Merge pull request #4260 from sanger/develop

develop into master

.github/workflows/check_docker_build.yml

@@ -15,17 +15,17 @@ jobs:
 
       - name: Build image
         run: >-
-          docker-compose build
+          docker compose build
 
       - name: Start stack and wait for all healthy
         run: |
-          RESET_DATABASE=true docker-compose -f docker-compose.yml up &
-          while docker-compose ps -q | xargs docker inspect --format '{{ .State.Health.Status }}' | grep -v '^healthy$' ; do
+          RESET_DATABASE=true docker compose -f docker-compose.yml up &
+          while docker compose ps -q | xargs docker inspect --format '{{ .State.Health.Status }}' | grep -v '^healthy$' ; do
             sleep 30
             echo "Waiting for healthy containers"
           done
         timeout-minutes: 5
 
       - name: Stop stack
         run: >-
-          docker-compose down
+          docker compose down

.release-version

@@ -1 +1 @@
-14.39.0
+14.40.0

Gemfile.lock

@@ -121,7 +121,7 @@ GEM
     bootsnap (1.18.3)
       msgpack (~> 1.2)
     builder (3.3.0)
-    bullet (7.1.6)
+    bullet (7.2.0)
       activesupport (>= 3.0.0)
       uniform_notifier (~> 1.11)
     bunny (2.22.0)
@@ -279,7 +279,7 @@ GEM
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
       minitest (>= 5.3.3)
-    mocha (2.4.0)
+    mocha (2.4.5)
       ruby2_keywords (>= 0.0.5)
     msgpack (1.7.2)
     multi_json (1.15.0)
@@ -387,7 +387,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.1)
+    rexml (3.3.4)
       strscan
     roo (2.10.1)
       nokogiri (~> 1)
@@ -560,7 +560,7 @@ GEM
       backports (>= 3.18)
       rainbow
       yard
-    zeitwerk (2.6.16)
+    zeitwerk (2.6.17)
 
 PLATFORMS
   arm64-darwin

app/api/io/study.rb

@@ -26,6 +26,7 @@ class Io::Study < Core::Io::Base
           study_metadata.commercially_available     => commercially_available
     study_metadata.data_release_study_type.name     => data_release_sort_of_study
            study_metadata.data_release_strategy     => data_release_strategy
+study_metadata.contaminated_human_data_access_group     => contaminated_human_data_access_group
   '
   )
 end

app/models/api/study_io.rb

@@ -99,5 +99,6 @@ def render_class
     map_attribute_to_json_attribute(:hmdmc_approval_number, 'hmdmc_number')
     map_attribute_to_json_attribute(:s3_email_list)
     map_attribute_to_json_attribute(:data_deletion_period)
+    map_attribute_to_json_attribute(:contaminated_human_data_access_group)
   end
 end

app/models/request.rb

@@ -563,6 +563,11 @@ def product_line
   def manifest_processed!
   end
 
+  def self.get_all_comments(request)
+    counts = Comment.counts_for_requests([request])
+    counts[request.id]
+  end
+
   private
 
   def calculate_next_request_type_id

app/models/study.rb

@@ -256,6 +256,7 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     # External Customers
     custom_attribute(:s3_email_list)
     custom_attribute(:data_deletion_period)
+    custom_attribute(:contaminated_human_data_access_group)
 
     REMAPPED_ATTRIBUTES =
       {

app/views/requests/show.html.erb

@@ -1,7 +1,7 @@
 
 <% add :about, "This page displays details of requests" %>
 <% add :menu, "View event history" => history_request_path(@request) -%>
-<% add :menu, (pluralize @request.comments.size, "comment") => request_comments_path(@request) -%>
+<% add :menu, (pluralize Request.get_all_comments(@request), "comment") => request_comments_path(@request) -%>
 
 <% if can?(:cancel, @request) && @request.try(:may_cancel_before_started?) %>
   <% add :menu, { "Cancel" => cancel_request_url(@request) }, { confirm: "Are you sure you want to cancel this request?" }  -%>

app/views/shared/_batch.html.erb

@@ -55,8 +55,8 @@
         <% end %>
 
         <td><%= request.state.humanize %></td>
-
-        <td><%= link_to (pluralize request.comments.size, 'comment'),  request_comments_url(request) %></td>
+        
+        <td><%= link_to (pluralize Request.get_all_comments(request), 'comment'),  request_comments_url(request) %></td>
 
       </tr>
     <% end -%>

app/views/shared/metadata/edit/_study.html.erb

@@ -89,6 +89,7 @@
 
     <%= metadata_fields.text_field(:s3_email_list) %>
     <%= metadata_fields.select(:data_deletion_period, ['','3 months']) %>
+    <%= metadata_fields.text_field(:contaminated_human_data_access_group) %>
 
     <% metadata_fields.finalize_related_fields %>
   <% end %>

app/views/shared/metadata/show/_study.html.erb

@@ -60,6 +60,7 @@
       <% end %>
       <%= metadata_fields.plain_value(:dac_policy_title) %>
       <%= metadata_fields.plain_value(:dac_policy) %>
+      <%= metadata_fields.plain_value(:contaminated_human_data_access_group) %>
     <% end %>
   <% end %>
 <% end %>

config/default_records/request_types/014_limber_scrna_core_cdna_prep_request_types.wip.yml

@@ -28,8 +28,8 @@ limber_scrna_core_cdna_prep_input:
     - LRC PBMC Pools Input
   library_types:
     - Chromium single cell GEM-X 5p v3 GE
-limber_scrna_core_chromium_gem_x_5p_aggregation:
-  name: scRNA Core Chromium GEM-X 5p Aggregation
+limber_scrna_core_aggregation:
+  name: scRNA Core Aggregation
   asset_type: Well
   order: 1
   request_class_name: CustomerRequest

config/default_records/submission_templates/012_scrna_core_library_prep_submission_templates.wip.yml

@@ -1,9 +1,9 @@
 # Submission templates for the aggregation and library prep parts of the scRNA Core pipeline.
 ---
-Limber-Htp - scRNA Core Chromium GEM-X 5p Aggregation:
+Limber-Htp - scRNA Core Aggregation:
   submission_class_name: "LinearSubmission"
   related_records:
-    request_type_keys: ["limber_scrna_core_chromium_gem_x_5p_aggregation"]
+    request_type_keys: ["limber_scrna_core_aggregation"]
     product_line_name: Short Read
     product_catalogue_name: scRNA Core
 Limber-Htp - scRNA Core Library Prep:

config/locales/metadata/en.yml

@@ -508,6 +508,9 @@ en:
         data_deletion_period:
           label: Data deletion period
 
+        contaminated_human_data_access_group:
+          label: Contaminated Human Data Access Group
+          help: "Allows specified Unix groups and users access to data segregated from the main data product, which is potentially contaminated with human data. This access is typically rarely used and is primarily for validating the separation process, as we may not have the ethical or legal clearance."
     project:
       metadata:
         project_manager_id:

db/migrate/20240730085322_add_contaminated_human_data_access_group_to_study_metadata.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+class AddContaminatedHumanDataAccessGroupToStudyMetadata < ActiveRecord::Migration[6.1]
+  def change
+    add_column :study_metadata, :contaminated_human_data_access_group, :string, default: nil
+  end
+end