renalware-core 2.0.121 → 2.0.123

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: a8947eece7d110e83bf494a41fd4f0c72fc654ca830236c6207abdd151d5d556
+  data.tar.gz: f7717b64d5286fcc533e247fd278653851f79c263fb928fa136f11630ccaa9dd
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+  data.tar.gz: 4fd87df55586b2a7043baef87043986d7791b5d3a9b3f16228fab25235b1837e3d686d3eefca9b4969c42140f69c6614efdc8f39e30a0d394dcb44fcaf953b86

data/Rakefile

@@ -51,6 +51,12 @@ namespace :yarn do
   end
 end
 
+namespace :webpacker do
+  task :compile do
+    Rake::Task["app:renalware:webpacker_compile"].invoke
+  end
+end
+
 # Default rake task to run all tests:
 #   bundle exec rake
 task :engine_default_task do

data/app/controllers/renalware/admin/users_controller.rb

@@ -17,26 +17,24 @@ module Renalware
     end
 
     def edit
-      load_user
+      render locals: { user: find_and_authorize_user }
     end
 
     def update
-      load_user
-
-      if update_user.call(update_params)
+      user = find_and_authorize_user
+      if System::UpdateUser.new(user).call(update_params)
         redirect_to admin_users_path,
                     notice: t(".success", model_name: "user")
       else
         flash.now[:error] = t(".failed", model_name: "user")
-        render :edit
+        render :edit, locals: { user: user }
       end
     end
 
     private
 
-    def load_user
-      @user = User.find(params[:id])
-      authorize @user
+    def find_and_authorize_user
+      User.find(params[:id]).tap { |user_| authorize user_ }
     end
 
     def update_params
@@ -45,15 +43,19 @@ module Renalware
     end
 
     def user_params
-      params.require(:user).permit(:approved, :unexpire, :telephone, role_ids: [])
+      params
+        .require(:user)
+        .permit(
+          :approved,
+          :unexpire,
+          :telephone,
+          :consultant,
+          role_ids: []
+        )
     end
 
     def role_ids
       (user_params[:role_ids] || []).reject(&:blank?)
     end
-
-    def update_user
-      @update_user ||= System::UpdateUser.new(@user)
-    end
   end
 end

data/app/controllers/renalware/clinical/profiles_controller.rb

@@ -4,6 +4,7 @@ require_dependency "renalware/clinical"
 
 module Renalware
   module Clinical
+    # Note that there is no concrete Clinical::Profile, most data here is persisted in the patient
     class ProfilesController < Clinical::BaseController
       def show
         authorize patient
@@ -31,24 +32,28 @@ module Renalware
       private
 
       def update_patient
+        patient.named_consultant_id = profile_params[:named_consultant_id]
         document = patient.document
+
         %i(diabetes history).each do |document_attribute|
           document.send(
             :"#{document_attribute}=",
-            profile_params[document_attribute].symbolize_keys
+            profile_params[:document][document_attribute].symbolize_keys
           )
         end
-        patient.by = current_user
-        patient.save!
+        patient.save_by! current_user
       end
 
       def profile_params
         params
           .require(:clinical_profile)
           .permit(
-            diabetes: %i(diagnosis diagnosed_on),
-            history: %i(alcohol smoking))
-          .to_h
+            :named_consultant_id,
+            document: {
+              diabetes: %i(diagnosis diagnosed_on),
+              history: %i(alcohol smoking)
+            }
+          ).to_h
       end
     end
   end

data/app/controllers/renalware/hd/sessions_controller.rb

@@ -69,6 +69,7 @@ module Renalware
         session = Session.for_patient(patient).find(params[:id])
         authorize session
         session.destroy!
+        regenerate_rolling_hd_statistics
         message = t(".success", model_name: "HD session")
         redirect_to patient_hd_dashboard_path(patient), notice: message
       end
@@ -145,6 +146,10 @@ module Renalware
           .fetch(:document, nil)
           .try(:permit!)
       end
+
+      def regenerate_rolling_hd_statistics
+        Delayed::Job.enqueue UpdateRollingPatientStatisticsDjJob.new(patient.id)
+      end
     end
     # rubocop:enable Metrics/ClassLength
   end

data/app/models/concerns/renalware/patient_pathology_scopes.rb

@@ -24,7 +24,7 @@ module Renalware
     #   = sort_link(<url>, :cre_date, "CRE date")
     #
     def self.extended(base)
-      %i(hgb ure cre urr phos pth).each do |code|
+      %i(hgb ure cre urr phos pthi pot).each do |code|
         base.ransacker(code) { pathology_result_sort_predicate(code) }
         base.ransacker(:"#{code}_date") { pathology_date_sort_predicate(code) }
       end

data/app/models/renalware/feeds/hl7_message.rb

@@ -134,6 +134,12 @@ module Renalware
           patient_id_list.split("^").first
         end
 
