renalware-core 2.0.55 → 2.0.56

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 894fbb8d8d83ab547c7a25dec9e6d41eca0a9f9181bd55aef8ece1c65bc26523
-  data.tar.gz: 468716265e6688e6d1e66fa3c6d606948531853285cacb9a1249914c02d6cb21
+  metadata.gz: b43e0abe941399d01e0ad556cd252275bee56352a1f93c36539047e23d494596
+  data.tar.gz: c01f1fb595e6349a0fe2cec92b9e1ece2051e46c3198bf4535206413a891dd4b
 SHA512:
-  metadata.gz: 2c62a3d4fba4c48455a0882e1b7a3d4353b08a0c557858af1bc27f73387f63a24471d15b0915bf2246836b87b3d3f5478a37e8dc3b427d312ea56ef9a7e09cbc
-  data.tar.gz: 34a24963e66f3d60d6776e63b4233b4ebd36eff7a35ac384f5640442e07e2f32841204503329eb1e8b51e5ca9c1b479b4ec3d7bd94489e88a0b4248c2a942a5e
+  metadata.gz: b1a75fd73bab54706788485f5c2d5a05f325f23d055aff0832f4a8e482ccc691ad6d654c1f94c279e4a0dbd9504cf10d244d1b7153f3660caf6f512ea1f5ab12
+  data.tar.gz: 272ff58c7269f6c12fce46cf38bea2826d77ff188241218380cd0f62f9d0a71e6aeed60ff238a467ee5266eb5e80692cb69444358ec9c5a9f1c7da97e9bbcbc4

data/app/controllers/renalware/admissions/requests_controller.rb

@@ -8,7 +8,11 @@ module Renalware
       include Renalware::Concerns::Pageable
 
       def index
-        requests = Request.ordered.all.page(page).per(per_page)
+        requests = Request
+          .ordered
+          .includes(:patient, :reason, :created_by, :updated_by, :hospital_unit)
+          .all
+          .page(page).per(per_page)
         authorize requests
         render locals: { requests: requests }
       end

data/app/controllers/renalware/hd/sessions_controller.rb

@@ -13,7 +13,11 @@ module Renalware
 
       def index
         query = sessions_query
-        sessions = query.call.includes(:hospital_unit, :patient).page(page).per(per_page || 15)
+        sessions = query
+          .call
+          .includes(:hospital_unit, :patient, :signed_on_by, :signed_off_by)
+          .page(page)
+          .per(per_page || 15)
         authorize sessions
         presenter = CollectionPresenter.new(sessions, SessionPresenter, view_context)
         @q = query.search

data/app/controllers/renalware/problems/problems_controller.rb

@@ -8,13 +8,13 @@ module Renalware
         authorize problems
         render locals: {
           patient: patient,
-          current_problems: problems.current.with_created_by.ordered,
+          current_problems: problems.current.with_updated_by.ordered,
           archived_problems: problems.archived.with_created_by.ordered
         }
       end
 
       def show
-        problem = patient.problems.with_archived.find(params[:id])
+        problem = patient.problems.with_archived.includes(versions: :item).find(params[:id])
         notes = problem.notes.with_updated_by.ordered
         authorize problem
         render locals: {

data/app/models/concerns/renalware/feeds/job.rb

@@ -19,7 +19,7 @@ module Renalware
       end
 
       def find_file_in(files, pattern)
-        file = files.select{ |f| f.basename.to_s.match(pattern) }.first
+        file = files.detect{ |f| f.basename.to_s.match(pattern) }
         if file.nil?
           msg = "Zip file does not contain a file with name matching #{pattern}!"
           log(msg)

data/app/models/renalware/admissions/consult_query.rb

@@ -33,6 +33,7 @@ module Renalware
             .includes(
               :consult_site,
               :hospital_ward,
+              :created_by,
               patient: { current_modality: :description }
             )
             .order(created_at: :desc)

data/app/models/renalware/admissions/request.rb

@@ -11,6 +11,7 @@ module Renalware
       acts_as_paranoid
 
       belongs_to :patient, touch: true
+      belongs_to :hospital_unit, class_name: "Hospitals::Unit"
       belongs_to :reason, class_name: "RequestReason"
 
