renalware-core 2.0.53 → 2.0.54

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5c36923d9a31021d45bae1db60627efefd8b843457cb6a7e102012cb989d254a
-  data.tar.gz: 86a0c83e095d0a70e3dbeb2905e44951e5553a3a7051977071e3ed302daee258
+  metadata.gz: 850fb8d5f1245a54162eaa4fb6e075f272563bac0729d30d4209fbf34c3fd378
+  data.tar.gz: 90e3476b1530fb2d49447bd9a882e456bcdabe533004be2d060993b361b6c076
 SHA512:
-  metadata.gz: 05e3cebc48a295074ac4ad1727debdee1c11b2a76c3a42d4fb973ad7393e3a2ee2697f7aac3dec3bb286d133a75c4e701f1ec6dd0d0aeef396c6877ffd217754
-  data.tar.gz: 07dd641741d884f975ac577f89ead6ef2ed8a33f11caabcab7ebe1921bbfe8e037f200fe00e5b5bc7ca2a89fecf4e04e008d6347528fb7b3929200943e315c38
+  metadata.gz: 63f4a175065d5c917e9e12b70466482fd0a9b8dad17122024909e6eb6a13b1f82183520346755ca72dfc8e3dbd0c450cd95351e9dfd2d95ff0fcaa8788a44d27
+  data.tar.gz: cd8734fc777f8dc1fcb54ff4814aa6a9e23a0628e774c5224b427873455d937f6a173a62779ffbbdf4ea2dafd40f4ee795a259a1e3affbb09390f348066b178d

data/app/documents/renalware/hd/session_document.rb

@@ -75,7 +75,7 @@ module Renalware
         ).each { |att| validates(att, numericality: { allow_blank: true }) }
 
         validates :machine_urr, inclusion: { in: 0..100, allow_blank: true }
-        validates :machine_ktv, inclusion: { in: (0.2..3.5), allow_blank: true }
+        validates :machine_ktv, inclusion: { in: (0.05..3.5), allow_blank: true }
         validates :blood_flow, numericality: {
           greater_than_or_equal_to: 50,
           less_than_or_equal_to: 800,

data/app/inputs/clock_picker_input.rb

@@ -28,7 +28,7 @@ class ClockPickerInput < SimpleForm::Inputs::StringInput
   end
 
   def icon_clock
-    "<span class='prefix'><i class='fa fa-clock-o'></i></span>".html_safe
+    "<span class='prefix'><i class='far fa-clock'></i></span>".html_safe
   end
 
   def input_type

data/app/inputs/date_picker_input.rb

@@ -30,7 +30,7 @@ class DatePickerInput < SimpleForm::Inputs::StringInput
   # rubocop:enable Metrics/AbcSize
 
   def icon_calendar
-    "<span class='prefix'><i class='fa fa-calendar'></i></span>".html_safe
+    "<span class='prefix'><i class='far fa-calendar'></i></span>".html_safe
   end
 
   def input_type

data/app/inputs/simple_time_input.rb

@@ -25,7 +25,7 @@ class SimpleTimeInput < SimpleForm::Inputs::StringInput
   end
 
   def icon_clock
-    "<span class='prefix'><i class='fa fa-clock-o'></i></span>".html_safe
+    "<span class='prefix'><i class='far fa-clock'></i></span>".html_safe
   end
 
   def input_type

data/app/mailers/renalware/previews/report_preview.rb

@@ -4,7 +4,7 @@ require_dependency "renalware/reporting"
 
 module Renalware
   module Reporting
-    # Preview all emails at http://localhost:3000/rails/mailers/report
+    # Preview all emails at http://localhost:3000/rails/mailers
     class ReportPreview < ActionMailer::Preview
       def daily_summary
         Reporting::ReportMailer.daily_summary

data/app/mailers/renalware/previews/ukrdc_summary_preview.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/reporting"
+
+module Renalware
+  module UKRDC
+    # Preview all emails at http://localhost:3000/rails/mailers
+    class SumaryPreview < ActionMailer::Preview
+      def daily_summary
+        summary = ExportSummary.new(
+          archive_folder: "/var/ukrdc/test",
+          num_changed_patients: 10,
+          milliseconds_taken: 123.0,
+          results: { sent: 1, unsent: 2 }
+        )
+        UKRDC::SummaryMailer.export_summary(summary: summary)
+      end
+    end
+  end
+end

