renalware-core 2.0.78 → 2.0.79

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: d6d87b6b9199f3f95e5ee6cf88b3a553eb819814db336e974e763fa35c5cc36b
+  metadata.gz: e498f337dc6db41cfb6478cd0241f19693a22f284ff95941a1756c32beb057d5
+  data.tar.gz: 45bf39706420b19adc516e7e2fc2effd4c095392a675d01af1e1a64892ba0420
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-  data.tar.gz: 41f49f78bab0117ee76308dcb1ae38009588098f197e28821a0cf11351549a16434f8001c01458b4915db06639e6e9f8bd0d7fc72f1f27fb0f438661cd75ffa6
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+  data.tar.gz: a14cb7fa2f36d3d40b3939715e485804b713b148dcd54dd68420eba7f1007a6cfbf31dde473952805ce79cae497276ae004e0734ee120f42b4affbe1c016a3d3

data/README.md

@@ -123,7 +123,7 @@ On a Mac:
 - Download chromedriver from eg [here](https://chromedriver.storage.googleapis.com/index.html?path=2.38/)
 - Unzip and place in location in your PATH eh `/usr/local/bin`
 - If you have chromedriver errors it maybe your installed version of Chrome is not
-compatible your chromedriver version. In this case check your versions with
+compatible your chromedriver version. In this case check your versions with:
 
 ```
 chromedriver -v

data/app/assets/javascripts/renalware/application.js.erb

@@ -36,6 +36,7 @@
 //= require jquery_nested_form
 //= require foundation-datepicker
 //= require renalware/clockpicker
+//= require renalware/double_scroll
 //= require cocoon
 //= require mousetrap
 //= require renalware/iframeResizer

data/app/assets/javascripts/renalware/layout.js

@@ -0,0 +1,3 @@
+$(document).ready(function() {
+  $('.double-scroll').doubleScroll({ resetOnWindowResize: true });
+});

data/app/assets/stylesheets/renalware/modules/_patients.scss

@@ -368,7 +368,8 @@ form {
   }
 
   .summary-part--events,
-  .summary-part--admissions {
+  .summary-part--admissions,
+  .summary-part--consults {
     @include grid-column(12);
 
     @media #{$xxlarge-up} {

data/app/controllers/renalware/admin/feeds/files_controller.rb

@@ -39,7 +39,13 @@ module Renalware
         private
 
         def files
-          @files ||= Renalware::Feeds::File.ordered.page(page).per(per_page)
+          @files ||= begin
+            Renalware::Feeds::File
+              .ordered
+              .includes(:file_type, :created_by)
+              .page(page)
+              .per(per_page)
+          end
         end
 
         def file_upload_params

data/app/controllers/renalware/patients/practices_controller.rb

@@ -31,7 +31,7 @@ module Renalware
         address = practice.address || null_address
         {
           id: practice.id,
-          name: practice.name,
+          name: "#{practice.name} (#{practice.code})",
           address: [
             address.street_1,
             address.town,

data/app/controllers/renalware/patients/primary_care_physician_controller.rb

@@ -35,10 +35,8 @@ module Renalware
       # So to allow the Practice and GP to be assigned to such a patient we have to skip validation
       # callbacks by using update_columns.
       def update_patient
-        return false unless selected_pyhsician
-
         patient.update_columns(
-          primary_care_physician_id: selected_pyhsician.id,
+          primary_care_physician_id: selected_physician_id,
           practice_id: patient_params[:practice_id],
           updated_by_id: current_user.id
         )
@@ -56,9 +54,12 @@ module Renalware
         }
       end
 
-      def selected_pyhsician
-        @selected_pyhsician ||= begin
-          PrimaryCarePhysician.find_by(id: patient_params[:primary_care_physician_id])
+      def selected_physician_id
+        @selected_physician_id ||= begin
+          PrimaryCarePhysician
+            .select(:id)
+            .find_by(id: patient_params[:primary_care_physician_id])
+            &.id
         end
       end
 
@@ -67,20 +68,38 @@ module Renalware
       end
 
       # Every time a practice is selected from the autocomplete list in the Find GP modal
-      # we re-render the edit form and inject the practice_id as a hidden field therein. This was
-      # its available in a form submission in the #update action.
+      # we re-render the edit form and inject the practice_id as a hidden field therein so it
+      # is available in a form submission in the #update action.