       validates :patient_id, presence: true, uniqueness: true

data/app/models/renalware/hd/session.rb

@@ -54,21 +54,24 @@ module Renalware
         datetime_at(end_time)
       end
 
+      def compute_duration
+        return unless start_time_changed? || end_time_changed?
+
+        self.duration = DurationCalculator.in_minutes(start_time, end_time)
+      end
+
       private
 
       def datetime_at(time)
+        return if performed_on.blank?
+        return performed_on.to_time if start_time.blank?
+
         Time.zone.parse("#{performed_on.strftime('%F')} #{time.strftime('%T')}")
       end
 
       def assign_modality
         self.modality_description = patient.modality_description
       end
-
-      def compute_duration
-        return unless start_time_changed? || end_time_changed?
-
-        self.duration = DurationCalculator.in_minutes(start_time, end_time)
-      end
     end
   end
 end

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

@@ -6,9 +6,15 @@ module Renalware
   module UKRDC
     class BatchNumber < ApplicationRecord
       def self.next
-        new_batcher_number = new
-        new_batcher_number.save!
-        new_batcher_number.id.to_s.rjust(6, "0")
+        create!
+      end
+
+      def number
+        id.to_s.rjust(6, "0")
+      end
+
+      def to_s
+        number
       end
     end
   end

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

@@ -29,22 +29,27 @@ module Renalware
         @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
           # Skipping transaction for now as worried about the quantity of rows and data invovled.
-          # ActiveRecord::Base.transaction do
-          @batch_number = BatchNumber.next
-          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
+          ActiveRecord::Base.transaction do
+            @batch_number = BatchNumber.next.number
+            @paths = Paths.new(
+              timestamp: timestamp,
+              batch_number: batch_number,
+              working_path: config.ukrdc_working_path
+            )
+            summary.milliseconds_taken = Benchmark.ms do
+              create_patient_xml_files
+              encrypt_patient_xml_files
+              copy_encrypted_xml_files_into_the_outgoing_folder
+            end
           end
-          # end
+          paths.create_symlink_to_latest_timestamped_folder_so_it_is_easier_to_eyeball
           build_summary
           print_summary
           email_summary

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

@@ -20,7 +20,7 @@ module Renalware
       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}"
+          logger.info "  Patient #{patient.ukrdc_external_id}"
           xml_payload = build_payload(log)
           if xml_payload_same_as_last_sent_payload?(xml_payload)
             logger.info "    skipping as no change in XML file"
@@ -98,19 +98,10 @@ module Renalware
       end
 
       def xml_filepath
+        xml_filename = Filename.new(patient: patient, batch_number: batch_number).to_s
         File.join(dir, xml_filename)
       end
 
-      def xml_filename
-        patient_identifier = patient.nhs_number || patient.local_patient_id
-        if patient_identifier.blank?
-          raise(ArgumentError, "Patient has no NHS number or local patient id")
-        end
-
-        site_code = Renalware.config.ukrdc_site_code # e.g. RJZ
-        "#{site_code}_#{batch_number}_#{patient_identifier.upcase}.xml"
-      end
-
       class Payload
         pattr_initialize :payload
         delegate :to_s, to: :payload

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

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+
+module Renalware
+  module UKRDC
+    # Formats a UKRDC patient XML filename
+    class Filename
+      pattr_initialize [:patient!, :batch_number!]
+
+      def to_s
+        "#{site_code}_#{batch_number}_#{sanitized_patient_identifier}.xml"
+      end
+
+      private
+
+      def sanitized_patient_identifier
+        patient_identifier.strip.upcase
+      end
+
+      def site_code
+        Renalware.config.ukrdc_site_code # e.g. RJZ
+      end
+
+      # For an patient identifer to put in the filename (to make it easierto look up the patient)
+      # choose the NHS Number is there is one, falling back to local_patient_id(2,3,4) then
+      # ukrdc_external_id - the latter at least is guaranteed to be present.
+      def patient_identifier
+        return patient.nhs_number if patient.nhs_number.present?
+
+        patient.hospital_identifier&.id || patient.ukrdc_external_id
+      end
+    end
+  end
+end

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

@@ -5,12 +5,13 @@ require_dependency "renalware/ukrdc"
 module Renalware
   module UKRDC
     class Paths
-      attr_reader :timestamp, :working_path
+      attr_reader :timestamp, :batch_number, :working_path
 
-      def initialize(timestamp: nil, working_path:)
+      def initialize(timestamp: nil, batch_number:, working_path:)
         raise(ArgumentError, "Invalid working_path") if working_path.blank?
 
         @timestamp = timestamp
+        @batch_number = batch_number
         @timestamp ||= Time.zone.now.strftime("%Y%m%d%H%M%S%L")
         @working_path = Pathname(working_path)
         create_folders
@@ -30,7 +31,7 @@ module Renalware
       end
 
       def timestamped_folder
-        @timestamped_folder ||= archive_folder.join(timestamp)
+        @timestamped_folder ||= archive_folder.join("#{batch_number}_#{timestamp}")
       end
 
       def timestamped_xml_folder

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

@@ -10,7 +10,7 @@ module Renalware
 
       def profiles
         @profiles ||= CollectionPresenter.new(
-          patient.profiles.past_and_future.ordered,
+          patient.profiles.past_and_future.ordered.includes(:type),
           ProfilePresenter
         )
       end
@@ -24,14 +24,14 @@ module Renalware
 
       def procedures
         @procedures ||= CollectionPresenter.new(
-          patient.procedures.ordered,
+          patient.procedures.ordered.includes(:type),
           ProcedurePresenter
         )
       end
 
       def assessments
         @assessments ||= CollectionPresenter.new(
-          patient.assessments.ordered,
+          patient.assessments.ordered.includes(:type),
           AssessmentPresenter
         )
       end

data/app/presenters/renalware/hd/dashboard_presenter.rb

@@ -47,7 +47,7 @@ module Renalware
 
       def sessions
         @sessions ||= begin
-          hd_sessions = Session.includes(:hospital_unit, :patient)
+          hd_sessions = Session.includes(:hospital_unit, :patient, :signed_on_by, :signed_off_by)
                                .for_patient(patient)
                                .limit(10).ordered
           CollectionPresenter.new(hd_sessions, SessionPresenter, view_context)

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

@@ -69,7 +69,10 @@ module Renalware
       end
 
       def schedule_definitions
-        ScheduleDefinition.ordered.map{ |definition| [definition.to_s, definition.id] }
+        ScheduleDefinition
+          .includes(:diurnal_period)
+          .ordered
+          .map{ |definition| [definition.to_s, definition.id] }
       end
 
       def last_update

data/app/presenters/renalware/hd/session_presenter.rb

@@ -8,6 +8,7 @@ module Renalware
                :observations_before,
                :observations_after,
                :dialysis,
+               :complications,
                to: :document, allow_nil: true
       delegate :access_type,
                :access_type_abbreviation,
@@ -27,6 +28,11 @@ module Renalware
                :renal_registry_code,
                to: :hospital_unit,
                prefix: true, allow_nil: true
+      delegate :username, :to_s, to: :updated_by, prefix: true, allow_nil: true
+      delegate :sodium_content, to: :dialysate, allow_nil: true
+      delegate :had_intradialytic_hypotension,
+               to: :complications,
+               allow_nil: true
       delegate :class, to: :__getobj__
 
       def initialize(session, view_context = nil)
@@ -35,6 +41,10 @@ module Renalware
         super(session)
       end
 
+      def had_intradialytic_hypotension?
+        had_intradialytic_hypotension&.yes? ? "Y" : "N"
+      end
+
       def state
         self.class.to_s.demodulize.downcase
       end
@@ -45,6 +55,10 @@ module Renalware
         view_context.link_to(text, url)
       end
 
+      def performed_on_date
+        __getobj__.performed_on
+      end
+
       def start_time
         ::I18n.l(super, format: :time)
       end
@@ -53,10 +67,16 @@ module Renalware
         ::I18n.l(super, format: :time)
       end
 
+      # Returns duration as e.g. "02:01"
       def duration
         super && ::Renalware::Duration.from_minutes(super)
       end
 
+      # Returns duration as e.g. 121 (minutes)
+      def duration_in_minutes
+        __getobj__.duration
+      end
+
       def before_measurement_for(measurement)
         observations_before.try(measurement.to_sym)
       end
@@ -87,7 +107,7 @@ module Renalware
       end
 
       def truncated_notes
-        return unless notes
+        return if notes.blank?
 
         notes.truncate(100, omission: "…").html_safe
       end

data/app/presenters/renalware/letters/letter_presenter.rb

@@ -85,7 +85,7 @@ module Renalware
       end
 
       def title
-        "TBC"
+        pdf_stateless_filename
       end
 
       def pdf_filename

data/app/views/renalware/admissions/requests/_request.html.slim

@@ -1,6 +1,5 @@
 ruby:
   patient = request.patient
-  unit = Renalware::Hospitals::Unit.find_by(id: request.hospital_unit_id)
   editing_history = "Created #{l(request.created_at)} by #{request.created_by}\n"\
                     "Updated #{l(request.updated_at)} by #{request.updated_by}"
 = content_tag_for(:tr,
@@ -13,7 +12,7 @@ ruby:
   td= default_patient_link(patient)
   td= patient.nhs_number
   td= patient.hospital_identifiers
-  td= unit&.name
+  td= request.hospital_unit&.name
   td.col-width-medium-with-ellipsis(title=request.notes)
     = request.notes
   td(title=editing_history)= l(request.created_at)

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

@@ -1,12 +1,12 @@
 # frozen_string_literal: true
 
-xml = builder
+# xml = builder
 
-xml.Encounters do
-  patient.finished_hd_sessions.each do |session|
-    render "renalware/api/ukrdc/patients/encounters/hd_session",
-           builder: xml,
-           patient: patient,
-           session: Renalware::HD::SessionPresenter.new(session)
-  end
-end
+# xml.Encounters do
+#   patient.finished_hd_sessions.each do |session|
+#     render "renalware/api/ukrdc/patients/encounters/hd_session",
+#            builder: xml,
+#            patient: patient,
+#            session: Renalware::HD::SessionPresenter.new(session)
+#   end
+# end

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

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+xml = builder
+
+xml.Procedures do
+  patient.finished_hd_sessions.each do |session|
+    render "renalware/api/ukrdc/patients/procedures/dialysis_session",
+           builder: xml,
+           patient: patient,
+           session: Renalware::HD::SessionPresenter.new(session)
+  end
+  # patient.prescriptions.each do |prescription|
+  #   xml.Medication do
+  #     xml.FromTime prescription.prescribed_on.to_datetime
+  #     if prescription.terminated_or_marked_for_termination?
+  #       xml.ToTime prescription.terminated_on&.to_datetime
+  #     end
+  #     xml.Route do
+  #       xml.CodingStandard "RR22"
+  #       xml.Code prescription.medication_route&.rr_code
+  #       xml.Description prescription.medication_route&.name
+  #     end
+  #     xml.DrugProduct do
+  #       xml.Generic prescription.drug
+  #       # xml.Id do
+  #       #   xml.CodingStandard "DM+D"
+  #       #   xml.Code "dm + d code for the drug - coming soon"
+  #       #   xml.Description prescription.drug
+  #       # end
+  #     end
+  #     xml.Frequency prescription.frequency
+  #     xml.Comments prescription.notes
+  #     # xml.DoseUoM
+  #     # xml.Indication
+  #   end
+  # end
+end

data/app/views/renalware/api/ukrdc/patients/procedures/_dialysis_session.xml.builder

