renalware-core 2.0.94 → 2.0.95

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 97f743d2f776695b7e406965b0c575158b831091441c6d687dc618755f503108
+  data.tar.gz: 7fa35c1012943e0e1da51d6268fbc38186bfac42eec755ac9319827ad20f9993
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+  data.tar.gz: cbf56881a9bdea06a338c2e9bce80daf3fc911248e9aeb0da125655cb5c87fd388b1872d536f8204faed4bc428b0d35953fbb2fcd96703e787373c5124f5e0df

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

@@ -21,6 +21,9 @@ module Renalware
         .order([:display_group, :display_order])
       }
 
+      enum rr_type: { rr_type_simple: 0, rr_type_interpretation: 1 }
+      enum rr_coding_standard: { ukrr: 0, pv: 1 }
+
       def self.for(codes)
         ObservationDescriptionsByCodeQuery.new(codes: codes).call
       end

data/app/models/renalware/ukrdc/pathology_observation_requests_query.rb

@@ -18,7 +18,7 @@ module Renalware
         Pathology::ObservationRequest
           .where(id: Pathology::ObservationRequest.distinct_for_patient_id(patient_id))
           .where("requested_at >= ?", changes_since)
-          .where("loinc_code is not null")
+          .where("coalesce(loinc_code, '') != ''") # excludes NULL and ''
           .eager_load(
             :description,
             observations: { description: :measurement_unit }

data/app/presenters/renalware/clinics/clinic_visit_presenter.rb

@@ -9,6 +9,12 @@ module Renalware
       def sanitized_notes
         ::Rails::Html::WhiteListSanitizer.new.sanitize(notes, tags: %w(p br ol li ul span div))
       end
+
+      def height_in_cm
+        return if height.blank?
+
+        height * 100
+      end
     end
   end
 end

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

@@ -5,7 +5,8 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class ObservationPresenter < SimpleDelegator
-      delegate :name, :code, :loinc_code, to: :description, prefix: true, allow_nil: true
+      delegate :name, :code, :loinc_code, :rr_type, :rr_coding_standard,
+               to: :description, prefix: true, allow_nil: true
       delegate :measurement_unit, to: :description, allow_nil: true
       delegate :name, to: :measurement_unit, prefix: true, allow_nil: true
 

data/app/presenters/renalware/ukrdc/pathology_observation_presenter.rb

@@ -2,7 +2,17 @@
 
 module Renalware
   module UKRDC
+    # Assumes the thing being passed to the ctor is of type Pathology::ObservationPresenter hence
+    # responds to #description_code
     class PathologyObservationPresenter < SimpleDelegator
+      delegate :rr_type_interpretation?, to: :description
+
+      INTERPRETATION_CODE_MAP = {
+        "positive" => "POS",
+        "negative" => "NEG"
+      }.freeze
+      DEFAULT_INTERPRETATION_CODE = "UNK"
+
       # The PrePost element in ResultItem
       # For HD patients, all bloods are PRE except the post dialysis urea,
       # For non-HD patients, all the tests are NA
@@ -19,6 +29,22 @@ module Renalware
       def result
         (super || "")[0..19]
       end
+
+      def coding_standard
+        return if description_rr_coding_standard.blank?
+
+        description_rr_coding_standard.to_s.upcase
+      end
+
+      def code
+        description_loinc_code.presence || description_code
+      end
+
+      def interpretation_code
+        sanitized_result = result&.downcase&.strip
+
+        INTERPRETATION_CODE_MAP.fetch(sanitized_result, DEFAULT_INTERPRETATION_CODE)
+      end
     end
   end
 end

data/app/presenters/renalware/ukrdc/patient_presenter.rb

@@ -94,10 +94,13 @@ module Renalware
       end
 
       def clinic_visits
-        clinics_patient
-          .clinic_visits
-          .where("date >= ?", changes_since)
-          .includes(:updated_by)
+        @clinic_visits ||= begin
+          visits = clinics_patient
+            .clinic_visits
+            .where("date >= ?", changes_since)
+            .includes(:updated_by)
+          CollectionPresenter.new(visits, Clinics::ClinicVisitPresenter)
+        end
       end
 
