renalware-core 2.0.79 → 2.0.80

checksums.yaml

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data/README.md

@@ -15,7 +15,7 @@ Rails application, and configure it to include the Renalware engine. The host ap
 extremely thin, adding no custom features other than site-specific configuration, or it may include
 Ruby, HTML and JavaScript to override or augment renalware-core's features.
 
-While the engine is indented to be deployed inside a host application in production, it can be run
+While the engine is intended to be deployed inside a host application in production, it can be run
 stand-alone in a local development environment (or indeed deployed  in a limited way to somewhere like Heroku) by employing
 the _dummy_ host application that ships inside the engine. This dummy app (in `./spec/dummy`)
 allows a developer to quickly mount the engine, and is used also used Rails integration tests (which is why

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

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    class Treatment < ApplicationRecord
+      belongs_to :patient
+      belongs_to :clinician, class_name: "Renalware::User"
+      belongs_to :modality_code
+      validates :patient, presence: true
+      validates :modality_code, presence: true
+
+      scope :ordered, -> { order(started_on: :asc, ended_on: :asc) }
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generate_timeline.rb

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+# rubocop:disable Rails/Output
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      #
+      # Re-generates the ukrdc_treatments for a patient from their modalities and other information.
+      #
+      class GenerateTimeline
+        pattr_initialize :patient
+
+        def call
+          PrepareTables.call
+          RemapModelTableNamesToTheirPreparedEquivalents.call
+
+          modalities.each do |modality|
+            print "#{modality.description.name} "
+            GeneratorFactory.call(modality).call
+          end
+        end
+
+        private
+
+        def modalities
+          patient.modalities.order(started_on: :asc, updated_at: :asc)
+        end
+      end
+    end
+  end
+end
+# rubocop:enable Rails/Output

data/app/models/renalware/ukrdc/treatment_timeline/generate_treatments.rb

@@ -0,0 +1,45 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+require "benchmark"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      # Re-generates the ukrdc_treatments table
+      class GenerateTreatments
+        def self.call
+          new.call
+        end
+
+        def call
+          elapsed_ms = Benchmark.ms do
+            generate_treatments
+          end
+          log("\nCreated #{UKRDC::Treatment.count} UKRDC Treatments in #{elapsed_ms / 1000.0}s")
+        end
+
+        private
+
+        def patient_scope
+          Renalware::Patient.select(:id)
+        end
+
+        # rubocop:disable Rails/Output
+        def generate_treatments
+          Rails.logger.info "#{patient_scope.count} patients"
+          patient_scope.find_each do |patient|
+            print "\n#{patient.id}: "
+            GenerateTimeline.new(patient).call
+          end
+        end
+        # rubocop:enable Rails/Output
+
+        def log(msg)
+          Rails.logger.info(msg)
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generator_factory.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+require "benchmark"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      class GeneratorFactory
+        DEFAULT_TYPE = "Generic"
+
+        # Returns the class of object to suitable for generating the treatment timeline for the
+        # requested modality. If the modality description type is nil then we use a generic
+        # generator. If no generator class is defined matching the description.type, we also
+        # return nil.
+        # Example:
+        # given the modality_description.type of Renalware::Bla::BlaModalityDescription
+        # we will look to see if the constant GenerateBlaBlaTimeline exists and return an instance
+        # if so - otherwise we return an instance of the default generator GenerateGenericTimeline.
+        def self.call(modality)
+          type = modality.description.type.presence || DEFAULT_TYPE
+          type = type.gsub("::", "").gsub(/^Renalware/, "").gsub(/ModalityDescription$/, "")
+          (klass_for(type) || klass_for(DEFAULT_TYPE)).new(modality)
+        end
+
+        def self.klass_for(type)
+          "Renalware::UKRDC::TreatmentTimeline::Generators::#{type}Timeline".safe_constantize
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generators/deaths_timeline.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Generators
+        class DeathsTimeline
+          pattr_initialize :modality
+
+          def call; end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generators/generic_timeline.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Generators
+        class GenericTimeline
+          pattr_initialize :modality
+
+          def call; end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generators/hd_timeline.rb

