renalware-core 2.0.155 → 2.0.160

data/app/presenters/renalware/transplants/donor_dashboard_presenter.rb

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 
 require_dependency "renalware/transplants"
-require "attr_extras"
 
 module Renalware
   module Transplants

data/app/presenters/renalware/transplants/recipient_dashboard_presenter.rb

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 
 require_dependency "renalware/transplants"
-require "attr_extras"
 
 module Renalware
   module Transplants

data/app/presenters/renalware/ukrdc/transplant_operation_presenter.rb

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 
 require_dependency "renalware/transplants"
-require "attr_extras"
 
 module Renalware
   module UKRDC

data/app/presenters/renalware/user_session_presenter.rb

@@ -21,8 +21,6 @@ module Renalware
     #       data-session-timeout="3600">
     # rubocop:disable Metrics/MethodLength
     def self.session_controller_data_attributes
-      return {} if Renalware.config.session_expiry_use_previous_mechansim
-
       urls = Renalware::Engine.routes.url_helpers
       {
         data: {
@@ -39,6 +37,6 @@ module Renalware
         }
       }
     end
+    # rubocop:enable Metrics/MethodLength
   end
-  # rubocop:enable Metrics/MethodLength
 end

data/app/values/renalware/bmi.rb

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
 
-require "attr_extras"
-
 module Renalware
   # Value object representing Body Mass Index. Accepts only meters and kg
   #

data/app/views/renalware/letters/contacts/_new_person.html.slim

@@ -10,7 +10,7 @@
                   class: "button secondary",
                   data: { behaviour: "toggle-section" }
       .right
-        = f.submit t(".save"), class: "button"
+        = f.submit t(".save"), class: "button", data: { disable_with: false }
         '  or
         = link_to t(".cancel"),
                "#",

data/app/views/renalware/letters/contacts/_person_from_directory.html.slim

@@ -16,7 +16,7 @@
   .row
     .large-12.columns
       br
-      = f.submit t(".save"), class: "button"
+      = f.submit t(".save"), class: "button", data: { disable_with: false }
       '  or
       = link_to t(".cancel"),
                "#",

data/app/views/renalware/letters/formatted_letters/_letter.html.slim

@@ -4,6 +4,10 @@ scss:
     font-family: Helvetica, Arial;
   }
 
+  .subtitle {
+    font-size: .9rem;
+  }
+
   .addressee {
     width: 50%;
     float: left;
@@ -153,12 +157,11 @@ scss:
     }
 
     .allergies {
-      margin-bottom: 1rem;
       float: left;
       clear: left;
       width: 50%;
 
-      h3 {
+      h3, b {
         padding-right: 1rem;
       }
 
@@ -221,10 +224,9 @@ scss:
     }
 
     .message {
-      margin-top: 30px;
-      margin-bottom: 20px;
+      margin-top: 20px;
+      margin-bottom: 0px;
       clear: both;
-
       p {
         margin-bottom: 15px;
       }
@@ -235,9 +237,6 @@ scss:
     }
 
     .author-signature {
-      .author-name {
-        font-weight: bold;
-      }
       margin-bottom: 20px;
     }
   }
@@ -320,10 +319,10 @@ scss:
       p= render "patient_summary", patient: letter.patient
 
     = render letter.parts, patient: letter.patient, letter: letter
-
-    .message
-      = letter.body&.html_safe
-
+    / empty small here is for RTF spacing
+    small  
+    .message= letter.body&.html_safe
+    br
     p Yours sincerely
 
     .signature.nobreak
@@ -332,7 +331,7 @@ scss:
 
       .author-signature
         p
-          span.author-name= letter.author.signature
+          b= letter.author.signature
           br
           = letter.author.professional_position
 
@@ -340,7 +339,7 @@ scss:
 
   .footer
     .ccs
-      h3 cc:
+      b cc:
 
       ul.electronic
         - letter.electronic_cc_recipients.each do |user|

data/app/views/renalware/letters/mailshots/mailshots/_form.html.slim

@@ -38,24 +38,28 @@
     br
     .panel
       h2
-        i.fas.fa-info-circle style="color: #00a499"
-        span(style="padding-left: 5px") Tips
-      p
-        | The list of patients to include in a mailshot it determined by the SQL View chosen above.
-        |  It is intended that a systems or database administrator create this view for you in the
-        |  renalware database. The view should have one column called 'patient_id' and return the ids
-        |  of all the patients you want to send this letter to.
-        |  You should ideally create the view in the hospital's
-        |  own postgres schema eg 'renalware_kch' in the case of Kings College Hospital.
-      p Here is a (somewhat pointless) example of a compatible SQL view definition:
-      p
-        code
-          | CREATE OR REPLACE VIEW
-          br
-          |  renalware_kch.letter_mailshot_patients_where_surname_starts_with_r AS
-          br
-          |  SELECT id as patient_id
-          br
-          |  FROM patients
-          br
-          |  WHERE family_name like 'R%';
+        i.fas.fa-info-circle
+        span.pl-3 Help
+
+      markdown:
+        The list of patients to include in a mailshot it determined by the SQL View chosen above.
+        It is intended that a systems or database administrator create this view for you in the
+        renalware database. The view should have one column called 'patient_id' and return the ids
+        of all the patients you want to send this letter to.
+
+        You should ideally create the view in the hospital's
+        own postgres schema (eg 'renalware_kch' in the case of Kings College Hospital) in order to
+        indicate your view is hospital-specific.
+
+        **Note that in order for your view to appear in the dropdown above, its name must start
+        with `letter_mailshot_`**
+
+        Here is a (somewhat pointless) example of a compatible SQL view definition:
+
+        ```
+          CREATE OR REPLACE VIEW
+          renalware_kch.letter_mailshot_patients_where_surname_starts_with_r AS
+          SELECT id as patient_id
+          FROM patients
+          WHERE family_name like 'R%';
+        ```

