renalware-core 2.0.132 → 2.0.133

data/app/models/renalware/pathology/code_group_membership.rb

@@ -10,6 +10,8 @@ module Renalware
     # together in groups on the page for clarity) and within that group might have a position wich
     # determines its order in the subgroup.
     class CodeGroupMembership < ApplicationRecord
+      include Accountable
+      has_paper_trail class_name: "Renalware::Pathology::Version", on: [:create, :update, :destroy]
       validates :position_within_subgroup, presence: true
       validates :subgroup, presence: true
       belongs_to :code_group

data/app/models/renalware/pathology/current_observation_set.rb

@@ -30,9 +30,18 @@ module Renalware
       validates :patient, presence: true
       serialize :values, ObservationsJsonbSerializer
 
+      # Select values frm the set where the code matches the code or array of codes
+      # requested. 
+      # When the code is not found in the set, return an empty hash for that code.
+      # When the patient has no current_observation_set, return an empty hash for each code. 
+      # We need to be sure to extend the HashWithIndifferentAccess returned from
+      # #select with the ObservationSetMethods so a user can call eg {..}.hgb_date
+      # or {..}.plt etc without error
       def values_for_codes(codes)
-        codes = Array(codes)
-        values.select { |code, _| codes.include?(code) }
+        hash = Array(codes).each_with_object(HashWithIndifferentAccess.new) do |code, hash| 
+          hash[code] = values[code] || CurrentObservationSet.null_values_hash
+        end
+        hash.extend(ObservationSetMethods)
       end
 
       def self.null_values_hash
@@ -42,7 +51,11 @@ module Renalware
 
     class NullObservationSet
       def values
-        ObservationsJsonbSerializer.load({})
+        ObservationsJsonbSerializer.load(HashWithIndifferentAccess.new)
+      end
+
+      def values_for_codes(codes)
+        CurrentObservationSet.null_values_hash
       end
     end
   end

data/app/models/renalware/pathology/observations_jsonb_serializer.rb

@@ -34,7 +34,7 @@ module Renalware
 
       def observation_hash_or_hash_element_for(code, suffix)
         obs_hash = self[code]
-        return nil if obs_hash.nil? # the patient may not have this observation in the set
+        return nil if obs_hash.blank? # the patient may not have this code in the set, or it might be {}
         return obs_hash[:result] if suffix == "_result"
         return Date.parse(obs_hash[:observed_at]) if suffix == "_observed_at"
 

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

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

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

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # A component is the description in data of an ActionView::Component
+    # in the app/components folder inside this engine.
+    # Components encapsulate reusable elements of the UI.
+    # Dashboard-compatible components must have a current_user arg in their
+    # ctor.
+    # A component can be included for example on a dashboard (see Dashboard
+    # and DashboardComponent) provided component.dashboard == true.
+    # A component has these properies
+    #  - class_name eg "Renalware::Letters::LettersInProgress"
+    #  - name eg "Letters In Progress"
+    #  - dashboard - if true then this component can be added to a dashboard
+    #  - roles - the roles required for a user to be able to add this component
+    #            to their dashboard
+    class Component < ApplicationRecord
+      validates :class_name, presence: true
+      validates :name, presence: true, uniqueness: true
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # The desription in data of a dashboard displayed in the UI, for example
+    # the 'default' dashboard a user see when they log in, a dashboard for
+    # an HD nurse, or a user's customised dashboard (if we get to build that!),
+    # A dashboard comprises components (see Component and DashboardComponent).
+    class Dashboard < ApplicationRecord
+      belongs_to :user
+      has_many :dashboard_components, dependent: :restrict_with_exception
+      has_many :components, through: :dashboard_components
+      validates :name, uniqueness: true
+      validates :name, presence: { if: -> { user_id.nil? } }
+      validates :user, presence: { if: -> { name.nil? } }
+    end
+  end
+end

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

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # Represents an instance of a component on a dashboard
+    class DashboardComponent < ApplicationRecord
+      belongs_to :component
+      belongs_to :dashboard
+      validates :position, presence: true
+      validates :position, uniqueness: { scope: [:dashboard_id] }
+      validates :dashboard, presence: true
+      validates :component, presence: true
+    end
+  end
+end

data/app/models/renalware/transplants.rb

@@ -2,7 +2,14 @@
 
 module Renalware
   module Transplants
-    WAITLIST_FILTERS = %w(active suspended active_and_suspended working_up status_mismatch).freeze
+    WAITLIST_FILTERS = %w(
+      all
+      active
+      suspended
+      active_and_suspended
+      working_up
+      status_mismatch
+    ).freeze
 
     def self.table_name_prefix
       "transplant_"

data/app/models/renalware/transplants/registrations/wait_list_form.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/transplants"
+
+module Renalware
+  module Transplants
+    module Registrations
+      class WaitListForm
+        include ActiveModel::Model
+        include Virtus::Model
+
+        attribute :ukt_recipient_number, String
+      end
+    end
+  end
+end

