renalware-core 2.0.0.pre.rc11 → 2.0.0.pre.rc13

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

@@ -8,7 +8,7 @@ module Renalware
       extend Enumerize
 
       belongs_to :patient, touch: true
-      belongs_to :recipient, class_name: "Patient", foreign_key: "recipient_id"
+      belongs_to :recipient, class_name: "Patient", foreign_key: "recipient_id", touch: true
 
       has_paper_trail class_name: "Renalware::Transplants::Version"
 

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

@@ -8,10 +8,12 @@ module Renalware
       include ModalityScopes
       include PatientPathologyScopes
       MODALITY_NAMES = ["Transplant"].freeze
+      DEFAULT_SEARCH_PREDICATE = "hgb_date DESC".freeze
       attr_reader :q, :relation, :named_filter
 
-      def initialize(relation: Transplants::Patient.all, named_filter: nil, q: {})
-        @q = q
+      def initialize(relation: Transplants::Patient.all, named_filter: nil, q: nil)
+        @q = q || {}
+        @q[:s] = DEFAULT_SEARCH_PREDICATE if @q[:s].blank?
         @relation = relation
         @named_filter = named_filter || :none
       end

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

@@ -12,8 +12,8 @@ module Renalware
                  foreign_key: "operation_id",
                  touch: true
       belongs_to :transplant_failure_cause_description,
-        class_name: "Transplants::FailureCauseDescription",
-        foreign_key: "transplant_failure_cause_description_id"
+                 class_name: "Transplants::FailureCauseDescription",
+                 foreign_key: "transplant_failure_cause_description_id"
 
       has_paper_trail class_name: "Renalware::Transplants::Version"
       has_document class_name: "Renalware::Transplants::RecipientFollowupDocument"

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

@@ -91,10 +91,16 @@ module Renalware
           end
 
           scope :ukt_status_is, lambda { |status|
-            where("transplant_registrations.document -> 'uk_transplant_centre' ->> 'status' ilike '#{status}'")
+            where(
+              "transplant_registrations.document -> 'uk_transplant_centre' ->> 'status' ilike ?",
+              status
+            )
           }
           scope :ukt_status_is_not, lambda { |status|
-            where.not("transplant_registrations.document -> 'uk_transplant_centre' ->> 'status' ilike '#{status}'")
+            where.not(
+              "transplant_registrations.document -> 'uk_transplant_centre' ->> 'status' ilike ?",
+              status
+            )
           }
           scope :current_status_is_active, ->{ current_status_in(:active) }
           scope :current_status_is_not_active, ->{ current_status_not_in(:active) }

data/app/models/renalware/ukrdc.rb

@@ -0,0 +1,9 @@
+require_dependency "renalware"
+
+module Renalware
+  module UKRDC
+    def self.table_name_prefix
+      "ukrdc_"
+    end
+  end
+end

