From b8245c39971c6d0fb07b9237f0652223948a0eeb Mon Sep 17 00:00:00 2001
From: shilpigoeldev <83065526+shilpigoeldev@users.noreply.github.com>
Date: Tue, 12 Nov 2024 09:53:06 +0000
Subject: [PATCH 1/3] Added another rule for missing SRI (#128)

* Added another rule for missing SRI

* Corrected the rule to single out particular case
---
 .../providers/leeds/leeds_handler_colorectal.rb       | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/lib/import/colorectal/providers/leeds/leeds_handler_colorectal.rb b/lib/import/colorectal/providers/leeds/leeds_handler_colorectal.rb
index 3c152006..695c33c0 100644
--- a/lib/import/colorectal/providers/leeds/leeds_handler_colorectal.rb
+++ b/lib/import/colorectal/providers/leeds/leeds_handler_colorectal.rb
@@ -369,6 +369,17 @@ def genes_from_mtype
               %w[MLH1 MSH2 MSH6 PMS2 EPCAM]
             when /r211/
               %w[APC BMPR1A EPCAM GREM1 MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN SMAD4 STK11]
+            when /confirmation/
+              genes_for_confirmation_mtype
+            else
+              []
+            end
+          end
+
+          def genes_for_confirmation_mtype
+            if @indicationcategory == '11450' && @geno == 'mlpa del confirmation +ve' &&
+               @report.match(/familial\spathogenic\sdeletion\sof\sexons\s16-19/ix)
+              %w[MLH1]
             else
               []
             end

From 57038a2ca0e7ca58b37819071ac9c50d848ba2c7 Mon Sep 17 00:00:00 2001
From: bshand <bshand@users.noreply.github.com>
Date: Fri, 22 Nov 2024 09:24:54 +0000
Subject: [PATCH 2/3] Use Rails 7.0 application defaults [NDRS2-2253] (#130)

---
 config/application.rb                         |  15 +-
 .../new_framework_defaults_7_0.rb             | 145 ------------------
 config/initializers/wrap_parameters.rb        |  14 --
 test/fixtures/project_outputs.yml             |   4 +-
 test/fixtures/pseudo/death_data.yml           |   3 +-
 test/fixtures/pseudo/ppatients.yml            |   6 +-
 test/fixtures/pseudo/prescription_data.yml    |   6 +-
 test/fixtures/users.yml                       |   6 +
 8 files changed, 31 insertions(+), 168 deletions(-)
 delete mode 100644 config/initializers/new_framework_defaults_7_0.rb
 delete mode 100644 config/initializers/wrap_parameters.rb

diff --git a/config/application.rb b/config/application.rb
index 073ba55b..135ca1f2 100644
--- a/config/application.rb
+++ b/config/application.rb
@@ -13,7 +13,7 @@
 module Mbis
   class Application < Rails::Application
     # Initialize configuration defaults for originally generated Rails version.
-    config.load_defaults 6.1
+    config.load_defaults 7.0
 
     # Configuration for the application, engines, and railties goes here.
     #
@@ -70,5 +70,18 @@ class Application < Rails::Application
 