@@ -0,0 +1,145 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+# rubocop:disable Rails/Output
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Generators
+        class HDTimeline
+          pattr_initialize :modality
+          delegate :patient, to: :modality
+
+          def call
+            create_treatment_from_modality
+            create_treatments_within_modality
+            deduplicate
+          end
+
+          private
+
+          def create_treatment_from_modality
+            print "[#{treatment.txt_code}] "
+            treatments << Treatment.create!(
+              patient: patient,
+              clinician: modality.created_by,
+              started_on: modality.started_on,
+              ended_on: modality.ended_on,
+              modality_code: treatment
+            )
+          end
+
+          class ProfileDecorator < DumbDelegator
+            def initialize(profile, last_profile:)
+              @last_profile = last_profile
+              super(profile)
+            end
+
+            def hd_type
+              document.dialysis.hd_type
+            end
+
+            def changed?
+              return true if last_profile.blank?
+
+              hd_type_changed? || hospital_unit_changed?
+            end
+
+            def unchanged?
+              !changed?
+            end
+
+            def hd_type_changed?
+              last_profile.document.dialysis.hd_type != hd_type
+            end
+
+            def hospital_unit_changed?
+              last_profile.hospital_unit_id != hospital_unit_id
+            end
+
+            private
+
+            attr_reader :last_profile
+          end
+
+          # 3 things trigger a new Treatment for an HD patient
+          # - change of site
+          # - change of hd_type to from hd and (hdf_pre || hdf_post)
+          # - change of hd prescription
+          # Looop through the hd_profiles and trigger an new treatment when these change
+          def create_treatments_within_modality
+            profiles = hd_profiles_for(patient, from: modality.started_on, to: modality.ended_on)
+            last_profile = NullObject.instance
+
+            profiles.each do |profile_|
+              profile = ProfileDecorator.new(profile_, last_profile: last_profile)
+              create_treatment_from(profile) if profile.changed?
+              last_profile = profile_
+            end
+          end
+
+          # - if modality started on same day as hd profile prescribed then use HD Profile hd_type
+          #   if present else hd
+          # - if modality started before hd_profile setup and hd_profile is hdf, we'll have
+          #   2 treatments: hd then hdf
+          # - if hosp unit changes within the modality timeframe, trigger a new treatment
+          # - if medications change? new treatment? Check with GS
+          def deduplicate
+            # p treatments.map(&:id)
+          end
+
+          # rubocop:disable Metrics/AbcSize
+          def create_treatment_from(profile)
+            code = treatment_for_hd_type(profile.hd_type)
+            print "[#{code.txt_code}] "
+            treatments << Treatment.create!(
+              patient: patient,
+              clinician: modality.created_by,
+              started_on: modality.started_on,
+              ended_on: modality.ended_on,
+              modality_code: treatment_for_hd_type(profile.hd_type)
+            )
+          end
+          # rubocop:enable Metrics/AbcSize
+
+          def treatments
+            @treatments ||= []
+          end
+
+          def treatment_for_hd_type(hd_type)
+            ukrr_name = case hd_type.to_s.downcase
+                        when "hd" then "Haemodialysis"
+                        when "hdf_pre", "hdf_post" then "Haemodiafiltration"
+                        end
+            UKRDC::ModalityCode.find_by!(description: ukrr_name)
+          end
+
+          def hd_profiles_for(patient, from:, to: Time.zone.now)
+            conditions = {
+              patient_id: patient.id,
+              prescribed_on: from..DateTime::Infinity.new
+            }
+
+            scope = Renalware::HD::Profile
+              .with_deactivated
+              .order(prescribed_on: :asc, deactivated_at: :desc)
+
+            scope
+              .where(conditions.merge(deactivated_at: from..to))
+              .or(scope.where(conditions.merge(deactivated_at: nil)))
+          end
+
+          def hd_patient
+            Renalware::HD.cast_patient(patient)
+          end
+
+          def treatment
+            ModalityCode.find_by!(description: "Haemodialysis")
+          end
+        end
+      end
+    end
+  end
+end
+# rubocop:enable Rails/Output

