renalware-core 2.0.99 → 2.0.100

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 688cbe6a0810acd8980722dbde29b68a21116d2e695a01bb0f71da9bef6c03c2
-  data.tar.gz: ca04c46a641c5214422e23f5b78e4872bccb5447691e5f02a1f76a049da16923
+  metadata.gz: 8aa7d57a0adfff2d76fadc4c11c9442fa83d82ca6dd5f01dcca5cfbf4226e0a9
+  data.tar.gz: 7a7c0329c9a32aac0da27b4165ab2bb1f1c9dd111729d4d86cbfaacab46040d8
 SHA512:
-  metadata.gz: 7585d9b098511c978d0b3f5b5f3b7ab7bcc89dc648e01943d7391694f69672afc07bf00451e9a65ab4f2caa622d2e7809aa8ade755d32428a208891c4332f223
-  data.tar.gz: 1c30a614fb4d0d85fc50a566ce141fd4aaf684ad6fed4080b32fd207e7bc2334e2f3c432d73899435826be964a67dc08078db6318846ab852ed1872751811f10
+  metadata.gz: 8f73fec51538a54fa18a57c9f3d2b009f8f64ce1253d7c9a43eb5cc1d19164fcba654b9ec43a976733359a833873299c1c7b199abe75e54d3baf9f3bb8478118
+  data.tar.gz: f9117254aad358aa7d265db64cfeeba583be6a8cac7c707e33440e8827659abe75529c4c8bcf17e92f4532d1eb10790fb3a498aaba4018f9ed39b9f82a8ef1cd

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

@@ -36,13 +36,11 @@ module Renalware
 
       def call
         logger.tagged(request_uuid) do
-          # ActiveRecord::Base.transaction do
           summary.milliseconds_taken = Benchmark.ms do
             create_patient_xml_files
             encrypt_patient_xml_files
             copy_encrypted_xml_files_into_the_outgoing_folder
           end
-          # end
           paths.create_symlink_to_latest_timestamped_folder_so_it_is_easier_to_eyeball
           build_summary
           print_summary
@@ -93,7 +91,7 @@ module Renalware
         summary.results = export_results
       end
 
-      # rubocop:disable Metrics/AbcSize
+      # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
       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")
@@ -115,7 +113,7 @@ module Renalware
           query.all
         end
       end
-      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/AbcSize, Metrics/MethodLength
 
       # rubocop:disable Metrics/AbcSize
       def print_summary

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

@@ -0,0 +1,89 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+module Renalware
+  module UKRDC
+    module Housekeeping
+      # Responsible for cleaning up old archive folders that are created each time the
+      # ukrdc:export task has run. Each archive folder's name has a batch number in it which is the
+      # id of the UKRDC::BatchNumber model created at the start of each export. We can find the
+      # folders to remove by extracting the batch number from the folder name and deleting the
+      # folder if that batch is no longer 'recent'.
+      # Called from a housekeeping rake task.
+      class RemoveOldExportArchiveFolders
+        def self.call
+          new.call
+        end
+
+        def call
+          remove_old_archives
+        end
+
+        private
+
+        class ArchiveFolder
+          pattr_initialize :folder
+
+          # Returns the integer batch number from the folder name
+          # e.g. 13 from /var/ukrdc/archive/000013_20190827081107620
+          def batch_number
+            matches = folder.match(%r(\/(\d{6})_))
+            return unless matches
+
+            matches[1].to_i
+          end
+        end
+
+        def remove_old_archives
+          log "Remove old archives"
+          log "Keeping archived batches #{batch_numbers_to_keep.join(', ')}"
+
+          Dir.glob(glob_pattern).each do |folder|
+            archive_folder = ArchiveFolder.new(folder)
+            next unless archive_folder.batch_number
+
+            if remove_folder?(archive_folder)
+              log "Removing #{folder}"
+              FileUtils.rm_rf folder
+            end
+          end
+        end
+
+        # Pattern to use to find batch-numbered folders in the archive directory
+        def glob_pattern
+          archive_path.join("??????_*")
+        end
+
+        def archive_path
+          Pathname(Renalware.config.ukrdc_working_path).join("archive")
+        end
+
+        def number_of_archived_folders_to_keep
+          Renalware.config.ukrdc_number_of_archived_folders_to_keep.to_i
+        end
+
+        # Returns the ids of a few of the most recent BatchNumbers rows (ie the batch number) that
+        # we should not delete - these being the most recent ones we want to stick around in case we
+        # need to inspect what was sent.
+        def batch_numbers_to_keep
+          @batch_numbers_to_keep ||= begin
+            BatchNumber
+              .limit(number_of_archived_folders_to_keep)
+              .order(created_at: :desc)
+              .pluck(:id)
+          end
+        end
+
+        def remove_folder?(archive_folder)
+          !batch_numbers_to_keep.include?(archive_folder.batch_number)
+        end
+
+        def log(msg)
+          Rails.logger.info(" " + msg)
+        end
+      end
+    end
+  end
+end