     # TODO: Old Rails 6.0 default; disable this
     ActiveSupport.utc_to_local_returns_utc_offset_times = false
+
+    # TODO: Old Rails 6.1 default; disable this
+    # Fails rails test test/models/concerns/workflow/model_test.rb:180
+    config.active_support.executor_around_test_case = false
+
+    # TODO: Old Rails 6.1 default; disable this
+    # Fixtures are incomplete, e.g. test/fixtures/memberships.yml needs to be defined
+    config.active_record.verify_foreign_keys_for_fixtures = false
+
+    # Old Rails 6.1 default, required by devise_saml_authenticatable version 1.9.1
+    # cf. https://github.com/apokalipto/devise_saml_authenticatable/issues/237
+    # If we don't have this, the redirect when logging out from ADFS throws an application error.
+    Rails.application.config.action_controller.raise_on_open_redirects = false
   end
 end
diff --git a/config/initializers/new_framework_defaults_7_0.rb b/config/initializers/new_framework_defaults_7_0.rb
deleted file mode 100644
index 099df580..00000000
--- a/config/initializers/new_framework_defaults_7_0.rb
+++ /dev/null
@@ -1,145 +0,0 @@
-# rubocop:disable Layout/LineLength, Layout/EmptyLines
-# Be sure to restart your server when you modify this file.
-#
-# This file eases your Rails 7.0 framework defaults upgrade.
-#
-# Uncomment each configuration one by one to switch to the new default.
-# Once your application is ready to run with all new defaults, you can remove
-# this file and set the `config.load_defaults` to `7.0`.
-#
-# Read the Guide for Upgrading Ruby on Rails for more info on each option.
-# https://guides.rubyonrails.org/upgrading_ruby_on_rails.html
-
-# `button_to` view helper will render `<button>` element, regardless of whether
-# or not the content is passed as the first argument or as a block.
-# Rails.application.config.action_view.button_to_generates_button_tag = true
-
-# `stylesheet_link_tag` view helper will not render the media attribute by default.
-# Rails.application.config.action_view.apply_stylesheet_media_default = false
-
-# Change the digest class for the key generators to `OpenSSL::Digest::SHA256`.
-# Changing this default means invalidate all encrypted messages generated by
-# your application and, all the encrypted cookies. Only change this after you
-# rotated all the messages using the key rotator.
-#
-# See upgrading guide for more information on how to build a rotator.
-# https://guides.rubyonrails.org/v7.0/upgrading_ruby_on_rails.html
-# Rails.application.config.active_support.key_generator_hash_digest_class = OpenSSL::Digest::SHA256
-
-# Change the digest class for ActiveSupport::Digest.
-# Changing this default means that for example Etags change and
-# various cache keys leading to cache invalidation.
-# Rails.application.config.active_support.hash_digest_class = OpenSSL::Digest::SHA256
-
-# Don't override ActiveSupport::TimeWithZone.name and use the default Ruby
-# implementation.
-# Rails.application.config.active_support.remove_deprecated_time_with_zone_name = true
-
-# Calls `Rails.application.executor.wrap` around test cases.
-# This makes test cases behave closer to an actual request or job.
-# Several features that are normally disabled in test, such as Active Record query cache
-# and asynchronous queries will then be enabled.
-# Rails.application.config.active_support.executor_around_test_case = true
-
-# Set both the `:open_timeout` and `:read_timeout` values for `:smtp` delivery method.
-# Rails.application.config.action_mailer.smtp_timeout = 5
-
-# The ActiveStorage video previewer will now use scene change detection to generate
-# better preview images (rather than the previous default of using the first frame
-# of the video).
-# Rails.application.config.active_storage.video_preview_arguments =
-#   "-vf 'select=eq(n\\,0)+eq(key\\,1)+gt(scene\\,0.015),loop=loop=-1:size=2,trim=start_frame=1' -frames:v 1 -f image2"
-
-# Automatically infer `inverse_of` for associations with a scope.
-# Rails.application.config.active_record.automatic_scope_inversing = true
-
-# Raise when running tests if fixtures contained foreign key violations
-# Rails.application.config.active_record.verify_foreign_keys_for_fixtures = true
-
-# Disable partial inserts.
-# This default means that all columns will be referenced in INSERT queries
-# regardless of whether they have a default or not.
-# Rails.application.config.active_record.partial_inserts = false
-
-# Protect from open redirect attacks in `redirect_back_or_to` and `redirect_to`.
-# Rails.application.config.action_controller.raise_on_open_redirects = true
-
-# Change the variant processor for Active Storage.
-# Changing this default means updating all places in your code that
-# generate variants to use image processing macros and ruby-vips
-# operations. See the upgrading guide for detail on the changes required.
-# The `:mini_magick` option is not deprecated; it's fine to keep using it.
