Infra/Refactor docker-based test runner and add linux container tests

.github/workflows/ruby-unit-test.yml

@@ -1,6 +1,12 @@
 name: Ruby Unit Test
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - '**'
+    tags-ignore:
+      - '**'   # ignore all tag pushes
+  pull_request:
 
 permissions:
   contents: read
@@ -13,11 +19,11 @@ jobs:
       fail-fast: false
       matrix:
         goo-slice: [ '100']
-        ruby-version: [ '3.2.0' ]
-        triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
+        ruby-version: [ '3.2' ]
+        triplestore: [ 'fs', 'ag', 'vo', 'gd' ]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install Dependencies
       run: sudo apt-get update && sudo apt-get -y install raptor2-utils
     - name: Set up Ruby
@@ -29,8 +35,8 @@ jobs:
       # tempoaray workaround for the config.rb file requirement
       run:  echo 'Goo.config do |config| end' > config/config.rb
     - name: List directory contents
-      run: ls -R ./test/data
+      run: ls -R ./test/fixtures
     - name: Run tests
       run: GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5

Dockerfile

@@ -0,0 +1,34 @@
+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 \
+    libxslt1-dev zlib1g-dev \
+    # openjdk-11-jre-headless \
+    raptor2-utils \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+COPY Gemfile* *.gemspec ./
+
+#Install the exact Bundler version from Gemfile.lock (if it exists)
+RUN gem update --system && \
+    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 --global no-document 'true'
+RUN bundle install --jobs 4 --retry 3
+
+COPY . ./
+
+CMD ["bundle", "exec", "rake"]

README.md

@@ -13,6 +13,42 @@ To see Goo in action browse to the following links:
 - [BioPortal New API Documentation](http://stagedata.bioontology.org/documentation)
 - [BioPortal New API Access](http://stagedata.bioontology.org/)
 
+## Tests
+
+Run the unit tests:
+
+```
+bundle exec rake test
+```
+
+Run docker-backed tests (host Ruby):
+
+```
+bundle exec rake test:docker:fs
+bundle exec rake test:docker:ag
+bundle exec rake test:docker:vo
+bundle exec rake test:docker:gd
+```
+
+Run docker-backed tests inside the Linux container:
+
+```
+bundle exec rake test:docker:fs:linux
+bundle exec rake test:docker:ag:linux
+bundle exec rake test:docker:vo:linux
+bundle exec rake test:docker:gd:linux
+```
+
+Start a shell in the Linux test container (default backend `fs`):
+
+```
+bundle exec rake test:docker:shell
+bundle exec rake test:docker:shell[ag]
+```
+
+Set `OP_KEEP_CONTAINERS=1` to keep services up after tests or shell exit.
+Set `OP_TEST_DOCKER_BACKEND=ag` (or `fs`, `vo`, `gd`) to change the default backend for `test:docker:shell`, `test:docker:up`, and `test:docker:down`.
+
 
 ## Schema Definitions (DSL)
 

config/config.rb.sample

@@ -1,23 +1,23 @@
 Goo.config do |config|
   # 4store
   config.goo_backend_name    = '4store'
-  config.goo_port            = 8080
+  config.goo_port            =  9000
   config.goo_host            = 'localhost'
   config.goo_path_query      = '/sparql/'
   config.goo_path_data       = '/data/'
   config.goo_path_update     = '/update/'
 
   # AllegroGraph
-  # config.goo_backend_name  = 'AG'
+  # config.goo_backend_name  = 'allegrograph'
   # config.goo_port          = 10035
   # config.goo_host          = 'localhost'
   # config.goo_path_query    = "/repositories/ontoportal"
   # config.goo_path_data     = "/repositories/ontoportal/statements/"
   # config.goo_path_update   = "/repositories/ontoportal/statements/"
 
   config.search_server_url   = 'http://localhost:8983/solr/'
-  config.redis_host          = 'localhost'
-  config.redis_port          = 6379
+  config.goo_redis_host      = 'localhost'
+  config.goo_redis_port      = 6379
   config.bioportal_namespace = 'http://data.bioontology.org/'
   config.queries_debug       = false
 end

dev/compose/linux/ag.yml

@@ -0,0 +1,16 @@
+services:
+  test-linux:
+    environment:
+      GOO_BACKEND_NAME: allegrograph
+      GOO_PORT: 10035
+      GOO_HOST: agraph-ut
+      GOO_PATH_QUERY: /repositories/ontoportal_test
+      GOO_PATH_DATA: /repositories/ontoportal_test/statements
+      GOO_PATH_UPDATE: /repositories/ontoportal_test/statements
+    depends_on:
+      solr-ut:
+        condition: service_healthy
+      redis-ut:
+        condition: service_healthy
+      agraph-ut:
+        condition: service_healthy

dev/compose/linux/fs.yml

@@ -0,0 +1,13 @@
+services:
+  test-linux:
+    environment:
+      GOO_BACKEND_NAME: '4store'
+      GOO_HOST: 4store-ut
+      GOO_PORT: 9000
+    depends_on:
+      solr-ut:
+        condition: service_healthy
+      redis-ut:
+        condition: service_healthy
+      4store-ut:
+        condition: service_healthy

dev/compose/linux/gd.yml

@@ -0,0 +1,19 @@
+services:
+  test-linux:
+    environment:
+      GOO_BACKEND_NAME: graphdb
+      GOO_PORT: 7200
+      GOO_HOST: graphdb-ut
+      GOO_PATH_QUERY: /repositories/ontoportal_test
+      GOO_PATH_DATA: /repositories/ontoportal_test/statements
+      GOO_PATH_UPDATE: /repositories/ontoportal_test/statements
+    depends_on:
+      solr-ut:
+        condition: service_healthy
+      redis-ut:
+        condition: service_healthy
+      graphdb-ut:
+        condition: service_healthy
+
+  graphdb-ut:
+    ports:

dev/compose/linux/no-ports.yml

@@ -0,0 +1,13 @@
+services:
+  redis-ut:
+    ports: []
+  solr-ut:
+    ports: []
+  agraph-ut:
+    ports: []
+  4store-ut:
+    ports: []
+  virtuoso-ut:
+    ports: []
+  graphdb-ut:
+    ports: []

dev/compose/linux/vo.yml

@@ -0,0 +1,16 @@
+services:
+  test-linux:
+    environment:
+      GOO_BACKEND_NAME: 'virtuoso'
+      GOO_HOST: virtuoso-ut
+      GOO_PORT: 8890
+      GOO_PATH_QUERY: /sparql
+      GOO_PATH_DATA: /sparql
+      GOO_PATH_UPDATE: /sparql
+    depends_on:
+      solr-ut:
+        condition: service_healthy
+      redis-ut:
+        condition: service_healthy
+      virtuoso-ut:
+        condition: service_healthy