renalware-core 2.0.18 → 2.0.20

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: ee61a87fbb969e571a1cd37d23446ce3d4c32ba439f768e73bcd6e1aeb2092de
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+  data.tar.gz: 57de76f0a5b9eb77cea4655a171d0b1d9c03df7d2ec525f505372e6802e6cd66b36642343601173cf78d51cf586c3509f066451fbfaa9f44139cf3a3ff39b4f4

data/app/controllers/renalware/events/events_controller.rb

@@ -108,7 +108,7 @@ module Renalware
 
       def build_new_event
         event = new_event_for_patient
-        event.date_time = Time.zone.now.beginning_of_hour
+        event.date_time = Time.zone.now
         event.event_type = event_type
         # disable_selection_of_event_type is a virtual attribute
         event.disable_selection_of_event_type = disable_selection_of_event_type?

data/app/jobs/renalware/hd/generate_monthly_statistics_job.rb

@@ -37,7 +37,7 @@ module Renalware
       end
 
       def date_falling_in_the_previous_month
-        @date ||= Time.zone.today - 1.month
+        @date_falling_in_the_previous_month ||= Time.zone.today - 1.month
       end
     end
   end

data/app/mailers/renalware/letters/delivery/errors.rb

@@ -5,7 +5,7 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     module Delivery
-      class PatientHasNoPracticeError < StandardError; end
+      class LetterIsNotApprovedOrCompletedError < StandardError; end
     end
   end
 end

data/app/mailers/renalware/letters/delivery/practice_mailer.rb

@@ -7,6 +7,8 @@ require_relative "./errors"
 module Renalware
   module Letters
     module Delivery
+      # Note PracticeMailer not the best name as we use this mailer to send a letter to any
+      # recipient (practices, hospital secretaries etc)
       class PracticeMailer < ApplicationMailer
         def patient_letter(letter:, to:)
           validate_letter(letter)
@@ -49,7 +51,9 @@ module Renalware
         end
 
         def validate_letter(letter)
-          raise Delivery::PatientHasNoPracticeError if letter.patient&.practice.blank?
+          unless letter.approved? || letter.completed?
+            raise Delivery::LetterIsNotApprovedOrCompletedError, letter.id
+          end
         end
       end
     end

data/app/models/concerns/renalware/letters/letter_pathology.rb

@@ -9,8 +9,6 @@ module Renalware
 
       # Filters a set of observations using a specific set of OBX codes
       class FilteredObservationSet
-        EMPTY_SNAPSHOT = {}.freeze
-
         def initialize(observation_set:, codes: nil)
           @codes = codes || RelevantObservationDescription.all.map(&:code)
           @observation_set = observation_set

data/app/models/renalware/admissions/consult_query.rb

@@ -24,6 +24,7 @@ module Renalware
         @search ||= begin
           Consult
             .joins(:patient)
+            .eager_load(patient: [current_modality: :description])
             .includes(
               :created_by,
               :consult_site,

data/app/models/renalware/hd/generate_monthly_statistics_for_patient.rb

@@ -24,6 +24,7 @@ module Renalware
         stats.hospital_unit = most_recently_used_hospital_unit(sessions)
         stats.assign_attributes(auditable_sessions(sessions).to_h)
         stats.session_count = sessions.length
+        stats.pathology_snapshot = capture_pathology_snapshot
         stats.save!
       end
 
@@ -43,6 +44,42 @@ module Renalware
       def most_recently_used_hospital_unit(sessions)
         sessions.last&.hospital_unit
       end
+
+      def capture_pathology_snapshot
+        FilteredObservationSet.new(patient: patient).to_h
+      end
+
+      # Filters a set of observations using a specific set of OBX codes.
+      # The snapshot is stored on the hd_patient_statistics table - i.e. it represents
+      # the state of the patient's pathology *at the time the hd_stats row is created*.
+      # So for an hd_stats row for say Patient X in the month of April 2018, the
+      # pathology_snapshot is a frozen snapshot of their pathology at 30/4/2018 23:59
+      # TODO: de-dupe this with the other FilteredObservationSet in Letters::?
+      class FilteredObservationSet
+        # These are the codes for the results we want to store in
+        # hd_patient_statics.pathology_snapshot - we are only interested in these
+        # results. They will be used for instance in reporting_hd_overall_audit
+        CODES = %w(HGB PTH PHOS CRE URE URR).freeze
+
+        def initialize(patient:)
+          @observation_set = Pathology.cast_patient(patient).fetch_current_observation_set
+        end
+
+        # Returns a hash of the filtered observations e.g.
+        # {
+        #   "HGB"=>{"result"=>"139", "observed_at"=>"2016-03-15T03:28:00"},
+        #   "URR"=>{"result"=>"49", "observed_at"=>"2016-03-15T03:28:00"},
+        #   ...
+        # }
+        def to_h
+          return {} if observation_set.blank?
+          observation_set.values.select { |code, _| CODES.include?(code.to_s) }
+        end
+
+        private
+
+        attr_reader :observation_set
+      end
     end
   end
 end