       # The practice_id in this method is supplied here as a query param by the JS that refreshes
       # the form when a practice is selected - it will be the same as that posted in the form when
-      # saved, but at this stage its  ephemeral and just here to let us build the PCP list to
+      # saved, but at this stage its ephemeral and just here to let us build the GP list to
       # render in the form.
       def available_primary_care_physicians
-        pratice_id = params[:practice_id]
-        return [] unless pratice_id
+        practice_id = params[:practice_id]
+        return [] unless practice_id
 
-        Practice.find(pratice_id).primary_care_physicians.map do |physician|
-          [physician.to_s, physician.id]
+        find_practice_memberships_for(practice_id).map do |membership|
+          [
+            format_gp_name(membership),
+            membership.primary_care_physician&.id
+          ]
         end
       end
+
+      def find_practice_memberships_for(practice_id)
+        PracticeMembership
+          .eager_load(:primary_care_physician)
+          .where(practice_id: practice_id)
+          .order(
+            "#{PracticeMembership.table_name}.left_on desc,"\
+            "#{PrimaryCarePhysician.table_name}.name asc"
+          )
+      end
+
+      def format_gp_name(membership)
+        left_on = " (Left #{I18n.l(membership.left_on)})" if membership.left_on.present?
+        "#{membership.primary_care_physician}#{left_on}"
+      end
     end
   end
 end

data/app/controllers/renalware/virology/dashboards_controller.rb

@@ -7,10 +7,7 @@ module Renalware
     class DashboardsController < BaseController
       def show
         authorize [:renalware, :virology, :dashboard], :show?
-        render locals: {
-          patient: patient,
-          vaccinations: Vaccination.for_patient(patient)
-        }
+        render locals: { dashboard: DashboardPresenter.new(patient) }
       end
     end
   end

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

@@ -32,15 +32,20 @@ module Renalware
       end
 
       def update_profile(profile)
-        document_params = profile_params[:document]
         document = profile.document
-        document.hiv = YearDatedDiagnosis.new(document_params[:hiv])
-        document.hepatitis_b = YearDatedDiagnosis.new(document_params[:hepatitis_b])
-        document.hepatitis_c = YearDatedDiagnosis.new(document_params[:hepatitis_c])
-        document.htlv = YearDatedDiagnosis.new(document_params[:htlv])
+        document.hiv = year_date_diagnosis_for(:hiv)
+        document.hepatitis_b = year_date_diagnosis_for(:hepatitis_b)
+        document.hepatitis_b_core_antibody = year_date_diagnosis_for(:hepatitis_b_core_antibody)
+        document.hepatitis_c = year_date_diagnosis_for(:hepatitis_c)
+        document.htlv = year_date_diagnosis_for(:htlv)
         profile.save_by(current_user)
       end
 
+      def year_date_diagnosis_for(condition)
+        document_params = profile_params[:document]
+        YearDatedDiagnosis.new(document_params[condition])
+      end
+
       def profile_params
         params.require(:virology_profile).permit(document: {})
       end

data/app/documents/renalware/hd/session_document.rb

@@ -34,11 +34,14 @@ module Renalware
         attribute :temperature, Float
         attribute :temperature_measured, Document::Enum, enums: %i(yes no), default: :yes
         attribute :bm_stix, Float
+        attribute :respiratory_rate, Integer
+        attribute :respiratory_rate_measured, Document::Enum, enums: %i(yes no), default: :yes
 
         %i(
           weight
           temperature
           bm_stix
+          respiratory_rate
           pulse
         ).each { |att| validates(att, numericality: { allow_blank: true }) }
 
@@ -46,6 +49,7 @@ module Renalware
         validates :temperature, "renalware/patients/temperature" => true
         validates :bm_stix, "renalware/patients/bm_stix" => true
         validates :pulse, "renalware/patients/pulse" => true
+        validates :respiratory_rate, "renalware/patients/respiratory_rate" => true
       end
       attribute :observations_before, Observations
       attribute :observations_after, Observations

data/app/documents/renalware/patient_document.rb

@@ -28,8 +28,22 @@ module Renalware
     attribute :psychosocial, Psychosocial
 
     class History < Document::Embedded
+      SMOKING_SNOMED_MAP = {
+        "yes" => { code: 77176002, description: "Current" },
+        "no" => { code: 8392000, description: "Non" },
+        "ex" => { code: 8517006, description: "Ex" }
+      }.freeze
+
       attribute :alcohol, Document::Enum, enums: %i(never rarely social heavy)
-      attribute :smoking, Document::Enum, enums: %i(no ex yes) # RRSMOKING %i(never former current)
+      attribute :smoking, Document::Enum, enums: %i(no ex yes)
+
+      def smoking_snomed
+        SMOKING_SNOMED_MAP[@smoking]
+      end
+
+      def smoking_rr
+        @smoking&.upcase
+      end
     end
     attribute :history, History
   end

data/app/documents/renalware/renal/profile_document.rb

@@ -7,6 +7,24 @@ module Renalware
   module Renal
     class ProfileDocument < Document::Embedded
       class Comorbidities < Document::Embedded
+        SMOMED_MAP = {
+          diabetes: 73211009,
+          ischaemic_heart_dis: 414545008,
+          cabg_or_angioplasty: 232717009,
+          heart_failure: 84114007,
+          atrial_fibrill: 49436004,
+          malignancy: 86049000,
+          cerebrovascular_dis: 62914000,
+          chronic_obstr_pulm_dis: 13645005,
+          liver_disease: 235856003,
+          periph_vascular_dis: 400047006,
+          amputation_for_pvd: 81723002,
+          claudication: 275520000,
+          ischaemic_neuropathic_ulcers: 13954005,
+          non_coronary_intervention: 418285008,
+          dementia: 52448006
+        }.freeze
+
         attribute :diabetes, YearDatedConfirmation
         attribute :ischaemic_heart_dis, YearDatedConfirmation
         attribute :cabg_or_angioplasty, YearDatedConfirmation
@@ -23,6 +41,10 @@ module Renalware
         attribute :non_coronary_intervention, YearDatedConfirmation
         attribute :dementia, YearDatedConfirmation
         attribute :smoking, SmokingStatus
+
+        def self.snomed_code_for(att)
+          SMOMED_MAP[att]
+        end
       end
       attribute :comorbidities, Comorbidities
     end

data/app/documents/renalware/virology/profile_document.rb

@@ -8,6 +8,7 @@ module Renalware
     class ProfileDocument < Document::Embedded
       attribute :hiv, YearDatedDiagnosis
       attribute :hepatitis_b, YearDatedDiagnosis
+      attribute :hepatitis_b_core_antibody, YearDatedDiagnosis
       attribute :hepatitis_c, YearDatedDiagnosis
       attribute :htlv, YearDatedDiagnosis
     end

data/app/models/renalware/clinics/remembered_clinic_visit_preferences.rb

@@ -6,7 +6,7 @@ module Renalware
   module Clinics
     class RememberedClinicVisitPreferences < RememberedPreferences
       SESSION_KEY = :clinic_visit_preferences
-      ATTRIBUTES_TO_REMEMBER = %i(date).freeze
+      ATTRIBUTES_TO_REMEMBER = %i(date clinic_id).freeze
     end
   end
 end

data/app/models/renalware/feeds/files/practice_memberships/import_job.rb

@@ -13,13 +13,11 @@ module Renalware
 
           def perform(file)
             logging_to_stringio(strio = StringIO.new)
-            log "Before upload there are #{practice_membership_count} active and "\
-                "#{inactive_practice_membership_count} inactive practice memberships"
+            log "Before upload there are #{practice_membership_count} practice memberships"
             file.update!(status: :processing, attempts: file.attempts + 1)
             status = :success
             elapsed_ms = Benchmark.ms { process_archive(file.location) }
-            log "After upload there are #{practice_membership_count} active and "\
-                "#{inactive_practice_membership_count} inactive practice memberships"
+            log "After upload there are #{practice_membership_count} practice memberships"
           rescue StandardError => e
             Rails.logger.error(formatted_exception(e))
             status = :failure
@@ -40,10 +38,6 @@ module Renalware
           def practice_membership_count
             Patients::PracticeMembership.count
           end
-
-          def inactive_practice_membership_count
-            Patients::PracticeMembership.deleted.count
-          end
         end
       end
     end

data/app/models/renalware/feeds/files/primary_care_physicians/import_csv.rb

@@ -11,13 +11,13 @@ module Renalware
           pattr_initialize :csv_path
 
           def call
-            import_practices_csv_using_sql_function
+            import_gp_csv_using_sql_function
           end
 
           private
 
           # See migration for SQL function definition
-          def import_practices_csv_using_sql_function
+          def import_gp_csv_using_sql_function
             conn = ActiveRecord::Base.connection
             conn.execute(
               "SELECT renalware.import_gps_csv(#{conn.quote(csv_path.realpath.to_s)}::text)"