data/app/mailers/renalware/previews/user_mailer_preview.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 module Renalware
+  # Preview all emails at http://localhost:3000/rails/mailers
   class Admin::UserMailerPreview < ActionMailer::Preview
     def approval
       user = User.first

data/app/mailers/renalware/ukrdc/summary_mailer.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/reporting"
+
+module Renalware
+  module UKRDC
+    class SummaryMailer < ApplicationMailer
+      def export_summary(to: "dev@airslie.com", **args)
+        mail(
+          to: Array(to),
+          subject: "UKRC export summary #{I18n.l(Time.zone.today)}"
+        ) do |format|
+          format.text { render(locals: args) }
+          format.html { render(locals: args) }
+        end
+      end
+    end
+  end
+end

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

@@ -0,0 +1,136 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "gpg_encrypt_folder"
+
+module Renalware
+  module UKRDC
+    # Using a working folder with a timestamp name, find matching patients and for each, generate
+    # an XML file (see UKRDC Schema) containing changes since the last time we sent the URDC data
+    # about them. Encrypt the xml files and copy to an outgoing folder
+    # which might for example be a symlink to an outgoing folder in /mmedia/ukrdc which in turn
+    # is mount on a remote share for example on an SFTP server.
+    #
+    class CreateEncryptedPatientXMLFiles
+      attr_reader :patient_ids, :changed_since, :logger, :request_uuid, :paths, :timestamp, :summary
+
+      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
+        @timestamp = Time.zone.now.strftime("%Y%m%d%H%M%S%L")
+        @paths = Paths.new(timestamp: @timestamp, working_path: config.ukrdc_working_path)
+        @summary = ExportSummary.new
+      end
+
+      def call
+        logger.tagged(request_uuid) do
+          summary.milliseconds_taken = Benchmark.ms do
+            create_patient_xml_files
+            encrypt_patient_xml_files
+            copy_encrypted_xml_files_into_the_outgoing_folder
+            paths.create_symlink_to_latest_timestamped_folder_so_it_is_easier_to_eyeball
+          end
+          build_summary
+          print_summary
+          email_summary
+        end
+      rescue StandardError => exception
+        Engine.exception_notifier.notify(exception)
+        raise exception
+      end
+
+      private
+
+      def create_patient_xml_files
+        patients = ukrdc_patients_who_have_changed_since_last_send
+        summary.num_changed_patients = patients.count
+        patients.find_each do |patient|
+          CreatePatientXMLFile.new(
+            patient: patient,
+            dir: paths.timestamped_xml_folder,
+            changes_since: changed_since,
+            request_uuid: request_uuid,
+            logger: logger
+          ).call
+        end
+      end
+
+      def build_summary
+        summary.count_of_files_in_outgoing_folder = count_of_files_in_outgoing_folder
+        summary.archive_folder = paths.timestamped_folder
+        summary.results = export_results
+      end
+
+      # rubocop:disable Metrics/AbcSize
+      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 = 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
+          query.all
+        end
+      end
+      # rubocop:enable Metrics/AbcSize
+
+      # rubocop:disable Metrics/AbcSize
+      def print_summary
+        logger.info("Files saved to #{summary.archive_folder}")
+        logger.info "*** Summary ***"
+        logger.info "Took #{summary.milliseconds_taken.to_i / 1000} seconds"
+        summary.results.map{ |key, value| logger.info("#{key}: #{value}") }
+      end
+      # rubocop:enable Metrics/AbcSize
+
+      def email_summary
+        UKRDC::SummaryMailer.export_summary(
+          to: email_recipients,
+          summary: summary
+        ).deliver
+      end
+
+      def email_recipients
+        Array(ENV.fetch("DAILY_REPORT_EMAIL_RECIPIENTS", "dev@airslie.com").split(","))
+      end
+
+      def export_results
+        TransmissionLog.where(request_uuid: request_uuid).group(:status).count(:status).to_h
+      end
+
+      def encrypt_patient_xml_files
+        logger.info "Encrypting..."
+        GpgEncryptFolder.new(folder: paths.timestamped_xml_folder, options: gpg_options).call
+      end
+
+      def copy_encrypted_xml_files_into_the_outgoing_folder
+        encrypted_files = Dir.glob(paths.timestamped_encrypted_folder.join("*.*"))
+        FileUtils.cp_r(encrypted_files, paths.outgoing_folder) if encrypted_files.any?
+      end
+
+      def count_of_files_in_outgoing_folder
+        Dir.glob(File.join(paths.outgoing_folder, "*.*")).count
+      end
+
+      def config
+        Renalware.config
+      end
+
+      def gpg_options
+        GpgOptions.new(
+          recipient: config.ukrdc_gpg_recipient,
+          keyring: config.ukrdc_gpg_keyring,
+          homedir: config.ukrdc_gpg_homedir,
+          destination_folder: paths.timestamped_encrypted_folder,
+          timestamp: timestamp
+        )
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/{send_patient.rb → create_patient_xml_file.rb}