data/app/models/renalware/letters/delivery/email_letter_to_practice.rb

@@ -28,9 +28,18 @@ module Renalware
         private
 
         def email_letter_to_the_patients_practice
+          # Note we cast the letter back to the superclass Letters::Letter here to prevent
+          # GlobalID from trying to load the letter using e.g. Letters::Approved.find(123), because
+          # in the meantime the letter's class might have progressed to Letters::Completed in which
+          # case GlobalId/ ActiveJob would not be able to find the letter!
+          # Casting to Letters::Letter means in the delayed job the handler says e.g.
+          #   - letter:
+          #    _aj_globalid: gid://dummy/Renalware::Letters::Letter/3
+          # which it turns out works fine when the letter is loaded by GlobalId/ActiveJob;
+          # it correctly casts the letter to its STI type e.g. Letters::Approved in the job.
           Letter.transaction do
             PracticeMailer.patient_letter(
-              letter: letter,
+              letter: letter.becomes(Letter),
               to: practice_email_address
             ).deliver_later
 

data/app/models/renalware/renal/aki_alert_query.rb

@@ -26,6 +26,7 @@ module Renalware
           AKIAlert
             .joins(:patient) # required for PatientsRansackHelper - see Admission
             .includes(:patient, :updated_by, :action, hospital_ward: :hospital_unit)
+            .eager_load(patient: [current_modality: :description])
             .public_send(query[:named_filter].to_s)
             .ransack(query)
         end

data/app/presenters/renalware/letters/practice_email_meta_data.rb

@@ -19,6 +19,7 @@ module Renalware
     #
     class PracticeEmailMetaData
       NullPrimaryCarePhysician = Naught.build(&:define_explicit_conversions)
+      NullPractice = Naught.build(&:define_explicit_conversions)
 
       pattr_initialize [
         :letter!,
@@ -82,6 +83,10 @@ module Renalware
       def primary_care_physician
         @primary_care_physician ||= NullPrimaryCarePhysician.new
       end
+
+      def practice
+        @practice ||= NullPractice.new
+      end
     end
   end
 end

data/app/views/renalware/admissions/consults/_filters.html.slim

@@ -11,10 +11,6 @@
         = f.input :consult_site_id_eq,
                   collection: Renalware::Admissions::ConsultSite.pluck(:name, :id),
                   label: "Site"
-      .columns.medium-1.large-1
-        = f.input :requires_aki_nurse_eq,
-                  collection: [["Yes", true], ["No", false]],
-                  label: "AKI Nurse?"
       .columns.medium-2.large-1
         = f.input :seen_by_id_eq,
                   include_blank: false,
@@ -30,11 +26,6 @@
                   include_blank: true,
                   collection: [["Yes", true], ["No", false]],
                   label: "Active"
-      .columns.medium-1.large-1
-        = f.input :rrt_eq,
-                  include_blank: true,
-                  collection: [["Yes", true], ["No", false]],
-                  label: "RRT"
       .columns.medium-2.large-2.actions.end
         = f.submit "Filter", class: "button"
         span= " or "

data/app/views/renalware/admissions/consults/_table.html.slim

@@ -13,13 +13,12 @@
                                       "Location")
         th.col-width-date.noprint= sort_link(query, :started_on, "Started")
         th.col-width-date.noprint= sort_link(query, :ended_on, "Ended")
-        th.col-width-small.show-for-large-up Modality
+        th.col-width-small.show-for-large-up
+          = sort_link([:renalware, query], :patient_current_modality_description_name, "Modality")
         th.col-width-tiny.show-for-large-up Sex
         th.col-width-date.show-for-large-up= sort_link(query, :patient_born_on, "DOB")
-        th.col-width-tiny.show-for-large-up.noprint Age
-        th.col-width-tiny RRT?
+        th.col-width-tiny.show-for-large-up Age
         th.col-width-tiny.noprint= sort_link(query, :aki_risk, "AKI Risk")
-        th.col-width-tiny.noprint= sort_link(query, :requires_aki_nurse, " AKI Nurse?")
         /th.show-for-large-up Author
         /th.col-width-medium.show-for-xlarge-up Description
 
