Updated mysql version to 8.0

.babelrc

@@ -1,16 +1,4 @@
 {
-  "presets": [
-    "@babel/preset-env",
-    "@babel/preset-react"
-  ],
-  "plugins": [
-    "syntax-dynamic-import",
-    "@babel/plugin-proposal-object-rest-spread",
-    [
-      "transform-class-properties",
-      {
-        "spec": true
-      }
-    ]
-  ]
+  "presets": ["@babel/preset-env", "@babel/preset-react"],
+  "plugins": ["@babel/plugin-syntax-dynamic-import", "@babel/plugin-proposal-object-rest-spread"]
 }

.dockerignore

@@ -0,0 +1,19 @@
+# See https://docs.docker.com/engine/reference/builder/#dockerignore-file
+# Avoids copying these files into our docker-container
+
+# Node modules can break docker-builds on the local machine if it gets
+# coppied to the container. (You'll see yarn integrity errors)
+node_modules
+# .bundle contains bundler configuration which is specific to our local system
+.bundle
+
+# These folders store transisent informatation and aren't relevant between
+# systems. They are in our .gitignore, so we also add them here to keep
+# local builds consistent.
+log
+tmp
+
+# We're building our container for production, so lets exclude the test and
+# spec folders. This will keep our container size a little smaller
+test
+spec

.github/workflows/docker.yml

@@ -4,35 +4,53 @@ on:
     branches:
       - develop
       - master
-      - release-2.0.8-docker
+    tags:
+      - release-*
+      - uat-*
+      - dev-*
 
 env:
-  IMAGE_NAME: ${{ github.repository }}/latest
+  IMAGE_NAME: ${{ github.repository }}/${{ github.event.repository.name }}
+
+permissions:
+  packages: write
 
 jobs:
   build_and_publish:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
 
     steps:
-    - run: env
+      - run: env
+
+      - uses: actions/checkout@v1
+      - uses: actions/cache@v1
+        with:
+          path: /var/lib/docker
+          key: ${{ runner.os }}-docker-${{ hashFiles('Dockerfile') }}
+          restore-keys: |
+            ${{ runner.os }}-docker-${{ hashFiles('Dockerfile') }}
+      - name: Build and tag the Docker image
+        run: docker build . --file Dockerfile --tag docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
+      - name: Tag (latest) the Docker image
+        run: docker tag docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/} docker.pkg.github.com/${IMAGE_NAME}:latest
+        if: github.ref == 'refs/heads/master'
 
-    - uses: actions/checkout@v1
-    - uses: actions/cache@v1
-      with:
-        path: /var/lib/docker
-        key: ${{ runner.os }}-docker-${{ hashFiles('Dockerfile') }}
-        restore-keys: |
-          ${{ runner.os }}-docker-
-    - name: Build and tag the Docker image
-      run: docker build . --file Dockerfile --tag docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
-    - name: Tag (latest) the Docker image
-      run: docker tag docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/} docker.pkg.github.com/${IMAGE_NAME}:latest
-      if: github.ref == 'refs/heads/master'
+      - name: Login to registry
+        run: docker login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} docker.pkg.github.com
+      - name: Publish image
+        run: docker push docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
+      - name: Publish image (latest)
+        run: docker push docker.pkg.github.com/${IMAGE_NAME}:latest
+        if: github.ref == 'refs/heads/master'
 
-    - name: Login to registry
-      run: docker login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} docker.pkg.github.com
-    - name: Publish image
-      run: docker push docker.pkg.github.com/${IMAGE_NAME}:${GITHUB_REF##*/}
-    - name: Publish image (latest)
-      run: docker push docker.pkg.github.com/${IMAGE_NAME}:latest
-      if: github.ref == 'refs/heads/master'
+      - name: Remove old releases
+        uses: snok/container-retention-policy@v2
+        with:
+          image-names: ${{ github.event.repository.name }}/*
+          cut-off: Ten months ago UTC
+          timestamp-to-use: updated_at
+          account-type: org
+          org-name: sanger
+          keep-at-least: 5
+          skip-tags: latest
+          token: ${{ secrets.REMOVE_OLD_IMAGES }}

.github/workflows/lint.yml

@@ -0,0 +1,30 @@
+name: Linting
+
+env:
+  TZ: Europe/London
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  ruby:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          bundler-cache:
+            true # Runs bundle install and caches gems. See the ruby_test.yml
+            # example if you need more control over bundler.
+      - name: Setup node
+        uses: actions/setup-node@v2
+        with:
+          node-version: ${{ steps.node_version.outputs.NODE_VERSION }}
+      - name: Install
+        run: yarn install
+      - name: Run prettier
+        run: yarn prettier --check .
+      - name: Run Rubocop
+        run: bundle exec rubocop --extra-details --display-style-guide --parallel

