hooks', "~> 1.5"
   gem 'minitest-stub_any_instance'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
+  gem 'webmock', '~> 3.19.1'
+  gem 'webrick'
 end