renalware-core 2.0.0.pre.rc6 → 2.0.0.pre.rc7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ce584cb7cbfefee7174f99e866b6a7955c12266f2fd6b0a60d86078dbf342ee2
-  data.tar.gz: 63261ae22a2fa334bb74777b0312ca3101a0cc38b45f964fd15ffaa82d62e7f6
+  metadata.gz: fe0192f8e977702f2adbf2a0f2893b3552b9e6bd573f721208e0250e03e03312
+  data.tar.gz: 87a77ba05e6a2dfb83cddbdb4d1d2de1bfe19aaf2c50515e57677db00588f7d5
 SHA512:
-  metadata.gz: e0f645e776c510e2b1f65c9b786b5838af19d350cc762d01ce6648f207881f6239ae131a10c980264cd123ed5ce6eaa0b1dcd13c2d0e62b2c6576df4feb32cc7
-  data.tar.gz: 0035ed970b1e8776a586398a8ad05e51373dff09467f833d6950f311eaf4e8508b63649849699e599b619c1fe4e689cb3334785ab91da31f1706bb677651ff02
+  metadata.gz: 3f6ef5e4f2f0fc65a67b0d6cb9c649685ec7ed98db4b0129a1ffb5f96d566e6a283f1fd436cff669188cd34778561b696f2a68c86b9d539790131110b6705e00
+  data.tar.gz: e61ff85f88683a31976a64dc74dfd65be9250168c7de67225c73db358591b387cef1f8add0ddb9bbf08cb6ade2becdbcc8e4f142de7c6893f4bde1c412dd027d

data/README.md

@@ -207,7 +207,6 @@ To make awesome_print the default formatter in irb, add the following to `~/.irb
     require "awesome_print"
     AwesomePrint.irb!
 
-
 #### Docker - WIP!
 
 ```

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

@@ -0,0 +1,10 @@
+require_dependency "renalware/events"
+
+# This controller is mostly empty - we are using it for mainly routing and to let us
+# override the events 'new' and 'edit' templates. See the base class for most functionality.
+module Renalware
+  module Events
+    class InvestigationsController < EventsController
+    end
+  end
+end

data/app/controllers/renalware/transplants/donor_dashboards_controller.rb

@@ -6,13 +6,7 @@ module Renalware
       before_action :load_patient
 
       def show
-        render locals: {
-          patient: patient,
-          donations: Donation.for_patient(patient).reversed,
-          donor_workup: DonorWorkup.for_patient(patient).first_or_initialize,
-          donor_operations: DonorOperation.for_patient(patient).reversed,
-          donor_stages: DonorStage.for_patient(patient).ordered
-        }
+        render locals: { dashboard: DonorDashboardPresenter.new(patient) }
       end
     end
   end

data/app/controllers/renalware/transplants/recipient_dashboards_controller.rb

@@ -5,27 +5,7 @@ module Renalware
     class RecipientDashboardsController < BaseController
       def show
         authorize patient
-        render locals: locals
-      end
-
-      private
-
-      def locals
-        {
-          patient: patient,
-          recipient_workup: RecipientWorkup.for_patient(patient).first_or_initialize,
-          registration: registration_presenter,
-          recipient_operations: RecipientOperation.for_patient(patient).reversed,
-          donations: Donation.for_recipient(patient).reversed
-        }
-      end
-
-      def registration_presenter
-        WaitListRegistrationPresenter.new(registration)
-      end
-
-      def registration
-        Registration.for_patient(patient).first_or_initialize
+        render locals: { dashboard: RecipientDashboardPresenter.new(patient) }
       end
     end
   end

data/app/models/renalware/events/investigation.rb

@@ -0,0 +1,31 @@
+require_dependency "renalware/events"
+require "document/base"
+require "document/embedded"
+require "document/enum"
+
+module Renalware
+  module Events
+    class Investigation < Event
+      include Document::Base
+
+      scope :transplant_donors, lambda{
+        where("document ->> 'modality' = ?", "transplant_donor")
+      }
+      scope :transplant_recipients, lambda{
+        where("document ->> 'modality' = ?", "transplant_recipient")
+      }
+
+      class Document < Document::Embedded
+        attribute :modality,
+                  ::Document::Enum,
+                  enums: %i(transplant_donor transplant_recipient other)
+        attribute :type, ::Document::Enum # See i18n for options
+        attribute :result, String
+        validates :modality, presence: true
+        validates :type, presence: true
+        validates :result, presence: true
+      end
+      has_document
+    end
+  end
+end

data/app/models/renalware/feeds/hl7_message.rb

@@ -15,8 +15,9 @@ module Renalware
       end
 
       class ObservationRequest < SimpleDelegator
-        def initialize(observation_request_segment, observations_segments)
-          @observations_segments = observations_segments
+        alias_attribute :date_time, :observation_date
+
+        def initialize(observation_request_segment)
           super(observation_request_segment)
         end
 
@@ -24,8 +25,14 @@ module Renalware
           universal_service_id.split("^").first
         end
 
+        # Select only OBX children. OBR can have other types of child
+        # segments but we want to ignore those.
