renalware-core 2.0.149 → 2.0.156

data/db/views/transplant_mdm_patients_v02.sql

@@ -0,0 +1,47 @@
+SELECT p.id,
+    p.secure_id,
+    (upper(p.family_name::text) || ', '::text) || p.given_name::text AS patient_name,
+    p.nhs_number,
+    p.local_patient_id AS hospital_numbers,
+    p.sex,
+    p.born_on,
+    rprof.esrf_on,
+    latest_op.performed_on AS last_operation_date,
+    date_part('year'::text, age(p.born_on::timestamp with time zone))::integer AS age,
+    mx.modality_name,
+    case when pw.id > 0 then 'Y' else 'N' end as on_worryboard,
+    (select bmi from clinic_visits cv2 where cv2.patient_id = P.id and bmi > 0 order by date desc limit 1) as bmi,
+    case when latest_op.performed_on >= (now() - interval '3 months') then true else false end as tx_in_past_3m,
+    case when latest_op.performed_on >= (now() - interval '12 months') then true else false end as tx_in_past_12m,
+    txrsd.name AS tx_status,
+    (pa."values" -> 'HGB'::text) ->> 'result'::text AS hgb,
+    ((pa."values" -> 'HGB'::text) ->> 'observed_at'::text)::date AS hgb_date,
+    (pa."values" -> 'URE'::text) ->> 'result'::text AS ure,
+    ((pa."values" -> 'URE'::text) ->> 'observed_at'::text)::date AS ure_date,
+    (pa."values" -> 'CRE'::text) ->> 'result'::text AS cre,
+    ((pa."values" -> 'CRE'::text) ->> 'observed_at'::text)::date AS cre_date,
+    (pa."values" -> 'EGFR'::text) ->> 'result'::text AS egfr_on
+   FROM patients p
+     JOIN patient_current_modalities mx ON mx.patient_id = p.id AND mx.modality_code::text = 'transplant'::text
+     LEFT JOIN pathology_current_observation_sets pa ON pa.patient_id = p.id
+     LEFT join patient_worries pw on pw.patient_id  = p.id
+     LEFT JOIN transplant_registrations txr ON txr.patient_id = p.id
+     LEFT JOIN transplant_registration_statuses txrs ON txrs.registration_id = txr.id AND txrs.terminated_on IS NULL
+     LEFT JOIN transplant_registration_status_descriptions txrsd ON txrsd.id = txrs.description_id
+     LEFT JOIN renal_profiles rprof ON rprof.patient_id = p.id
+     LEFT JOIN ( SELECT DISTINCT ON (transplant_recipient_operations.patient_id) transplant_recipient_operations.id,
+            transplant_recipient_operations.patient_id,
+            transplant_recipient_operations.performed_on,
+            transplant_recipient_operations.theatre_case_start_time,
+            transplant_recipient_operations.donor_kidney_removed_from_ice_at,
+            transplant_recipient_operations.operation_type,
+            transplant_recipient_operations.hospital_centre_id,
+            transplant_recipient_operations.kidney_perfused_with_blood_at,
+            transplant_recipient_operations.cold_ischaemic_time,
+            transplant_recipient_operations.warm_ischaemic_time,
+            transplant_recipient_operations.notes,
+            transplant_recipient_operations.document,
+            transplant_recipient_operations.created_at,
+            transplant_recipient_operations.updated_at
+           FROM transplant_recipient_operations
+          ORDER BY transplant_recipient_operations.patient_id, transplant_recipient_operations.performed_on DESC) latest_op ON latest_op.patient_id = p.id;

data/lib/renalware/configuration.rb

@@ -108,6 +108,7 @@ module Renalware
     config_accessor(:generate_pathology_request_forms_from_hd_mdm_listing) { true }
     config_accessor(:disable_inputs_controlled_by_tissue_typing_feed) { false }
     config_accessor(:disable_inputs_controlled_by_demographics_feed) { false }
+    config_accessor(:enforce_user_prescriber_flag) { false }
     config_accessor(:medication_delivery_purchase_order_prefix) { "R" }
     config_accessor(:medication_homecare_pdf_forms) do
       # esa: { provider: :generic, version: 1 },
@@ -128,6 +129,7 @@ module Renalware
           Renalware::Admissions::SummaryPart
           Renalware::Admissions::ConsultSummaryPart
           Renalware::Patients::SummaryPart
+          Renalware::Patients::MessagesComponent
         )
       }
     }

