renalware-core 2.0.0.pre.beta8 → 2.0.0.pre.beta9

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

@@ -0,0 +1,15 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    class AKIAlert < ApplicationRecord
+      include Accountable
+      scope :ordered, ->{ order(created_at: :desc) }
+      belongs_to :patient, class_name: "Renal::Patient"
+      belongs_to :action, class_name: "Renal::AKIAlertAction"
+      belongs_to :hospital_ward, class_name: "Hospitals::Ward"
+      validates :patient, presence: true
+      alias_attribute :decided_by, :updated_by
+    end
+  end
+end

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

@@ -0,0 +1,10 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    class AKIAlertAction < ApplicationRecord
+      validates :name, presence: true, uniqueness: true
+      delegate :to_s, to: :name
+    end
+  end
+end

data/app/models/renalware/reporting/audit.rb

@@ -4,12 +4,11 @@ module Renalware
   module Reporting
     class Audit < ApplicationRecord
       validates :name, presence: true
-      validates :materialized_view_name, presence: true
-      validates :refresh_schedule, presence: true
+      validates :view_name, presence: true
 
       def self.available_audit_materialized_views
         result = connection.execute("SELECT oid::regclass::text FROM pg_class
-                                     WHERE  relkind = 'm' and relname like 'reporting_%';")
+                                     WHERE  relkind in ('m', 'v') and relname like 'reporting_%';")
         result.values.flatten
       end
     end

data/app/models/renalware/reporting/generate_audit_json.rb

@@ -3,17 +3,33 @@ require_dependency "renalware/reporting"
 module Renalware
   module Reporting
     class GenerateAuditJson
-      def self.call(materialized_view_name)
-        result = ActiveRecord::Base.connection.execute(
-          "select * from #{materialized_view_name};"
-        )
-        # Build a datatables compatible columnDefs hash
+      def self.call(view_name)
+        conn = ActiveRecord::Base.connection
+        result = conn.execute("select * from #{conn.quote_column_name(view_name)};")
+
+        # Build a JS DataTables-compatible columnDefs hash
         columns = result.fields.each_with_index.inject([]) do |array, data|
           column_name, index = data
           array << { title: column_name, target: index }
         end
         [columns.to_json, result.values]
       end
+
+      # A WIP to translate audit column names into human friendly ones.
+      # May need to establish guidelines for instance apply text case in the view itself so
+      # eg pct_HGB = % HGB without having to know to upcase certain bits of the name but
+      # capitalise others etc.
+      # def self.humanize_column_name(column)
+      #   column
+      #     .gsub("pct_", "% ")
+      #     .gsub("count_", "No.")
+      #     .gsub("avg_", "Avg ")
+      #     .gsub("max", "Max ")
+      #     .gsub("gt_eq_", "≥ ")
+      #     .gsub("lt_eq_", "≤ ")
+      #     .gsub("gt_", "> ")
+      #     .gsub("lt_", "< ")
+      # end
     end
   end
 end

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

@@ -0,0 +1,21 @@
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    class Country < ApplicationRecord
+      validates :name, presence: true, uniqueness: true
+      validates :alpha2, presence: true, uniqueness: true
+      validates :alpha3, presence: true, uniqueness: true
+
+      default_scope ->{ order(position: :asc) }
+
+      def to_s
+        name
+      end
+
+      def uk?
+        (alpha3 || "").casecmp("GBR").zero?
+      end
+    end
+  end
+end

data/app/models/renalware/transplants/create_donor_stage.rb

@@ -1,4 +1,6 @@
 require_dependency "renalware/transplants"
+require_dependency "renalware/success"
+require_dependency "renalware/failure"
 
 # Service object responsible for creating a new DonorStage and terminated the previous one
 # if found.
@@ -15,9 +17,9 @@ module Renalware
           terminate_current_stage if current_stage.present?
           stage = build_new_stage
           if stage.save
-            Success.new(stage)
+            ::Renalware::Success.new(stage)
           else
-            Failure.new(stage)
+            ::Renalware::Failure.new(stage)
           end
         end
       end

data/app/policies/renalware/base_policy.rb

@@ -45,6 +45,10 @@ module Renalware
       update?
     end
 
+    def debug?
+      user_is_super_admin?
+    end
+
     protected
 
     # For each role define e.g. user_is_admin?

data/app/policies/renalware/renal/aki_alert_policy.rb

@@ -0,0 +1,9 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    class AKIAlertPolicy < BasePolicy
+
+    end
+  end
+end

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

@@ -16,6 +16,11 @@ module Renalware
         super(HD.cast_patient(patient.__getobj__))
       end
 
+      def finished_hd_sessions
+        # TODO: standardise on a way to get closed sessions - a scope on patient maybe?
+        hd_sessions.eager_load(:hospital_unit).where(type: "Renalware::HD::Session::Closed")
+      end
+
       private
 
       def hd_profile

data/app/presenters/renalware/reporting/audit_presenter.rb

@@ -5,6 +5,7 @@ module Renalware
   module Reporting
     class AuditPresenter < SimpleDelegator
       def refresh_schedule
+        return if super.blank?
         Cronex::ExpressionDescriptor.new(super).description
       end
     end

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

@@ -3,7 +3,8 @@ module Renalware
     class PatientPresenter < SimpleDelegator
 
       def initialize(patient)
-        super(Transplants.cast_patient(patient.__getobj__))
+        patient = patient.__getobj__ if patient.respond_to?(:__getobj__)
+        super(Transplants.cast_patient(patient))
       end
 
       def current_registration_status

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

@@ -6,6 +6,14 @@ module Renalware
       delegate :allergies, to: :clinical_patient
       delegate :clinic_visits, to: :clinics_patient
       delegate :observation_requests, to: :pathology_patient
+      delegate :profile, to: :renal_patient, allow_nil: true
+      delegate :first_seen_on, to: :profile, allow_nil: true
+      alias_attribute :home_telephone, :telephone1
+      alias_attribute :mobile_telephone, :telephone2
+
+      def dead?
+        current_modality_death?
+      end
 
       def smoking_history
         @smoking_history ||= document.history&.smoking&.upcase
@@ -18,10 +26,21 @@ module Renalware
         )
       end
 
+      def current_registration_status_rr_code
+        @current_registration_status_rr_code ||= begin
+          status = transplant_patient.current_registration_status
+          status&.description&.rr_code
+        end
+      end
+
       def hospital_unit_code
         letter_head.site_code
       end
 
+      def contact_details?
+        email || home_telephone || mobile_telephone
+      end
+
       private
 
       def clinical_patient
@@ -39,6 +58,14 @@ module Renalware
       def pathology_patient
         @pathology_patient ||= Renalware::Pathology.cast_patient(__getobj__)
       end
+
+      def renal_patient
+        @renal_patient ||= Renalware::Renal.cast_patient(__getobj__)
+      end
+
+      def transplant_patient
+        @transplant_patient ||= Transplants::PatientPresenter.new(__getobj__)
+      end
     end
   end
 end

data/app/values/renalware/address.rb

@@ -1,14 +1,8 @@
 module Renalware
   class Address < ApplicationRecord
-    UK_COUNTRIES = [
-      "united kingdom",
-      "england",
-      "scotland",
-      "wales",
-      "northern ireland"
-    ].freeze
-
+    belongs_to :country, class_name: "System::Country"
     validates :email, email: true, allow_blank: true
+    delegate :uk?, to: :country, allow_nil: true
     validates_with AddressValidator
 
     belongs_to :addressable, polymorphic: true
@@ -20,11 +14,6 @@ module Renalware
       }
     end
 
