renalware-core 2.0.25 → 2.0.26

data/app/models/renalware/pathology/adjust_observation.rb

@@ -0,0 +1,72 @@
+require_dependency "renalware/pathology"
+require "attr_extras"
+
+module Renalware
+  module Pathology
+    # A utility class used for example by the host app to provide a generic way of adjusting
+    # an observation, usually in a Wisper listener on receipt of a broadcast pathology message
+    # probably 'after_observation_request_persisted'.
+    #
+    # Example usage:
+    #
+    # # Subscribe our class to pathology messages.
+    # Renalware.configure do |config|
+    #   map = config.broadcast_subscription_map
+    #   map["Renalware::Pathology::CreateObservationRequests"] << "MyListener"
+    # end
+    #
+    # class MyListener
+    #   def after_observation_request_persisted(observation_request)
+    #     service = Renalware::Pathology::AdjustObservation.new(
+    #       observation_request: observation_request,
+    #       code: "EGFR",
+    #       policy: ->(patient, observation){
+    #         .. some logic returning true or false to indicate to adjust or not
+    #       }
+    #     )
+    #     service.call do |egfr_observation_requiring_adjustment|
+    #       egfr_observation_requiring_adjustment.result += 1 or whatever
+    #       egfr_observation_requiring_adjustment.comment = "adjusted (original = 123)"
+    #       egfr_observation_requiring_adjustment.save!
+    #     end
+    #   end
+    # end
+    class AdjustObservation
+      pattr_initialize [:observation_request!, :code!, :policy!]
+      delegate :patient, to: :observation_request
+
+      # Will yield the requested observation if one found - the caller is responsible for
+      # making and saving the adjustment.
+      def call
+        return unless request_has_the_relevant_observation?
+        return if observation_result_is_zero?
+        return unless adjustment_required?
+
+        yield observation
+      end
+
+      def request_has_the_relevant_observation?
+        observation.present?
+      end
+
+      def observation_result_is_zero?
+        observation.result.to_f.zero?
+      end
+
+      def adjustment_required?
+        policy.call(patient, observation)
+      end
+
+      def observation
+        @observation ||= begin
+          observation_request
+            .observations
+            .joins(:description)
+            .find_by(
+              pathology_observation_descriptions: { code: code }
+            ) || Renalware::NullObject.instance
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/pathology/create_observation_requests.rb

@@ -10,11 +10,15 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class CreateObservationRequests
+      include Wisper::Publisher
+
       def call(params)
         Array(params).each do |request|
           patient = find_patient(request.fetch(:patient_id))
           observation_params = request.fetch(:observation_request)
-          patient.observation_requests.create!(observation_params)
+          broadcast :before_observation_request_persisted, observation_params
+          obr = patient.observation_requests.create!(observation_params)
+          broadcast :after_observation_request_persisted, obr
         end
       end
 

data/app/models/renalware/pathology/message_listener.rb

@@ -9,6 +9,7 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class MessageListener
+      # Note: We are already inside a transaction here
       def message_processed(message_payload)
         pathology_params = parse_pathology_params(message_payload)
         create_observation_requests_and_their_child_observations_from(pathology_params)

data/app/models/renalware/pathology/observation_requests_attributes_builder.rb

@@ -9,7 +9,7 @@ module Renalware
     # Note:
     # - A message can have multiple observation_requests, each with its own observations.
     # - This class could be removed and a Builder class used to create the database models
-    # directly - this would remove the extra level of indirection that this class introduces.
+    #   directly - this would remove the extra level of indirection that this class introduces.
     class ObservationRequestsAttributesBuilder
       DEFAULT_REQUESTOR_NAME = "UNKNOWN"
       delegate :patient_identification, :observation_requests, to: :message_payload
@@ -87,10 +87,14 @@ module Renalware
 
       def find_request_description(code)
         RequestDescription.find_by!(code: code)
+      rescue ActiveRecord::RecordNotFound
+        raise MissingRequestDescriptionError, code
       end
 
       def find_observation_description(code)
         ObservationDescription.find_by!(code: code)
+      rescue ActiveRecord::RecordNotFound
+        raise MissingObservationDescriptionError, code
       end
 
       def validate_observation(observation, observation_description)

