renalware-core 2.0.146 → 2.0.152

data/app/models/renalware/transplants/recipient_operation.rb

@@ -19,8 +19,11 @@ module Renalware
       scope :reversed, -> { order(performed_on: :desc) }
       scope :most_recent, -> { order(performed_on: :desc).first }
 
-      has_paper_trail class_name: "Renalware::Transplants::Version",
-                      on: [:create, :update, :destroy]
+      has_paper_trail(
+        versions: { class_name: "Renalware::Transplants::Version" },
+        on: [:create, :update, :destroy]
+      )
+
       has_document class_name: "Renalware::Transplants::RecipientOperationDocument"
 
       validates :performed_on, presence: true

data/app/models/renalware/transplants/recipient_workup.rb

@@ -12,8 +12,11 @@ module Renalware
 
       belongs_to :patient, touch: true
 
-      has_paper_trail class_name: "Renalware::Transplants::Version",
-                      on: [:create, :update, :destroy]
+      has_paper_trail(
+        versions: { class_name: "Renalware::Transplants::Version" },
+        on: [:create, :update, :destroy]
+      )
+
       has_document class_name: "Renalware::Transplants::RecipientWorkupDocument"
     end
   end

data/app/models/renalware/transplants/recipient_workup_builder.rb

@@ -20,6 +20,7 @@ module Renalware
       private
 
       attr_reader :workup, :default_consenter_name
+
       delegate :document, to: :workup
 
       def assign_default_consenter

data/app/models/renalware/transplants/registration.rb

@@ -18,8 +18,11 @@ module Renalware
               class_name: "RegistrationStatus",
               foreign_key: "registration_id"
 
-      has_paper_trail class_name: "Renalware::Transplants::Version",
-                      on: [:create, :update, :destroy]
+      has_paper_trail(
+        versions: { class_name: "Renalware::Transplants::Version" },
+        on: [:create, :update, :destroy]
+      )
+
       has_document class_name: "Renalware::Transplants::RegistrationDocument"
 
       accepts_nested_attributes_for :statuses

data/app/models/renalware/transplants/registration_status.rb

@@ -14,7 +14,7 @@ module Renalware
       scope :reversed, -> { order(started_on: :desc, created_at: :desc) }
 
       validates :description_id, presence: true
-      validates :started_on, timeliness: { type: :date, allow_blank: false }
+      validates :started_on, presence: true, timeliness: { type: :date, allow_blank: false }
       validates :terminated_on, timeliness: { type: :date, allow_blank: true }
 
       validate :constraint_started_on_today_or_before, if: :started_on

data/app/models/renalware/transplants/rejection_episode.rb

@@ -7,7 +7,7 @@ module Renalware
     class RejectionEpisode < ApplicationRecord
       include Accountable
       has_paper_trail(
-        class_name: "Renalware::Transplants::Version",
+        versions: { class_name: "Renalware::Transplants::Version" },
         on: [:create, :update, :destroy]
       )
       belongs_to :followup, class_name: "RecipientFollowup", touch: true

data/app/models/renalware/ukrdc/{batch_number.rb → batch.rb}

@@ -4,7 +4,7 @@ require_dependency "renalware/ukrdc"
 
 module Renalware
   module UKRDC
-    class BatchNumber < ApplicationRecord
+    class Batch < ApplicationRecord
       def self.next
         create!
       end

data/app/models/renalware/ukrdc/create_encrypted_patient_xml_files.rb

@@ -16,9 +16,8 @@ module Renalware
         :patient_ids,
         :changed_since,
         :logger,
-        :request_uuid,
         :timestamp,
-        :batch_number,
+        :batch,
         :summary,
         :force_send
       )
@@ -27,16 +26,15 @@ module Renalware
         @changed_since = Time.zone.parse(changed_since) if changed_since.present?
         @patient_ids = Array(patient_ids)
         @logger = logger || Rails.logger
-        @request_uuid = SecureRandom.uuid # helps group logs together
         @timestamp = Time.zone.now.strftime("%Y%m%d%H%M%S%L")
-        @batch_number ||= BatchNumber.next.number
+        @batch ||= Batch.next
         @summary = ExportSummary.new
         @force_send = force_send
       end
 
