add ontoportal testkit

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

@@ -0,0 +1,62 @@
+name: Docker Unit Tests
+
+on:
+  push:
+    branches:
+      - '**'
+    tags-ignore:
+      - '**'
+  pull_request:
+
+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
+
+      - name: Checkout ontoportal_testkit
+        uses: actions/checkout@v4
+        with:
+          repository: alexskr/ontoportal_testkit
+          path: .tooling/ontoportal_testkit
+
+      - name: Run unit tests in linux container
+        env:
+          CI: "true"
+          TESTOPTS: "-v"
+          BACKEND: ${{ matrix.backend }}
+        run: |
+          ruby -I .tooling/ontoportal_testkit/lib -e 'require "rake"; require "ontoportal/testkit/tasks"; Rake::Task["test:docker:#{ENV.fetch("BACKEND")}:linux"].invoke'
+
+      - 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-linux
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services:
+  - mgrep

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

@@ -17,6 +17,7 @@ group :test do
   gem 'pry'
   gem 'simplecov'
   gem 'simplecov-cobertura' # for codecov.io
+  gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main'
 end
 
 # NCBO gems (can be from a local dev path or from rubygems/git)

Gemfile.lock

@@ -1,6 +1,14 @@
+GIT
+  remote: https://github.com/alexskr/ontoportal_testkit.git
+  revision: c1eb12818b208f6d9ed46c6793e6115135052f16
+  branch: main
+  specs:
+    ontoportal_testkit (0.1.0)
+      rake (>= 13.0)
+
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 13a8559a2346cc8320d7d36046646907bfa8a27c
+  revision: f6310650f578200f0e1465bd013dc5a737ef0170
   branch: ontoportal-lirmm-development
   specs:
     goo (0.0.2)
@@ -18,7 +26,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 3204c0a830d344eb9ae1db82c22b46be1ef468b3
+  revision: 637fdfcfc0f9201a631b4d827d34aa8993325565
   branch: chore/ontoportal-lirmm-goo-compat
   specs:
     ontologies_linked_data (0.0.1)
@@ -148,7 +156,7 @@ GEM
       uri (>= 0.11.1)
     net-http-persistent (4.0.8)
       connection_pool (>= 2.2.4, < 4)
-    net-imap (0.6.2)
+    net-imap (0.6.3)
       date
       net-protocol
     net-pop (0.1.2)
@@ -245,7 +253,6 @@ PLATFORMS
   arm-linux-gnu
   arm-linux-musl
   arm64-darwin
-  ruby
   x86-linux-gnu
   x86-linux-musl
   x86_64-darwin
@@ -263,6 +270,7 @@ DEPENDENCIES
   minitest-reporters
   oj (~> 3.0)
   ontologies_linked_data!
+  ontoportal_testkit!
   parallel
   pry
   rake
@@ -327,14 +335,15 @@ CHECKSUMS
   net-ftp (0.3.9) sha256=307817ccf7f428f79d083f7e36dbb46a9d1d375e0d23027824de1866f0b13b65
   net-http (0.9.1) sha256=25ba0b67c63e89df626ed8fac771d0ad24ad151a858af2cc8e6a716ca4336996
   net-http-persistent (4.0.8) sha256=ef3de8319d691537b329053fae3a33195f8b070bbbfae8bf1a58c796081960e6
-  net-imap (0.6.2) sha256=08caacad486853c61676cca0c0c47df93db02abc4a8239a8b67eb0981428acc6
+  net-imap (0.6.3) sha256=9bab75f876596d09ee7bf911a291da478e0cd6badc54dfb82874855ccc82f2ad
   net-pop (0.1.2) sha256=848b4e982013c15b2f0382792268763b748cce91c9e91e36b0f27ed26420dff3
   net-protocol (0.2.2) sha256=aa73e0cba6a125369de9837b8d8ef82a61849360eba0521900e2c3713aa162a8
   net-smtp (0.5.1) sha256=ed96a0af63c524fceb4b29b0d352195c30d82dd916a42f03c62a3a70e5b70736
   netrc (0.11.0) sha256=de1ce33da8c99ab1d97871726cba75151113f117146becbe45aa85cb3dabee3f
   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

config/config.test.rb

@@ -16,20 +16,27 @@
 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_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.goo_redis_host                = REDIS_HOST.to_s
+  config.goo_redis_port                = REDIS_PORT.to_i
+  config.http_redis_host               = REDIS_HOST.to_s
+  config.http_redis_port               = REDIS_PORT.to_i
+  config.ontology_analytics_redis_host = REDIS_HOST.to_s
+  config.ontology_analytics_redis_port = REDIS_PORT.to_i
+  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_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

rakelib/ontoportal_testkit.rake

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

test/test_case.rb

@@ -16,7 +16,7 @@
 end
 
 require_relative '../lib/ncbo_annotator'
-require_relative '../config/config'
+require_relative '../config/config.test'
 
 # Check to make sure you want to run if not pointed at localhost
 safe_host = Regexp.new(/localhost|-ut|ncbo-dev*|ncbo-unittest*/)