renalware-core 2.0.41 → 2.0.42

data/app/views/renalware/navigation/_renal.html.slim

@@ -10,6 +10,6 @@ li.has-dropdown
     li= link_to t(".letters"), letters_list_path
     li= link_to t(".esa_prescriptions"), medications_esa_prescriptions_path
     li= link_to t(".audits"), reporting_audits_path
-    li= link_to t(".aki_alerts"), renal_filtered_aki_alerts_path(named_filter: :today)
+    li= link_to t(".aki_alerts"), renal_aki_alerts_path
     li= link_to t(".studies"), research_studies_path
     li= link_to t(".renal_registry_checks"), patients_renal_registry_preflight_checks_path

data/app/views/renalware/navigation/_super_admin.html.slim

@@ -11,3 +11,5 @@ li.has-dropdown
     li= link_to "User Feedback", system_user_feedback_index_path
     li= link_to "System Messages", system_messages_path
     li= link_to "HD Dialysates", hd_dialysates_path
+    li= link_to "HD Dialysers", hd_dialysers_path
+    li= link_to "HD Cannulation Types", hd_cannulation_types_path

data/app/views/renalware/renal/aki_alerts/_aki_alert.html.slim

@@ -12,8 +12,7 @@ tr(class="#{'aki_alert--hotlist' if aki_alert.hotlist?}")
   td= aki_alert.patient.sex
   td= aki_alert.patient.age
   td= aki_alert.action
-  td= [aki_alert.hospital_ward, aki_alert.hospital_ward&.hospital_unit&.unit_code]\
-      .compact.join(" - ")
+  td= "#{aki_alert.hospital_ward} @#{aki_alert.hospital_ward&.hospital_unit&.unit_code}"
   td= yes_no aki_alert.hotlist?
   td= aki_alert.max_aki
   td= l(aki_alert.aki_date)
@@ -23,4 +22,3 @@ tr(class="#{'aki_alert--hotlist' if aki_alert.hotlist?}")
   td(colspan=10)
     .quick-preview
       =aki_alert.notes
-

data/app/views/renalware/renal/aki_alerts/_filters.html.slim

@@ -4,36 +4,56 @@ ruby:
     suspended: "All"
   }
 
-h2.print-only= filters[path_params[:named_filter].to_sym]
+scss:
+  .link_to_right_of_input_label {
+    position: absolute;
+    top: 0;
+    right: 0;
+    padding-right: .2rem;
+  }
+
+/h2.print-only= filters[path_params[:named_filter].to_sym]
 
-dl.sub-nav
-  - Renalware::Renal::AKI_ALERT_FILTERS.each do |key|
-    - options = path_params.merge(named_filter: key).to_h.symbolize_keys
-    - path = Renalware::Engine.routes.url_for(options.merge!(only_path: true))
-    = sub_nav_item(key.to_s.humanize, path)
+/ dl.sub-nav
+/   - Renalware::Renal::AKI_ALERT_FILTERS.each do |key|
+/     - options = path_params.merge(named_filter: key).to_h.symbolize_keys
+/     - path = Renalware::Engine.routes.url_for(options.merge!(only_path: true))
+/     = sub_nav_item(key.to_s.humanize, path)
 
 .search-form.filters
   = simple_form_for form,
       as: :q,
-      url: renal_filtered_aki_alerts_path,
+      url: renal_aki_alerts_path,
       method: :get do |f|
 