@@ -5,10 +5,12 @@ require "attr_extras"
 
 module Renalware
   module UKRDC
-    class SendPatient
+    class CreatePatientXMLFile
       pattr_initialize [:patient!, :dir!, :request_uuid!, :renderer, :changes_since, :logger]
 
+      # rubocop:disable Metrics/AbcSize
       def call
+        update_patient_to_indicated_we_checked_them_for_any_relevant_changes
         UKRDC::TransmissionLog.with_logging(patient, request_uuid) do |log|
           logger.info "  Patient #{patient.to_param}"
           xml_payload = build_payload(log)
@@ -16,17 +18,13 @@ module Renalware
             logger.info "    skipping as no change in XML file"
             log.unsent_no_change_since_last_send!
           else
-            send_file(xml_payload, log)
-            # Important we use update_column here so we don't trigger updated_at to change
-            # on the patient, which affects the results of PatientsQuery next time.
-            patient.update_column(:sent_to_ukrdc_at, Time.zone.now)
-            logger.info(
-              "    sending file and setting patient.sent_to_ukrdc_at = #{patient.sent_to_ukrdc_at}"
-            )
+            create_xml_file(xml_payload, log)
+            update_patient_to_indicate_we_have_sent_their_data_to_ukrdc
           end
           logger.info "    Status: #{log.status}"
         end
       end
+      # rubocop:enable Metrics/AbcSize
 
       private
 
@@ -34,11 +32,26 @@ module Renalware
         @logger ||= Rails.logger
       end
 
+      # Important we use update_column here so we don't trigger updated_at to change
+      # on the patient, which affects the results of PatientsQuery next time.
+      def update_patient_to_indicated_we_checked_them_for_any_relevant_changes
+        patient.update_column(:checked_for_ukrdc_changes_at, Time.zone.now)
+      end
+
+      # Important we use update_column here so we don't trigger updated_at to change
+      # on the patient, which affects the results of PatientsQuery next time.
+      def update_patient_to_indicate_we_have_sent_their_data_to_ukrdc
+        patient.update_column(:sent_to_ukrdc_at, Time.zone.now)
+        logger.info(
+          "    sending file and setting patient.sent_to_ukrdc_at = #{patient.sent_to_ukrdc_at}"
+        )
+      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)
+      def create_xml_file(payload, log)
         File.open(xml_filepath, "w") { |file| file.write(payload) }
         log.file_path = xml_filepath
         log.sent!
@@ -99,9 +112,9 @@ module 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(%r{<Stream>[^<]*<\/Stream>}, "<Stream>removed</Stream>")
             .gsub(/ (time|start|stop)=["'][^'"]*['"]/, "")
-            .gsub(/<UpdatedOn>[^<]*<\/UpdatedOn>/, "<UpdatedOn>removed</UpdatedOn>")
+            .gsub(%r{<UpdatedOn>[^<]*<\/UpdatedOn>}, "<UpdatedOn>removed</UpdatedOn>")
         end
       end
     end

