ncbo · alexskr · Mar 9, 2026 · Mar 7, 2026 · Mar 7, 2026 · Mar 7, 2026
diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
diff --git a/.github/workflows/testkit-unit-tests.yml b/.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
diff --git a/.ontoportal-testkit.yml b/.ontoportal-testkit.yml
@@ -0,0 +1,9 @@
+component_name: ontologies_api
+app_service: test-container
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services:
+  - mgrep
diff --git a/Dockerfile b/Dockerfile
@@ -1,24 +1,20 @@
-ARG RUBY_VERSION=3.1
-ARG DISTRO_NAME=bullseye
+ARG RUBY_VERSION=3.2
+ARG DISTRO=bullseye
+ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO}
+FROM ${TESTKIT_BASE_IMAGE}
 
-FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+WORKDIR /app
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
-  openjdk-11-jre-headless \
-  raptor2-utils \
-  && rm -rf /var/lib/apt/lists/*
+COPY Gemfile* *.gemspec ./
 
-RUN mkdir -p /srv/ontoportal/ontologies_api
-RUN mkdir -p /srv/ontoportal/bundle
-COPY Gemfile* /srv/ontoportal/ontologies_api/
+# 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
 
-WORKDIR /srv/ontoportal/ontologies_api
+RUN bundle install --jobs 4 --retry 3
 
-ENV BUNDLE_PATH=/srv/ontoportal/bundle
-RUN bundle install
+COPY . ./
 
-COPY . /srv/ontoportal/ontologies_api
-RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
-
-EXPOSE 9393
 CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]
diff --git a/Gemfile b/Gemfile
@@ -78,8 +78,9 @@ group :test do
   gem 'crack', '0.4.5'
   gem 'minitest'
   gem 'minitest-hooks'
-  gem 'minitest-stub_any_instance'
   gem 'minitest-reporters'
+  gem 'minitest-stub_any_instance'
+  gem 'ontoportal_testkit', github: 'alexskr/ontoportal_testkit', branch: 'main'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,3 +1,11 @@
+GIT
+  remote: https://github.com/alexskr/ontoportal_testkit.git
+  revision: 9944d1d5f57b11e8ae9ccda11a83c7c5b2348870
+  branch: main
+  specs:
+    ontoportal_testkit (0.1.0)
+      rake (>= 13.0)
+
 GIT
   remote: https://github.com/ncbo/goo.git
   revision: 93c8ade0f7ef56fa4ad4fbdee0f9c6c4553be287
@@ -183,15 +191,9 @@ GEM
       faraday (~> 2.0)
     ffi (1.17.3)
     ffi (1.17.3-aarch64-linux-gnu)
-    ffi (1.17.3-aarch64-linux-musl)
-    ffi (1.17.3-arm-linux-gnu)
-    ffi (1.17.3-arm-linux-musl)
     ffi (1.17.3-arm64-darwin)
-    ffi (1.17.3-x86-linux-gnu)
-    ffi (1.17.3-x86-linux-musl)
     ffi (1.17.3-x86_64-darwin)
     ffi (1.17.3-x86_64-linux-gnu)
-    ffi (1.17.3-x86_64-linux-musl)
     fugit (1.12.1)
       et-orbi (~> 1.4)
       raabro (~> 1.4)
@@ -224,7 +226,6 @@ GEM
     google-protobuf (3.25.3)
     google-protobuf (3.25.3-aarch64-linux)
     google-protobuf (3.25.3-arm64-darwin)
-    google-protobuf (3.25.3-x86-linux)
     google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.8.0)
@@ -250,9 +251,6 @@ GEM
     grpc (1.70.1-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.70.1-x86-linux)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
     grpc (1.70.1-x86_64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
@@ -515,20 +513,11 @@ GEM
     webrick (1.9.2)
 
 PLATFORMS
-  aarch64-linux
   aarch64-linux-gnu
-  aarch64-linux-musl
-  arm-linux-gnu
-  arm-linux-musl
   arm64-darwin
   ruby
-  x86-linux
-  x86-linux-gnu
-  x86-linux-musl
   x86_64-darwin
-  x86_64-linux
   x86_64-linux-gnu
-  x86_64-linux-musl
 
