renalware-core 2.0.149 → 2.0.151

data/app/views/renalware/transplants/mdm/_bottom.html.slim

@@ -9,4 +9,6 @@
     = render "measurements", mdm: mdm
 
   .columns.medium-12.large-4
-    = render Renalware::Events::BiopsiesComponent.new(patient: current_patient)
+    = render Renalware::Events::EventListComponent.new(\
+        patient: current_patient,
+        event_class: Renalware::Events::Biopsy)

data/app/views/renalware/transplants/recipient_followups/show.html.slim

@@ -10,7 +10,7 @@
   .edit_timestamp= render "renalware/shared/last_update", record: recipient_followup
 
   .document-view
-    .grid
+    .mgrid
       .row
         = render "renalware/shared/attributes_group",
             legend: "Transplant Outcomes", destination: "transplant_failure",

data/app/views/renalware/transplants/recipient_operations/show.html.slim

@@ -10,7 +10,7 @@
   .edit_timestamp= render "renalware/shared/last_update", record: recipient_operation
 
   .document-view
-    .grid
+    .mgrid
       .row
         = render "operation", recipient_operation: recipient_operation
 

data/app/views/renalware/transplants/recipient_workups/show.html.slim

@@ -9,7 +9,7 @@
   .edit_timestamp= render "renalware/shared/last_update", record: workup
 
   .document-view
-   .grid
+   .mgrid
      .row
         - ["Historicals", "Scores"].each do |group|
           = render "renalware/shared/documents/attributes_group",

data/app/views/renalware/transplants/registrations/show.html.slim

@@ -9,7 +9,7 @@
   .edit_timestamp= render "renalware/shared/last_update", record: registration
 
   .document-view
-    .grid
+    .mgrid
       .row
           - ["Codes", "CRF", "HLA", "Transplant", "Organs"].each do |group|
             = render "renalware/shared/documents/attributes_group",

data/config/initializers/inflections.rb

@@ -14,6 +14,14 @@
 
 # These inflection rules are supported but not enabled by default:
 ActiveSupport::Inflector.inflections(:en) do |inflect|
+  # For zeitwerk, handle the gem convention where the file version.rb
+  # does not define a constant Version. Alternatively we could move
+  # the version number someone else.
+  # (untested!)
+  # def camelize(basename, abspath)
+  #   abspath == app_version ? "VERSION" : basename.camelize
+  # end
+
   inflect.acronym "AKI"
   inflect.acronym "APD"
   inflect.acronym "API"

data/config/initializers/wicked_pdf.rb

@@ -20,3 +20,15 @@ WickedPdf.config = {
   # (but can be overridden in `render :pdf` calls)
   # layout: 'pdf.html',
 }
+
+# This is a hack to get ViewComponent and WickedPDF to work together.
+# See https://github.com/github/view_component/issues/288
+# Basically in Rails 5.x, both gems monkey patch ActionView render_to_string
+# and we can get an infinite loop when rendering PDFs.
+# Once we move to Rails 6 I think think this can be removed
+class WickedPdf
+  module PdfHelper
+    remove_method(:render_to_string)
+    remove_method(:render)
+  end
+end

data/config/locales/en-GB.yml

@@ -39,7 +39,7 @@ en-GB:
     - Saturday
     formats:
       default: "%d-%b-%Y"
-      long: "%a %e %b %Y"
+      long: "%a %d %b %Y"
       short: "%d %b"
       compact: "%d-%b-%y"
     month_names:

data/config/locales/renalware/events/advanced_care_plan.en.yml

@@ -0,0 +1,12 @@
+en:
+  renalware/events/advanced_care_plan:
+    title: "Advanced Care Plans"
+    description_column_title: State
+  enumerize:
+    renalware/events/advanced_care_plan/document:
+      state:
+        not_required: "ACP not required"
+        required_but_not_started: "ACP required but not started"
+        acp_in_progress: "ACP in progress"
+        acp_complete: "ACP complete"
+        acp_declined: "ACP declined"

