Release DPL-977, DPL-1043 & DPL-1059

.github/workflows/compile_test.yml

@@ -0,0 +1,39 @@
+name: Test compilation
+
+on:
+  - push
+  - pull_request
+
+env:
+  BUNDLE_WITHOUT: 'test lint'
+
+jobs:
+  Build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: nelonoel/[email protected]
+
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version-file: '.nvmrc'
+
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+
+      # Actually run our build
+      - name: Create Build
+        run: ./compile-build
+
+      # Create a release tag based on the branch name and .release-version file
+      - name: Set release tag
+        # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
+        # On the develop branch this might create RELEASE_VERSION=2.4.6-987654321-develop
+        # On the master branch this would then only create RELEASE_VERSION=2.4.6
+        run: echo "RELEASE_VERSION=$(printf -- '%s%s\n' $(cat .release-version) $([ ${BRANCH_NAME} = "develop" ] && printf -- '-%s-develop' ${GITHUB_RUN_ID} || echo ""))" >> $GITHUB_ENV
+
+    # Do not actually save build or create release itself

.github/workflows/test_js.yml

@@ -0,0 +1,33 @@
+name: Javascript testing
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  js_test:
+    runs-on: ubuntu-latest
+    env:
+      TZ: Europe/London
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version-file: '.nvmrc'
+      - name: Node Information
+        run: node --version
+      - name: Install
+        run: yarn install
+      - name: Run yarn test
+        run: yarn test
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: javascript,${{ github.event_name }}
+          fail_ci_if_error: true
+          disable_search: true
+          files: ${{ github.workspace }}/app/javascript/coverage/lcov.info
+          # Note: see codecov.yml for more additional settings

.github/workflows/ruby_test.yml → .github/workflows/test_ruby.yml

@@ -27,9 +27,17 @@ jobs:
             # example if you need more control over bundler.
       - name: Additional setup
         run: bin/setup
-      - name: Test & publish code coverage
+      - name: Run rspec
+        run: bundle exec rspec
+      - name: Publish code coverage to Code Climate
         uses: paambaati/[email protected]
         env:
           CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID || '1735fdb62543d410c5ed4469e402641a7986f1ebf62ff7398f3ab8ccc98069ef' }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
         with:
-          coverageCommand: bundle exec rspec
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: ruby,${{ github.event_name }}
+          fail_ci_if_error: true
+          disable_search: true
+          files: ${{ github.workspace }}/lcov.info

.release-version

@@ -1 +1 @@
-3.45.0
+3.46.0

Gemfile

@@ -46,7 +46,7 @@ group :test do
   gem 'launchy' # Used by capybara for eg. save_and_open_screenshot
   gem 'rails-controller-testing'
   gem 'rspec-json_expectations'
-  gem 'rspec-rails', '6.1.0'
+  gem 'rspec-rails', '6.1.1'
   gem 'selenium-webdriver', '~> 4.1', require: false
   gem 'simplecov', require: false
   gem 'simplecov-lcov', require: false

