renalware-core 2.0.149 → 2.0.156

data/app/models/renalware/system/update_user.rb

@@ -20,12 +20,16 @@ module Renalware
 
       private
 
+      # rubocop:disable Metrics/MethodLength
       def update!(params)
         User.transaction do
           approve if can_approve?(params)
           unexpire if can_unexpire?(params)
           user.consultant = true?(params[:consultant])
           user.hidden = true?(params[:hidden])
+          if params[:prescriber] # if not a supperadmin, may not be submitted
+            user.prescriber = true?(params[:prescriber])
+          end
           authorise(params)
           user.telephone = params[:telephone]
           user.save!
@@ -33,6 +37,7 @@ module Renalware
       rescue ActiveRecord::RecordInvalid
         false
       end
+      # rubocop:enable Metrics/MethodLength
 
       def notify!
         notifications.each { |n| n.public_send(delivery_method) } if notifications.any?

data/app/models/renalware/system/version.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/problems"
+
+module Renalware
+  module System
+    class Version < PaperTrail::Version
+      self.table_name = :system_versions
+    end
+  end
+end

data/app/models/renalware/system/view_metadata.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # Information on SQL views used to build parts of the UI
+    class ViewMetadata < ApplicationRecord
+      has_paper_trail(
+        versions: { class_name: "Renalware::System::Version" },
+        on: [:create, :update, :destroy]
+      )
+
+      attribute :columns, ColumnDefinition.to_array_type
+      validates :columns, store_model: true
+
+      attribute :filters, FilterDefinition.to_array_type
+      validates :filters, store_model: true
+
+      # This maps to a PG enum
+      enum display_type: { tabular: "tabular" }
+      enum category: { mdm: "mdm", report: "report" }
+    end
+  end
+end

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

@@ -10,7 +10,7 @@ module Renalware
       extend Enumerize
 
       belongs_to :patient, touch: true
-      belongs_to :recipient, class_name: "Patient", foreign_key: "recipient_id", touch: true
+      belongs_to :recipient, class_name: "Patient", touch: true
 
       has_paper_trail(
         versions: { class_name: "Renalware::Transplants::Version" },

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

@@ -8,7 +8,6 @@ module Renalware
     class DonorFollowup < ApplicationRecord
       belongs_to :operation,
                  class_name: "DonorOperation",
-                 foreign_key: "operation_id",
                  touch: true
 
       has_paper_trail(

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

@@ -5,7 +5,7 @@ require_dependency "renalware/transplants"
 module Renalware
   module Transplants
     class FailureCauseDescription < ApplicationRecord
-      belongs_to :group, class_name: "FailureCauseDescriptionGroup", foreign_key: "group_id"
+      belongs_to :group, class_name: "FailureCauseDescriptionGroup"
 
       scope :ordered, -> { order(name: :asc) }
 

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

@@ -44,7 +44,7 @@ module Renalware
         end
 
         def patients_with_a_transplant_date_in_the_past_3_months
-          joins(<<-SQL)
+          joins(<<-SQL.squish)
             LEFT JOIN transplant_recipient_operations
             ON patients.id = transplant_recipient_operations.patient_id
           SQL
@@ -58,7 +58,7 @@ module Renalware
         alias_method :on_worryboard, :patients_on_the_worry_board
 
         def patients_with_a_transplant_operation_in_the_past_year
-          joins(<<-SQL)
+          joins(<<-SQL.squish)
             LEFT JOIN transplant_recipient_operations
             ON patients.id = transplant_recipient_operations.patient_id
           SQL

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

@@ -8,7 +8,7 @@ module Renalware
       has_one :current_donor_stage, -> { current }, class_name: "DonorStage"
 
       scope :with_registration_statuses, lambda {
-        joins(<<-SQL)
+        joins(<<-SQL.squish)
           left outer join transplant_registrations
             on transplant_registrations.patient_id = patients.id
           left outer join transplant_registration_statuses

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

@@ -13,11 +13,9 @@ module Renalware
 
       belongs_to :operation,
                  class_name: "RecipientOperation",
-                 foreign_key: "operation_id",
                  touch: true
       belongs_to :transplant_failure_cause_description,
-                 class_name: "Transplants::FailureCauseDescription",
-                 foreign_key: "transplant_failure_cause_description_id"
+                 class_name: "Transplants::FailureCauseDescription"
       has_many :rejection_episodes,
                class_name: "RejectionEpisode",
                dependent: :restrict_with_exception,

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

@@ -10,9 +10,7 @@ module Renalware
       include PatientScope
 
       belongs_to :patient, touch: true
-      has_many :statuses,
-               class_name: "RegistrationStatus",
-               foreign_key: "registration_id"
+      has_many :statuses, class_name: "RegistrationStatus"
       has_one :current_status,
               -> { where(terminated_on: nil).order([:started_on, :created_at]) },
               class_name: "RegistrationStatus",

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/registrations/wait_list_query.rb

@@ -42,7 +42,7 @@ module Renalware
           def having_ukt_recipient_number(number)
             return all if number.blank?
 