data/app/models/renalware/ukrdc/treatment_timeline/generators/low_clearance_timelinex.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimelinex
+      module Generators
+        class LowClearanceTimeline
+          pattr_initialize :modality
+
+          def call; end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generators/pd_timeline.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Generators
+        class PDTimeline
+          pattr_initialize :modality
+          delegate :patient, to: :modality
+
+          def call; end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generators/transplants_donor_timeline.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Generators
+        class TransplantsDonorTimeline
+          pattr_initialize :modality
+
+          def call; end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/generators/transplants_recipient_timeline.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Generators
+        class TransplantsRecipientTimeline
+          pattr_initialize :modality
+
+          def call; end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/prepare_tables.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      # If the host site has defined a SQL function called ukrdc_prepare_tables() in any schema in
+      # the current SEARCH_PATH, then we call it here. It will (we hope) generate massaged copies of
+      # tables needed to later generate e.g. UKRDC treatments - for example at KCH the hd_profiles
+      # table is massaged to correct migration artefacts and issues prior to the generation of the
+      # UKRDC Treatment Timeline. Elsewhere we detect the presence of these prepared
+      # tables (eg ukrdc_prepared_hd_profiles) and use them as the underlying table behind, in this
+      # example, Renalware::HD::Profile, by setting class.table_name = 'ukrdc_prepared_hd_profiles'.
+      # If the site has not defined the ukrdc_prepare_tables SQL function then we exit gracefully.
+      class PrepareTables
+        def self.call
+          connection = ActiveRecord::Base.connection
+          result = connection.execute(<<-SQL)
+            select 1 where exists(select 1 from pg_proc where proname = 'ukrdc_prepare_tables');
+          SQL
+          if result.ntuples == 1
+            connection.execute("select ukrdc_prepare_tables();")
+            return true
+          end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/remap_model_table_names_to_their_prepared_equivalents.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+# For use only in rake task! See comments below
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      # Wehen generating the tratment timeline, sites may want to pre-prepare a massaged version
+      # of say hd_profiles, in order to correct any anomalies. This service object
+      # will remap the table_name of the supplied (or default models) to the
+      # 'ukrdc_prepared_*' version if it exists. Otrherwise it will not change the table name.
+      # Note that this can only be done when executing as a rake task (which has its own process)
+      # as I beleive changing the table_name will affect all threads in the same process - so doing
+      # this in a puma process would mean users start to see only the contents of the
+      # ukrdc_prepared_tables. Not good :0.
+      class RemapModelTableNamesToTheirPreparedEquivalents
+        ALLOWED_PROCESSES = %w(rake rspec).freeze
+        MODELS = [
+          Renalware::HD::Profile
+        ].freeze
+        class ExecutionNotAllowedError < StandardError; end
+
+        def self.call(models = MODELS)
+          new.call(models)
+        end
+
+        def call(models)
+          fail_unless_running_in_rake_or_rspec
+          Array(models).each do |model_class|
+            prepared_table_name = prepared_table_name_for(model_class.table_name)
+            model_class.table_name = prepared_table_name if table_exists?(prepared_table_name)
+          end
+        end
+
+        private
+
+        def fail_unless_running_in_rake_or_rspec
+          unless ALLOWED_PROCESSES.include?(File.basename($PROGRAM_NAME))
+            raise(
+              ExecutionNotAllowedError,
+              "Can only be called from #{ALLOWED_PROCESSES.join(', ')}"
+            )
+          end
+        end
+
+        def prepared_table_name_for(table_name)
+          "ukrdc_prepared_#{table_name}"
+        end
+
+        def table_exists?(table_name)
+          result = connection.execute(<<-SQL)
+            SELECT 1
+            WHERE EXISTS (
+              SELECT 1 FROM information_schema.tables WHERE table_name = '#{table_name}')
+          SQL
+          result.ntuples == 1
+        end
+
+        def connection
+          ActiveRecord::Base.connection
+        end
+      end
+
+      module X
+        def table_name
+          "ukrdc_prepared_#{super}"
+        end
+      end
+    end
+  end
+end

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

@@ -96,7 +96,10 @@ module Renalware
 
       # We always send the patients current prescriptions.
       def prescriptions
-        __getobj__.prescriptions.current.includes(:termination, :medication_route, :drug)
+        __getobj__
+          .prescriptions
+          .includes(:termination, :medication_route, :drug)
+          .order(:prescribed_on)
       end
 
       def observation_requests

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

@@ -3,15 +3,6 @@
 # https://github.com/renalreg/ukrdc/blob/6d95e364dd8de857839fe6cdbd4e7fc3fb4c1d42/Schema/Diagnoses/Diagnosis.xsd
 xml = builder
 xml.Diagnoses do
-  if patient.dead? && patient.first_cause.present?
-    # Only 1 CauseOfDeath element is allowed so we ignore patient.second_cause
-    render(
-      "renalware/api/ukrdc/patients/diagnoses/cause_of_death",
-      builder: xml,
-      cause: patient.first_cause
-    )
-  end
-
   patient.yes_comorbidities.each do |comorb|
     xml.Diagnosis do
       xml.Diagnosis do
@@ -44,6 +35,15 @@ xml.Diagnoses do
     end
   end
 
