renalware-core 2.0.92 → 2.0.93

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/models/renalware/ukrdc/treatment_timeline/generate_timeline.rb

@@ -3,7 +3,6 @@
 require_dependency "renalware/ukrdc"
 require "attr_extras"
 
-# rubocop:disable Rails/Output
 module Renalware
   module UKRDC
     module TreatmentTimeline
@@ -14,7 +13,7 @@ module Renalware
         pattr_initialize :patient
 
         def call
-         # RemapModelTableNamesToTheirPreparedEquivalents.new.call do
+          # RemapModelTableNamesToTheirPreparedEquivalents.new.call do
           Rails.logger.info "    Generating Treatment rows for modalities #{modality_names}"
           modalities.each do |modality|
             generator = GeneratorFactory.call(modality)
@@ -27,7 +26,10 @@ module Renalware
 
         def modalities
           @modalities ||= begin
-            patient.modalities.includes(:description).order(started_on: :asc, updated_at: :asc)
+            patient
+              .modalities
+              .includes(:description, :created_by)
+              .order(started_on: :asc, updated_at: :asc)
           end
         end
 
@@ -38,4 +40,3 @@ module Renalware
     end
   end
 end
-# rubocop:enable Rails/Output

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

@@ -10,17 +10,9 @@ module Renalware
       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.
+        # Each modality_description has a :code fiekd
         def self.call(modality)
-          type = modality.description.type.presence || DEFAULT_TYPE
-          type = type.gsub("::", "").gsub(/^Renalware/, "").gsub(/ModalityDescription$/, "")
+          type = modality.description.code&.to_s&.camelize
           (klass_for(type) || klass_for(DEFAULT_TYPE)).new(modality)
         end
 

data/app/models/renalware/ukrdc/treatment_timeline/transfer_out/generator.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module TransferOut
+        class Generator
+          RR7_DISCHARGE_CODE_TRANSFER_OUT = 38
+          pattr_initialize :modality
+          delegate :patient, to: :modality
+
+          def call
+            update_discharge_reason_on_most_recent_treatment
+          end
+
+          private
+
+          def most_recent_treatment
+            @most_recent_treatment ||= begin
+              Treatment.where(patient_id: patient.id).order(started_on: :desc).first
+            end
+          end
+
+          def update_discharge_reason_on_most_recent_treatment
+            return if most_recent_treatment.blank?
+
+            most_recent_treatment.update!(
+              discharge_reason_code: RR7_DISCHARGE_CODE_TRANSFER_OUT,
+              discharge_reason_comment: "transfer_out"
+            )
+          end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/treatment_timeline/transplant/generator.rb.wip

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+# QBL   TXT   Description
+# "20"  "20"  "Transplant ; Cadaver donor"
+# "21"  "21"  "Transplant ; Live related - sibling"
+# "74"  "74"  "Transplant ; Live related - father"
+# "75"  "75"  "Transplant ; Live related - mother"
+# "77"  "77"  "Transplant ; Live related - child"
+# "23"  "23"  "Transplant ; Live related - other"
+# "24"  "24"  "Transplant ; Live genetically unrelated"
+# "25"  "25"  "Transplant ; Cadaver donor + transp other organ"
+# "26"  "26"  "Transplant ; Live donor + transplant other organ"
+# "27"  "27"  "Transplant ; Live donor non-UK transplant"
+# "28"  "28"  "Transplant ; non-heart-beating donor"
+# "29"  "29"  "Transplant ; type unknown"
+module Renalware
+  module UKRDC
+    module TreatmentTimeline
+      module Transplant
+        class Generator
+          pattr_initialize :modality
+          delegate :patient, to: :modality
+
+          # We need to create a treatment record to match the UKRDC code expectations
+          # based on donor relationship.
+          # Otherwise Default to 29 Transplant ; type unknown
+          def call
+
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -55,7 +55,7 @@ module Renalware
         current_modality.description.is_a?(Renalware::HD::ModalityDescription)
       end
 