         def observations
-          Array(@observations_segments).map { |segment| Observation.new(segment) }
+          @observations ||= begin
+            children
+              .select{ |segment| segment.is_a? HL7::Message::Segment::OBX }
+              .map{ |obx_segment| Observation.new(obx_segment) }
+          end
         end
 
         def ordering_provider_name
@@ -36,10 +43,6 @@ module Renalware
           super.split("^").first
         end
 
-        def date_time
-          observation_date
-        end
-
         private
 
         def ordering_provider
@@ -48,6 +51,9 @@ module Renalware
       end
 
       class Observation < SimpleDelegator
+        alias_attribute :date_time, :observation_date
+        alias_attribute :value, :observation_value
+
         def identifier
           observation_id.split("^").first
         end
@@ -57,14 +63,6 @@ module Renalware
           ""
         end
 
-        def date_time
-          observation_date
-        end
-
-        def value
-          observation_value
-        end
-
         # Because some units of measurement, such as 10^12/L for WBC, contain a caret, the caret
         # will initially have been encoded by Mirth as \S\ (a Mirth escape sequence for ^
         # or whatever the mirth component separator character is configured to be)
@@ -72,28 +70,33 @@ module Renalware
         # the `\12` within the message is interpreted as a `\n` (form feed) by
         # delayed_job when it is read into the yaml format string in the HL7 messages.
         # While it might be possible to write out yaml into delayed_job using a format
-        # that will not un-escape on reading, the approach here is that the Mirth channel must
-        # encode \S\ as \\S\\ in the message before inserting.
-        # Thus the raw data for units might look like `10\\S\\12/L` and this will work
-        # by the fact that the backslashes are escaped and a significant `\12` is not found.
+        # that will not un-escape on reading, the approach here is that the we have preprocessed
+        # the message using a trigger (at the point it is inserted into delayed_jobs) by
+        # replacing any instance of \S\ with \\S\\ in the message.
+        # Thus the raw data for units in the database will look like `10\\S\\12/L`.
+        # When ever this string is loaded by Ruby it will un-escaped and become "\S\"
+        # No `\12` is not found and un-escaped to \n"
+        # Note in the gsub here we double escape the \'s
         def units
           super&.gsub("\\S\\", "^")
         end
       end
 
-      def observation_request
-        ObservationRequest.new(self[:OBR], self[:OBX])
+      # There is a problem here is there are < 1 OBR
+      # i.e. self[:OBR] could be an array
+      def observation_requests
+        Array(self[:OBR]).map{ |obr| ObservationRequest.new(obr) }
       end
 
       class PatientIdentification < SimpleDelegator
+        alias_attribute :external_id, :patient_id
+        alias_attribute :sex, :admin_sex
+        alias_attribute :dob, :patient_dob
+
         def internal_id
           patient_id_list.split("^").first
         end
 
-        def external_id
-          patient_id
-        end
-
         def name
           Name.new(patient_name)
         end
@@ -106,14 +109,6 @@ module Renalware
           patient_name[1]
         end
 
-        def sex
-          admin_sex
-        end
-
-        def dob
-          patient_dob
-        end
-
         private
 
         def patient_name
@@ -134,7 +129,7 @@ module Renalware
       end
 
       def to_s
-        @message_string
+        @message_string.tr("\r", "\n")
       end
     end
   end

data/app/models/renalware/feeds/message_parser.rb

@@ -7,7 +7,8 @@ module Renalware
     #
     class MessageParser
       def parse(message_string)
-        HL7Message.new(message_string)
+        lines = message_string.split("\n").join("\r")
+        HL7Message.new(lines)
       end
     end
   end

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

@@ -0,0 +1,25 @@
+require_dependency "renalware/pathology"
+
+#
+# Create pathology observations requests and their child observations for an existing
+# patient from HL7 message content.
+#
+module Renalware
+  module Pathology
+    class CreateObservationRequests
+      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)
+        end
+      end
+
+      private
+
+      def find_patient(id)
+        ::Renalware::Pathology::Patient.find_by(id: id) || NullObject.instance
+      end
+    end
+  end
+end

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

@@ -9,19 +9,21 @@ module Renalware
     class MessageListener
       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
+        create_observation_requests_and_their_child_observations_from(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(message_payload).parse
+        ObservationRequestsAttributesBuilder.new(message_payload).parse
       end
 
-      def create_observations(pathology_params)
+      def create_observation_requests_and_their_child_observations_from(pathology_params)
         return if pathology_params.nil? # eg patient does not exist
-        CreateObservations.new.call(pathology_params)
+        CreateObservationRequests.new.call(pathology_params)
       end
     end
   end

data/app/models/renalware/pathology/{message_param_parser.rb → observation_requests_attributes_builder.rb}

@@ -4,12 +4,14 @@ module Renalware
   module Pathology
     # Responsible for transforming an HL7 message payload into a params hash
     # that can be persisted by ObservationRequest.
-    #
-    class MessageParamParser
-      delegate :patient_identification, :observation_request, to: :message_payload
+    # 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.
