RubyGems - renalware-core - Versions diffs - 2.0.159 → 2.0.164 - Mend

renalware-core 2.0.159 → 2.0.164

Files changed (208) hide show

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

@@ -9,7 +9,7 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class MessageListener
-      # Note: We are already inside a transaction here
+      # NOTE: We are already inside a transaction here
       def oru_message_arrived(hl7_message:, **)
         pathology_params = parse_pathology_params(hl7_message)
         create_observation_requests_and_their_child_observations_from(pathology_params)

data/app/models/renalware/pathology/observation.rb CHANGED

@@ -19,7 +19,7 @@ module Renalware
       scope :ordered, -> { order(observed_at: :desc) }
       scope :for_description, ->(description) { where(description: description) }
-      scope :having_a_loinc_code, -> { joins(:description).where("loinc_code is not null") }
+      scope :having_a_loinc_code, -> { joins(:description).where.not(loinc_code: nil) }
       def observed_on
         observed_at.to_date

data/app/models/renalware/pathology/observation_descriptions_by_code_query.rb CHANGED

@@ -28,7 +28,7 @@ module Renalware
       #     ...
       #   ]
       def call
-        stmt = SQL::IndexedCaseStmt.new(:code, @codes) # Generate a CASE statement for ordering
+        stmt = Sql::IndexedCaseStmt.new(:code, @codes) # Generate a CASE statement for ordering
         records = @relation.where(code: @codes).order(stmt.generate)
         verify_all_records_found(records)
         records

data/app/models/renalware/pathology/observations_grouped_by_date_query.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/pathology"
-require "attr_extras"
 module Renalware
   module Pathology

data/app/models/renalware/pathology/observations_grouped_by_date_table.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/pathology"
-require "attr_extras"
 module Renalware
   module Pathology

data/app/models/renalware/pathology/ordered_patient_query.rb CHANGED

@@ -19,7 +19,7 @@ module Renalware
       private
       def ids_index
-        ::SQL::IndexedCaseStmt.new("patients.id", @patient_ids).generate
+        ::Sql::IndexedCaseStmt.new("patients.id", @patient_ids).generate
       end
     end
   end

data/app/models/renalware/pathology/requests/request_params_factory.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/pathology"
-require "attr_extras"
 module Renalware
   module Pathology

data/app/models/renalware/patients/calculate_age.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/patients"
-require "attr_extras"
 module Renalware
   module Patients

data/app/models/renalware/patients/clear_patient_ukrdc_data.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/patients"
-require "attr_extras"
 module Renalware
   module Patients

data/app/models/renalware/patients/ingestion/update_master_patient_index.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require "renalware/feeds"
-require "attr_extras"
 module Renalware
   module Patients

data/app/models/renalware/patients/last_successful_practice_sync_date_query.rb CHANGED

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
-require "attr_extras"
 module Renalware
   module Patients
     class LastSuccessfulPracticeSyncDateQuery

data/app/models/renalware/patients/primary_care_physician.rb CHANGED

@@ -57,6 +57,7 @@ module Renalware
       end
       class PrimaryCarePhysicianAddressAccessError < StandardError; end
       def current_address
         raise PrimaryCarePhysicianAddressAccessError,
               "primary_care_physician#current_address should not be called: "\

data/app/models/renalware/patients/sync_ods_job.rb CHANGED

@@ -33,7 +33,7 @@ module Renalware
       # practices. On successive runs it will just find changes since the last run.
       def sync_practices(dry_run)
         Renalware::System::APILog.with_log("nhs_data_api", dry_run: dry_run) do |api_log|
-          Renalware::Patients::SyncPracticesViaApi.call(
+          Renalware::Patients::SyncPracticesViaAPI.call(
             dry_run: dry_run,
             api_log: api_log
           )

data/app/models/renalware/patients/sync_practices_via_api.rb CHANGED

@@ -7,7 +7,7 @@ module Renalware
     # Fetches pratice changes and additions from the NHS ODS API.
     # Called from a rake task.
     # See doc/ods.md
-    class SyncPracticesViaApi
+    class SyncPracticesViaAPI
       def self.call(**args)
         new(**args).call
       end

data/app/models/renalware/pd.rb CHANGED

@@ -39,5 +39,10 @@ module Renalware
     def self.configure
       yield config
     end
+    module APD
+      class NonUniqueOvernightVolumeError < StandardError
+      end
+    end
   end
 end

data/app/models/renalware/pd/{apd/exceptions.rb → apd.rb.dead} RENAMED

File without changes

data/app/models/renalware/pd/apd/available_overnight_volume.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/pd"
-require_dependency "renalware/pd/apd/exceptions"
 module Renalware
   module PD

data/app/models/renalware/pd/apd/regime_calculations.rb CHANGED

@@ -19,7 +19,7 @@ module Renalware
             calculated_overnight_volume,
             effective_last_fill_volume,
             effective_additional_manual_exchange_volume
-          ].compact.inject(0, :+)
+          ].compact.sum
           vol == 0 ? nil : vol
         end

data/app/models/renalware/pd/create_regime.rb CHANGED

@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 require_dependency "renalware/pd"
-require_dependency "renalware/success"
-require_dependency "renalware/failure"
+require "success"
+require "failure"
 module Renalware
   module PD
@@ -14,9 +14,9 @@ module Renalware
       def call(by:, params:)
         regime = patient.pd_regimes.new(params)
         if regime.valid? && save_regime(regime, by)
-          ::Renalware::Success.new(regime)
+          ::Success.new(regime)
         else
-          ::Renalware::Failure.new(regime)
+          ::Failure.new(regime)
         end
       end