       # rubocop:disable Metrics/MethodLength
       def call
-        logger.tagged(request_uuid) do
+        logger.tagged(batch.number) do
           summary.milliseconds_taken = Benchmark.ms do
             create_patient_xml_files
             encrypt_patient_xml_files
@@ -48,7 +46,7 @@ module Renalware
           email_summary
         end
       rescue StandardError => e
-        # TODO: if fails before copying to outgoing then we should roll back BatchNumber
+        # TODO: if fails before copying to outgoing then we should roll back Batch
         Engine.exception_notifier.notify(e)
         raise e
       end
@@ -60,37 +58,64 @@ module Renalware
         @paths ||= begin
           Paths.new(
             timestamp: timestamp,
-            batch_number: batch_number,
+            batch_number: batch.number,
             working_path: config.ukrdc_working_path
           )
         end
       end
 
-      # rubocop:disable Metrics/MethodLength
+      # If UKRDC_THREADS is set to a nonzero value (eg 4 but depending on CPUs/cores),
+      # a threadpool containing that number of threads is created and XML creation
+      # (including PDF letter rendering) for that patient happens in a separate thread.
+      # The performance increase in doing it this way is marginal unless there are
+      # PDFs to be rendered, which can introduce significant IO wait. As PDFs are cached
+      # by the PDFLetterCache, using threads may have limited benefit but
+      # rubocop:disable Metrics/MethodLength, Metrics/AbcSize
       def create_patient_xml_files
         count = 0
         patients = ukrdc_patients_who_have_changed_since_last_send
         summary.num_changed_patients = patients.count
         schema = UKRDC::XsdSchema.new
-        patients.find_each do |patient|
+        thread_count = ENV["UKRDC_THREADS"].to_i
+        use_threads = thread_count.nonzero?
+
+        if use_threads
+          thread_pool = Concurrent::ThreadPoolExecutor.new(max_threads: thread_count)
+        end
+
+        patients.map do |patient|
           count += 1
           Rails.logger.info count
-          CreatePatientXMLFile.new(
-            patient: patient,
-            dir: paths.timestamped_xml_folder,
-            changes_since: changed_since,
-            request_uuid: request_uuid,
-            batch_number: batch_number,
-            logger: logger,
-            force_send: force_send,
-            schema: schema
-          ).call
-
-          # Every n patients, force the garbage collector to kick in
-          # GC.start if (count % 10).zero?
+          if use_threads
+            thread_pool.post do
+              Rails.logger.info "Thread #{Thread.current.object_id}"
+              ActiveRecord::Base.connection_pool.with_connection do
+                create_xml_file(patient: patient, schema: schema)
+              end
+            end
+          else
+            create_xml_file(patient: patient, schema: schema)
+          end
+        end
+      ensure
+        if use_threads
+          thread_pool.shutdown
+          thread_pool.wait_for_termination
         end
       end
-      # rubocop:enable Metrics/MethodLength
+      # rubocop:enable Metrics/MethodLength, Metrics/AbcSize
+
+      def create_xml_file(patient:, schema:)
+        CreatePatientXMLFile.new(
+          patient: patient,
+          dir: paths.timestamped_xml_folder,
+          changes_since: changed_since,
+          batch: batch,
+          logger: logger,
+          force_send: force_send,
+          schema: schema
+        ).call
+      end
 
       def build_summary
         summary.count_of_files_in_outgoing_folder = count_of_files_in_outgoing_folder
@@ -141,7 +166,7 @@ module Renalware
       end
 
       def export_results
-        TransmissionLog.where(request_uuid: request_uuid).group(:status).count(:status).to_h
+        TransmissionLog.where(batch_id: batch.id).group(:status).count(:status).to_h
       end
 
