renalware-core 2.0.148 → 2.0.155

data/db/views/patient_current_modalities_v02.sql

@@ -0,0 +1,18 @@
+select
+  patients.id as patient_id,
+  patients.secure_id as patient_secure_id,
+  current_modality.id as modality_id,
+  modality_descriptions.id as modality_description_id,
+  modality_descriptions.name as modality_name,
+  current_modality.started_on as started_on,
+  modality_descriptions.code as modality_code
+from patients
+  -- this join only required as currently there can be > 1 current modality for a patient
+  -- here we select the current modality with the most recent started_on
+  left outer join (
+    select distinct on (patient_id) * from modality_modalities
+    where ended_on is null
+    order by patient_id, started_on desc, created_at desc
+) as current_modality
+on patients.id = current_modality.patient_id
+left outer join modality_descriptions on modality_descriptions.id = current_modality.description_id;

data/db/views/pd_mdm_patients_v01.sql

@@ -0,0 +1,42 @@
+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,
+  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
+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/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

@@ -14,6 +14,7 @@
 # To access configuration settings use e.g.
 #   Renalware.config.x
 #
+# rubocop:disable Metrics/ClassLength
 module Renalware
   class Configuration
     include ActiveSupport::Configurable
@@ -35,6 +36,10 @@ module Renalware
     config_accessor(:page_title_spearator) { " : " }
     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 }
@@ -103,6 +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 },
@@ -123,6 +129,7 @@ module Renalware
           Renalware::Admissions::SummaryPart
           Renalware::Admissions::ConsultSummaryPart
           Renalware::Patients::SummaryPart
+          Renalware::Patients::MessagesComponent
         )
       }
     }
@@ -154,3 +161,4 @@ module Renalware
     yield config
   end
 end
+# rubocop:enable Metrics/ClassLength

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
@@ -110,7 +112,8 @@ module Renalware
         # need to see them. 100 users with an active session polling every minute will add
         # up to fair number of log entries.
         app.config.lograge.ignore_actions = [
-          "Renalware::SessionTimeoutController#has_user_timed_out"
+          "Renalware::SessionTimeoutController#check_session_expired",
+          "Renalware::SessionTimeoutController#keep_session_alive"
         ]
       end
     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 = "2.0.155"
+  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