data/lib/renalware/engine.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 require "rubygems"
-require "action_view/component/railtie"
+require "view_component/engine"
 require "active_type"
 require "activerecord-import"
 require "ahoy"
@@ -22,7 +22,6 @@ require "dumb_delegator"
 require "email_validator"
 require "enumerize"
 require "font-awesome-sass"
-require "foundation-rails"
 require "friendly_id"
 require "groupdate"
 require "hashdiff"
@@ -53,6 +52,7 @@ require "ruby-hl7"
 require "sass-rails"
 require "scenic"
 require "slim-rails"
+require "store_model"
 require "uglifier"
 require "validates_timeliness"
 require "virtus"
@@ -75,12 +75,14 @@ module Renalware
     # Errors in the UI are bubbled up and handled in the host app in the usual way.
     class << self
       attr_writer :exception_notifier
+
       def exception_notifier
         @exception_notifier ||= NullExceptionNotifier.new
       end
     end
 
-    config.action_view_component.test_controller = "Renalware::BaseController"
+    # config.view_component.test_controller = "Renalware::BaseController"
+
     config.autoload_paths += Dir["#{config.root}/lib/**/"]
     config.autoload_paths += %W(#{config.root}/app/validators/concerns)
 
@@ -90,7 +92,7 @@ module Renalware
     end
 
     initializer :add_locales do |app|
-      app.config.i18n.load_path += Dir[config.root.join("config", "locales", "**", "*.{rb,yml}")]
+      app.config.i18n.load_path += Dir[config.root.join("config/locales/**/*.{rb,yml}")]
       app.config.i18n.default_locale = "en-GB"
       app.config.i18n.fallbacks = [:en]
     end

data/lib/renalware/version_number.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+module Renalware
+  # To satisfy zeitwerk we have renamed this file version_number and make sure
+  # to creat that class even though its not used. If we don't do this zeitwerk
+  # complains that version.rb does export a constant called Version.
+  class VersionNumber
+    VERSION = "2.0.156"
+  end
+end

data/lib/tasks/db.rake

@@ -3,6 +3,14 @@
 require "benchmark"
 
 namespace :db do
+  desc "Check that we are not about to drop an anonymised database"
+  task drop_check: :environment do
+    db_name = "rw_anon"
+    if Rails.configuration.database_configuration[Rails.env]["database"] == db_name
+      raise ActiveRecord::ProtectedEnvironmentError, "Cannot drop #{db_name}"
+    end
+  end
+
   desc "Refreshes all materialized views e.g. audits. May take a while so only run overnight."
   task refresh_all_materialized_views: :environment do
     ms = Benchmark.ms do
@@ -22,3 +30,4 @@ namespace :db do
     end
   end
 end
+task("db:drop").enhance ["db:drop_check"]

data/lib/tasks/pd.rake

@@ -29,4 +29,32 @@ namespace :pd do
       end
     end
   end
+
+  desc "Useful to call this after migrating PET and Adequacy results from the legacy "\
+       "pd_pet_adequacies table. It simulates eding a result and saving it in the UI, which "\
+       "triggers the calculations to be redone"
+  task apply_pet_adequacy_calculations: :environment do
+    Rails.logger = Logger.new(STDOUT)
+    Rails.logger.info "Regenerate all PET calcs"
+    count = 0
+    Renalware::PD::PETResult.find_in_batches(batch_size: 500) do |group|
+      count += group.length
+      group.each do |pet|
+        pet.by = pet.updated_by
+        pet.save(validate: false)
+      end
+    end
+    Rails.logger.info "Total PETResults = #{count}"
+
+    Rails.logger.info "Regenerate all Adequacy calcs"
+    count = 0
+    Renalware::PD::AdequacyResult.find_in_batches(batch_size: 500) do |group|
+      count += group.length
+      group.each do |adequacy|
+        adequacy.by = adequacy.updated_by
+        adequacy.save(validate: false)
+      end
+    end
+    Rails.logger.info "Total AdequacyResults = #{count}"
+  end
 end

