Adding CONTRIBUTING.md

.nvmrc

@@ -1 +1 @@
-v24.13.1
+v24.14.0

.prettierignore

@@ -1,3 +1,4 @@
+*.md
 .bundle
 db/*.sqlite3
 log/*.log*

.release-version

@@ -1 +1 @@
-3.96.1
+3.96.0

.rubocop.yml

@@ -15,6 +15,9 @@ AllCops:
     - vendor/**/*
   NewCops: enable
 
+Layout/IndentationWidth:
+  EnforcedStyleAlignWith: relative_to_receiver
+
 Layout/LeadingCommentSpace:
   AllowRBSInlineAnnotation: true
 

.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config --no-exclude-limit`
-# on 2025-12-03 11:51:13 UTC using RuboCop version 1.81.7.
+# on 2026-03-16 10:14:34 UTC using RuboCop version 1.85.1.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
@@ -298,7 +298,7 @@ RSpec/MultipleDescribes:
     - 'spec/models/utility/normalised_binning_calculator_spec.rb'
     - 'spec/models/utility/pcr_cycles_binning_calculator_spec.rb'
 
-# Offense count: 248
+# Offense count: 249
 # Configuration parameters: Max.
 RSpec/MultipleExpectations:
   Exclude:
@@ -569,12 +569,37 @@ RSpecRails/TravelAround:
     - 'spec/models/presenters/permissive_submission_presenter_spec.rb'
     - 'spec/models/presenters/submission_plate_presenter_spec.rb'
 
+# Offense count: 2
+Style/FileOpen:
+  Exclude:
+    - 'script/limber'
+
 # Offense count: 2
 Style/MultilineBlockChain:
   Exclude:
     - 'app/controllers/pipelines_controller.rb'
     - 'app/models/labware_creators/tubes_from_plate_well.rb'
 
+# Offense count: 2
+# Configuration parameters: AllowedClasses.
+Style/OneClassPerFile:
+  Exclude:
+    - 'config/initializers/json_api_casters.rb'
+    - 'spec/models/concerns/presenters/statemachine/feature_in_states_spec.rb'
+
+# Offense count: 8
+# This cop supports unsafe autocorrection (--autocorrect-all).
+Style/ReduceToHash:
+  Exclude:
+    - 'app/helpers/exports_helper.rb'
+    - 'app/integrations/sequencescape/api/v2/tag_layout_template.rb'
+    - 'app/models/plate_walking.rb'
+    - 'app/models/tube_rack_walking.rb'
+    - 'app/models/utility/common_dilution_calculations.rb'
+    - 'lib/tasks/config.rake'
+    - 'lib/well_helpers.rb'
+    - 'spec/models/labware_creators/plate_split_to_tube_racks_spec.rb'
+
 # Offense count: 4
 # Configuration parameters: Max.
 Style/SafeNavigationChainLength:

.ruby-version

@@ -1 +1 @@
-3.4.8
+3.4.9

CONTRIBUTING.md

@@ -0,0 +1,30 @@
+# Contributing
+
+All contributions to this project are subject to the [MIT License](https://foss-haas.mit-license.org/). By submitting a contribution, you agree to license your work under these terms.
+
+## Contribution Process
+
+### 1. Issue First
+
+All contributions from outside the core team require an **Issue First** approach. Before submitting a pull request (PR), you must:
+
+- Open an issue in the repository.
+- Ensure the issue includes:
+  - **Clear problem statement:** Describe the issue or feature request.
+  - **Reproduction steps:** If reporting a bug, provide steps to reproduce it.
+  - **Proposed approach:** Outline your suggested solution or implementation.
+  - **Why this change matters:** Explain the impact or necessity of the change.
+- Tag `@sanger/psd-developers` in the issue to bring it to the attention of a maintainer.
+- Wait for the issue to be assigned or approved by a maintainer.
+
+### 2. Pull Request
+
+Once your issue is approved:
+
+- Fork the repository and create a branch for your changes.
+- Submit a PR referencing the approved issue.
+- Ensure your code adheres to the project's coding standards and passes all tests.
+
+### 3. Review
+
+Maintainers will review your PR. Address any feedback before merging.