-# Rails.application.config.active_storage.variant_processor = :vips
-
-# Enable parameter wrapping for JSON.
-# Previously this was set in an initializer. It's fine to keep using that initializer if you've customized it.
-# To disable parameter wrapping entirely, set this config to `false`.
-# Rails.application.config.action_controller.wrap_parameters_by_default = true
-
-# Specifies whether generated namespaced UUIDs follow the RFC 4122 standard for namespace IDs provided as a
-# `String` to `Digest::UUID.uuid_v3` or `Digest::UUID.uuid_v5` method calls.
-#
-# See https://guides.rubyonrails.org/configuring.html#config-active-support-use-rfc4122-namespaced-uuids for
-# more information.
-# Rails.application.config.active_support.use_rfc4122_namespaced_uuids = true
-
-# Change the default headers to disable browsers' flawed legacy XSS protection.
-Rails.application.config.action_dispatch.default_headers = {
-  'X-Frame-Options' => 'SAMEORIGIN',
-  'X-XSS-Protection' => '0',
-  'X-Content-Type-Options' => 'nosniff',
-  'X-Download-Options' => 'noopen',
-  'X-Permitted-Cross-Domain-Policies' => 'none',
-  'Referrer-Policy' => 'strict-origin-when-cross-origin'
-}
-
-
-# ** Please read carefully, this must be configured in config/application.rb **
-# Change the format of the cache entry.
-# Changing this default means that all new cache entries added to the cache
-# will have a different format that is not supported by Rails 6.1 applications.
-# Only change this value after your application is fully deployed to Rails 7.0
-# and you have no plans to rollback.
-# When you're ready to change format, add this to `config/application.rb` (NOT this file):
-#  config.active_support.cache_format_version = 7.0
-
-
-# Cookie serializer: 2 options
-#
-# If you're upgrading and haven't set `cookies_serializer` previously, your cookie serializer
-# is `:marshal`. The default for new apps is `:json`.
-#
-# Rails.application.config.action_dispatch.cookies_serializer = :json
-#
-#
-# To migrate an existing application to the `:json` serializer, use the `:hybrid` option.
-#
-# Rails transparently deserializes existing (Marshal-serialized) cookies on read and
-# re-writes them in the JSON format.
-#
-# It is fine to use `:hybrid` long term; you should do that until you're confident *all* your cookies
-# have been converted to JSON. To keep using `:hybrid` long term, move this config to its own
-# initializer or to `config/application.rb`.
-#
-# Rails.application.config.action_dispatch.cookies_serializer = :hybrid
-#
-#
-# If your cookies can't yet be serialized to JSON, keep using `:marshal` for backward-compatibility.
-#
-# If you have configured the serializer elsewhere, you can remove this section of the file.
-#
-# See https://guides.rubyonrails.org/action_controller_overview.html#cookies for more information.
-
-# Change the return value of `ActionDispatch::Request#content_type` to the Content-Type header without modification.
-# Rails.application.config.action_dispatch.return_only_request_media_type_on_content_type = false
-
-# Active Storage `has_many_attached` relationships will default to replacing the current collection instead of appending to it.
-# Thus, to support submitting an empty collection, the `file_field` helper will render an hidden field `include_hidden` by default when `multiple_file_field_include_hidden` is set to `true`.
-# See https://guides.rubyonrails.org/configuring.html#config-active-storage-multiple-file-field-include-hidden for more information.
-# Rails.application.config.active_storage.multiple_file_field_include_hidden = true
-
-# ** Please read carefully, this must be configured in config/application.rb (NOT this file) **
-# Disables the deprecated #to_s override in some Ruby core classes
-# See https://guides.rubyonrails.org/configuring.html#config-active-support-disable-to-s-conversion for more information.
-# config.active_support.disable_to_s_conversion = true
-# rubocop:enable Layout/LineLength, Layout/EmptyLines
diff --git a/config/initializers/wrap_parameters.rb b/config/initializers/wrap_parameters.rb
deleted file mode 100644
index bbfc3961..00000000
--- a/config/initializers/wrap_parameters.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-# Be sure to restart your server when you modify this file.
-
-# This file contains settings for ActionController::ParamsWrapper which
-# is enabled by default.
-
-# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
-ActiveSupport.on_load(:action_controller) do
-  wrap_parameters format: [:json]
-end
-
-# To enable root element in JSON for ActiveRecord objects.
-# ActiveSupport.on_load(:active_record) do
-#   self.include_root_in_json = true
-# end
diff --git a/test/fixtures/project_outputs.yml b/test/fixtures/project_outputs.yml
index 0c60fe33..015371e4 100644
--- a/test/fixtures/project_outputs.yml
+++ b/test/fixtures/project_outputs.yml
@@ -2,8 +2,8 @@
 