+    class ObservationRequestsAttributesBuilder
+      delegate :patient_identification, :observation_requests, to: :message_payload
       delegate :internal_id, to: :patient_identification
-      delegate :observations, to: :observation_request
-      alias_attribute :request, :observation_request
+      alias_attribute :requests, :observation_requests
 
       # message_payload is an HL7Message (a decorator around an ::HL7::Message)
       def initialize(message_payload, logger = Delayed::Worker.logger)
@@ -17,6 +19,9 @@ module Renalware
         @logger = logger
       end
 
+      # Return an array of observation request attributes (with a nested array of
+      # child observation attributes) for each OBR in the HL7 message.
+      # The resulting array will be used to create the corresponding database records.
       def parse
         if renalware_patient?
           build_patient_params
@@ -34,32 +39,38 @@ module Renalware
 
       attr_reader :message_payload, :logger
 
-      def observations_params
-        @observations_params ||= build_observations_params
+      def build_patient_params
+        patient = find_patient(internal_id)
+        request_params.each do |request_param|
+          request_param[:patient_id] = patient.id
+        end
       end
 
       def request_params
         @request_params ||= build_observation_request_params
       end
 
+      # rubocop:disable Metrics/MethodLength
       def build_observation_request_params
-        request_description = find_request_description(request.identifier)
-
-        {
-          observation_request: {
-            description_id: request_description.id,
-            requestor_name: request.ordering_provider_name,
-            requestor_order_number: request.placer_order_number,
-            requested_at: parse_time(request.date_time),
-            observations_attributes: observations_params
+        requests.each_with_object([]) do |request, arr|
+          request_description = find_request_description(request.identifier)
+          hash = {
+            observation_request: {
+              description_id: request_description.id,
+              requestor_name: request.ordering_provider_name,
+              requestor_order_number: request.placer_order_number,
+              requested_at: parse_time(request.date_time),
+              observations_attributes: build_observations_params(request)
+            }
           }
-        }
+          arr << hash
+        end
       end
+      # rubocop:enable Metrics/MethodLength
 
-      def build_observations_params
-        observations.map do |observation|
+      def build_observations_params(request)
+        request.observations.map do |observation|
           observation_description = find_observation_description(observation.identifier)
-
           {
             description_id: observation_description.id,
             observed_at: parse_time(observation.date_time),
@@ -69,13 +80,6 @@ module Renalware
         end
       end
 
-      def build_patient_params
-        request_params.tap do |p|
-          patient = find_patient(internal_id)
-          p[:patient_id] = patient.id
-        end
-      end
-
       def find_request_description(code)
         RequestDescription.find_by!(code: code)
       end

data/app/models/renalware/patients/practice_search_query.rb

@@ -12,7 +12,7 @@ module Renalware
 
         term = "%#{search_term}%"
         Practice.select(:id, :name)
-                .joins(:address)
+                .left_outer_joins(:address)
                 .where("patient_practices.name ILIKE ? OR addresses.postcode ILIKE ?", term, term)
         # .select("patient_practices.id", "patient_practices.name")
       end

data/app/policies/renalware/events/investigation_policy.rb

@@ -0,0 +1,8 @@
+require_dependency "renalware/events"
+
+module Renalware
+  module Events
+    class InvestigationPolicy < BasePolicy
+    end
+  end
+end

data/app/presenters/renalware/pathology/observation_presenter.rb

@@ -3,7 +3,7 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class ObservationPresenter < SimpleDelegator
-      delegate :name, :code, to: :description, prefix: true, allow_nil: true
+      delegate :name, :code, :loinc_code, to: :description, prefix: true, allow_nil: true
       delegate :measurement_unit, to: :description
       delegate :name, to: :measurement_unit, prefix: true
 

data/app/presenters/renalware/transplants/consent_presenter.rb

@@ -1,4 +1,4 @@
-require_dependency "renalware"
+require_dependency "renalware/transplants"
 
 module Renalware
   module Transplants

data/app/presenters/renalware/transplants/donor_dashboard_presenter.rb

@@ -0,0 +1,35 @@
+require_dependency "renalware/transplants"
+require "attr_extras"
+
+module Renalware
+  module Transplants
+    class DonorDashboardPresenter
+      attr_reader_initialize :patient
+
+      def donor_stages
+        @donor_stages ||= DonorStage.for_patient(patient).ordered
+      end
+
+      def donor_workup
+        @donor_workups ||= DonorWorkup.for_patient(patient).first_or_initialize
+      end
+
+      def donations
+        @donations ||= Donation.for_patient(patient).reversed
+      end
+
+      def donor_operations
+        @donor_operations ||= DonorOperation.for_patient(patient).reversed
+      end
+
+      def investigations
+        @investigations ||= begin
+          Events::Investigation
+            .for_patient(patient)
+            .transplant_donors
+            .ordered
+        end
+      end
+    end
+  end
+end