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

data/app/models/renalware/drugs/classification.rb

@@ -4,8 +4,8 @@ module Renalware
   module Drugs
     class Classification < ApplicationRecord
       self.table_name = "drug_types_drugs" # a relic from migrating from habtm
-      belongs_to :drug
-      belongs_to :drug_type, class_name: "Type"
+      belongs_to :drug, touch: true
+      belongs_to :drug_type, class_name: "Type", inverse_of: :classifications
     end
   end
 end

data/app/models/renalware/drugs/drug.rb

@@ -6,7 +6,7 @@ module Renalware
       acts_as_paranoid
 
       has_many :classifications, dependent: :destroy
-      has_many :drug_types, through: :classifications
+      has_many :drug_types, through: :classifications, after_remove: proc { |drug| drug.touch }
 
       scope :ordered, -> { order(:name) }
 

data/app/models/renalware/feeds/files/import_job_factory.rb

@@ -4,7 +4,6 @@ module Renalware
   module Feeds
     module Files
       class ImportJobFactory
-
         # Returns the active job class required to process files of type file_type
         def self.job_class_for(file_type)
           "Renalware::Feeds::Files::#{file_type.name.camelize}::ImportJob".constantize

data/app/models/renalware/feeds/files/practices/import_job.rb

@@ -43,6 +43,7 @@ module Renalware
             ZipArchive.new(zipfile).unzip do |files|
               xml_pathname = find_file_in(files, FILE_TO_EXTRACT_FROM_ARCHIVE)
               csv_path = Practices::ConvertXmlToCsv.call(xml_pathname)
+              FileUtils.copy(csv_path, Rails.root.join("generated_organisations.csv"))
               Practices::ImportCSV.new(csv_path).call
             end
             log "Practice count after update: #{practice_count}"

data/app/models/renalware/feeds/message_processor.rb

@@ -9,10 +9,11 @@ module Renalware
       include Wisper::Publisher
 
       def call(raw_message)
-        message_payload = parse_message(raw_message)
-        persist_message(message_payload)
-
-        broadcast(:message_processed, message_payload)
+        ActiveRecord::Base.transaction do
+          message_payload = parse_message(raw_message)
+          persist_message(message_payload)
+          broadcast(:message_processed, message_payload)
+        end
       rescue StandardError => exception
         notify_exception(exception)
         raise exception

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

@@ -2,6 +2,7 @@ require_dependency "renalware/hd"
 
 module Renalware
   module HD
+    # TODO: Document
     class DiarySlot < ApplicationRecord
       # Changing to_ary from private to public here is a hack required to remove a SimpleDelgator
       # warning in eg Renalware::HD::WeeklyDiary::WeeklySlotDecorator:
@@ -26,8 +27,8 @@ module Renalware
       attr_accessor :change_type
 
       include Accountable
-      belongs_to :diary, class_name: "Renalware::HD::Diary"
-      belongs_to :patient
+      belongs_to :diary, class_name: "Renalware::HD::Diary", touch: true
+      belongs_to :patient, touch: true
       belongs_to :station, class_name: "Renalware::HD::Station"
       belongs_to :diurnal_period_code
 

data/app/models/renalware/letters/archive.rb

@@ -5,7 +5,7 @@ module Renalware
     class Archive < ApplicationRecord
       include Accountable
 
-      belongs_to :letter
+      belongs_to :letter, touch: true
 
       validates :content, presence: true
     end

data/app/models/renalware/letters/complete_letter.rb

@@ -1,18 +1,22 @@
 require_dependency "renalware/letters"
+require "attr_extras"
 
 module Renalware
   module Letters
     class CompleteLetter
+      include Broadcasting
+      pattr_initialize :letter
+
       class << self
         alias_method :build, :new
       end
 