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

@@ -45,6 +45,8 @@ module Renalware
           validates :blood_pressure, presence: true
           validates :weight_measured, presence: true
           validates :temperature_measured, presence: true
+          validates :respiratory_rate_measured, presence: true
+          validates :respiratory_rate, presence: { if: -> { respiratory_rate_measured&.yes? } }
           validates :weight, presence: { if: -> { weight_measured&.yes? } }
           validates :temperature, presence: { if: -> { temperature_measured&.yes? } }
           validates :blood_pressure, "renalware/patients/blood_pressure_presence" => true

data/app/models/renalware/patients/last_successful_practice_sync_date_query.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+require "attr_extras"
+
+module Renalware
+  module Patients
+    class LastSuccessfulPracticeSyncDateQuery
+      pattr_initialize :identifier
+
+      def call
+        max_created_at&.to_date&.to_s
+      end
+
+      private
+
+      def max_created_at
+        System::APILog
+          .where(
+            identifier: identifier,
+            dry_run: false,
+            status: Renalware::System::APILog::STATUS_DONE
+          )
+          .group(:identifier)
+          .maximum(:created_at)[identifier]
+      end
+    end
+  end
+end

data/app/models/renalware/patients/practice.rb

@@ -5,8 +5,6 @@ require_dependency "renalware/patients"
 module Renalware
   module Patients
     class Practice < ApplicationRecord
-      acts_as_paranoid
-
       has_one :address, as: :addressable
       has_many :practice_memberships, dependent: :restrict_with_exception
       has_many :primary_care_physicians, through: :practice_memberships

data/app/models/renalware/patients/practice_search_query.rb

@@ -13,12 +13,14 @@ module Renalware
         return [] if search_term.blank?
 
         term = "%#{search_term}%"
-        Practice.select(:id, :name)
+        Practice.select(:id, :name, :code)
                 .left_outer_joins(:address)
                 .includes(:address)
                 .where("patient_practices.name ILIKE ? "\
+                       "OR patient_practices.code = ? " \
                        "OR addresses.street_1 ILIKE ? " \
-                       "OR addresses.postcode ILIKE ?", term, term, term)
+                       "OR addresses.postcode ILIKE ?", term, search_term, term, term)
+                .where(active: true)
                 .limit(50)
       end
     end

data/app/models/renalware/patients/sync_gps_via_file_download_job.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/patients"
+
+module Renalware
+  module Patients
+    class SyncGpsViaFileDownloadJob < ApplicationJob
+      ODS_DOWNLOADABLES = {
+        primary_care_physicians: {
+          url: "https://files.digital.nhs.uk/assets/ods/current/egpcur.zip",
+          filename: "egpcur.zip"
+        },
+        practice_memberships: {
+          url: "https://files.digital.nhs.uk/assets/ods/current/epracmem.zip",
+          filename: "epracmem.zip"
+        }
+      }.freeze
+
+      # Do not retry this job
+      discard_on(StandardError) do |_job, exception|
+        Renalware::Engine.exception_notifier.notify(exception)
+        Rails.logger.error exception
+      end
+
+      # Now we have brought practices up to date, update GPs and their membership in practices.
+      # Download the relevant zip file, save it as a Feeds::File (the zip file will be copied to
+      # the uploads dir) and kick off a sync job to import the data, which it does by unzipping
+      # the file, extracting the csv and using a PG function to upsert the contents.
+      # Note we cannot reliably use an aysnc job here as the order of execution of the 3 updates -
+      # practices, gps, practice memberships - is strict.
+      def perform
+        ODS_DOWNLOADABLES.each do |type, options|
+          # Download the ODS file to a temporary location
+          tmp_file = Rails.root.join("tmp").join(options[:filename])
+          `wget -O #{tmp_file} #{options[:url]}`
+          file = create_feed_file(type, tmp_file)
+          Renalware::Feeds::Files::ImportJobFactory.job_class_for(file.file_type).perform_now(file)
+        end
+      end
+
+      private
+
+      def create_feed_file(type, tmp_file)
+        Renalware::Feeds::Files::CreateFeedFile.call(
+          uploaded_file: tmp_file,
+          file_type: Renalware::Feeds::FileType.find_by(name: type),
+          user: Renalware::SystemUser.find
+        )
+      end
+    end
+  end
+end