data/app/views/renalware/accesses/procedures/_form.html.slim

@@ -16,7 +16,8 @@ ruby:
     = f.association :type,
         collection: Renalware::Accesses::Type.ordered,
         label_method: :long_name,
-        wrapper: :horizontal_medium
+        wrapper: :horizontal_medium,
+        input_html: { class: "searchable_select" }
     = f.input :side, wrapper: :horizontal_small
     = f.association :pd_catheter_insertion_technique,
                     collection: Renalware::Accesses::CatheterInsertionTechnique.ordered,

data/app/views/renalware/pd/exit_site_infections/_details.html.slim

@@ -9,7 +9,7 @@
     dt Treatment:
     dd= exit_site_infection.treatment
     dt Notes:
-    dd= exit_site_infection.notes
+    dd= simple_format(exit_site_infection.notes)
     dt= attr_name(exit_site_infection, :clinical_presentation)
     dd= exit_site_infection.clinical_presentation&.texts&.join(", ")
     - %i(recurrent cleared catheter_removed).each do |option|

data/app/views/renalware/pd/peritonitis_episodes/_details.html.slim

@@ -41,7 +41,7 @@
   .row
     .large-12.columns
       = article_tag "Peritonitis Episode Notes" do
-        p= peritonitis_episode.notes
+        = simple_format(peritonitis_episode.notes)
 
   .right
     = link_to "Edit",

data/db/seeds.rb

@@ -20,6 +20,7 @@ def log(msg, type: :full)
   end
 end
 
+PaperTrail.enabled = false
 
 # Seed the database with data common to all installations.
 # Site specific data should be seeded from the host application.

data/db/seeds/seeds_helper.rb

@@ -1,10 +1,9 @@
 # frozen_string_literal: true
 
 module SeedsHelper
-  def without_papertrail_versioning_for(klass)
-    raise ArgumentError unless klass.is_a? Class
-    klass.paper_trail.disable
+  def without_papertrail_versioning_for(klasses)
+    Array(klasses).each { |klass| klass.paper_trail.disable }
     yield
-    klass.paper_trail.enable
+    Array(klasses).each { |klass| klass.paper_trail.enable }
   end
 end

data/lib/renalware/configuration.rb

@@ -66,6 +66,9 @@ module Renalware
       ENV.fetch("UKRDC_WORKING_PATH", File.join("/var", "ukrdc"))
     end
     config_accessor(:ukrdc_site_code) { ENV.fetch("UKRDC_PREFIX", "RJZ") }
+    config_accessor(:ukrdc_number_of_archived_folders_to_keep) do
+      ENV.fetch("UKRDC_NUMBER_OF_ARCHIVED_FOLDERS_TO_KEEP", "3")
+    end
 
     # To use a date other that the default changes_since date when
     # compiling pathology to send to UKRDC, you can set an ENV var as follows:

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.99"
+  VERSION = "2.0.100"
 end

data/lib/tasks/ukrdc.rake

@@ -47,4 +47,12 @@ namespace :ukrdc do
     Rails.logger     = logger
     Renalware::UKRDC::TreatmentTimeline::GenerateTreatments.call
   end
+
+  task housekeeping: :environment do
+    logger           = ActiveSupport::TaggedLogging.new(Logger.new(STDOUT))
+    logger.level     = Logger::INFO
+    Rails.logger     = logger
+    logger.info "UKRDC housekeeping"
+    Renalware::UKRDC::Housekeeping::RemoveOldExportArchiveFolders.call
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.99
+  version: 2.0.100
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-23 00:00:00.000000000 Z
+date: 2019-08-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1840,6 +1840,7 @@ files:
 - 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/housekeeping/remove_old_export_archive_folders.rb
 - app/models/renalware/ukrdc/modality_code.rb
 - app/models/renalware/ukrdc/pathology_observation_requests_query.rb
 - app/models/renalware/ukrdc/paths.rb