@@ -68,14 +67,12 @@
           td.show-for-large-up.col-width-medium-with-ellipsis= consult.patient_current_modality
           td.show-for-large-up= consult.patient_sex
           td.show-for-large-up= l(consult.patient.born_on)
-          td.show-for-large-up.noprint= consult.patient_age
-          td= yes_no(consult.rrt)
+          td.show-for-large-up= consult.patient_age
           td.noprint= consult.aki_risk&.text
-          td.noprint= yes_no(consult.requires_aki_nurse)
           /td.show-for-xlarge-up.consult-author.col-width-medium-with-ellipsis(title=consult.created_by)= consult.created_by
           /td.col-width-medium-with-ellipsis(title=consult.description)= consult.description
         = content_tag(:tr, id: "consult-quick-preview-#{consult.id}", style: "display: none")
-          td(colspan=12)
+          td(colspan=11)
             .quick-preview
               dl.dl-horizontal
                 dt Author

data/app/views/renalware/dashboard/bookmarks/_table.html.slim

@@ -7,7 +7,7 @@ table.auto-layout
       th.col-width-date= t(".born_on")
       th.col-width-tiny= t(".age")
       th.col-width-tiny= t(".sex")
-      th.col-width-small= t(".modality")
+      th.col-width-medium= t(".modality")
       th= t(".notes")
       th= t(".tags")
       th.col-width-date-time= t(".bookmarked_on")

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

@@ -8,6 +8,7 @@ tr(class="#{'aki_alert--hotlist' if aki_alert.hotlist?}")
               data: { behaviour: "toggler" })
   td= default_patient_link(aki_alert.patient)
   td= aki_alert.patient.hospital_identifiers
+  td.show-for-large-up.col-width-medium-with-ellipsis= aki_alert.patient.current_modality
   td= aki_alert.patient.sex
   td= aki_alert.patient.age
   td= aki_alert.action

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

@@ -1,8 +1,10 @@
 table.aki-alerts
   thead
     th.col-width-small
-    th.col-width-large Patient
+    th.col-width-large= sort_link(search, :patient_family_name, "Patient")
     th.col-width-reference-no Hosp. No.
+    th.col-width-small.show-for-large-up
+        = sort_link([:renalware, search], :patient_current_modality_description_name, "Modality")
     th.col-width-tiny Sex
     th.col-width-tiny Age
     th= sort_link(search, :action_name, "Action")

data/db/migrate/20180419141524_add_cols_to_hd_patient_statistics.rb

@@ -0,0 +1,10 @@
+class AddColsToHDPatientStatistics < ActiveRecord::Migration[5.1]
+  def change
+    add_column :hd_patient_statistics,
+               :pathology_snapshot,
+               :jsonb,
+               index: { using: :gin },
+               default: {},
+               null: false
+  end
+end

data/db/migrate/20180422090043_update_hd_overall_audit_to_version_6.rb

@@ -0,0 +1,91 @@
+# rubocop:disable Metrics/MethodLength
+class UpdateHDOverallAuditToVersion6 < ActiveRecord::Migration[5.1]
+  def change
+    update_view :reporting_hd_overall_audit,
+                materialized: true,
+                version: 6,
+                revert_to_version: 5
+
+    reversible do |direction|
+      direction.up do
+        connection.execute <<-SQL
+          update reporting_audits set display_configuration = '
+          {
+            "columnDefs": [
+              {
+                "title": "Unit",
+                "width": "300",
+                "data": "name"
+              },
+              {
+                "title": "Year",
+                "width": "100",
+                "data": "year"
+              },
+              {
+                "title": "Month",
+                "width": "100",
+                "data": "month"
+              },
+              {
+                "title": "No. patients",
+                "width": "100",
+                "data": "patient_count"
+              },
+              {
+                "title": "% HGB > 100",
+                "width": "120",
+                "data": "percentage_hgb_gt_100"
+              },
+              {
+                "title": "% HGB > 130",
+                "width": "120",
+                "data": "percentage_hgb_gt_130"
+              },
+              {
+                "title": "% Phosphate < 1.8",
+                "width": "120",
+                "data": "percentage_phosphate_lt_1_8"
+              },
+              {
+                "title": "% PTH < 300",
+                "width": "120",
+                "data": "percentage_pth_lt_300"
+              },
+              {
+                "title": "% URR > 64",
+                "width": "120",
+                "data": "percentage_urr_gt_64"
+              },
+              {
+                "title": "% URR > 69",
+                "width": "120",
+                "data": "percentage_urr_gt_69"
+              },
+              {
+                "title": "% w/fistula or graft",
+                "width": "120",
+                "data": "percentage_access_fistula_or_graft"
+              },
+              {
+                "title": "Avg. missed HD time",
+                "width": "120",
+                "data": "avg_missed_hd_time"
+              },
+              {
+                "title": "% sessions >5% dialysis time missed",
+                "width": "200",
+                "data": "pct_missed_sessions_gt_10_pct"
+              },
+              {
+                "title": "% missing >10% HD sessions",
+                "width": "150",
+                "data": "pct_shortfall_gt_5_pct"
+              }
+            ]
+          }';
+        SQL
+      end
+    end
+  end
+end