data/config/locales/renalware/events/biopsy.en.yml

@@ -1,4 +1,6 @@
 en:
+  renalware/events/biopsy:
+    title: "Biopsies"
   activemodel:
     attributes:
       renalware/events/biopsy/document:

data/config/locales/renalware/events/clinical_frailty_score.en.yml

@@ -0,0 +1,16 @@
+en:
+  renalware/events/clinical_frailty_score:
+    title: "Clinical Frailty Scores"
+    description_column_title: Score
+  enumerize:
+    renalware/events/clinical_frailty_score/document:
+      score:
+        1: 1
+        2: 2
+        3: 3
+        4: 4
+        5: 5
+        6: 6
+        7: 7
+        8: 8
+        9: 9

data/config/locales/renalware/events/clinical_frailty_score_component.en.yml

@@ -0,0 +1,8 @@
+en:
+  renalware:
+    events:
+      clinical_frailty_score_component:
+        date_time: Date time
+        score: Score
+        created_at: Created
+        created_by: By

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

@@ -0,0 +1,6 @@
+en:
+  activerecord:
+    errors:
+      messages:
+        nhs_number_invalid_checkdigit: "is invalid - please check"
+        nhs_number_not_numeric: "is invalid -  must be 10 digits"

data/config/locales/renalware/pd/adequacy_result.en.yml

@@ -0,0 +1,9 @@
+en:
+  activerecord:
+    attributes:
+      renalware/pd/adequacy_result:
+        dial_24_vol_in: Dial 24 vol in (ml)
+        dial_24_vol_out: Dial 24 vol out (ml)
+        urine_24_vol: Urine 24 vol (ml)
+        height: Height (m)
+        weight: Weight (kg)

data/config/locales/renalware/pd/dashboard.en.yml

@@ -8,6 +8,9 @@ en:
             add_capd_regime: CAPD Regime
             add_apd_regime: APD Regime
             add_pet_adequacy: PET Adequacy
+            add_unified_pet_adequacy: PET & Adequacy
+            add_pet: PET
+            add_adequacy: Adequacy
             add_exit_site_infection: Exit Site Infection
             add_peritonitis_episode: Peritonitis Episode
             add_pd_assessment: PD Assessment

data/config/locales/renalware/pd/pet_result.en.yml

@@ -0,0 +1,23 @@
+en:
+  activerecord:
+    attributes:
+      renalware/pd/pet_result:
+        net_uf: PET_netUF
+        d_pcr: PET_D_Pcr
+        dextrose_concentration: Dextrose
+        dextrose_concentration_id: Dextrose
+        volume_in: Volume in (ml)
+        volume_out: Volume out (ml)
+        infusion_time: Infusion time (min)
+        drain_time: Drain time (min)
+        overnight_dextrose_concentration: Overnight dextrose
+        overnight_dextrose_concentration_id: Overnight dextrose
+        overnight_volume_in: Overnight vol in (ml)
+        overnight_volume_out: Overnight vol out (ml)
+        overnight_dwell_time: Overnight dwell time (min)
+
+  enumerize:
+    renalware/pd/pet_result:
+      pet_type:
+        fast: Fast
+        full: Full

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

@@ -8,3 +8,4 @@ en:
           comorbidities_at_esrf: Comorbidities
           first_seen_on: Date first seen
           cause_of_death: Cause of death
+          esrf: ESRF

data/config/routes/pathology.rb

@@ -2,6 +2,7 @@
 
 resources :patients, only: [] do
   namespace :pathology do
+    resources :charts, only: [:show]
     get "observations/current",
         to: "current_observation_results#index",
         as: "current_observations"
@@ -11,6 +12,11 @@ resources :patients, only: [] do
     get "observations/historical",
         to: "historical_observation_results#index",
         as: "historical_observations"
+    scope constraints: { format: :json, date: /\d{4}-\d{2}-\d{2}/ } do
+      get "observations/nearest/code_group/:code_group_id/date/:date",
+          to: "nearest_observation_results#index",
+          as: "nearest_observations"
+    end
     resources :observation_requests, only: [:index, :show]
     resources :patient_rules
     get "descriptions/:description_id/observations",