 DEPENDENCIES
   activesupport
@@ -559,6 +548,7 @@ DEPENDENCIES
   net-ftp
   oj
   ontologies_linked_data!
+  ontoportal_testkit!
   pandoc-ruby
   parallel
   parseconfig
@@ -629,15 +619,9 @@ CHECKSUMS
   faraday-retry (2.4.0) sha256=7b79c48fb7e56526faf247b12d94a680071ff40c9fda7cf1ec1549439ad11ebe
   ffi (1.17.3) sha256=0e9f39f7bb3934f77ad6feab49662be77e87eedcdeb2a3f5c0234c2938563d4c
   ffi (1.17.3-aarch64-linux-gnu) sha256=28ad573df26560f0aedd8a90c3371279a0b2bd0b4e834b16a2baa10bd7a97068
-  ffi (1.17.3-aarch64-linux-musl) sha256=020b33b76775b1abacc3b7d86b287cef3251f66d747092deec592c7f5df764b2
-  ffi (1.17.3-arm-linux-gnu) sha256=5bd4cea83b68b5ec0037f99c57d5ce2dd5aa438f35decc5ef68a7d085c785668
-  ffi (1.17.3-arm-linux-musl) sha256=0d7626bb96265f9af78afa33e267d71cfef9d9a8eb8f5525344f8da6c7d76053
   ffi (1.17.3-arm64-darwin) sha256=0c690555d4cee17a7f07c04d59df39b2fba74ec440b19da1f685c6579bb0717f
-  ffi (1.17.3-x86-linux-gnu) sha256=868a88fcaf5186c3a46b7c7c2b2c34550e1e61a405670ab23f5b6c9971529089
-  ffi (1.17.3-x86-linux-musl) sha256=f0286aa6ef40605cf586e61406c446de34397b85dbb08cc99fdaddaef8343945
   ffi (1.17.3-x86_64-darwin) sha256=1f211811eb5cfaa25998322cdd92ab104bfbd26d1c4c08471599c511f2c00bb5
   ffi (1.17.3-x86_64-linux-gnu) sha256=3746b01f677aae7b16dc1acb7cb3cc17b3e35bdae7676a3f568153fb0e2c887f
-  ffi (1.17.3-x86_64-linux-musl) sha256=086b221c3a68320b7564066f46fed23449a44f7a1935f1fe5a245bd89d9aea56
   fugit (1.12.1) sha256=5898f478ede9b415f0804e42b8f3fd53f814bd85eebffceebdbc34e1107aaf68
   gapic-common (1.1.0) sha256=3270ab3c5135012a4ab4d8848f945cf35014192f24504cdb40c66fc67f1beaa3
   get_process_mem (0.2.7) sha256=4afd3c3641dd6a817c09806c7d6d509d8a9984512ac38dea8b917426bbf77eba
@@ -651,7 +635,6 @@ CHECKSUMS
   google-protobuf (3.25.3) sha256=39bd97cbc7631905e76cdf8f1bf3dda1c3d05200d7e23f575aced78930fbddd6
   google-protobuf (3.25.3-aarch64-linux) sha256=5ea9d20d60e5d3bef8d881b426946345e5ac6cf4779ac81cd900e45f40567243
   google-protobuf (3.25.3-arm64-darwin) sha256=c42cddd21c4f09fd756fe0efd70ab6c8006dd67ffbb04e99fe7310f49923d18c
-  google-protobuf (3.25.3-x86-linux) sha256=7a0e74f14affbce6024595cdb55e7e8c5a51716f0bb11b103c63cbe3a3a0e348
   google-protobuf (3.25.3-x86_64-darwin) sha256=13d27e96e89835f642c444e32414fd50fabc29a125d78760ad067d6536214f02
   google-protobuf (3.25.3-x86_64-linux) sha256=ceeba879d9313a2bd0600a97d6fe3cf529a9b37d12ca026f891996c118b7ffb2
   googleapis-common-protos (1.8.0) sha256=bfe89cb75d1a8f13e4591d262a20333e145481d803adb74dd13ac0517decdffe
@@ -660,7 +643,6 @@ CHECKSUMS
   grpc (1.70.1) sha256=174594605c96df3caed44a83221665aa6e11f554e56028f89bef82c07ffb83cb
   grpc (1.70.1-aarch64-linux) sha256=48e0b22b8b96e61ca7054a7fea894a4845498e6bf366b50eff03e588f714ed96
   grpc (1.70.1-arm64-darwin) sha256=eeb6758dd58135e4e5fcd78726b9a18d34d7313e41bc81528ff4b3dce65cf525
-  grpc (1.70.1-x86-linux) sha256=cb7921614fec4f90f888637736b7ede85305ad94a869f736176f9ebede98c4f1
   grpc (1.70.1-x86_64-darwin) sha256=628cb929542c277b6e5f638b6b8575b3bdcde250a2a70bddf8c0be1bf77e6781
   grpc (1.70.1-x86_64-linux) sha256=ed12eea749127119c9761a58ba17ce92aadbc35b0b4fa27e4bd8ec84047d63be
   haml (5.2.2) sha256=6e759246556145642ef832d670fc06f9bd8539159a0e600847a00291dd7aae0c
@@ -712,6 +694,7 @@ 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)
   os (1.1.4) sha256=57816d6a334e7bd6aed048f4b0308226c5fb027433b67d90a9ab435f35108d3f
   ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912
   pandoc-ruby (2.1.10) sha256=37653d6b5e71657fb25b3cb230e6eebbfb8c925c7f1fcf69dfb6b929d12b74b2