       def encrypt_patient_xml_files

data/app/models/renalware/ukrdc/create_patient_xml_file.rb

@@ -9,11 +9,10 @@ module Renalware
       pattr_initialize [
         :patient!,
         :dir!,
-        :request_uuid!,
         :schema!,
         :changes_since,
         :logger,
-        :batch_number,
+        :batch,
         :renderer, # so we can pass a test renderer to bypass real rendering
         :log,
         :force_send
@@ -24,7 +23,7 @@ module Renalware
       # send. This is primarily for debugging and testing phases with UKRDC
       def call
         update_patient_to_indicated_we_checked_them_for_any_relevant_changes
-        UKRDC::TransmissionLog.with_logging(patient, request_uuid) do |log|
+        UKRDC::TransmissionLog.with_logging(patient: patient, batch: batch) do |log|
           @log = log
           logger.info "  Patient #{patient.ukrdc_external_id}"
           xml_payload = build_payload(log)
@@ -86,7 +85,7 @@ module Renalware
           nil
         else
           Payload.new(result.xml).tap do |payload|
-            log.payload = payload.to_s
+            # log.payload = payload.to_s
             log.payload_hash = payload.to_md5_hash
           end
         end
@@ -117,7 +116,7 @@ module Renalware
       end
 
       def xml_filepath
-        xml_filename = Filename.new(patient: patient, batch_number: batch_number).to_s
+        xml_filename = Filename.new(patient: patient, batch_number: batch.number).to_s
         File.join(dir, xml_filename)
       end
 

data/app/models/renalware/ukrdc/housekeeping/remove_old_export_archive_folders.rb

@@ -8,7 +8,7 @@ module Renalware
     module Housekeeping
       # Responsible for cleaning up old archive folders that are created each time the
       # ukrdc:export task has run. Each archive folder's name has a batch number in it which is the
-      # id of the UKRDC::BatchNumber model created at the start of each export. We can find the
+      # id of the UKRDC::Batch model created at the start of each export. We can find the
       # folders to remove by extracting the batch number from the folder name and deleting the
       # folder if that batch is no longer 'recent'.
       # Called from a housekeeping rake task.
@@ -64,12 +64,12 @@ module Renalware
           Renalware.config.ukrdc_number_of_archived_folders_to_keep.to_i
         end
 
-        # Returns the ids of a few of the most recent BatchNumbers rows (ie the batch number) that
+        # Returns the ids of a few of the most recent Batch rows (ie the batch number) that
         # we should not delete - these being the most recent ones we want to stick around in case we
         # need to inspect what was sent.
         def batch_numbers_to_keep
           @batch_numbers_to_keep ||= begin
-            BatchNumber
+            Batch
               .limit(number_of_archived_folders_to_keep)
               .order(created_at: :desc)
               .pluck(:id)

data/app/models/renalware/ukrdc/housekeeping/remove_stale_files.rb

@@ -53,11 +53,11 @@ module Renalware
           Renalware.config.ukrdc_number_of_archived_folders_to_keep.to_i
         end
 
-        # Returns the ids of a few of the most recent BatchNumbers rows (ie the batch number) that
+        # Returns the ids of a few of the most recent Batch rows (ie the batch number) that
         # we should not delete - these being the most recent ones
         def batch_numbers_to_keep
           @batch_numbers_to_keep ||= begin
-            BatchNumber
+            Batch
               .limit(number_of_batches_to_keep)
               .order(created_at: :desc)
               .pluck(:id)

data/app/models/renalware/ukrdc/incoming/import_surveys.rb

@@ -23,7 +23,6 @@ module Renalware
               FileUtils.mv filepath, paths.archive.join(filepath.basename)
               next
             end
-
             logger.info "Processing: #{filepath}"
             import_surveys_from_file(filepath)
           end
@@ -49,7 +48,7 @@ module Renalware
         def import_surveys_from_file(file)
           # Important to create the log before we do anything that might cause an error
           # eg parse the xml etc.
-          TransmissionLog.with_logging(nil, batch_uuid, log_options(file)) do |log|
+          TransmissionLog.with_logging(request_uuid: batch_uuid, **log_options(file)) do |log|
             doc = XmlDocument.new(file)
             patient = find_patient(doc.nhs_number)
             log.update!(patient_id: patient.id)

