Feature: Align Bioportal and AgroPortal - part 1 - Configuration code and Docker

.dockerignore

@@ -0,0 +1,25 @@
+.git/
+log/*
+!log/.keep
+app/assets/builds/*
+!app/assets/builds/.keep
+node_modules/
+public/assets/
+storage/*
+!storage/.keep
+tmp/*
+!tmp/.keep
+
+.bundle
+.byebug_history
+.dockerignore
+.env*
+!.env.example
+config/master.key
+docker-compose.override.yml
+yarn-error.log
+yarn-debug.log*
+.yarn-integrity
+
+config/credentials/*
+config/credentials.yml.enc

.env.sample

@@ -0,0 +1,43 @@
+##################### UI configuration ####################
+RAILS_ENV=development
+SITE=Testportal
+ORG=LIRMM
+ORG_URL=http://www.lirmm.fr
+
+UI_URL=http://localhost:3000
+API_URL=http://localhost:9393
+API_KEY=
+
+UI_THEME=ontoportal
+
+BIOMIXER_URL=
+BIOMIXER_APIKEY=
+
+ANNOTATOR_URL=
+
+FAIRNESS_DISABLED=false
+FAIRNESS_URL=
+
+NCBO_ANNOTATORPLUS_ENABLED=false
+NCBO_ANNOTATOR_URL=
+NCBO_API_KEY=
+
+[email protected]
+RELEASE_VERSION="OntoPortal Appliance 3.0.1"
+
+ANALYTICS_ID=
+USE_RECAPTCHA=false
+####################  Buidling the API for running tests ####################
+## 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"
+
+## Image repositroy from which the ontoportal api will be built
+API_IMAGE_REPOSITORY=agroportal
+## Image tag/version from which the ontoportal api will be built
+API_IMAGE_TAG=master
+
+

.gitignore

@@ -17,8 +17,9 @@ rerun.txt
 pickle-email-*.html
 config/bioportal_config*.rb
 config/database.yml
-config/secrets.yml
 config/deploy/*
+config/locales/en.rb
+config/secrets.yml
 **.DS_Store
 /public/**/cache/**
 /public/umls/*
@@ -28,23 +29,28 @@ nohup.out
 # Ignore editor files
 .idea
 *.swp
+.rbenv-gemsets
 
 .tags
 
 .tags_sorted_by_file
 
-config/newrelic.yml
-
 node_modules
-
-# Ignore keys for decrypting credentials
-/config/credentials/development.key
-/config/credentials/test.key
-/config/credentials/staging.key
-/config/credentials/production.key
-/config/credentials/appliance.key
+.env
+config/site_config.rb
+docker-sync.yml
+.docker-sync/daemon.log
+.docker-sync/daemon.pid
 
 /app/assets/builds/*
 !/app/assets/builds/.keep
 
 /node_modules
+
+# Encryption keys
+/config/master.key
+/config/credentials/development.key
+/config/credentials/test.key
+/config/credentials/staging.key
+/config/credentials/production.key
+/config/credentials/appliance.key

Dockerfile

@@ -0,0 +1,53 @@
+# Make sure it matches the Ruby version in .ruby-version and Gemfile
+ARG RUBY_VERSION=3.2.0
+FROM ruby:${RUBY_VERSION}-alpine
+
+# Install libvips for Active Storage preview support
+RUN apk add --no-cache build-base \
+                       libxml2-dev \
+                       libxslt-dev \
+                       mariadb-dev \
+                       git \
+                       tzdata \
+                       nodejs yarn \
+                       less \
+                       bash \
+                       docker \
+                       docker-compose \
+    && mkdir /node_modules
+
+# Rails app lives here
+WORKDIR /app
+
+# Set production environment
+ARG RAILS_ENV="production"
+ARG BUNDLE_WITHOUT="development test"
+
+ENV RAILS_LOG_TO_STDOUT="1" \
+    RAILS_SERVE_STATIC_FILES="true" \
+    RAILS_ENV="${RAILS_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 . .
+
+RUN bundle install
+RUN yarn install && yarn build
+
+
+
+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
+
+# Precompile bootsnap code for faster boot times
+RUN bundle exec bootsnap precompile --gemfile app/ lib/
+
+RUN SECRET_KEY_BASE_DUMMY="1" ./bin/rails assets:precompile
+
+ENV BINDING="0.0.0.0"
+EXPOSE 3000
+
+CMD ["bash"]