-    def uk?
-      return if country.blank?
-      UK_COUNTRIES.include?(country.downcase)
-    end
-
     def copy_from(source)
       self.name = source.name
       self.organisation_name = source.organisation_name

data/app/views/renalware/addresses/_form.html.slim

@@ -7,8 +7,10 @@
 = a.input :town, wrapper: :horizontal_medium
 = a.input :county, wrapper: :horizontal_small
 = a.input :postcode, wrapper: :horizontal_small
-= a.input :country,
-          collection: Renalware::Country.all.map(&:name),
+= a.input :country_id,
+          collection: Renalware::System::Country.pluck(:name, :id),
           wrapper: :horizontal_small
 = a.input :telephone, wrapper: :horizontal_medium
 = a.input :email, wrapper: :horizontal_medium
+
+

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

@@ -10,7 +10,7 @@ xml.Address(use: "H") do
   xml.Postcode address.postcode
   xml.Country do
     xml.CodingStandard "ISO3166-1"
-    xml.Code Renalware::Country.code_for(address.country)
-    xml.Description address.country
+    xml.Code address&.country&.alpha3
+    xml.Description address&.country&.to_s
   end
 end

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

@@ -1,7 +1,10 @@
 # https://github.com/renalreg/ukrdc/blob/6d95e364dd8de857839fe6cdbd4e7fc3fb4c1d42/Schema/Diagnoses/Diagnosis.xsd
 # This is snomed-based, so might not be possible?
 xml = builder
-
 xml.Diagnoses do
-  xml.comment! "TODO"
+  if patient.dead?
+    [patient.first_cause, patient.second_cause].compact.each do |cause|
+      render "renalware/api/ukrdc/patients/diagnoses/cause_of_death", builder: xml, cause: cause
+    end
+  end
 end

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

@@ -1,5 +1,12 @@
 xml = builder
+hd_patient = Renalware::HD::PatientPresenter.new(patient)
 
 xml.Encounters do
-  xml.comment! "TODO"
+  hd_patient.finished_hd_sessions.each do |session|
+    render "renalware/api/ukrdc/patients/encounters/hd_session",
+           builder: xml,
+           patient: patient,
+           hd_patient: hd_patient,
+           session: Renalware::HD::SessionPresenter.new(session)
+  end
 end

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

@@ -0,0 +1,30 @@
+xml = builder
+
+xml.Medications do
+  patient.prescriptions.each do |prescription|
+    xml.Medication do
+      xml.PrescriptionNumber
+      xml.FromTime prescription.prescribed_on.to_datetime
+      if prescription.terminated_or_marked_for_termination?
+        xml.ToTime prescription.terminated_on&.to_datetime
+      end
+      xml.OrderedBy
+      xml.Route do
+        xml.CodingStandard "RR22"
+        xml.Code prescription.medication_route&.rr_code
+        xml.Description prescription.medication_route&.name
+      end
+      xml.DrugProduct do
+        xml.Id do
+          xml.CodingStandard "DM+D"
+          xml.Code "dm + d code for the drug - coming soon"
+          xml.Description prescription.drug
+        end
+      end
+      xml.Frequency prescription.frequency
+      xml.Comments prescription.notes
+      # xml.DoseUoM
+      # xml.Indication
+    end
+  end
+end

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

@@ -2,7 +2,6 @@
 # Things we are not going to include in RW2.0
 # - PersonToContact
 # - Occupation
-# - CountryOfBirth
 #
 xml = builder
 path = "renalware/api/ukrdc/patients" # or "."
@@ -30,7 +29,7 @@ xml.Patient do
 
   xml.BirthTime patient.born_on.to_datetime
 
-  if patient.current_modality_death? && patient.died_on.present?
+  if patient.dead? && patient.died_on.present?
     xml.DeathTime(patient.died_on.to_datetime)
   end
 
