Sync with BioPortal release 6.20.0 and Alignement with Agroportal work

.dockerignore

@@ -1,4 +1,5 @@
 .git/
+.github/
 log/*
 !log/.keep
 app/assets/builds/*
@@ -21,5 +22,9 @@ yarn-error.log
 yarn-debug.log*
 .yarn-integrity
 
+# Ruby version is set in Dockerfile
+.ruby-version
+
 config/credentials/*
-config/credentials.yml.enc
+config/credentials.yml.enc
+config/deploy/*

.env.sample

@@ -40,4 +40,6 @@ API_IMAGE_REPOSITORY=agroportal
 ## Image tag/version from which the ontoportal api will be built
 API_IMAGE_TAG=master
 
-
+## Tests
+# List of Ontologies to test in test/controllers/ontologies_controller_test.rb
+# ONTOLOGIES_TO_TEST="NCIT,GO,SNOMEDCT"

.github/workflows/docker-image.yml

@@ -0,0 +1,40 @@
+name: Publish Docker Image to hub.docker.com
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: bioportal/bioportal_web_ui
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -1,53 +1,55 @@
 # Make sure it matches the Ruby version in .ruby-version and Gemfile
-ARG RUBY_VERSION=3.2.0
-FROM ruby:${RUBY_VERSION}-alpine
-
-# Install libvips for Active Storage preview support
-RUN apk add --no-cache build-base \
-                       libxml2-dev \
-                       libxslt-dev \
-                       mariadb-dev \
-                       git \
-                       tzdata \
-                       nodejs yarn \
-                       less \
-                       bash \
-                       docker \
-                       docker-compose \
-    && mkdir /node_modules
-
-# Rails app lives here
+ARG RUBY_VERSION=3.2
+FROM ruby:${RUBY_VERSION}-slim-bookworm
+
 WORKDIR /app
 
-# Set production environment
+RUN bash -c "set -o pipefail && apt-get update && \
+  apt-get install -y --no-install-recommends \
+     build-essential \
+     libxml2 \
+     libxslt-dev \
+     libmariadb-dev \
+     git \
+     curl \
+  && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key -o /etc/apt/keyrings/nodesource.asc \
+  && echo 'deb [signed-by=/etc/apt/keyrings/nodesource.asc] https://deb.nodesource.com/node_20.x nodistro main' | tee /etc/apt/sources.list.d/nodesource.list \
+  && apt-get update \
+  && apt-get install -y --no-install-recommends nodejs \
+  && corepack enable \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/* /usr/share/doc /usr/share/man \
+  && mkdir /node_modules"
+
 ARG RAILS_ENV="production"
+ARG NODE_ENV="production"
 ARG BUNDLE_WITHOUT="development test"
 
 ENV RAILS_LOG_TO_STDOUT="1" \
     RAILS_SERVE_STATIC_FILES="true" \
     RAILS_ENV="${RAILS_ENV}" \
+    NODE_ENV="${NODE_ENV}" \
     BUNDLE_PATH=/usr/local/bundle \
     BUNDLE_WITHOUT="${BUNDLE_WITHOUT}"
 
-RUN gem update --system 3.4.22 # the 3.4.22 can be removed if we support Ruby version > 3.0
-
-COPY . .
-
+#PATH="${PATH}:/node_modules/.bin"
+COPY Gemfile* .
 RUN bundle install
-RUN yarn install && yarn build
-
 
+COPY package.json *yarn* .
+RUN yarn install
 
-RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_production.rb
-RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_development.rb
-RUN cp config/database.yml.sample config/database.yml
+COPY . .
 
-# Precompile bootsnap code for faster boot times
-RUN bundle exec bootsnap precompile --gemfile app/ lib/
+RUN cp config/bioportal_config_env.rb.sample config/bioportal_config_production.rb \
+ && cp config/bioportal_config_env.rb.sample config/bioportal_config_development.rb \
+ && cp config/bioportal_config_env.rb.sample config/bioportal_config_test.rb \
+ && cp config/database.yml.sample config/database.yml
 
-RUN SECRET_KEY_BASE_DUMMY="1" ./bin/rails assets:precompile
+RUN if [ "${RAILS_ENV}" != "development" ]; then \
+  bundle exec bootsnap precompile --gemfile app/ lib/ && \
+  SECRET_KEY_BASE_DUMMY=1 ./bin/rails assets:precompile; fi
 
-ENV BINDING="0.0.0.0"
 EXPOSE 3000
 
-CMD ["bash"]
+CMD ["rails", "s"]

Gemfile

@@ -21,7 +21,7 @@ gem 'sassc-rails' # sass-rails replacement
 gem 'terser' # uglifier replacement
 
 # Bootstrap front-end framework
-gem 'bootstrap',  '~> 5.2.3'
+gem 'bootstrap', '~> 5.2.3'
 
 # jQuery integration for Rails
 gem 'jquery-rails'
@@ -67,7 +67,6 @@ gem 'dalli'
 gem 'graphql', '~> 2.0.27'
 gem 'graphql-client'
 
-
 # Haml template engine for Ruby on Rails
 gem 'haml', '~> 5.1'
 
@@ -104,12 +103,21 @@ gem 'flag-icons-rails', '~> 3.4'
 gem 'iso-639', '~> 0.3.6'
 
 # Custom API client
-gem 'ontologies_api_client', git: 'https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git', branch: 'master'
+gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.4.0'
+
+# compatibilty pin https://github.com/ncbo/bioportal_web_ui/issues/293
+gem 'base64', '0.1.0'
+gem 'rexml', '~> 3'
 
 # Ruby 2.7.8 pinned gems (to remove when migrating to Ruby >= 3.0)
-gem 'ffi', '~> 1.16.3'
-gem 'net-ftp', '~> 0.2.0', require: false
-gem 'net-http', '~> 0.3.2'
+# gem 'ffi', '~> 1.16.3'
+# gem 'net-ftp', '~> 0.2.0', require: false
+# gem 'net-http', '~> 0.3.2'
+
+gem 'ffi'
+gem 'net-ftp', require: false
+gem 'net-http'
+
 
 # Multi-Provider Authentication
 gem 'omniauth'
@@ -125,10 +133,6 @@ group :staging, :production, :appliance do
 
   # Error monitoring
   gem 'bugsnag', '~> 6.26'
-
-  # Logs in JSON format, useful for shipping logs to logstash
-  # gem 'rackstash', git: 'https://github.com/planio-gmbh/rackstash.git'
-  # gem 'logstash-logger'
 end
 
 group :development do