renalware-core 2.0.0.pre.beta9 → 2.0.0.pre.beta10

data/config/locales/renalware/hd/session.en.yml

@@ -11,6 +11,7 @@ en:
         end_time: Session End Time
         hd_type: HD Type
         modality_description: Modality
+        dialysate: Dialysis Solution Used
   activemodel:
     attributes:
       renalware/hd/session/dna/document:
@@ -25,7 +26,6 @@ en:
         lines_reversed: "Lines Reversed?"
         had_blood_transfusion: "Had blood transfusion?"
         machine_no: Machine No
-        dialysis_fluid_used: Dialysis Solution Used
       renalware/hd/session_document/observations:
         weight: Weight (kg)
         weight_measured: Weight taken
@@ -89,12 +89,6 @@ en:
               invalid_number: Please enter a number with up to 1 decimal place, for example 20 or 20.1
 
   enumerize:
-    renalware/hd/session_document/info:
-      dialysis_fluid_used:
-        a7: Fresenius A7
-        a10: Fresenius A10
-        a17: Fresenius A17
-        a27: Fresenius A27
     renalware/hd/session_document/observations:
       weight_measured:
         "yes": "Yes"

data/config/locales/renalware/hospitals/unit.yml

@@ -10,4 +10,3 @@ en:
         renal_registry_code: NRD Code
         unit_type: Unit Type
         is_hd_site: Can provide HD treatments?
-        number_of_hd_stations: Maximum number of stations

data/config/locales/renalware/mdm.yml

@@ -2,7 +2,7 @@ en:
   renalware:
     mdm_patients:
       patient:
-        view: "View"
+        view: "MDM"
       table:
         name: Name
         nhs_no: NHS No.

data/config/locales/renalware/messaging/internal/messages.en.yml

@@ -25,6 +25,7 @@ en:
             body: Body
             urgent: Urgent
             age: Age
+            nhs_no: NHS Number
             hosp_no: Hosp No.
             recipients: Recipients
           sent_table:

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

@@ -13,6 +13,8 @@ en:
         esa_prescriptions: ESA Patients
         audits: Audits
         aki_alerts: AKI Alerts
+        studies: Clinical Studies
+        renal_registry_checks: Renal Registry Checks
       mdms:
         menu_title: MDMs
         hd: HD

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

@@ -0,0 +1,12 @@
+en:
+  renalware:
+    renal:
+      registry_preflight_checks:
+        table:
+          ethnicity: Ethnicity
+          prd: PRD
+          comorbidities_at_esrf: Comorbidities
+          first_seen_on: Date first seen
+          cause_of_death: Cause of death
+
+

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

@@ -0,0 +1,11 @@
+en:
+  activerecord:
+    attributes:
+      renalware/research/study_participant:
+        participant_id: "Patient"
+    errors:
+      models:
+        renalware/research/study_participant:
+          participant_id:
+            taken: is already in this study
+

data/config/routes.rb

@@ -46,6 +46,7 @@ Renalware::Engine.routes.draw do
     resources :requests do
       post :sort, on: :collection
     end
+    resources :consults
   end
 
   namespace :messaging do
@@ -76,6 +77,12 @@ Renalware::Engine.routes.draw do
     end
   end
 
+  namespace :research do
+    resources :studies, except: :show do
+      resources :participants, controller: :study_participants
+    end
+  end
+
   resources :snippets, controller: "snippets/snippets", except: :show do
     resources :snippet_clones,
               controller: "snippets/snippet_clones",
@@ -127,6 +134,11 @@ Renalware::Engine.routes.draw do
   end
 
   namespace :hd do
+    scope format: true, constraints: { format: :json } do
+      get "patients_dialysing_at_unit" => "patients#dialysing_at_unit"
+      get "patients_dialysing_at_hospital" => "patients#dialysing_at_hospital"
+    end
+
     resources :cannulation_types, except: :show
     resources :dialysers, except: :show
     resource :ongoing_sessions, only: :show
@@ -136,11 +148,23 @@ Renalware::Engine.routes.draw do
       resources :stations do
         post :sort, on: :collection
       end
+      resources :diaries, only: [:index, :show]
+      get "diaries/:year/:week_number/edit", to: "diaries#edit", as: :edit_diary
+    end
+    resources :diaries, only: [] do
+      resources :slots, except: :show, controller: :diary_slots
+      get "slots/day/:day_of_week/period/:diurnal_period_code_id/station/:station_id",
+          to: "diary_slots#show",
+          as: :refresh_slot
     end
   end
 