+        def nhs_number
+          return unless defined?(patient_id)
+
+          patient_id.split("^").first
+        end
+
         def name
           Name.new(patient_name)
         end

data/app/models/renalware/hd/prescription_administration.rb

@@ -6,6 +6,7 @@ module Renalware
   module HD
     class PrescriptionAdministration < ApplicationRecord
       include Accountable
+      acts_as_paranoid
       attr_accessor :administrator_authorisation_token
       attr_accessor :witness_authorisation_token
 

data/app/models/renalware/hd/session.rb

@@ -10,6 +10,8 @@ module Renalware
       include Accountable
       include ExplicitStateModel
 
+      acts_as_paranoid
+
       # Prevent instances of this of this base class from being saved
       validates :type, presence: true
 

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

@@ -5,15 +5,12 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class ObservationForPatientObservationDescriptionQuery
-      def initialize(patient, observation_description)
-        @patient = patient
-        @observation_description = observation_description
-      end
+      pattr_initialize :patient, :observation_description
 
       def call
-        @patient
+        patient
           .observations
-          .where(description: @observation_description)
+          .where(description: observation_description)
           .order(observed_at: :desc)
           .first
       end

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

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/pathology"
+
+module Renalware
+  module Pathology
+    class ObservationForPatientObservationDescriptionUsingSetQuery
+      pattr_initialize :patient, :observation_description
+
+      # Fetches the patient's most recent observation for the supplied observation_description.code
+      # (eg 'HGB') using the patient's current_observation_set jsonb hash and returnd something
+      # like { "result" => "123", "observed_on" => "2019-01-01" }
+      def call
+        return {} unless patient.current_observation_set
+
+        patient.current_observation_set.values.fetch(observation_description.code, {})
+      end
+    end
+  end
+end

data/app/models/renalware/pathology/requests/global_rule/observation_result.rb

@@ -36,23 +36,21 @@ module Renalware
         end
 
         class PatientGlobalRuleDecision
-          def initialize(patient, rule)
-            @patient = patient
-            @rule = rule
-          end
+          pattr_initialize :patient, :rule
+          delegate :param_comparison_operator, :param_comparison_value, :param_id, to: :rule
 
           def observation_required_for_patient?
-            return true if observation.nil?
+            return true if observation.blank?
 
-            if [">", "<", ">=", "<="].include?(@rule.param_comparison_operator)
-              observation.result.to_i.send(
-                @rule.param_comparison_operator.to_sym,
-                @rule.param_comparison_value.to_i
+            if [">", "<", ">=", "<="].include?(rule.param_comparison_operator)
+              observation.to_i.send(
+                param_comparison_operator.to_sym,
+                param_comparison_value.to_i
               )
             else
-              observation.result.send(
-                @rule.param_comparison_operator.to_sym,
-                @rule.param_comparison_value
+              observation.send(
+                param_comparison_operator.to_sym,
+                param_comparison_value
               )
             end
           end
@@ -60,15 +58,23 @@ module Renalware
           private
 
           def observation
-            @observation ||=
-              ObservationForPatientObservationDescriptionQuery.new(
-                @patient,
+            @observation ||= begin
+              # This fetches the observation from the patient.current_observation_set jsonb hash.
+              # The call returns eg { "result" => "123", "observed_on" => "2019-01-01" }
+              ObservationForPatientObservationDescriptionUsingSetQuery.new(
+                patient,
                 observation_description
-              ).call
+              ).call["result"]
+
+              # ObservationForPatientObservationDescriptionQuery.new(
+              #     @patient,
+              #     observation_description
+              #   ).call&.result
+            end
           end
 
           def observation_description
-            @observation_description ||= ObservationDescription.new(id: @rule.param_id)
+            rule.observation_description ||= ObservationDescription.new(id: param_id)
           end
         end
       end

data/app/models/renalware/pathology/requests/global_rule/prescription_drug.rb

@@ -10,7 +10,7 @@ module Renalware
           validate :drug_present
 
           def observation_required_for_patient?(patient, _date)
-            patient.drugs.include?(drug)
+            patient.drugs.exists?(id: param_id)
           end
 
           def to_s
@@ -24,7 +24,7 @@ module Renalware
           end
 
           def drug_present
-            return if drug.present?
+            return if Drugs::Drug.exists?(id: param_id)
 
             errors.add(:param_id, "param_id must be the id of a Drug")
           end

data/app/models/renalware/pathology/requests/global_rule/prescription_drug_category.rb

@@ -10,7 +10,7 @@ module Renalware
           validate :drug_category_present
 
           def observation_required_for_patient?(patient, _date)
-            (patient.drugs.map(&:id) & drug_ids).any?
+            (patient.drugs.pluck(&:id) & drug_ids).any?
           end
 
           def to_s
@@ -20,7 +20,7 @@ module Renalware
           private
 
           def drug_ids
-            drug_category.drugs.map(&:id)
+            drug_category.drugs.pluck(&:id)
           end
 
           def drug_category

data/app/models/renalware/pathology/requests/global_rule/prescription_drug_type.rb

