renalware-core 2.0.152 → 2.0.158

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

@@ -6,7 +6,7 @@ require "sql/indexed_case_stmt"
 module Renalware
   module Pathology
     class ObservationDescriptionsByCodeQuery
-      def initialize(relation: ObservationDescription, codes:)
+      def initialize(codes:, relation: ObservationDescription)
         @relation = relation
         @codes = Array(codes)
       end

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

@@ -8,8 +8,15 @@ module Renalware
     # that can be persisted by ObservationRequest.
     # Note:
     # - A message can have multiple observation_requests, each with its own observations.
-    # - This class could be removed and a Builder class used to create the database models
-    #   directly - this would remove the extra level of indirection that this class introduces.
+    # - We create any missing *_description or measurement_unit rows - ie if a new OBR 'ABC' arrives
+    # - from the lab and we have not seen it before, we create a corresponding
+    # - observation_request_description first. Likewise for previously unseen OBX codes we will
+    # - create a new observation_description in realtime. If a OBC has a unit we have not seen
+    #   before eg MW (Megawatts!) we create that also. In this way the pathology 'metadata' is
+    #   keep up to date based on what the lab/send.
+    #
+    # Note this class could be removed and a Builder class used to create the database models
+    # directly - this would remove the extra level of indirection that this class introduces.
     class ObservationRequestsAttributesBuilder
       DEFAULT_REQUESTOR_NAME = "UNKNOWN"
       delegate :patient_identification, :observation_requests, to: :hl7_message
@@ -53,6 +60,10 @@ module Renalware
         @request_params ||= build_observation_request_params
       end
 
+      # Returns an array of hashes each containing an observation_request entry
+      # that wil be used to create associatwd database rows
+      # e.g. [ { observation_request: {..} }, {...} ]
+      #
       # rubocop:disable Metrics/MethodLength
       def build_observation_request_params
         requests.each_with_object([]) do |request, arr|
@@ -74,12 +85,19 @@ module Renalware
       end
       # rubocop:enable Metrics/MethodLength
 
+      # Returns an array of hashes where each has the attributes used to create a new
+      # pathology_observation in the datbase when passed inside the observation_request hash]
+      # built in build_observation_request_params { observations_attributes: [..] }
       # rubocop:disable Metrics/MethodLength
       def build_observations_params(request)
         request.observations.map do |observation|
+          unit = if observation.units.present?
+                   MeasurementUnit.find_or_create_by!(name: observation.units)
+                 end
           observation_description = find_observation_description(
             code: observation.identifier,
-            name: observation.name
+            name: observation.name,
+            measurement_unit: unit
           )
           next unless validate_observation(observation, observation_description)
 
@@ -103,8 +121,30 @@ module Renalware
         raise MissingRequestDescriptionError, code
       end
 
-      def find_observation_description(code:, name:)
-        ObservationDescription.find_or_create_by!(code: code) { |desc| desc.name = name || code }
+      # Finds an observation_description or creates one if not found.
+      # Makes sure the description.measurement_unit, if unset, is set to the HL7 unit (eg mg) if
+      # passed in. Also set the suggested_measurement_unit, which may be different to the
+      # observation_description if was set uncorrectly at some point.
+      # The idea of suggested_measurement_unit is that it always updated dynamically if missing,
+      # whereas measurement_unit is only updated if missing. This is to cope with the case where
+      # the units of an OBX changes (eg by a factor of 10 as HB was a while back at KCH); in this
+      # instance we only update the suggested_measurement_unit so its clear(ish) what the correct
+      # value should be.
+      def find_observation_description(code:, name:, measurement_unit:)
+        created_jit = false
+        desc = ObservationDescription.find_or_create_by!(code: code) do |desc|
+          desc.name = name || code
+          desc.measurement_unit = measurement_unit
+          desc.suggested_measurement_unit = measurement_unit
+          created_jit = true
+        end
+
+        if created_jit == false && measurement_unit.present?
+          desc.measurement_unit ||= measurement_unit
+          desc.suggested_measurement_unit = measurement_unit
+          desc.save! if desc.changed?
+        end
+        desc
       rescue ActiveRecord::RecordNotFound
         raise MissingObservationDescriptionError, code
       end

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

@@ -8,7 +8,7 @@ module Renalware
     # the specified date range.
     #
     class ObservationsWithinDateRangeQuery
-      def initialize(relation: Observation.all, date_range:)
+      def initialize(date_range:, relation: Observation.all)
         @relation = relation
         @date_range = date_range
       end

data/app/models/renalware/patient.rb

@@ -54,8 +54,8 @@ module Renalware
     has_many :alerts, class_name: "Patients::Alert"
     has_one :worry, class_name: "Patients::Worry"
 
-    belongs_to :first_cause, class_name: "Deaths::Cause", foreign_key: :first_cause_id
-    belongs_to :second_cause, class_name: "Deaths::Cause", foreign_key: :second_cause_id
+    belongs_to :first_cause, class_name: "Deaths::Cause"
+    belongs_to :second_cause, class_name: "Deaths::Cause"
 
     belongs_to :primary_care_physician, class_name: "Patients::PrimaryCarePhysician"
     belongs_to :practice, class_name: "Patients::Practice"

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

@@ -7,9 +7,9 @@ module Renalware
     class Bookmark < ApplicationRecord
       acts_as_paranoid
 
-      belongs_to :user, class_name: "Renalware::Patients::User", foreign_key: :user_id
+      belongs_to :user, class_name: "Renalware::Patients::User"
       # No touch required on patient
-      belongs_to :patient, class_name: "Renalware::Patient", foreign_key: :patient_id
+      belongs_to :patient, class_name: "Renalware::Patient"
 
       validates :patient, presence: true
       validates :user, presence: true

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

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+module Renalware
+  module Patients
+    # Queries for and stores in a class variable the list of MDM 'scopes' to use when building
+    # the MDM menu. An example of a scope is "transplant" or "low_clearance".
+    # If you make changes to the system_view_metadata table to add/edit/remove a scope,
+    # you will need to restart the app for changes to to reflect in the menu. It is done this
+    # way as a changes are rare and we want to avoid running this query too many times.
+    # I think it will run once per procethread
+    class MDMMenu
+      thread_cattr_accessor :cached_items
+
+      def self.items
+        return cached_items if cached_items
+
+        self.cached_items = array_of_distinct_scopes_for_all_mdm_list_views
+        cached_items
+      end
+
+      def self.array_of_distinct_scopes_for_all_mdm_list_views
+        Rails.logger.info "#### Loading MDM scope names! ####"
+        scopes = Renalware::System::ViewMetadata
+          .distinct("scope")
+          .where(category: :mdm)
+          .pluck(:scope)
+
+        remove_invalid_scope_names_that_could_break_menu_rendering(scopes)
+      end
+
+      # Only accept MDM scopes names that are simple lower case underscored
+      # strings eg "my_view_name".
+      def self.remove_invalid_scope_names_that_could_break_menu_rendering(scopes)
+        scopes.select { |scope| scope.match?(/^[a-z0-9_]*$/) }
+      end
+
+      private_class_method :array_of_distinct_scopes_for_all_mdm_list_views
+      private_class_method :cached_items
+    end
+  end
+end

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

@@ -8,7 +8,7 @@ module Renalware
       attr_reader :modality_names, :q, :relation
 
       # modality_names: eg "HD" or "PD"
-      def initialize(relation: Patient.all, q:, modality_names:)
+      def initialize(q:, modality_names:, relation: Patient.all)
         @modality_names = modality_names
         @q = q
         @relation = relation

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

@@ -18,7 +18,7 @@ module Renalware
       # FIELDS = %i(id family_name given_name nhs_number).freeze
       attr_reader :term, :scope
 
-      def initialize(scope: Patient.all, term:)
+      def initialize(term:, scope: Patient.all)
         @term = term
         @scope = scope
       end

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

@@ -14,7 +14,6 @@ module Renalware
 
       belongs_to :patient,
                  class_name: "Renalware::Patient",
-                 foreign_key: :patient_id,
                  touch: true
 
       validates :patient, presence: true, uniqueness: true

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

@@ -8,7 +8,7 @@ module Renalware
       DEFAULT_SEARCH_PREDICATE = "hgb_date desc"
       attr_reader :q, :relation, :named_filter
 
-      def initialize(relation: PD::Patient.all, q:, named_filter: nil)
+      def initialize(q:, relation: PD::Patient.all, named_filter: nil)
         @q = q || {}
         @q[:s] = DEFAULT_SEARCH_PREDICATE if @q[:s].blank?
         @relation = relation

data/app/models/renalware/problems/problem.rb

@@ -7,6 +7,7 @@ module Renalware
     class Problem < ApplicationRecord
       include PatientScope
       include Accountable
+      include Sortable
 
       acts_as_paranoid
 
@@ -23,7 +24,7 @@ module Renalware
       scope :with_patient, -> { includes(:patient) }
       scope :with_versions, -> { includes(versions: :item) }
 
-      # This scope is called by CoreExtensions::ActiveRecord::Sort
+      # This scope is called by Sortable concern
       scope :position_sorting_scope, ->(problem) { where(patient_id: problem.patient.id) }
 
       validates :patient, presence: true

data/app/models/renalware/snippets/snippet_query.rb

@@ -5,7 +5,7 @@ module Renalware
     class SnippetQuery
       attr_reader :author, :relation
 
-      def initialize(relation: nil, author:)
+      def initialize(author:, relation: nil)
         @relation = relation || Snippet.includes(:author).all
         @author = author
       end

data/app/models/renalware/surveys/question.rb

@@ -11,8 +11,7 @@ module Renalware
       has_many(
         :responses,
         class_name: "Response",
-        dependent: :nullify,
-        foreign_key: :question_id
+        dependent: :nullify
       )
       validates :code, presence: true, uniqueness: { scope: :survey_id }
       validates :label, presence: true

data/app/models/renalware/system/column_definition.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # Backed by Jsonb, stored in view_metadata.columns, a model to allow
+    # us to specify how a SQL view column is displayed in an HTML table in the
+    # UI.
+    class ColumnDefinition
+      include StoreModel::Model
+      attribute :code, :string
+      # An optional title for the column. Code will be used if title is missing
+      attribute :name, :string
+      attribute :hidden, :boolean, default: false
+      # The width enum corresponds to various classes we apply to columns, e.g.
+      # if tiny is chosen, then class applied to the th will be col-width-tiny
+      enum(
+        :width,
+        %i(
+          tiny
+          small
+          medium
+          large
+          date
+          datetime
+          nhs_number
+          hospital_numbers
+          patient_name
+        )
+      )
+      # If truncate_with_ellipsis is true we add a class to the td so that it
+      # will truncate the text and add .. onm the end
+      attribute :truncate, :boolean, default: false
+
+      validates :code, presence: true
+
+      def title
+        @title ||= name.presence || code.humanize
+      end
+    end
+  end
+end

data/app/models/renalware/system/filter_definition.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # Backed by JSONB, stored in view_metadata.fitlers, a model to allow
+    # us to specify how filters for a SQL view are displayed in HTML
+    class FilterDefinition
+      include StoreModel::Model
+      attribute :code, :string
+      # The type enum detemines how the filter is constructed eg as a list of distinct values
+      enum(
+        :type,
+        %i(
+          list
+          search
+        )
+      )
+      validates :code, presence: true
+      validates :type, presence: true
+
+      def title
+        code.humanize
+        # @title ||= name.presence || code.humanize
+      end
+    end
+  end
+end