   namespace :hospitals do
-    resources :units, except: :show
+    resources :units, except: :show do
+      scope format: true, constraints: { format: :json } do
+        resources :wards, only: :index
+      end
+    end
   end
 
   namespace :modalities do
@@ -204,6 +228,12 @@ Renalware::Engine.routes.draw do
       end
     end
     resources :aki_alerts, except: [:new, :create, :destroy]
+    resources :registry_preflight_checks, only: [] do
+      collection do
+        get :patients
+        get :deaths
+      end
+    end
   end
 
   namespace :system do

data/db/migrate/20170831082043_create_hd_diaries.rb

@@ -0,0 +1,57 @@
+class CreateHDDiaries < ActiveRecord::Migration[5.1]
+  def change
+    create_table :hd_diaries do |t|
+      # Ensure the base Diary class is abstract, ie you can only save STI sub-classes like
+      # MasterDiary, which have an STI type.
+      t.string :type, index: true, null: false
+      t.references :hospital_unit, null: false, foreign_key: true, index: true
+      t.integer :master_diary_id, null: true, foreign_key: true, index: true
+      t.integer :week_number, null: true, index: true
+      t.integer :year, null: true, index: true
+      t.boolean :master, null: false, default: false
+      t.integer :updated_by_id, null: false, index: true
+      t.integer :created_by_id, null: false, index: true
+      t.datetime :deleted_at, index: true
+      t.timestamps null: false
+    end
+
+    add_foreign_key :hd_diaries, :users, column: :created_by_id
+    add_foreign_key :hd_diaries, :users, column: :updated_by_id
+    add_foreign_key :hd_diaries, :hd_diaries, column: :master_diary_id
+
+    # If this is
+    add_index :hd_diaries,
+              [:hospital_unit_id, :week_number, :year],
+              unique: true,
+              where: "master = false"
+    add_index :hd_diaries,
+              :hospital_unit_id,
+              unique: true,
+              where: "master = true",
+              name: "master_index_hd_diaries_on_hospital_unit_id"
+
+    # Add CHECK constraint to ensure week_number and year are in valid ranges
+    reversible do |direction|
+      direction.up do
+        execute <<-SQL
+          ALTER TABLE hd_diaries ADD CONSTRAINT week_number_in_valid_range CHECK (week_number >= 1 AND week_number <= 53);
+          ALTER TABLE hd_diaries ADD CONSTRAINT year_in_valid_range CHECK (year >= 2017 AND year <= 2050);
+        SQL
+      end
+      direction.down do
+        execute <<-SQL
+          ALTER TABLE hd_diaries DROP CONSTRAINT week_number_in_valid_range;
+          ALTER TABLE hd_diaries DROP CONSTRAINT year_in_valid_range;
+        SQL
+      end
+    end
+
+    # Would like to add an index here for WeeklyDiary implementation, but as this table is shared
+    # with MasterDiary, we can't do this unless we use partial indexes?
+    # add_index :hd_diaries, [:hospital_unit_id, :week_number, :year], unique: true
+
+    # Would like to add an index here for MasterDiary implementation (allow only one per hospital)
+    # but as this table is shared with WeeklyDiary, we can't do this  unless we use partial indexes?
+    # add_index :hd_diaries, [:hospital_unit_id, :week_number, :year], unique: true
+  end
+end