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:3.4.8-slim
+FROM ruby:3.4.9-slim
 
 # Major version of Node.js to install
 ARG nodeVersion=22

Gemfile

@@ -57,7 +57,7 @@ group :development do
   gem 'guard-rspec', require: false
   gem 'pry'
   gem 'pry-byebug'
-  gem 'web-console'
+  gem 'web-console', '~> 4.2.1' # version 4.3.0 requires Rails 8.0
 
   # MiniProfiler allows you to see the speed of a request conveniently on the page.
   gem 'rack-mini-profiler'

Gemfile.lock

@@ -101,8 +101,8 @@ GEM
       minitest (>= 5.1)
       securerandom (>= 0.3)
       tzinfo (~> 2.0, >= 2.0.5)
-    addressable (2.8.7)
-      public_suffix (>= 2.0.2, < 7.0)
+    addressable (2.8.9)
+      public_suffix (>= 2.0.2, < 8.0)
     ast (2.4.3)
     base64 (0.3.0)
     benchmark (0.5.0)
@@ -113,9 +113,9 @@ GEM
       erubi (~> 1.4)
       parser (>= 2.4)
       smart_properties
-    bigdecimal (4.0.1)
+    bigdecimal (4.1.0)
     bindex (0.8.1)
-    bootsnap (1.22.0)
+    bootsnap (1.23.0)
       msgpack (~> 1.2)
     builder (3.3.0)
     byebug (13.0.0)
@@ -220,7 +220,10 @@ GEM
       prism (>= 1.3.0)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
-    json (2.18.1)
+    json (2.19.2)
+    json-schema (6.2.0)
+      addressable (~> 2.8)
+      bigdecimal (>= 3.1, < 5)
     language_server-protocol (3.17.0.5)
     launchy (3.1.1)
       addressable (~> 2.8)
@@ -231,7 +234,7 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     logger (1.7.0)
-    loofah (2.25.0)
+    loofah (2.25.1)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lumberjack (1.2.10)
@@ -243,6 +246,8 @@ GEM
       net-smtp
     marcel (1.1.0)
     matrix (0.4.2)
+    mcp (0.9.2)
+      json-schema (>= 4.1)
     method_source (1.1.0)
     mini_mime (1.1.5)
     mini_portile2 (2.8.9)
@@ -263,18 +268,18 @@ GEM
     net-smtp (0.5.1)
       net-protocol
     nio4r (2.7.5)
-    nokogiri (1.19.1)
+    nokogiri (1.19.2)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    oj (3.16.15)
+    oj (3.16.16)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     ostruct (0.6.3)
     parallel (1.27.0)
-    parser (3.3.10.1)
+    parser (3.3.10.2)
       ast (~> 2.4.1)
       racc
     pp (0.6.3)
@@ -292,7 +297,7 @@ GEM
     psych (5.3.1)
       date
       stringio
-    public_suffix (6.0.2)
+    public_suffix (7.0.5)
     puma (7.2.0)
       nio4r (~> 2.0)
     racc (1.8.1)
@@ -368,30 +373,31 @@ GEM
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-json_expectations (2.2.0)
-    rspec-mocks (3.13.7)
+    rspec-mocks (3.13.8)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (8.0.3)
+    rspec-rails (8.0.4)
       actionpack (>= 7.2)
       activesupport (>= 7.2)
       railties (>= 7.2)
-      rspec-core (~> 3.13)
-      rspec-expectations (~> 3.13)
-      rspec-mocks (~> 3.13)
-      rspec-support (~> 3.13)
+      rspec-core (>= 3.13.0, < 5.0.0)
+      rspec-expectations (>= 3.13.0, < 5.0.0)
+      rspec-mocks (>= 3.13.0, < 5.0.0)
+      rspec-support (>= 3.13.0, < 5.0.0)
     rspec-support (3.13.7)
-    rubocop (1.84.1)
+    rubocop (1.85.1)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
+      mcp (~> 0.6)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 2.9.3, < 3.0)
       rubocop-ast (>= 1.49.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.49.0)
+    rubocop-ast (1.49.1)
       parser (>= 3.3.7.2)
       prism (~> 1.7)
     rubocop-capybara (2.22.1)
@@ -419,7 +425,7 @@ GEM
     ruby2_keywords (0.0.5)
     rubyzip (3.2.2)
     securerandom (0.4.1)
-    selenium-webdriver (4.40.0)
+    selenium-webdriver (4.41.0)
       base64 (~> 0.2)
       logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)
@@ -460,10 +466,10 @@ GEM
       unicode-emoji (~> 4.1)
     unicode-emoji (4.2.0)
     useragent (0.16.11)
-    vite_rails (3.0.20)
+    vite_rails (3.10.0)
       railties (>= 5.1, < 9)
       vite_ruby (~> 3.0, >= 3.2.2)
-    vite_ruby (3.9.2)
+    vite_ruby (3.10.0)
       dry-cli (>= 0.7, < 2)
       logger (~> 1.6)
       mutex_m
@@ -474,7 +480,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.26.1)
+    webmock (3.26.2)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -534,7 +540,7 @@ DEPENDENCIES
   syslog
   vite_rails
   vite_ruby
-  web-console
+  web-console (~> 4.2.1)
   webmock
   yard
 

