renalware-core 2.0.0.pre.beta8 → 2.0.0.pre.beta9

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -27,7 +27,7 @@ for example `renalware-ukrdc` which enables sending data to the UKRDC.
 
 ### Stack
 
-- Ruby 2.4.1
+- Ruby 2.x
 - Ruby on Rails 5
 - Postgres 9.6+
 
@@ -161,6 +161,15 @@ to just create
 `config.active_record.schema_format = :sql` in `application.rb` is used the engine
 uses Postgres views and functions which are not properly supported in a `schema.rb`
 
+##### Creating scenic views
+
+As we are an engine this is the workaround for now.
+```sh
+  bundle exec spec/dummy/bin/rails generate scenic:view my_view_name
+```
+Then copy the new files from spec/dummy/db/views and spec/dummy/db/migrations
+to ./db/views and ./db/migrations
+
 #### Throttling login attempts
 
 [rack-attack](https://github.com/kickstarter/rack-attack) is configured to throttle login attempts.
@@ -182,3 +191,12 @@ To make awesome_print the default formatter in irb, add the following to `~/.irb
 
     require "awesome_print"
     AwesomePrint.irb!
+
+
+#### Docker - WIP!
+
+```
+docker build -t renalware .
+docker-compose run web rake db:create
+docker-compose run web rake app:db:create
+```

data/app/assets/stylesheets/renalware/lib/_select2-foundation5-overrides.scss

@@ -1,6 +1,6 @@
 span.select2 {
   margin: 0;
-  // margin: 0 0 0.75rem 0;
+  margin: 0 0 0.75rem 0;
 }
 
 .grouped_select {
@@ -19,6 +19,6 @@ span.select2 {
 
 .horizontal_medium {
   span.select2.select2-container.select2-container--default {
-    min-width: 500px !important;
+    // min-width: 500px !important;
   }
 }

data/app/controllers/renalware/directory/people_controller.rb

@@ -94,7 +94,7 @@ module Renalware
       def address_attributes
         [
           :id, :name, :organisation_name, :street_1, :street_2, :street_3, :town, :county,
-          :postcode, :country, :telephone, :email, :_destroy
+          :postcode, :country_id, :telephone, :email, :_destroy
         ]
       end
     end

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

@@ -69,7 +69,7 @@ module Renalware
       def person_address_attributes
         [
           :id, :name, :organisation_name, :street_1, :street_2, :street_3, :town, :county,
-          :postcode, :country, :telephone, :email
+          :postcode, :country_id, :telephone, :email
         ]
       end
 

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

@@ -212,7 +212,7 @@ module Renalware
       def address_attributes
         [
           :id, :name, :organisation_name, :street_1, :street_2, :street_3, :town, :county,
-          :postcode, :country, :telephone, :email, :_destroy
+          :postcode, :country_id, :telephone, :email, :_destroy
         ]
       end
     end

data/app/controllers/renalware/patients/patients_controller.rb

@@ -22,7 +22,7 @@ module Renalware
       end
 
       def new
-        patient = Patient.new
+        patient = Patient.new.tap(&:build_current_address)
         authorize patient
         render locals: { patient: patient }
       end
@@ -83,10 +83,9 @@ module Renalware
           .merge(by: current_user)
       end
 
-      # rubocop:disable Metrics/MethodLength
       def patient_attributes
         [
-          :nhs_number, :family_name, :given_name, :sex,
+          :nhs_number, :family_name, :given_name, :sex, :country_of_birth_id,
           :ethnicity_id, :born_on, :paediatric_patient_indicator, :cc_on_all_letters,
           :title, :suffix, :marital_status, :telephone1, :telephone2, :email, :religion_id,
           :language_id, :cc_decision_on,
@@ -97,10 +96,9 @@ module Renalware
           current_address_attributes: address_params
         ]
       end
-      # rubocop:enable Metrics/MethodLength
 
       def address_params
-        [:id, :name, :organisation_name, :street_1, :street_2, :street_3, :county, :country,
+        [:id, :name, :organisation_name, :street_1, :street_2, :street_3, :county, :country_id,
           :town, :postcode, :telephone, :email]
       end
 

data/app/controllers/renalware/patients/primary_care_physicians_controller.rb

@@ -90,7 +90,7 @@ module Renalware
           practice_ids: [],
           address_attributes: [
             :id, :name, :organisation_name, :street_1, :street_2, :street_3, :town, :county,
-            :postcode, :country, :telephone, :email
+            :postcode, :country_id, :telephone, :email
           ]
         )
       end

data/app/controllers/renalware/renal/aki_alerts_controller.rb

@@ -0,0 +1,44 @@
+require_dependency("renalware/renal")
+
+module Renalware
+  module Renal
+    class AKIAlertsController < BaseController
+      include Renalware::Concerns::Pageable
+
+      def index
+        alerts = AKIAlert.includes(:updated_by, :action, :hospital_ward, :patient)
+                         .ordered.page(page).per(per_page)
+        authorize alerts
+        render locals: { alerts: alerts }
+      end
+
+      def edit
+        authorize alert
+        render_edit(alert)
+      end
+
+      def update
+        authorize alert
+        if alert.update_attributes(aki_alert_params.merge(by: current_user))
+          redirect_to renal_aki_alerts_path
+        else
+          render_edit(alert)
+        end
+      end
+
+      private
+
+      def render_edit(alert)
+        render :edit, locals: { alert: alert }
+      end
+
+      def alert
+        @alert ||= AKIAlert.find(params[:id])
+      end
+
+      def aki_alert_params
+        params.require(:renal_aki_alert).permit(:notes, :action_id, :hotlist, :hospital_ward_id)
+      end
+    end
+  end
+end

data/app/controllers/renalware/renal/profiles_controller.rb

@@ -49,7 +49,7 @@ module Renalware
       end
 
       def address_params
-        [:id, :name, :organisation_name, :street_1, :street_2, :street_3, :county, :country,
+        [:id, :name, :organisation_name, :street_1, :street_2, :street_3, :county, :country_id,
           :town, :postcode, :telephone, :email]
       end
 

data/app/controllers/renalware/reporting/audits_controller.rb

@@ -12,12 +12,12 @@ module Renalware
 
       def show
         authorize audit
-        columns, values = GenerateAuditJson.call(audit.materialized_view_name)
+        columns, values = GenerateAuditJson.call(audit.view_name)
         render(
           locals: {
             audit: audit,
             columns: columns,
-            values: values
+            values: replace_nils_with_empty_string(values)
           }
         )
       end
@@ -42,6 +42,12 @@ module Renalware
         @audit ||= Audit.find(params[:id])
       end
 
+      # Takes an array (rows) of arrays (cells) and replaces any nil elements
+      # with an empty string so JS data tables does not baulk with 'nil undefined' error.
+      def replace_nils_with_empty_string(values)
+        values.map{ |row| row.map{ |cell| cell || "" } }
+      end
+
       def render_edit
         render :edit, locals: {
           audit: audit,
@@ -54,7 +60,7 @@ module Renalware
               .permit(
                 :name,
                 :description,
-                :materialized_view_name,
+                :view_name,
                 :display_configuration,
                 :refresh_schedule
               )

data/app/documents/renalware/patient_document.rb

@@ -15,19 +15,6 @@ module Renalware
     end
     attribute :diabetes, Diabetes
 
-    # TODO: Check if this is used?
-    class Address < Document::Embedded
-      attribute :name, String
-      attribute :organisation_name, String
-      attribute :street_1, String
-      attribute :street_2, String
-      attribute :street_3, String
-      attribute :town, String
-      attribute :county, String
-      attribute :postcode, String
-      attribute :country, String
-    end
-
     class Referral < Document::Embedded
       attribute :referring_physician_name, String
       attribute :referral_date, Date

data/app/jobs/hl7_message_example.yml

@@ -7,7 +7,7 @@ raw_message: |
   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|HB^Hb^MB||11.8||||||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|

data/app/jobs/renalware/reporting/refresh_audit_data_job.rb

@@ -7,14 +7,18 @@ module Renalware
 
       # :reek:UtilityFunction
       def perform(audit)
-        refresh_materialized_view_associated_with_audit(audit)
-        update_audit_refreshment_date(audit)
+        if audit.materialized?
+          refresh_materialized_view_associated_with_audit(audit)
+          update_audit_refreshment_date(audit)
+        else
+          Rails.logger.warn("Cannot refresh an view that is not materialized: #{audit.view_name}")
+        end
       end
 
       private
 
       def refresh_materialized_view_associated_with_audit(audit)
-        Scenic.database.refresh_materialized_view(audit.materialized_view_name,
+        Scenic.database.refresh_materialized_view(audit.view_name,
                                                   concurrently: false,
                                                   cascade: false)
       end

data/app/models/renalware/clinical/create_allergy.rb

@@ -1,4 +1,6 @@
 require_dependency "renalware/clinical"
+require_dependency "renalware/success"
+require_dependency "renalware/failure"
 
 module Renalware
   module Clinical
@@ -14,9 +16,9 @@ module Renalware
         yield allergy if block_given?
         if allergy.valid?
           save_allergy(allergy)
-          Success.new(allergy)
+          ::Renalware::Success.new(allergy)
         else
-          Failure.new(allergy)
+          ::Renalware::Failure.new(allergy)
         end
       end
 

data/app/models/renalware/clinics/create_clinic_visit.rb

@@ -1,3 +1,7 @@
+require_dependency "renalware/clinics"
+require_dependency "renalware/success"
+require_dependency "renalware/failure"
+
 module Renalware
   module Clinics
     class CreateClinicVisit
@@ -17,9 +21,9 @@ module Renalware
           visit = patient.clinic_visits.new(params)
           objects = OpenStruct.new(clinic_visit: visit, appointment: appointment)
           if visit.save && update_appointment_with(visit.id)
-            return Success.new(objects)
+            return ::Renalware::Success.new(objects)
           else
-            return Failure.new(objects)
+            return ::Renalware::Failure.new(objects)
           end
         end
       end

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

@@ -42,8 +42,20 @@ module Renalware
 
       delegate :hospital_centre, to: :hospital_unit, allow_nil: true
 
+      def start_datetime
+        datetime_at(start_time)
+      end
+
+      def stop_datetime
+        datetime_at(end_time)
+      end
+
       private
 
+      def datetime_at(time)
+        Time.zone.parse("#{performed_on.strftime('%F')} #{time.strftime('%T')}")
+      end
+
       def assign_modality
         self.modality_description = patient.modality_description
       end

data/app/models/renalware/hospitals/unit.rb

@@ -6,6 +6,10 @@ module Renalware
       extend Enumerize
 
       belongs_to :hospital_centre, class_name: "Hospitals::Centre"
+      has_many :wards,
+               class_name: "Hospitals::Ward",
+               foreign_key: :hospital_unit_id,
+               dependent: :destroy
 
       validates :hospital_centre, presence: true
       validates :unit_code, presence: true

data/app/models/renalware/hospitals/ward.rb

@@ -0,0 +1,22 @@
+require_dependency "renalware/hospitals"
+
+module Renalware
+  module Hospitals
+    class Ward < ApplicationRecord
+      belongs_to :hospital_unit, class_name: "Hospitals::Unit"
+
+      validates :hospital_unit, presence: true
+      validates :name, presence: true, uniqueness: { scope: :hospital_unit_id }
+
+      scope :ordered, -> { order(:name) }
+
+      def self.policy_class
+        BasePolicy
+      end
+
+      def to_s
+        name
+      end
+    end
+  end
+end

data/app/models/renalware/modalities/change_patient_modality.rb

@@ -1,4 +1,6 @@
 require_dependency "renalware/modalities"
+require_dependency "renalware/success"
+require_dependency "renalware/failure"
 
 module Renalware
   module Modalities
@@ -46,9 +48,9 @@ module Renalware
         if new_modality.valid?
           make_new_modality_the_current_one(new_modality)
           broadcast_modality_change_event_to_any_listeners(new_modality)
-          Success.new(new_modality)
+          ::Renalware::Success.new(new_modality)
         else
-          Failure.new(new_modality)
+          ::Renalware::Failure.new(new_modality)
         end
       end
 

data/app/models/renalware/patient.rb

@@ -31,6 +31,7 @@ module Renalware
     has_one :current_address, as: :addressable, class_name: "Address"
     has_one :summary, class_name: "Patients::Summary"
     belongs_to :ethnicity, class_name: "Patients::Ethnicity"
+    belongs_to :country_of_birth, class_name: "System::Country"
     belongs_to :religion, class_name: "Patients::Religion"
     belongs_to :language, class_name: "Patients::Language"
     has_many :bookmarks, class_name: "Patients::Bookmark"

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

@@ -4,6 +4,7 @@ module Renalware
   module Patients
     class Language < ApplicationRecord
       validates :name, presence: true
+      validates :code, presence: true
 
       def to_s
         name

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

@@ -1,4 +1,6 @@
 require_dependency "renalware/pd"
+require_dependency "renalware/success"
+require_dependency "renalware/failure"
 
 module Renalware
   module PD
@@ -10,9 +12,9 @@ module Renalware
       def call(by:, params:)
         regime = patient.pd_regimes.new(params)
         if regime.valid? && save_regime(regime, by)
-          return Success.new(regime)
+          return ::Renalware::Success.new(regime)
         else
-          return Failure.new(regime)
+          return ::Renalware::Failure.new(regime)
         end
       end
 

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

@@ -1,4 +1,6 @@
 require_dependency "renalware/pd"
+require_dependency "renalware/success"
+require_dependency "renalware/failure"
 
 module Renalware
   module PD
@@ -11,11 +13,11 @@ module Renalware
       def call(by:, params:)
         Regime.transaction do
           regime.assign_attributes(params)
-          return Success.new(regime) unless regime.anything_changed?
-          return Failure.new(regime.with_bag_destruction_marks_removed) unless regime.valid?
+          return ::Renalware::Success.new(regime) unless regime.anything_changed?
+          return ::Renalware::Failure.new(regime.with_bag_destruction_marks_removed) unless regime.valid?
 
           new_regime = revise_regime(by: by)
-          Success.new(new_regime)
+          ::Renalware::Success.new(new_regime)
         end
       end