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

@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+module Renalware
+  module UKRDC
+    class ExportSummary
+      attr_accessor_initialize [
+        :milliseconds_taken,
+        :num_changed_patients,
+        :results,
+        :archive_folder,
+        :count_of_files_in_outgoing_folder
+      ]
+
+      def elapsed_time
+        (milliseconds_taken.to_f / 1000.0).round(2)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    class Paths
+      attr_reader :timestamp, :working_path
+
+      def initialize(timestamp: nil, working_path:)
+        raise(ArgumentError, "Invalid working_path") if working_path.blank?
+
+        @timestamp = timestamp
+        @timestamp ||= Time.zone.now.strftime("%Y%m%d%H%M%S%L")
+        @working_path = Pathname(working_path)
+        create_folders
+      end
+
+      def archive_folder
+        @archive_folder ||= working_path.join("archive")
+      end
+
+      # Name for the symlink to the latest archive folder
+      def latest_archive_symlink_name
+        @latest_archive_symlink_name ||= archive_folder.join("latest")
+      end
+
+      def outgoing_folder
+        @outgoing_folder ||= working_path.join("outgoing")
+      end
+
+      def timestamped_folder
+        @timestamped_folder ||= archive_folder.join(timestamp)
+      end
+
+      def timestamped_xml_folder
+        @timestamped_xml_folder ||= timestamped_folder.join("xml")
+      end
+
+      def timestamped_encrypted_folder
+        @timestamped_encrypted_folder ||= timestamped_folder.join("encrypted")
+      end
+
+      def create_symlink_to_latest_timestamped_folder_so_it_is_easier_to_eyeball
+        if File.exist?(latest_archive_symlink_name)
+          FileUtils.rm(latest_archive_symlink_name)
+        end
+        FileUtils.ln_sf(timestamped_folder, latest_archive_symlink_name)
+      end
+
+      def create_folders
+        FileUtils.mkdir_p timestamped_xml_folder
+        FileUtils.mkdir_p timestamped_encrypted_folder
+        FileUtils.mkdir_p outgoing_folder
+      end
+    end
+  end
+end

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

@@ -7,6 +7,16 @@ module Renalware
     # 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.
+    # A patient has a sent_to_ukrdc_at datetime which is the last time the data was actually sent.
+    # It maybe be that something about the patient has changed and updated_at > sent_to_ukrdc_at
+    # however when compiled to xml there are no effective changes, for example because some notes
+    # were added somewhere on the patient's data but those notes don't make it into the XML. So
+    # therefore no effective changes and we don't send the file to UKRDC.
+    # However a downside of this approach is that we always find updated patients and generate
+    # an XML for them, in order to compare an MD5 hash of the XML with what was previously sent, and
+    # *sometimes* this is waste of time if the MD5 hash has not changed. However we will live with
+    # 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)
         if changed_since.present?

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

@@ -78,7 +78,7 @@ module Renalware
       end
 
       def contact_details?
-        email || home_telephone || mobile_telephone
+        email.present? || home_telephone.present? || mobile_telephone.present?
       end
 
       def allergies

data/app/validators/renalware/patients/hdf_presence_validator.rb

@@ -10,7 +10,7 @@ module Renalware
     class HDFPresenceValidator < ActiveModel::EachValidator
       def validate_each(_record, _attribute, value)
         hdf = value
-        attribute_names = hdf.attributes.map(&:first)
+        attribute_names = [:subs_volume]
         attribute_names.each do |attribute_name|
           hdf.errors.add(attribute_name, :blank) if value[attribute_name].blank?
         end

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

@@ -23,12 +23,10 @@ xml.Documents do
       xml.EnteredAt do
         xml.CodingStandard "ODS"
         xml.Code letter.hospital_unit_code
-        xml.Description ""
       end
       xml.FileType "application/pdf"
       xml.FileName letter.pdf_stateless_filename
       xml.Stream Base64.encode64(Renalware::Letters::PdfRenderer.call(letter))
-      xml.DocumentURL
     end
   end
 end

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

@@ -5,12 +5,10 @@ xml = builder
 xml.Medications do
   patient.prescriptions.each do |prescription|
     xml.Medication do
-      xml.PrescriptionNumber
       xml.FromTime prescription.prescribed_on.to_datetime
       if prescription.terminated_or_marked_for_termination?
         xml.ToTime prescription.terminated_on&.to_datetime
       end
-      xml.OrderedBy
       xml.Route do
         xml.CodingStandard "RR22"
         xml.Code prescription.medication_route&.rr_code

