renalware-core 2.0.0.pre.rc1 → 2.0.0.pre.rc3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 661e00b27713f1b17a461bfff57e9afda54ce746
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+  data.tar.gz: cdcad7175c0fe8258a43f4dced4e0d3f159683bc
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+  data.tar.gz: a06f5d25faccc97b6374a910b9d3cd4ecf8c23a493bf329dc85e3ab8920cd0c203fbfecb251d60c3ac833b7dce6adb510a7fbf54db9403807c2eab14bbbc6abe

data/app/assets/stylesheets/renalware/modules/_dashboard.scss

@@ -1,13 +1,14 @@
 .dashboard-content {
   margin-top: 10px;
 
-  section {
-    // TODO: Style sections
-  }
-
   p.empty-section {
     padding-left: 0;
     color: $dashboard-muted-color;
     clear: both;
   }
 }
+
+.dashboard-owner {
+  color: $mid-grey;
+  font-style: normal;
+}

data/app/controllers/renalware/admin/users_controller.rb

@@ -3,10 +3,14 @@ module Renalware
     include Renalware::Concerns::Pageable
 
     def index
-      search = User.search(params[:q])
+      query = params.fetch(:q, {})
+      query[:s] ||= "family_name"
+      search = User
+        .where.not(username: :systemuser)
+        .search(query)
       users = search.result(distinct: true).page(page).per(per_page)
       authorize users
-      render locals: { users: users }
+      render locals: { users: users, user_search: search }
     end
 
     def edit

data/app/controllers/renalware/admissions/consults_controller.rb

@@ -70,7 +70,7 @@ module Renalware
         params
           .require(:admissions_consult)
           .permit(
-            :hospital_unit_id, :hospital_ward_id, :patient_id, :q,
+            :consult_site_id, :hospital_ward_id, :patient_id, :q, :other_site_or_ward,
             :decided_on, :transferred_on, :started_on, :ended_on, :decided_on,
             :aki_risk, :transfer_priority, :seen_by_id, :consult_type,
             :requires_aki_nurse, :description, :contact_number

data/app/controllers/renalware/letters/contacts_controller.rb

@@ -38,7 +38,10 @@ module Renalware
       end
 
       def find_contacts
-        CollectionPresenter.new(@patient.contacts.includes(:description).ordered, ContactPresenter)
+        CollectionPresenter.new(
+          @patient.contacts.includes(:description).ordered,
+          ContactPresenter
+        )
       end
 
       def find_contact_descriptions

data/app/controllers/renalware/pathology/current_observation_results_controller.rb

@@ -3,18 +3,12 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class CurrentObservationResultsController < Pathology::BaseController
-      before_action :load_patient
-
       def index
-        table_view = CurrentObservationResults::HTMLTableView.new(view_context)
-        presenter = CurrentObservationResults::Presenter.new
-        service = ViewCurrentObservationResults.new(@patient, presenter)
-        service.call
-
-        render :index, locals: {
-          rows: presenter.view_model,
-          table: table_view
-        }
+        patient = load_patient
+        observation_set = ObservationSetPresenter.new(
+          patient.fetch_current_observation_set
+        )
+        render :index, locals: { observation_set: observation_set }
       end
     end
   end

data/app/controllers/renalware/research/study_participants_controller.rb

@@ -52,7 +52,7 @@ module Renalware
       private
 
       def participants
-        @participants ||= study.participants.page(page).per(per_page)
+        @participants ||= study.participants.includes(:patient).page(page).per(per_page)
       end
 
       def render_edit(participant)

data/app/helpers/renalware/dashboards_helper.rb

@@ -0,0 +1,10 @@
+module Renalware
+  module DashboardsHelper
+    def composed_dashboard_title(user_name)
+      capture do
+        concat content_tag(:span, I18n.t("renalware.dashboard.dashboards.title"))
+        concat content_tag(:span, user_name, class: "dashboard-owner")
+      end
+    end
+  end
+end

data/app/helpers/renalware/layout_helper.rb

@@ -1,8 +1,10 @@
 module Renalware
   module LayoutHelper
+    # If you don't want the title argument to be used in the browser bar, pass in
+    # page_title: in opts also.
     def within_admin_layout(title: nil, **opts)
       within_layout(layout: "renalware/layouts/non_patient",
-                    title: title,
+                    title: opts.fetch(:page_title, title),
                     **opts) { yield }
     end
 

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

@@ -0,0 +1,20 @@
+require_dependency "renalware/letters"
+
+module Renalware
+  module Letters
+    module LetterPathology
+      extend ActiveSupport::Concern
+
+      # Update a letter's pathology snapshot to the current point in time
+      def build_pathology_snapshot(patient, letter)
+        return if patient.current_observation_set.nil?
+        possible_letter_codes = Renalware::Letters::RelevantObservationDescription.all.map(&:code)
+        letter.pathology_snapshot = begin
+          patient.current_observation_set.values.select do |code, _|
+            possible_letter_codes.include?(code.to_s)
+          end
+        end
+      end
+    end
+  end
+end

data/app/models/concerns/renalware/patient_pathology_scopes.rb

@@ -6,8 +6,8 @@ require_dependency "renalware"
 #
 module Renalware
   module PatientPathologyScopes
-    def with_current_key_pathology
-      includes(:current_key_observation_set).joins(:current_key_observation_set)
+    def with_current_pathology
+      includes(:current_observation_set)
     end
 
     # Define some ransackers to make it easier to sort the table (using sort_link)
@@ -23,17 +23,25 @@ module Renalware
     #
     def self.extended(base)
       %i(hgb ure cre).each do |code|
-        base.ransacker(code) { pathology_sort_predicate("#{code}_result") }
-        base.ransacker(:"#{code}_date") { pathology_sort_predicate("#{code}_observed_at") }
+        base.ransacker(code) { pathology_result_sort_predicate(code) }
+        base.ransacker(:"#{code}_date") { pathology_date_sort_predicate(code) }
       end
 
       %i(mdrd).each do |code|
-        base.ransacker(code) { pathology_sort_predicate("#{code}_result") }
+        base.ransacker(code) { pathology_result_sort_predicate(code) }
       end
     end
 
-    def self.pathology_sort_predicate(column)
-      Arel.sql("pathology_current_key_observation_sets.#{column}")
+    def self.pathology_result_sort_predicate(column)
+      Arel.sql(
+        "cast(values -> '#{column.upcase}' ->> 'result' as float)"
+      )
+    end
+
+    def self.pathology_date_sort_predicate(column)
+      Arel.sql(
+        "cast(values -> '#{column.upcase}' ->> 'observed_at' as date)"
+      )
     end
   end
 end

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

@@ -7,14 +7,15 @@ module Renalware
       extend Enumerize
       acts_as_paranoid
       validates :patient_id, presence: true
-      validates :hospital_unit_id, presence: true
-      validates :hospital_ward_id, presence: true
       validates :started_on, presence: true
       validates :description, presence: true
       validates :consult_type, presence: true
+      validates :other_site_or_ward, presence: {
+        if: ->(consult){ consult.consult_site_id.blank? && consult.hospital_ward_id.blank? }
+      }
 
       belongs_to :patient
-      belongs_to :hospital_unit, class_name: "Hospitals::Unit"
+      belongs_to :consult_site, class_name: "Admissions::ConsultSite"
       belongs_to :hospital_ward, class_name: "Hospitals::Ward"
       belongs_to :seen_by, class_name: "User"
 

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

@@ -0,0 +1,9 @@
+require_dependency "renalware/admissions"
+
+module Renalware
+  module Admissions
+    class ConsultSite < ApplicationRecord
+      validates :name, presence: true
+    end
+  end
+end

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

@@ -2,6 +2,7 @@ module Renalware
   module HD
     class MDMPatientsQuery
       include ModalityScopes
+      include PatientPathologyScopes
       MODALITY_NAMES = "HD".freeze
       DEFAULT_SEARCH_PREDICATE = "hgb_date".freeze
       attr_reader :q, :relation
@@ -22,7 +23,7 @@ module Renalware
             .includes(:hd_profile)
             .extending(ModalityScopes)
             .extending(PatientPathologyScopes)
-            .with_current_key_pathology
+            .with_current_pathology
             .with_current_modality_matching(MODALITY_NAMES)
             .search(q)
         end

data/app/models/renalware/letters/draft_letter.rb

@@ -4,6 +4,7 @@ module Renalware
   module Letters
     class DraftLetter
       include Wisper::Publisher
+      include LetterPathology
 
       def self.build
         new
@@ -11,7 +12,7 @@ module Renalware
 
       def call(patient, params = {})
         letter = LetterFactory.new(patient, params).build
-        # Rails.logger.info "Drafting letter of class #{letter.class} with type #{letter.type}"
+        build_pathology_snapshot(patient, letter)
         letter.save!
         letter.reload
         broadcast(:draft_letter_successful, letter)

data/app/models/renalware/letters/letter.rb

@@ -26,6 +26,7 @@ module Renalware
                source: :recipient
       has_one :signature, dependent: :destroy
       has_one :archive, foreign_key: "letter_id"
+      serialize :pathology_snapshot, Pathology::ObservationsJsonbSerializer
 
       accepts_nested_attributes_for :main_recipient
       accepts_nested_attributes_for :cc_recipients, reject_if: :all_blank, allow_destroy: true

data/app/models/renalware/letters/part/recent_pathology_results.rb

@@ -14,22 +14,8 @@ module Renalware
       private
 
       def recent_pathology_results
-        @recent_pathology_results ||= find_recent_pathology_results
-      end
-
-      def find_recent_pathology_results
-        check_letter
-        range = Time.zone.at(1)..letter.pathology_timestamp
-        Renalware::Pathology::CurrentObservationsForDescriptionsQuery.new(
-          patient: patient,
-          descriptions: Renalware::Letters::RelevantObservationDescription.all
-        ).call.where(observed_at: range).reject{ |obs| obs.id.nil? }
-      end
-
-      def check_letter
-        if letter.pathology_timestamp.blank?
-          raise ArgumentError,
-                "letter.pathology_timestamp cannot be nil when rendering letter pathology!"
+        @recent_pathology_results ||= begin
+          letter.pathology_snapshot
         end
       end
     end