data/app/models/renalware/pathology/observations_grouped_by_date_query.rb

@@ -68,7 +68,7 @@ module Renalware
       def to_sql
         <<-SQL.squish
           select obs_req.patient_id, cast(observed_at as date) as observed_on,
-          jsonb_object_agg(obs_desc.code, obs.result) results
+          jsonb_object_agg(obs_desc.code, ARRAY[obs.result, obs.comment]) results
           from pathology_observations obs
           inner join pathology_observation_requests obs_req on obs.request_id = obs_req.id
           inner join pathology_observation_descriptions obs_desc on obs.description_id = obs_desc.id

data/app/models/renalware/pathology/observations_grouped_by_date_table.rb

@@ -41,6 +41,10 @@ module Renalware
         @rows ||= relation.all.map(&:with_indifferent_access).map { |row| Row.new(row) }
       end
 
+      # Each row wraps a PGResult (database row).
+      # Each row is all the pathology results for this patient on a particular day.
+      # Hence there is one observed_on date but multiple results which are the columns going across
+      # the table.
       class Row
         pattr_initialize :row
 
@@ -49,11 +53,21 @@ module Renalware
         end
 
         def result_for(code)
-          results[code&.to_sym]
+          row_hash[code&.to_sym]&.first
         end
 
-        def results
-          @results = JSON.parse(row[:results]).with_indifferent_access
+        def comment_for(code)
+          row_hash[code&.to_sym]&.last
+        end
+
+        # A hash keyed by OBX code, containing an array of [result, comment] arrays, e.g.
+        #
+        #  { "HGB": [[123,nil],[124,'Some comment about the result',[..]], "PLT": [..] }
+        #
+        # This is a compressed format (as opposed to returning more verbose json) to
+        # improve performance. Just remember that for any result, its an array of [result, comment]
+        def row_hash
+          @row_hash = JSON.parse(row[:results]).with_indifferent_access
         end
       end
     end

data/app/models/renalware/pathology.rb

@@ -19,5 +19,8 @@ module Renalware
     def configure
       SubscriptionRegistry.instance.register(Feeds::MessageProcessor, MessageListener)
     end
+
+    class MissingRequestDescriptionError < StandardError; end
+    class MissingObservationDescriptionError < StandardError; end
   end
 end

data/app/models/renalware/system/message.rb

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    class Message < ApplicationRecord
+      extend Enumerize
+      validates :body, presence: true
+      validates :display_from, timeliness: { type: :datetime }, presence: true
+      validates :display_until,
+                timeliness: { type: :datetime, allow_blank: true, after: :display_from }
+      enumerize :severity, in: %i(default warning info success)
+
+      scope :active, lambda{
+        where(
+          "display_from <= ? and (display_until is null or display_until >= ?)",
+          Time.zone.now,
+          Time.zone.now
+        )
+      }
+
+      # Return true if the message should be visible.
+      # A message is visible if display_from is in the past and display_until is nil
+      # or in the future
+      def active?
+        return false if display_from.nil?
+        now = Time.zone.now
+        self.display_until ||= far_future_date
+        return true if display_from < now && display_until > now
+        false
+      end
+
+      private
+
+      def far_future_date
+        Time.zone.parse("2999-01-01 00:00:01")
+      end
+    end
+  end
+end

data/app/policies/renalware/system/message_policy.rb

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/snippets"
+
+module Renalware
+  module System
+    class MessagePolicy < BasePolicy
+      def new?
+        user_is_super_admin?
+      end
+
+      def create?
+        user_is_super_admin?
+      end
+
+      def destroy?
+        user_is_super_admin?
+      end
+    end
+  end
+end

data/app/views/renalware/admin/cache/show.html.slim

@@ -34,8 +34,8 @@
       |  source for PDF letters, rather a volatile cache to aid performance. EPR should be the place
       |  to look for letter content - or just view the PDF through the UI.
     p
-      | You may wish to clear the PDF Letter Cache if you notice any anomalies in the PDFs. Please
-      | raise a GitHub issue after clearing the cache so we can look into it.
+      | You may wish to clear the PDF Letter Cache if you notice any anomalies in the PDFs.
+      |  Please raise a GitHub issue after clearing the cache so we can look into it.
 