data/lib/tasks/renalware.rake

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+# rubocop:disable Rails/RakeEnvironment
 namespace :renalware do
   desc "Install package.json dependencies with yarn for the renalware-core engine - "\
        "without this <path to installed gem>/renalware-core/node_modules is not populated "\
@@ -7,7 +8,11 @@ namespace :renalware do
   task :yarn_install do
     puts "Installing renalware-core/package.json dependencies with yarn"
     Dir.chdir(File.join(__dir__, "../..")) do
-      system "yarn install --no-progress --production"
+      if ENV["RAILS_ENV"] == "production"
+        system "yarn install --no-progress --production"
+      else
+        system "yarn install"
+      end
     end
   end
 end
@@ -17,3 +22,4 @@ if Rake::Task.task_defined?("yarn:install")
 else
   Rake::Task.define_task("yarn:install" => "renalware:yarn_install")
 end
+# rubocop:enable Rails/RakeEnvironment

data/spec/factories/accesses/profiles.rb

@@ -7,6 +7,7 @@ FactoryBot.define do
     type { create(:access_type) }
     side { :right }
     formed_on { Time.zone.today }
+    started_on { Time.zone.today }
 
     trait :current do
       started_on { 1.day.ago }

data/spec/factories/drugs/drug_types.rb

@@ -2,8 +2,12 @@
 
 FactoryBot.define do
   factory :drug_type, class: "Renalware::Drugs::Type" do
+    initialize_with do
+      Renalware::Drugs::Type.find_or_create_by!(code: code, name: name)
+    end
+
     code { "immuno" }
-    name { "Immunosuppressant" }
+    name { "immuno" }
 
     trait :immunosuppressant do
       code { "immunosuppressant" }

data/spec/factories/events/events_types.rb

@@ -36,5 +36,17 @@ FactoryBot.define do
       slug { "vaccinations" }
       event_class_name { "Renalware::Virology::Vaccination" }
     end
+
+    factory :advanced_care_plan do
+      name { "AdvancedCarePlan" }
+      slug { "advanced_care_plans" }
+      event_class_name { "Renalware::Events::AdvancedCarePlan" }
+    end
+
+    factory :clinical_frailty_score do
+      name { "Clinical Frailty Score" }
+      slug { "clinical_frailty_scores" }
+      event_class_name { "Renalware::Events::ClinicalFrailtyScore" }
+    end
   end
 end

data/spec/factories/messaging/internal/messages.rb

@@ -9,6 +9,7 @@ FactoryBot.define do
     association :author, factory: :author
     sent_at { Time.zone.now }
     association :patient
+    public { true }
     receipts { [] }
   end
 end

data/spec/factories/patients/patients.rb

@@ -2,7 +2,28 @@
 
 FactoryBot.define do
   sequence :nhs_number do |n|
-    n.to_s.rjust(10, "0000000000")
+    %w(
+      6393739592
+      4414733227
+      5552737601
+      4696133478
+      4904230000
+      5477425407
+      7465613493
+      9827026836
+      2132173117
+      2717073604
+      3477113764
+      7114008236
+      9660350961
+      2637392835
+      1833834704
+      9707196408
+      0676304567
+      0558366333
+      1573555126
+      5543098111
+    )[n]
   end
 
   sequence :local_patient_id do |n|

data/spec/factories/patients/practices.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   sequence :practice_code do |n|
-    "M" + n.to_s.rjust(5, "0")
+    "M#{n.to_s.rjust(5, '0')}"
   end
 
   factory :practice, class: "Renalware::Patients::Practice" do

data/spec/factories/patients/primary_care_physicians.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   sequence :gp_code do |n|
-    "G" + n.to_s.rjust(7, "0")
+    "G#{n.to_s.rjust(7, '0')}"
   end
 
   factory :primary_care_physician, class: "Renalware::Patients::PrimaryCarePhysician" do

data/spec/factories/pd/adequacy_results.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :pd_adequacy_result, class: "Renalware::PD::AdequacyResult" do
+    accountable
+    performed_on { I18n.l(Time.zone.today) }
+    urine_urea { 10 }
+    urine_creatinine { 10 }
+    urine_24_vol { 1000 }
+    dialysate_urea { 10 }
+    dialysate_creatinine { 10 }
+    dial_24_vol_out { 1500 }
+    serum_urea { 10 }
+    serum_creatinine { 10 }
+  end
+end

data/spec/factories/pd/pet_results.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :pd_pet_result, class: "Renalware::PD::PETResult" do
+    accountable
+    performed_on { I18n.l(Time.zone.today) }
+    test_type { :full }
+  end
+end

data/spec/factories/system/users.rb

@@ -18,6 +18,7 @@ FactoryBot.define do
     approved { true }
     professional_position { "Health Minister" }
     signature { Faker::Name.name }
+    prescriber { true }
 
