Infra: upgrade ncbo_annotator to Ruby 3.2 and Minitest 6

.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: "-v"
+          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: ncbo_annotator
+app_service: test-container
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services:
+  - mgrep

.ruby-version

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

Dockerfile

@@ -1,38 +1,18 @@
-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
 
-# Use a dedicated bundle path
-ENV BUNDLE_PATH=/usr/local/bundle
-ENV GEM_HOME=/usr/local/bundle
-ENV PATH="$BUNDLE_PATH/bin:$PATH"
-
 COPY Gemfile* *.gemspec ./
 
-RUN gem update --system
-
-#I nstall the exact Bundler version from Gemfile.lock (if it exists)
+# 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 --local path '/usr/local/bundle'
-RUN bundle config set --global no-document 'true'
 RUN bundle install --jobs 4 --retry 3
 
 COPY . ./

Gemfile

@@ -1,20 +1,26 @@
 source 'https://rubygems.org'
 
-gem 'cube-ruby'
 gem 'faraday'
 gem 'ffi'
 gem 'oj', '~> 3.0'
-gem 'rake', '~> 10.0'
+gem 'rake'
+gem 'request_store'
+gem 'parallel'
+gem 'json-ld'
+gem 'jwt'
 gem 'ruby-xxHash'
+gem 'activesupport'
 
-group :development do
-  gem 'minitest', '~> 4.0'
+group :test do
+  gem 'minitest'
+  gem 'minitest-reporters'
+  gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main'
   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: 'ncbo/goo', 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 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'chore/ontoportal-lirmm-goo-compat'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'main'