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

@@ -0,0 +1,24 @@
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    # If the optional :changed_since argument is passed we select all RPV
+    # patients how have been updated since that date. Otherwise we select all RPV
+    # patients who have changed since the last time they were exported.
+    class PatientsQuery
+      def call(changed_since: nil)
+        if changed_since.present?
+          rpv_patients.where("updated_at > ?", changed_since)
+        else
+          rpv_patients.where("updated_at > sent_to_ukrdc_at")
+        end
+      end
+
+      private
+
+      def rpv_patients
+        Renalware::Patient.where(send_to_rpv: true)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,97 @@
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+module Renalware
+  module UKRDC
+    class SendPatient
+      pattr_initialize [:patient!, :dir!, :request_uuid!, :renderer, :changes_since, :logger]
+
+      def call
+        UKRDC::TransmissionLog.with_logging(patient, request_uuid) do |log|
+          logger.info "  Patient #{patient.to_param}"
+          xml_payload = build_payload(log)
+          if xml_payload_same_as_last_sent_payload?(xml_payload)
+            log.unsent_no_change_since_last_send!
+          else
+            send_file(xml_payload, log)
+          end
+          logger.info "    Status: #{log.status}"
+        end
+      end
+
+      private
+
+      def logger
+        @logger ||= Rails.logger
+      end
+
+      def xml_payload_same_as_last_sent_payload?(payload)
+        payload.to_md5_hash == last_sent_transmission_log.payload_hash
+      end
+
+      def send_file(payload, log)
+        File.open(xml_filepath, "w") { |file| file.write(payload) }
+        log.file_path = xml_filepath
+        log.sent!
+      end
+
+      def last_sent_transmission_log
+        @last_sent_transmission_log ||= begin
+          TransmissionLog.where(patient: patient, status: :sent).ordered.last || NullObject.instance
+        end
+      end
+
+      def build_payload(log)
+        Payload.new(render_xml_for(patient)).tap do |payload|
+          log.payload = payload.to_s
+          log.payload_hash = payload.to_md5_hash
+        end
+      end
+
+      def render_xml_for(patient)
+        renderer.render(
+          "renalware/api/ukrdc/patients/show",
+          locals: { patient: presenter_for(patient) }
+        )
+      end
+
+      def presenter_for(patient)
+        Renalware::UKRDC::PatientPresenter.new(patient, changes_since: changes_since)
+      end
+
+      # Note a test might have passed in a mock renderer
+      def renderer
+        @renderer ||= Renalware::API::UKRDC::PatientsController.renderer
+      end
+
+      def xml_filepath
+        raise(ArgumentError, "Patient has no ukrdc_external_id") if patient.ukrdc_external_id.blank?
+        filename = "#{patient.ukrdc_external_id}.xml"
+        File.join(dir, filename)
+      end
+
+      class Payload
+        pattr_initialize :payload
+        delegate :to_s, to: :payload
+
+        def to_md5_hash
+          @to_md5_hash ||= Digest::MD5.hexdigest(time_neutral_payload)
+        end
+
+        private
+
+        # Remove the time elements from SendingFacility
+        # e.g.
+        #   <SendingFacility channelName='Renalware' time='2018-02-26T13:18:02+00:00'/>
+        # becomes
+        #   <SendingFacility channelName='Renalware'/>
+        # This allows us to do payload comparisons independent of the time they were sent.
+        def time_neutral_payload
+          payload
+            .gsub(/<Stream>[^<]*<\/Stream>/, "<Stream>removed</Stream>")
+            .gsub(/ (time|start|stop)=["'][^'"]*['"]/, '')
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,91 @@
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    class SendPatients
+      attr_reader :patient_ids, :changed_since, :logger, :request_uuid
+
+      def initialize(changed_since: nil, patient_ids: nil, logger: nil)
+        @changed_since = Time.zone.parse(changed_since) if changed_since.present?
+        @patient_ids = Array(patient_ids)
+        @logger = logger || Rails.logger
+        @request_uuid = SecureRandom.uuid # helps group logs together
+      end
+
+      def call
+        logger.info "Request #{request_uuid}"
+
+        ms = Benchmark.ms do
+          send_patients
+        end
+        print_summary(ms)
+      end
+
+      private
+
+      def send_patients
+        logger.info("Generating XML files for #{patient_ids&.any? ? patient_ids : 'all'} patients")
+        query = Renalware::UKRDC::PatientsQuery.new.call(changed_since: changed_since)
+        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}")
+        else
+          logger.info("#{query.count} patients have changed since the last send")
+        end
+
+        folder_name = within_new_folder do |dir|
+          xml_path = dir.join("xml")
+          query.all.find_each do |patient|
+            SendPatient.new(
+              patient: patient,
+              dir: xml_path,
+              changes_since: changed_since,
+              request_uuid: request_uuid,
+              logger: logger
+            ).call
+          end
+        end
+        logger.info("Files saved to #{folder_name}")
+      end
+
+      def gpg_encrypt(filepath, output_filepath)
+        path_to_key = File.open(Rails.root.join("key.gpg"))
+        # only needed if the key has not been imported previously
+        GPGME::Key.import(path_to_key)
+        crypto = GPGME::Crypto.new(always_trust: true)
+        File.open(filepath) do |in_file|
+          File.open(output_filepath, "wb") do |out_file|
+            crypto.encrypt in_file, output: out_file, recipients: "Patient View"
+          end
+        end
+      end
+
+      def timestamp
+        Time.zone.now.strftime("%Y%m%d%H%M%S%L")
+      end
+
+      def within_new_folder
+        dir = Rails.root.join("tmp", timestamp)
+        FileUtils.mkdir_p dir
+        FileUtils.mkdir_p File.join(dir, "xml")
+        FileUtils.mkdir_p File.join(dir, "encrypted")
+        yield dir if block_given?
+        dir
+      end
+
+      def filepath_for(patient, dir, sub_folder)
+        raise(ArgumentError, "Patient has no ukrdc_external_id") if patient.ukrdc_external_id.blank?
+        filename = "#{patient.ukrdc_external_id}.xml"
+        File.join(dir, sub_folder.to_s, filename)
+      end
+
+      def print_summary(ms)
+        logger.info "*** Summary ***"
+        logger.info "Took #{ms.to_i / 1000} seconds"
+        results = TransmissionLog.where(request_uuid: request_uuid).group(:status).count(:status)
+        results.to_h.map{ |key, value| logger.info("#{key}: #{value}") }
+      end
+    end
+  end
+end