data/app/models/renalware/system/update_user.rb

@@ -20,12 +20,16 @@ module Renalware
 
       private
 
+      # rubocop:disable Metrics/MethodLength
       def update!(params)
         User.transaction do
           approve if can_approve?(params)
           unexpire if can_unexpire?(params)
           user.consultant = true?(params[:consultant])
           user.hidden = true?(params[:hidden])
+          if params[:prescriber] # if not a supperadmin, may not be submitted
+            user.prescriber = true?(params[:prescriber])
+          end
           authorise(params)
           user.telephone = params[:telephone]
           user.save!
@@ -33,6 +37,7 @@ module Renalware
       rescue ActiveRecord::RecordInvalid
         false
       end
+      # rubocop:enable Metrics/MethodLength
 
       def notify!
         notifications.each { |n| n.public_send(delivery_method) } if notifications.any?

data/app/models/renalware/system/version.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/problems"
+
+module Renalware
+  module System
+    class Version < PaperTrail::Version
+      self.table_name = :system_versions
+    end
+  end
+end

data/app/models/renalware/system/view_metadata.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    # Information on SQL views used to build parts of the UI
+    class ViewMetadata < ApplicationRecord
+      has_paper_trail(
+        versions: { class_name: "Renalware::System::Version" },
+        on: [:create, :update, :destroy]
+      )
+
+      attribute :columns, ColumnDefinition.to_array_type
+      validates :columns, store_model: true
+
+      attribute :filters, FilterDefinition.to_array_type
+      validates :filters, store_model: true
+
+      # This maps to a PG enum
+      enum display_type: { tabular: "tabular" }
+      enum category: { mdm: "mdm", report: "report" }
+    end
+  end
+end

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

@@ -10,7 +10,7 @@ module Renalware
       extend Enumerize
 
       belongs_to :patient, touch: true
-      belongs_to :recipient, class_name: "Patient", foreign_key: "recipient_id", touch: true
+      belongs_to :recipient, class_name: "Patient", touch: true
 
       has_paper_trail(
         versions: { class_name: "Renalware::Transplants::Version" },

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

@@ -8,7 +8,6 @@ module Renalware
     class DonorFollowup < ApplicationRecord
       belongs_to :operation,
                  class_name: "DonorOperation",
-                 foreign_key: "operation_id",
                  touch: true
 
       has_paper_trail(

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

@@ -5,7 +5,7 @@ require_dependency "renalware/transplants"
 module Renalware
   module Transplants
     class FailureCauseDescription < ApplicationRecord
-      belongs_to :group, class_name: "FailureCauseDescriptionGroup", foreign_key: "group_id"
+      belongs_to :group, class_name: "FailureCauseDescriptionGroup"
 
       scope :ordered, -> { order(name: :asc) }
 

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

@@ -44,7 +44,7 @@ module Renalware
         end
 
         def patients_with_a_transplant_date_in_the_past_3_months
-          joins(<<-SQL)
+          joins(<<-SQL.squish)
             LEFT JOIN transplant_recipient_operations
             ON patients.id = transplant_recipient_operations.patient_id
           SQL
@@ -58,7 +58,7 @@ module Renalware
         alias_method :on_worryboard, :patients_on_the_worry_board
 
         def patients_with_a_transplant_operation_in_the_past_year
-          joins(<<-SQL)
+          joins(<<-SQL.squish)
             LEFT JOIN transplant_recipient_operations
             ON patients.id = transplant_recipient_operations.patient_id
           SQL

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

@@ -8,7 +8,7 @@ module Renalware
       has_one :current_donor_stage, -> { current }, class_name: "DonorStage"
 
       scope :with_registration_statuses, lambda {
-        joins(<<-SQL)
+        joins(<<-SQL.squish)
           left outer join transplant_registrations
             on transplant_registrations.patient_id = patients.id
           left outer join transplant_registration_statuses

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

@@ -13,11 +13,9 @@ module Renalware
 
       belongs_to :operation,
                  class_name: "RecipientOperation",
-                 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"
       has_many :rejection_episodes,
                class_name: "RejectionEpisode",
                dependent: :restrict_with_exception,