   = link_to "Clear the PDF Letter Cache",
             letters_pdf_letter_cache_path,

data/app/views/renalware/devise/sessions/new.html.slim

@@ -2,6 +2,7 @@
   .row.small-8.large-12
     h3 Log in to Renalware
 
+    = render "renalware/system/messages/list"
     = render "warning"
 
   .row.small-6.large-3

data/app/views/renalware/hospitals/units/index.html.slim

@@ -14,7 +14,7 @@
         th.col-width-small NRD Code
         th.col-width-small HD Site?
         th.col-width-tiny Stations
-        th.col-width-medium
+        th.col-width-largish
     tbody
       - hospital_units.each do |unit|
         tr
@@ -36,3 +36,5 @@
             = link_to("HD Stations", hd_unit_stations_path(unit))
             = pipe_separator
             = link_to("HD Diaries", hd_unit_diaries_path(unit))
+            = pipe_separator
+            = link_to("Wards", hospitals_unit_wards_path(unit))

data/app/views/renalware/hospitals/wards/_form.html.slim

@@ -0,0 +1,3 @@
+= f.input :code, wrapper: :horizontal_small
+= f.input :name, wrapper: :horizontal_medium
+= f.submit class: :button

data/app/views/renalware/hospitals/wards/edit.html.slim

@@ -0,0 +1,12 @@
+= within_admin_layout(title: "Edit", breadcrumbs: [ \
+      breadcrumb_for(ward.hospital_unit.name, hospitals_units_path),
+      breadcrumb_for("Wards", hospitals_unit_wards_path(ward.hospital_unit)) \
+  ]) do
+
+  = simple_form_for ward,
+        url: hospitals_unit_ward_path(ward.hospital_unit, ward),
+        html: { autocomplete: "off" },
+        as: :ward,
+        wrapper: "horizontal_form" do |f|
+
+      = render "form", f: f

data/app/views/renalware/hospitals/wards/index.html.slim

@@ -0,0 +1,27 @@
+= content_for(:actions) do
+  = link_to "Add",
+          new_hospitals_unit_ward_path(unit),
+          class: "button"
+
+= within_admin_layout(title: "Wards", breadcrumbs: \
+    breadcrumb_for(unit.name, hospitals_units_path)) do
+
+  table.hospital-wards
+    thead
+      th.col-width-tiny
+      th.col-width-medium Code
+      th Name
+    tbody
+      - wards.each do |ward|
+        tr
+          td
+            - if policy(ward).edit?
+              = link_to "Edit", edit_hospitals_unit_ward_path(unit, ward)
+            - if policy(ward).destroy?
+              = pipe_separator
+              = link_to "Delete",
+                        hospitals_unit_ward_path(unit, ward),
+                        method: :delete,
+                        data: { confirm: "Are you sure?" }
+          td= ward.code
+          td= ward.name

data/app/views/renalware/hospitals/wards/new.html.slim

@@ -0,0 +1,12 @@
+= within_admin_layout(title: "New", breadcrumbs: [ \
+      breadcrumb_for(ward.hospital_unit.name, hospitals_units_path),
+      breadcrumb_for("Wards", hospitals_unit_wards_path(ward.hospital_unit)) \
+  ]) do
+
+  = simple_form_for ward,
+        url: hospitals_unit_wards_path(unit_id: ward.hospital_unit.id),
+        html: { autocomplete: "off" },
+        as: :ward,
+        wrapper: "horizontal_form" do |f|
+
+      = render "form", f: f

data/app/views/renalware/letters/formatted_letters/_letter.html.slim

@@ -154,6 +154,9 @@ scss:
 
     .allergies {
       margin-bottom: 1rem;
+      float: left;
+      clear: left;
+      width: 50%;
 
       h3 {
         padding-right: 1rem;
@@ -220,6 +223,7 @@ scss:
     .message {
       margin-top: 30px;
       margin-bottom: 20px;
+      clear: both;
 
       p {
         margin-bottom: 15px;

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

@@ -9,3 +9,4 @@ li.has-dropdown
     li= link_to "Cache", admin_cache_path
     li= link_to "File Imports", admin_feeds_files_path
     li= link_to "User Feedback", system_user_feedback_index_path
+    li= link_to "System Messages", system_messages_path

data/app/views/renalware/pathology/historical_observation_results/_table.html.slim

