renalware-core 2.0.164 → 2.1.1

data/config/locales/renalware/renal/registry.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   renalware:
     renal:

data/config/locales/renalware/reporting/audit.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/research/study_participant.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/{shared.yml → shared.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   prompts:
     confirm_delete: "Are you sure you want to delete?"

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

@@ -1,3 +1,4 @@
+---
 en:
   snippets:
     insert: Insert snippet

data/config/locales/renalware/transplants/{donation.yml → donation.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/transplants/donor_dashboard.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   renalware:
     transplants:

data/config/locales/renalware/transplants/{donor_followup.yml → donor_followup.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/transplants/{donor_operation.yml → donor_operation.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/transplants/{donor_workup.yml → donor_workup.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activemodel:
     attributes:

data/config/locales/renalware/transplants/live_donors.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   renalware:
     transplants:

data/config/locales/renalware/transplants/mdm.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   renalware:
     transplants:

data/config/locales/renalware/transplants/recipient_dashboards.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   renalware:
     transplants:

data/config/locales/renalware/transplants/{recipient_followup.yml → recipient_followup.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/transplants/{recipient_operation.yml → recipient_operation.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/transplants/{recipient_workup.yml → recipient_workup.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activemodel:
     attributes:

data/config/locales/renalware/transplants/{registration.yml → registration.en.yml}

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

data/config/locales/renalware/transplants/rejection_episode.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   activerecord:
     attributes:

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

@@ -1,10 +1,10 @@
+---
 en:
   renalware:
     virology:
       vaccinations:
         list:
           title: Vaccinations
-          add: Add
       dashboards:
         actions:
           add_vaccination: Vaccination

data/config/locales/simple_form.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   simple_form:
     "yes": 'Yes'

data/config/locales/validates_timeliness.en.yml

@@ -1,3 +1,4 @@
+---
 en:
   errors:
     messages:

data/config/permissions.yml

@@ -8,6 +8,7 @@ super_admin:
   - Renalware::HD::CannulationType
   - Renalware::System::Download
   - Renalware::Pathology::ObservationDescription
+  - Renalware::Virology::VaccinationType
 admin:
   - Renalware::User
   - Renalware::BagType

data/config/routes/events.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 resources :patients, only: [] do
-  resources :events, only: [:new, :create, :index], controller: "events/events"
+  resources :events, except: :show, controller: "events/events"
   constraints(format: /(pdf)/) do
     resources :events, only: :show, controller: "events/events"
   end

data/config/routes/virology.rb

@@ -10,3 +10,9 @@ resources :patients, only: [] do
               defaults: { slug: :vaccinations }
   end
 end
+
+namespace :virology do
+  resources :vaccination_types do
+    post :sort, on: :collection
+  end
+end

data/db/migrate/20180112151706_create_low_clearance_profiles.rb

@@ -13,7 +13,7 @@ class CreateLowClearanceProfiles < ActiveRecord::Migration[5.1]
       sql_for_modality_type = lambda { |mod_desc_type|
         <<-SQL.squish
           UPDATE modality_descriptions SET type = #{connection.quote(mod_desc_type)}
-          WHERE name = 'Low Clearance';
+          WHERE name = 'Low Clearance' or name = 'Advanced Kidney Care';
         SQL
       }
 

data/db/migrate/20190131152758_create_event_categories.rb

@@ -0,0 +1,36 @@
+class CreateEventCategories < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :event_categories do |t|
+        t.string :name, null: false, index: { unique: true }
+        t.integer :position, null: false, default: 10
+        t.datetime :deleted_at, index: true
+        t.timestamps null: false
+      end
+
+      add_reference(
+        :event_types,
+        :category,
+        references: :event_categories,
+        index: true,
+        null: true,
+        foreign_key: { to_table: :event_categories }
+      )
+
+      reversible do |direction|
+        direction.up do
+          category = Renalware::Events::Category.find_or_create_by!(name: "General")
+          Renalware::Events::Type
+            .with_deleted
+            .where(category_id: nil)
+            .update_all(category_id: category.id)
+        end
+        direction.down do
+          # noop
+        end
+      end
+
+      change_column_null(:event_types, :category_id, false)
+    end
+  end
+end

