renalware-core 2.0.88 → 2.0.89

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: c722f3506055163495fabcf33d586d83597be269f5b40998cec8605236e6400a
+  metadata.gz: dea8d3ef3c91160dead8c1db92b9a131b218f2ab1001c2acd0ad6698f6b83e33
+  data.tar.gz: 4a19dba06dfd48d8973e103dd3cb950162bf3fe038af55acbd5cee991e240b17
 SHA512:
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-  data.tar.gz: 8f954eeaebce032662556e9b2bb2b4984479f7b13c27ee814e63b17a154836a5c91f596107cbc2e0961c2c32daf3849045f29caea5f39805483ae9ffff3a9d77
+  metadata.gz: de2b1c0d56675e5e23607cca2729c9864516ff919e838a278dcc84a15598b72ed2ab26b0be8894894a8cb10d5c1229213af78a6001bbfcc723ec881e5f43e52b
+  data.tar.gz: a8c732dfd1caba2154487c21c8f557ba52e09f161b71886262516938b2331399c33806d9fe292b961ad08d60d373baf55e632c1754d7cddfdcebe76922d5259f

data/Rakefile

@@ -43,3 +43,12 @@ namespace :assets do
     Rake::Task["app:assets:clobber"].invoke
   end
 end
+
+# Default rake task to run all tests:
+#   bundle exec rake
+task :engine_default_task do
+  sh "bin/rspec"
+  sh "bin/cucumber"
+  sh "bin/cucumber TEST_DEPTH=web --profile rake_web"
+end
+task(:default).clear.enhance(["engine_default_task"])

data/app/models/renalware/hospitals/unit.rb

@@ -7,6 +7,12 @@ module Renalware
     class Unit < ApplicationRecord
       extend Enumerize
 
+      UNIT_TYPE_RR8_MAP = {
+        hospital: "HOSP",
+        satellite: "SATL",
+        home: "HOME"
+      }.freeze
+
       belongs_to :hospital_centre, class_name: "Hospitals::Centre"
       has_many :wards,
                class_name: "Hospitals::Ward",
@@ -32,6 +38,11 @@ module Renalware
       def to_s
         "#{name} (#{unit_code})"
       end
+
+      # Map unit_type to its equivalent Renal Registry RR8 code.
+      def unit_type_rr8
+        UNIT_TYPE_RR8_MAP[unit_type.to_sym]
+      end
     end
   end
 end

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

@@ -19,10 +19,11 @@ module Renalware
         :request_uuid,
         :timestamp,
         :batch_number,
-        :summary
+        :summary,
+        :force_send
       )
 
-      def initialize(changed_since: nil, patient_ids: nil, logger: nil)
+      def initialize(changed_since: nil, patient_ids: nil, logger: nil, force_send: false)
         @changed_since = Time.zone.parse(changed_since) if changed_since.present?
         @patient_ids = Array(patient_ids)
         @logger = logger || Rails.logger
@@ -30,6 +31,7 @@ module Renalware
         @timestamp = Time.zone.now.strftime("%Y%m%d%H%M%S%L")
         @batch_number ||= BatchNumber.next.number
         @summary = ExportSummary.new
+        @force_send = force_send
       end
 
       def call
@@ -74,7 +76,8 @@ module Renalware
             changes_since: changed_since,
             request_uuid: request_uuid,
             batch_number: batch_number,
-            logger: logger
+            logger: logger,
+            force_send: force_send
           ).call
         end
       end
@@ -89,11 +92,18 @@ module Renalware
       def ukrdc_patients_who_have_changed_since_last_send
         @ukrdc_patients_who_have_changed_since_last_send ||= begin
           logger.info("Finding #{patient_ids&.any? ? patient_ids : 'all ukrdc'} patients")
-          query = Renalware::UKRDC::PatientsQuery.new.call(changed_since: changed_since)
+          query = Renalware::UKRDC::PatientsQuery.new.call(
+            changed_since: changed_since,
+            changed_since_last_send: !force_send
+          )
           query = query.where(id: Array(patient_ids)) if patient_ids.present?
 
           if changed_since.present?
-            logger.info("#{query.count} patients have changed since #{changed_since}")
+            if force_send
+              logger.info("sending #{query.count} patients, taking changes since #{changed_since}")
+            else
+              logger.info("#{query.count} patients have changed since #{changed_since}")
+            end
           else
             logger.info("#{query.count} patients have changed since the last send")
           end

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

@@ -14,10 +14,13 @@ module Renalware
         :logger,
         :batch_number,
         :renderer, # so we can pass a test renderer to bypass real rendering
-        :log
+        :log,
+        :force_send
       ]
 