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

@@ -31,16 +31,8 @@ xml.Treatment do
     xml.HDP03 session.document.dialysis.flow_rate
     xml.HDP04 session&.dialysate&.sodium_content
     xml.QBL05 session.access_type
-    xml.comment! "QBL06 HD Shared Care - including as XSD requires it, but not implemented yet"
-    xml.QBL06 ""
-    xml.comment! "QBL07 HD Shared Care - including as XSD requires it, but not implemented yet"
-    xml.QBL07 ""
     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
-
-  # xml.UpdatedOn
-  # xml.ActionCode
-  # xml.ExternalId
 end

data/app/views/renalware/api/ukrdc/patients/lab_orders/_lab_order.xml.builder

@@ -40,9 +40,6 @@ xml.LabOrder do
   end
   # xml.SpecimenCollectedTime request.requested_at.iso8601
   # xml.SpecimenReceivedTime "TODO"
-  # xml.Priority do
-  #   xml.Code "TODO: Probably n/a"
-  # end
   xml.SpecimenSource request.description.bottle_type
   # xml.Duration "OBR:27.3 but no available in the example messages I have"
 

data/app/views/renalware/api/ukrdc/patients/lab_orders/_result_item.xml.builder

@@ -5,7 +5,6 @@ observation = Renalware::Pathology::ObservationPresenter.new(observation)
 observation = Renalware::UKRDC::PathologyObservationPresenter.new(observation)
 
 xml.ResultItem do
-  # xml.ResultType
   xml.EnteredOn observation.updated_at&.iso8601
   xml.PrePost observation.pre_post(patient_is_on_hd: patient.current_modality_hd?)
   xml.ServiceId do
@@ -18,12 +17,7 @@ xml.ResultItem do
     end
     xml.Description observation.description_name
   end
-  # xml.SubId
   xml.ResultValue observation.result
   xml.ResultValueUnits observation.measurement_unit_name
-  # xml.AbnormalFlags
-  # xml.Status
   xml.ObservationTime observation.observed_at&.iso8601
-  # xml.Comments
-  # xml.ReferenceComment
 end

data/app/views/renalware/problems/problems/_archived_table.html.slim

@@ -5,7 +5,7 @@ table#archived_problems.manual-stripes.auto-layout
       th Description
       th.col-width-date Archived on
       th.nowrap Archived by
-      th.col-width-date Recorded on
+      th.col-width-date Updated on
       th.nowrap Recorded by
 
   = content_tag(:tbody, class: "sortables", data: { rel: sort_patient_problems_path(@patient) }) do

data/app/views/renalware/problems/problems/_current_table.html.slim

@@ -3,8 +3,8 @@ table#current_problems.manual-stripes.auto-layout
     tr
       th.options.col-width-small
       th Description
-      th.col-width-date Recorded on
-      td.nowrap Recorded by
+      th.col-width-date Updated on
+      td.nowrap Updated by
       th.col-width-tiny Reorder
   = content_tag(:tbody, class: "sortables", data: { rel: sort_patient_problems_path(@patient) }) do
     - problems.each do |problem|
@@ -22,6 +22,6 @@ table#current_problems.manual-stripes.auto-layout
             - problem.notes.each do |note|
               li= note.description
         td= l problem.updated_on
-        td= problem.created_by.full_name
+        td= problem.updated_by.full_name
         td.handle
           i.fas.fa-bars

data/app/views/renalware/ukrdc/summary_mailer/export_summary.html.slim

@@ -0,0 +1,13 @@
+p= l(Time.zone.now)
+p= "XML files archived to #{summary.archive_folder} and took #{summary.elapsed_time} seconds"
+p= "Count of patients changed since the last time they were sent: #{summary.num_changed_patients}"
+
+- if summary.results.empty?
+  p Nothing to send
+- else
+  ul
+    - summary.results.each do |key, value|
+      li= "#{key.to_s.humanize}: #{value}"
+
+
+p= "Count of files waiting in outgoing folder: #{summary.count_of_files_in_outgoing_folder}"

data/app/views/renalware/ukrdc/summary_mailer/export_summary.text.erb

@@ -0,0 +1,11 @@
+<%= l(Time.zone.now) %>
+
+XML files archived to <%=summary.archive_folder%> and took <%=summary.elapsed_time %> seconds.
+
+Results
+
+<% summary.results.each do |key, value| %>
+  <%= %"#{key.to_s.humanize}: #{value}" %>
+<% end %>
+
+Count of files waiting in outgoing folder: <%= summary.count_of_files_in_outgoing_folder %>

data/db/migrate/20181025170410_add_ukrdc_helper_column_to_patients.rb

@@ -0,0 +1,9 @@
+class AddUKRDCHelperColumnToPatients < ActiveRecord::Migration[5.2]
+  include MigrationHelper
+
+  def change
+    within_renalware_schema do
+      add_column :patients, :checked_for_ukrdc_changes_at, :datetime
+    end
+  end
+end

data/db/views/reporting_daily_pathology_v02.sql

@@ -9,7 +9,7 @@ select
   (select max(created_at) from delayed_jobs) as delayed_jobs_latest_entry,
   (select count(*) from delayed_jobs where created_at >= now()::date) as delayed_jobs_added_today,
   (select json_object_agg(priority, count) from (select priority, count(*) from delayed_jobs group by priority ) query) as delayed_jobs_priority_counts,
-  (select json_object_agg(queue, count) from (select queue, count(*) from delayed_jobs group by queue ) query) as delayed_jobs_queue_counts,
+  (select json_object_agg(coalesce(queue, 'unset'), count) from (select queue, count(*) from delayed_jobs group by queue ) query) as delayed_jobs_queue_counts,
   (select json_object_agg(attempts, count) from (select attempts, count(*) from delayed_jobs group by attempts ) query) as delayed_jobs_attempts_counts,
   (select count(*) from feed_messages) as feed_messages_total,
   (select count(*) from feed_messages where created_at >= now()::date) as feed_messages_added_today,

data/lib/gpg_encrypt_folder.rb

@@ -18,14 +18,19 @@ class GpgEncryptFolder
   pattr_initialize [:folder!, :options!]
 
   def call
-    Dir.glob(folder.join("xml", "*.xml")) do |file|
+    Dir.glob(folder.join("*.xml")) do |file|
       GpgEncryptFile.new(file: file, options: options).call
     end
   end
 end
 
 class GpgOptions
-  attr_reader_initialize [:recipient, :keyring, :homedir, :filename_transform]
+  attr_reader_initialize [
+    :recipient,
+    :keyring,
+    :homedir,
+    :destination_folder,
+    :timestamp]
 end
 
 class GpgEncryptFile
@@ -67,8 +72,15 @@ class GpgCommand
     "--keyring #{options.keyring}"
   end
 
-  # Calls a proc to transform the in file name into an out file name
+  def filename_with_extension
+    File.basename(file, ".xml")
+  end
+
+  def output_filename
+    "#{options.timestamp}_#{filename_with_extension}.gpg"
+  end
+
   def encrypted_filename
-    options.filename_transform.call(file)
+    options.destination_folder.join(output_filename)
   end
 end

data/lib/renalware/configuration.rb

@@ -61,6 +61,9 @@ module Renalware
     config_accessor(:ukrdc_gpg_keyring) do
       ENV.fetch("UKRDC_GPG_KEYRING", Engine.root.join("config", "gpg", "renalware_test.gpg"))
     end
+    config_accessor(:ukrdc_working_path) do
+      ENV.fetch("UKRDC_WORKING_PATH", File.join("/var", "ukrdc"))
+    end
 
     # We override this in some tests as a means of getting wicked_Pdf to generate an HTML version
     # of the PDF so we can examine its content

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.53"
+  VERSION = "2.0.54"
 end

data/lib/tasks/ukrdc.rake

@@ -33,10 +33,10 @@ namespace :ukrdc do
          bundle exec rake ukrdc:export\["2018-02-23","1 2"\]
   DESC
   task :export, [:changed_since, :patient_ids] => [:environment] do |_task, args|
-    logger           = Logger.new(STDOUT)
+    logger           = ActiveSupport::TaggedLogging.new(Logger.new(STDOUT))
     logger.level     = Logger::INFO
     Rails.logger     = logger
-    Renalware::UKRDC::SendPatients.new(
+    Renalware::UKRDC::CreateEncryptedPatientXMLFiles.new(
       changed_since: args[:changed_since],
       patient_ids: args.fetch(:patient_ids, "").split(" ").map(&:to_i)
     ).call