-      def initialize(letter)
-        @letter = letter
-      end
-
       def call(by:)
-        @letter.complete(by: by).save!
+        Letter.transaction do
+          @letter = letter.complete(by: by)
+          letter.save!
+          broadcast(:letter_completed, letter)
+        end
       end
     end
   end

data/app/models/renalware/letters/contact.rb

@@ -3,7 +3,7 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class Contact < ApplicationRecord
-      belongs_to :patient
+      belongs_to :patient, touch: true
       belongs_to :person, class_name: "Directory::Person"
       belongs_to :description, class_name: "ContactDescription"
 

data/app/models/renalware/letters/electronic_receipt.rb

@@ -7,7 +7,7 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class ElectronicReceipt < ApplicationRecord
-      belongs_to :letter
+      belongs_to :letter, touch: true
       belongs_to :recipient, class_name: "Renalware::User"
       validates :letter, presence: true
       validates :recipient_id, presence: true

data/app/models/renalware/letters/letter.rb

@@ -12,6 +12,9 @@ module Renalware
 
       belongs_to :event, polymorphic: true
       belongs_to :author, class_name: "User"
+      belongs_to :submitted_for_approval_by, class_name: "User"
+      belongs_to :approved_by, class_name: "User"
+      belongs_to :completed_by, class_name: "User"
       belongs_to :patient, touch: true
       belongs_to :letterhead
       has_one :main_recipient,

data/app/models/renalware/letters/letter/approved.rb

@@ -10,6 +10,8 @@ module Renalware
       def complete(by:)
         becomes!(Completed).tap do |letter|
           letter.by = by
+          letter.completed_by = by
+          letter.completed_at = Time.current
         end
       end
     end

data/app/models/renalware/letters/letter/draft.rb

@@ -13,7 +13,11 @@ module Renalware
       end
 
       def submit(by:)
-        becomes!(PendingReview).tap { |letter| letter.by = by }
+        becomes!(PendingReview).tap do |letter|
+          letter.by = by
+          letter.submitted_for_approval_by = by
+          letter.submitted_for_approval_at = Time.current
+        end
       end
     end
   end

data/app/models/renalware/letters/letter/pending_review.rb

@@ -18,6 +18,8 @@ module Renalware
 
       def sign(by:)
         build_signature(user: by, signed_at: Time.current)
+        self.approved_by = by
+        self.approved_at = Time.current
         self.by = by
         self
       end

data/app/models/renalware/letters/pdf_letter_cache.rb

@@ -2,13 +2,18 @@
 # 2.5 seconds and a fair chunk of memory to convert html to pdf, so we want to cache generated PDFs
 # for a period of time.
 #
+# Note that the cache in question here is not intended to be a canonical archive of PDFs for
+# future reference; it is up to the host application to move the PDFs into EPR folders etc
+# for archiving. This cache could be cleared at any time.
+#
 # Note that even when checking to see if the PDF exists in the cache, we *always* regenerate at
 # least the HTML letter content (i.e. the letter content wrapped in a layout) as we want to make
-# sure we picking up any view and layout changes (Rails fragment caching could possibly be levered
+# sure we are picking up any view and layout changes (fragment caching could possibly be levered
 # here as it knows the MD5 of the views and layouts used, and thus might help us to avoid having
 # to re-render the letter HTML each time - but I have started by taking the less `magical` route
 # of rendering the entire HTML letter to get its MD5 hash, which is then used in trying to find a
-# PDF file cache hit for that filename.
+# PDF file cache hit for that filename).
+#
 # Note that PDF Letters are stored in the rails cache, which is currently Filestore. If we move
 # to a multi-server environment we would need to switch to Memcached or Redis, and the PDF files
 # would be poked into that - using quite a lot of memory I am sure (ag 25k per PDF), so would be
@@ -29,19 +34,28 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class PdfLetterCache
-      def self.fetch(letter)
-        Rails.cache.fetch(cache_key_for(letter), expires_in: 1.month) do
-          yield
+      class << self
+        def fetch(letter)
+          store.fetch(cache_key_for(letter)) { yield }
+        end
+
+        # Note the letter must be a LetterPresenter which has a #to_html method
+        # The to_html method should (and does on the LetterPrsenter class) render the complete
+        # html including surrounding layout with inline css and images. This way if the
+        # layout changes or the image is changed for example, the cache for the pdf is no longer
+        # valid and a new key and cache entry will be created.
+        def cache_key_for(letter)
+          timestamp = letter&.updated_at&.strftime("%Y%m%d%H%M%S")
+          "letter-pdf-#{letter.id}-#{timestamp}-#{Digest::MD5.hexdigest(letter.to_html)}"
+        end
+
+        def cache_path
+          Rails.root.join("tmp", "pdf_letter_cache")
         end
-      end
 