     # By default a user has no roles.
     # If you want a use with a role, use a trait, e.g. create(:user, :clinical)

data/spec/factories/system/view_metadata.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :view_metadata, class: "Renalware::System::ViewMetadata" do
+    schema_name { "renalware" }
+    view_name { "transplant_mdm_patients" }
+    title { "Title" }
+    slug { "all" }
+    category { "mdm" }
+    scope { "transplant" }
+    columns { [] }
+    filters {
+      [
+        Renalware::System::FilterDefinition.new(code: :sex, type: :list),
+        Renalware::System::FilterDefinition.new(code: :age, type: :search)
+      ]
+    }
+    position { 1 }
+  end
+end

data/spec/support/capybara_helper.rb

@@ -9,9 +9,7 @@ module CapybaraHelper
     select_nth_option_from(selector)
   end
 
-  def within_article(title)
-    within(:css, "article", text: title) do
-      yield
-    end
+  def within_article(title, &block)
+    within(:css, "article", text: title, &block)
   end
 end

data/spec/support/letters_spec_helper.rb

@@ -2,7 +2,7 @@
 
 # rubocop:disable Metrics/MethodLength
 module LettersSpecHelper
-  def build_letter(state: :draft, to:, patient:, **args)
+  def build_letter(to:, patient:, state: :draft, **args)
     trait = "#{state}_letter".to_sym
     letter = build(trait, **args)
     letter.patient = patient

data/spec/support/matchers/validate_timeliness_of.rb

@@ -3,7 +3,7 @@
 RSpec::Matchers.define :validate_timeliness_of do |attribute|
   match do |model|
     model._validators[attribute.to_sym].detect do |validator|
-      validator.class == ActiveModel::Validations::TimelinessValidator &&
+      validator.instance_of?(ActiveModel::Validations::TimelinessValidator) &&
         validator.attributes.include?(attribute)
     end
   end

data/spec/support/pathology_spec_helper.rb

@@ -20,11 +20,10 @@ module PathologySpecHelper
   end
 
   # rubocop:disable Metrics/ParameterLists, Metrics/MethodLength
-  def create_request_with_observations(requestor_order_number: "123",
+  def create_request_with_observations(patient:, requestor_order_number: "123",
                                        obr_code: "OBR1",
                                        obx_codes: ["OBX1"],
                                        requested_at: 1.year.ago,
-                                       patient:,
                                        created_at: nil,
                                        count: 1,
                                        result: "1.1")

data/spec/support/policy_spec_helper.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module PolicySpecHelper
+  def user_double_with_role(role)
+    instance_double(Renalware::User).tap do |user|
+      allow(user).to receive(:has_role?).and_return(false)
+      allow(user).to receive(:has_role?).with(role).and_return(true)
+      allow(user).to receive(:roles).and_return([role])
+      allow(user).to receive(:role_names).and_return([role.to_s])
+    end
+  end
+end

data/vendor/assets/javascripts/foundation/foundation.alert.js

@@ -0,0 +1,43 @@
+;(function ($, window, document, undefined) {
+  'use strict';
+
+  Foundation.libs.alert = {
+    name : 'alert',
+
+    version : '5.5.3',
+
+    settings : {
+      callback : function () {}
+    },
+
+    init : function (scope, method, options) {
+      this.bindings(method, options);
+    },
+
+    events : function () {
+      var self = this,
+          S = this.S;
+
+      $(this.scope).off('.alert').on('click.fndtn.alert', '[' + this.attr_name() + '] .close', function (e) {
+        var alertBox = S(this).closest('[' + self.attr_name() + ']'),
+            settings = alertBox.data(self.attr_name(true) + '-init') || self.settings;
+
+        e.preventDefault();
+        if (Modernizr.csstransitions) {
+          alertBox.addClass('alert-close');
+          alertBox.on('transitionend webkitTransitionEnd oTransitionEnd', function (e) {
+            S(this).trigger('close.fndtn.alert').remove();
+            settings.callback();
+          });
+        } else {
+          alertBox.fadeOut(300, function () {
+            S(this).trigger('close.fndtn.alert').remove();
+            settings.callback();
+          });
+        }
+      });
+    },
+
+    reflow : function () {}
+  };
+}(jQuery, window, window.document));