Sync: align ncbo/ontologies_api with the AgroPortal codebase

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

@@ -0,0 +1,87 @@
+name: Docker Unit Tests
+
+on:
+  push:
+    branches:
+      - '**'
+    tags-ignore:
+      - '**'
+  pull_request:
+
+env:
+  # CI execution mode for backend tests:
+  # - container: run `test:docker:<backend>:container` (default)
+  # - native: run `test:docker:<backend>` on host Ruby
+  OPTK_CI_RUN_MODE: ${{ vars.OPTK_CI_RUN_MODE || 'container' }}
+  # Example override to force native mode in this workflow file:
+  # OPTK_CI_RUN_MODE: native
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      backends: ${{ steps.cfg.outputs.backends }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - id: cfg
+        name: Read backend matrix from .ontoportal-testkit.yml
+        run: |
+          BACKENDS=$(ruby -ryaml -rjson -e 'c=YAML.safe_load_file(".ontoportal-testkit.yml") || {}; b=c["backends"] || %w[fs ag vo gd]; puts JSON.generate(b)')
+          echo "backends=$BACKENDS" >> "$GITHUB_OUTPUT"
+
+  test:
+    needs: prepare
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
+    strategy:
+      fail-fast: false
+      matrix:
+        backend: ${{ fromJson(needs.prepare.outputs.backends) }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Ruby from .ruby-version
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: .ruby-version
+          bundler-cache: true
+
+      - name: Set up Java 11 (native mode)
+        if: env.OPTK_CI_RUN_MODE == 'native'
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: '11'
+
+      - name: Install native system dependencies
+        if: env.OPTK_CI_RUN_MODE == 'native'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y raptor2-utils
+
+      - name: Run unit tests
+        env:
+          CI: "true"
+          TESTOPTS: "--verbose"
+          BACKEND: ${{ matrix.backend }}
+        run: |
+          MODE="${OPTK_CI_RUN_MODE:-container}"
+          TASK="test:docker:${BACKEND}"
+          if [ "$MODE" = "container" ]; then
+            TASK="${TASK}:container"
+          elif [ "$MODE" != "native" ]; then
+            echo "Invalid OPTK_CI_RUN_MODE=$MODE (expected container or native)"
+            exit 1
+          fi
+
+          bundle exec rake "$TASK"
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: unittests,${{ matrix.backend }}
+          verbose: true
+          fail_ci_if_error: false

.ontoportal-testkit.yml

@@ -0,0 +1,9 @@
+component_name: ontologies_api
+app_service: test-container
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services:
+  - mgrep

.ruby-version

@@ -1 +1 @@
-3.1.6
+3.2.10

Capfile

@@ -22,6 +22,5 @@ require 'capistrano/bundler'
 # require 'capistrano/rails/assets'
 # require 'capistrano/rails/migrations'
 require 'capistrano/locally'
-require 'new_relic/recipes' # announce deployments in NewRelic
 # Loads custom tasks from `lib/capistrano/tasks' if you have any defined.
 Dir.glob('lib/capistrano/tasks/*.cap').each { |r| import r }

Dockerfile

@@ -1,24 +1,20 @@
-ARG RUBY_VERSION=3.1
-ARG DISTRO_NAME=bullseye
+ARG RUBY_VERSION=3.2
+ARG DISTRO=bullseye
+ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO}
+FROM ${TESTKIT_BASE_IMAGE}
 
-FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+WORKDIR /app
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
-  openjdk-11-jre-headless \
-  raptor2-utils \
-  && rm -rf /var/lib/apt/lists/*
+COPY Gemfile* *.gemspec ./
 
-RUN mkdir -p /srv/ontoportal/ontologies_api
-RUN mkdir -p /srv/ontoportal/bundle
-COPY Gemfile* /srv/ontoportal/ontologies_api/
+# Respect the project's Bundler lock when present.
+RUN if [ -f Gemfile.lock ]; then \
+      BUNDLER_VERSION=$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1 | tr -d ' '); \
+      gem install bundler -v "$BUNDLER_VERSION"; \
+    fi
 