data/app/models/renalware/transplants/registrations/wait_list_query.rb

@@ -6,9 +6,10 @@ module Renalware
   module Transplants
     module Registrations
       class WaitListQuery
-        def initialize(named_filter:, q: nil)
+        def initialize(named_filter:, ukt_recipient_number: nil, q: nil)
           @named_filter = named_filter&.to_sym || :active
           @q = (q || ActionController::Parameters.new).permit(:s, :q)
+          @ukt_recipient_number = ukt_recipient_number
         end
 
         def call
@@ -16,6 +17,7 @@ module Renalware
             .result
             .extending(Scopes)
             .apply_filter(named_filter)
+            .having_ukt_recipient_number(ukt_recipient_number)
         end
 
         def search
@@ -37,6 +39,14 @@ module Renalware
         # At some point we will have turn this into a mapping object or hash because there will
         # probably not be a 1 to 1 mapping from wait list to UKT status.
         module Scopes
+          def having_ukt_recipient_number(number)
+            return all if number.blank?
+
+            where(<<-SQL, number)
+              transplant_registrations.document -> 'codes' ->> 'uk_transplant_patient_recipient_number' = ?
+            SQL
+          end
+
           # rubocop:disable Metrics/MethodLength
           def apply_filter(filter)
             case filter
@@ -71,10 +81,13 @@ module Renalware
 
         private
 
-        attr_reader :q, :named_filter
+        attr_reader :q, :named_filter, :ukt_recipient_number
 
+        # rubocop:disable Metrics/CyclomaticComplexity, Metrics/MethodLength
         def query_for_filter(filter)
           case filter
+          when :all
+            {}
           when :active
             { current_status_in: :active }
           when :suspended
@@ -89,6 +102,7 @@ module Renalware
             {} # See Scopes
           end
         end
+        # rubocop:enable Metrics/CyclomaticComplexity, Metrics/MethodLength
 
         class QueryableRegistration < ActiveType::Record[Registration]
           scope :current_status_in, lambda { |codes|
@@ -133,7 +147,7 @@ module Renalware
           private_class_method :ransackable_scopes
 
           def self.ransackable_scopes(_auth_object = nil)
-            %i(current_status_in)
+            %i(current_status_in ukt_recipient_number_eq)
           end
         end
       end

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

@@ -6,7 +6,7 @@ module Renalware
   module UKRDC
     module Incoming
       class FileList
-        pattr_initialize [pattern: "*.xml", paths: Paths.new]
+        pattr_initialize [pattern: "survey*.xml", paths: Paths.new]
 
         # Helper which yields each file in the incoming folder.
         def each_file

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

@@ -18,6 +18,13 @@ module Renalware
 
         def call
           Incoming::FileList.new(paths: paths).each_file do |filepath|
+            if already_imported?(filepath)
+              logger.info "Skipping: #{filepath} already successfully imported"
+              FileUtils.mv filepath, paths.archive.join(filepath.basename)
+              next
+            end
+            
+            logger.info "Processing: #{filepath}"
             import_surveys_from_file(filepath)
           end
         rescue StandardError => e
@@ -27,6 +34,15 @@ module Renalware
 
         private
 
+        # If a file arrives that we have already imported successfully then skip it.
+        # This assumes filenames are unique across time, which they should be.
+        # Note we match on the whole file path, so if the location of the folder changes
+        # and we are presented with familiar files, then they will be imported again. Its unlikely
+        # those two things will happen together though. 
+        def already_imported?(filepath)
+          TransmissionLog.exists?(file_path: filepath.to_s, status: :imported)
+        end
+
         # Import all surverys (they will be for the same patient) in the XML file.
         # Note that #with_logging yields a block that will catch and save any error to
         # ukrdc_transmission_logs

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

@@ -13,6 +13,28 @@ module Renalware
             yield(elem) if block_given?
             elem
           end
+
+          # Example output:
+          #   "123 approx" => 123
+          #   "123" => 123
+          #   123 => 123
+          #   123.1 => 123
+          #   0 => nil
+          #   "n/a" => nil
+          def coerce_to_integer(value)
+            value.to_i > 0 && value.presence&.to_i
+          end
+
+          # Example output:
+          #   "123 approx" => 123.0
+          #   "123" => 123.0
+          #   123 => 123.0
+          #   123.1 => 123.1
+          #   0 => nil
+          #   "n/a" => nil
+          def coerce_to_float(value)
+            value.to_f > 0.0 && value.presence&.to_f
+          end
         end
       end
     end

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

@@ -67,8 +67,8 @@ module Renalware
               elem << create_node("QHD20", session.access_rr02_code)
               elem << create_node("QHD21", session.access_rr41_code)
               elem << create_node("QHD22", "N") # Access in two sites simultaneously
-              elem << create_node("QHD30", session.blood_flow)
-              elem << create_node("QHD31", session.duration_in_minutes) # Time Dialysed in Minutes
+              elem << create_node("QHD30", coerce_to_integer(session.blood_flow))
+              elem << create_node("QHD31", coerce_to_integer(session.duration_in_minutes))
               elem << create_node("QHD32", session.sodium_content) # Sodium in Dialysate
               elem << create_node("QHD33") # TODO: Needling Method
             end