     .row
-      .columns.medium-2.large-3
-        = f.input :term, label: "Hosp/NHS no or name"
+      .columns.medium-3.large-2
+        = f.input :term, label: "Hosp/NHS No. or name"
+      .columns.medium-2.large-2
+        = f.input :date, as: :date_picker
+        .link_to_right_of_input_label
+          a.set_filter_date_to_today(href="") Today
+          |  | 
+          a.set_filter_date_to_any_date(href="") Clear
       .columns.medium-1.large-1
         = f.input :on_hotlist,
-                  collection: [["Yes",true],["No",false]]
+                  collection: [["Yes",true],["No",false]],
+                  label: "Hotlist"
       .columns.medium-2.large-2
         = f.input :action,
                   collection: Renalware::Renal::AKIAlertAction.pluck(:name, :id)
-      .columns.medium-3.large-2
-        = f.input :hospital_unit_id,
-                  collection: Renalware::Hospitals::Unit.pluck(:name, :id)
       .columns.medium-2.large-2
         = f.input :hospital_ward_id,
-                  collection: Renalware::Hospitals::Ward.pluck(:name, :id)
+                  as: :grouped_select,
+                  group_method: :wards,
+                  collection: Renalware::Hospitals::Unit.joins(:wards).includes(:wards).ordered,
+                  label_method: ->(s) { "#{s.name} @#{s.hospital_unit.unit_code}" },
+                  input_html: { class: "searchable_select" },
+                  label: "Ward"
+
+        a.link_to_right_of_input_label(href="javascript:$('#q_hospital_ward_id').val(null).trigger('change');") Clear
       .columns.medium-2.large-2.actions.end
         = f.submit "Filter", class: "button"
         span= " or "
-        = link_to t("helpers.reset"), renal_filtered_aki_alerts_path
+        = link_to t("helpers.reset"), renal_aki_alerts_path
+br

data/app/views/renalware/renal/aki_alerts/_filters.pdf.slim

@@ -8,6 +8,9 @@
       - if filters.empty?
         td None
       - else
+        - if filters[:date].present?
+          th Date:
+          td= filters[:date]
         - if filters[:term].present?
           th Query:
           td= filters[:term]
@@ -16,7 +19,7 @@
           td= yes_no(filters[:on_hotlist] == "true")
         - if filters[:action].present?
           th Action:
-          td=  Renalware::Renal::AKIAlertAction.find(filters[:action])&.to_s
+          td= Renalware::Renal::AKIAlertAction.find(filters[:action])&.to_s
         - if filters[:hospital_unit_id].present?
           th Site:
           td= Renalware::Hospitals::Unit.find_by(id: filters[:hospital_unit_id])

data/app/views/renalware/renal/aki_alerts/edit.html.slim

@@ -1,5 +1,5 @@
 = within_admin_layout(title: "Edit",
-                      breadcrumbs: breadcrumb_for("AKI Alerts", renal_filtered_aki_alerts_path(named_filter: :today))) do
+                      breadcrumbs: breadcrumb_for("AKI Alerts", renal_aki_alerts_path)) do
 
   = simple_form_for(alert, wrapper: :horizontal_form) do |f|
     = f.association :action, wrapper: :horizontal_small
@@ -17,4 +17,4 @@
     = f.input :notes, wrapper: :horizontal_large, input_html: { rows: 5 }
     = f.submit class: "button"
     span= " or "
-    = link_to "cancel", renal_filtered_aki_alerts_path(named_filter: :today)
+    = link_to "cancel", renal_aki_alerts_path

data/app/views/renalware/renal/aki_alerts/index.html.slim

@@ -3,7 +3,7 @@
   / An alternative to what we have used here is to use
   /   url_for(request.filtered_parameters&.merge({format: :pdf})
   / however this seems to loose the ransack sort option in  params[:q][:s]
-  = link_to(renal_filtered_aki_alerts_path(q: params[:q]&.permit!, format: :pdf), class: "button secondary") do
+  = link_to(renal_aki_alerts_path(q: params[:q]&.permit!, format: :pdf), class: "button secondary") do
     i.fa.fa-print
     | Print (PDF)
 

data/app/views/renalware/renal/aki_alerts/index.pdf.slim

@@ -4,11 +4,6 @@
 .pdf
   .header
     h1 AKI Alerts
-    - if params[:named_filter].present?
-      h1.muted
-        |  / 
-        = params[:named_filter]&.humanize
     h2.muted= I18n.l(Time.zone.today)
   = render "filters"
   = render "table", alerts: alerts
-

data/config/initializers/ransack.rb

@@ -7,10 +7,24 @@ Ransack.configure do |config|
 
   # Raise errors if a query contains an unknown predicate or attribute.
   # Default is true (do not raise error on unknown conditions).
-  # config.ignore_unknown_conditions = false
+  config.ignore_unknown_conditions = !Rails.env.development?
 
   # Globally display sort links without the order indicator arrow.
   # Default is false (sort order indicators are displayed).
   # This can also be configured individually in each sort link (see the README).
   # config.hide_sort_order_indicators = true
+  #
+
+  # Add a predicate to allow a datepicker for instance to find all items
+  # with a certain created_at. It ensures the datetime is resolved as a date.
+  # See
+  # - https://github.com/activerecord-hackery/ransack/issues/101
+  # - https://github.com/activerecord-hackery/ransack/wiki/Custom-Predicates
+  config.add_predicate(
+    "date_equals",
+    arel_predicate: "eq",
+    formatter: proc { |val| val&.to_date },
+    validator: proc { |val| val.present? },
+    type: :string
+  )
 end

data/config/permissions.yml

@@ -2,6 +2,8 @@ super_admin:
   - Renalware::Role
   - Renalware::Hospitals::Ward
   - Renalware::HD::Dialysate
+  - Renalware::HD::Dialyser
+  - Renalware::HD::CannulationType
 admin:
   - Renalware::User
   - Renalware::BagType
@@ -15,3 +17,4 @@ admin:
   - Renalware::PRDDescription
   - Renalware::Hospitals::Unit
   - Renalware::HD::Station
+  - Renalware::HD::TransmissionLog

data/config/routes.rb

@@ -156,6 +156,7 @@ Renalware::Engine.routes.draw do
       get "patients_dialysing_at_hospital" => "patients#dialysing_at_hospital"
     end
 
+    resources :transmission_logs, only: [:show, :index]
     resources :cannulation_types, except: :show
     resources :dialysers, except: :show
     resources :dialysates, except: :show
@@ -247,10 +248,7 @@ Renalware::Engine.routes.draw do
         get :search
       end
     end
-    resources :aki_alerts, only: [:edit, :update]
-    constraints(named_filter: /#{Renalware::Renal::AKI_ALERT_FILTERS.join("|")}/) do
-      get "aki_alerts/:named_filter", to: "aki_alerts#index", as: :filtered_aki_alerts
-    end
+    resources :aki_alerts, only: [:edit, :update, :index]
     resources :registry_preflight_checks, only: [] do
       collection do
         get :patients

data/db/migrate/20151116170200_create_transplant_versions.rb

@@ -1,9 +1,9 @@
 class CreateTransplantVersions < ActiveRecord::Migration[4.2]
   def change
     create_table :transplant_versions do |t|
-      t.string   :item_type, :null => false
-      t.integer  :item_id,   :null => false
-      t.string   :event,     :null => false
+      t.string   :item_type, null: false
+      t.integer  :item_id,   null: false
+      t.string   :event,     null: false
       t.string   :whodunnit
       t.jsonb    :object
       t.jsonb    :object_changes

data/db/migrate/20180622130552_add_external_id_to_hd_sessions.rb

@@ -0,0 +1,6 @@
+class AddExternalIdToHDSessions < ActiveRecord::Migration[5.1]
+  def change
+    add_column :hd_sessions, :external_id, :bigint
+    add_index :hd_sessions, :external_id, unique: true
+  end
+end

data/db/migrate/20180625124431_add_patient_identifier_to_feed_messages.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+
+class AddPatientIdentifierToFeedMessages < ActiveRecord::Migration[5.1]
+  def change
+    add_column :feed_messages, :patient_identifier, :string, index: true
+  end
+end

data/db/migrate/20180702091222_create_hd_providers.rb

@@ -0,0 +1,8 @@
+class CreateHDProviders < ActiveRecord::Migration[5.1]
+  def change
+    create_table "renalware.hd_providers" do |t|
+      t.string :name
+      t.timestamps null: false
+    end
+  end
+end

data/db/migrate/20180702091237_create_hd_provider_units.rb

@@ -0,0 +1,11 @@
+class CreateHDProviderUnits < ActiveRecord::Migration[5.1]
+  def change
+    create_table "renalware.hd_provider_units" do |t|
+      t.references :hospital_unit, foreign_key: true, null: false
+      t.references :hd_provider, foreign_key: true, null: false
+      t.string :providers_reference, index: true
+      t.timestamps null: false
+    end
+    add_index :hd_provider_units, [:hd_provider_id, :hospital_unit_id], unique: true
+  end
+end

data/db/migrate/20180702091352_create_hd_transmission_log.rb

@@ -0,0 +1,18 @@
+class CreateHDTransmissionLog < ActiveRecord::Migration[5.1]
+  def change
+    create_table "renalware.hd_transmission_logs" do |t|
+      t.references :parent, index: true
+      t.string :direction, null: false, index: true
+      t.string :format, null: false, index: true
+      t.string :status, index: true
+      t.references :hd_provider_unit, foreign_key: true, index: true
+      t.references :patient, foreign_key: true, index: true
+      t.string :filepath
+      t.text :payload
+      t.jsonb :result, index: { using: :gin }, default: {}
+      t.text :error_messages, array: true, default: []
+      t.datetime :transmitted_at, index: true
+      t.timestamps null: false
+    end
+  end
+end

data/db/migrate/20180730154454_add_external_session_id_to_hd_transmission_logs.rb

@@ -0,0 +1,9 @@
+class AddExternalSessionIdToHDTransmissionLogs < ActiveRecord::Migration[5.1]
+  def change
+    add_column :hd_transmission_logs,
+               :external_session_id,
+               :string,
+               index: true
+    add_reference :hd_transmission_logs, :session, index: true, null: true
+  end
+end

data/db/migrate/20180802132417_add_missing_indexes_2.rb

@@ -0,0 +1,18 @@
+class AddMissingIndexes2 < ActiveRecord::Migration[5.1]
+  def change
+    # These indexes where missed as we had used the add_column method passing in index: true
+    # but that is not supported so no index was created
+    add_index :addresses, :country_id
+    add_index :patients, :country_of_birth_id
+    add_index :patients, :sent_to_ukrdc_at
+    add_index :patients, :send_to_renalreg
+    add_index :patients, :send_to_rpv
+    add_index :patient_bookmarks, :urgent
+    add_index :letter_recipients, :emailed_at
+    add_index :letter_recipients, :printed_at
+    add_index :hospital_wards, :code
+    add_index :feed_messages, :patient_identifier
+    add_index :access_procedures, :performed_by
+    add_index :patient_ethnicities, :cfh_name
+  end
+end

data/db/migrate/20180802144507_add_missing_foreign_key_indexes.rb

@@ -0,0 +1,17 @@
+class AddMissingForeignKeyIndexes < ActiveRecord::Migration[5.1]
+  # Found using https://github.com/gregnavis/active_record_doctor
+  def change
+    add_index :drug_types_drugs, :drug_type_id
+    add_index :hd_stations, :location_id
+    add_index :letter_contacts, :patient_id
+    add_index :messaging_messages, :replying_to_message_id
+    add_index :pathology_observation_descriptions, :measurement_unit_id
+    add_index :patient_bookmarks, :user_id
+    add_index(
+      :pd_peritonitis_episode_types, :peritonitis_episode_type_description_id,
+      name: "index_pd_peritonitis_episode_types_description_id"
+    )
+    add_index :pd_pet_adequacy_results, :patient_id
+    add_index :roles_users, :role_id
+  end
+end

data/db/migrate/20180803131157_add_uuid_to_hd_transmission_logs.rb

@@ -0,0 +1,5 @@
+class AddUuidToHDTransmissionLogs < ActiveRecord::Migration[5.1]
+  def change
+    add_column :hd_transmission_logs, :uuid, :uuid, default: "uuid_generate_v4()", null: false
+  end
+end