       # rubocop:disable Metrics/AbcSize
+      # If force_send is true then send all files even if they have not changed since the last
+      # send. This is primarily for debugging and testing phases with UKRDC
       def call
         update_patient_to_indicated_we_checked_them_for_any_relevant_changes
         UKRDC::TransmissionLog.with_logging(patient, request_uuid) do |log|
@@ -25,7 +28,7 @@ module Renalware
           logger.info "  Patient #{patient.ukrdc_external_id}"
           xml_payload = build_payload(log)
           if xml_payload.present?
-            if xml_payload_same_as_last_sent_payload?(xml_payload)
+            if !force_send && xml_payload_same_as_last_sent_payload?(xml_payload)
               logger.info "    skipping as no change in XML file"
               log.unsent_no_change_since_last_send!
             else

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

@@ -18,11 +18,15 @@ module Renalware
     # this for now I think. If it is a problem we can use the checked_for_ukrdc_changes_at column
     # on patients.
     class PatientsQuery
-      def call(changed_since: nil)
+      def call(changed_since: nil, changed_since_last_send: true)
         if changed_since.present?
-          sendable_patients.where("updated_at > ?", changed_since)
-        else
+          # patients who changed since a specific date (inclusive)
+          sendable_patients.where("updated_at >= ?", changed_since)
+        elsif changed_since_last_send
+          # patients who have never been sent, or have changed since the last time they were sent
           sendable_patients.where("(sent_to_ukrdc_at is null) or (updated_at > sent_to_ukrdc_at)")
+        else
+          sendable_patients
         end
       end
 
@@ -31,7 +35,7 @@ module Renalware
       def sendable_patients
         Renalware::Patient.where(send_to_rpv: true).or(
           Renalware::Patient.where(send_to_renalreg: true)
-        )
+        ).order(family_name: :asc, given_name: :asc)
       end
     end
   end

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

@@ -15,11 +15,11 @@ module Renalware
 
         def call
           PrepareTables.call
-          RemapModelTableNamesToTheirPreparedEquivalents.call
-
-          modalities.each do |modality|
-            print "#{modality.description.name} "
-            GeneratorFactory.call(modality).call
+          RemapModelTableNamesToTheirPreparedEquivalents.new.call do
+            modalities.each do |modality|
+              print "#{modality.description.name} "
+              GeneratorFactory.call(modality).call
+            end
           end
         end
 

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

@@ -4,7 +4,7 @@
 module Renalware
   module UKRDC
     module TreatmentTimeline
-      # Wehen generating the tratment timeline, sites may want to pre-prepare a massaged version
+      # When generating the treatment 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.
@@ -19,16 +19,25 @@ module Renalware
         ].freeze
         class ExecutionNotAllowedError < StandardError; end
 
-        def self.call(models = MODELS)
-          new.call(models)
-        end
-
-        def call(models)
+        # Saves the original table names for the array of models classes
+        # remaps to its ukrdc_prepared_* varaient if it exists, yields to allow
+        # the claling process to do its thing, then importantly winds back to
+        # the original table names.
+        def call(models = MODELS)
           fail_unless_running_in_rake_or_rspec
-          Array(models).each do |model_class|
+          models = Array(models)
+          original_table_names = models.map(&:table_name)
+
+          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
+
+          yield if block_given?
+
+          models.each_with_index do |model_class, index|
+            model_class.table_name = original_table_names[index]
+          end
         end
 
         private

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

@@ -39,7 +39,10 @@ module Renalware
       end
 
       def modalities
-        __getobj__.modalities.includes(:description).order(started_on: :asc, created_at: :asc)
+        __getobj__
+          .modalities
+          .includes(:description)
+          .order(started_on: :asc, created_at: :asc)
       end
 
       def dead?
@@ -52,6 +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.
       def letters
         return ::Renalware::Letters::Letter.none if send_to_rpv == false
 

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

@@ -8,6 +8,7 @@ xml = builder
 # like CAPD and HDF are not yet implemented, just the top level modality.
 patient.modalities.each do |modality|
   ukrdc_modality_code_id = modality.description.ukrdc_modality_code_id
+
   next if ukrdc_modality_code_id.blank?
 
   ukrdc_modality_code = Renalware::UKRDC::ModalityCode.find(ukrdc_modality_code_id)
@@ -28,24 +29,25 @@ patient.modalities.each do |modality|
       xml.Code ukrdc_modality_code.txt_code
     end
 