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+xml = builder
+
+xml.DialysisSession(
+  start: session.performed_on_date,
+  stop: session.performed_on_date
+) do
+
+  xml.ProcedureType do
+    xml.CodingStandard "SNOMED"
+    xml.Code "19647005"
+    xml.Description "Plasma Exchange"
+  end
+
+  xml.Clinician do
+    xml.Description session.updated_by
+  end
+
+  xml.ProcedureTime session.start_datetime.to_datetime
+
+  xml.EnteredBy do
+    xml.CodingStandard "LOCAL"
+    xml.Code session.updated_by_username
+    xml.Description session.updated_by
+  end
+
+  xml.EnteredAt do
+    xml.Code session.hospital_unit_renal_registry_code
+  end
+
+  xml.ExternalId session.uuid
+  xml.Attributes do
+    xml.QHD19 session.had_intradialytic_hypotension?
+    xml.QHD20 session.access_type
+    xml.QHD21 session.access_side
+    xml.QHD22 "N" # Access in two sites simultaneously
+    xml.QHD30 session.blood_flow
+    xml.QHD31 session.duration_in_minutes # Time Dialysed in Minutes
+    xml.QHD32 session.sodium_content # Sodium in Dialysate
+    xml.QHD33 # Needling Method
+  end
+end

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

@@ -21,6 +21,7 @@ xml.ukrdc(:PatientRecord, namespace_and_schema) do
   render "allergies", builder: xml, patient: patient
   render "diagnoses", builder: xml, patient: patient
   render "medications", builder: xml, patient: patient
+  render "procedures", builder: xml, patient: patient
   render "documents", builder: xml, patient: patient
   render "encounters", builder: xml, patient: patient
   render "program_memberships", builder: xml, patient: patient

data/lib/gpg_encrypt_folder.rb

@@ -40,13 +40,13 @@ class GpgEncryptFile
     err = Open3.popen3(gpg_command) do |_stdin, _stdout, stderr|
       stderr.read
     end
-    raise "Error encrypting UKRDC files: #{err}" unless err.empty?
+    raise "Error encrypting UKRDC files: #{err}, #{gpg_command}" unless err.empty?
   end
 
   private
 
   def gpg_command
-    GpgCommand.new(file: file, options: options).to_s
+    @gpg_command ||= GpgCommand.new(file: file, options: options).to_s
   end
 end
 
@@ -56,8 +56,8 @@ class GpgCommand
   def to_s
     "gpg --armor --no-default-keyring --trust-model always "\
       "#{keyring} #{homedir} #{recipient} "\
-      "-o #{encrypted_filename} "\
-      "--encrypt #{file}"
+      "-o \"#{encrypted_filename}\" "\
+      "--encrypt \"#{file}\""
   end
 
   def recipient

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.55"
+  VERSION = "2.0.56"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.55
+  version: 2.0.56
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-10-26 00:00:00.000000000 Z
+date: 2018-10-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1763,6 +1763,7 @@ files:
 - 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/filename.rb
 - app/models/renalware/ukrdc/paths.rb
 - app/models/renalware/ukrdc/patients_query.rb
 - app/models/renalware/ukrdc/transmission_log.rb
@@ -2043,6 +2044,7 @@ files:
 - app/views/renalware/api/ukrdc/patients/_name.xml.builder
 - app/views/renalware/api/ukrdc/patients/_observations.xml.builder
 - app/views/renalware/api/ukrdc/patients/_patient.xml.builder
+- app/views/renalware/api/ukrdc/patients/_procedures.xml.builder
 - app/views/renalware/api/ukrdc/patients/_program_memberships.xml.builder
 - app/views/renalware/api/ukrdc/patients/_sending_facility.xml.builder
 - app/views/renalware/api/ukrdc/patients/_social_histories.xml.builder
@@ -2054,6 +2056,7 @@ files:
 - app/views/renalware/api/ukrdc/patients/observations/_blood_pressure.xml.builder
 - app/views/renalware/api/ukrdc/patients/observations/_standing_blood_pressure.xml.builder
 - app/views/renalware/api/ukrdc/patients/observations/_weight.xml.builder
+- app/views/renalware/api/ukrdc/patients/procedures/_dialysis_session.xml.builder
 - app/views/renalware/api/ukrdc/patients/show.xml.builder
 - app/views/renalware/api/v1/medications/prescriptions/index.json.jbuilder
 - app/views/renalware/api/v1/patients/patients/index.json.jbuilder