data/db/migrate/20201217154345_update_reporting_anaemia_audit.rb

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

data/db/migrate/20201217155107_update_reporting_bone_audit.rb

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

data/db/migrate/20201229174653_add_language_to_users.rb

@@ -0,0 +1,5 @@
+class AddLanguageToUsers < ActiveRecord::Migration[5.2]
+  def change
+    add_column :users, :language, :string
+  end
+end

data/db/migrate/20210305100015_add_named_nurse_to_patients.rb

@@ -0,0 +1,33 @@
+class AddNamedNurseToPatients < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_reference :patients, :named_nurse, references: :users, index: true
+      add_foreign_key :patients, :users, column: :named_nurse_id
+
+      reversible do |direction|
+        direction.up do
+          # Migrate the named_nurse_id column from hd_profiles to patients
+          sql = <<-SQL.squish
+            UPDATE renalware.patients P
+            SET named_nurse_id = HP.named_nurse_id
+            FROM renalware.hd_profiles HP
+            WHERE
+              HP.patient_id = P.id
+              and P.named_nurse_id is null
+              and HP.named_nurse_id is not null
+              and HP.deactivated_at is null;
+          SQL
+          connection.execute sql
+        end
+        direction.down do
+          # noop
+        end
+      end
+
+      # Rename hd_profiles.named_nurse_id to named_nurse_id_legacy so it is not used
+      change_table :hd_profiles do |t|
+        t.rename :named_nurse_id, :named_nurse_id_legacy
+      end
+    end
+  end
+end

data/db/migrate/20210305105830_update_mdm_views_for_named_nurse_changes.rb

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

data/db/migrate/20210305181345_deprecate_issued_on_in_letters.rb

@@ -0,0 +1,8 @@
+class DeprecateIssuedOnInLetters < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      change_column_null :letter_letters, :issued_on, true # allow nulls
+      rename_column :letter_letters, :issued_on, :legacy_issued_on
+    end
+  end
+end

data/db/migrate/20210305191214_update_reporting_daily_letters_view.rb

@@ -0,0 +1,11 @@
+class UpdateReportingDailyLettersView < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view(
+        :reporting_daily_letters,
+        version: 3,
+        revert_to_version: 2
+      )
+    end
+  end
+end

data/db/migrate/20210310154134_create_akcc_mdm_patients_view.rb

@@ -0,0 +1,7 @@
+class CreateAKCCMDMPatientsView < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_view :akcc_mdm_patients
+    end
+  end
+end

data/db/seeds/default/clinics/clinics.rb

@@ -16,7 +16,7 @@ module Renalware
       "Haemodialysis",
       "Home Haemodialysis",
       "Iron",
-      "Low Clearance",
+      "Advanced Kidney Care",
       "Transplant",
       "Walk-in",
       "Woolwich Outreach"

data/db/seeds/default/events/event_categories.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Renalware
+  log "Adding Default Event Categories" do
+    Events::Category.find_or_create_by!(name: "General") do |category|
+      category.position = 1
+    end
+  end
+end

data/db/seeds/default/events/event_types.csv

@@ -1,10 +1,10 @@
-"name","event_class_name","slug"
-"Renal Biopsy Native","Renalware::Events::Biopsy","native_biopsies"
-"Renal Biopsy Transplant","Renalware::Events::Biopsy","transplant_biopsies"
-"Swab","Renalware::Events::Swab","swabs"
-"Plasma Exchange",,
-"PD Line Change",,"pd_line_changes"
-"Investigation","Renalware::Events::Investigation","investigations"
-"Vaccination","Renalware::Virology::Vaccination","vaccinations"
-"Advanced Care Plan","Renalware::Events::AdvancedCarePlan","advanced_care_plans"
-"Clinical Frailty Score","Renalware::Events::ClinicalFrailtyScore","clinical_frailty_score"
+"name","event_class_name","slug","category_id"
+"Renal Biopsy Native","Renalware::Events::Biopsy","native_biopsies",1
+"Renal Biopsy Transplant","Renalware::Events::Biopsy","transplant_biopsies",1
+"Swab","Renalware::Events::Swab","swabs",1
+"Plasma Exchange",,,1
+"PD Line Change",,"pd_line_changes",1
+"Investigation","Renalware::Events::Investigation","investigations",1
+"Vaccination","Renalware::Virology::Vaccination","vaccinations",1
+"Advanced Care Plan","Renalware::Events::AdvancedCarePlan","advanced_care_plans",1
+"Clinical Frailty Score","Renalware::Events::ClinicalFrailtyScore","clinical_frailty_score",1

