Update to latest AgroPortal code

.env.sample

@@ -1,4 +1,15 @@
 API_URL=http://localhost:9393
 ONTOLOGIES_LINKED_DATA_PATH=
 GOO_PATH=
-SPARQL_CLIENT_PATH=
+SPARQL_CLIENT_PATH=
+
+REDIS_GOO_CACHE_HOST=redis-ut
+REDIS_HTTP_CACHE_HOST=redis-ut
+REDIS_PERSISTENT_HOST=redis-ut
+
+## An ontology that will be imported in the starting of the API server
+STARTER_ONTOLOGY=STY
+## API key of a remote API used to download the starter ontology
+OP_API_KEY=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+## API url of the remote API used to download the starter ontology
+OP_API_URL="https://data.bioontology.org"

.github/workflows/deploy.yml

@@ -69,7 +69,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: 2.7.8 # Not needed with a .ruby-version file
+          ruby-version: 3.1.0 # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
       - name: get-deployment-config
         uses: actions/checkout@v3

.github/workflows/docker-image.yml

@@ -1,5 +1,4 @@
 name: Docker branch Images build
-
 on:
   push:
     branches:
@@ -9,48 +8,54 @@ on:
       - test
   release:
     types: [ published ]
+
 jobs:
   push_to_registry:
     name: Push Docker branch image to Docker Hub
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
+        with:
+          platforms: linux/amd64,linux/arm64
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Log in to the Container registry
-        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: |
             agroportal/ontologies_api
             ghcr.io/${{ github.repository }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64,linux/arm64
           build-args: |
-            RUBY_VERSION=2.7.8
+            RUBY_VERSION=3.1
+            BUILDPLATFORM=${{ github.job_name }}
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

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

@@ -2,15 +2,14 @@ name: Ruby Unit Tests
 
 on:
   push:
-  pull_request:
 
 jobs:
   test:
     strategy:
       fail-fast: false
       matrix:
-        goo-slice: [ '20', '100', '500' ]
-        ruby-version: [ '2.7' ]
+        goo-slice: [ '100' ]
+        ruby-version: [ '3.2.0' ]
         triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
     runs-on: ubuntu-latest
     steps:
@@ -28,11 +27,10 @@ jobs:
           ruby-version: ${{ matrix.ruby-version }}
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
       - name: Run unit tests
-        # unit tests are run inside a container
-        # http://docs.codecov.io/docs/testing-with-docker
         run: |
           ci_env=`bash <(curl -s https://codecov.io/env)`
-          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
+          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }}
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:

.ruby-version

@@ -0,0 +1 @@
+3.1.0

Dockerfile

@@ -1,29 +1,57 @@
-ARG RUBY_VERSION=3.0
-ARG DISTRO_NAME=bullseye
+# syntax=docker/dockerfile:1
 
-FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+# Build arguments with specific versions for better reproducibility
+ARG RUBY_VERSION=3.1
+ARG DISTRO_NAME=slim-bookworm
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
-  openjdk-11-jre-headless \
-  raptor2-utils \
-  wait-for-it \
-  libraptor2-dev \
-  && rm -rf /var/lib/apt/lists/*
-
-RUN mkdir -p /srv/ontoportal/ontologies_api
-RUN mkdir -p /srv/ontoportal/bundle
-COPY Gemfile* /srv/ontoportal/ontologies_api/
+FROM ruby:${RUBY_VERSION}-${DISTRO_NAME}
 
 WORKDIR /srv/ontoportal/ontologies_api
 
-RUN gem update --system 3.4.22 # the 3.4.22 can be removed if we support Ruby version > 3.0
+# Set environment variables
+ENV BUNDLE_PATH=/srv/ontoportal/bundle \
+    BUNDLE_JOBS=4 \
+    BUNDLE_RETRY=5 \
+    RAILS_ENV=production \
+    DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        ca-certificates \
+        openjdk-17-jre-headless \
+        raptor2-utils \
+        wait-for-it \
+        libraptor2-dev \
+        build-essential \
+         libxml2 \
+         libxslt-dev \
+         libmariadb-dev \
+         git \
+         curl \
+         libffi-dev \
+         file \
+         pandoc \
+     pkg-config && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
 RUN gem install bundler
-ENV BUNDLE_PATH=/srv/ontoportal/bundle
-RUN bundle install
 