-WORKDIR /srv/ontoportal/ontologies_api
+RUN bundle install --jobs 4 --retry 3
 
-ENV BUNDLE_PATH=/srv/ontoportal/bundle
-RUN bundle install
+COPY . ./
 
-COPY . /srv/ontoportal/ontologies_api
-RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
-
-EXPOSE 9393
 CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]

Gemfile

@@ -1,58 +1,61 @@
 source 'https://rubygems.org'
 
-gem 'activesupport', '~> 5'
+gem 'activesupport'
 # see https://github.com/ncbo/ontologies_api/issues/69
 gem 'bigdecimal'
-# gem 'faraday', '~> 1.9'
-gem 'json-schema', '~> 2.0'
+gem 'json-schema'
 gem 'multi_json'
 gem 'oj'
 gem 'parseconfig'
 gem 'rack'
-gem 'rake', '~> 10.0'
+gem 'rake'
 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'
+gem 'rackup'
+gem 'sinatra'
+gem 'sinatra-contrib'
+
+gem 'request_store'
+gem 'parallel'
+gem 'google-protobuf', '3.25.3'
+gem 'grpc', '1.70.1'
+gem 'net-ftp'
+gem 'json-ld', '~> 3.2.0'
+gem 'rdf-raptor', github:'ruby-rdf/rdf-raptor', ref: '6392ceabf71c3233b0f7f0172f662bd4a22cd534' # use version 3.3.0 when available
 
 # Rack middleware
 gem 'ffi'
-gem 'rack-accept', '~> 0.4'
-gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
-gem 'rack-cache', '~> 1.13.0' # see https://github.com/ncbo/ontologies_api/issues/118
+gem 'rack-accept'
+gem 'rack-attack', require: 'rack/attack'
+gem 'rack-cache' # see https://github.com/ncbo/ontologies_api/issues/118
 gem 'rack-cors', require: 'rack/cors'
 # GitHub dependency can be removed when https://github.com/niko/rack-post-body-to-params/pull/6 is merged and released
 gem 'rack-post-body-to-params', github: 'palexander/rack-post-body-to-params', branch: 'multipart_support'
 gem 'rack-timeout'
-gem 'redis-rack-cache', '~> 2.0'
+gem 'redis-rack-cache'
 
 # Data access (caching)
 gem 'redis'
-gem 'redis-store', '~>1.10'
-
-# Monitoring
-gem 'cube-ruby', require: 'cube'
-gem 'newrelic_rpm', group: [:default, :deployment]
+gem 'redis-store'
 
 # HTTP server
 gem 'unicorn'
 gem 'unicorn-worker-killer'
 
 # Templating
 gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
-gem 'redcarpet'
+gem 'rack-contrib'
+gem 'pandoc-ruby'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'develop'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
-gem 'sparql-client', github: 'ncbo/sparql-client', tag: 'v6.3.0'
+gem 'goo', github: 'ncbo/goo', branch: 'main'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'main'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'chore/ruby3.2-minitest6-compat'
+gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'chore/ontoportal-lirmm-goo-compat'
+gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'chore/ruby3.2-minitest6-compat'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'chore/ontoportal-lirmm-goo-compat'
 
 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
-  gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
+  gem 'shotgun', github: 'syphax-bouazzouni/shotgun', branch: 'master'
   gem 'rubocop'
 end
 
@@ -73,13 +76,14 @@ end
 group :test do
   gem 'byebug', '~> 12.0'
   gem 'crack', '0.4.5'
-  gem 'minitest', '~> 5.0'
-  gem 'minitest-hooks', "~> 1.5"
+  gem 'minitest'
+  gem 'minitest-hooks'
+  gem 'minitest-reporters'
   gem 'minitest-stub_any_instance'
+  gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-  gem 'webmock', '~> 3.19.1'
+  gem 'webmock'
   gem 'webrick'
-  gem 'minitest-bisect'
-end
+end