+  if patient.dead? && patient.first_cause.present?
+    # Only 1 CauseOfDeath element is allowed so we ignore patient.second_cause
+    render(
+      "renalware/api/ukrdc/patients/diagnoses/cause_of_death",
+      builder: xml,
+      cause: patient.first_cause
+    )
+  end
+
   if patient.prd_description_code.present?
     xml.RenalDiagnosis do
       xml.Diagnosis do

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

@@ -3,10 +3,5 @@
 xml = builder
 
 xml.Encounters do
-  patient.modalities.each do |session|
-    render "renalware/api/ukrdc/patients/encounters/treatment",
-           builder: xml,
-           patient: patient,
-           session: Renalware::HD::SessionPresenter.new(session)
-  end
+  render "treatments", builder: xml, patient: patient
 end

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

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+xml = builder
+
+# A temporary output ot the treatment timeline using just this modality descriptions with a
+# crude renal reg modality code assigned to them - HD PD Transplant vCKD - all other modalities
+# fall through the gaps at this stage until we implement this properly. Also sub RR modal codes
+# like CAPD and HDF are not yet implemented, just the top level modality.
+patient.modalities.each do |modality|
+  next if modality.description.ukrdc_modality_code_id.blank?
+
+  xml.Treatment do
+    xml.EncounterNumber modality.id
+    xml.EncounterType "N"
+    xml.FromTime modality.started_on.to_time&.iso8601
+    xml.ToTime modality.ended_on.to_time&.iso8601
+
+    xml.HealthCareFacility do
+      xml.CodingStandard "ODS"
+      xml.Code Renalware.config.ukrdc_site_code
+    end
+
+    xml.AdmitReason do
+      xml.CodingStandard "CF_RR7_TREATMENT"
+      xml.Code Renalware::UKRDC::ModalityCode.find(modality.description.ukrdc_modality_code_id).txt_code
+    end
+  end
+end

data/app/views/renalware/api/ukrdc/patients/procedures/_dialysis_session.xml.builder

@@ -6,7 +6,6 @@ xml.DialysisSession(
   start: session.performed_on_date,
   stop: session.performed_on_date
 ) do
-
   xml.ProcedureType do
     xml.CodingStandard "SNOMED"
     xml.Code "302497006"

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

@@ -23,7 +23,7 @@ xml.ukrdc(:PatientRecord, namespace_and_schema) do
   render "medications", builder: xml, patient: patient
   render "procedures", builder: xml, patient: patient
   render "documents", builder: xml, patient: patient
-  # render "encounters", builder: xml, patient: patient
+  render "encounters", builder: xml, patient: patient
   render "program_memberships", builder: xml, patient: patient
   render "clinical_relationships", builder: xml, patient: patient
   render "surveys", builder: xml, patient: patient

data/db/migrate/20190520091324_create_ukrdc_treatments.rb

@@ -0,0 +1,18 @@
+class CreateUKRDCTreatments < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :ukrdc_treatments do |t|
+        t.references :patient, foreign_key: true, index: true, null: false
+        t.references :clinician, foreign_key: { to_table: :users }, index: true, null: true
+        t.references :modality_code, foreign_key: { to_table: :ukrdc_modality_codes }, index: true, null: false
+        t.references :modality, index: true, null: true
+        t.references :modality_description, index: true, null: true, foreign_key: true
+        t.references :hospital_centre, null: true, foreign_key: true, index: true
+        t.references :hospital_unit, null: true, foreign_key: true, index: true
+        t.date :started_on, null: false
+        t.date :ended_on
+        t.timestamps null: false
+      end
+    end
+  end
+end

data/db/migrate/20190607134717_add_ukrdc_modality_code_id_to_modality_descriptions.rb