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.53
+  version: 2.0.54
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-10-24 00:00:00.000000000 Z
+date: 2018-10-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1297,8 +1297,10 @@ files:
 - app/mailers/renalware/letters/delivery/errors.rb
 - app/mailers/renalware/letters/delivery/practice_mailer.rb
 - app/mailers/renalware/previews/report_preview.rb
+- app/mailers/renalware/previews/ukrdc_summary_preview.rb
 - app/mailers/renalware/previews/user_mailer_preview.rb
 - app/mailers/renalware/reporting/report_mailer.rb
+- app/mailers/renalware/ukrdc/summary_mailer.rb
 - app/models/application_record.rb
 - app/models/concerns/renalware/accountable.rb
 - app/models/concerns/renalware/broadcasting.rb
@@ -1757,9 +1759,11 @@ files:
 - app/models/renalware/transplants/registrations/wait_list_query.rb
 - app/models/renalware/transplants/version.rb
 - app/models/renalware/ukrdc.rb
+- app/models/renalware/ukrdc/create_encrypted_patient_xml_files.rb
+- app/models/renalware/ukrdc/create_patient_xml_file.rb
+- app/models/renalware/ukrdc/export_summary.rb
+- app/models/renalware/ukrdc/paths.rb
 - app/models/renalware/ukrdc/patients_query.rb
-- app/models/renalware/ukrdc/send_patient.rb
-- app/models/renalware/ukrdc/send_patients.rb
 - app/models/renalware/ukrdc/transmission_log.rb
 - app/models/renalware/user.rb
 - app/models/renalware/version.rb
@@ -2764,6 +2768,8 @@ files:
 - app/views/renalware/transplants/registrations/show.html.slim
 - app/views/renalware/transplants/wait_lists/_registration.html.slim
 - app/views/renalware/transplants/wait_lists/show.html.slim
+- app/views/renalware/ukrdc/summary_mailer/export_summary.html.slim
+- app/views/renalware/ukrdc/summary_mailer/export_summary.text.erb
 - app/views/renalware/virology/dashboards/_actions.html.slim
 - app/views/renalware/virology/dashboards/show.html.slim
 - app/views/renalware/virology/profiles/_summary.html.slim
@@ -3330,6 +3336,7 @@ files:
 - db/migrate/20181008144324_update_daily_letters_report_view_to_version_2.rb
 - db/migrate/20181008145159_create_reporting_daily_ukrdc_view.rb
 - db/migrate/20181013115138_update_reporting_daily_pathology_view_to_v2.rb
+- db/migrate/20181025170410_add_ukrdc_helper_column_to_patients.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3713,7 +3720,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.4
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: Renalware core functionality as a mountable engine.

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

@@ -1,112 +0,0 @@
-# frozen_string_literal: true
-
-require_dependency "renalware/ukrdc"
-require "gpg_encrypt_folder"
-
-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)
-      rescue StandardError => exception
-        notify_exception(exception)
-        raise exception
-      end
-
-      private
-
-      def notify_exception(exception)
-        Engine.exception_notifier.notify(exception)
-      end
-
-      # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
-      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
-          encrypt_xml_files_in(dir)
-        end
-        logger.info("Files saved to #{folder_name}")
-      end
-      # rubocop:enable Metrics/AbcSize, Metrics/MethodLength
-
-      def timestamp
-        Time.zone.now.strftime("%Y%m%d%H%M%S%L")
-      end
-
-      def within_new_folder
-        dir = Pathname(File.join("/var", "ukrdc", timestamp))
-        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
-
-      def encrypt_xml_files_in(dir)
-        logger.info "Encrypting..."
-        GpgEncryptFolder.new(folder: dir, options: gpg_options).call
-      end
-
-      def config
-        Renalware.config
-      end
-
-      def gpg_options
-        GpgOptions.new(
-          recipient: config.ukrdc_gpg_recipient,
-          keyring: config.ukrdc_gpg_keyring,
-          homedir: config.ukrdc_gpg_homedir,
-          filename_transform: lambda do |filename|
-            filename.to_s.gsub("/xml/", "/encrypted/").gsub(".xml", ".gpg")
-          end
-        )
-      end
-    end
-  end
-end