-COPY . /srv/ontoportal/ontologies_api
-RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
-RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/production.rb
+COPY Gemfile* ./
+
+# Install dependencies
+RUN bundle install --jobs ${BUNDLE_JOBS} --retry ${BUNDLE_RETRY}
 
+# Copy application code
+COPY . .
+
+# Copy config files
+RUN cp config/environments/config.rb.sample config/environments/development.rb && \
+    cp config/environments/config.rb.sample config/environments/production.rb
+
+# Expose port
 EXPOSE 9393
+
+# Start command
 CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]

Gemfile

@@ -1,62 +1,65 @@
 source 'https://rubygems.org'
-gem 'activesupport', '~> 5'
-# see https://github.com/ncbo/ontologies_api/issues/69
+gem 'activesupport'
 gem 'bigdecimal'
-# gem 'faraday', '~> 1.9'
-gem 'json-schema', '~> 2.0'
+gem 'json-schema'
 gem 'multi_json'
 gem 'oj'
 gem 'parseconfig'
 gem 'rack'
-gem 'rake', '~> 10.0'
+gem 'rake'
 gem 'rexml' # Investigate why unicorn fails to start under ruby 3 without adding rexml gem to the Gemfile
-gem 'sinatra', '~> 1.0'
-gem 'sinatra-advanced-routes'
-gem 'sinatra-contrib', '~> 1.0'
+gem 'sinatra'
+gem 'rackup'
+
+github 'sinatra/sinatra' do
+  gem 'sinatra-contrib'
+end
+
 gem 'request_store'
 gem 'parallel'
-gem 'json-ld'
-gem 'google-protobuf', '3.25.3'
+gem 'google-protobuf'
+gem 'net-ftp'
+gem 'json-ld', '~> 3.2.0'
+gem 'rdf-raptor', github:'ruby-rdf/rdf-raptor', ref: '6392ceabf71c3233b0f7f0172f662bd4a22cd534' # use version 3.3.0 when available
 
 # Rack middleware
-gem 'ffi', '~> 1.16.3'
-gem 'rack-accept', '~> 0.4'
-gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
-gem 'rack-cache', '~> 1.13.0'
+gem 'ffi', '~> 1.15.0'
+gem 'rack-accept'
+gem 'rack-attack', require: 'rack/attack'
+gem 'rack-cache'
 gem 'rack-cors', require: 'rack/cors'
 # GitHub dependency can be removed when https://github.com/niko/rack-post-body-to-params/pull/6 is merged and released
 gem 'rack-post-body-to-params', github: 'palexander/rack-post-body-to-params', branch: 'multipart_support'
 gem 'rack-timeout'
-gem 'redis-rack-cache', '~> 2.0'
+gem 'redis-rack-cache'
 
 # Data access (caching)
 gem 'redis'
-gem 'redis-store', '~>1.10'
+gem 'redis-store'
 
 # Monitoring
-gem 'cube-ruby', require: 'cube'
 gem 'newrelic_rpm', group: [:default, :deployment]
 
 # HTTP server
 gem 'unicorn'
 gem 'unicorn-worker-killer'
 
 # Templating
-gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
-gem 'redcarpet'
+gem 'haml', '~> 5.2.2'
+gem 'rack-contrib'
+gem 'pandoc-ruby'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git', branch: 'development'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
-
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
-  gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
+  gem 'shotgun', github: 'syphax-bouazzouni/shotgun', branch: 'master'
   gem 'rubocop'
 end
 
@@ -77,12 +80,14 @@ end
 
 group :test do
   gem 'crack', '0.4.5'
-  gem 'minitest', '~> 5.0'
-  gem 'minitest-hooks', "~> 1.5"
+  gem 'minitest'
+  gem 'minitest-hooks'
   gem 'minitest-stub_any_instance'
+  gem 'minitest-reporters'
+  gem 'minitest-fail-fast'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-  gem 'webmock', '~> 3.19.1'
+  gem 'webmock'
   gem 'webrick'
 end