data/app/models/renalware/ukrdc/outgoing/rendering/patient_number.rb

@@ -15,7 +15,7 @@ module Renalware
 
           def name_element
             create_node("PatientNumber") do |elem|
-              elem << create_node("Number", number)
+              elem << create_node("Number", number&.delete(" "))
               elem << create_node("Organization", organisation)
               elem << create_node("NumberType", type)
             end

data/app/models/renalware/ukrdc/transmission_log.rb

@@ -17,12 +17,13 @@ module Renalware
       }
       enum direction: { out: 0, in: 1 }
       scope :ordered, -> { order(sent_at: :asc) }
+      belongs_to :batch
 
-      def self.with_logging(patient, request_uuid, **options)
+      def self.with_logging(patient: nil, batch: nil, **options)
         log = new(
           patient: patient,
           sent_at: Time.zone.now,
-          request_uuid: request_uuid,
+          batch: batch,
           **options)
         yield log if block_given?
         log.save!

data/app/models/renalware/user.rb

@@ -42,6 +42,8 @@ module Renalware
     scope :hidden, -> { where(hidden: true) }
     scope :picklist, -> { visible.ordered }
 
+    store_accessor :preferences, :experimental_features
+
     # Non-persistent attribute to signify we want to use extended validation.
     # We need to refactor this by ising a form object for updating a user.
     attr_accessor :with_extended_validation
@@ -100,6 +102,14 @@ module Renalware
     #   Pundit.policy(self, record).public_send(method.to_sym)
     # end
 
+    # We can enable experiment features for particular users using the bitmask user#feature_flags
+    # property and bitwise operators.
+    # For example given the the feature flag FANCY_GRAPHS = 2, we if they user should see these with
+    #   FANCY_GRAPHS & feature_flags == FANCY_GRAPHS
+    def wants_feature?(flag)
+      (flag & feature_flags) == flag
+    end
+
     private
 
     def build_authentication_token

data/app/pdfs/renalware/events/event_pdf.rb

@@ -12,6 +12,7 @@ module Renalware
     class EventPdf
       include Prawn::View
       attr_reader :event
+
       delegate :patient, :event_type, to: :event
 
       def initialize(event)

data/app/policies/renalware/events/advanced_care_plan_policy.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/messaging"
+
+module Renalware
+  module Events
+    class AdvancedCarePlanPolicy < BasePolicy
+    end
+  end
+end

data/app/policies/renalware/events/clinical_frailty_score_policy.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/messaging"
+
+module Renalware
+  module Events
+    class ClinicalFrailtyScorePolicy < BasePolicy
+    end
+  end
+end

data/app/policies/renalware/pd/adequacy_result_policy.rb

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+module Renalware
+  module PD
+    class AdequacyResultPolicy < BasePolicy
+      def destroy?
+        user_is_admin? || user_is_super_admin?
+      end
+
+      def edit?
+        destroy?
+      end
+    end
+  end
+end

data/app/policies/renalware/pd/pet_result_policy.rb

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+module Renalware
+  module PD
+    class PETResultPolicy < BasePolicy
+      def destroy?
+        user_is_admin? || user_is_super_admin?
+      end
+
+      def edit?
+        destroy?
+      end
+    end
+  end
+end

data/app/policies/renalware/renal/registry_preflight_check_policy.rb

@@ -12,6 +12,10 @@ module Renalware
       def patients?
         index?
       end
+
+      def missing_esrf?
+        index?
+      end
     end
   end
 end

data/app/presenters/renalware/clinical/profile_presenter.rb

@@ -6,6 +6,7 @@ module Renalware
   module Clinical
     class ProfilePresenter
       attr_reader :patient, :params
+
       delegate :allergies, :document, to: :patient
 
       def initialize(patient:, params:)

data/app/presenters/renalware/hd/dashboard_presenter.rb

@@ -6,6 +6,7 @@ module Renalware
   module HD
     class DashboardPresenter
       attr_accessor :patient
+
       delegate :has_ever_been_on_hd?, to: :patient
 
       def initialize(patient, view_context, current_user)