 one:
   project: one
-  output: MyString
+  output: one
 
 two:
   project: two
-  output: MyString
+  output: one
diff --git a/test/fixtures/pseudo/death_data.yml b/test/fixtures/pseudo/death_data.yml
index 52d5f908..4338d9a6 100644
--- a/test/fixtures/pseudo/death_data.yml
+++ b/test/fixtures/pseudo/death_data.yml
@@ -1,4 +1,5 @@
 death1:
   death_dataid: 1
 # created in ppatients.yml
-  ppatient: patient3
+#  ppatient: patient3
+  ppatient_id: 3
diff --git a/test/fixtures/pseudo/ppatients.yml b/test/fixtures/pseudo/ppatients.yml
index 79b1ccd0..0c11d862 100644
--- a/test/fixtures/pseudo/ppatients.yml
+++ b/test/fixtures/pseudo/ppatients.yml
@@ -8,20 +8,20 @@ patient1:
 patient2:
   id: 2
   e_batch_id: 1
-  type: Pseudo::Pbirth
+  type: Pseudo::Birth
   pseudo_id1: some_long_id_2_1
   pseudo_id2: ""
 
 patient3:
   id: 3
   e_batch_id: 1
-  type: Pseudo::Pdeath
+  type: Pseudo::Death
   pseudo_id1: some_long_id_3_1
   pseudo_id2: ""
 
 patient4:
   id: 4
   e_batch_id: 1
-  type: Pseudo::Pmolecular
+  type: Pseudo::Molecular
   pseudo_id1: some_long_id_4_1
   pseudo_id2: ""
diff --git a/test/fixtures/pseudo/prescription_data.yml b/test/fixtures/pseudo/prescription_data.yml
index e050e2c4..b621ac1c 100644
--- a/test/fixtures/pseudo/prescription_data.yml
+++ b/test/fixtures/pseudo/prescription_data.yml
@@ -6,7 +6,8 @@ prescription1:
   bnf_code: XYZ45
   pat_age: 44
 # created in ppatients.yml
-  ppatient: patient1
+#  ppatient: patient1
+  ppatient_id: 1
 
 prescription2:
   prescription_dataid: 2
@@ -15,4 +16,5 @@ prescription2:
   drug_paid: £99.98
   bnf_code: FML02
   pat_age: 28
-  ppatient: patient1
+#  ppatient: patient1
+  ppatient_id: 1
diff --git a/test/fixtures/users.yml b/test/fixtures/users.yml
index c11c903f..a6f0fff7 100644
--- a/test/fixtures/users.yml
+++ b/test/fixtures/users.yml
@@ -298,6 +298,12 @@ delegate_user3:
   division_id: 1
   delegate_user: true
 
+mbis_delegate:
+  email: mbis.delegate@phe.gov.uk
+  first_name: mbis
+  last_name: delegate
+  delegate_user: true
+
 approved_project_user:
   email: approved_project_user@phe.gov.uk
   first_name: Approved

From 82f2220663f6918dd96a12d15bb1ab1f8643b71f Mon Sep 17 00:00:00 2001
From: bshand <bshand@users.noreply.github.com>
Date: Fri, 22 Nov 2024 09:25:51 +0000
Subject: [PATCH 3/3] Run tests faster in parallel groups on GitHub Actions
 (#131)

