Feature: Align to AgroPortal 3.0

.dockerignore

@@ -1,6 +1,7 @@
 # Git
 .git
 .gitignore
+.github
 create_permissions.log
 # Logs
 log/*
@@ -9,4 +10,8 @@ tmp/*
 # Editor temp files
 *.swp
 *.swo
-test/solr
+coverage
+# Ignore generated test data
+test/data/uploaded_ontologies/**/*
+test/data/ontology_files/repo/**/*
+test/log

.github/workflows/deploy.yml

@@ -1,85 +1,92 @@
-# Workflow for deploying ontologies_api to stage/prod systems via capistrano.
-# This workflow runs after a successeful execution of the unit test workflow and it
-# can also be triggered manually.
+# Workflow to deploy OntoPortal API to stage/prod systems
 #
 # Required github secrets:
 #
-# CONFIG_REPO - github repo containing config and customizations for the API. Format 'author/private_config_repo'
+# CONFIG_REPO - github repo containing config and customizations for API. Format 'author/private_config_repo'
 # it is used for getting capistrano deployment configuration for stages on the github actions runner and
-# PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the remote servers for pulling configs.
+# PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the API hosts for pulling configs.
 #
-# GH_PAT - github Personal Access Token for accessing PRIVATE_CONFIG_REPO
+# GH_PAT - github Personal Access Token for accessing private config repo
 #
-# SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if app servers are hosted on private network.
+# SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if API nodes live on private network.
+# SSH_JUMPHOST_USER - username  to use to connect to the ssh jump/proxy.
 #
-# DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/deploy_id_rsa_enc (see miloserdow/capistrano-deploy)
-# this SSH key is used for accessing jump host, UI nodes, and private github repo.
+# DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/
+# this SSH key is used for accessing jump host, API nodes, and private github repo.
 
 name: Capistrano Deployment
 # Controls when the action will run.
 on:
-  # Trigger deployment to staging after unit test action completes
-  workflow_run:
-    workflows: ["Ruby Unit Tests"]
-    types:
-      - completed
-    branches: [master, develop]
+  push:
+    branches:
+      - stage
+      - test
   # Allows running this workflow manually from the Actions tab
   workflow_dispatch:
-    branches: [master, develop]
     inputs:
       BRANCH:
-        description: 'Branch/tag to deploy'
-        default: develop
+        description: "Branch/tag to deploy"
+        options:
+          - stage
+          - test
+          - master
+        default: stage
         required: true
       environment:
-        description: 'target environment to deploy to'
+        description: "target environment to deploy to"
         type: choice
         options:
           - staging
-          - production
-        default: staging
-
+          - agroportal
+          - test
+        default: stage
 jobs:
   deploy:
     runs-on: ubuntu-latest
-    # run deployment only if "Ruby Unit Tests" workflow completes sucessefully or when manually triggered
-    if: ${{ (github.event.workflow_run.conclusion == 'success') || (github.event_name == 'workflow_dispatch') }}
     env:
-      BUNDLE_WITHOUT: default #install gems required primarily for the deployment in order to speed this workflow
+      BUNDLE_WITHOUT: default #install gems required primarely for deployment in order to speed up workflow
       PRIVATE_CONFIG_REPO: ${{ format('[email protected]:{0}.git', secrets.CONFIG_REPO) }}
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-    - name: set branch/tag and environment to deploy from inputs
-      run: |
-        # workflow_dispatch default input doesn't get set on push so we need to set defaults
-        # via shell parameter expansion
-        # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g
-        USER_INPUT_BRANCH=${{ inputs.branch }}
-        echo "BRANCH=${USER_INPUT_BRANCH:-develop}" >> $GITHUB_ENV
-        USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
-        echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
-    - uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: 2.7.6 # 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
-      with:
-        repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
-        token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
-        path:  deploy_config
-    - name: copy-deployment-config
-      run:  cp -r deploy_config/ontologies_api/* .
-    # add ssh hostkey so that capistrano doesn't complain
-    - name: Add jumphost's hostkey to Known Hosts
-      run: |
-        mkdir -p ~/.ssh
-        ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts
-      shell: bash
-    - uses: miloserdow/capistrano-deploy@master
-      with:
-        target: ${{ env.TARGET }} # which environment to deploy
-        deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project
+      - name: set branch/tag and environment to deploy from inputs
+        run: |
+          # workflow_dispatch default input doesn't get set on push so we need to set defaults
+          # via shell parameter expansion
+          # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g
+          USER_INPUT_BRANCH=${{ inputs.branch }}
+          echo "BRANCH=${USER_INPUT_BRANCH:github.head_ref:-master}" >> $GITHUB_ENV
+
+          USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
+          echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV
+
+          CONFIG_REPO=${{ secrets.CONFIG_REPO }}
+          GH_PAT=${{ secrets.GH_PAT }}
+          echo "PRIVATE_CONFIG_REPO=https://${GH_PAT}@github.com/${CONFIG_REPO}" >> $GITHUB_ENV
+
+          echo "SSH_JUMPHOST=${{ secrets.SSH_JUMPHOST }}" >> $GITHUB_ENV
+          echo "SSH_JUMPHOST_USER=${{ secrets.SSH_JUMPHOST_USER }}" >> $GITHUB_ENV
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 2.7.8 # 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
+        with:
+          repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
+          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
+          path: deploy_config
+      - name: copy-deployment-config
+        run: cp -r deploy_config/ontologies_api/${{ inputs.environment }}/* .
+        # add ssh hostkey so that capistrano doesn't complain
+      - name: Add jumphost's hostkey to Known Hosts
+        run: |
+          mkdir -p ~/.ssh
+          echo "${{ secrets.SSH_JUMPHOST }}"
+          ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts
+        shell: bash
+      - uses: miloserdow/capistrano-deploy@master
+        with:
+          target: ${{ env.TARGET }} # which environment to deploy
+          deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project