@@ -10,7 +10,12 @@ module Renalware
           validate :drug_type_present
 
           def observation_required_for_patient?(patient, _date)
-            patient.drugs.flat_map(&:drug_types).include?(drug_type)
+            patient
+              .drugs
+              .select(:id)
+              .joins(:classifications)
+              .where("drug_types_drugs.drug_type_id = ?", param_id)
+              .count > 0
           end
 
           def to_s
@@ -24,7 +29,7 @@ module Renalware
           end
 
           def drug_type_present
-            return if drug_type.present?
+            return if Drugs::Type.exists?(param_id)
 
             errors.add(:param_id, "param_id must be the id of a DrugType")
           end

data/app/models/renalware/pathology/requests/global_rule_set/patient_rule_set_decision.rb

@@ -7,12 +7,7 @@ module Renalware
         class PatientRuleSetDecision
           OBSERVATION_REQUIRED = true
           OBSERVATION_NOT_REQUIRED = false
-
-          def initialize(patient, rule_set, date)
-            @rule_set = rule_set
-            @patient = patient
-            @date = date
-          end
+          pattr_initialize :patient, :rule_set, :date
 
           # NOTE: Decide if a rule_set applies to a patient
           def call
@@ -32,26 +27,26 @@ module Renalware
           def last_observation_too_recent?
             return false if last_observation.nil?
 
-            observed_days_ago = @date - last_observation.observed_on
-            !@rule_set.frequency.observation_required?(observed_days_ago)
+            observed_days_ago = date - last_observation.observed_on
+            !rule_set.frequency.observation_required?(observed_days_ago)
           end
 
           def last_request_still_being_processed?
             return false if last_request.nil? || last_request_has_an_observation_result?
 
-            expiration_days = @rule_set.request_description.expiration_days
+            expiration_days = rule_set.request_description.expiration_days
             return false if expiration_days == 0
 
             # This subtraction works because ActiveSupport::TimeWithZone works in days
             # e.g. TimeWithZone1 - TimeWithZone2 = 3 days
-            requested_days_ago = @date - last_request.requested_on
+            requested_days_ago = date - last_request.requested_on
             requested_days_ago < expiration_days
           end
 
           def required_from_rules?
-            @rule_set
+            rule_set
               .rules
-              .map { |rule| rule.observation_required_for_patient?(@patient, @date) }
+              .map { |rule| rule.observation_required_for_patient?(patient, date) }
               .all?
           end
 
@@ -64,16 +59,16 @@ module Renalware
           def last_observation
             @last_observation ||=
               ObservationForPatientRequestDescriptionQuery.new(
-                @patient,
-                @rule_set.request_description
+                patient,
+                rule_set.request_description
               ).call
           end
 
           def last_request
             @last_request ||=
               RequestForPatientRequestDescriptionQuery.new(
-                @patient,
-                @rule_set.request_description
+                patient,
+                rule_set.request_description
               ).call
           end
         end

data/app/models/renalware/pathology/requests/request_factory.rb

@@ -6,10 +6,7 @@ module Renalware
   module Pathology
     module Requests
       class RequestFactory
-        def initialize(patient, params)
-          @patient = patient
-          @params = params
-        end
+        pattr_initialize :patient, :params
 
         def build
           Request.new(request_params)
@@ -19,24 +16,24 @@ module Renalware
 
         def request_params
           {
-            patient: @patient,
-            clinic: @params[:clinic],
-            consultant: @params[:consultant],
-            telephone: @params[:telephone],
-            template: @params[:template],
+            patient: patient,
+            clinic: params[:clinic],
+            consultant: params[:consultant],
+            telephone: params[:telephone],
+            template: params[:template],
             request_descriptions: request_descriptions,
             patient_rules: patient_rules,
-            high_risk: @patient.high_risk?,
-            by: @params[:by]
+            high_risk: patient.high_risk?,
+            by: params[:by]
           }
         end
 
         def request_descriptions
-          @patient.required_observation_requests(@params[:clinic])
+          patient.required_observation_requests(params[:clinic])
         end
 
         def patient_rules
-          @patient.required_patient_pathology
+          patient.required_patient_pathology
         end
       end
     end

data/app/models/renalware/pathology/requests/requests_factory.rb

@@ -6,14 +6,11 @@ module Renalware
   module Pathology
     module Requests
       class RequestsFactory
-        def initialize(patients, params)
-          @patients = patients
-          @params = params
-        end
+        pattr_initialize :patients, :params
 
         def build
-          @patients.map do |patient|
-            RequestFactory.new(patient, @params).build
+          patients.map do |patient|
+            RequestFactory.new(patient, params).build
           end
         end
       end

data/app/models/renalware/patient.rb

@@ -45,6 +45,7 @@ module Renalware
     belongs_to :country_of_birth, class_name: "System::Country"
     belongs_to :religion, class_name: "Patients::Religion"
     belongs_to :language, class_name: "Patients::Language"
+    belongs_to :named_consultant, class_name: "User"
     has_many :bookmarks, class_name: "Patients::Bookmark"
     has_many :alerts, class_name: "Patients::Alert"
     has_one :worry, class_name: "Patients::Worry"

data/app/models/renalware/patients/ingestion/commands/add_or_update_patient.rb

@@ -35,15 +35,15 @@ module Renalware
           attr_reader :mapper_factory
 
           def call
-            # For now skip updating the patient, just update the index ie create/update a
-            # patient abridgement
-            # update_patient_if_exists
+            update_patient_if_exists
             UpdateMasterPatientIndex.new(message).call
           end
 
           private
 
           def update_patient_if_exists
+            return if ENV.key?("ADT_SKIP_UPDATE_PATIENT")
+
             patient = find_patient
             return if patient.blank?
 