app/integrations/sequencescape/api/v2/plate.rb

@@ -16,7 +16,7 @@ class Sequencescape::Api::V2::Plate < Sequencescape::Api::V2::Base
 
   DEFAULT_INCLUDES = [
     :purpose,
-    { wells: [requests_as_source: %i[primer_panel], aliquots: [request: %i[primer_panel request_type]]] }
+    { wells: [{ requests_as_source: %i[primer_panel], aliquots: [{ request: %i[primer_panel request_type] }] }] }
   ].freeze
 
   self.plate = true

app/models/concerns/presenters/statemachine/submission_when_input_and_when_passed.rb

@@ -0,0 +1,92 @@
+# frozen_string_literal: true
+
+require_dependency 'presenters/statemachine'
+module Presenters::Statemachine
+  #
+  # Presenters::Statemachine::SubmissionWhenInputAndWhenPassed can be included in a class to
+  # provide a state machine with the following behaviour:
+  # - When plates are 'pending' the submission sidebar will be displayed.
+  #   This sidebar allows the user to build a submission for an input plate.
+  # - When plates are 'passed' the submission sidebar will also be displayed.
+  #   This sidebar allows the user to build a submission for a plate that has already been through
+  #   the pipeline before. Used for repeating runs.
+  # - In all other states the default sidebar will be used
+  # - When the plate is passed, the user will be allowed to create the child plates
+  # - In all other states the user will be unable to advanced the plate
+  #
+  # Typically this state machine should be used in conjunction with an input
+  # plate purpose. {file:docs/purposes_yaml_files.md See the purposes yaml configuration.}
+  # Purposes with input_plate set to true use the PlatePurpose::Input class in sequencescape.
+  # These plates show the following states:
+  # Pending: No submission made, or some wells with samples have no submissions
+  # Passed: Initial Submission has been made, and the plate is ready to proceed, or previous run has
+  # completed, but ready for a repeat run.
+  # Cancelled/Failed: Seen when all requests out of the plate have these states.
+  #
+  # Other states: Typically not seen in standard scenarios.
+  module SubmissionWhenInputAndWhenPassed
+    extend ActiveSupport::Concern
+
+    included do
+      include Shared
+
+      # The state machine for plates which has knock-on effects on the plates that can be created
+      state_machine :state, initial: :pending do
+        StateTransitions.inject(self)
+
+        # These are the states, which are really the only things we need ...
+        state :pending do
+          include StateDoesNotAllowChildCreation
+
+          def sidebar_partial
+            'submission'
+          end
+        end
+
+        state :started do
+          include StateDoesNotAllowChildCreation
+        end
+
+        state :processed_1 do
+          include StateAllowsChildCreation
+        end
+
+        state :processed_2 do
+          include StateDoesNotAllowChildCreation
+        end
+
+        state :processed_3 do
+          include StateDoesNotAllowChildCreation
+        end
+
+        state :processed_4 do
+          include StateDoesNotAllowChildCreation
+        end
+
+        state :passed do
+          include StateAllowsChildCreation
+
+          def sidebar_partial
+            'submission_default'
+          end
+        end
+
+        state :qc_complete, human_name: 'QC Complete' do
+          include StateAllowsChildCreation
+        end
+
+        state :cancelled do
+          include StateDoesNotAllowChildCreation
+        end
+
+        state :failed do
+          include StateDoesNotAllowChildCreation
+        end
+
+        state :unknown do
+          include StateDoesNotAllowChildCreation
+        end
+      end
+    end
+  end
+end