@@ -57,9 +56,41 @@ xml.Patient do
     end
   end
 
-  xml.PrimaryLanguage patient.language
+  if patient.language.present?
+    xml.PrimaryLanguage do
+      xml.CodingStandard "NHS_DATA_DICTIONARY_LANGUAGE_CODE" # ISO 639-1 plus braille an sign
+      xml.Code patient.language&.code
+      xml.Description patient.language
+    end
+  end
+
+  if patient.contact_details?
+    xml.ContactDetails do
+      if patient.email.present?
+        xml.ContactDetail(use: "NET") do
+          xml.Value patient.email
+        end
+      end
+      if patient.home_telephone.present?
+        xml.ContactDetail(use: "PRN") do
+          xml.Value patient.home_telephone
+        end
+      end
+      if patient.mobile_telephone.present?
+        xml.ContactDetail(use: "PRS") do
+          xml.Value patient.mobile_telephone
+        end
+      end
+    end
+  end
 
-  if patient.current_modality_death?
+  xml.comment! "Inclusion of CountryOfBirth causes XSD error so temporarily excluded"
+  # Inclusion strangley causes an XSD error
+  # if patient.country_of_birth.present?
+  #   xml.CountryOfBirth patient.country_of_birth.alpha3
+  # end
+
+  if patient.dead?
     xml.Death true
   end
 
@@ -67,4 +98,5 @@ xml.Patient do
   xml.UpdatedOn patient.updated_at&.to_datetime
   xml.ActionCode "A" # A = added/updated. If we are posting this XML isn't only going to be 'A'?
   xml.ExternalId patient.ukrdc_external_id
+
 end

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

@@ -5,3 +5,4 @@ xml.SendingFacility(
   channelId: "TODO",
   time: Time.zone.now.to_datetime) do
 end
+xml.SendingExtract "???"

data/app/views/renalware/api/ukrdc/patients/diagnoses/_cause_of_death.xml.builder

@@ -0,0 +1,10 @@
+xml = builder
+
+xml.CauseOfDeath do
+  xml.DiagnosisType "final"
+  xml.Diagnosis do
+    xml.CodingStandard "EDTA"
+    xml.Code cause.code
+  end
+  xml.EnteredOn cause.created_at.to_datetime
+end

data/app/views/renalware/api/ukrdc/patients/encounters/_hd_session.xml.builder

@@ -0,0 +1,40 @@
+xml = builder
+
+xml.Treatment do
+  xml.EncounterNumber "?can supply uuid if required?"
+  xml.comment! "What EncounterType for HD Session?"
+  xml.EncounterType "R"
+  xml.FromTime session.start_datetime&.to_datetime
+  xml.ToTime session.stop_datetime&.to_datetime
+  xml.HealthCareFacility
+  xml.EnteredAt do
+    xml.Code session.hospital_unit.renal_registry_code
+  end
+
+  xml.Attributes do
+    xml.HDP01 "Times per week - to confirm"
+    xml.HDP02 session.duration
+    xml.HDP03 session.document.dialysis.flow_rate
+    xml.comment! "HDP04 Sodium in Dialysate - to follow."
+    xml.HDP04 ""
+    xml.QBL05 session.access_type
+    xml.QBL06 ""
+    xml.comment! "QBL06 HD Shared Care - not implemented yet"
+    xml.QBL07 ""
+    xml.comment! "QBL07 HD Shared Care - not implemented yet"
+    xml.comment! "ERF61 - defaulting to 5 if not present, as element is required"
+    xml.ERF61 patient.current_registration_status_rr_code || "5" # 5= not assessed
+    xml.PAT35 patient.first_seen_on
+  end
+  xml.comment! "TODO: AdmitReason fails xsd validation with "\
+             "Element 'AdmitReason': This element is not expected. Expected is one of "\
+             "( VisitDescription, Attributes, UpdatedOn, ActionCode, ExternalId )."
+  # xml.AdmitReason do
+  #   xml.comment! "I think AdmitReason 1 is Haemodialysis"
+  #   xml.CodingStandard "CF_RR7_TREATMENT"
+  #   xml.Code "1"
+  # end
+  # xml.UpdatedOn
+  # xml.ActionCode
+  # xml.ExternalId
+end