data/app/models/renalware/patients/ingestion/message_mappers/patient.rb

@@ -30,9 +30,9 @@ module Renalware
 
           # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
           def map_attributes
-            patient.attributes = {
+            attrs = {
               local_patient_id: patient_identification.internal_id,
-              nhs_number: patient_identification.external_id,
+              nhs_number: patient_identification.nhs_number,
               given_name: patient_identification.given_name,
               family_name: patient_identification.family_name,
               suffix: patient_identification.suffix,
@@ -43,6 +43,28 @@ module Renalware
               practice: find_practice(message.practice_code) || patient.practice,
               primary_care_physician: find_primary_care_physician(message.gp_code)
             }
+
+            # Don't overwrite existing patient data if the new data is blank?
+            attrs.reject! { |_key, value| value.blank? }
+            patient.attributes = attrs
+
+            # patient.given_name = patient_identification.given_name
+            # patient.family_name = patient_identification.family_name
+            # patient.suffix = patient_identification.suffix
+            # patient.title = patient_identification.title
+            # patient.attributes = {
+            #   local_patient_id: patient_identification.internal_id,
+            #   nhs_number: patient_identification.nhs_number,
+            #   given_name: patient_identification.given_name,
+            #   family_name: patient_identification.family_name,
+            #   suffix: patient_identification.suffix,
+            #   title: patient_identification.title,
+            #   born_on: Time.zone.parse(patient_identification.dob)&.to_date,
+            #   died_on: Time.zone.parse(patient_identification.death_date)&.to_date,
+            #   sex: patient_identification.sex,
+            #   practice: find_practice(message.practice_code) || patient.practice,
+            #   primary_care_physician: find_primary_care_physician(message.gp_code)
+            # }
             patient.build_current_address if patient.current_address.blank?
             patient.current_address.attributes = {
               street_1: address[0],

data/app/models/renalware/patients/ingestion/update_master_patient_index.rb

@@ -20,8 +20,6 @@ module Renalware
 
           @rw_patient = find_patient_in_renalware
           update_or_create_abridged_patient
-          # update_primary_care_physician
-          # update_practice
         end
 
         private
@@ -32,9 +30,10 @@ module Renalware
           ) || NullObject.instance
         end
 
-        # rubocop:disable Metrics/AbcSize
+        # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
         def update_or_create_abridged_patient
           find_or_initialize_abridged_patient.update!(
+            nhs_number: patient_identification.nhs_number,
             given_name: patient_identification.given_name,
             family_name: patient_identification.family_name,
             sex: patient_identification.sex,
@@ -47,7 +46,7 @@ module Renalware
             gp_code: hl7_message.gp_code
           )
         end
-        # rubocop:enable Metrics/AbcSize
+        # rubocop:enable Metrics/AbcSize, Metrics/MethodLength
 
         def find_or_initialize_abridged_patient
           Patients::Abridgement.find_or_initialize_by(

data/app/models/renalware/problems/note.rb

@@ -6,10 +6,14 @@ module Renalware
   module Problems
     class Note < ApplicationRecord
       include Accountable
+      acts_as_paranoid
+      alias archived? deleted?
 
       belongs_to :problem, touch: true
 
       scope :ordered, -> { order(created_at: :asc) }
+      scope :archived, -> { only_deleted }
+      scope :with_archived, -> { with_deleted }
 
       validates :description, presence: true
 

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

@@ -24,6 +24,7 @@ module Renalware
         User.transaction do
           approve if can_approve?(params)
           unexpire if can_unexpire?(params)
+          user.consultant = true?(params[:consultant])
           authorise(params)
           user.telephone = params[:telephone]
           user.save!

data/app/models/renalware/user.rb

@@ -37,6 +37,7 @@ module Renalware
         .distinct("roles_users.user_id")
         .where("roles_users.user_id is null")
     }
+    scope :consultants, -> { where(consultant: true).excluding_system_user.ordered }
 
     # 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.

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

@@ -8,7 +8,9 @@ module Renalware
       end
 
       def edit?
-        !record.immutable?
+        return false unless record.persisted?
+
+        user_is_super_admin? || !record.immutable?
       end
     end
   end

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

@@ -8,7 +8,9 @@ module Renalware
       end
 
       def edit?
-        record.persisted? && !record.immutable?
+        return false unless record.persisted?
+
+        user_is_super_admin? || !record.immutable?
       end
     end
   end

data/app/views/renalware/admin/users/edit.html.slim

@@ -1,47 +1,52 @@
 = within_admin_layout(title: "Edit",
                       breadcrumbs: breadcrumb_for("Users", admin_users_path)) do
 
-  h2= @user
+  h2= user
 
-  = simple_form_for @user,
+  = simple_form_for user,
                     html: { autocomplete: "off" },
-                    url: admin_user_path(@user) do |f|
+                    url: admin_user_path(user) do |f|
     = f.input :approved, as: :hidden, input_html: { value: true }
 
-    - if @user.errors.any?
+    - if user.errors.any?
       ul.error-messages
-        - @user.errors.full_messages.each do |msg|
+        - user.errors.full_messages.each do |msg|
           li= msg
 
-    - if @user.expired?
+    - if user.expired?
       .row
         = check_box_tag "user[unexpire]", true, false, class: "inline"
         = label_tag :user_unexpire, "Reactivate account"
 
     span
       | Requested write access:  
-      = yes_no(@user.asked_for_write_access)
+      = yes_no(user.asked_for_write_access)
 
     br
     br
     - Renalware::Role.all.order(id: :asc).each_with_index do |role, index|
       - element_id = "user_role_ids_#{index}"
-      - policy = Pundit.policy(current_user, @user)
+      - policy = Pundit.policy(current_user, user)
       = check_box_tag "user[role_ids][]",
                       role.id,
-                      @user.has_role?(role.name),
+                      user.has_role?(role.name),
                       disabled: !(policy.assign_role?(role)),
                       id: element_id,
                       class: "inline"
       = label_tag element_id, role.name.humanize
     br
-    br
 
     = f.input :telephone,
               input_html: { class: "input small" },
               wrapper: :horizontal_small
 
-    - msg = @user.approved? ? "Update" : "Approve"
+    = f.input :consultant,
+              as: :boolean,
+              checked_value: "true",
+              unchecked_value: "false",
+              wrapper: :horizontal_small
+
+    - msg = user.approved? ? "Update" : "Approve"
     = f.submit msg, class: "button"
     span= " or "
     = link_to "cancel", admin_users_path

data/app/views/renalware/admin/users/index.html.slim

@@ -19,6 +19,7 @@
       th.col-width-small Requested write access
       th.col-width-medium Role
       th.col-width-tiny= sort_link(user_search, :approved, "Approved")
+      th.col-width-tiny= sort_link(user_search, :consultant, "Consultant")
       th.col-width-date= sort_link(user_search, :expired_at, "Expired On")
       th.col-width-date-time.show-for-large-up= sort_link(user_search, :current_sign_in_at, "Current sign in")
       th.col-width-date-time.show-for-large-up= sort_link(user_search, :last_sign_in_at, "Last sign in")
@@ -47,6 +48,11 @@
               i.far.fa-check-square
             - else
               i.muted.unapproved.far.fa-square
+          td
+            - if user.consultant?
+              i.far.fa-check-square
+            - else
+              i.muted.unapproved.far.fa-square
           td.expired= l(user.expired_at&.to_date)
           td.show-for-large-up= l(user.current_sign_in_at)
           td.show-for-large-up= l(user.last_sign_in_at)

data/app/views/renalware/clinical/profiles/edit.html.slim

@@ -2,7 +2,7 @@
   breadcrumbs: breadcrumb_for("Clinical Profile", patient_clinical_profile_path)) do
 
   .row.document
-    = simple_form_for patient.document,
+    = simple_form_for patient,
                       url: patient_clinical_profile_path(patient),
                       method: :patch,
                       as: :clinical_profile,
@@ -12,19 +12,29 @@
       .columns.large-12
         article
           header
-            h2 Diabetes
-          .hint If YES, enter year of diagnosis
-          = render_input f, :diabetes
+            h2 General
+          = f.association :named_consultant,
+                          as: :user_picker,
+                          collection: Renalware::User.consultants,
+                          wrapper: :horizontal_medium
 
-        article
-          header
-            h2 History
+      = f.simple_fields_for :document, patient.document do |fdoc|
+        .columns.large-12
+          article
+            header
+              h2 Diabetes
+            .hint If YES, enter year of diagnosis
+            = render_input fdoc, :diabetes
 
-          = f.simple_fields_for :history, patient.document.history do |fd|
-            = fd.input :alcohol, input_html: { class: "small-input" }
-            = fd.input :smoking, input_html: { class: "small-input" }
+          article
+            header
+              h2 History
 
-        .columns.large-12
-          = submit_tag "Update", class: "button"
-          span= " or "
-          = link_to "Cancel", patient_clinical_profile_path(patient)
+            = fdoc.simple_fields_for :history, patient.document.history do |fh|
+              = fh.input :alcohol, input_html: { class: "small-input" }
+              = fh.input :smoking, input_html: { class: "small-input" }
+
+          .columns.large-12.form-actions
+            = submit_tag "Update", class: "button"
+            span= " or "
+            = link_to "Cancel", patient_clinical_profile_path(patient)

data/app/views/renalware/clinical/profiles/show.html.slim

@@ -5,7 +5,11 @@
   .grid
     .row
       .columns.medium-6
+        = article_tag("General") do
+          = definition_list_for(patient) do |list|
+            = list.definition(:named_consultant)
 
+      .columns.medium-6
         article
           header
             h2 Diabetes

data/app/views/renalware/hd/mdm_patients/_patient.html.slim

@@ -20,8 +20,10 @@ tr
   td= l(patient.current_observation_set.hgb_observed_at)
   td.show-for-xlarge-up= patient.current_observation_set.phos_result
   td.show-for-xlarge-up= l(patient.current_observation_set.phos_observed_at)
-  td.show-for-xlarge-up= patient.current_observation_set.pth_result
-  td.show-for-xlarge-up= l(patient.current_observation_set.pth_observed_at)
+  td.show-for-xlarge-up= patient.current_observation_set.pot_result
+  td.show-for-xlarge-up= l(patient.current_observation_set.pot_observed_at)
+  td.show-for-xlarge-up= patient.current_observation_set.pthi_result
+  td.show-for-xlarge-up= l(patient.current_observation_set.pthi_observed_at)
   td.show-for-xlarge-up= patient.current_observation_set.urr_result
   td.show-for-xlarge-up= l(patient.current_observation_set.urr_observed_at)
   td.actions= link_to t(".view"), view_proc.call(patient)

data/app/views/renalware/hd/mdm_patients/_table.html.slim

@@ -19,8 +19,10 @@ table#patients.mdm-patients.columns
       th.col-width-date= sort_link(path, :hgb_date, t(".hgb_date"))
       th.show-for-xlarge-up.col-width-tiny= sort_link(path, :phos, t(".phos"))
       th.show-for-xlarge-up.col-width-date= sort_link(path, :phos_date, t(".phos_date"))
-      th.show-for-xlarge-up.col-width-tiny= sort_link(path, :pth, t(".pth"))
-      th.show-for-xlarge-up.col-width-date= sort_link(path, :pth_date, t(".pth_date"))
+      th.show-for-xlarge-up.col-width-tiny= sort_link(path, :pot, t(".pot"))
+      th.show-for-xlarge-up.col-width-date= sort_link(path, :pot_date, t(".pot_date"))
+      th.show-for-xlarge-up.col-width-tiny= sort_link(path, :pthi, t(".pthi"))
+      th.show-for-xlarge-up.col-width-date= sort_link(path, :pthi_date, t(".pthi_date"))
       th.show-for-xlarge-up.col-width-tiny= sort_link(path, :urr, t(".urr"))
       th.show-for-xlarge-up.col-width-date= sort_link(path, :urr_date, t(".urr_date"))
       th.col-width-tiny

data/app/views/renalware/medications/home_delivery/prescriptions/index.pdf.slim

@@ -77,15 +77,18 @@ html
     section.consultant
       p
         b Consultant:
-        span  
+        / TODO: Move this logic to a presenter
+        - consultant = patient.named_consultant
+        - if consultant.present?
+          |   
+          - name = consultant.signature.presence || consultant.to_s
+          = [name, consultant.professional_position].compact.join(", ")
+        - else
+          span  
     section.signoff
       table
         tr
-          td Prescriber:
-          td
-          td
-        tr
-          td.prescriber= [current_user.signature, current_user.professional_position].compact.join(", ")
+          td.prescriber Prescriber:
           td.signature Signature:
           td Date:
 

data/app/views/renalware/medications/prescriptions/_table.html.slim

@@ -19,7 +19,7 @@
             th Notes
             th.col-width-date.wide
               = sort_link_if(treatable.sortable?, search, :prescribed_on, "Prescribed on")
-            th Prescribed By
+            th Recorded By
             - unless current_scope
               th.col-width-date Terminated On
               th Terminated By

data/app/views/renalware/problems/problems/_archived_table.html.slim

@@ -16,7 +16,7 @@ table#archived_problems.manual-stripes.auto-layout
         td
           = problem.description
           ol
-            - problem.notes.each do |note|
+            - problem.notes.with_archived.each do |note|
               li= note.description
         td= l problem.updated_on
         td= problem.updated_by.full_name

data/config/locales/renalware/hd/mdm_patients.yml

@@ -30,10 +30,10 @@ en:
           urr_date: URR Date
           phos: PO4
           phos_date: PO4 Date
-          pth: PTH
-          pth_date: PTH Date
           pthi: PTHI
           pthi_date: PTHI Date
+          pot: POT
+          pot_date: POT Date
           cre: CRE
           cre_date: CRE Date
           egfr: EGFR

data/db/migrate/20190925161724_change_path_request_consultant_id.rb

@@ -1,12 +1,8 @@
 class ChangePathRequestConsultantId < ActiveRecord::Migration[5.2]
   def change
     within_renalware_schema do
-      remove_reference(
-        :pathology_requests_requests,
-        :consultant,
-        foreign_key: { to_table: :users },
-        index: true
-      )
+      remove_column(:pathology_requests_requests, :consultant_id, :integer)
+
       add_reference(
         :pathology_requests_requests,
         :consultant,

data/db/migrate/20191026120029_add_deleted_at_to_hd_sessions.rb

@@ -0,0 +1,11 @@
+class AddDeletedAtToHDSessions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :hd_sessions, :deleted_at, :datetime
+      add_index :hd_sessions, :deleted_at
+
+      add_column :hd_prescription_administrations, :deleted_at, :datetime
+      add_index :hd_prescription_administrations, :deleted_at
+    end
+  end
+end