-      # Note we of course only send letters for RPV patients and exlcude them for all others.
+      # Note we of course only send letters for RPV patients and exclude them for all others.
       def letters
         return ::Renalware::Letters::Letter.none if send_to_rpv == false
 

data/app/views/renalware/api/ukrdc/patients/treatments/_discharge_reason.xml.builder

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+xml = builder
+
+if treatment&.discharge_reason_code.present?
+  xml.DischargeReason do
+    xml.CodingStandard "CF_RR7_DISCHARGE"
+    xml.Code treatment.discharge_reason_code
+  end
+end

data/app/views/renalware/api/ukrdc/patients/treatments/_generic.xml.builder

@@ -12,4 +12,10 @@ xml.Treatment do
     xml.CodingStandard "CF_RR7_TREATMENT"
     xml.Code treatment.modality_code.txt_code
   end
+
+  render(
+    "renalware/api/ukrdc/patients/treatments/discharge_reason",
+    treatment: treatment,
+    builder: builder
+  )
 end

data/app/views/renalware/api/ukrdc/patients/treatments/_hd.xml.builder

@@ -20,6 +20,12 @@ xml.Treatment do
     xml.Code treatment.modality_code.txt_code
   end
 
+  render(
+    "renalware/api/ukrdc/patients/treatments/discharge_reason",
+    treatment: treatment,
+    builder: builder
+  )
+
   # HD
   rr8 = treatment.hospital_unit&.unit_type_rr8
   if rr8.present?

data/app/views/renalware/api/ukrdc/patients/treatments/_pd.xml.builder

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 xml = builder
 
 xml.Treatment do
@@ -15,4 +17,10 @@ xml.Treatment do
     xml.CodingStandard "CF_RR7_TREATMENT"
     xml.Code treatment.modality_code.txt_code
   end
+
+  render(
+    "renalware/api/ukrdc/patients/treatments/discharge_reason",
+    treatment: treatment,
+    builder: builder
+  )
 end

data/db/migrate/20190718091430_add_code_to_modality_descriptions.rb

@@ -0,0 +1,8 @@
+class AddCodeToModalityDescriptions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :modality_descriptions, :code, :string
+      add_index  :modality_descriptions, :code, unique: true
+    end
+  end
+end

data/db/migrate/20190718095851_add_discharge_reason_code_to_ukrdc_treatments.rb

@@ -0,0 +1,8 @@
+class AddDischargeReasonCodeToUKRDCTreatments < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :ukrdc_treatments, :discharge_reason_code, :integer
+      add_column :ukrdc_treatments, :discharge_reason_comment, :string
+    end
+  end
+end

data/db/seeds/default/modalities/descriptions.rb

@@ -2,11 +2,11 @@
 
 module Renalware
   log "Adding Modality Descriptions" do
-    Deaths::ModalityDescription.find_or_create_by!(name: "Death")
-    Transplants::DonorModalityDescription.find_or_create_by!(name: "Live Donor")
-    Transplants::RecipientModalityDescription.find_or_create_by!(name: "Transplant")
-    PD::ModalityDescription.find_or_create_by!(name: "PD")
-    HD::ModalityDescription.find_or_create_by!(name: "HD")
-    LowClearance::ModalityDescription.find_or_create_by!(name: "Low Clearance")
+    Deaths::ModalityDescription.find_or_create_by!(name: "Death", code: "death")
+    Transplants::DonorModalityDescription.find_or_create_by!(name: "Live Donor", code: "live_donor")
+    Transplants::RecipientModalityDescription.find_or_create_by!(name: "Transplant", code: "transplant")
+    PD::ModalityDescription.find_or_create_by!(name: "PD", code: "pd")
+    HD::ModalityDescription.find_or_create_by!(name: "HD", code: "hd")
+    LowClearance::ModalityDescription.find_or_create_by!(name: "Low Clearance", code: "low_clearance")
   end
 end

data/lib/gpg_encrypt_folder.rb

@@ -53,8 +53,12 @@ end
 class GpgCommand
   pattr_initialize [:file!, :options!]
 
+  # Note we skip using a random seed file (normally created at var/ukrdc/gpgkey/random_seed)
+  # because we had problems at KCH where the file would become corrupt, breaking the export, and
+  # fixable only by deleting the random_seed file and letting gpg re-create one.
+  # Using the --no-random-seed-file option the file is not used so we avoid that problem.
   def to_s
-    "gpg --armor --no-default-keyring --trust-model always "\
+    "gpg --armor --no-default-keyring --trust-model always --no-random-seed-file "\
       "#{keyring} #{homedir} #{recipient} "\
       "-o \"#{encrypted_filename}\" "\
       "--encrypt \"#{file}\""

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.92"
+  VERSION = "2.0.93"
 end

data/spec/factories/hd/modality_descriptions.rb

@@ -3,5 +3,6 @@
 FactoryBot.define do
   factory :hd_modality_description, class: "Renalware::HD::ModalityDescription" do
     initialize_with { Renalware::HD::ModalityDescription.find_or_create_by(name: "HD") }
+    code { "hd" }
   end
 end

data/spec/factories/modalities/modality_descriptions.rb

@@ -6,34 +6,45 @@ FactoryBot.define do
 
     initialize_with { Renalware::Modalities::Description.find_or_create_by(name: name) }
 
+    trait :transfer_out do
+      name { "Transfer Out" }
+      code { "transfer_out" }
+    end
+
     trait :pd do
       name { "PD" }
       type { "Renalware::PD::ModalityDescription" }
+      code { "pd" }
     end
 
     trait :hd do
       name { "HD" }
       type { "Renalware::HD::ModalityDescription" }
+      code { "hd" }
     end
 
     trait :transplant do
       name { "Transplant" }
       type { "Renalware::Transplants::RecipientModalityDescription" }
+      code { "transplant" }
     end
 
     trait :low_clearance do
       name { "Low Clearance" }
       type { "Renalware::LowClearance::ModalityDescription" }
+      code { "low_clearance" }
     end
 
     trait :death do
       name { "Death" }
       type { "Renalware::Deaths::ModalityDescription" }
+      code { "death" }
     end
 
     trait :live_donor do
       name { "Live Donor" }
       type { "Renalware::Transplants::DonorModalityDescription" }
+      code { "live_donor" }
     end
   end
 end

data/spec/factories/pd/modality_descriptions.rb

@@ -6,5 +6,6 @@ FactoryBot.define do
       Renalware::PD::ModalityDescription.find_or_create_by!(name: name)
     end
     name { "PD" }
+    code { "pd" }
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.92
+  version: 2.0.93
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-11 00:00:00.000000000 Z
+date: 2019-07-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1858,6 +1858,8 @@ files:
 - app/models/renalware/ukrdc/treatment_timeline/pd/regime_decorator.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/treatment_timeline/transfer_out/generator.rb
+- app/models/renalware/ukrdc/treatment_timeline/transplant/generator.rb.wip
 - app/models/renalware/ukrdc/xml_renderer.rb
 - app/models/renalware/user.rb
 - app/models/renalware/version.rb
@@ -2165,6 +2167,7 @@ files:
 - app/views/renalware/api/ukrdc/patients/procedures/_dialysis_session.xml.builder
 - app/views/renalware/api/ukrdc/patients/procedures/_transplant_operation.xml.builder
 - app/views/renalware/api/ukrdc/patients/show.xml.builder
+- app/views/renalware/api/ukrdc/patients/treatments/_discharge_reason.xml.builder
 - app/views/renalware/api/ukrdc/patients/treatments/_generic.xml.builder
 - app/views/renalware/api/ukrdc/patients/treatments/_hd.xml.builder
 - app/views/renalware/api/ukrdc/patients/treatments/_pd.xml.builder
@@ -3530,6 +3533,8 @@ files:
 - db/migrate/20190705083727_alter_ukrdc_treatments.rb
 - db/migrate/20190705105921_create_hd_profile_for_modalites.rb
 - 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/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb