Merge pull request #4045 from sanger/develop

DPL-1101: Accept RVI Barcodes

.release-version

@@ -1 +1 @@
-14.31.0
+14.31.1

Gemfile

@@ -62,7 +62,17 @@ group :default do
   # https://github.com/JamesGlover/sequencescape/tree/depfu/update/jsonapi-resources-0.9.5
   # but not only is there a failing test, but performance was tanking in a few places
   # due to not correctly eager loading dependencies on nested resources.
-  gem 'jsonapi-resources', '0.9.0'
+
+  # Versions above 0.9.0 are incompatible and it is too much work to upgrade at
+  # this time. Implementing new patches for updates is not a long term solution
+  # as the internals keep changing. However, version 0.9.0 is blocking us from
+  # updating rails to version 6.1 . The following steps show the process for an
+  # alternative solution:
+  # - Fork jsonpi-resources repository
+  # - Create a branch off version 0.9.0
+  # - Remove the ActionController::ForceSSL module
+  # - Load the gem from the branch
+  gem 'jsonapi-resources', github: 'sanger/jsonapi-resources', branch: 'develop'
 
   # Wraps bunny with connection pooling ad consumer process handling
   gem 'sanger_warren'

Gemfile.lock

@@ -7,6 +7,16 @@ GIT
       activemodel
       activerecord (>= 4.0.0)
 
+GIT
+  remote: https://github.com/sanger/jsonapi-resources.git
+  revision: be2fb43f5f8da2e632fb5f48200928b2dd3d8bf9
+  branch: develop
+  specs:
+    jsonapi-resources (0.9.0)
+      activerecord (>= 4.1)
+      concurrent-ruby
+      railties (>= 4.1)
+
 GIT
   remote: https://github.com/sanger/record_loader
   revision: 9e7481f4d2342f042ab13465962e5d6689863198
@@ -76,7 +86,7 @@ GEM
     activerecord (6.0.6.1)
       activemodel (= 6.0.6.1)
       activesupport (= 6.0.6.1)
-    activerecord-import (1.5.0)
+    activerecord-import (1.5.1)
       activerecord (>= 4.2)
     activeresource (6.0.0)
       activemodel (>= 6.0)
@@ -103,7 +113,7 @@ GEM
     bootsnap (1.16.0)
       msgpack (~> 1.2)
     builder (3.2.4)
-    bullet (7.1.1)
+    bullet (7.1.6)
       activesupport (>= 3.0.0)
       uniform_notifier (~> 1.11)
     bunny (2.22.0)
@@ -135,7 +145,7 @@ GEM
     choice (0.2.0)
     chronic (0.10.2)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     configatron (4.5.1)
     connection_pool (2.4.1)
     crack (0.4.5)
@@ -184,7 +194,7 @@ GEM
     date (3.3.3)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
-    delayed_job_active_record (4.1.7)
+    delayed_job_active_record (4.1.8)
       activerecord (>= 3.0, < 8.0)
       delayed_job (>= 3.0, < 5)
     diff-lcs (1.5.0)
@@ -221,16 +231,12 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    i18n (1.14.1)
+    i18n (1.14.4)
       concurrent-ruby (~> 1.0)
     image_processing (1.12.2)
       mini_magick (>= 4.9.5, < 5)
       ruby-vips (>= 2.0.17, < 3)
     json (2.6.3)
-    jsonapi-resources (0.9.0)
-      activerecord (>= 4.1)
-      concurrent-ruby
-      railties (>= 4.1)
     jsonapi-resources-matchers (1.0.0)
       jsonapi-resources (>= 0.9.0)
     knapsack_pro (5.7.0)
@@ -257,8 +263,8 @@ GEM
     mime-types-data (3.2023.0808)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.4)
-    minitest (5.20.0)
+    mini_portile2 (2.8.5)
+    minitest (5.22.2)
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
       minitest (>= 5.3.3)
@@ -282,7 +288,7 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.0)
-    nokogiri (1.15.4)
+    nokogiri (1.16.2)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     parallel (1.23.0)
@@ -301,10 +307,10 @@ GEM
     puma (6.4.2)
       nio4r (~> 2.0)
     racc (1.7.3)
-    rack (2.2.8)
+    rack (2.2.8.1)
     rack-acceptable (0.1.0)
       rack (>= 1.1.0)
-    rack-cors (2.0.1)
+    rack-cors (2.0.2)
       rack (>= 2.0.0)
     rack-mini-profiler (3.1.1)
       rack (>= 1.2.0)
@@ -520,10 +526,10 @@ GEM
       will_paginate (>= 3.0.3)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    yard (0.9.34)
+    yard (0.9.36)
     yard-activerecord (0.0.16)
       yard (>= 0.8.3)
-    zeitwerk (2.6.12)
+    zeitwerk (2.6.13)
 
 PLATFORMS
   ruby
@@ -555,7 +561,7 @@ DEPENDENCIES
   flipper-ui (~> 0.25.0)
   formtastic
   json
-  jsonapi-resources (= 0.9.0)
+  jsonapi-resources!
   jsonapi-resources-matchers
   knapsack_pro
   launchy

LICENSE

@@ -1,55 +1,21 @@
-Sequencescape - A open source project and lab management systems
+MIT License
 