* Run tests single-threaded to reduce test brittleness.
* Rename tests to ensure better test timing spread across the alphabet.
---
 .github/workflows/static_code_analysis.yml    |  69 ++++++++
 .github/workflows/test.yml                    | 133 ---------------
 .github/workflows/tests.yml                   | 154 ++++++++++++++++++
 ...tems_test.rb => manage_data_items_test.rb} |   2 +-
 ...dataset_test.rb => manage_dataset_test.rb} |   2 +-
 ...est.rb => manage_dataset_versions_test.rb} |   2 +-
 ...age_users_test.rb => manage_users_test.rb} |   2 +-
 7 files changed, 227 insertions(+), 137 deletions(-)
 create mode 100644 .github/workflows/static_code_analysis.yml
 delete mode 100644 .github/workflows/test.yml
 create mode 100644 .github/workflows/tests.yml
 rename test/integration/admin/{can_manage_data_items_test.rb => manage_data_items_test.rb} (99%)
 rename test/integration/admin/{can_manage_dataset_test.rb => manage_dataset_test.rb} (91%)
 rename test/integration/admin/{can_manage_dataset_versions_test.rb => manage_dataset_versions_test.rb} (95%)
 rename test/integration/admin/{can_manage_users_test.rb => manage_users_test.rb} (96%)