.gitignore

@@ -36,7 +36,6 @@ config/environments/*
 !config/environments/config.rb.sample
 
 #ignore capistrano deployment
-config/deploy/*
 config/*.p12
 
 # Ignore generated test data
@@ -56,8 +55,6 @@ test/data/ontology_files/repo/**/*
 
 *.swp
 
-.ruby-version
-
 config/environments/console.rb
 
 config/environments/development.rb.sample

.ruby-version

@@ -0,0 +1 @@
+3.0.6

Capfile

@@ -16,12 +16,12 @@ install_plugin Capistrano::SCM::Git
 #   https://github.com/capistrano/rails
 #
 # require 'capistrano/rvm'
-# require 'capistrano/rbenv'
+require 'capistrano/rbenv'
 # require 'capistrano/chruby'
 require 'capistrano/bundler'
 # require 'capistrano/rails/assets'
 # require 'capistrano/rails/migrations'
 require 'capistrano/locally'
-
+require 'new_relic/recipes' # announce deployments in NewRelic
 # Loads custom tasks from `lib/capistrano/tasks' if you have any defined.
 Dir.glob('lib/capistrano/tasks/*.cap').each { |r| import r }

Dockerfile

@@ -1,4 +1,4 @@
-ARG RUBY_VERSION
+ARG RUBY_VERSION=3.0
 ARG DISTRO_NAME=bullseye
 
 FROM ruby:$RUBY_VERSION-$DISTRO_NAME

Gemfile

@@ -1,25 +1,25 @@
 source 'https://rubygems.org'
-
-gem 'activesupport', '~> 3.2'
+gem 'activesupport', '~> 5'
 # see https://github.com/ncbo/ontologies_api/issues/69
-gem 'bigdecimal', '1.4.2'
-gem 'faraday', '~> 1.9'
+gem 'bigdecimal'
+# gem 'faraday', '~> 1.9'
 gem 'json-schema', '~> 2.0'
-gem 'multi_json', '~> 1.0'
+gem 'multi_json'
 gem 'oj'
 gem 'parseconfig'
 gem 'rack'
 gem 'rake', '~> 10.0'
+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 'request_store'
 gem 'parallel'
 gem 'json-ld'
-
+gem 'google-protobuf', '3.25.3'
 
 # Rack middleware
-gem 'ffi', '~> 1.15.5'
+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'
@@ -35,7 +35,7 @@ gem 'redis-store', '~>1.10'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
-gem 'newrelic_rpm'
+gem 'newrelic_rpm', group: [:default, :deployment]
 
 # HTTP server
 gem 'unicorn'
@@ -53,16 +53,21 @@ gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'developm
 gem 'ontologies_linked_data', git: 'https://github.com/lifewatch-eric/ontologies_linked_data.git', branch: 'master'
 gem 'ncbo_cron', git: 'https://github.com/lifewatch-eric/ncbo_cron.git', branch: 'master'
 
+
 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 'rubocop'
+end
+
+group :deployment do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
   gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false
   gem 'capistrano', '~> 3', require: false
   gem 'capistrano-bundler', require: false
   gem 'capistrano-locally', require: false
   gem 'capistrano-rbenv', require: false
   gem 'ed25519', '>= 1.2', '< 2.0', require: false
-  gem 'pry'
-  gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
 end
 
 
@@ -71,10 +76,13 @@ group :profiling do
 end
 
 group :test do
-  gem 'minitest', '~> 4.0'
+  gem 'crack', '0.4.5'
+  gem 'minitest', '~> 5.0'
+  gem 'minitest-hooks', "~> 1.5"
   gem 'minitest-stub_any_instance'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
   gem 'webmock', '~> 3.19.1'
+  gem 'webrick'
 end