data/app/models/renalware/letters/revise_letter.rb

@@ -4,6 +4,7 @@ module Renalware
   module Letters
     class ReviseLetter
       include Wisper::Publisher
+      include LetterPathology
 
       def self.build
         new
@@ -13,6 +14,7 @@ module Renalware
         letter = patient.letters.pending.find(letter_id)
         Letter.transaction do
           letter.revise(params)
+          build_pathology_snapshot(patient, letter) if letter.changes.key?(:pathology_timestamp)
           letter.save!
         end
         broadcast(:revise_letter_successful, letter)

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

@@ -0,0 +1,35 @@
+require_dependency "renalware/pathology"
+
+module Renalware
+  module Pathology
+    # We maintain current observations for each patient in their #current_observation_set.
+    # CurrentObservationSet#values is a hash (stored as jsonb) where the OBX code
+    # is the key and the result value and observation date are themselves a hash.
+    # So values looks like this
+    # {
+    #   "HGB": {
+    #     "result": 123,
+    #     observed_at: "2017-12-12 12:12:12"
+    #   },
+    #   "CRE": {
+    #     ...
+    #   }
+    # }
+    # and *always* contains the very latest pathology result for any code.
+    # We store all incoming OBX codes, not just a restricted list.
+    # Legacy data might only contain a subset of codes, so #values should not be relied on
+    # to cover current observations for the patients entire history, just key ones.
+    # When displaying or using a patient's current_observation_set the consuming code
+    # must filter out the codes it wants.
+    class CurrentObservationSet < ApplicationRecord
+      belongs_to :patient, class_name: "Renalware::Pathology::Patient"
+      validates :patient, presence: true
+      serialize :values, ObservationsJsonbSerializer
+
+      def values_for_codes(codes)
+        codes = Array(codes)
+        values.select{ |code, _| codes.include?(code) }
+      end
+    end
+  end
+end

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

@@ -10,16 +10,18 @@ module Renalware
       def message_processed(message_payload)
         pathology_params = parse_pathology_params(message_payload)
         create_observations(pathology_params)
+        # Note the the current_observation_set for the patient is updated by a trigger here
       end
 
       private
 
       def parse_pathology_params(message_payload)
-        MessageParamParser.new.parse(message_payload)
+        MessageParamParser.new(message_payload).parse
       end
 
-      def create_observations(params)
-        CreateObservations.new.call(params)
+      def create_observations(pathology_params)
+        return if pathology_params.nil? # eg patient does not exist
+        CreateObservations.new.call(pathology_params)
       end
     end
   end

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

@@ -6,18 +6,43 @@ module Renalware
     # that can be persisted by ObservationRequest.
     #
     class MessageParamParser
+      delegate :patient_identification, :observation_request, to: :message_payload
+      delegate :internal_id, to: :patient_identification
+      delegate :observations, to: :observation_request
+      alias_attribute :request, :observation_request
+
       # message_payload is an HL7Message (a decorator around an ::HL7::Message)
-      def parse(message_payload)
-        request = message_payload.observation_request
+      def initialize(message_payload, logger = Delayed::Worker.logger)
+        @message_payload = message_payload
+        @logger = logger
+      end
+
+      def parse
+        if renalware_patient?
+          build_patient_params
+        else
+          logger.warn("Did not process pathology for #{internal_id}: not a renalware patient")
+          nil
+        end
+      end
 
-        observations_params = build_observations_params(request.observations)
-        request_params = build_observation_request_params(request, observations_params)
-        build_patient_params(message_payload.patient_identification, request_params)
+      def renalware_patient?
+        Patient.exists?(local_patient_id: internal_id)
       end
 
       private
 
-      def build_observation_request_params(request, observations_params)
+      attr_reader :message_payload, :logger
+
+      def observations_params
+        @observations_params ||= build_observations_params
+      end
+
+      def request_params
+        @request_params ||= build_observation_request_params
+      end
+
+      def build_observation_request_params
         request_description = find_request_description(request.identifier)
 
         {
@@ -31,7 +56,7 @@ module Renalware
         }
       end
 
-      def build_observations_params(observations)
+      def build_observations_params
         observations.map do |observation|
           observation_description = find_observation_description(observation.identifier)
 
@@ -44,9 +69,9 @@ module Renalware
         end
       end
 
-      def build_patient_params(patient_identification, params)
-        params.tap do |p|
-          patient = find_patient(patient_identification.internal_id)
+      def build_patient_params
+        request_params.tap do |p|
+          patient = find_patient(internal_id)
           p[:patient_id] = patient.id
         end
       end