.github/workflows/test.yml

@@ -0,0 +1,64 @@
+name: Tests
+
+env:
+  TZ: Europe/London
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  ruby:
+    runs-on: ubuntu-latest
+
+    env:
+      RAILS_ENV: test
+
+    services:
+      mysql:
+        # Use the Mysql docker image https://hub.docker.com/_/mysql
+        image: mysql:8.0
+        ports:
+          - 3306 # Default port mappings
+        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
+        env:
+          MYSQL_ALLOW_EMPTY_PASSWORD: yes
+          MYSQL_ROOT_PASSWORD: ''
+          MYSQL_DATABASE: samples_extraction_test
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          bundler-cache:
+            true # Runs bundle install and caches gems. See the ruby_test.yml
+            # example if you need more control over bundler.
+      - name: Set up environment
+        env:
+          DBPORT: ${{ job.services.mysql.ports[3306] }}
+        run: bin/setup
+
+      - name: Run tests
+        env:
+          DBPORT: ${{ job.services.mysql.ports[3306] }}
+        run: bundle exec rake
+
+  yarn:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Export node version
+        id: node_version
+        run: echo ::set-output name=NODE_VERSION::$(cat .nvmrc)
+      - name: Setup node
+        uses: actions/setup-node@v2
+        with:
+          node-version: ${{ steps.node_version.outputs.NODE_VERSION }}
+
+      - name: Install
+        run: yarn install
+
+      - name: Run yarn test
+        run: yarn test

.gitignore

@@ -48,3 +48,6 @@ bower.json
 /node_modules
 yarn-debug.log*
 .yarn-integrity
+
+# Ignore Rediscache
+dump.rdb

.nvmrc

@@ -0,0 +1 @@
+v16.14.2

.postcssrc.yml

@@ -1,3 +1,3 @@
 plugins:
   postcss-import: {}
-  postcss-cssnext: {}
+  postcss-preset-env: {}

.prettierignore

@@ -0,0 +1,53 @@
+*.rbc
+.DS_Store
+*~
+capybara-*.html
+.rspec
+/log
+/tmp
+/db/*.sqlite3
+/db/*.sqlite3-journal
+/public/system
+/public/assets
+/coverage/
+/spec/tmp
+**.orig
+rerun.txt
+pickle-email-*.html
+
+# TODO Comment out these rules if you are OK with secrets being uploaded to the repo
+config/initializers/secret_token.rb
+config/secrets.yml
+
+# dotenv
+# TODO Comment out this rule if environment variables can be committed
+.env
+
+## Environment normalization:
+/.bundle
+/vendor/bundle
+
+# these should all be checked in to normalize the environment:
+# Gemfile.lock, .ruby-version, .ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+
+# if using bower-rails ignore default bower_components path bower.json files
+/vendor/assets/bower_components
+*.bowerrc
+bower.json
+
+# Ignore pow environment settings
+.powenv
+
+# Ignore Byebug command history file.
+.byebug_history
+/public/packs
+/public/packs-test
+/node_modules
+yarn-debug.log*
+.yarn-integrity
+
+# Ignore Rediscache
+dump.rdb

.prettierrc.json

@@ -0,0 +1,5 @@
+{
+  "printWidth": 120,
+  "semi": false,
+  "singleQuote": true
+}

.rubocop.yml

@@ -1,2 +1,60 @@
-require: rubocop-performance
-require: rubocop-rails
+inherit_from:
+  - .rubocop_todo.yml
+  - node_modules/@prettier/plugin-ruby/rubocop.yml
+
+require:
+  - rubocop-performance
+  - rubocop-rails
+
+AllCops:
+  NewCops: enable
+  inherit_mode:
+    merge:
+      - Exclude
+  Exclude:
+    - 'db/views_schema.rb'
+
+# Blocks are used to structure tests and are part of the rspec dsl.
+# The standard BlockLength limits are too stringent for this purpose.
+# Block DSL is also used in routes
+# We should be careful keeping rake tasks here, as large tasks are still an issue.
+# Not sure if we need to split namespaces across several files though.
+Metrics/BlockLength:
+  Exclude:
+    - Gemfile
+  IgnoredMethods:
+    - describe
+    - context
+    - background
+    - scenario
+    - namespace
+    - task
+    - included
+    - shared_context
+    - shared_examples
+    - shared_examples_for
+    - state_machine
+    - configure
+    - draw
+    - feature
+    - subject
+    - let
+    - let!
+    - factory
+    - define
+    - guard
+    - transient
+    - with_nested_has_many_association
+    - with_association
+    - it
+    - class_eval
+    - has_metadata
+    - resources
+
+# Rubocop is choking on this file, so we're excluding it for now.
+Rails/NegateInclude:
+  inherit_mode:
+    merge:
+      - Exclude
+  Exclude:
+    - 'lib/changes_support/disjoint_list.rb'