data/db/migrate/20180814103916_create_index_on_lower_patient_family_name.rb

@@ -0,0 +1,7 @@
+class CreateIndexOnLowerPatientFamilyName < ActiveRecord::Migration[5.1]
+  def change
+    add_index :patients,
+            "lower(family_name), given_name",
+            name: "idx_patients_on_lower_family_name"
+  end
+end

data/db/migrate/20180815144429_update_hd_overall_audit_to_version_8.rb

@@ -0,0 +1,6 @@
+class UpdateHDOverallAuditToVersion8 < ActiveRecord::Migration[5.1]
+  update_view :reporting_hd_overall_audit,
+              materialized: true,
+              version: 8,
+              revert_to_version: 7
+end

data/db/views/reporting_hd_overall_audit_v08.sql

@@ -0,0 +1,46 @@
+WITH fistula_or_graft_access_types AS (
+  select id from access_types where name ilike '%fistula%' or name ilike '%graft%'
+)
+, patients_w_fistula_or_graft as (
+  select patient_id from access_profiles where type_id in (select id from  fistula_or_graft_access_types)
+),
+stats as (
+  select
+  s.patient_id,
+  s.hospital_unit_id,
+  s.month,
+  s.year,
+  s.session_count,
+  s.number_of_missed_sessions,
+  s.number_of_sessions_with_dialysis_minutes_shortfall_gt_5_pct,
+  exists(select x.patient_id from patients_w_fistula_or_graft x where x.patient_id = s.patient_id) as has_fistula_or_graft,
+  ((number_of_missed_sessions::float / NULLIF(session_count::float, 0)) * 100.0) > 10.0 as missed_sessions_gt_10_pct,
+  s.dialysis_minutes_shortfall::float,
+  convert_to_float(s.pathology_snapshot -> 'HGB' ->> 'result') > 100 as hgb_gt_100,
+  convert_to_float(s.pathology_snapshot -> 'HGB' ->> 'result') > 130 as hgb_gt_130,
+  convert_to_float(s.pathology_snapshot -> 'PTH' ->> 'result') < 300 as pth_lt_300,
+  convert_to_float(s.pathology_snapshot -> 'URR' ->> 'result') > 64 as urr_gt_64,
+  convert_to_float(s.pathology_snapshot -> 'URR' ->> 'result') > 69 as urr_gt_69,
+  convert_to_float(s.pathology_snapshot -> 'PHOS' ->> 'result') < 1.8 as phos_lt_1_8
+  from hd_patient_statistics s
+  where s.rolling is null
+)
+select
+  hu.name,
+  stats.year,
+  stats.month,
+  count(*) as patient_count,
+  round(avg(stats.dialysis_minutes_shortfall)::decimal, 2) as avg_missed_hd_time,
+  round(avg(number_of_sessions_with_dialysis_minutes_shortfall_gt_5_pct),2) as pct_shortfall_gt_5_pct,
+  round(((count(*) filter(where missed_sessions_gt_10_pct = true))::float / count(*)::float * 100)::decimal, 2) as pct_missed_sessions_gt_10_pct,
+  round(((count(*) filter(where hgb_gt_100 = true))::float / count(*)::float * 100)::decimal, 2) as percentage_hgb_gt_100,
+  round(((count(*) filter(where hgb_gt_130 = true))::float / count(*)::float * 100)::decimal, 2) as percentage_hgb_gt_130,
+  round(((count(*) filter(where pth_lt_300 = true))::float / count(*)::float * 100)::decimal, 2) as percentage_pth_lt_300,
+  round(((count(*) filter(where urr_gt_64 = true))::float / count(*)::float * 100)::decimal, 2) as percentage_urr_gt_64,
+  round(((count(*) filter(where urr_gt_69 = true))::float / count(*)::float * 100)::decimal, 2) as percentage_urr_gt_69,
+  round(((count(*) filter(where phos_lt_1_8 = true))::float / count(*)::float * 100)::decimal, 2) as percentage_phosphate_lt_1_8,
+  round(((((count(*) FILTER (WHERE (stats.has_fistula_or_graft = true)))::double precision / (count(*))::double precision) * (100)::double precision))::numeric, 2) AS percentage_access_fistula_or_graft
+  from stats
+inner join hospital_units hu on hu.id = stats.hospital_unit_id
+group by hu.name, stats.year, stats.month
+order by hu.name, stats.year asc, stats.month asc;