data/db/seeds/default/reporting/audits.yml

@@ -84,6 +84,16 @@
           "width": "300",
           "data": "name"
         },
+        {
+          "title": "Year",
+          "width": "100",
+          "data": "year"
+        },
+        {
+          "title": "Month",
+          "width": "100",
+          "data": "month"
+        },
         {
           "title": "No. patients",
           "width": "120",
@@ -92,18 +102,33 @@
         {
           "title": "% HGB > 100",
           "width": "120",
-          "data": "percentage_hb_gt_100"
+          "data": "percentage_hgb_gt_100"
         },
         {
-          "title": "% URR > 65",
+          "title": "% HGB > 130",
           "width": "120",
-          "data": "percentage_urr_gt_65"
+          "data": "percentage_hgb_gt_130"
         },
         {
           "title": "% Phosphate < 1.8",
           "width": "200",
           "data": "percentage_phosphate_lt_1_8"
         },
+        {
+          "title": "% PTH < 300",
+          "width": "200",
+          "data": "percentage_pth_lt_300"
+        },
+        {
+          "title": "% URR > 64",
+          "width": "120",
+          "data": "percentage_urr_gt_64"
+        },
+        {
+          "title": "% URR > 69",
+          "width": "120",
+          "data": "percentage_urr_gt_69"
+        },
         {
           "title": "% w/fistula or graft",
           "width": "200",
@@ -115,9 +140,9 @@
           "data": "avg_missed_hd_time"
         },
         {
-          "title": "% missing >5% HD time",
+          "title": "% missing >10% HD time",
           "width": "200",
-          "data": "pct_shortfall_gt_5_pct"
+          "data": "pct_shortfall_gt_10_pct"
         }
       ]
     }

data/db/views/reporting_hd_overall_audit_v06.sql

@@ -0,0 +1,44 @@
+with fistula_or_graft_access_types as (
+    select id
+    from access_types
+    where name ilike '%fistula%' or name ilike '%graft%'
+),
+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,
+  ((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,
+  avg(stats.dialysis_minutes_shortfall) as avg_missed_hd_time,
+  avg(number_of_sessions_with_dialysis_minutes_shortfall_gt_5_pct) as pct_shortfall_gt_5_pct,
+  (count(*) filter(where missed_sessions_gt_10_pct = true))::float / count(*)::float * 100 as pct_missed_sessions_gt_10_pct,
+  (count(*) filter(where hgb_gt_100 = true))::float / count(*)::float * 100 as percentage_hgb_gt_100,
+  (count(*) filter(where hgb_gt_130 = true))::float / count(*)::float * 100 as percentage_hgb_gt_130,
+  (count(*) filter(where pth_lt_300 = true))::float / count(*)::float * 100 as percentage_pth_lt_300,
+  (count(*) filter(where urr_gt_64 = true))::float / count(*)::float * 100 as percentage_urr_gt_64,
+  (count(*) filter(where urr_gt_69 = true))::float / count(*)::float * 100 as percentage_urr_gt_69,
+  (count(*) filter(where phos_lt_1_8 = true))::float / count(*)::float * 100 as percentage_phosphate_lt_1_8,
+  'TBC' 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 = "2.0.18"
+  VERSION = "2.0.20"
 end

data/lib/tasks/ukrdc.rake

@@ -1,16 +1,43 @@
 require "fileutils"
 require "gpgme"
 