diff --git a/config/environments/test.rb b/config/environments/test.rb
@@ -1,31 +1,16 @@
 # conig file for unit tests
 
-# GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "AG"
-# GOO_HOST         = ENV.include?("GOO_HOST")         ? ENV["GOO_HOST"]         : "localhost"
-# GOO_PATH_QUERY   = ENV.include?("GOO_PATH_QUERY")   ? ENV["GOO_PATH_QUERY"]   : "/repositories/bioportal"
-# GOO_PATH_DATA    = ENV.include?("GOO_PATH_DATA")    ? ENV["GOO_PATH_DATA"]    : "/repositories/bioportal/statements"
-# GOO_PATH_UPDATE  = ENV.include?("GOO_PATH_UPDATE")  ? ENV["GOO_PATH_UPDATE"]  : "/repositories/bioportal/statements"
-# GOO_PORT         = ENV.include?("GOO_PORT")         ? ENV["GOO_PORT"]         : 10035
-
-GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "4store"
-GOO_HOST         = ENV.include?("GOO_HOST")         ? ENV["GOO_HOST"]         : "localhost"
-GOO_PATH_DATA    = ENV.include?("GOO_PATH_DATA")    ? ENV["GOO_PATH_DATA"]    : "/data/"
-GOO_PATH_QUERY   = ENV.include?("GOO_PATH_QUERY")   ? ENV["GOO_PATH_QUERY"]   : "/sparql/"
-GOO_PATH_UPDATE  = ENV.include?("GOO_PATH_UPDATE")  ? ENV["GOO_PATH_UPDATE"]  : "/update/"
-GOO_PORT         = ENV.include?("GOO_PORT")         ? ENV["GOO_PORT"]         : 9000
-
-MGREP_DICTIONARY_FILE = ENV.include?("MGREP_DICTIONARY_FILE") ? ENV["MGREP_DICTIONARY_FILE"] : "./test/data/dictionary.txt"
-MGREP_HOST       = ENV.include?("MGREP_HOST")       ? ENV["MGREP_HOST"]       : "localhost"
-MGREP_PORT       = ENV.include?("MGREP_PORT")       ? ENV["MGREP_PORT"]       : 55555
-
-REDIS_GOO_CACHE_HOST  = ENV.include?("REDIS_GOO_CACHE_HOST")  ? ENV["REDIS_GOO_CACHE_HOST"]  : "localhost"
-REDIS_HTTP_CACHE_HOST = ENV.include?("REDIS_HTTP_CACHE_HOST") ? ENV["REDIS_HTTP_CACHE_HOST"] : "localhost"
-REDIS_PERSISTENT_HOST = ENV.include?("REDIS_PERSISTENT_HOST") ? ENV["REDIS_PERSISTENT_HOST"] : "localhost"
-REDIS_PORT            = ENV.include?("REDIS_PORT")            ? ENV["REDIS_PORT"]            : 6379
-REPORT_PATH           = ENV.include?("REPORT_PATH")           ? ENV["REPORT_PATH"]           : "./test/ontologies_report.json"
-REPOSITORY_FOLDER     = ENV.include?("REPOSITORY_FOLDER")     ? ENV["REPOSITORY_FOLDER"]     : "./test/data/ontology_files/repo"
-SOLR_PROP_SEARCH_URL  = ENV.include?("SOLR_PROP_SEARCH_URL")  ? ENV["SOLR_PROP_SEARCH_URL"]  : "http://localhost:8983/solr"
-SOLR_TERM_SEARCH_URL  = ENV.include?("SOLR_TERM_SEARCH_URL")  ? ENV["SOLR_TERM_SEARCH_URL"]  : "http://localhost:8983/solr"
+GOO_BACKEND_NAME  = ENV.include?("GOO_BACKEND_NAME")  ? ENV["GOO_BACKEND_NAME"]  : "4store"
+GOO_HOST          = ENV.include?("GOO_HOST")          ? ENV["GOO_HOST"]          : "localhost"
+GOO_PATH_DATA     = ENV.include?("GOO_PATH_DATA")     ? ENV["GOO_PATH_DATA"]     : "/data/"
+GOO_PATH_QUERY    = ENV.include?("GOO_PATH_QUERY")    ? ENV["GOO_PATH_QUERY"]    : "/sparql/"
+GOO_PATH_UPDATE   = ENV.include?("GOO_PATH_UPDATE")   ? ENV["GOO_PATH_UPDATE"]   : "/update/"
+GOO_PORT          = ENV.include?("GOO_PORT")          ? ENV["GOO_PORT"]          : 9000
+MGREP_HOST        = ENV.include?("MGREP_HOST")        ? ENV["MGREP_HOST"]        : "localhost"
+MGREP_PORT        = ENV.include?("MGREP_PORT")        ? ENV["MGREP_PORT"]        : 55556
+REDIS_HOST        = ENV.include?("REDIS_HOST")        ? ENV["REDIS_HOST"]        : "localhost"
+REDIS_PORT        = ENV.include?("REDIS_PORT")        ? ENV["REDIS_PORT"]        : 6379
+SEARCH_SERVER_URL = ENV.include?('SEARCH_SERVER_URL') ? ENV['SEARCH_SERVER_URL'] : 'http://localhost:8983/solr'
 
