Sync: align ncbo/goo 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: ${{ steps.cfg.outputs.backends }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - id: cfg
+        name: Read backend matrix from .ontoportal-testkit.yml
+        run: |
+          BACKENDS=$(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@v6
+
+      - 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@v5
+        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

@@ -4,6 +4,7 @@
 *.tags*
 .bundle
 .config
+.serena
 coverage
 InstalledFiles
 lib/bundler/man
@@ -25,3 +26,8 @@ doc/
 
 .idea/*
 projectFilesBackup/*
+
+config/config.rb
+queries.txt
+
+*.iml

.ontoportal-testkit.yml

@@ -0,0 +1,8 @@
+component_name: goo
+app_service: test-container
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services: []

.ruby-version

@@ -0,0 +1 @@
+3.2.10

Dockerfile

@@ -0,0 +1,20 @@
+ARG RUBY_VERSION=3.2
+ARG DISTRO=bullseye
+ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO}
+FROM ${TESTKIT_BASE_IMAGE}
+
+WORKDIR /app
+
+COPY Gemfile* *.gemspec ./
+
+# Respect the project's Bundler lock when present.
+RUN if [ -f Gemfile.lock ]; then \
+      BUNDLER_VERSION=$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1 | tr -d ' '); \
+      gem install bundler -v "$BUNDLER_VERSION"; \
+    fi
+
+RUN bundle install --jobs 4 --retry 3
+
+COPY . ./
+
+CMD ["bundle", "exec", "rake"]

Gemfile

@@ -3,16 +3,16 @@ source 'https://rubygems.org'
 gemspec
 
 gem "activesupport"
-gem "cube-ruby", require: "cube"
-gem "faraday", '~> 1.9'
 gem "rake"
 gem "uuid"
+gem "request_store"
 
 group :test do
   gem "minitest", '< 5.0'
   gem "pry"
   gem 'simplecov'
   gem 'simplecov-cobertura' # for submitting code coverage results to codecov.io
+  gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main'
 end
 
 group :profiling do
@@ -22,4 +22,6 @@ group :profiling do
   gem "thin"
 end
 
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'ontoportal-lirmm-development'
+gem "rdf-raptor", github: "ruby-rdf/rdf-raptor", ref: "6392ceabf71c3233b0f7f0172f662bd4a22cd534" # use version 3.3.0 when available
+gem 'net-ftp'