Gemfile.lock

@@ -110,19 +110,19 @@ GEM
     base64 (0.2.0)
     bigdecimal (3.1.6)
     bindex (0.8.1)
-    bootsnap (1.17.1)
+    bootsnap (1.18.3)
       msgpack (~> 1.2)
     bootstrap (4.6.2)
       autoprefixer-rails (>= 9.1.0)
       popper_js (>= 1.16.1, < 2)
       sassc-rails (>= 2.0.0)
     builder (3.2.4)
     byebug (11.1.3)
-    capybara (3.39.2)
+    capybara (3.40.0)
       addressable
       matrix
       mini_mime (>= 0.1.3)
-      nokogiri (~> 1.8)
+      nokogiri (~> 1.11)
       rack (>= 1.6.0)
       rack-test (>= 0.6.3)
       regexp_parser (>= 1.5, < 3.0)
@@ -133,11 +133,12 @@ GEM
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
-    crack (0.4.5)
+    crack (1.0.0)
+      bigdecimal
       rexml
     crass (1.0.6)
     date (3.3.4)
-    diff-lcs (1.5.0)
+    diff-lcs (1.5.1)
     docile (1.4.0)
     drb (2.2.0)
       ruby2_keywords
@@ -146,7 +147,7 @@ GEM
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
     execjs (2.9.1)
-    factory_bot (6.4.5)
+    factory_bot (6.4.6)
       activesupport (>= 5.0.0)
     faraday (1.10.3)
       faraday-em_http (~> 1.0)
@@ -199,7 +200,7 @@ GEM
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
     io-console (0.7.2)
-    irb (1.11.1)
+    irb (1.11.2)
       rdoc
       reline (>= 0.4.2)
     jquery-rails (4.6.0)
@@ -229,13 +230,13 @@ GEM
     method_source (1.0.0)
     mini_mime (1.1.5)
     mini_portile2 (2.8.5)
-    minitest (5.21.2)
+    minitest (5.22.2)
     msgpack (1.7.2)
     multi_json (1.15.0)
-    multipart-post (2.3.0)
+    multipart-post (2.4.0)
     mutex_m (0.2.0)
     nenv (0.3.0)
-    net-imap (0.4.9.1)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
@@ -245,7 +246,7 @@ GEM
     net-smtp (0.4.0.1)
       net-protocol
     nio4r (2.7.0)
-    nokogiri (1.16.0)
+    nokogiri (1.16.2)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -254,7 +255,7 @@ GEM
     oj (3.16.3)
       bigdecimal (>= 3.0)
     parallel (1.24.0)
-    parser (3.3.0.4)
+    parser (3.3.0.5)
       ast (~> 2.4.1)
       racc
     popper_js (1.16.1)
@@ -270,7 +271,7 @@ GEM
     puma (6.4.2)
       nio4r (~> 2.0)
     racc (1.7.3)
-    rack (3.0.8)
+    rack (3.0.9)
     rack-mini-profiler (3.3.0)
       rack (>= 1.2.0)
     rack-proxy (0.7.7)
@@ -326,29 +327,29 @@ GEM
     reline (0.4.2)
       io-console (~> 0.5)
     rexml (3.2.6)
-    rspec (3.12.0)
-      rspec-core (~> 3.12.0)
-      rspec-expectations (~> 3.12.0)
-      rspec-mocks (~> 3.12.0)
-    rspec-core (3.12.2)
-      rspec-support (~> 3.12.0)
-    rspec-expectations (3.12.3)
+    rspec (3.13.0)
+      rspec-core (~> 3.13.0)
+      rspec-expectations (~> 3.13.0)
+      rspec-mocks (~> 3.13.0)
+    rspec-core (3.13.0)
+      rspec-support (~> 3.13.0)
+    rspec-expectations (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
+      rspec-support (~> 3.13.0)
     rspec-json_expectations (2.2.0)
-    rspec-mocks (3.12.6)
+    rspec-mocks (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-rails (6.1.0)
+      rspec-support (~> 3.13.0)
+    rspec-rails (6.1.1)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       railties (>= 6.1)
       rspec-core (~> 3.12)
       rspec-expectations (~> 3.12)
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
-    rspec-support (3.12.1)
-    rubocop (1.60.1)
+    rspec-support (3.13.0)
+    rubocop (1.60.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -370,7 +371,7 @@ GEM
       rubocop (>= 1.33.0, < 2.0)
       rubocop-ast (>= 1.30.0, < 2.0)
     ruby-progressbar (1.13.0)
-    ruby-units (4.0.1)
+    ruby-units (4.0.2)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
     sass-rails (6.0.0)
@@ -384,7 +385,8 @@ GEM
       sprockets-rails
       tilt
     select2-rails (4.0.13)
-    selenium-webdriver (4.16.0)
+    selenium-webdriver (4.17.0)
+      base64 (~> 0.2)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
@@ -425,7 +427,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.19.1)
+    webmock (3.20.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -442,7 +444,7 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     yard (0.9.34)
-    zeitwerk (2.6.12)
+    zeitwerk (2.6.13)
 
 PLATFORMS
   ruby
@@ -471,7 +473,7 @@ DEPENDENCIES
   rails-controller-testing
   rake
   rspec-json_expectations
-  rspec-rails (= 6.1.0)
+  rspec-rails (= 6.1.1)
   rubocop
   rubocop-performance
   rubocop-rails

LICENSE

@@ -1,22 +1,21 @@
-Copyright (c) 2011-2021 Genome Research Ltd.
+MIT License
 
-Author:
-Eduardo Martin Rojo <[email protected]>
-James Glover <[email protected]>
-Matthew Denner <[email protected]>
-Sean Dunn <[email protected]>
-Stephen Inglis <[email protected]>
-Yana Proskurina <[email protected]>
+Copyright (c) 2024 Wellcome Sanger Institute - PSD
 
-This program is free software: you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 3 of the License, or (at your option) any later
-version.
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-This program is distributed in the hope that it will be useful, but WITHOUT
-ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
-details.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
-You should have received a copy of the GNU General Public License along with
-this program. If not, see <http://www.gnu.org/licenses/>.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

app/assets/stylesheets/limber/pipeline-graph.scss

@@ -89,7 +89,7 @@
     ul {
       @extend .list-group;
       @extend .list-group-flush;
-      max-height: 500px;
+      max-height: 50vh;
       overflow-y: auto;
 
       li {

app/assets/stylesheets/limber/screen.scss

@@ -535,7 +535,13 @@ footer.version-info {
   /* Set the fixed height of the footer here */
   height: 50px;
   line-height: 50px; /* Vertically center the text there */
+  overflow: hidden;
   background-color: $gray-100;
+
+  .container {
+    @extend .text-center;
+    @extend .text-nowrap;
+  }
 }
 
 .asset-warnings {

app/models/labels/base.rb

@@ -49,10 +49,6 @@ def label_template
   end
 
   def label_templates_by_service
-    # NB. Make sure label_templates.yml contains settings for label definitions
-    # explicity, in order to avoid incorrect results. The lines below do not
-    # work as intended because the config is filled with default values for
-    # missing settings by PurposeConfig class.
     pmb_template = config[:pmb_template] || default_label_template
     sprint_template = config[:sprint_template] || default_sprint_label_template
     { 'PMB' => pmb_template, 'SPrint' => sprint_template }