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.41"
+  VERSION = "2.0.42"
 end

data/lib/tasks/db.rake

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "benchmark"
 
 namespace :db do
@@ -8,4 +10,15 @@ namespace :db do
     end
     puts "Refreshing materialized views took #{ms}"
   end
+
+  namespace :demo do
+    desc "Loads demo seed data from the renalware-core gem"
+    task seed: :environment do
+      if Rails.env.development?
+        require Renalware::Engine.root.join("spec/dummy/db/seeds")
+      else
+        puts "Task currently only possible in development environment"
+      end
+    end
+  end
 end

data/lib/tasks/pathology.rake

@@ -0,0 +1,29 @@
+require "benchmark"
+
+namespace :pathology do
+  namespace :test do
+    desc "In development only, import a test HL7 message. Useful for testing listeners."
+    task import_one: :environment do
+      raise NotImplementedError unless Rails.env.development?
+
+      # Load the example HL7 file.
+      path = Renalware::Engine.root.join("app", "jobs", "hl7_message_example.yml")
+      raw_message = File.read(path)
+
+      # It has a struct header at the top so it can also be dumped into
+      # the delayed_job queue, but we want to skip queuing so strip out that header and simulate
+      # the message being passed directly to the FeedJob which will persist and process the message.
+      raw_message = raw_message.gsub("--- !ruby/struct:FeedJob\n", "")
+
+      # Replace the MSH date with now() to guarantee a unique message. not doing so results in
+      # an index violation becuase we calc am MD5 hash of the message and this has to be unique -
+      # this prevents us importing the same message twice.
+      raw_message = raw_message.gsub("20091112164645", Time.zone.now.strftime("%Y%m%d%H%M%S"))
+
+      # 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
+    end
+  end
+end

data/spec/factories/hd/transmission_logs.rb

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :hd_transmission_log, class: "Renalware::HD::TransmissionLog" do
+    trait :outgoing_hl7 do
+      direction :out
+      format :hl7
+    end
+
+    trait :incoming_xml do
+      direction :in
+      format :xml
+    end
+  end
+end

data/spec/support/capybara.rb

@@ -1,22 +1,23 @@
 # frozen_string_literal: true
 
 # # frozen_string_literal: true
+if defined?(Capybara)
+  Capybara.register_driver(:headless_chrome) do |app|
+    capabilities = Selenium::WebDriver::Remote::Capabilities.chrome(
+      chromeOptions: { args: %w(headless disable-gpu window-size=1366,1768) }
+    )
 
-Capybara.register_driver(:headless_chrome) do |app|
-  capabilities = Selenium::WebDriver::Remote::Capabilities.chrome(
-    chromeOptions: { args: %w(headless disable-gpu window-size=1366,1768) }
-  )
-
-  Capybara::Selenium::Driver.new(
-    app,
-    browser: :chrome,
-    desired_capabilities: capabilities
-  )
-end
+    Capybara::Selenium::Driver.new(
+      app,
+      browser: :chrome,
+      desired_capabilities: capabilities
+    )
+  end
 
-if RUBY_PLATFORM.match?(/darwin/)
-  Capybara::Screenshot.register_driver(:headless_chrome) do |driver, path|
-    driver.browser.save_screenshot(path)
+  if RUBY_PLATFORM.match?(/darwin/)
+    Capybara::Screenshot.register_driver(:headless_chrome) do |driver, path|
+      driver.browser.save_screenshot(path)
+    end
   end
+  Capybara.javascript_driver = :headless_chrome
 end
-Capybara.javascript_driver = :headless_chrome