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

@@ -0,0 +1,30 @@
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    class TransmissionLog < ApplicationRecord
+      validates :sent_at, presence: true
+      validates :status, presence: true
+      belongs_to :patient, class_name: "Renalware::Patient"
+      enum status: [:undefined, :error, :unsent_no_change_since_last_send, :sent]
+      scope :ordered, ->{ order(sent_at: :asc) }
+
+      def self.with_logging(patient, request_uuid)
+        log = new(patient: patient, sent_at: Time.zone.now, request_uuid: request_uuid)
+        yield log if block_given?
+        log.save!
+      rescue StandardError => error
+        log.error = formatted_exception(error)
+        log.status = :error
+        log.save!
+      end
+
+      def self.formatted_exception(error)
+        [
+          "#{error.backtrace.first}: #{error.message} (#{error.class})",
+          error.backtrace.drop(1).map{ |s| "\t#{s}" }
+        ].join("\n")
+      end
+    end
+  end
+end

data/app/models/renalware/virology/profile.rb

@@ -3,6 +3,7 @@ require_dependency "renalware/virology"
 module Renalware
   module Virology
     class Profile < ApplicationRecord
+      belongs_to :patient, touch: true
     end
   end
 end

data/app/presenters/date_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class DatePresenter < SimpleDelegator
   def to_s
     ::I18n.l self

data/app/presenters/date_time_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class DateTimePresenter < SimpleDelegator
   def to_s
     ::I18n.l self

data/app/presenters/enumerize/value_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Enumerize
   class ValuePresenter < SimpleDelegator
     def to_s

data/app/presenters/false_class_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class FalseClassPresenter < SimpleDelegator
   def to_s
     # rubocop:disable Lint/BooleanSymbol

data/app/presenters/presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Presenter
   def self.for(value)
     klass = "#{value.class.name}Presenter".constantize

data/app/presenters/renalware/accesses/assessment_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Renalware
   module Accesses
     class AssessmentPresenter < DumbDelegator

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

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "renalware"
 require "renalware/accesses"
 

data/app/presenters/renalware/accesses/plan_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Renalware
   module Accesses
     class PlanPresenter < DumbDelegator

data/app/presenters/renalware/accesses/procedure_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Renalware
   module Accesses
     class ProcedurePresenter < DumbDelegator

data/app/presenters/renalware/accesses/profile_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Renalware
   module Accesses
     class ProfilePresenter < DumbDelegator

data/app/presenters/renalware/address_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_dependency "renalware"
 
 module Renalware

data/app/presenters/renalware/address_presenter/block.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_dependency "renalware/address_presenter"
 
 module Renalware

data/app/presenters/renalware/address_presenter/short.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_dependency "renalware/address_presenter"
 
 module Renalware

data/app/presenters/renalware/address_presenter/single_line.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_dependency "renalware/address_presenter"
 
 module Renalware

data/app/presenters/renalware/admin/users/summary_part.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Renalware
   module Admin
     module Users

data/app/presenters/renalware/admissions/admission_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_dependency "renalware/admissions"
 
 module Renalware

data/app/presenters/renalware/admissions/consult_presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_dependency "renalware/admissions"
 
 module Renalware