-            where(<<-SQL, number)
+            where(<<-SQL.squish, number)
               transplant_registrations.document -> 'codes' ->> 'uk_transplant_patient_recipient_number' = ?
             SQL
           end
@@ -83,7 +83,7 @@ module Renalware
 
         attr_reader :q, :named_filter, :ukt_recipient_number
 
-        # rubocop:disable Metrics/CyclomaticComplexity, Metrics/MethodLength
+        # rubocop:disable Metrics/MethodLength
         def query_for_filter(filter)
           case filter
           when :all
@@ -102,7 +102,7 @@ module Renalware
             {} # See Scopes
           end
         end
-        # rubocop:enable Metrics/CyclomaticComplexity, Metrics/MethodLength
+        # rubocop:enable Metrics/MethodLength
 
         class QueryableRegistration < ActiveType::Record[Registration]
           scope :current_status_in, lambda { |codes|
@@ -136,7 +136,7 @@ module Renalware
           end
 
           ransacker :ukt_status do
-            Arel.sql(<<-SQL)
+            Arel.sql(<<-SQL.squish)
               COALESCE(
                 transplant_registrations.document -> 'uk_transplant_centre' ->> 'status',
                 ''

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

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    # Represents a valid UKRDC pathology test result measurement unit e.g. "mg".
+    # See https://github.com/renalreg/ukrdc/blob/master/Schema/Types/CF_RR23.xsd
+    class MeasurementUnit < ApplicationRecord
+      validates :name, presence: true
+
+      # A friendly string containing the name folllowed by the description (if present)
+      # in parentheses e.g. "l (litres)"
+      def title
+        return name if description.blank? || name == description
+
+        "#{name} (#{description})"
+      end
+    end
+  end
+end

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

@@ -16,12 +16,16 @@ module Renalware
 
           def lab_order_element
             Ox::Element.new("LabOrder").tap do |lab_order|
+              lab_order << receiving_location_element
               lab_order << create_node("PlacerId", request.placer_id)
               lab_order << order_category_element
               lab_order << create_node("SpecimenCollectedTime", request.requested_at&.iso8601)
               lab_order << create_node("SpecimenSource", request.description.bottle_type)
               lab_order << result_items_element
               lab_order << create_node("EnteredOn", request.requested_at.iso8601)
+              lab_order << entered_at_element
+              lab_order << entering_organisation_element
+              lab_order << create_node("ExternalId", request.placer_id)
             end
           end
 
@@ -63,15 +67,39 @@ module Renalware
           end
 
           # If the rr_type of the observation_description is interpretation (ie an interpretted
-          # result like POS NEG the out
+          # result like POS NEG then output the interpretation_code
           def rr_type_value_elements_for(observation, append_to:)
             if observation.rr_type_interpretation?
               append_to << create_node("InterpretationCodes", observation.interpretation_code)
             else
-              append_to << create_node("ResultValue", observation.result)
+              append_to << create_node("ResultValue", observation.result.strip)
               append_to << create_node("ResultValueUnits", observation.measurement_unit_name)
             end
           end
+
+          def entered_at_element
+            create_node("EnteredAt").tap do |elem|
+              elem << create_node("CodingStandard", "RR1+")
+              elem << create_node("Code", Renalware.config.ukrdc_sending_facility_name)
+              elem << create_node("Description", Renalware.config.ukrdc_sending_facility_name)
+            end
+          end
+
+          def entering_organisation_element
+            create_node("EnteringOrganization").tap do |elem|
+              elem << create_node("CodingStandard", "RR1+")
+              elem << create_node("Code", Renalware.config.ukrdc_sending_facility_name)
+              elem << create_node("Description", Renalware.config.ukrdc_sending_facility_name)
+            end
+          end
+
+          def receiving_location_element
+            create_node("ReceivingLocation").tap do |elem|
+              elem << create_node("CodingStandard", "RR1+")
+              elem << create_node("Code", Renalware.config.ukrdc_sending_facility_name)
+              elem << create_node("Description", Renalware.config.ukrdc_sending_facility_name)
+            end
+          end
         end
       end
     end

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/paths.rb

@@ -7,7 +7,7 @@ module Renalware
     class Paths
       attr_reader :timestamp, :batch_number, :working_path
 
-      def initialize(timestamp: nil, batch_number:, working_path:)
+      def initialize(batch_number:, working_path:, timestamp: nil)
         raise(ArgumentError, "Invalid working_path") if working_path.blank?
 
         @timestamp = timestamp

data/app/models/renalware/ukrdc/treatment_timeline/prepare_tables.rb

@@ -15,7 +15,7 @@ module Renalware
         def self.call
           Treatment.delete_all
           connection = ActiveRecord::Base.connection
-          result = connection.execute(<<-SQL)
+          result = connection.execute(<<-SQL.squish)
             select 1 where exists(select 1 from pg_proc where proname = 'ukrdc_prepare_tables');
           SQL
           if result.ntuples == 1

data/app/models/renalware/ukrdc/treatment_timeline/remap_model_table_names_to_their_prepared_equivalents.rb

@@ -56,7 +56,7 @@ module Renalware
         end
 
         def table_exists?(table_name)
-          result = connection.execute(<<-SQL)
+          result = connection.execute(<<-SQL.squish)
             SELECT 1
             WHERE EXISTS (
               SELECT 1 FROM information_schema.tables WHERE table_name = '#{table_name}')

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/application_policy.rb

@@ -13,7 +13,7 @@ class ApplicationPolicy
   end
 
   def show?
-    scope.where(id: record.id).exists?
+    scope.exists?(id: record.id)
   end
 
   def new?

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/medications/prescription_policy.rb

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module Renalware
+  module Medications
+    class PrescriptionPolicy < BasePolicy
+      def new?
+        super && user_is_a_prescriber?
+      end
+
+      def create?
+        super && user_is_a_prescriber?
+      end
+
+      def edit?
+        super && user_is_a_prescriber?
+      end
+
+      def update?
+        super && user_is_a_prescriber?
+      end
+
+      def destroy?
+        super && user_is_a_prescriber?
+      end
+
+      private
+
+      def user_is_a_prescriber?
+        return true unless Renalware.config.enforce_user_prescriber_flag
+
+        user.prescriber?
+      end
+    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