       def treatments

data/app/views/renalware/api/ukrdc/patients/_observations.xml.builder

@@ -31,7 +31,7 @@ xml.Observations(
 
     render "clinic_visit_observation",
            visit: visit,
-           method: :height,
+           method: :height_in_cm,
            i18n_key: "height",
            builder: builder
   end

data/app/views/renalware/api/ukrdc/patients/lab_orders/_result_item.xml.builder

@@ -8,17 +8,19 @@ xml.ResultItem do
   xml.EnteredOn observation.updated_at&.iso8601
   xml.PrePost observation.pre_post(patient_is_on_hd: patient.current_modality_hd?)
   xml.ServiceId do
-    if observation.description_loinc_code.present?
-      xml.CodingStandard "PV"
-      xml.Code observation.description_loinc_code
-    else
-      xml.CodingStandard "LOCAL"
-      xml.Code observation.description_code
-    end
+    xml.CodingStandard observation.coding_standard
+    xml.Code observation.code
     xml.Description observation.description_name
   end
 
-  xml.ResultValue observation.result
-  xml.ResultValueUnits observation.measurement_unit_name
+  # If the rrr_type of the observation_descriptions is interpretation (ie an interpretted result
+  # like POS NEG)
+  if observation.rr_type_interpretation?
+    xml.InterpretationCodes observation.interpretation_code
+  else
+    xml.ResultValue observation.result
+    xml.ResultValueUnits observation.measurement_unit_name
+  end
+
   xml.ObservationTime observation.observed_at&.iso8601
 end

data/config/locales/loinc_codes.yml

@@ -19,4 +19,4 @@ en:
     height:
       code: height
       description: Height Measured
-      units: "m"
+      units: "cm"

data/db/migrate/20190722145936_change_type_of_patients_ukrdc_external_id.rb

@@ -0,0 +1,17 @@
+class ChangeTypeOfPatientsUKRDCExternalId < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      reversible do |dir|
+        dir.up do
+          change_column :patients, :ukrdc_external_id, :text, null: true
+        end
+        dir.down do
+          change_column :patients, :ukrdc_external_id, "uuid USING UUID(ukrdc_external_id)", null: true
+        end
+      end
+
+      remove_index :patients, :ukrdc_external_id
+      add_index :patients, :ukrdc_external_id, unique: true
+    end
+  end
+end

data/db/migrate/20190723150737_add_result_type_to_pathology_observation_descriptions.rb

@@ -0,0 +1,21 @@
+class AddResultTypeToPathologyObservationDescriptions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :pathology_observation_descriptions,
+        :rr_type,
+        :integer,
+        default: 0,
+        null: false
+      )
+
+      add_column(
+        :pathology_observation_descriptions,
+        :rr_coding_standard,
+        :integer,
+        default: 0,
+        null: false
+      )
+    end
+  end
+end

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.94"
+  VERSION = "2.0.95"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.94
+  version: 2.0.95
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-19 00:00:00.000000000 Z
+date: 2019-07-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -2038,7 +2038,7 @@ files:
 - app/presenters/renalware/transplants/patient_presenter.rb
 - app/presenters/renalware/transplants/recipient_dashboard_presenter.rb
 - app/presenters/renalware/transplants/wait_list_registration_presenter.rb
-- app/presenters/renalware/ukrdc/modality_presenter.rb
+- app/presenters/renalware/ukrdc/modality_presenter.rb.dead
 - app/presenters/renalware/ukrdc/pathology_observation_presenter.rb
 - app/presenters/renalware/ukrdc/pathology_observation_request_presenter.rb
 - app/presenters/renalware/ukrdc/patient_presenter.rb
@@ -3535,6 +3535,8 @@ files:
 - db/migrate/20190709101610_create_pd_regime_for_modalities.rb
 - db/migrate/20190718091430_add_code_to_modality_descriptions.rb
 - db/migrate/20190718095851_add_discharge_reason_code_to_ukrdc_treatments.rb
+- db/migrate/20190722145936_change_type_of_patients_ukrdc_external_id.rb
+- db/migrate/20190723150737_add_result_type_to_pathology_observation_descriptions.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb