renalware-core 2.0.156 → 2.0.161

data/app/views/renalware/virology/vaccinations/_cell.html.slim

@@ -1,2 +1,2 @@
 / See Vaccination.to_partial_path etc
-= event.document.type.text
+= event.document.to_s

data/app/views/renalware/virology/vaccinations/_inputs.html.slim

@@ -1,4 +1,6 @@
 / See Vaccination.to_partial_path etc
 / Pulled into the New Event form via a js get to EventsController#new
 = f.simple_fields_for :document, event.document do |fd|
-  = fd.input :type, wrapper: :horizontal_medium
+  /= fd.input :type, wrapper: :horizontal_medium
+  = fd.input :type, wrapper: :horizontal_medium, collection: Renalware::Virology::VaccinationType.ordered.pluck(:name, :code)
+  = fd.input :drug, wrapper: :horizontal_medium, collection: Renalware::Drugs::Drug.for(:vaccine).pluck(:name, :name)

data/app/views/renalware/virology/vaccinations/_toggled_cell.html.slim

@@ -3,6 +3,8 @@
 
 dl.dl-horizontal
   dt= attr_name(document, :type, suffix: ":")
-  dd= document.type&.text || t("unspecified")
+  dd= document.type_name.presence || t("unspecified")
+  dt= attr_name(document, :drug, suffix: ":")
+  dd= document.drug.presence || t("unspecified")
   dt= attr_name(event, :notes, suffix: ":")
   dd= event.notes&.html_safe || t("unspecified")

data/config/initializers/core_extensions.rb

@@ -5,7 +5,7 @@ require "core_extensions/i18n/always_cascade"
 require "core_extensions/dumb_delegator"
 # require "core_extensions/active_record/sort"
 require "core_extensions/date"
-require "core_extensions/active_support/duration"
+require "core_extensions/active_support/duration_additions"
 require "core_extensions/scenic"
 require "core_extensions/hash"
 require "core_extensions/active_record/migration_helpers"

data/config/initializers/inflections.rb

@@ -32,6 +32,7 @@ ActiveSupport::Inflector.inflections(:en) do |inflect|
   inflect.acronym "CCs"
   inflect.acronym "CM"
   inflect.acronym "CSV"
+  inflect.acronym "CRF"
   inflect.acronym "DNA"
   inflect.acronym "EDTA"
   inflect.acronym "ESRF"
@@ -55,6 +56,7 @@ ActiveSupport::Inflector.inflections(:en) do |inflect|
   inflect.acronym "EQ5D"
   inflect.acronym "EQ5D5L"
   inflect.acronym "POS"
+  inflect.acronym "YAML"
   inflect.irregular "feedback", "feedback"
   inflect.acronym "NHS"
   inflect.uncountable %w(cache)

data/config/locales/renalware/virology/virology.en.yml

@@ -24,4 +24,8 @@ en:
         hbv3: HBV Vaccination 3
         hbv4: HBV Vaccination 4
         hbv_booster: HBV Booster
+        influenza: Influenza
+        pneumococcus: Pneumococcus
+        covid19_1: COVID-19 1
+        covid19_2: COVID-19 2
         patient_refused: Patient Refused

data/db/migrate/20201020155510_add_bmi_to_clinic_visits.rb

@@ -5,7 +5,7 @@ class AddBMIToClinicVisits < ActiveRecord::Migration[5.2]
         :clinic_visits,
         :bmi,
         :decimal,
-        precision: 4,
+        precision: 10,
         scale: 1,
         null: true,
         comment: "Body Mass Index calculated using a before_save when the clinic visit is updated"
@@ -13,10 +13,13 @@ class AddBMIToClinicVisits < ActiveRecord::Migration[5.2]
 
       reversible do |direction|
         direction.up do
+          # Update the bmi for existing clinic visits, but restrict to avoid generating a
+          # non-sense value in case height or weight were entered incorrectly.
+          # NB: height is in metres and weight in kg
           connection.execute(
             "update renalware.clinic_visits "\
             "set bmi = round(((weight / height)::decimal / height::decimal), 1) "\
-            "where height > 0 and weight > 0;"
+            "where height > 0 and height < 3 and weight > 0 and weight < 500;"
           )
         end
         direction.down do

data/db/migrate/20201105153422_update_medication_current_prescriptions_view.rb

@@ -0,0 +1,7 @@
+class UpdateMedicationCurrentPrescriptionsView < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      replace_view :medication_current_prescriptions, version: 2, revert_to_version: 1
+    end
+  end
+end

data/db/migrate/20201112152752_update_pd_mdm_patients_view1.rb

@@ -0,0 +1,7 @@
+class UpdatePDMDMPatientsView1 < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view :pd_mdm_patients, version: 3, revert_to_version: 2
+    end
+  end
+end

data/db/migrate/20210105163944_create_virology_vaccination_types.rb

@@ -0,0 +1,13 @@
+class CreateVirologyVaccinationTypes < ActiveRecord::Migration[5.2]
+  within_renalware_schema do
+    def change
+      create_table :virology_vaccination_types do |t|
+        t.string :code, null: false, index: { unique: true }
+        t.string :name, null: false, index: { unique: true }
+        t.integer :position, null: false, default: 0
+        t.datetime :deleted_at
+        t.timestamps null: false
+      end
+    end
+  end
+end

data/db/seeds/default/seeds.rb

@@ -20,3 +20,4 @@ require_relative "./practices/seeds"
 require_relative "./pd/seeds"
 require_relative "./renal/seeds"
 require_relative "./transplants/seeds"
+require_relative "./virology/seeds"

data/db/seeds/default/virology/seeds.rb

@@ -0,0 +1,3 @@
+# frozen_string_literal: true
+
+require_relative "./vaccination_types"

data/db/seeds/default/virology/vaccination_types.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+module Renalware
+  module Virology
+    log "Adding virology vaccination types" do
+      {
+        hbv1: "HBV Vaccination 1",
+        hbv2: "HBV Vaccination 2",
+        hbv3: "HBV Vaccination 3",
+        hbv4: "HBV Vaccination 4",
+        hbv_booster: "HBV Booster",
+        influenza: "Influenza",
+        pneumococcus: "Pneumococcus",
+        covid19_1: "COVID-19 1",
+        covid19_2: "COVID-19 2",
+        patient_refused: "Patient Refused",
+        patient_refused_covid19: "Patient refused Covid-19 vaccine",
+        patient_refused_covid19_pfizer: "Patient refused Covid-19 vaccine Pfizer",
+        patient_refused_covid19_astrazenica: "Patient refused Covid-19 vaccine Astra Zeneca"
+      }.each do |code, name|
+        VaccinationType.find_or_create_by!(code: code, name: name)
+      end
+    end
+  end
+end

data/db/views/medication_current_prescriptions_v01.sql

@@ -1,4 +1,5 @@
- SELECT mp.id,
+ SELECT
+    mp.id,
     mp.patient_id,
     mp.drug_id,
     mp.treatable_type,

data/db/views/medication_current_prescriptions_v02.sql

@@ -0,0 +1,30 @@
+ SELECT distinct on (mp.patient_id, mp.id)
+     mp.id,
+    mp.patient_id,
+    mp.drug_id,
+    mp.treatable_type,
+    mp.treatable_id,
+    mp.dose_amount,
+    mp.dose_unit,
+    mp.medication_route_id,
+    mp.route_description,
+    mp.frequency,
+    mp.notes,
+    mp.prescribed_on,
+    mp.provider,
+    mp.created_at,
+    mp.updated_at,
+    mp.created_by_id,
+    mp.updated_by_id,
+    mp.administer_on_hd,
+    mp.last_delivery_date,
+    drugs.name as drug_name,
+    drug_types.code AS drug_type_code,
+    drug_types.name AS drug_type_name
+  FROM medication_prescriptions mp
+  left outer join medication_prescription_terminations mpt ON mpt.prescription_id = mp.id
+  inner JOIN drugs ON drugs.id = mp.drug_id
+  left outer join drug_types_drugs ON drug_types_drugs.drug_id = drugs.id
+  left outer join drug_types ON drug_types_drugs.drug_type_id = drug_types.id
+  where (mpt.terminated_on IS NULL OR mpt.terminated_on > current_date)
+  order by mp.patient_id asc, mp.id asc;

data/db/views/pd_mdm_patients_v03.sql

@@ -0,0 +1,50 @@
+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,
+   (select
+       date(date_time)
+       from events e
+       inner join event_types et on et.id = e.event_type_id
+       where et.slug = 'pd_line_changes'
+       and e.patient_id  = P.id
+       order by date_time desc limit 1) as last_line_change_date,
+  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/reporting_anaemia_audit_v01.sql

@@ -1,5 +1,3 @@
-
---explain analyze
 select
   modality_desc       modality,
   count(e1.patient_id)  patient_count,

data/lib/failure.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+
+require "service_result"
+
+class Failure < ServiceResult
+end

data/lib/gpg_encrypt_folder.rb

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
 
-require "attr_extras"
-
 # Shell out to gpg with a a command like this
 # gpg --armor --no-default-keyring --keyring keyring.gpg
 #     --trust-model always -r 'renalware_test'

data/lib/month_period.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+class MonthPeriod
+  attr_reader :month, :year, :start, :finish
+
+  def initialize(month:, year:)
+    @month = month
+    @year = year
+    @start = Time.new(year, month, 1, 0, 0, 0)
+    @finish = start.end_of_month.end_of_day
+  end
+
+  def to_range
+    start..finish
+  end
+end

data/lib/renalware/configuration.rb

@@ -14,7 +14,6 @@
 # To access configuration settings use e.g.
 #   Renalware.config.x
 #
-# rubocop:disable Metrics/ClassLength
 module Renalware
   class Configuration
     include ActiveSupport::Configurable
@@ -37,9 +36,6 @@ module Renalware
     config_accessor(:patient_hospital_identifiers) { {} }
     config_accessor(:session_timeout_polling_frequency) { 1.minute }
     config_accessor(:session_register_user_user_activity_after) { 2.minutes }
-    config_accessor(:session_expiry_use_previous_mechansim) {
-      ENV["SESSION_EXPIRY_USE_PREVIOUS_MECHANSIM"] == "true"
-    }
     config_accessor(:duration_of_last_url_memory_after_session_expiry) { 30.minutes }
     config_accessor(:broadcast_subscription_map) { {} }
     config_accessor(:include_sunday_on_hd_diaries) { false }
@@ -140,6 +136,9 @@ module Renalware
     # Note that the standard HL7 PID admin sex values are not adhered to here. For reference
     # they are:
     # F Female, M Male, O Other, U Unknown, A Ambiguous, N Not applicable
+    # Note
+    # - NS = Not Stated
+    # - NK = Not Known
     config_accessor(:hl7_pid_sex_map) do
       {
         "MALE" => "M",
@@ -148,7 +147,8 @@ module Renalware
         "UNKNOWN" => "NK",
         "NOTKNOWN" => "NK",
         "AMBIGUOUS" => "NS",
-        "NOT APPLICABLE" => "NS"
+        "NOT APPLICABLE" => "NS",
+        "BOTH" => "NS"
       }.freeze
     end
   end
@@ -161,4 +161,3 @@ module Renalware
     yield config
   end
 end
-# rubocop:enable Metrics/ClassLength

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 = "2.0.156"
+    VERSION = "2.0.161"
   end
 end

data/lib/service_result.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+class ServiceResult
+  attr_reader :object
+
+  def initialize(object)
+    @object = object
+  end
+
+  def success?
+    false
+  end
+
+  def failure?
+    !success?
+  end
+end

data/lib/sql/indexed_case_stmt.rb

@@ -1,8 +1,6 @@
 # frozen_string_literal: true
 
-require "attr_extras"
-
-module SQL
+module Sql
   # Example:
   #
   #     indexed_case_stmt(:code, "DT", "AC", "XY")

data/lib/success.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+require "service_result"
+
+class Success < ServiceResult
+  def success?
+    true
+  end
+end

data/lib/tasks/ukrdc.rake

@@ -39,7 +39,7 @@ namespace :ukrdc do
       RubyProf.start
     end
     # Renalware::UKRDC::TreatmentTimeline::GenerateTreatments.call
-    Renalware::UKRDC::CreateEncryptedPatientXMLFiles.new(
+    Renalware::UKRDC::CreateEncryptedPatientXmlFiles.new(
       changed_since: ENV["changed_since"],
       patient_ids: ENV.fetch("patient_ids", "").split(",").map(&:to_i),
       force_send: ENV["force_send"] == "true"

data/lib/week_period.rb

@@ -0,0 +1,57 @@
+# frozen_string_literal: true
+
+class WeekPeriod
+  attr_reader :year, :week_number, :date_on_first_day_of_week
+
+  def self.from_date(date)
+    date = date.to_date
+    new(week_number: date.cweek, year: date.cwyear)
+  end
+
+  def initialize(week_number:, year:)
+    @week_number = week_number.to_i
+    @year = year.to_i
+    validate_week_number
+    validate_year
+    @date_on_first_day_of_week = Date.commercial(@year, @week_number)
+  end
+
+  def next
+    self.class.from_date(date_on_first_day_of_week + 1.week)
+  end
+
+  def previous
+    self.class.from_date(date_on_first_day_of_week - 1.week)
+  end
+
+  def to_a
+    [week_number, year]
+  end
+
+  def to_s
+    "#{I18n.l(date_on_first_day_of_week, format: :long)} " \
+    "to #{I18n.l(last_day_of_week, format: :long)}"
+  end
+
+  # The date of last day of the week (a Sunday)
+  def last_day_of_week
+    @last_day_of_week ||= (date_on_first_day_of_week + 1.week - 1.minute).to_date
+  end
+
+  def validate_week_number
+    if week_number < 1 || week_number > 53
+      raise(ArgumentError, "invalid date: week_number must be 1-53")
+    end
+  end
+
+  def validate_year
+    raise(ArgumentError, "invalid date year must be >= 2000") if year <= 2000
+  end
+
+  def to_h
+    {
+      year: year,
+      week_number: week_number
+    }
+  end
+end