 LinkedData.config do |config|
   config.goo_backend_name              = GOO_BACKEND_NAME.to_s
@@ -34,16 +19,15 @@
   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_GOO_CACHE_HOST.to_s
+  config.goo_redis_host                = REDIS_HOST.to_s
   config.goo_redis_port                = REDIS_PORT.to_i
-  config.http_redis_host               = REDIS_HTTP_CACHE_HOST.to_s
+  config.http_redis_host               = REDIS_HOST.to_s
   config.http_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
-  #config.enable_notifications          = false
+  config.search_server_url             = SEARCH_SERVER_URL.to_s
+  config.property_search_server_url    = SEARCH_SERVER_URL.to_s
 
   # Ontology analytics
-  config.ontology_analytics_redis_host  = REDIS_PERSISTENT_HOST.to_s
+  config.ontology_analytics_redis_host  = REDIS_HOST.to_s
   config.ontology_analytics_redis_port  = REDIS_PORT.to_i
   config.ontology_analytics_redis_field = 'test_analytics'
   config.oauth_providers = {
@@ -67,20 +51,18 @@
 end
 
 Annotator.config do |config|
-  config.annotator_redis_host  = REDIS_PERSISTENT_HOST.to_s
+  config.annotator_redis_host  = REDIS_HOST.to_s
   config.annotator_redis_port  = REDIS_PORT.to_i
   config.mgrep_host            = MGREP_HOST.to_s
   config.mgrep_port            = MGREP_PORT.to_i
-  config.mgrep_dictionary_file = MGREP_DICTIONARY_FILE.to_s
 end
 
 LinkedData::OntologiesAPI.config do |config|
-  config.http_redis_host = REDIS_HTTP_CACHE_HOST.to_s
+  config.http_redis_host = REDIS_HOST.to_s
   config.http_redis_port = REDIS_PORT.to_i
 end
 
 NcboCron.config do |config|
-  config.redis_host = REDIS_PERSISTENT_HOST.to_s
+  config.redis_host = REDIS_HOST.to_s
   config.redis_port = REDIS_PORT.to_i
-#  config.ontology_report_path = REPORT_PATH
 end