data/app/views/renalware/letters/parts/_allergies.html.slim

@@ -1,5 +1,5 @@
 .list.allergies
-  h3 Allergies:
+  b.subtitle Allergies:
   - if allergies.any?
     ul
       - allergies.each do |allergy|

data/app/views/renalware/letters/parts/_problems.html.slim

@@ -1,5 +1,5 @@
 .list.problems
-  h3 Problems
+  b.subtitle Problems
 
   - if problems.any?
     ul.indented

data/app/views/renalware/letters/parts/_recent_pathology_results.html.slim

@@ -1,3 +1,3 @@
 .list.investigations
-  h3 Recent Investigations
+  b.subtitle Recent Investigations
   p= recent_pathology_results.results || " None"

data/app/views/renalware/medications/prescriptions/_current.html.slim

@@ -1,4 +1,4 @@
-h3 Current Medications
+b.subtitle Current Medications
 
 - if prescriptions.blank?
   p.prescription No medications listed

data/app/views/renalware/medications/prescriptions/_current_hd.html.slim

@@ -1,5 +1,5 @@
 - if prescriptions.any?
-  h3 Drugs to give on Haemodialysis
+  b.subtitle Drugs to give on Haemodialysis
 
   ul
       - prescriptions.each do |prescription|

data/app/views/renalware/medications/prescriptions/_prescription.html.slim

@@ -1,5 +1,4 @@
 - recently_changed = defined?(recently_changed) && recently_changed
-
 li.prescription class=("recently_changed" if recently_changed)
   = prescription.drug.name
   = blank_separator
@@ -8,6 +7,9 @@ li.prescription class=("recently_changed" if recently_changed)
   = prescription.medication_route.code
   = blank_separator
   = prescription.frequency
+  = blank_separator
+  i
+    b= prescription.provider_suffix
 
   / We pass in date_changed if the prescription is recently_changed or recently_stopped
   / It could be the prescribed_on or terminated_on date

data/app/views/renalware/medications/prescriptions/_recently_stopped.html.slim

@@ -1,4 +1,4 @@
-h3 Recently Stopped Medications
+b.subtitle Recently Stopped Medications
 
 - if prescriptions.blank?
   p.prescription None

data/app/views/renalware/system/view_metadata/_columns_table.html.slim

@@ -28,9 +28,9 @@ table.sortables(style="list-style-type: none;")
           td.border-0
             code= col.code
           td.text-center.border-0
-            input.m-0(type="checkbox" name="view_metadata[columns][][hidden]" checked=col.hidden)
+            input.m-0(type="checkbox" name="view_metadata[columns][][hidden]" checked=col.hidden style="margin:0")
           td.border-0
-            input.m-0(type="text" name="view_metadata[columns][][name]" value=col.name)
+            input.m-0(type="text" name="view_metadata[columns][][name]" value=col.name style="margin:0")
           td.border-0
             select.m-0(name="view_metadata[columns][][width]")
               option(value="")

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

@@ -2,3 +2,4 @@
 / 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 :drug, wrapper: :horizontal_medium, collection: Renalware::Drugs::Drug.for(:vaccine).pluck(:name, :name)

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

@@ -4,5 +4,7 @@
 dl.dl-horizontal
   dt= attr_name(document, :type, suffix: ":")
   dd= document.type&.text || 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/20201020171139_update_low_clearance_mdm_patients_view.rb

@@ -1,4 +1,4 @@
-class UpdateLowClearanceMDMPatientsView < ActiveRecord::Migration[6.0]
+class UpdateLowClearanceMDMPatientsView < ActiveRecord::Migration[5.2]
   def change
     within_renalware_schema do
       update_view :low_clearance_mdm_patients, version: 2, revert_to_version: 1

data/db/migrate/20201021153832_update_supportive_care_mdm_patients_view.rb

@@ -1,4 +1,4 @@
-class UpdateSupportiveCareMDMPatientsView < ActiveRecord::Migration[6.0]
+class UpdateSupportiveCareMDMPatientsView < ActiveRecord::Migration[5.2]
   def change
     within_renalware_schema do
       update_view :supportive_care_mdm_patients, version: 2, revert_to_version: 1

data/db/migrate/20201021154809_update_transplant_mdm_patients_view.rb

@@ -1,4 +1,4 @@
-class UpdateTransplantMDMPatientsView < ActiveRecord::Migration[6.0]
+class UpdateTransplantMDMPatientsView < ActiveRecord::Migration[5.2]
   def change
     within_renalware_schema do
       update_view :transplant_mdm_patients, version: 2, revert_to_version: 1

data/db/migrate/20201023092859_remove_unused_indexes.rb

@@ -1,4 +1,4 @@
-class RemoveUnusedIndexes < ActiveRecord::Migration[6.0]
+class RemoveUnusedIndexes < ActiveRecord::Migration[5.2]
   def change
     within_renalware_schema do
       # Covered by index_admission_requests_on_patient_id_and_deleted_at

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/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;