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

@@ -41,7 +41,7 @@ module Renalware
             {
               "blood_pressure.systolic" => observations.blood_pressure&.systolic,
               "blood_pressure.diastolic" => observations.blood_pressure&.diastolic,
-              "weight" => observations.weight
+              "weight" => coerce_to_float(observations.weight)
             }
           end
         end

data/app/models/renalware/user.rb

@@ -92,6 +92,15 @@ module Renalware
       OpenSSL::HMAC.hexdigest(digest, key, id.to_s)
     end
 
+
+    # We implement a simple can? method ion the use because in places we pass a current user
+    # from an ActionView::Component to a partial, and in the specs the partial says it cannot
+    # Example usage user.can?(:edit, letter)
+    # def can?(method, record)
+    #   method = :"#{method}?" unless method.to_s.ends_with("?")
+    #   Pundit.policy(self, record).public_send(method.to_sym)
+    # end
+
     private
 
     def build_authentication_token

data/app/policies/renalware/hd/closed_session_policy.rb

@@ -10,7 +10,7 @@ module Renalware
       def edit?
         return false unless record.persisted?
 
-        user_is_super_admin? || !record.immutable?
+        user_is_admin? || user_is_super_admin? || !record.immutable?
       end
     end
   end

data/app/policies/renalware/pathology/code_group_policy.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module Renalware
+  module Pathology
+    class CodeGroupPolicy < BasePolicy
+      def create?
+        user_is_super_admin?
+      end
+
+      def update?
+        create?
+      end
+
+      def destroy?
+        create?
+      end
+
+      def edit?
+        create?
+      end
+    end
+  end
+end

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

@@ -56,8 +56,14 @@ module Renalware
       end
 
       def recent_pathology
-        current_observation_set = Pathology.cast_patient(patient).current_observation_set
-        current_observation_set&.values || Pathology::CurrentObservationSet.null_values_hash
+        current_observation_set = Pathology.cast_patient(patient).fetch_current_observation_set 
+        current_observation_set ||= Pathology::NullObservationSet.new
+        current_observation_set.values_for_codes(codes_to_show)
+      end
+
+      def codes_to_show
+        code_group_name = "hd_session_form_recent"
+        @codes_to_show ||= Pathology::CodeGroup.descriptions_for_group(code_group_name).pluck(:code)
       end
 
       def patient_title

data/app/views/renalware/clinical/body_compositions/_form.html.slim

@@ -6,6 +6,12 @@
             as: :user_picker,
             collection: Renalware::User.ordered,
             wrapper: :horizontal_medium
+  = f.input :pre_post_hd,
+            collection: Renalware::Clinical::BodyComposition.pre_post_hds.collect{ |c| [c[0].titleize, c[0]] },
+            include_blank: "Not Applicable",
+            wrapper: :horizontal_small
+  = f.input :weight,
+            wrapper: :horizontal_tiny
   = f.input :overhydration,
             wrapper: :horizontal_small
   = f.input :volume_of_distribution,

data/app/views/renalware/clinical/body_compositions/_table.html.slim

@@ -6,6 +6,8 @@ table
       th.col-width-date= t(".assessed_on")
       th= t(".modality_description")
       th= t(".assessor")
+      th.col-width-tiny= t(".pre_post_hd")
+      th.col-width-tiny= t(".weight")
       th.col-width-tiny= t(".overhydration")
       th.col-width-tiny= t(".volume_of_distribution")
       th.col-width-tiny= t(".total_body_water")
@@ -29,6 +31,8 @@ table
         td= body_composition.assessed_on
         td= body_composition.modality_description&.name
         td= body_composition.assessor
+        td= body_composition.pre_post_hd&.titleize
+        td= body_composition.weight
         td= body_composition.overhydration
         td= body_composition.volume_of_distribution
         td= body_composition.total_body_water

data/app/views/renalware/dashboard/bookmarks/_bookmark.html.slim

@@ -4,13 +4,13 @@ tr class=("urgent" if bookmark.urgent?)
   td= default_patient_link(patient)
   td= patient.nhs_number
   td= patient.hospital_identifier
-  td= I18n.l(patient.born_on)
+  td.show-for-medium-up= I18n.l(patient.born_on)
   td= patient.age
   td= patient.sex
-  td= patient.current_modality
-  td= bookmark.notes
-  td= bookmark.tags
-  td= I18n.l bookmark.created_at
+  td.col-width-medium-with-ellipsis= patient.current_modality
+  td.show-for-medium-up= bookmark.notes
+  td.show-for-medium-up= bookmark.tags
+  td= I18n.l bookmark.created_at&.to_date
   td.nowrap= render "renalware/patients/bookmarks/delete",
                     bookmark: bookmark,
                     link_text: "Remove"