data/config/routes/pd.rb

@@ -15,6 +15,9 @@ resources :patients, only: [] do
     resources :peritonitis_episodes, only: [:new, :create, :show, :edit, :update]
     resources :exit_site_infections, only: [:new, :create, :show, :edit, :update]
     resources :pet_adequacy_results, except: [:destroy]
+    resources :unified_pet_adequacies, only: [:new, :create]
+    resources :pet_results
+    resources :adequacy_results
     resources :assessments, except: [:index, :destroy]
     resources :training_sessions, except: [:index, :destroy]
     resource :mdm, only: :show, controller: "mdm"
@@ -22,6 +25,8 @@ resources :patients, only: [] do
 end
 
 namespace :pd do
+  resources :pet_completions, only: :index
+  resources :adequacy_completions, only: :index
   resources :bag_types, except: [:show]
   resources :infection_organisms
   resources :mdm_patients, only: :index

data/config/routes/renal.rb

@@ -12,6 +12,7 @@ namespace :renal do
     collection do
       get :patients
       get :deaths
+      get :missing_esrf
     end
   end
 end

data/db/functions/generate_secure_id_v01.sql

@@ -9,7 +9,7 @@ CREATE OR REPLACE FUNCTION generate_secure_id(length integer default 24)
   */
   RETURNS text AS
   $body$
-  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789',
+  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ9999999999',
                      ceil (random() * 62)::integer,
                      1), '')
   FROM   generate_series(1, length)

data/db/migrate/20200226145010_add_unique_indexes.rb

@@ -0,0 +1,46 @@
+class AddUniqueIndexes < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      # Allow only one transplant_registration per patient
+      remove_index :transplant_registrations, :patient_id
+      add_index :transplant_registrations, :patient_id, unique: true
+
+      # Allow only one un-terminated transplant_registration_status per patient
+      # Removed this for now as the way we update the terminated_on in the model
+      # prevents us from enforcing this constraint atm.
+      # remove_index :transplant_registration_statuses, :registration_id
+      # add_index(
+      #   :transplant_registration_statuses,
+      #   :registration_id,
+      #   unique: true,
+      #   where: "terminated_on is null"
+      # )
+
+      # Allow only one current modality_modalities per patient
+      add_index(
+        :modality_modalities,
+        :patient_id,
+        unique: true,
+        where: "ended_on is null",
+        name: :index_modality_modalities_on_patient_id_current
+      )
+
+      # Removed this for now as prevents adding new profiles. Need to address holistically in
+      # a separate PR
+      # # An access profile must have a start date
+      # change_column_null :access_profiles, :started_on, false
+      # # Allow only on unterminated access profile per patient
+      # add_index(
+      #   :access_profiles,
+      #   :patient_id,
+      #   unique: true,
+      #   where: "terminated_on is null",
+      #   name: :index_access_profiles_on_patient_id_current
+      # )
+
+      # Allow only one renal_profile per patient
+      remove_index :renal_profiles, :patient_id
+      add_index :renal_profiles, :patient_id, unique: true
+    end
+  end
+end

data/db/migrate/20200421082715_add_body_surface_area_to_clinic_visits.rb

@@ -0,0 +1,8 @@
+class AddBodySurfaceAreaToClinicVisits < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :clinic_visits, :body_surface_area, :decimal, precision: 8, scale: 2
+      add_column :clinic_visits, :total_body_water, :decimal, precision: 8, scale: 2
+    end
+  end
+end

data/db/migrate/20200421132911_create_pd_pet_dextrose_concentrations.rb

@@ -0,0 +1,13 @@
+class CreatePDPETDextroseConcentrations < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :pd_pet_dextrose_concentrations do |t|
+        t.string :name, null: false, index: { unique: true }
+        t.float :value, null: false, index: { unique: true }
+        t.boolean :hidden, null: false, default: false
+        t.integer :position, null: false, default: 0
+        t.timestamps null: false
+      end
+    end
+  end
+end

