Infra/ontoportal testkit integration

.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 @@
-3.2.2
+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

@@ -14,6 +14,7 @@ gem 'activesupport'
 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

Gemfile.lock

@@ -1,3 +1,11 @@
+GIT
+  remote: https://github.com/alexskr/ontoportal_testkit.git
+  revision: 5138aa94c028ec97adeaf1f7a5ed9f1c40b12950
+  branch: main
+  specs:
+    ontoportal_testkit (0.1.0)
+      rake (>= 13.0)
+
 GIT
   remote: https://github.com/ncbo/goo.git
   revision: 13a8559a2346cc8320d7d36046646907bfa8a27c
@@ -263,6 +271,7 @@ DEPENDENCIES
   minitest-reporters
   oj (~> 3.0)
   ontologies_linked_data!
+  ontoportal_testkit!
   parallel
   pry
   rake
@@ -335,6 +344,7 @@ CHECKSUMS
   oj (3.16.15) sha256=4d3324cac3e8fef54c0fa250b2af26a16dadd9f9788a1d6b1b2098b793a1b2cd
   omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e
   ontologies_linked_data (0.0.1)
+  ontoportal_testkit (0.1.0)
   ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912
   parallel (1.27.0) sha256=4ac151e1806b755fb4e2dc2332cbf0e54f2e24ba821ff2d3dcf86bf6dc4ae130
   pony (1.13.1) sha256=ab507c8ade8b35de96f1e75c0ae4566a3c40ac8a0d5101433969b6fd29c718a7
@@ -374,4 +384,4 @@ CHECKSUMS
   uuid (2.3.9) sha256=aec0cf592053cd6e07c13c1ef94c440aba705f22eb1ee767b39631f2760124d7
 
 BUNDLED WITH
-  4.0.5
+  4.0.7

config/config.test.rb

@@ -16,21 +16,23 @@
 SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr"
 SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr"
 
-
 LinkedData.config do |config|
-  config.goo_backend_name           = GOO_BACKEND_NAME.to_s
-  config.goo_host                   = GOO_HOST.to_s
-  config.goo_port                   = GOO_PORT.to_i
-  config.goo_path_query             = GOO_PATH_QUERY.to_s
-  config.goo_path_data              = GOO_PATH_DATA.to_s
-  config.goo_path_update            = GOO_PATH_UPDATE.to_s
-  config.search_server_url          = SOLR_TERM_SEARCH_URL.to_s
-  config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s
+ config.goo_backend_name           = GOO_BACKEND_NAME.to_s
+ config.goo_host                   = GOO_HOST.to_s
+ config.goo_port                   = GOO_PORT.to_s
+ config.goo_path_query             = GOO_PATH_QUERY.to_s
+ config.goo_path_data              = GOO_PATH_DATA.to_s
+ config.goo_path_update            = GOO_PATH_UPDATE.to_s
+ config.search_server_url          = SOLR_TERM_SEARCH_URL.to_s
+ config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s
 end
+
 Annotator.config do |config|
   config.mgrep_host            = MGREP_HOST.to_s
-  config.mgrep_port            = MGREP_PORT.to_i
+  config.mgrep_port            = MGREP_PORT.to_s
+  config.mgrep_alt_host        = MGREP_HOST.to_s
+  config.mgrep_alt_port        = MGREP_PORT.to_s
   config.mgrep_dictionary_file = './test/data/dictionary.txt'
   config.annotator_redis_host  = REDIS_HOST.to_s
-  config.annotator_redis_port  = REDIS_PORT.to_i
+  config.annotator_redis_port  = REDIS_PORT.to_s
 end

rakelib/ontoportal_testkit.rake

@@ -0,0 +1,2 @@
+# Loads shared OntoPortal testkit rake tasks into this component.
+require "ontoportal/testkit/tasks"