data/db/seeds/default/events/event_types.rb

@@ -5,9 +5,12 @@ module Renalware
     file_path = File.join(File.dirname(__FILE__), "event_types.csv")
 
     CSV.foreach(file_path, headers: true) do |row|
-      Events::Type.find_or_create_by!(name: row["name"],
-                                      event_class_name: row["event_class_name"],
-                                      slug: row["slug"])
+      Events::Type.find_or_create_by!(
+        name: row["name"],
+        event_class_name: row["event_class_name"],
+        slug: row["slug"],
+        category_id: row["category_id"]
+      )
     end
   end
 end

data/db/seeds/default/events/seeds.rb

@@ -1,3 +1,4 @@
 # frozen_string_literal: true
 
+require_relative "./event_categories"
 require_relative "./event_types"

data/db/seeds/default/modalities/descriptions.rb

@@ -2,11 +2,23 @@
 
 module Renalware
   log "Adding Modality Descriptions" do
-    Deaths::ModalityDescription.find_or_create_by!(name: "Death", code: "death")
-    Transplants::DonorModalityDescription.find_or_create_by!(name: "Live Donor", code: "live_donor")
-    Transplants::RecipientModalityDescription.find_or_create_by!(name: "Transplant", code: "transplant")
-    PD::ModalityDescription.find_or_create_by!(name: "PD", code: "pd")
-    HD::ModalityDescription.find_or_create_by!(name: "HD", code: "hd")
-    LowClearance::ModalityDescription.find_or_create_by!(name: "Low Clearance", code: "low_clearance")
+    Deaths::ModalityDescription.find_or_create_by!(
+      name: "Death", code: "death"
+    )
+    Transplants::DonorModalityDescription.find_or_create_by!(
+      name: "Live Donor", code: "live_donor"
+    )
+    Transplants::RecipientModalityDescription.find_or_create_by!(
+      name: "Transplant", code: "transplant"
+    )
+    PD::ModalityDescription.find_or_create_by!(
+      name: "PD", code: "pd"
+    )
+    HD::ModalityDescription.find_or_create_by!(
+      name: "HD", code: "hd"
+    )
+    LowClearance::ModalityDescription.find_or_create_by!(
+      name: "Advanced Kidney Care", code: "low_clearance"
+    )
   end
 end

data/db/seeds/default/system/view_metadata.rb

@@ -71,8 +71,8 @@ module Renalware
     end
 
     Renalware::System::ViewMetadata.find_or_create_by!(
-      view_name: "low_clearance_mdm_patients",
-      scope: "low_clearance",
+      view_name: "akcc_mdm_patients",
+      scope: "akcc",
       category: "mdm",
       slug: "all",
       schema_name: "renalware"

data/db/views/akcc_mdm_patients_v01.sql

@@ -0,0 +1,39 @@
+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 where 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,
+  case when TXRSD.code not ilike '%permanent' then true else false end as tx_candidate,
+  case
+    when (convert_to_float(PA.values->'HGB'->>'result') < 100.0) then '< 100'
+    when (convert_to_float(PA.values->'HGB'->>'result') > 130.0) then '> 130'
+    else NULL
+  end as hgb_range,
+  case
+    when (convert_to_float(values->'URE'->>'result') >= 30.0) then '>= 30'
+    else NULL
+  end as urea_range
+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 and TXRS.started_on <= current_date
+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 = 'low_clearance'