Merge branch 'develop' into 1390-dpl-916-pbmc-donor-pooling-create-plate

.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
+3.47.0

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/labware_creators/pcr_cycles_binned_plate/csv_file/duplex_seq/row.rb

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+# Part of the Labware creator classes
+module LabwareCreators
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_for_duplex_seq'
+
+  module PcrCyclesBinnedPlate::CsvFile
+    #
+    # This version of the row is for the Duplex Seq pipeline.
+    #
+    class DuplexSeq::Row < RowBase
+      include ActiveModel::Validations
+
+      SUB_POOL_NOT_BLANK = 'has a value when Submit for Sequencing is N, it should be empty, in %s'
+      SUBMIT_FOR_SEQ_INVALID = 'is empty or has an unrecognised value (should be Y or N), in %s'
+      COVERAGE_MISSING = 'is missing but should be present when Submit for Sequencing is Y, in %s'
+      COVERAGE_NEGATIVE = 'is negative but should be a positive value, in %s'
+
+      attr_reader :submit_for_sequencing, :sub_pool, :coverage
+
+      validate :submit_for_sequencing_has_expected_value
+      validate :sub_pool_within_expected_range
+      validates :coverage,
+                presence: {
+                  message: ->(object, _data) { COVERAGE_MISSING % object }
+                },
+                numericality: {
+                  greater_than: 0,
+                  message: ->(object, _data) { COVERAGE_NEGATIVE % object }
+                },
+                unless: -> { empty? || !submit_for_sequencing? }
+
+      delegate :submit_for_sequencing_column, :sub_pool_column, :coverage_column, to: :header
+
+      def initialize_pipeline_specific_columns
+        @submit_for_sequencing_as_string = @row_data[submit_for_sequencing_column]&.strip&.upcase
+        @sub_pool = @row_data[sub_pool_column]&.strip&.to_i
+        @coverage = @row_data[coverage_column]&.strip&.to_i
+      end
+
+      def submit_for_sequencing?
+        @submit_for_sequencing ||= (@submit_for_sequencing_as_string == 'Y')
+      end
+
+      def submit_for_sequencing_has_expected_value
+        return if empty?
+
+        return if %w[Y N].include? @submit_for_sequencing_as_string
+
+        errors.add('submit_for_sequencing', format(SUBMIT_FOR_SEQ_INVALID, to_s))
+      end
+
+      def sub_pool_within_expected_range
+        return if empty?
+
+        # check the value is within range when we do expect a value to be present
+        if submit_for_sequencing?
+          in_range('sub_pool', sub_pool, @row_config.sub_pool_min, @row_config.sub_pool_max)
+        else
+          # expect sub-pool field to be blank, possible mistake by user if not
+          return if sub_pool.blank?
+
+          # sub-pool is NOT blank and should be
+          errors.add('sub_pool', format(SUB_POOL_NOT_BLANK, to_s))
+        end
+      end
+    end
+  end
+end

app/models/labware_creators/pcr_cycles_binned_plate/csv_file/duplex_seq/well_details_header.rb

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+# Part of the Labware creator classes
+module LabwareCreators
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_for_duplex_seq'
+
+  module PcrCyclesBinnedPlate::CsvFile
+    #
+    # Class WellDetailsHeader provides a simple wrapper for handling and validating
+    # the plate barcode header row from the customer csv file
+    #
+    class DuplexSeq::WellDetailsHeader < WellDetailsHeaderBase
+      # Return the index of the respective column.
+      attr_reader :submit_for_sequencing_column, :sub_pool_column, :coverage_column
+
+      SUBMIT_FOR_SEQUENCING_COLUMN = 'Submit for sequencing (Y/N)?'
+      SUB_POOL_COLUMN = 'Sub-Pool'
+      COVERAGE_COLUMN = 'Coverage'
+      NOT_FOUND = 'could not be found in: '
+
+      validates :submit_for_sequencing_column, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+      validates :sub_pool_column, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+      validates :coverage_column, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+
+      private
+
+      def initialize_pipeline_specific_columns
+        @submit_for_sequencing_column = index_of_header(SUBMIT_FOR_SEQUENCING_COLUMN)
+        @sub_pool_column = index_of_header(SUB_POOL_COLUMN)
+        @coverage_column = index_of_header(COVERAGE_COLUMN)
+      end
+    end
+  end
+end

app/models/labware_creators/pcr_cycles_binned_plate/csv_file/plate_barcode_header.rb

@@ -2,7 +2,7 @@
 
 # Part of the Labware creator classes
 module LabwareCreators
-  require_dependency 'labware_creators/custom_pooled_tubes/csv_file'
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_base'
 
   #
   # Class PlateBarcodeHeader provides a simple wrapper for handling and validating
@@ -22,9 +22,10 @@ class PcrCyclesBinnedPlate::CsvFile::PlateBarcodeHeader
     BARCODE_NOT_MATCHING =
       'The plate barcode in the file (%s) does not match the barcode of ' \
         'the plate being uploaded to (%s), please check you have the correct file.'
+    NOT_FOUND = 'could not be found in: '
 
-    validates :barcode_lbl_index, presence: { message: ->(object, _data) { "could not be found in: '#{object}'" } }
-    validates :plate_barcode, presence: { message: ->(object, _data) { "could not be found in: '#{object}'" } }
+    validates :barcode_lbl_index, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+    validates :plate_barcode, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
     validate :plate_barcode_matches_parent?
 
     #