@@ -0,0 +1,22 @@
+class AddUKRDCModalityCodeIdToModalityDescriptions < ActiveRecord::Migration[5.2]
+  def change
+    # add_column :modality_descriptions, :ukrdc_modality_code_id, :integer
+    add_reference :modality_descriptions,
+                  :ukrdc_modality_code,
+                  foreign_key: true
+
+    reversible do |direction|
+      direction.up do
+        connection.execute(<<-SQL.squish)
+          update renalware.modality_descriptions set ukrdc_modality_code_id = (select id from renalware.ukrdc_modality_codes where qbl_code = '19') where name = 'PD';
+          update renalware.modality_descriptions set ukrdc_modality_code_id = (select id from renalware.ukrdc_modality_codes where qbl_code = '1') where name = 'HD';
+          update renalware.modality_descriptions set ukrdc_modality_code_id = (select id from renalware.ukrdc_modality_codes where qbl_code = '29') where name = 'Transplant';
+          update renalware.modality_descriptions set ukrdc_modality_code_id = (select id from renalware.ukrdc_modality_codes where qbl_code = '900') where name = 'vCKD';
+        SQL
+      end
+      direction.down do
+        # noop
+      end
+    end
+  end
+end

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.79"
+  VERSION = "2.0.80"
 end

data/lib/tasks/ukrdc.rake

@@ -41,4 +41,12 @@ namespace :ukrdc do
       patient_ids: args.fetch(:patient_ids, "").split(" ").map(&:to_i)
     ).call
   end
+
+  desc "Regenerates the ukrdc_treatments table ready for exporting to UKRDC in another task"
+  task generate_treatments: :environment do
+    logger           = ActiveSupport::TaggedLogging.new(Logger.new(STDOUT))
+    logger.level     = Logger::INFO
+    Rails.logger     = logger
+    Renalware::UKRDC::TreatmentTimeline::GenerateTreatments.call
+  end
 end

data/spec/factories/ukrdc/modality_codes.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :ukrdc_modality_code, class: Renalware::UKRDC::ModalityCode do
+    trait :hd do
+      description { "Haemodialysis" }
+      txt_code { 1 }
+      qbl_code { 1 }
+    end
+
+    trait :hdf do
+      description { "Haemodiafiltration" }
+      txt_code { 3 }
+      qbl_code { 3 }
+    end
+  end
+end

data/spec/support/patients_spec_helper.rb

@@ -6,7 +6,8 @@ module PatientsSpecHelper
                    started_on: Time.zone.today,
                    by: Renalware::User.first)
 
-    Renalware::Modalities::ChangePatientModality
+    # ChangePatientModality returns a Success or Failure object
+    new_modality = Renalware::Modalities::ChangePatientModality
       .new(patient: patient, user: by)
       .call(
         description: modality_description,
@@ -14,5 +15,8 @@ module PatientsSpecHelper
       )
 
