renalware-core 2.0.113 → 2.0.115

data/config/routes/hd.rb

@@ -41,14 +41,18 @@ namespace :hd 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
+  namespace :scheduling do
+    resources :units, only: [] do
+      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 :session_forms do
     resources :batches, only: [:create, :show] do

data/config/routes/letters.rb

@@ -27,11 +27,6 @@ namespace :letters do
     resources :completions, only: [:new, :create], controller: "completed_batches"
   end
   resource :pdf_letter_cache, only: [:destroy], controller: "pdf_letter_cache"
-  resources :descriptions, only: :search do
-    collection do
-      get :search
-    end
-  end
 
   # Letters::ListsController displays prefined lists of letters. The default list is :all
   # We want to support dynamic urls with letters_list_path(named_parameeter: :all)

data/config/routes/patients.rb

@@ -10,6 +10,7 @@ namespace :patients do
               only: :index,
               controller: "practices/primary_care_physicians"
   end
+  resources :abridgements, only: :index
 end
 
 resources :bookmarks, controller: "patients/bookmarks", only: [:destroy, :index]

data/config/routes/pd.rb

@@ -6,11 +6,11 @@ resources :patients, only: [] do
     resources :apd_regimes,
               controller: "regimes",
               type: "PD::APDRegime",
-              only: [:new, :create, :edit, :update, :show]
+              only: [:new, :create, :edit, :update, :show, :index]
     resources :capd_regimes,
               controller: "regimes",
               type: "PD::CAPDRegime",
-              only: [:new, :create, :edit, :update, :show]
+              only: [:new, :create, :edit, :update, :show, :index]
     resources :regimes, only: [:new, :create, :edit, :update, :show]
     resources :peritonitis_episodes, only: [:new, :create, :show, :edit, :update]
     resources :exit_site_infections, only: [:new, :create, :show, :edit, :update]

data/config/routes/renal.rb

@@ -7,11 +7,6 @@ resources :patients, only: [] do
 end
 
 namespace :renal do
-  resources :prd_descriptions, only: [:search] do
-    collection do
-      get :search
-    end
-  end
   resources :aki_alerts, only: [:edit, :update, :index]
   resources :registry_preflight_checks, only: [] do
     collection do

data/config/routes.rb

@@ -11,6 +11,7 @@ Renalware::Engine.routes.draw do
   draw :directory
   draw :drugs
   draw :events
+  draw :feeds
   draw :hd
   draw :hospitals
   draw :letters

data/config/webpack/development.js

@@ -0,0 +1,5 @@
+process.env.NODE_ENV = process.env.NODE_ENV || 'development'
+
+const environment = require('./environment')
+
+module.exports = environment.toWebpackConfig()

data/config/webpack/environment.js

@@ -0,0 +1,3 @@
+const { environment } = require('@rails/webpacker')
+
+module.exports = environment

data/config/webpack/production.js

@@ -0,0 +1,5 @@
+process.env.NODE_ENV = process.env.NODE_ENV || 'production'
+
+const environment = require('./environment')
+
+module.exports = environment.toWebpackConfig()

data/config/webpack/test.js

@@ -0,0 +1,5 @@
+process.env.NODE_ENV = process.env.NODE_ENV || 'development'
+
+const environment = require('./environment')
+
+module.exports = environment.toWebpackConfig()