data/db/migrate/20191029095202_add_deleted_at_to_problem_notes.rb

@@ -0,0 +1,8 @@
+class AddDeletedAtToProblemNotes < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :problem_notes, :deleted_at, :datetime
+      add_index :problem_notes, :deleted_at
+    end
+  end
+end

data/db/migrate/20191105095304_update_views_to_exclude_deleted_sessions.rb

@@ -0,0 +1,12 @@
+class UpdateViewsToExcludeDeletedSessions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view(
+        :reporting_hd_blood_pressures_audit,
+        version: 2,
+        revert_to_version: 1,
+        materialized: true
+      )
+    end
+  end
+end

data/db/migrate/20191108105923_add_named_consultant_to_patients.rb

@@ -0,0 +1,11 @@
+class AddNamedConsultantToPatients < ActiveRecord::Migration[5.2]
+  def change
+    add_reference(
+      :patients,
+      :named_consultant,
+      foreign_key: { to_table: :users },
+      index: true,
+      null: true
+    )
+  end
+end

data/db/views/reporting_hd_blood_pressures_audit_v02.sql

@@ -0,0 +1,80 @@
+/*
+This is just a starter for 10 equivalent for the HaemoBPaudit4 audit.
+Lots missing for example
+- only do this for the last 30 days?
+- selecting patients with a current modality of HD
+- filtering out null or 0 bps
+- the 140 130 etc percentages
+*/
+
+WITH
+  blood_pressures AS (
+  SELECT
+    hd_sessions.id as session_id,
+    patients.id as patient_id,
+    hd_sessions.hospital_unit_id,
+    hd_sessions.document->'observations_before'->'blood_pressure'->>'systolic' as systolic_pre,
+    hd_sessions.document->'observations_before'->'blood_pressure'->>'diastolic' as diastolic_pre,
+    hd_sessions.document->'observations_after'->'blood_pressure'->>'systolic' as systolic_post,
+    hd_sessions.document->'observations_after'->'blood_pressure'->>'diastolic' as diastolic_post
+    FROM hd_sessions
+  INNER JOIN patients on patients.id = hd_sessions.patient_id
+  WHERE hd_sessions.signed_off_at IS NOT NULL
+  AND hd_sessions.deleted_at IS NULL
+  ),
+  some_other_derived_table_variable AS (
+   SELECT 1 FROM blood_pressures
+  )
+SELECT
+  hu.name as hospital_unit_name,
+  ROUND(AVG(systolic_pre::int)) as systolic_pre_avg,
+  ROUND(AVG(diastolic_pre::int)) as diastolic_pre_avg,
+  ROUND(AVG(systolic_post::int)) as systolic_post_avg,
+  ROUND(AVG(diastolic_post::int)) as distolic_post_avg
+  FROM blood_pressures
+  INNER JOIN hospital_units as hu on hu.id = blood_pressures.hospital_unit_id
+        GROUP BY hu.name
+
+/*
+Here is the original for reference
+use audits;
+DROP TABLE IF EXISTS hdbpdata;
+DROP TABLE IF EXISTS hdpatbpavg;
+DROP TABLE IF EXISTS hdpatbpsite;
+DROP TABLE IF EXISTS HDpatBPsitemain;
+SET @mintotal=6;
+CREATE TEMPORARY TABLE hdbpdata SELECT hdsesszid, modalsite as currsite, sex,
+year(CURDATE())-year(birthdate) as age, syst_pre, syst_post, diast_pre, diast_post FROM
+renalware.hdsessiondata JOIN renalware.patientdata ON hdsesszid=patzid WHERE DATEDIFF(CURDATE(),
+hdsessdate)<30 and patientdata.modalcode LIKE '%HD%';
+CREATE TABLE hdpatbpavg as SELECT hdsesszid, currsite, ROUND(AVG(syst_pre),0) as avgpresyst,
+ROUND(AVG(syst_post),0) as avgpostsyst, ROUND(AVG(diast_pre),0) as avgprediast,
+ ROUND(AVG(diast_post),0) as avgpostdiast, syst_pre, syst_post, diast_pre, diast_post FROM hdbpdata
+ GROUP BY hdsesszid;
+CREATE TABLE hdpatbpsite as SELECT currsite as currentsite, count(hdsesszid) as patcount,
+ROUND(AVG(avgpresyst),0) as presyst_avg,
+round(100*(sum(IF(syst_pre<140, '1','0'))/count(hdsesszid)),1) as pctpresysless140,
+ROUND(AVG(avgpostsyst),0) as postsys_avg,
+round(100*(sum(IF(syst_post<130, '1','0'))/count(hdsesszid)),1) as pctpostsysless130,
+ROUND(AVG(avgprediast),0) as prediast_avg,
+round(100*(sum(IF(diast_pre<90, '1','0'))/count(hdsesszid)),1) as pctprediastless90,
+ROUND(AVG(avgpostdiast),0) as postdiast_avg,
+round(100*(sum(IF(diast_post<80, '1','0'))/count(hdsesszid)),1) as pctpostdiastless80
+FROM hdpatbpavg GROUP BY currentsite
+UNION
+SELECT 'Total', count(hdsesszid) as patcount, ROUND(AVG(avgpresyst),0) as presyst_avg,
+round(100*(sum(IF(syst_pre<140, '1','0'))/count(hdsesszid)),1) as pctpresysless140,
+ROUND(AVG(avgpostsyst),0) as postsys_avg,
+round(100*(sum(IF(syst_post<130, '1','0'))/count(hdsesszid)),1) as pctpostsysless130,
+ROUND(AVG(avgprediast),0) as prediast_avg,
+round(100*(sum(IF(diast_pre<90, '1','0'))/count(hdsesszid)),1) as pctprediastless90,
+ROUND(AVG(avgpostdiast),0) as postdiast_avg,
+round(100*(sum(IF(diast_post<80, '1','0'))/count(hdsesszid)),1) as pctpostdiastless80
+FROM hdpatbpavg;
+Create TABLE HDpatBPsitemain as select * from hdpatbpsite WHERE patcount>@mintotal
+ORDER BY patcount DESC;
+UPDATE auditslist SET lastrun=NOW() WHERE auditcode='hdbpaudit';
+DROP TABLE IF EXISTS hdbpdata;
+DROP TABLE IF EXISTS hdpatbpavg;
+DROP TABLE IF EXISTS hdpatbpsite;
+*/