     patient.reload # need to do this in order for current_modality to be set
+
+    # Return ther object associated with the returned Success or Failure object
+    new_modality.object
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.79
+  version: 2.0.80
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-06 00:00:00.000000000 Z
+date: 2019-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1825,6 +1825,19 @@ files:
 - app/models/renalware/ukrdc/paths.rb
 - app/models/renalware/ukrdc/patients_query.rb
 - app/models/renalware/ukrdc/transmission_log.rb
+- app/models/renalware/ukrdc/treatment.rb
+- app/models/renalware/ukrdc/treatment_timeline/generate_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generate_treatments.rb
+- app/models/renalware/ukrdc/treatment_timeline/generator_factory.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/deaths_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/generic_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/hd_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/low_clearance_timelinex.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/pd_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/transplants_donor_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generators/transplants_recipient_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/prepare_tables.rb
+- app/models/renalware/ukrdc/treatment_timeline/remap_model_table_names_to_their_prepared_equivalents.rb
 - app/models/renalware/ukrdc/xml_renderer.rb
 - app/models/renalware/user.rb
 - app/models/renalware/version.rb
@@ -2118,9 +2131,8 @@ files:
 - app/views/renalware/api/ukrdc/patients/_sending_facility.xml.builder
 - app/views/renalware/api/ukrdc/patients/_social_histories.xml.builder
 - app/views/renalware/api/ukrdc/patients/_surveys.xml.builder
+- app/views/renalware/api/ukrdc/patients/_treatments.xml.builder
 - app/views/renalware/api/ukrdc/patients/diagnoses/_cause_of_death.xml.builder
-- app/views/renalware/api/ukrdc/patients/encounters/_hd_session.xml.builder
-- app/views/renalware/api/ukrdc/patients/encounters/_treatment.xml.builder
 - app/views/renalware/api/ukrdc/patients/lab_orders/_lab_order.xml.builder
 - app/views/renalware/api/ukrdc/patients/lab_orders/_result_item.xml.builder
 - app/views/renalware/api/ukrdc/patients/observations/_blood_pressure.xml.builder
@@ -3472,12 +3484,14 @@ files:
 - db/migrate/20190513131826_add_view_count_to_system_help.rb
 - db/migrate/20190513135312_create_pathology_code_groups.rb
 - db/migrate/20190516093707_add_graft_nephectomy_on_to_tx_op_followup.rb
+- db/migrate/20190520091324_create_ukrdc_treatments.rb
 - db/migrate/20190531172829_add_last_change_date_to_patient_practices.rb
 - db/migrate/20190602114659_create_system_api_logs.rb
 - db/migrate/20190603084428_add_pages_to_system_api_logs.rb
 - db/migrate/20190603135247_add_columns_to_patient_primary_care_physicians.rb
 - db/migrate/20190603143834_update_import_practice_memberships_csv.rb
 - db/migrate/20190603165812_drop_import_practices_csv_function.rb
+- db/migrate/20190607134717_add_ukrdc_modality_code_id_to_modality_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
@@ -3804,6 +3818,7 @@ files:
 - spec/factories/transplants/registration_status_descriptions.rb
 - spec/factories/transplants/registration_statuses.rb
 - spec/factories/transplants/registrations.rb
+- spec/factories/ukrdc/modality_codes.rb
 - spec/factories/virology/patients.rb
 - spec/factories/virology/vaccinations.rb
 - spec/support/capybara_helper.rb

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

@@ -1,38 +0,0 @@
-# frozen_string_literal: true
-
-# xml = builder
-
-# xml.Treatment do
-#   xml.EncounterNumber session.uuid
-#   xml.comment! "TODO: EncounterType TBC"
-#   xml.EncounterType "R"
-#   xml.FromTime session.start_datetime&.to_datetime
-#   xml.ToTime session.stop_datetime&.to_datetime
-
-#   xml.HealthCareFacility do
-#     xml.CodingStandard "ODS"
-#     xml.Code session.hospital_unit_renal_registry_code
-#     xml.Description session.hospital_unit_name
-#   end
-
-#   xml.AdmitReason do
-#     xml.comment! "AdmitReason 1 == Haemodialysis - TBC - may need to capture/derive"
-#     xml.CodingStandard "CF_RR7_TREATMENT"
-#     xml.Code "1"
-#   end
-
-#   xml.EnteredAt do
-#     xml.Code session.hospital_unit_renal_registry_code
-#   end
-
-#   xml.Attributes do
-#     xml.HDP01 session.patient&.hd_profile&.schedule_definition&.days_per_week
-#     xml.HDP02 session.duration
-#     xml.HDP03 session.document.dialysis.flow_rate
-#     xml.HDP04 session&.dialysate&.sodium_content
-#     xml.QBL05 session.access_type
-#     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
-# end

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

@@ -1,34 +0,0 @@
-# frozen_string_literal: true
-
-xml = builder
-
-xml.Treatment do
-  xml.FromTime modality.started_on
-  xml.ToTime modality.ended_on
-
-  xml.HealthCareFacility do
-    xml.CodingStandard "ODS"
-    xml.Code Renalware.config.ukrdc_site_code
-  end
-
-  # xml.AdmitReason do
-  #   xml.comment! "AdmitReason 1 == Haemodialysis - TBC - may need to capture/derive"
-  #   xml.CodingStandard "CF_RR7_TREATMENT"
-  #   xml.Code "1"
-  # end
-
-  # xml.EnteredAt do
-  #   xml.Code session.hospital_unit_renal_registry_code
-  # end
-
-  # xml.Attributes do
-  #   xml.HDP01 session.patient&.hd_profile&.schedule_definition&.days_per_week
-  #   xml.HDP02 session.duration
-  #   xml.HDP03 session.document.dialysis.flow_rate
-  #   xml.HDP04 session&.dialysate&.sodium_content
-  #   xml.QBL05 session.access_type
-  #   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
-end