-Authors:
-Andrew Page <andrewjpage@gmail.com>
-Andrew Sparkes <as28@sanger.ac.uk>
-Arfon Smith <as8@sanger.ac.uk>
-Beth Jones <bj2@sanger.ac.uk>
-Cinzia Malangone <cm10@sanger.ac.uk>
-Conny Brunnkvist <cb16@sanger.ac.uk>
-Constantine Nicolou <cn5@sanger.ac.uk>
-David Franklin <df2@sanger.ac.uk>
-Eduardo Martin Rojo <emr@sanger.ac.uk>
-Harriet Craven <hc6@sanger.ac.uk>
-James Glover <james.glover@sanger.ac.uk>
-Jens Raaby <jr16@sanger.ac.uk>
-Kate Taylor <kt6@sanger.ac.uk>
-Lars G T Jorgensen <lj3@sanger.ac.uk>
-Luca Da Rin Fioretto <ldrf@sanger.ac.uk>
-Matthew Astley <mca@sanger.ac.uk>
-Matthew Denner <md12@sanger.ac.uk>
-Matt Wood <mw4@sanger.ac.uk>
-Maxime Bourget <mb14@sanger.ac.uk>
-Neil Sycamore <nts@sanger.ac.uk>
-Niels Jansen <nj3@sanger.ac.uk>
-Paul Thornthwaite <pt2@sanger.ac.uk>
-Paul Western <pw6@sanger.ac.uk>
-Sean Dunn <sd9@sanger.ac.uk>
-Simon Holroyd <holroyd@sanger.ac.uk>
-Stephen Inglis <si5@sanger.ac.uk>
-Yana Proskurina <yp3@sanger.ac.uk>
+Copyright (c) 2024 Wellcome Sanger Institute - PSD
 
+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 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 1, or (at your option)
-any later version.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
-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.
-
-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 usage of a range of years within a copyright statement contained within
-this distribution should be interpreted as being equivalent to a list of years
-including the first and last year specified and all consecutive years between
-them. For example, a copyright statement that reads "Copyright (c) 2005, 2007-
-2009, 2011-2012" should be interpreted as being identical to a statement that
-reads "Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright
-statement that reads "Copyright (c) 2005-2012" should be interpreted as being
-identical to a statement that reads "Copyright (c) 2005, 2006, 2007, 2008, 2009
-, 2010 , 2011 , 2012".
+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/models/barcode.rb

@@ -65,7 +65,8 @@ class Barcode < ApplicationRecord
          plymouth_v2: 43,
          leamington_spa_v3: 44,
          brants_bridge_v3: 45,
-         ibd_response: 46
+         ibd_response: 46,
+         rvi: 47
        }
 
   # Barcode formats which may be submitted via sample manifests
@@ -112,6 +113,7 @@ class Barcode < ApplicationRecord
     leamington_spa_v3
     brants_bridge_v3
     ibd_response
+    rvi
   ].freeze
 
   validate :barcode_valid?

app/models/barcode/format_handlers.rb

@@ -569,4 +569,12 @@ class EastLondonGenesAndHealthV2 < BaseRegExBarcode
   class IbdResponse < BaseRegExBarcode
     self.format = /\A(?<prefix>IBDR)(?<number>[0-9]{6})\z/
   end
+
+  # Support for RVI barcodes.
+  # Expected formats:
+  # RVI-nnnnnn
+  # where n is a digit
+  class Rvi < BaseRegExBarcode
+    self.format = /\A(?<prefix>RVI)-(?<number>[0-9]{6,})\z/
+  end
 end

app/models/labware.rb

@@ -231,6 +231,15 @@ def scanned_in_date
     scanned_into_lab_event.try(:content) || ''
   end
 
+  def received_date
+    self
+      &.asset_audits
+      &.where(key: 'slf_receive_plates')
+      &.where('message LIKE ?', '%Reception fridge%')
+      &.last
+      &.created_at
+  end
+
   def retention_instructions
     @retention_instructions ||= obtain_retention_instructions
   end

app/models/location_report.rb

@@ -80,7 +80,19 @@ def check_maxlength_of_barcodes
   end
 
   def column_headers
-    %w[ScannedBarcode HumanBarcode Type Created Location Service RetentionInstructions StudyName StudyId FacultySponsor]
+    %w[
+      ScannedBarcode
+      HumanBarcode
+      Type
+      Created
+      ReceivedDate
+      Location
+      Service
+      RetentionInstructions
+      StudyName
+      StudyId
+      FacultySponsor
+    ]
   end
 
   def generate!
@@ -140,15 +152,16 @@ def generate_report_row(cur_plate, cur_study)
   end
 
   def generate_plate_cols_for_row(cur_plate)
-    cols = [] << cur_plate.machine_barcode
-    cols << cur_plate.human_barcode
-
-    # NB. some older plates do not have a purpose
-    cols << (cur_plate.plate_purpose&.name || 'Unknown')
-    cols << cur_plate.created_at.strftime('%Y-%m-%d %H:%M:%S')
-    cols << cur_plate.storage_location
-    cols << cur_plate.storage_location_service
-    cols << (cur_plate.retention_instructions || 'Unknown')
+    [
+      cur_plate.machine_barcode,
+      cur_plate.human_barcode,
+      cur_plate.plate_purpose&.name || 'Unknown', # NB. some older plates do not have a purpose
+      cur_plate.created_at.strftime('%Y-%m-%d %H:%M:%S'),
+      cur_plate.received_date&.strftime('%Y-%m-%d %H:%M:%S') || 'Unknown',
+      cur_plate.storage_location,
+      cur_plate.storage_location_service,
+      cur_plate.retention_instructions || 'Unknown'
+    ]
   end
 
   def generate_study_cols_for_row(cur_study)

app/models/study.rb

@@ -262,6 +262,8 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     # This excludes supplementary characters, which include emoji and rare kanji
     validates :study_abstract, :study_study_title, :study_description, :s3_email_list, utf8mb3: true
 
+    validates :data_release_delay_other_comment, length: { maximum: 255 }
+
     # These fields are restricted further as they aren't expected to ever contain anything more than ASCII
     validates :study_project_id,
               :ega_dac_accession_number,