data/db/migrate/20170831084331_create_hd_diary_slots.rb

@@ -0,0 +1,36 @@
+class CreateHDDiarySlots < ActiveRecord::Migration[5.1]
+  def change
+    create_table :hd_diary_slots do |t|
+      t.integer :diary_id, null: false, index: true
+      t.integer :station_id, null: false, index: true
+      t.integer :day_of_week, null: false, index: true
+      t.integer :diurnal_period_code_id, null: false, index: true
+      t.references :patient, null: false, foreign_key: true, index: true
+      t.integer :updated_by_id, null: false, index: true
+      t.integer :created_by_id, null: false, index: true
+      t.datetime :deleted_at, index: true
+      t.timestamps null: false
+    end
+
+    # Add CHECK constraint to ensure week and year are in valid ranges
+    reversible do |direction|
+      direction.up do
+        execute <<-SQL
+          ALTER TABLE hd_diary_slots
+            ADD CONSTRAINT day_of_week_in_valid_range CHECK (day_of_week >= 1 AND day_of_week <= 7);
+        SQL
+      end
+      direction.down do
+        execute <<-SQL
+          ALTER TABLE hd_diary_slots DROP CONSTRAINT day_of_week_in_valid_range;
+        SQL
+      end
+    end
+
+    add_foreign_key :hd_diary_slots, :hd_stations, column: :station_id
+    add_foreign_key :hd_diary_slots, :hd_diaries, column: :diary_id
+    add_foreign_key :hd_diary_slots, :users, column: :created_by_id
+    add_foreign_key :hd_diary_slots, :users, column: :updated_by_id
+    add_foreign_key :hd_diary_slots, :hd_diurnal_period_codes, column: :diurnal_period_code_id
+  end
+end

data/db/migrate/20170831142819_enable_crosstab_extension.rb

@@ -0,0 +1,9 @@
+class EnableCrosstabExtension < ActiveRecord::Migration[5.1]
+  def up
+    ActiveRecord::Base.connection.execute("CREATE extension IF NOT EXISTS tablefunc;")
+  end
+
+  def down
+    ActiveRecord::Base.connection.execute("DROP extension IF EXISTS tablefunc;")
+  end
+end

data/db/migrate/20170915090544_create_hd_station_locations.rb

@@ -0,0 +1,12 @@
+class CreateHDStationLocations < ActiveRecord::Migration[5.1]
+  def change
+    create_table :hd_station_locations do |t|
+      t.string :name, null: false, index: :unique
+      t.string :colour, null: false
+    end
+
+    remove_column :hd_stations, :location, :string
+    add_column :hd_stations, :location_id, :integer, null: true
+    add_foreign_key :hd_stations, :hd_station_locations, column: :location_id
+  end
+end

data/db/migrate/20170915115228_add_schedule_diurnal_period_id_to_hd_profiles.rb

@@ -0,0 +1,52 @@
+class AddScheduleDiurnalPeriodIdToHDProfiles < ActiveRecord::Migration[5.1]
+  def change
+
+    #ActiveRecord::Base.clear_all_connections!
+    conn = ActiveRecord::Base.connection
+
+    # Enable the intarray extension which is required if we want to index the days[] array
+    # - see below
+    conn.execute(
+      "CREATE EXTENSION IF NOT EXISTS btree_gist;
+       CREATE EXTENSION IF NOT EXISTS intarray;"
+    )
+
+    create_table :hd_schedule_definitions do |t|
+      t.integer :days, null: false, array: true, default: []
+      t.integer :diurnal_period_id, null: false, index: true
+      t.datetime :deleted_at
+      t.timestamps null: false
+    end
+
+    add_foreign_key :hd_schedule_definitions, :hd_diurnal_period_codes, column: :diurnal_period_id
+    add_index :hd_schedule_definitions, :days, using: 'gin'
+
+    reversible do |direction|
+      direction.up do
+        # Create an index to make the days of week array eg [1 ,3, 5] unique within the scope
+        # of a diurnal period. So for the AM period, Mon Wed Fri ([1,3,5]) can only appear once.
+        conn.execute(
+          "ALTER TABLE hd_schedule_definitions ADD constraint "\
+          "days_array_unique_scoped_to_period EXCLUDE "\
+          "USING gist(diurnal_period_id WITH =, days WITH = );"
+        )
+      end
+      direction.down do
+        conn.execute(
+          "ALTER TABLE hd_schedule_definitions DROP CONSTRAINT days_array_unique_scoped_to_period;"
+        )
+      end
+    end
+
+    remove_column :hd_profiles, :schedule, :string
+    add_column :hd_profiles, :schedule_definition_id, :integer, null: true
+    add_foreign_key :hd_profiles, :hd_schedule_definitions, column: :schedule_definition_id
+    add_index :hd_profiles, :schedule_definition_id
+
+    remove_column :hd_preference_sets, :schedule, :string
+    add_column :hd_preference_sets, :schedule_definition_id, :integer, null: true
+    add_foreign_key :hd_preference_sets, :hd_schedule_definitions, column: :schedule_definition_id
+    add_index :hd_preference_sets, :schedule_definition_id
+
+  end
+end

data/db/migrate/20170916121019_remove_number_of_hd_stations_from_hospital_units.rb

@@ -0,0 +1,5 @@
+class RemoveNumberOfHDStationsFromHospitalUnits < ActiveRecord::Migration[5.1]
+  def change
+    remove_column :hospital_units, :number_of_hd_stations, :integer
+  end
+end

data/db/migrate/20170917185426_add_indexes_to_diary_slots.rb

@@ -0,0 +1,19 @@
+class AddIndexesToDiarySlots < ActiveRecord::Migration[5.1]
+  def change
+    # This unique index ensures that, for a diary (weekly or master), the same patient can
+    # only be added to one station in any period (am pm etc) on any day of the week
+    add_index :hd_diary_slots,
+              [
+                :diary_id,
+                :diurnal_period_code_id,
+                :day_of_week,
+                :patient_id
+              ],
+              unique: true,
+              name: "idx_unique_diaryslot_patients"
+
+    add_column :hd_diary_slots, :archived, :boolean, null: false, default: false
+    add_index :hd_diary_slots, :archived
+    add_column :hd_diary_slots, :archived_at, :datetime
+  end
+end

data/db/migrate/20171004092235_create_hd_dialysates.rb

@@ -0,0 +1,13 @@
+class CreateHDDialysates < ActiveRecord::Migration[5.1]
+  def change
+    create_table :hd_dialysates do |t|
+      t.string :name, null: false
+      t.text :description
+      t.integer :sodium_content, null: false
+      t.string :sodium_content_uom, null: false
+
+      t.datetime :deleted_at, index: true
+      t.timestamps null: false
+    end
+  end
+end

data/db/migrate/20171004110909_add_dialysate_id_to_profile_and_session.rb

@@ -0,0 +1,9 @@
+class AddDialysateIdToProfileAndSession < ActiveRecord::Migration[5.1]
+  def change
+    add_reference :hd_profiles, :dialysate, references: :hd_dialysates, index: true
+    add_foreign_key :hd_profiles, :hd_dialysates, column: :dialysate_id
+
+    add_reference :hd_sessions, :dialysate, references: :hd_dialysates, index: true
+    add_foreign_key :hd_sessions, :hd_dialysates, column: :dialysate_id
+  end
+end

data/db/migrate/20171012110133_create_research_studies.rb

@@ -0,0 +1,22 @@
+class CreateResearchStudies < ActiveRecord::Migration[5.1]
+  def change
+    create_table :research_studies do |t|
+      t.string :code, null: false
+      t.string :description, null: false, index: true
+      t.string :leader, index: true
+      t.text :notes
+      t.date :started_on
+      t.date :terminated_on
+      t.datetime :deleted_at
+      t.references :updated_by, foreign_key: { to_table: :users }, index: true
+      t.references :created_by, foreign_key: { to_table: :users }, index: true
+      t.timestamps null: false
+    end
+
+    # This create a postgres partial index
+    add_index :research_studies,
+              :code,
+              unique: true,
+              where: "deleted_at IS NULL"
+  end
+end

data/db/migrate/20171012143050_create_research_study_participants.rb

@@ -0,0 +1,30 @@
+class CreateResearchStudyParticipants < ActiveRecord::Migration[5.1]
+  def change
+    create_table :research_study_participants do |t|
+      t.references :participant,
+                   null: false,
+                   foreign_key: { to_table: :patients },
+                   index: true
+      t.references :study,
+                   null: false,
+                   foreign_key: { to_table: :research_studies },
+                   index: true
+      t.date :joined_on, null: false
+      t.date :left_on
+      t.datetime :deleted_at
+      t.references :updated_by, foreign_key: { to_table: :users }, index: true
+      t.references :created_by, foreign_key: { to_table: :users }, index: true
+      t.timestamps null: false
+    end
+
+    # This create a postgres partial index
+    # A participant can only be enrolled once in a study  must be unique in for any unit
+    # Ignoring any times there were deleted (for example because they were added in error and so
+    # removed, but subsequently added again)
+    add_index :research_study_participants,
+              [:participant_id, :study_id],
+              name: :unique_study_participants,
+              unique: true,
+              where: "deleted_at IS NULL"
+  end
+end