-# Need to bear in mind we if we find a patient with changes, we still don't take everything
-# the patient has but only those bits modified since the last export or :since_date
-#
+# Note you can print out the help for this task and others with `rake -D`
 namespace :ukrdc do
-  desc "Creates a folder of UKRDC XML files containing any changes to PV patients since "\
-       "their last export"
-  task :export, [:changed_since, :patient_ids] => [:environment] do |t, args|
+  desc <<-DESC
+    Creates a folder of UKRDC XML files with any changes to PV patients since their last export
+    Notes:
+      1. Running the rake task updates the sent_to_ukrdc_at for each patient exported.
+         If you don't want to do this you may need to edit this task to wrpt the code in a
+         transaction you can optionally roll back.
+     2: If testing this inside the renalware-core gem, you will need to append app: e.g.
+        app:ukrdc:export ...
+
+    Example usage
+      1. To get all patients with send_to_rpv=true who have changed since the last time they
+         were sent, or have not been sent to the UKRDC yet:
+
+         bundle exec rake ukrdc:export
+
+      2. To get all patients with send_to_rpv=true who have changed since a certain date:
+
+         bundle exec rake ukrdc:export["2018-02-23"]
+         or in zsh shell
+         bundle exec rake ukrdc:export\["2018-02-23"\]
+
+      3. To get only certain RPV patients (by their id eg ids 1 and 2) who with changes since
+         a certain time (not pass patient ids in a space delimited string:
+
+         bundle exec rake ukrdc:export["2018-02-23","1 2"]
+         or in the zsh shell
+         bundle exec rake ukrdc:export\["2018-02-23","1 2"\]
+  DESC
+  task :export, [:changed_since, :patient_ids] => [:environment] do |_task, args|
     logger           = Logger.new(STDOUT)
     logger.level     = Logger::INFO
     Rails.logger     = logger
-    Renalware::UKRDC::SendPatients.new(**args.to_h).call
+    Renalware::UKRDC::SendPatients.new(
+      changed_since: args[:changed_since],
+      patient_ids: args.fetch(:patient_ids, "").split(" ").map(&:to_i)
+    ).call
   end
 end

data/spec/factories/hd/patient_statistics.rb

@@ -4,7 +4,26 @@ FactoryBot.define do
   factory :hd_patient_statistics, class: "Renalware::HD::PatientStatistics" do
     patient factory: :hd_patient
     association :hospital_unit, factory: :hospital_unit
-    month 0 # rolling
-    year 0  # rolling
+    month 1
+    year 2018
+    # rolling false
+    pre_mean_systolic_blood_pressure 0
+    pre_mean_diastolic_blood_pressure 0
+    post_mean_systolic_blood_pressure 0
+    post_mean_diastolic_blood_pressure 0
+    lowest_systolic_blood_pressure 0
+    highest_systolic_blood_pressure 0
+    mean_fluid_removal 0
+    mean_weight_loss 0
+    mean_machine_ktv 0
+    mean_blood_flow 0
+    mean_litres_processed 0
+    session_count 0
+    number_of_missed_sessions 0
+    dialysis_minutes_shortfall 0
+    dialysis_minutes_shortfall_percentage 0
+    mean_ufr 0
+    mean_weight_loss_as_percentage_of_body_weight 0
+    number_of_sessions_with_dialysis_minutes_shortfall_gt_5_pct 0
   end
 end

data/spec/factories/pathology/observation_descriptions.rb

@@ -15,5 +15,12 @@ FactoryBot.define do
     display_order 1
     letter_group 1
     letter_order 1
+
+    %i(urr ure hgb cre phos pth).each do |code|
+      trait code do
+        code code.to_s.upcase
+        name code.to_s.upcase
+      end
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.18
+  version: 2.0.20
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-04-24 00:00:00.000000000 Z
+date: 2018-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -3213,6 +3213,8 @@ files:
 - db/migrate/20180326155400_add_admin_notes_to_system_user_feedback.rb
 - db/migrate/20180327100423_add_constraints_to_recipient_operations.rb
 - db/migrate/20180328210434_add_rrt_to_admission_consults.rb
+- db/migrate/20180419141524_add_cols_to_hd_patient_statistics.rb
+- db/migrate/20180422090043_update_hd_overall_audit_to_version_6.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3315,6 +3317,7 @@ files:
 - db/views/reporting_hd_overall_audit_v02.sql
 - db/views/reporting_hd_overall_audit_v04.sql
 - db/views/reporting_hd_overall_audit_v05.sql
+- db/views/reporting_hd_overall_audit_v06.sql
 - db/views/reporting_main_authors_audit_v01.sql
 - db/views/reporting_main_authors_audit_v02.sql
 - db/views/reporting_pd_audit_v01.sql