data/config/webpacker.yml

@@ -0,0 +1,103 @@
+# Note: You must restart bin/webpack-dev-server for changes to take effect
+
+default: &default
+  source_path: app/javascript
+  source_entry_path: packs
+  # public_root_path: /Users/tim/Sites/airslie/renalware/renalwarev2/spec/dummy/public
+  public_root_path: public
+  public_output_path: renalware-core-packs
+  cache_path: tmp/cache/webpacker
+  check_yarn_integrity: false
+  webpack_compile_output: true
+
+  # Additional paths webpack should lookup modules
+  # ['app/assets', 'engine/foo/app/assets']
+  resolved_paths: []
+
+  # Reload manifest.json on all requests so we reload latest compiled packs
+  cache_manifest: false
+
+  # Extract and emit a css file
+  extract_css: false
+
+  static_assets_extensions:
+    - .jpg
+    - .jpeg
+    - .png
+    - .gif
+    - .tiff
+    - .ico
+    - .svg
+    - .eot
+    - .otf
+    - .ttf
+    - .woff
+    - .woff2
+
+  extensions:
+    - .mjs
+    - .js
+    - .sass
+    - .scss
+    - .css
+    - .module.sass
+    - .module.scss
+    - .module.css
+    - .png
+    - .svg
+    - .gif
+    - .jpeg
+    - .jpg
+
+development:
+  <<: *default
+  compile: true
+
+  # Verifies that correct packages and versions are installed by inspecting package.json, yarn.lock, and node_modules
+  check_yarn_integrity: false
+
+  # Reference: https://webpack.js.org/configuration/dev-server/
+  dev_server:
+    https: false
+    host: localhost
+    port: 3035
+    public: localhost:3035
+    hmr: false
+    # Inline should be set to true if using HMR
+    inline: true
+    overlay: true
+    compress: true
+    disable_host_check: true
+    use_local_ip: false
+    quiet: false
+    headers:
+      'Access-Control-Allow-Origin': '*'
+    watch_options:
+      ignored: '**/node_modules/**'
+
+
+test:
+  <<: *default
+  compile: true
+
+  # Compile test packs to a separate directory
+  # public_output_path: packs-test
+
+staging:
+  <<: *default
+
+  compile: false
+  extract_css: true
+  cache_manifest: true
+
+production:
+  <<: *default
+
+  # Production depends on precompilation of packs prior to booting for performance.
+  compile: false
+
+  # Extract and emit a css file
+  extract_css: true
+
+  # Cache manifest.json for performance
+  cache_manifest: true

data/db/functions/hd_diary_archive_elapsed_master_slots_v01.sql

@@ -0,0 +1,40 @@
+CREATE OR REPLACE FUNCTION renalware.hd_diary_archive_elapsed_master_slots()
+RETURNS void
+  AS $$
+  BEGIN
+
+INSERT into hd_diary_slots
+(
+    diary_id,
+    station_id,
+    day_of_week,
+    diurnal_period_code_id,
+    patient_id,
+    created_by_id,
+    updated_by_id,
+    created_at,
+    updated_at,
+    deleted_at
+)
+(
+    select
+        weekly_diary_id,
+        station_id,
+        day_of_week,
+        diurnal_period_code_id,
+        patient_id,
+        master_slot_created_by_id,
+        master_slot_updated_by_id,
+        master_slot_created_at,
+        master_slot_updated_at,
+        deleted_at
+    from renalware.hd_diary_matrix -- a SQL view
+    where
+        weekly_slot_id is null
+        and master_slot_id is not null
+        and master_slot_created_at <= slot_date
+        and slot_date >= now() - interval '3 months'
+);
+
+END;
+$$ LANGUAGE plpgsql;

data/db/migrate/20190322120025_create_feed_hl7_test_messages.rb

@@ -0,0 +1,12 @@
+class CreateFeedHL7TestMessages < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :feed_hl7_test_messages do |t|
+        t.string :name, null: false, index: true
+        t.string :description
+        t.text :body, null: false
+        t.timestamps
+      end
+    end
+  end
+end

data/db/migrate/20190325134823_create_patients_master_index.rb

@@ -0,0 +1,24 @@
+class CreatePatientsMasterIndex < ActiveRecord::Migration[5.2]
+  def change
+    create_table :patient_master_index do |t|
+      t.references :patient, null: true, foreign_key: true
+      t.timestamps null: false
+      t.string :nhs_number, index: true
+      t.string :hospital_number, index: true
+      t.string :title
+      t.string :family_name
+      t.string :middle_name
+      t.string :given_name
+      t.string :suffix
+      t.string :sex
+      t.date :born_on
+      t.datetime :died_at
+      t.string :ethnicity
+      t.string :practice_code
+      t.string :gp_code
+      t.timestamps null: false
+    end
+
+    add_index :patient_master_index, [:family_name, :given_name]
+  end
+end