-      # Note the letter must be a LetterPresenter which has a #to_html method
-      # The to_html method should (and does on the LetterPrsenter class) render the complete
-      # html including surrounding layout with inline css and images. This way if the layout changes
-      # or the image is changed for example, the cache for the pdf is no longer valid and a new
-      # key and cache entry will be created.
-      def self.cache_key_for(letter)
-        "letter:pdf:#{letter.id}:#{Digest::MD5.hexdigest(letter.to_html)}"
+        def store
+          @store ||= ActiveSupport::Cache::FileStore.new(cache_path)
+        end
       end
     end
   end

data/app/models/renalware/letters/signature.rb

@@ -3,8 +3,8 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class Signature < ApplicationRecord
-      belongs_to :user
-      belongs_to :letter
+      belongs_to :user, touch: true
+      belongs_to :letter, touch: true
 
       validates :user, presence: true
       validates :letter, presence: true

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

@@ -4,7 +4,7 @@ module Renalware
   module LowClearance
     class MDMPatientsQuery
       include ModalityScopes
-      DEFAULT_SEARCH_PREDICATE = "ure_date ASC".freeze
+      DEFAULT_SEARCH_PREDICATE = "hgb_date DESC".freeze
       attr_reader :query, :relation, :named_filter
 
       def initialize(relation: Patient.all, query: nil, named_filter: nil)

data/app/models/renalware/messaging/internal/author.rb

@@ -2,6 +2,7 @@ require_dependency "renalware/messaging"
 
 module Renalware
   module Messaging
+    # TODO: Document the Internal module
     module Internal
       class Author < ActiveType::Record[Renalware::User]
         has_many :messages

data/app/models/renalware/messaging/message.rb

@@ -13,7 +13,7 @@ module Renalware
       validates :patient, presence: true
       validates :sent_at, presence: true
 
-      belongs_to :patient
+      belongs_to :patient # no touch required
       belongs_to :author
     end
   end

data/app/models/renalware/pathology/measurement_unit.rb

@@ -4,7 +4,7 @@ module Renalware
   module Pathology
     class MeasurementUnit < ApplicationRecord
       validates :name, presence: true
-      has_many :observation_descriptions
+      has_many :observation_descriptions, inverse_of: :measurement_unit
     end
   end
 end

data/app/models/renalware/pathology/observation.rb

@@ -3,8 +3,13 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class Observation < ApplicationRecord
-      belongs_to :request, class_name: "ObservationRequest", touch: true, inverse_of: :observations
-      belongs_to :description, class_name: "ObservationDescription"
+      belongs_to :request,
+                 class_name: "ObservationRequest",
+                 touch: true,
+                 inverse_of: :observations
+      belongs_to :description,
+                 class_name: "ObservationDescription",
+                 inverse_of: :observations
 
       validates :description, presence: true
       validates :result, presence: true, unless: ->(obs) { obs.cancelled? }

data/app/models/renalware/pathology/observation_description.rb

@@ -3,9 +3,15 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class ObservationDescription < ApplicationRecord
+      has_many :observations,
+               class_name: "Pathology::Observation",
+               inverse_of: :description
       belongs_to :measurement_unit
-      validates :display_order, uniqueness: { allow_nil: true }
-      validates :display_order_letters, uniqueness: { allow_nil: true }
+
+      scope :in_display_order, lambda {
+        where("display_group is not null and display_order is not null")
+        .order([:display_group, :display_order])
+      }
 
       def self.for(codes)
         ObservationDescriptionsByCodeQuery.new(codes: codes).call

data/app/models/renalware/pathology/observation_request.rb

@@ -7,7 +7,7 @@ module Renalware
                foreign_key: :request_id,
                inverse_of: :request,
                dependent: :destroy
-      belongs_to :description, class_name: "RequestDescription"
+      belongs_to :description, class_name: "RequestDescription", inverse_of: :requests
       belongs_to :patient, class_name: "Patient", touch: true
 
       accepts_nested_attributes_for :observations
@@ -17,9 +17,6 @@ module Renalware
       validates :requested_at, presence: true
 
       scope :ordered, -> { order(requested_at: :desc) }
-      scope :having_observations_with_a_loinc_code, lambda {
-        joins(observations: :description).where("loinc_code is not null") # TODO: use a merge
-      }
 
       def requested_on
         requested_at.to_date

data/app/models/renalware/patients/alert.rb

@@ -9,7 +9,7 @@ module Renalware
       validates :patient, presence: true
       validates :notes, presence: true
 
-      belongs_to :patient
+      belongs_to :patient, touch: true
     end
   end
 end

data/app/models/renalware/patients/bookmark.rb

@@ -6,6 +6,7 @@ module Renalware
       acts_as_paranoid
 
       belongs_to :user, class_name: "Renalware::Patients::User", foreign_key: :user_id
+      # No touch required on patient
       belongs_to :patient, class_name: "Renalware::Patient", foreign_key: :patient_id
 
       validates :patient, presence: true

data/app/models/renalware/patients/worry.rb

@@ -6,7 +6,10 @@ module Renalware
       include Accountable
       has_paper_trail class_name: "Renalware::Patients::Version"
 
-      belongs_to :patient, class_name: "Renalware::Patient", foreign_key: :patient_id
+      belongs_to :patient,
+                 class_name: "Renalware::Patient",
+                 foreign_key: :patient_id,
+                 touch: true
 
       validates :patient, presence: true, uniqueness: true
     end

data/app/models/renalware/pd/peritonitis_episode_type.rb

@@ -6,7 +6,8 @@ module Renalware
       belongs_to :peritonitis_episode_type_description,
                  class_name: "PD::PeritonitisEpisodeTypeDescription"
       belongs_to :peritonitis_episode,
-                 class_name: "PD::PeritonitisEpisode"
+                 class_name: "PD::PeritonitisEpisode",
+                 touch: true
     end
   end
 end

data/app/models/renalware/pd/regime_bag.rb

@@ -14,7 +14,7 @@ module Renalware
       before_save :assign_days_per_week
 
       belongs_to :bag_type
-      belongs_to :regime
+      belongs_to :regime, touch: true
 
       validates :bag_type, presence: true
       validates :volume, presence: true

data/app/models/renalware/renal/aki_alert.rb

@@ -5,7 +5,7 @@ module Renalware
     class AKIAlert < ApplicationRecord
       include Accountable
       scope :ordered, ->{ order(created_at: :desc) }
-      belongs_to :patient, class_name: "Renal::Patient"
+      belongs_to :patient, class_name: "Renal::Patient", touch: true
       belongs_to :action, class_name: "Renal::AKIAlertAction"
       belongs_to :hospital_ward, class_name: "Hospitals::Ward"
       validates :patient, presence: true

data/app/models/renalware/research/study.rb

@@ -11,9 +11,12 @@ module Renalware
       validates :started_on, timeliness: { type: :date, allow_blank: true }
       validates :terminated_on, timeliness: { type: :date, allow_blank: true, after: :started_on }
 
-      scope :ordered, -> { order(created_at: :asc) }
+      scope :ordered, -> { order(code: :asc) }
 
-      has_many :participants, class_name: "StudyParticipant", dependent: :destroy
+      has_many :participants,
+               class_name: "StudyParticipant",
+               dependent: :destroy,
+               inverse_of: :study
     end
   end
 end

data/app/models/renalware/research/study_participant.rb

@@ -7,8 +7,11 @@ module Renalware
       acts_as_paranoid
       validates :participant_id, presence: true, uniqueness: { scope: :study }
       validates :study, presence: true
-      belongs_to :study
-      belongs_to :patient, class_name: "Renalware::Patient", foreign_key: :participant_id
+      belongs_to :study, touch: true
+      belongs_to :patient,
+                 class_name: "Renalware::Patient",
+                 foreign_key: :participant_id,
+                 touch: true
 
       def to_s
         patient&.to_s
@@ -16,15 +19,3 @@ module Renalware
     end
   end
 end
-#       include Accountable
-#       acts_as_paranoid
-
-#       validates :code, presence: true
-#       validates :description, presence: true
-#       validates :started_on, timeliness: { type: :date, allow_blank: true }
-#       validates :terminated_on, timeliness: { type: :date, allow_blank: true, after: :started_on }
-
-#       scope :ordered, -> { order(created_at: :asc) }
-#     end
-#   end
-# end