@@ -7,7 +7,12 @@ table#observations
   tbody
     - table.rows.each do |row|
       tr
-        td.date= l(row.observed_on)
+        th.date= l(row.observed_on)
         - table.observation_descriptions.each do |desc|
           - code = desc.code
-          td(class=code.downcase)= row.result_for(code)
+          - if row.comment_for(code).present?
+            td(class=code.downcase data-balloon=row.comment_for(code) data-balloon-pos="up")
+              .triangle-top-right
+              = row.result_for(code)
+          - else
+            td(class=code.downcase)= row.result_for(code)

data/app/views/renalware/pathology/historical_observation_results/index.html.slim

@@ -2,11 +2,9 @@
                         navigation_partial: "renalware/pathology/navigation" do
   - if table.rows.empty?
     p No results available for this patient.
-
   - else
-    p.hint Hover over table then scroll horizontally to view more results.
-
     .embedded-scroll
+      p.hint Hover over table then scroll horizontally to view more results.
       = render "table", table: table
 
     = paginate(table)

data/app/views/renalware/pathology/recent_observation_results/_table.html.slim

@@ -2,17 +2,25 @@
 / historical results, we transpose the cols and rows so we have
 / dates along the top and OBX codes down the left.
 table#observations
-  tr
-    th Year
-    - table.rows.each do |row|
-      th.date= row.observed_on.year
-  tr
-    th Date
-    - table.rows.each do |row|
-      th= row.observed_on.strftime("%d/%m")
-  - table.observation_descriptions.each do |desc|
-    - code = desc.code
+  thead
     tr
-      th(title=desc.name)= code
+      th Year
       - table.rows.each do |row|
-        td(class=code.downcase)= row.results[code]
+        th.date= row.observed_on.year
+  thead
+    tr
+      th Date
+      - table.rows.each do |row|
+        th= row.observed_on.strftime("%d/%m")
+  tbody
+    - table.observation_descriptions.each do |desc|
+      - code = desc.code
+      tr
+        th(title=desc.name)= code
+        - table.rows.each do |row|
+          - if row.comment_for(code).present?
+            td(class=code.downcase data-balloon=row.comment_for(code) data-balloon-pos="up")
+              .triangle-top-right
+              = row.result_for(code)
+          - else
+            td(class=code.downcase)= row.result_for(code)

data/app/views/renalware/system/messages/_form.html.slim

@@ -0,0 +1,18 @@
+- severities = Renalware::System::Message.severity.values.map{|val| [val&.humanize, val] }
+= simple_form_for(message,
+                  as: :message,
+                  html: { autocomplete: "off" }) do |f|
+
+  = render "renalware/shared/errors", model: f.object
+
+  = f.input :title, placeholder: "An optional title"
+  = f.trix_editor :body, wrapper: :horizontal_large
+  br
+  = f.input :severity,
+            collection: severities,
+            input_html: { style: "width:100px" },
+            include_blank: nil
+  = f.input :display_from, as: :datetime_picker
+  = f.input :display_until, as: :datetime_picker
+  br
+  = f.submit "Save", class: :button

data/app/views/renalware/system/messages/_list.html.slim

@@ -0,0 +1,4 @@
+- messages = Renalware::System::Message.active
+- return if messages.empty?
+.system-messages
+  = render messages

data/app/views/renalware/system/messages/_message.html.slim

@@ -0,0 +1,4 @@
+div.system-message.alert-box.radius(class=message.severity)
+  - if message.title.present?
+    h1= message.title
+  = simple_format(message.body)

data/app/views/renalware/system/messages/edit.html.slim

@@ -0,0 +1,3 @@
+= within_admin_layout(title: "Edit",
+  breadcrumbs: breadcrumb_for("System Messages", system_messages_path)) do
+  = render "form", message: message