diff --git a/.github/workflows/static_code_analysis.yml b/.github/workflows/static_code_analysis.yml
new file mode 100644
index 00000000..55c2b7d6
--- /dev/null
+++ b/.github/workflows/static_code_analysis.yml
@@ -0,0 +1,69 @@
+---
+name: Static Code Analysis
+
+on: [pull_request]
+
+jobs:
+  brakeman:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Ruby + Bundle
+        uses: ruby/setup-ruby@v1
+        with:
+          bundler-cache: true
+      - name: Run Brakeman analysis
+        run: bundle exec brakeman --parser-timeout 60
+
+  bundle-audit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Ruby + Bundle
+        uses: ruby/setup-ruby@v1
+        with:
+          bundler-cache: true
+      - name: Audit the bundle
+        # Ignore bootstrap version 3 warning: https://nhsd-jira.digital.nhs.uk/browse/NDRS2-1676
+        run: bundle exec bundle-audit check --update --ignore CVE-2024-6484
+        # run: bundle exec bundle-audit check --update
+
+  notify:
+    # Run only on main, but regardless of whether tests past:
+    if: ${{ always() }}
+    # if: ${{ always() && github.ref == 'refs/heads/main' }}
+
+    needs:
+      - brakeman
+      - bundle-audit
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: 8398a7/action-slack@v3
+        with:
+          status: custom
+          fields: workflow,commit,author
+          custom_payload: |
+            {
+              channel: '${{ secrets.SLACK_CHANNEL }}',
+              username: 'GitHub CI',
+              icon_emoji: ':robot_face:',
+              attachments: [{
+                text: '${{ github.event.commits[0].message }}',
+                fields: [
+                  { title: 'Author', value: '${{ github.actor }}', short: true },
+                  { title: 'Revision', value: '${{ github.sha }}', short: true }
+                ]
+              },{
+                color: '${{ needs.brakeman.result }}' === 'success' ? 'good' : '${{ needs.brakeman.result }}' === 'failure' ? 'danger' : 'warning',
+                text: `Brakeman checks returned *${{ needs.brakeman.result }}*.`
+              },{
+                color: '${{ needs.bundle-audit.result }}' === 'success' ? 'good' : '${{ needs.bundle-audit.result }}' === 'failure' ? 'danger' : 'warning',
+                text: `Bundle Audit checks returned *${{ needs.bundle-audit.result }}*.`
+              }]
+            }
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index 71973e5b..00000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,133 +0,0 @@
-name: Test
-
-on: [pull_request]
-
-jobs:
-  test:
-    strategy:
-      matrix:
-        ruby-version:
-          - '3.1.6'
-          # - '3.2' # Not yet tested on CentOS 7. Ideally move to rails 7.0 first
-
-    name: Ruby ${{ matrix.ruby-version }}
-
-    runs-on: ubuntu-latest
-
-    services:
-      postgres:
-        image: postgres
-        env:
-          POSTGRES_USER: rails
-          POSTGRES_PASSWORD: rails_password
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-          - 5432:5432
-
-    env:
-      DB_HOST: localhost
-      DB_PORT: 5432
-      DB_USERNAME: rails
-      DB_PASSWORD: rails_password
-
-      # Prep the whole stack in test-only mode:
-      RAILS_ENV: test
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Ruby + Bundle
-      uses: ruby/setup-ruby@v1
-      with:
-        bundler-cache: true
-        ruby-version: ${{ matrix.ruby-version }}
-    - name: Inject configuration
-      run: cp config/database.yml{.ci,}
-    - name: Prepare the database
-      run: bin/rails db:setup
-    - name: Precompile assets
-      # Since ruby/setup-ruby@v1 moved to Node.js v18 we need the extra options
-      # until we move to newer webpacker / stop using it.
-      # I've tried using a newer hash function in config/webpack/environment.js
-      # by adding the following line, but this didn't help with github actions
-      # # environment.config.set('output.hashFunction', 'sha256')
-      # https://stackoverflow.com/questions/69692842/error-message-error0308010cdigital-envelope-routinesunsupported/73465262#73465262
-      run: NODE_OPTIONS=--openssl-legacy-provider bin/rails yarn:install assets:clobber assets:precompile
-    - name: Run tests
-      run: bin/rails test
-
-  brakeman:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Ruby + Bundle
-      uses: ruby/setup-ruby@v1
-      with:
-        bundler-cache: true
-    - name: Run Brakeman analysis
-      run: bundle exec brakeman
-
-  bundle-audit:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Ruby + Bundle
-      uses: ruby/setup-ruby@v1
-      with:
-        bundler-cache: true
-    - name: Audit the bundle
-      # Ignore bootstrap version 3 warning: https://nhsd-jira.digital.nhs.uk/browse/NDRS2-1676
-      run: bundle exec bundle-audit check --update --ignore CVE-2024-6484
-      # run: bundle exec bundle-audit check --update
-
-  # A utility job upon which Branch Protection can depend,
-  # thus remaining agnostic of the matrix.
-  test_matrix:
-    if: ${{ always() }}
-    runs-on: ubuntu-latest
-    name: Matrix
-    needs: test
-    steps:
-    - name: Check build matrix status
-      if: ${{ needs.test.result != 'success' }}
-      run: exit 1
-
-  notify:
-    # Run only on master, but regardless of whether tests past:
-    if: ${{ always() && github.ref == 'refs/heads/master' }}
-
-    needs:
-      - test_matrix
-      - brakeman
-      - bundle-audit
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: 8398a7/action-slack@v3
-      with:
-        status: custom
-        fields: workflow,commit,author
-        custom_payload: |
-          {
-            channel: 'CSEPN7EES',
-            username: 'CI',
-            icon_emoji: ':hammer_and_wrench:',
-            attachments: [{
-              color: '${{ needs.test.result }}' === 'success' ? 'good' : '${{ needs.test.result }}' === 'failure' ? 'danger' : 'warning',
-              text: `${process.env.AS_WORKFLOW} against \`${{ github.ref }}\` (${process.env.AS_COMMIT}) for ${{ github.actor }} resulted in *${{ needs.test.result }}*.`
-            },{
-              color: '${{ needs.brakeman.result }}' === 'success' ? 'good' : '${{ needs.brakeman.result }}' === 'failure' ? 'danger' : 'warning',
-              text: `Brakeman checks returned *${{ needs.brakeman.result }}*.`
-            },{
-              color: '${{ needs.bundle-audit.result }}' === 'success' ? 'good' : '${{ needs.bundle-audit.result }}' === 'failure' ? 'danger' : 'warning',
-              text: `Bundle Audit checks returned *${{ needs.bundle-audit.result }}*.`
-            }]
-          }
-      env:
-        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 00000000..a3984e3d
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,154 @@
+---
+# This file is @generated by `bin/rails generate test_strategy test_strategy_timings.csv`
+# Please edit the template and regenerate, rather than edit this file.
+
+name: Tests
+
+on: [pull_request]
+
+permissions:
+  contents: read
+  actions: read
+
+jobs:
+  remaining_test_matrix:
+    strategy:
+      fail-fast: false
+      matrix:
+        ruby-version:
+          - '3.1.6'
+        test-group:
+          - "[a-b]"
+          - "[c]"
+          - "[d-m]"
+          - "[n-z]"
+
+    name: "Ruby ${{ matrix.ruby-version }} Tests (${{ matrix.test-group }})"
+
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_USER: rails
+          POSTGRES_PASSWORD: rails_password
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+          --name postgres
+        ports:
+          - 5432:5432
+
+    env:
+      DB_HOST: localhost
+      DB_PORT: 5432
+      DB_USERNAME: rails
+      DB_PASSWORD: rails_password
+
+      # Prep the whole stack in test-only mode:
+      RAILS_ENV: test
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set timezone to Europe/London
+        run: sudo timedatectl set-timezone Europe/London
+      - name: Use bundled npm files
+        run: printf 'disable-self-update-check true\nyarn-offline-mirror "./vendor/npm-packages-offline-cache"\nyarn-offline-mirror-pruning false\n' > .yarnrc
+      - name: Set up Ruby + Bundle
+        uses: ruby/setup-ruby@v1
+        with:
+          bundler-cache: true
+          ruby-version: ${{ matrix.ruby-version }}
+      - name: Inject configuration
+        run: cp config/database.yml{.ci,}
+      - name: Prepare the database
+        run: bin/rails db:setup
+      - name: Precompile assets
+        # Since ruby/setup-ruby@v1 moved to Node.js v18 we need the extra options
+        # until we move to newer webpacker / stop using it.
+        # I've tried using a newer hash function in config/webpack/environment.js
+        # by adding the following line, but this didn't help with github actions
+        # # environment.config.set('output.hashFunction', 'sha256')
+        # https://stackoverflow.com/questions/69692842/error-message-error0308010cdigital-envelope-routinesunsupported/73465262#73465262
+        run: NODE_OPTIONS=--openssl-legacy-provider bin/rails yarn:install assets:clobber assets:precompile
+      - name: Run tests
+        run: PARALLEL_WORKERS=1 bin/rails test 'test/**/${{ matrix.test-group }}*_test.rb'
+
+  # A utility job upon which Branch Protection can depend,
+  # thus remaining agnostic of the matrix.
+  remaining_tests:
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    # name: Matrix
+    needs: remaining_test_matrix
+    steps:
+      - name: Check build matrix status
+        if: ${{ needs.remaining_test_matrix.result != 'success' }}
+        run: exit 1
+
+  notify:
+    # Run only on master, but regardless of whether tests past:
+    if: ${{ always() }}
+    # if: ${{ always() && github.ref == 'refs/heads/master' }}
+
+    needs:
+      - remaining_tests
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-node@v3
+        # with:
+        #   node-version: '16.x'
+      - id: slack-payload-generator
+        env:
+          COMMIT_MESSAGE: ${{ github.event.commits[0].message }}
+        run: |-
+          node -e "
+            const passed = '${{ needs.integration_tests.result }}' === 'success' && '${{ needs.models_tests.result }}' === 'success' && '${{ needs.remaining_tests.result }}' === 'success'
+
+            const text = process.env.COMMIT_MESSAGE
+
+            let attachments = [
+              {
+                fallback: text,
+                text: text,
+                fields: [
+                  { title: 'Author', value: '${{ github.actor }}', short: true },
+                  { title: 'Revision', value: '${{ github.sha }}', short: true }
+                ]
+                // ts: @commit.author[:time].to_i
+              }
+            ]
+
+            if (passed) {
+              attachments.push({
+                color: 'good',
+                text: 'Tests passed'
+              })
+            } else {
+              attachments.push({
+                color: 'danger',
+                text: 'Test(s) failed'
+              })
+            }
+
+            let payload = {
+              channel: '${{ secrets.SLACK_CHANNEL }}',
+              username: 'GitHub CI',
+              icon_emoji: ':robot_face:',
+              attachments: attachments
+            }
+
+            console.log('json=' + JSON.stringify(payload))
+          " >> "$GITHUB_OUTPUT"
+      - uses: 8398a7/action-slack@v3
+        with:
+          status: custom
+          fields: workflow,commit,author
+          custom_payload: ${{ steps.slack-payload-generator.outputs.json }}
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
diff --git a/test/integration/admin/can_manage_data_items_test.rb b/test/integration/admin/manage_data_items_test.rb
similarity index 99%
rename from test/integration/admin/can_manage_data_items_test.rb
rename to test/integration/admin/manage_data_items_test.rb
index 48c33951..e0f34284 100644
--- a/test/integration/admin/can_manage_data_items_test.rb
+++ b/test/integration/admin/manage_data_items_test.rb
@@ -1,6 +1,6 @@
 require 'test_helper'
 
