Merge branch 'develop' into develop-Y24-190

# Conflicts:
#	app/controllers/api/v2/tag_layouts_controller.rb

Gemfile.lock

@@ -34,72 +34,72 @@ GEM
   specs:
     aasm (5.5.0)
       concurrent-ruby (~> 1.0)
-    actioncable (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actioncable (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activestorage (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionmailbox (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      actionview (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionmailer (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      actionview (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.8.1)
-      actionview (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionpack (7.0.8.7)
+      actionview (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
     actionpack-xml_parser (2.0.1)
       actionpack (>= 5.0)
       railties (>= 5.0)
-    actiontext (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activestorage (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actiontext (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.8.1)
-      activesupport (= 7.0.8.1)
+    actionview (7.0.8.7)
+      activesupport (= 7.0.8.7)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (7.0.8.1)
-      activesupport (= 7.0.8.1)
+    activejob (7.0.8.7)
+      activesupport (= 7.0.8.7)
       globalid (>= 0.3.6)
-    activemodel (7.0.8.1)
-      activesupport (= 7.0.8.1)
-    activerecord (7.0.8.1)
-      activemodel (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    activemodel (7.0.8.7)
+      activesupport (= 7.0.8.7)
+    activerecord (7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
     activerecord-import (1.7.0)
       activerecord (>= 4.2)
-    activestorage (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    activestorage (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.8.1)
+    activesupport (7.0.8.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -196,7 +196,7 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
-    date (3.4.0)
+    date (3.4.1)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
     delayed_job_active_record (4.1.8)
@@ -206,7 +206,7 @@ GEM
     docile (1.4.0)
     domain_name (0.6.20240107)
     dry-cli (1.0.0)
-    erubi (1.13.0)
+    erubi (1.13.1)
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
@@ -257,7 +257,7 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     logger (1.6.1)
-    loofah (2.23.1)
+    loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.8.1)
@@ -273,7 +273,7 @@ GEM
     mime-types-data (3.2024.0305)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    minitest (5.25.1)
+    minitest (5.25.4)
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
       minitest (>= 5.3.3)
@@ -285,7 +285,7 @@ GEM
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
     mysql2 (0.5.6)
-    net-imap (0.5.1)
+    net-imap (0.5.5)
       date
       net-protocol
     net-ldap (0.19.0)
@@ -297,11 +297,11 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.4)
-    nokogiri (1.16.7-arm64-darwin)
+    nokogiri (1.18.1-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-darwin)
+    nokogiri (1.18.1-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-linux)
+    nokogiri (1.18.1-x86_64-linux-gnu)
       racc (~> 1.4)
     ostruct (0.6.0)
     parallel (1.26.3)
@@ -334,22 +334,22 @@ GEM
       rack (~> 2.2, >= 2.2.4)
     rack-proxy (0.7.7)
       rack
-    rack-test (2.1.0)
+    rack-test (2.2.0)
       rack (>= 1.3)
-    rails (7.0.8.1)
-      actioncable (= 7.0.8.1)
-      actionmailbox (= 7.0.8.1)
-      actionmailer (= 7.0.8.1)
-      actionpack (= 7.0.8.1)
-      actiontext (= 7.0.8.1)
-      actionview (= 7.0.8.1)
-      activejob (= 7.0.8.1)
-      activemodel (= 7.0.8.1)
-      activerecord (= 7.0.8.1)
-      activestorage (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    rails (7.0.8.7)
+      actioncable (= 7.0.8.7)
+      actionmailbox (= 7.0.8.7)
+      actionmailer (= 7.0.8.7)
+      actionpack (= 7.0.8.7)
+      actiontext (= 7.0.8.7)
+      actionview (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       bundler (>= 1.15.0)
-      railties (= 7.0.8.1)
+      railties (= 7.0.8.7)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -363,13 +363,13 @@ GEM
       activesupport (>= 4.2)
       choice (~> 0.2.0)
       ruby-graphviz (~> 1.2)
-    rails-html-sanitizer (1.6.0)
+    rails-html-sanitizer (1.6.2)
       loofah (~> 2.21)
-      nokogiri (~> 1.14)
+      nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     rails-perftest (0.0.7)
-    railties (7.0.8.1)
-      actionpack (= 7.0.8.1)
-      activesupport (= 7.0.8.1)
+    railties (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -515,7 +515,7 @@ GEM
     thor (1.3.2)
     tilt (2.4.0)
     timecop (0.9.10)
-    timeout (0.4.2)
+    timeout (0.4.3)
     traceroute (0.8.1)
       rails (>= 3.0.0)
     tzinfo (2.0.6)
@@ -535,7 +535,8 @@ GEM
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
     websocket (1.2.11)
-    websocket-driver (0.7.6)
+    websocket-driver (0.7.7)
+      base64
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     whenever (1.0.0)