data/db/migrate/20190327100851_add_handled_to_feed_messages.rb

@@ -0,0 +1,5 @@
+class AddHandledToFeedMessages < ActiveRecord::Migration[5.2]
+  def change
+    add_column :feed_messages, :processed, :boolean, default: false
+  end
+end

data/db/migrate/20191012121433_add_consultant_to_users.rb

@@ -0,0 +1,7 @@
+class AddConsultantToUsers < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :users, :consultant, :boolean, default: false, null: false, index: true
+    end
+  end
+end

data/db/migrate/20191018143635_create_hd_diary_matrix_view.rb

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

data/db/migrate/20191018144917_create_fn_to_archive_master_slots.rb

@@ -0,0 +1,9 @@
+class CreateFnToArchiveMasterSlots < ActiveRecord::Migration[5.2]
+  def up
+    load_function("hd_diary_archive_elapsed_master_slots_v01.sql")
+  end
+
+  def down
+    connection.execute("DROP FUNCTION IF EXISTS hd_diary_archive_elapsed_master_slots();")
+  end
+end

data/db/views/hd_diary_matrix_v01.sql

@@ -0,0 +1,38 @@
+-- First build a matrix of 'virtual' empty slots - by creating a cartesian product
+-- of weeks in the last year, unit, stations, days and periods (am pm eve)
+-- This can creates 50,0000+ rows
+with hd_empty_diary_matrix as (
+    SELECT
+        extract(YEAR from the_date) as year,
+        extract(WEEK from the_date) as week_number,
+        h.id as hospital_unit_id,
+        s.id as station_id,
+        day_of_week,
+        period.id as diurnal_period_code_id
+    from generate_series(now() - interval '1 year', now() - interval '1 week', '1 week') as the_date
+    cross join hospital_units h
+    cross join hd_stations s
+    CROSS JOIN (SELECT generate_series(1, 7) AS day_of_week) as A
+    CROSS JOIN hd_diurnal_period_codes period
+    where h.is_hd_site = TRUE
+    order by year, week_number, hospital_unit_id, station_id, day_of_week, diurnal_period_code_id
+)
+-- Now decorate the previous query by adding columns for the slots (master and weekly) that we actually have
+select
+    M.*
+    ,WD.id as weekly_diary_id
+    ,MD.id as master_diary_id
+    ,WS.id as weekly_slot_id
+    ,MS.id as master_slot_id
+    ,coalesce(WS.patient_id, MS.patient_id) as patient_id
+    ,MS.deleted_at
+    ,MS.created_by_id as master_slot_created_by_id
+    ,MS.updated_by_id as master_slot_updated_by_id
+    ,MS.created_at::date as master_slot_created_at
+    ,MS.updated_at::date as master_slot_updated_at
+    ,to_date(WD.year::text || '-' ||  WD.week_number::text || '-' || MS.day_of_week::text , 'iyyy-iw-ID') slot_date
+    from hd_empty_diary_matrix M
+    left outer join hd_diaries WD on WD.hospital_unit_id = M.hospital_unit_id AND WD.year = M.year AND WD.week_number = M.week_number AND WD.master = false
+    left outer join hd_diaries MD on MD.hospital_unit_id = M.hospital_unit_id AND MD.master = true
+    left outer join hd_diary_slots WS on WS.diary_id = WD.id AND WS.station_id = M.station_id and WS.day_of_week = M.day_of_week AND WS.diurnal_period_code_id = M.diurnal_period_code_id
+    left outer join hd_diary_slots MS on MS.diary_id = MD.id AND MS.station_id = M.station_id and MS.day_of_week = M.day_of_week AND MS.diurnal_period_code_id = M.diurnal_period_code_id

