Sync: align ncbo/ontologies_linked_data 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

.gitignore

@@ -2,6 +2,7 @@
 *.swp
 *.gemtags
 .bundle
+.serena
 *.tags*
 .DS_Store
 

.ontoportal-testkit.yml

@@ -0,0 +1,8 @@
+component_name: ontologies_linked_data
+app_service: test-container
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services: {}

.ruby-version

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

Dockerfile

@@ -1,34 +1,21 @@
-ARG RUBY_VERSION=3.1
+ARG RUBY_VERSION=3.2
 ARG DISTRO=bullseye
-
-FROM ruby:$RUBY_VERSION-$DISTRO
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential \
-    git \
-    libxml2 \
-    libxslt-dev \
-    openjdk-11-jre-headless \
-    raptor2-utils \
-    && rm -rf /var/lib/apt/lists/*
+ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO}
+FROM ${TESTKIT_BASE_IMAGE}
 
 WORKDIR /app
 
-COPY Gemfile* *.gemspec ./
-
-# Copy only the `version.rb` file to prevent missing file errors!
+# Copy only the `version.rb` file to prevent missing file errors
 COPY lib/ontologies_linked_data/version.rb lib/ontologies_linked_data/
 
-#Install the exact Bundler version from Gemfile.lock (if it exists)
-RUN gem update --system && \
-    if [ -f Gemfile.lock ]; then \
+COPY Gemfile* *.gemspec ./
+
+# 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"; \
-    else \
-      gem install bundler; \
     fi
 
-RUN bundle config set --global no-document 'true'
 RUN bundle install --jobs 4 --retry 3
 
 COPY . ./

Gemfile

@@ -2,43 +2,46 @@ source 'https://rubygems.org'
 
 gemspec
 
-gem 'activesupport', '~> 4'
+gem 'activesupport'
 gem 'addressable', '~> 2.8'
 gem 'bcrypt', '~> 3.0'
-gem 'cube-ruby', require: 'cube'
 gem 'ffi'
 gem 'libxml-ruby'
 gem 'multi_json', '~> 1.0'
 gem 'oj', '~> 3.0'
 gem 'omni_logger'
 gem 'pony'
 gem 'rack'
-gem 'rake', '~> 10.0'
+gem 'rake'
 gem 'request_store'
 gem 'rest-client'
 gem 'rsolr'
-gem 'thin', '~> 1.0' # compatibility version pin. thin should be replaced with webmoc
-gem "down", "~> 5.0"
+gem 'jwt'
+gem 'json-ld', '~> 3.2.0'
 
 # Testing
 group :test do
   gem 'email_spec'
-  gem 'minitest', '~> 4'
-  gem 'minitest-reporters', '>= 0.5.0'
+  gem 'minitest'
+  gem 'minitest-reporters'
   gem 'mocha', '~> 2.7'
   gem 'mock_redis', '~> 0.5'
+  gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main'
   gem 'pry'
   gem 'rack-test', '~> 0.6'
   gem 'simplecov'
   gem 'simplecov-cobertura' # for codecov.io
+  gem "thin", "~> 1.8.2"
+  gem 'webmock'
 end
 
 group :development do
   gem 'rubocop', require: false
 end
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', 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 'public_suffix', '~> 5.1.1'
 gem 'net-imap', '~> 0.4.18'