data/app/models/renalware/pd/regimes_in_date_range_query.rb CHANGED

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
-require "attr_extras"
 module Renalware
   module PD
     class RegimesInDateRangeQuery

data/app/models/renalware/pd/revise_regime.rb CHANGED

@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 require_dependency "renalware/pd"
-require_dependency "renalware/success"
-require_dependency "renalware/failure"
+require "success"
+require "failure"
 module Renalware
   module PD
@@ -14,13 +14,13 @@ module Renalware
       def call(by:, params:)
         Regime.transaction do
           regime.assign_attributes(params)
-          return ::Renalware::Success.new(regime) unless regime.anything_changed?
+          return ::Success.new(regime) unless regime.anything_changed?
           unless regime.valid?
-            return ::Renalware::Failure.new(regime.with_bag_destruction_marks_removed)
+            return ::Failure.new(regime.with_bag_destruction_marks_removed)
           end
           new_regime = revise_regime(by: by)
-          ::Renalware::Success.new(new_regime)
+          ::Success.new(new_regime)
         end
       end

data/{lib → app/models}/renalware/remembered_preferences.rb RENAMED

File without changes

data/app/models/renalware/research/study_participants_query.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/research"
-require "attr_extras"
 module Renalware
   module Research

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

@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 require_dependency "renalware/transplants"
-require_dependency "renalware/success"
-require_dependency "renalware/failure"
+require "success"
+require "failure"
 # Service object responsible for creating a new DonorStage and terminated the previous one
 # if found.
@@ -19,9 +19,9 @@ module Renalware
           terminate_current_stage if current_stage.present?
           stage = build_new_stage
           if stage.save
-            ::Renalware::Success.new(stage)
+            ::Success.new(stage)
           else
-            ::Renalware::Failure.new(stage)
+            ::Failure.new(stage)
           end
         end
       end

data/app/models/renalware/transplants/registrations/wait_list_query.rb CHANGED

@@ -93,7 +93,7 @@ module Renalware
           when :suspended
             { current_status_in: :suspended }
           when :active_and_suspended
-            # note: array must be embedded in another array as mentioned here:
+            # NOTE: array must be embedded in another array as mentioned here:
             # https://github.com/activerecord-hackery/ransack#using-scopesclass-methods
             { current_status_in: [%w(active suspended)] }
           when :working_up

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

@@ -5,6 +5,7 @@ require_dependency "renalware"
 module Renalware
   module UKRDC
     class SurveyNotFoundError < StandardError; end
     class QuestionNotFoundError < StandardError; end
     def self.table_name_prefix

data/app/models/renalware/ukrdc/create_encrypted_patient_xml_files.rb CHANGED

@@ -11,7 +11,7 @@ module Renalware
     # which might for example be a symlink to an outgoing folder in /media/ukrdc which in turn
     # is mount on a remote share for example on an SFTP server.
     # rubocop:disable Metrics/ClassLength:
-    class CreateEncryptedPatientXMLFiles
+    class CreateEncryptedPatientXmlFiles
       attr_reader(
         :patient_ids,
         :changed_since,
@@ -106,7 +106,7 @@ module Renalware
       # rubocop:enable Metrics/MethodLength, Metrics/AbcSize
       def create_xml_file(patient:, schema:)
-        CreatePatientXMLFile.new(
+        CreatePatientXmlFile.new(
           patient: patient,
           dir: paths.timestamped_xml_folder,
           changes_since: changed_since,

data/app/models/renalware/ukrdc/create_patient_xml_file.rb CHANGED

@@ -1,11 +1,10 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC
-    class CreatePatientXMLFile
+    class CreatePatientXmlFile
       pattr_initialize [
         :patient!,
         :dir!,

data/app/models/renalware/ukrdc/export_summary.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

data/app/models/renalware/ukrdc/housekeeping/remove_old_export_archive_folders.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

data/app/models/renalware/ukrdc/incoming/file_list.rb CHANGED

@@ -1,7 +1,5 @@
 # frozen_string_literal: true
-require "attr_extras"
 module Renalware
   module UKRDC
     module Incoming

data/app/models/renalware/ukrdc/incoming/import_survey.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

data/app/models/renalware/ukrdc/incoming/import_surveys.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

data/app/models/renalware/ukrdc/incoming/xml_document.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

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

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC
@@ -18,7 +17,7 @@ module Renalware
         Pathology::ObservationRequest
           .where(id: Pathology::ObservationRequest.distinct_for_patient_id(patient_id))
           .where("requested_at >= ?", effective_changes_since)
-          .where("loinc_code is not null")
+          .where("loinc_code is not null") # NOTE: fails using where.not(loinc_code: nil)
           .eager_load(
             :description,
             observations: { description: :measurement_unit }

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

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

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

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 require "benchmark"
 module Renalware

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

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 require "benchmark"
 module Renalware

data/app/models/renalware/ukrdc/treatment_timeline/hd/generator.rb CHANGED

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
 module Renalware
   module UKRDC

data/app/models/renalware/ukrdc/treatment_timeline/pd/generator.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

data/app/models/renalware/ukrdc/treatment_timeline/pd/regime_decorator.rb CHANGED

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

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

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 module Renalware
   module UKRDC

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

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 require_dependency "renalware/ukrdc"
-require "attr_extras"
 # QBL   TXT   Description
 # "20"  "20"  "Transplant ; Cadaver donor"