renalware-core 2.0.0.pre.rc9 → 2.0.0.pre.rc10

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/assets/stylesheets/renalware/modules/_clinics.scss

@@ -1,4 +1,4 @@
-.page--cinic-visits {
+.page--visits {
 
   .filters__output {
     display: none;

data/app/assets/stylesheets/renalware/modules/_letters.scss

@@ -1,3 +1,10 @@
+// When the letter summary part is included in the clinical summary, make it 12 cols wide.
+.page--clinical_summaries {
+  .summary-part--letters {
+    @include grid-column(12);
+  }
+}
+
 table.contacts tbody td{
   vertical-align: top;
 }

data/app/assets/stylesheets/renalware/partials/_navigation.scss

@@ -78,7 +78,7 @@ dd.patient-name {
   }
 
   ul.side-nav {
-    margin: .1rem 0 0 0;
+    margin: 0;
     padding: 0;
 
     li {

data/app/controllers/renalware/api/ukrdc/patients_controller.rb

@@ -1,7 +1,7 @@
 module Renalware
   module API
     module UKRDC
-      class PatientsController < ApplicationController
+      class PatientsController < BaseController
         respond_to :xml
 
         def show
@@ -18,6 +18,7 @@ module Renalware
 
         def patient_presenter
           patient = Renalware::Patient.find_by!(secure_id: params[:id])
+          authorize patient
           Renalware::UKRDC::PatientPresenter.new(patient)
         end
       end

data/app/controllers/renalware/application_controller.rb

@@ -0,0 +1,13 @@
+require_dependency "renalware"
+
+module Renalware
+  # Note that we inherit from ::ApplicationController which is defined in the host application.
+  # This allows application to
+  # - define the default layout
+  # - intercept requests with before_action etc.
+  class ApplicationController < ::ApplicationController
+    # Prevent CSRF attacks by raising an exception.
+    # For APIs, you may want to use :null_session instead.
+    protect_from_forgery with: :exception
+  end
+end

data/app/controllers/renalware/base_controller.rb

@@ -10,8 +10,6 @@ module Renalware
 
     rescue_from Pundit::NotAuthorizedError, with: :user_not_authorized
 
-    layout "renalware/layouts/application"
-
     # Expose a few attributes for use in the patient layout and its partials.
     # As a rule, we should be passing variables explicitly to all view using `locals`;
     # however, while not a fan of `helper_method`, exposing e.g. current_patient this (akin to

data/app/controllers/renalware/concerns/cache_busting.rb

@@ -0,0 +1,21 @@
+require "active_support/concern"
+
+# The host Rails application's ApplicationController could choose to mix-in this concern in order to
+# prevent the browser from being able navigate Back to logged-in pages once the user has logged out.
+module Renalware
+  module Concerns::CacheBusting
+    extend ActiveSupport::Concern
+
+    included do
+      class_eval do
+        before_action :bust_cache
+      end
+    end
+
+    def bust_cache
+      response.headers["Cache-Control"] = "no-cache, no-store, max-age=0, must-revalidate"
+      response.headers["Pragma"] = "no-cache"
+      response.headers["Expires"] = "Fri, 01 Jan 1990 00:00:00 GMT"
+    end
+  end
+end

data/app/controllers/renalware/devise/passwords_controller.rb

@@ -1,6 +1,4 @@
 class Renalware::Devise::PasswordsController < ::Devise::PasswordsController
   helper Renalware::ApplicationHelper
   include Renalware::Concerns::DeviseControllerMethods
-
-  layout "renalware/layouts/application"
 end

data/app/controllers/renalware/devise/registrations_controller.rb

@@ -1,6 +1,4 @@
 class Renalware::Devise::RegistrationsController < ::Devise::RegistrationsController
   helper Renalware::ApplicationHelper
   include Renalware::Concerns::DeviseControllerMethods
-
-  layout "renalware/layouts/application"
 end

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

@@ -2,8 +2,6 @@ module Renalware
   class Devise::SessionsController < ::Devise::SessionsController
     include Concerns::DeviseControllerMethods
 
-    layout "renalware/layouts/application"
-
     # Define the path to go to after logging in:
     # - if the user has never before logged-in, devise will take them to the root path (dashboard)
     # - if the user's session timed-out less that 30 minutes ago, we take them back to the

data/app/controllers/renalware/events/events_controller.rb

@@ -6,6 +6,8 @@ module Renalware
     class EventsController < BaseController
       include Renalware::Concerns::Pageable
 
+      # HTML GET when rendering the new form
+      # JS GET after user selects event type, prompting us to return event-specific form fields
       def new
         save_path_to_return_to
         render locals: {

data/app/controllers/renalware/letters/letters_controller.rb

@@ -8,7 +8,7 @@ module Renalware
       before_action :load_patient, except: [:author]
 
       def index
-        render :index, locals: { letters: present_letters(find_letters) }
+        render :index, locals: { letters: present_letters(find_letters), patient: patient }
       end
 
       def author

data/app/controllers/renalware/pd/bag_types_controller.rb

@@ -23,7 +23,7 @@ module Renalware
       end
 
       def index
-        bag_types = BagType.all
+        bag_types = BagType.ordered
         authorize bag_types
         render locals: { bag_types: bag_types }
       end

data/app/controllers/renalware/virology/dashboards_controller.rb

@@ -0,0 +1,15 @@
+require_dependency "renalware/virology"
+
+module Renalware
+  module Virology
+    class DashboardsController < BaseController
+      def show
+        authorize patient
+        render locals: {
+          patient: patient,
+          vaccinations: Vaccination.for_patient(patient)
+        }
+      end
+    end
+  end
+end

data/app/controllers/renalware/virology/vaccinations_controller.rb

@@ -0,0 +1,11 @@
+require_dependency "renalware/events"
+require_dependency "renalware/virology"
+
+# This controller is mostly empty - we are using it for mainly routing and to let us
+# override the events 'new' and 'edit' templates. See the base class for most functionality.
+module Renalware
+  module Virology
+    class VaccinationsController < Events::EventsController
+    end
+  end
+end

data/app/documents/renalware/patient_document.rb

@@ -23,6 +23,15 @@ module Renalware
     end
     attribute :referral, Referral
 
+    class Psychosocial < Document::Embedded
+      attribute :housing, String
+      attribute :social_network, String
+      attribute :care_package, String
+      attribute :other, String
+      attribute :updated_at, Date
+    end
+    attribute :psychosocial, Psychosocial
+
     class History < Document::Embedded
       attribute :alcohol, Document::Enum, enums: %i(never rarely social heavy)
       attribute :smoking, Document::Enum, enums: %i(no ex yes) # RRSMOKING %i(never former current)

data/app/jobs/hl7_message_example.yml

@@ -5,18 +5,18 @@ raw_message: |
   PV1||Inpatient|NIBC^^^^^^^^|||||MID^KINGS MIDWIVES||||||||||NHS|HXF888888^^^Visit Number|||||||||
   ORC|RE|^PCS|09B0099478^LA||CM||||200911111841|||MID^KINGS MIDWIVES|||||||
   OBR|1|^PCS|09B0099478^LA|FBC^FULL BLOOD COUNT^MB||200911111841|200911111841|||||||200911111841|B^Blood|MID^KINGS MIDWIVES||09B0099478||||200911121646||HM|F||||||||||||||||||
-  OBX|1|TX|WBC^WBC^MB||6.09||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|2|TX|RBC^RBC^MB||4.00||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|3|TX|HGB^Hb^MB||11.8||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|4|TX|PCV^PCV^MB||0.344||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|5|TX|MCV^MCV^MB||85.9||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|6|TX|MCH^MCH^MB||29.5||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|7|TX|MCHC^MCHC^MB||34.4||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|8|TX|RDW^RDW^MB||13.3||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|9|TX|PLT^PLT^MB||259||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|10|TX|MPV^Mean Platelet Volume^MB||8.3||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|11|TX|NRBC^Machine NRBC^MB||<0.2%||||||F|||200911112026||BBKA^Kenneth AMENYAH|
-  OBX|12|TX|HYPO^% HYPO^MB||0.2||||||F|||200911112026||BBKA^Kenneth AMENYAH|
+  OBX|1|TX|WBC^WBC^MB||6.09||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|2|TX|RBC^RBC^MB||4.00||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|3|TX|HGB^Hb^MB||11.8||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|4|TX|PCV^PCV^MB||0.344||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|5|TX|MCV^MCV^MB||85.9||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|6|TX|MCH^MCH^MB||29.5||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|7|TX|MCHC^MCHC^MB||34.4||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|8|TX|RDW^RDW^MB||13.3||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|9|TX|PLT^PLT^MB||259||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|10|TX|MPV^Mean Platelet Volume^MB||8.3||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|11|TX|NRBC^Machine NRBC^MB||<0.2%||||||F|||200911112026||BBKA^Donald DUCK|
+  OBX|12|TX|HYPO^% HYPO^MB||0.2||||||F|||200911112026||BBKA^Donald DUCK|
   OBX|13|TX|NEUT^Neutrophil Count^MB||  3.16||||||F|||200911121646||BHISVC01^BHI Authchecker|
   OBX|14|TX|LYM^Lymphocyte Count^MB||  2.32||||||F|||200911121646||BHISVC01^BHI Authchecker|
   OBX|15|TX|MON^Monocyte Count^MB||  0.44||||||F|||200911121646||BHISVC01^BHI Authchecker|

data/app/models/renalware/events/event.rb

@@ -29,12 +29,37 @@ module Renalware
         NullObject.instance
       end
 
+      def to_s
+        description
+      end
+
+      # As Events are a cross domain model, a subclass can choose to override to_partial_path etc
+      # in order to use events from another namespace for instance.
       def to_partial_path
-        self.class.name.demodulize.underscore
+        partial_for "inputs"
       end
+      alias :to_input_partial_path :to_partial_path
 
-      def to_s
-        description
+      def to_cell_partial_path
+        partial_for "cell"
+      end
+
+      def to_toggled_cell_partial_path
+        partial_for "toggled_cell"
+      end
+
+      def partial_for(partial_type)
+        File.join(
+          "renalware/events/events",
+          partial_type,
+          self.class.name.demodulize.underscore
+        )
+      end
+
+      private
+
+      def our_class_name
+        self.class.name.demodulize.underscore
       end
     end
   end

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

@@ -2,7 +2,8 @@ require_dependency "renalware/pathology"
 
 #
 # Create pathology observations requests and their child observations for an existing
-# patient from HL7 message content.
+# patient from HL7 message content previously parsed into an array of hashes (there can be > 1 OBR
+# in each message).
 #
 module Renalware
   module Pathology

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

@@ -4,6 +4,8 @@ module Renalware
   module Pathology
     class ObservationDescription < ApplicationRecord
       belongs_to :measurement_unit
+      validates :display_order, uniqueness: { allow_nil: true }
+      validates :display_order_letters, uniqueness: { allow_nil: true }
 
       def self.for(codes)
         ObservationDescriptionsByCodeQuery.new(codes: codes).call

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

@@ -6,7 +6,7 @@ module Renalware
     class ObservationDescriptionsByCodeQuery
       def initialize(relation: ObservationDescription, codes:)
         @relation = relation
-        @codes = codes
+        @codes = Array(codes)
       end
 
       # Executes SQL that looks like this:
@@ -37,6 +37,7 @@ module Renalware
       def verify_all_records_found(records)
         found_codes = records.map(&:code)
 
+        # TODO: Bug? Shouldn't this be @codes - found_codes?
         missing_records = found_codes - @codes
         if missing_records.present?
           raise ActiveRecord::RecordNotFound, "Missing records for #{missing_records}"

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

@@ -71,13 +71,14 @@ module Renalware
       def build_observations_params(request)
         request.observations.map do |observation|
           observation_description = find_observation_description(observation.identifier)
+          next unless validate_observation(observation, observation_description)
           {
             description_id: observation_description.id,
             observed_at: parse_time(observation.date_time),
             result: observation.value,
             comment: observation.comment
           }
-        end
+        end.compact
       end
 
       def find_request_description(code)
@@ -88,6 +89,18 @@ module Renalware
         ObservationDescription.find_by!(code: code)
       end
 
+      def validate_observation(observation, observation_description)
+        if observation.date_time.blank?
+          logger.warn(
+            "Skipped observation with blank `observed_at` (date_time) "\
+            "in OBX with code #{observation_description.code}"
+          )
+          false
+        else
+          true
+        end
+      end
+
       # TODO: Support searching by other local patient ids?
       def find_patient(local_patient_id)
         Patient.find_by!(local_patient_id: local_patient_id)

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

@@ -6,6 +6,8 @@ module Renalware
       acts_as_paranoid
       extend Enumerize
 
+      scope :ordered, ->{ order(manufacturer: :asc, description: :asc) }
+
       enumerize :glucose_strength, in: { not_applicable: 0, low: 1, medium: 2, high: 3 }
 
       has_many :bags, class_name: "Renalware::PD::RegimeBag"

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

@@ -6,7 +6,9 @@ module Renalware
       include OrderedScope
       include PatientScope
 
-      BAG_VOLUMES = [1000, 1200, 1500, 1800, 2000, 2200, 2500].freeze
+      BAG_VOLUMES = [
+        500, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2200, 2500
+      ].freeze
 
       before_save :set_glucose_volume_low_strength
       before_save :set_glucose_volume_medium_strength
@@ -18,6 +20,7 @@ module Renalware
 
       private
 
+      # rubocop:disable Metrics/MethodLength
       def match_bag_type
         @match_bag_type ||= begin
           glucose_types = [[], [], []]
@@ -34,6 +37,7 @@ module Renalware
           glucose_types
         end
       end
+      # rubocop:enable Metrics/MethodLength
 
       def set_glucose_volume_low_strength
         if match_bag_type[0].empty?

data/app/models/renalware/virology.rb

@@ -0,0 +1,13 @@
+require_dependency "renalware"
+
+module Renalware
+  module Virology
+    def self.table_name_prefix
+      "virology_"
+    end
+
+    def self.cast_patient(patient)
+      ActiveType.cast(patient, ::Renalware::Virology::Patient)
+    end
+  end
+end

data/app/models/renalware/virology/profile.rb

@@ -0,0 +1,8 @@
+require_dependency "renalware/virology"
+
+module Renalware
+  module Virology
+    class Profile < ApplicationRecord
+    end
+  end
+end

data/app/models/renalware/virology/vaccination.rb

@@ -0,0 +1,24 @@
+require_dependency "renalware/virology"
+require_dependency "renalware/events"
+require "document/base"
+require "document/embedded"
+require "document/enum"
+
+module Renalware
+  module Virology
+    class Vaccination < Events::Event
+      include Document::Base
+
+      # Return e.g. "renalware/virology/vaccinations/toggled_cell
+      def partial_for(partial_type)
+        File.join("renalware/virology/vaccinations", partial_type)
+      end
+
+      class Document < Document::Embedded
+        attribute :type, ::Document::Enum # See i18n for options
+        validates :type, presence: true
+      end
+      has_document
+    end
+  end
+end