data/db/migrate/20200421143546_create_pet_results.rb

@@ -0,0 +1,66 @@
+class CreatePETResults < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_enum :pd_pet_type, %w(full fast)
+
+      create_table :pd_pet_results do |t|
+        t.references :patient, null: false, foreign_key: true
+
+        # The first set are inputs when seeing the patient
+        t.date :performed_on, null: false
+        t.enum :test_type, enum_name: :pd_pet_type, null: false
+        t.integer :volume_in
+        t.integer :volume_out
+        t.references(
+          :dextrose_concentration,
+          foreign_key: { to_table: :pd_pet_dextrose_concentrations },
+          index: true,
+          null: true
+        )
+        t.integer :infusion_time
+        t.integer :drain_time
+        t.integer :overnight_volume_in
+        t.integer :overnight_volume_out
+        t.references(
+          :overnight_dextrose_concentration,
+          foreign_key: { to_table: :pd_pet_dextrose_concentrations },
+          index: true,
+          null: true
+        )
+        t.integer :overnight_dwell_time
+
+        # This set is manually or automatically added pathology after the fact
+        # Refers to dialysate samples
+        [0, 2, 4, 6].each do |hr|
+          t.float :"sample_#{hr}hr_time"
+          t.float :"sample_#{hr}hr_urea"
+          t.float :"sample_#{hr}hr_creatinine"
+          t.float :"sample_#{hr}hr_glc"
+          t.float :"sample_#{hr}hr_sodium"
+          t.float :"sample_#{hr}hr_protein"
+        end
+
+        # Blood results back from the lab
+        t.float :serum_time
+        t.float :serum_urea
+        t.float :serum_creatinine
+        t.float :plasma_glc
+        t.float :serum_ab
+        t.float :serum_na
+
+        # This set is for calculated fields
+        t.integer :net_uf
+        t.float :d_pcr
+        t.boolean :complete, default: false, null: false, indeex: true
+
+        t.datetime :deleted_at, index: true
+        t.references :created_by, index: true, null: false
+        t.references :updated_by, index: true, null: false
+        t.timestamps null: false
+      end
+
+      add_foreign_key :pd_pet_results, :users, column: :created_by_id
+      add_foreign_key :pd_pet_results, :users, column: :updated_by_id
+    end
+  end
+end

data/db/migrate/20200427123229_create_adequacy_results.rb

@@ -0,0 +1,54 @@
+class CreateAdequacyResults < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :pd_adequacy_results do |t|
+        t.references :patient, null: false, foreign_key: true
+
+        # The first set are inputs after seeing the patient
+        t.date :performed_on, null: false
+        t.integer :dial_24_vol_in
+        t.integer :dial_24_vol_out
+        t.boolean :dial_24_missing, null: false, default: false
+        t.integer :urine_24_vol
+        t.boolean :urine_24_missing, null: false, default: false
+
+        # Blood results back from the lab
+        t.float :serum_urea
+        t.float :serum_creatinine
+        t.float :plasma_glc
+        t.float :serum_ab
+
+        # Dialysate results back from the lab
+        t.float :dialysate_urea
+        t.float :dialysate_creatinine
+        t.float :dialysate_glu
+        t.float :dialysate_na
+        t.float :dialysate_protein
+
+        # Urine results back from the lab
+        t.float :urine_urea
+        t.float :urine_creatinine
+        t.float :urine_na
+        t.float :urine_k
+
+        # Calculations
+        t.float :total_creatinine_clearance
+        t.float :pertitoneal_creatinine_clearance
+        t.float :renal_creatinine_clearance
+        t.float :total_ktv
+        t.float :pertitoneal_ktv
+        t.float :renal_ktv
+        t.float :dietry_protein_intake
+        t.boolean :complete, default: false, null: false, indeex: true
+
+        t.datetime :deleted_at, index: true
+        t.references :created_by, index: true, null: false
+        t.references :updated_by, index: true, null: false
+        t.timestamps null: false
+      end
+
+      add_foreign_key :pd_adequacy_results, :users, column: :created_by_id
+      add_foreign_key :pd_adequacy_results, :users, column: :updated_by_id
+    end
+  end
+end