data/app/views/renalware/system/messages/index.html.slim

@@ -0,0 +1,30 @@
+= content_for(:actions) do
+  = link_to "Add", new_system_message_path, class: :button
+
+= within_admin_layout(title: "System Messages") do
+  .system-messages
+    table
+      thead
+        th
+        th
+        th.col-width-tiny Severity
+        th.col-width-date-time Display from
+        th.col-width-date-time Display until
+        th.col-width-tiny Active now
+      tbody
+        - messages.each do |message|
+          tr
+            td
+              = link_to "Edit", edit_system_message_path(message)
+              = pipe_separator
+              = link_to "Delete",
+                        system_message_path(message),
+                        method: :delete,
+                        data: { confirm: I18n.t("prompts.confirm_delete") }
+            td
+              = render message
+            /td= simple_format(message.body)
+            td= message.severity&.humanize
+            td= l(message.display_from)
+            td= l(message.display_until)
+            td= yes_no(message.active?)

data/app/views/renalware/system/messages/new.html.slim

@@ -0,0 +1,3 @@
+= within_admin_layout(title: "New",
+    breadcrumbs: breadcrumb_for("System Messages", system_messages_path)) do
+  = render "form", message: message

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

@@ -8,10 +8,10 @@
   .columns.small-12.medium-4
     = render "measurements", mdm: mdm
 .row
-  .columns.medium-12.large-6
+  .columns.medium-12
     = render "clinic_visits", mdm: mdm
 
-  .columns.medium-12.large-6
+  .columns.medium-12.large-4
     = render "biopsies", mdm: mdm
 .row
   .columns.medium-12.large-12

data/config/initializers/renalware.rb

@@ -11,7 +11,8 @@ Renalware.configure do |config|
       "Renalware::Letters::PatientListener",
       "Renalware::HD::PatientListener"
     ],
-    "Renalware::Letters::ApproveLetter" => []
+    "Renalware::Letters::ApproveLetter" => [],
+    "Renalware::Pathology::CreateObservationRequests" => []
   }
 end
 

data/config/permissions.yml

@@ -1,5 +1,6 @@
 super_admin:
   - Renalware::Role
+  - Renalware::Hospitals::Ward
 admin:
   - Renalware::User
   - Renalware::BagType

data/config/routes.rb

@@ -178,6 +178,7 @@ Renalware::Engine.routes.draw do
 
   namespace :hospitals do
     resources :units, except: :show do
+      resources :wards
       scope format: true, constraints: { format: :json } do
         resources :wards, only: :index
       end
@@ -267,6 +268,7 @@ Renalware::Engine.routes.draw do
   namespace :system do
     resources :email_templates, only: :index
     resources :user_feedback, except: :destroy, controller: "user_feedback"
+    resources :messages
   end
 
   namespace :transplants do

data/db/migrate/20180514151627_create_system_messages.rb

@@ -0,0 +1,13 @@
+class CreateSystemMessages < ActiveRecord::Migration[5.1]
+  def change
+    create_table :system_messages do |t|
+      t.string :title, null: true
+      t.text :body, null: false
+      t.integer :message_type, null: false, default: 0
+      t.string :severity
+      t.datetime :display_from, null: false
+      t.datetime :display_until
+      t.timestamps null: false
+    end
+  end
+end

data/db/migrate/20180516111411_create_view_patient_current_modalities.rb

@@ -0,0 +1,5 @@
+class CreateViewPatientCurrentModalities < ActiveRecord::Migration[5.1]
+  def change
+    create_view :patient_current_modalities
+  end
+end

data/db/views/patient_current_modalities_v01.sql

@@ -0,0 +1,16 @@
+select
+  patients.id as patient_id,
+  patients.secure_id as patient_secure_id,
+  current_modality.id as modality_id,
+  modality_descriptions.id as modality_description_id,
+  modality_descriptions.name as modality_name,
+  current_modality.started_on as started_on
+from patients
+  -- this join only required as currently there can be > 1 current modality for a patient
+  -- here we select the current modality with the most recent started_on
+  left outer join (
+    select distinct on (patient_id) * from modality_modalities
+    order by patient_id, started_on desc
+) as current_modality
+on patients.id = current_modality.patient_id
+left outer join modality_descriptions on modality_descriptions.id = current_modality.description_id;

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.25"
+  VERSION = "2.0.26"
 end

data/spec/factories/system/messages.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :system_message, class: "Renalware::System::Message" do
+    title "Test title"
+    body "Test body"
+    display_from { Time.zone.now }
+  end
+end