renalware-core 2.0.152 → 2.0.158

data/db/views/pd_mdm_patients_v02.sql

@@ -0,0 +1,43 @@
+select
+  distinct on (P.id)
+  P.id,
+  P.secure_id,
+  (upper(P.family_name) || ', ' || P.given_name) as "patient_name",
+  P.nhs_number,
+  P.local_patient_id as hospital_numbers,
+  P.sex,
+  P.born_on,
+  date_part('year', age(P.born_on)) as "age",
+  RPROF.esrf_on,
+  Mx.modality_name,
+  case
+    when pw.id > 0 then true
+    else false
+    end as on_worryboard,
+  TXRSD."name" tx_status,
+  case pr.type
+    when 'Renalware::PD::APDRegime' then 'APD'
+    when 'Renalware::PD::CAPDRegime' then 'CAPD'
+    end as pd_type,
+  pesi.diagnosis_date as last_esi_date,
+  ppe.diagnosis_date as last_peritonitis_date,
+  (select bmi from clinic_visits cv2 where cv2.patient_id = P.id and bmi > 0 order by date desc limit 1) as bmi,
+  PA.values -> 'HGB' ->> 'result' as hgb,
+  (PA.values -> 'HGB' ->> 'observed_at')::date as hgb_date,
+  PA.values -> 'URE' ->> 'result' as ure,
+  (PA.values -> 'URE' ->> 'observed_at')::date as ure_date,
+  PA.values -> 'CRE' ->> 'result' as cre,
+  (PA.values -> 'CRE' ->> 'observed_at')::date as cre_date,
+  PA.values -> 'EGFR' ->> 'result' as egfr
+from renalware.patients P
+left outer join patient_worries pw on pw.patient_id = p.id
+left outer join renalware.pathology_current_observation_sets PA on PA.patient_id = P.id
+left outer join renalware.renal_profiles RPROF on RPROF.patient_id = P.id
+left outer join renalware.transplant_registrations TXR on TXR.patient_id = P.id
+left outer join renalware.transplant_registration_statuses TXRS on TXRS.registration_id = TXR.id AND TXRS.terminated_on IS NULL
+left outer join renalware.transplant_registration_status_descriptions TXRSD on TXRSD.id = TXRS.description_id
+left outer join renalware.pd_regimes pr on pr.patient_id = P.id and pr.start_date <= current_date and pr.end_date is null
+left outer join renalware.pd_exit_site_infections pesi on pesi.patient_id = P.id
+left outer join pd_peritonitis_episodes ppe on ppe.patient_id = P.id
+inner join renalware.patient_current_modalities Mx on Mx.patient_id = P.id and Mx.modality_code = 'pd'
+order by P.id, pr.start_date desc, pr.created_at desc, pesi.diagnosis_date desc, ppe.diagnosis_date desc;

data/db/views/supportive_care_mdm_patients_v01.sql

@@ -0,0 +1,28 @@
+select
+  P.id,
+  P.secure_id,
+  (upper(P.family_name) || ', ' || P.given_name) as "patient_name",
+  P.nhs_number,
+  P.local_patient_id as hospital_numbers,
+  P.sex,
+  P.born_on,
+  date_part('year', age(P.born_on)) as "age",
+  RPROF.esrf_on,
+  Mx.modality_name,
+  case when pw.id > 0 then true else false end as on_worryboard,
+  TXRSD."name" tx_status,
+  PA.values -> 'HGB' ->> 'result' as hgb,
+  (PA.values -> 'HGB' ->> 'observed_at')::date as hgb_date,
+  PA.values -> 'URE' ->> 'result' as ure,
+  (PA.values -> 'URE' ->> 'observed_at')::date as ure_date,
+  PA.values -> 'CRE' ->> 'result' as cre,
+  (PA.values -> 'CRE' ->> 'observed_at')::date as cre_date,
+  PA.values -> 'EGFR' ->> 'result' as egfr
+from renalware.patients P
+left join patient_worries pw on pw.patient_id  = p.id
+left outer join renalware.pathology_current_observation_sets PA on PA.patient_id = P.id
+left outer join renalware.renal_profiles RPROF on RPROF.patient_id = P.id
+left outer join renalware.transplant_registrations TXR on TXR.patient_id = P.id
+left outer join renalware.transplant_registration_statuses TXRS on TXRS.registration_id = TXR.id AND TXRS.terminated_on IS NULL
+left outer join renalware.transplant_registration_status_descriptions TXRSD on TXRSD.id = TXRS.description_id
+inner join renalware.patient_current_modalities Mx on Mx.patient_id = P.id and Mx.modality_code = 'supportive_care'

data/db/views/supportive_care_mdm_patients_v02.sql

@@ -0,0 +1,29 @@
+select
+  P.id,
+  P.secure_id,
+  (upper(P.family_name) || ', ' || P.given_name) as "patient_name",
+  P.nhs_number,
+  P.local_patient_id as hospital_numbers,
+  P.sex,
+  P.born_on,
+  date_part('year', age(P.born_on)) as "age",
+  RPROF.esrf_on,
+  Mx.modality_name,
+  case when pw.id > 0 then true else false 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,
+  TXRSD."name" tx_status,
+  PA.values -> 'HGB' ->> 'result' as hgb,
+  (PA.values -> 'HGB' ->> 'observed_at')::date as hgb_date,
+  PA.values -> 'URE' ->> 'result' as ure,
+  (PA.values -> 'URE' ->> 'observed_at')::date as ure_date,
+  PA.values -> 'CRE' ->> 'result' as cre,
+  (PA.values -> 'CRE' ->> 'observed_at')::date as cre_date,
+  PA.values -> 'EGFR' ->> 'result' as egfr
+from renalware.patients P
+left join patient_worries pw on pw.patient_id  = p.id
+left outer join renalware.pathology_current_observation_sets PA on PA.patient_id = P.id
+left outer join renalware.renal_profiles RPROF on RPROF.patient_id = P.id
+left outer join renalware.transplant_registrations TXR on TXR.patient_id = P.id
+left outer join renalware.transplant_registration_statuses TXRS on TXRS.registration_id = TXR.id AND TXRS.terminated_on IS NULL
+left outer join renalware.transplant_registration_status_descriptions TXRSD on TXRSD.id = TXRS.description_id
+inner join renalware.patient_current_modalities Mx on Mx.patient_id = P.id and Mx.modality_code = 'supportive_care'

data/db/views/transplant_mdm_patients_v01.sql

@@ -0,0 +1,46 @@
+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,
+    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/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

@@ -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"
@@ -92,7 +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

@@ -5,6 +5,6 @@ module Renalware
   # 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 = "2.0.152"
+    VERSION = "2.0.158"
   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/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/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/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/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));