-    # # This is a bit of hack to get the HD Profile location for the current modality
-    # if [1, 2, 3, 4, 5, 9].include?(ukrdc_modality_code.txt_code.to_i) # HD
-    #   profile = Renalware::HD::Profile
-    #     .for_patient(patient)
-    #     .where(<<-SQL).first
-    #     created_at::date <= '#{modality.started_on}'
-    #     and (
-    #       deactivated_at is NULL or
-    #       (
-    #         deactivated_at >= '#{modality.started_on}'
-    #       )
-    #     )
-    #     SQL
-    #   if profile&.hospital_unit.present?
-    #     xml.Attributes do
-    #       xml.QBL05 profile.hospital_unit.unit_type # eg home
-    #     end
-    #   end
-    # end
+    # This is a bit of hack to get the HD Profile location for the current modality
+    if [1, 2, 3, 4, 5, 9].include?(ukrdc_modality_code.txt_code.to_i) # HD
+      profile = Renalware::HD::Profile
+        .where(patient_id: patient.id)
+        .where(<<-SQL).order(created_at: :desc).first
+        created_at::date <= '#{modality.started_on}'
+        and (
+          deactivated_at is NULL or
+          (
+            deactivated_at > '#{modality.started_on}'
+          )
+        )
+        SQL
+
+      if profile&.hospital_unit&.unit_type_rr8.present?
+        xml.Attributes do
+          xml.QBL05 profile.hospital_unit.unit_type_rr8 # eg HOME
+        end
+      end
+    end
   end
 end

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.88"
+  VERSION = "2.0.89"
 end

data/lib/tasks/ukrdc.rake

@@ -5,40 +5,37 @@ require "fileutils"
 # Note you can print out the help for this task and others with `rake -D`
 namespace :ukrdc do
   desc <<-DESC
-    Creates a folder of UKRDC XML files with any changes to PV patients since their last export
+    Creates a folder of UKRDC XML files with any changes to PV + RR patients since their last export
     Notes:
       1. Running the rake task updates the sent_to_ukrdc_at for each patient exported.
-         If you don't want to do this you may need to edit this task to wrpt the code in a
+         If you don't want to do this you may need to edit this task to wrap the code in a
          transaction you can optionally roll back.
      2: If testing this inside the renalware-core gem, you will need to append app: e.g.
         app:ukrdc:export ...
 
     Example usage
-      1. To get all patients with send_to_rpv=true who have changed since the last time they
-         were sent, or have not been sent to the UKRDC yet:
+      1. To get all RR and RPV patients with who have changed
+         since the last time they were sent, or have not been sent to the UKRDC yet:
 
          bundle exec rake ukrdc:export
 
-      2. To get all patients with send_to_rpv=true who have changed since a certain date:
+      2. To get all RR and RPV patients who have changed since a certain date:
 
-         bundle exec rake ukrdc:export["2018-02-23"]
-         or in zsh shell
-         bundle exec rake ukrdc:export\["2018-02-23"\]
+         bundle exec rake ukrdc:export changed_since="2018-02-23"
 
-      3. To get only certain RPV patients (by their id eg ids 1 and 2) who with changes since
-         a certain time (not pass patient ids in a space delimited string:
+      3. To get only certain RR and RPV patients (by their id eg ids 1 and 2) with changes since
+         a certain date:
 
-         bundle exec rake ukrdc:export["2018-02-23","1 2"]
-         or in the zsh shell
-         bundle exec rake ukrdc:export\["2018-02-23","1 2"\]
+         bundle exec rake ukrdc:export changed_since=2018-02-23 patient_ids=1,2
   DESC
-  task :export, [:changed_since, :patient_ids] => [:environment] do |_task, args|
+  task :export => :environment do |_task, args|
     logger           = ActiveSupport::TaggedLogging.new(Logger.new(STDOUT))
     logger.level     = Logger::INFO
     Rails.logger     = logger
     Renalware::UKRDC::CreateEncryptedPatientXMLFiles.new(
-      changed_since: args[:changed_since],
-      patient_ids: args.fetch(:patient_ids, "").split(" ").map(&:to_i)
+      changed_since: ENV["changed_since"],
+      patient_ids: ENV.fetch("patient_ids", "").split(",").map(&:to_i),
+      force_send: ENV["force_send"] == "true"
     ).call
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.88
+  version: 2.0.89
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-26 00:00:00.000000000 Z
+date: 2019-07-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -72,14 +72,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 9.4.2
+        version: '9.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 9.4.2
+        version: '9.6'
 - !ruby/object:Gem::Dependency
   name: client_side_validations
   requirement: !ruby/object:Gem::Requirement
@@ -938,16 +938,16 @@ dependencies:
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.15
+        version: 0.9.20
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.15
+        version: 0.9.20
 description: Renalware uses demographic, clinical, pathology, and nephrology datasets
   to improve patient care, undertake clinical and administrative audits and share
   data with external systems.