data/lib/core_extensions/active_record/sort.rb

@@ -1,14 +1,15 @@
 # frozen_string_literal: true
 
-# Adds a sort method to ActiveRecord class.  Given a list of IDs, it will sort
-# the records in the order of the ids.  Assumes that the model has the :position attribute.
-#
-# ActiveRecord::Base.class_eval do
-#    include RailsExtensions::ActiveRecord::Sort
-# end
-
 module CoreExtensions
   module ActiveRecord
+    # Assumes that the model has the #position attribute and adds 2 features to a model that
+    # includes it:
+    # 1. Set the :position to the next highest value when a new row is added. If the model has a
+    #    position_sorting_scope scope or class method, this is used to narrow the range of records
+    #    searched when finding the current max position
+    # 2. Add ability to sort rows based on an array of ids.
+    #
+    # TODO: move to a model concern and include selectively rather than globally.
     module Sort
       def self.included(base)
         base.extend ClassMethods
@@ -17,17 +18,34 @@ module CoreExtensions
       end
 
       module ClassMethods
+        # A controller #sort action might for instance invoke this class method on an object.
+        # The array of ids are the model to sort, and sorting is done by updating each model's
+        # position to reflect their place in the array.
         def sort(ids)
-          ids.each_with_index do |id, index|
+          Array(ids).each_with_index do |id, index|
             where(id: id).update_all(["position=?", index + 1])
           end
         end
       end
 
+      # Invoked by the callback when a record is created to set the initial value of #position.
+      # If no position_sorting_scope is defined on the model class, we set position to the max
+      # position in the whole table. If position_sorting_scope is provided we use it to refine the
+      # grouping and hence the max(position) found - for example to get the max position where
+      # patient_id = 123
+      #
+      # Example scope in a model:
+      #   scope :position_sorting_scope, ->(problem) { where(patient_id: problem.patient.id) }
+      #
       def set_position
         return unless respond_to?(:position)
 
-        self.position = (self.class.where("position < 99999").maximum(:position) || 0) + 1
+        scope = if self.class.respond_to?(:position_sorting_scope)
+                  self.class.position_sorting_scope(self)
+                else
+                  self.class
+                end
+        self.position = (scope.maximum(:position) || 0) + 1
       end
     end
   end

data/lib/renalware/configuration.rb

@@ -86,6 +86,9 @@ module Renalware
 
     config_accessor(:hd_session_prescriptions_require_signoff) { true }
     config_accessor(:batch_printing_enabled) { true }
+    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 }
 
     # A host app can override this to add/remove/re-order the clinical summary display
     # Note these have to be strings - they mapped to constants in ClinicalSummaryPresenter.

data/lib/renalware/engine.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require "rubygems"
+require "action_view/component/base"
 require "active_type"
 require "activerecord-import"
 require "ahoy"
@@ -49,8 +50,10 @@ require "sass-rails"
 require "scenic"
 require "slim-rails"
 require "trix"
+require "uglifier"
 require "validates_timeliness"
 require "virtus"
+require "webpacker"
 require "wicked_pdf"
 require "wisper"
 require "wisper/activejob"
@@ -62,9 +65,36 @@ module Renalware
   # This will keep Rails Engine from generating all table prefixes with the engines name
   def self.table_name_prefix; end
 
+  # rubocop:disable Metrics/ClassLength
   class Engine < ::Rails::Engine
     isolate_namespace Renalware
 
+    # Configure webpacker dev server proxy
+    # rubocop:disable Style/RescueStandardError
+    initializer "webpacker.proxy" do |app|
+      insert_middleware = begin
+                            Renalware.webpacker.config.dev_server.present?
+                          rescue
+                            nil
+                          end
+      next unless insert_middleware
+
+      app.middleware.insert_before(
+        0, Webpacker::DevServerProxy, # "Webpacker::DevServerProxy" if Rails version < 5
+        ssl_verify_none: true,
+        webpacker: Renalware.webpacker
+      )
+    end
+    # rubocop:enable Style/RescueStandardError
+
+    # Allow the host app to consume webpacker-compiled packs in the engine's public folder.
+    initializer :packs do |_app|
+      config.app_middleware.use(
+        Rack::Static,
+        urls: ["/renalware-core-packs"], root: Engine.root.join("public")
+      )
+    end
+
     # Define a attr on the Engine's eigenclass so a host application
     # can set an exception handler instance. It must accept a .notify(excetion) method.
     # We use the exception handler when logging errors in background jobs only.
@@ -192,3 +222,4 @@ module Renalware
     end
   end
 end
+# rubocop:enable Metrics/ClassLength

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.113"
+  VERSION = "2.0.115"
 end

data/lib/renalware/week_period.rb

@@ -2,11 +2,11 @@
 
 module Renalware
   class WeekPeriod
-    attr_reader :year, :week_number, :first_day_of_week
+    attr_reader :year, :week_number, :date_on_first_day_of_week
 
     def self.from_date(date)
       date = date.to_date
-      new(week_number: date.cweek, year: date.year)
+      new(week_number: date.cweek, year: date.cwyear)
     end
 
     def initialize(week_number:, year:)
@@ -14,15 +14,15 @@ module Renalware
       @year = year.to_i
       validate_week_number
       validate_year
-      @first_day_of_week = Date.commercial(@year, @week_number)
+      @date_on_first_day_of_week = Date.commercial(@year, @week_number)
     end
 
     def next
-      self.class.from_date(first_day_of_week + 1.week)
+      self.class.from_date(date_on_first_day_of_week + 1.week)
     end
 
     def previous
-      self.class.from_date(first_day_of_week - 1.week)
+      self.class.from_date(date_on_first_day_of_week - 1.week)
     end
 
     def to_a
@@ -30,12 +30,13 @@ module Renalware
     end
 
     def to_s
-      "#{I18n.l(first_day_of_week, format: :long)} to #{I18n.l(last_day_of_week, format: :long)}"
+      "#{I18n.l(date_on_first_day_of_week, format: :long)} " \
+      "to #{I18n.l(last_day_of_week, format: :long)}"
     end
 
     # The date of last day of the week (a Sunday)
     def last_day_of_week
-      @last_day_of_week ||= (first_day_of_week + 1.week - 1.minute).to_date
+      @last_day_of_week ||= (date_on_first_day_of_week + 1.week - 1.minute).to_date
     end
 
     def validate_week_number

data/lib/renalware.rb

@@ -4,5 +4,17 @@ require "renalware/engine"
 require "renalware/configuration"
 
 module Renalware
-  # Your code goes here...
+  # Configure Webpacker instance.
+  # See https://github.com/rails/webpacker/blob/master/docs/engines.md
+  class << self
+    def webpacker
+      @webpacker ||= begin
+        root_path = Pathname.new(File.join(__dir__, ".."))
+        ::Webpacker::Instance.new(
+          root_path: root_path,
+          config_path: root_path.join("config/webpacker.yml")
+        )
+      end
+    end
+  end
 end

data/lib/tasks/hd.rake

@@ -12,4 +12,11 @@ namespace :hd do
       performed_before: 3.days.ago
     )
   end
+
+  namespace :diary do
+    task housekeeping: :environment do
+      Rails.logger = Logger.new(STDOUT)
+      Delayed::Job.enqueue Renalware::HD::Scheduling::ArchiveYesterdaysSlotsJob.new
+    end
+  end
 end

data/lib/tasks/pathology.rake

@@ -23,7 +23,7 @@ namespace :pathology do
       # Load the message into a hash as delayed_Job would do and splat the hash keys as keyword args
       # into the FeedJob ctor.
       hash = YAML.safe_load(*raw_message).symbolize_keys
-      FeedJob.new(hash[:raw_message]).perform
+      Delayed::Job.enqueue FeedJob.new(hash[:raw_message])
     end
 
     desc "In development only, enqueue a test HL7 message"