-class CanManageDataItemsTest < ActionDispatch::IntegrationTest
+class ManageDataItemsTest < ActionDispatch::IntegrationTest
   def setup
     @admin = users(:admin_user)
     login_and_accept_terms(@admin)
diff --git a/test/integration/admin/can_manage_dataset_test.rb b/test/integration/admin/manage_dataset_test.rb
similarity index 91%
rename from test/integration/admin/can_manage_dataset_test.rb
rename to test/integration/admin/manage_dataset_test.rb
index d8391dd9..fa24f06e 100644
--- a/test/integration/admin/can_manage_dataset_test.rb
+++ b/test/integration/admin/manage_dataset_test.rb
@@ -1,7 +1,7 @@
 require 'test_helper'
 require 'project_helper'
 
-class CanManageDatasetTest < ActionDispatch::IntegrationTest
+class ManageDatasetTest < ActionDispatch::IntegrationTest
   def setup
     @admin = users(:admin_user)
     login_and_accept_terms(@admin)
diff --git a/test/integration/admin/can_manage_dataset_versions_test.rb b/test/integration/admin/manage_dataset_versions_test.rb
similarity index 95%
rename from test/integration/admin/can_manage_dataset_versions_test.rb
rename to test/integration/admin/manage_dataset_versions_test.rb
index 45227d3f..e597910c 100644
--- a/test/integration/admin/can_manage_dataset_versions_test.rb
+++ b/test/integration/admin/manage_dataset_versions_test.rb
@@ -1,6 +1,6 @@
 require 'test_helper'
 
-class CanManageDatasetVersionsTest < ActionDispatch::IntegrationTest
+class ManageDatasetVersionsTest < ActionDispatch::IntegrationTest
   def setup
     @admin = users(:admin_user)
     @dataset_manager = users(:team_dataset_manager)
diff --git a/test/integration/admin/can_manage_users_test.rb b/test/integration/admin/manage_users_test.rb
similarity index 96%
rename from test/integration/admin/can_manage_users_test.rb
rename to test/integration/admin/manage_users_test.rb
index a40c9dc0..dce69cd0 100644
--- a/test/integration/admin/can_manage_users_test.rb
+++ b/test/integration/admin/manage_users_test.rb
@@ -1,6 +1,6 @@
 require 'test_helper'
 
-class CanManageUsersTest < ActionDispatch::IntegrationTest
+class ManageUsersTest < ActionDispatch::IntegrationTest
   def setup
     @admin = users(:admin_user)
     login_and_accept_terms(@admin)