app/controllers/api/v2/orders_controller.rb

@@ -8,5 +8,82 @@ class OrdersController < JSONAPI::ResourceController
       # By default JSONAPI::ResourceController provides most the standard
       # behaviour, and in many cases this file may be left empty.
     end
+
+    class OrderProcessor < JSONAPI::Processor
+      before_create_resource :prepare_context
+
+      private
+
+      def prepare_context
+        context[:template] = find_template
+        context[:template_attributes] = template_attributes unless context[:template].nil?
+      end
+
+      def find_template
+        template_uuid = params[:data][:attributes][:submission_template_uuid]
+        return nil if template_uuid.nil? # No errors -- we just don't have a template.
+
+        template = SubmissionTemplate.with_uuid(template_uuid).first
+        raise JSONAPI::Exceptions::InvalidFieldValue.new(:submission_template_uuid, template_uuid) if template.nil?
+
+        template
+      end
+
+      def template_attributes
+        parameters = params[:data][:attributes][:submission_template_attributes]
+
+        raise JSONAPI::Exceptions::ParameterMissing, :submission_template_attributes if parameters.nil?
+
+        make_template_attributes(permitted_attributes(parameters))
+      end
+
+      def permitted_attributes(attributes)
+        attributes.permit(
+          { asset_uuids: [], request_options: {} },
+          :autodetect_projects,
+          :autodetect_studies,
+          :user_uuid
+        )
+      end
+
+      def make_template_attributes(attributes)
+        {
+          assets: extract_assets(attributes),
+          autodetect_projects: attributes[:autodetect_projects],
+          autodetect_studies: attributes[:autodetect_studies],
+          request_options: require_attribute(attributes, :request_options),
+          user: extract_user(attributes)
+        }.compact
+      end
+
+      def extract_assets(attributes)
+        asset_uuids = require_attribute(attributes, :asset_uuids)
+        return nil if asset_uuids.nil?
+
+        asset_uuids.map do |uuid|
+          uuid_obj = Uuid.find_by(external_id: uuid)
+          raise JSONAPI::Exceptions::InvalidFieldValue.new(:asset_uuids, uuid) if uuid_obj.nil?
+          uuid_obj&.resource
+        end
+      end
+
+      def extract_user(attributes)
+        user_uuid = require_attribute(attributes, :user_uuid)
+        return nil if user_uuid.nil?
+
+        user = User.with_uuid(user_uuid).first
+        raise JSONAPI::Exceptions::InvalidFieldValue.new(:user_uuid, user_uuid) if user.nil?
+
+        user
+      end
+
+      def require_attribute(attributes, key)
+        value = attributes.require(key)
+        value = value.to_h if value.instance_of?(ActionController::Parameters) && value.permitted?
+        value
+      rescue ActionController::ParameterMissing
+        raise JSONAPI::Exceptions::ParameterMissing, "submission_template_attributes.#{key}"
+      end
+    end
   end
 end

app/controllers/samples_controller.rb

@@ -248,6 +248,7 @@ def default_permitted_metadata_fields
         subject
         treatment
         donor_id
+        huMFre_code
       ]
     }
   end

app/models/api/sample_io.rb

@@ -98,6 +98,7 @@ def json_root
     map_attribute_to_json_attribute(:treatment)
     map_attribute_to_json_attribute(:date_of_consent_withdrawn)
     map_attribute_to_json_attribute(:user_id_of_consent_withdrawn, 'marked_as_consent_withdrawn_by')
+    map_attribute_to_json_attribute(:huMFre_code)
   end
 
   extra_json_attributes do |_object, json_attributes|

app/models/order_template.rb

@@ -3,3 +3,6 @@
 # If we remove this, then we break our API endpoints. Some of which, at least at one point, actually had
 # external users.
 OrderTemplate = SubmissionTemplate
+
+# TODO: {API v1 removal} this alias was created for v1 and should not be in v2. When v1 is removed, we should try
+#       to remove this alias as well.

app/models/sample.rb

@@ -147,6 +147,8 @@ class Current < ActiveSupport::CurrentAttributes
     custom_attribute(:date_of_consent_withdrawn)
     custom_attribute(:user_id_of_consent_withdrawn)
 
+    custom_attribute(:huMFre_code)
+
     # These fields are warehoused, so need to match the encoding restrictions there
     # This excludes supplementary characters, which include emoji and rare kanji
     # @note phenotype isn't currently broadcast but has a field waiting in the warehouse
@@ -226,6 +228,17 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
+    # HuMFre numbers contain tissue information, which is only relevant for human samples.
+    validates :huMFre_code,
+              length: {
+                maximum: 16
+              },
+              format: {
+                with: %r{\A(?:\d{2}/\d{2,}|\d{2}/\d{4}-\d{3})\z},
+                message: 'must match a valid format, e.g. 12/34 or 12/2023-001'
+              },
+              allow_blank: true
+
     # This constraint doesn't match that described in the manifest, and is more permissive
     # It was added on conversion of out database to utf8 to address concerns that this would
     # lead to an increase in characters that their pipeline cannot process. Only a handful

app/resources/api/v2/base_resource.rb

@@ -17,6 +17,7 @@ class BaseResource < JSONAPI::Resource
       abstract
 
       # Loaded on the base class so that they can be loaded globally.
+      Order.descendants.each { |subclass| model_hint model: subclass, resource: :order }
       Purpose.descendants.each { |subclass| model_hint model: subclass, resource: :purpose }
       Plate.descendants.each { |subclass| model_hint model: subclass, resource: :plate }
       Tube.descendants.each { |subclass| model_hint model: subclass, resource: :tube }