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.121"
+  VERSION = "2.0.123"
 end

data/spec/factories/system/users.rb

@@ -29,6 +29,10 @@ FactoryBot.define do
       user.roles << create(:role, obj.role) if obj.role.present?
     end
 
+    trait :consultant do
+      consultant { true }
+    end
+
     trait :unapproved do
       approved { false }
     end

data/spec/support/pages/clinical/profile_page.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+require_relative "../page_object"
+
+module Pages
+  module Clinical
+    class ProfilePage < Pages::PageObject
+      pattr_initialize :patient
+
+      def edit
+        visit patient_clinical_profile_path(patient)
+        within ".page-actions" do
+          click_on "Edit"
+        end
+      end
+
+      def save
+        within ".form-actions" do
+          find('input[name="commit"]').click
+        end
+      end
+
+      def named_consultant=(user)
+        select user.to_s, from: "Named consultant"
+      end
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.121
+  version: 2.0.123
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-04 00:00:00.000000000 Z
+date: 2019-11-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: actionview-component
@@ -1697,6 +1697,7 @@ files:
 - app/models/renalware/pathology/observation_descriptions_by_code_query.rb
 - app/models/renalware/pathology/observation_digest.rb
 - app/models/renalware/pathology/observation_for_patient_observation_description_query.rb
+- app/models/renalware/pathology/observation_for_patient_observation_description_using_set_query.rb
 - app/models/renalware/pathology/observation_for_patient_request_description_query.rb
 - app/models/renalware/pathology/observation_request.rb
 - app/models/renalware/pathology/observation_requests_attributes_builder.rb
@@ -1749,7 +1750,7 @@ files:
 - app/models/renalware/pathology/requests/requests_factory.rb
 - app/models/renalware/pathology/requests/sample_type.rb
 - app/models/renalware/pathology/results.rb
-- app/models/renalware/pathology/view_observation_results.rb
+- app/models/renalware/pathology/view_observation_results.rb.dead
 - app/models/renalware/patient.rb
 - app/models/renalware/patients.rb
 - app/models/renalware/patients/abridgement.rb
@@ -3691,6 +3692,10 @@ files:
 - db/migrate/20191012121433_add_consultant_to_users.rb
 - db/migrate/20191018143635_create_hd_diary_matrix_view.rb
 - db/migrate/20191018144917_create_fn_to_archive_master_slots.rb
+- db/migrate/20191026120029_add_deleted_at_to_hd_sessions.rb
+- db/migrate/20191029095202_add_deleted_at_to_problem_notes.rb
+- db/migrate/20191105095304_update_views_to_exclude_deleted_sessions.rb
+- db/migrate/20191108105923_add_named_consultant_to_patients.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3808,6 +3813,7 @@ files:
 - db/views/reporting_daily_pathology_v03.sql
 - db/views/reporting_daily_ukrdc_v01.sql
 - db/views/reporting_hd_blood_pressures_audit_v01.sql
+- db/views/reporting_hd_blood_pressures_audit_v02.sql
 - db/views/reporting_hd_overall_audit_v01.sql
 - db/views/reporting_hd_overall_audit_v02.sql
 - db/views/reporting_hd_overall_audit_v04.sql
@@ -4049,6 +4055,7 @@ files:
 - spec/support/matchers/have_pdf_page_text.rb
 - spec/support/matchers/validate_timeliness_of.rb
 - spec/support/pages/admissions/consults_page.rb
+- spec/support/pages/clinical/profile_page.rb
 - spec/support/pages/letters/form.rb
 - spec/support/pages/letters/patient_letters.rb
 - spec/support/pages/medications/prescription_fom.rb