renalware-core 2.0.0.pre.beta12 → 2.0.0.pre.rc1

checksums.yaml

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

@@ -29,7 +29,7 @@ for example `renalware-ukrdc` which enables sending data to the UKRDC.
 
 - Ruby 2.x
 - Ruby on Rails 5
-- Postgres 9.6+
+- Postgres 10.1+
 
 ## Get up and running locally
 

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

@@ -1,4 +1,3 @@
-
 .electronic-ccs {
   ul.actions {
     list-style: none;

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

@@ -1,3 +1,7 @@
+table.pathology-observation-diff {
+  width: auto;
+}
+
 table#observations {
   border-collapse: collapse;
   white-space: nowrap;

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

@@ -0,0 +1,26 @@
+.beta_banner {
+  background-color: $nhs-orange;
+  padding: 0.4rem 1rem;
+  color: $white;
+  text-align: center;
+
+  span {
+    font-size: 1.1rem;
+  }
+
+  .button {
+    margin: 0;
+    margin-left: 1rem;
+    padding: 0.3rem 0.8rem;
+  }
+}
+
+.new_feedback {
+  .radio {
+    label {
+      input {
+        margin: 0 1rem 0.5rem 0
+      }
+    }
+  }
+}

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

@@ -1,3 +1,7 @@
+.alert-box.warning {
+  background-color: $nhs-orange;
+}
+
 .error-page {
   .title-area .name {
     color: $white;

data/app/controllers/renalware/admissions/consults_controller.rb

@@ -52,13 +52,6 @@ module Renalware
 
       private
 
-      def present(consults)
-        CollectionPresenter.new(
-          Consult.all.order(created_at: :desc).page(page).per(per_page),
-          ConsultPresenter
-        )
-      end
-
       def find_and_authorize_consult
         Consult.find(params[:id]).tap do |consult|
           authorize consult

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

@@ -41,15 +41,15 @@ module Renalware
         devise_parameter_sanitizer.permit(
           :account_update,
           keys: [
-              :given_name,
-              :family_name,
-              :username,
-              :email,
-              :password,
-              :password_confirmation,
-              :current_password,
-              :professional_position,
-              :signature
+            :given_name,
+            :family_name,
+            :username,
+            :email,
+            :password,
+            :password_confirmation,
+            :current_password,
+            :professional_position,
+            :signature
           ]
         )
       end

data/app/controllers/renalware/hd/mdm_controller.rb

@@ -1,11 +1,10 @@
-require_dependency "renalware/hd/base_controller"
+require_dependency "renalware/hd"
 
 module Renalware
   module HD
     class MDMController < Renalware::MDMController
-      before_action :load_patient
-
       def show
+        authorize patient
         mdm_presenter = HD::MDMPresenter.new(patient: patient, view_context: view_context)
         render_show(mdm_presenter: mdm_presenter)
       end

data/app/controllers/renalware/hd/mdm_patients_controller.rb

@@ -1,3 +1,5 @@
+require_dependency "renalware/hd"
+
 module Renalware
   module HD
     class MDMPatientsController < Renalware::MDMPatientsController
@@ -8,7 +10,11 @@ module Renalware
       end
 
       def index
-        render_index(query: MDMPatientsQuery.new(q: params[:q]),
+        query = HD::MDMPatientsQuery.new(
+          relation: HD::Patient.eager_load(hd_profile: [:hospital_unit]),
+          q: params[:q]
+        )
+        render_index(query: query,
                      page_title: t(".page_title"),
                      view_proc: ->(patient) { patient_hd_mdm_path(patient) },
                      patient_presenter_class: HD::PatientPresenter)

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

@@ -184,7 +184,7 @@ module Renalware
         [
           :event_type, :event_id, :clinical,
           :letterhead_id, :author_id, :description, :issued_on, :enclosures,
-          :salutation, :body, :notes,
+          :salutation, :body, :notes, :pathology_timestamp,
           main_recipient_attributes: main_recipient_attributes,
           cc_recipients_attributes: cc_recipients_attributes,
           electronic_cc_recipient_ids: []

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

@@ -7,14 +7,21 @@ module Renalware
 
       def show
         query = LetterQuery.new(q: params[:q])
-        collection = call_query(query).page(page).per(per_page)
-        @letters = present_letters(collection)
-        authorize @letters
+        letters = find_and_authorize_letters(query)
+
+        render locals: {
+          letters: letters,
+          authors: User.author.ordered,
+          typists: User.ordered,
+          q: query.search
+        }
+      end
 
-        @q = query.search
+      private
 
-        @authors = User.author.ordered
-        @typists = User.ordered
+      def find_and_authorize_letters(query)
+        collection = call_query(query).page(page).per(per_page)
+        present_letters(collection).tap { |letters| authorize letters }
       end
 
       def present_letters(letters)

data/app/controllers/renalware/mdm_controller.rb

@@ -1,4 +1,4 @@
-require_dependency "renalware/hd/base_controller"
+require_dependency "renalware"
 
 module Renalware
   class MDMController < BaseController

data/app/controllers/renalware/mdm_patients_controller.rb

@@ -1,4 +1,4 @@
-require_dependency "renalware/base_controller"
+require_dependency "renalware"
 
 # Note we rely on template inheritance with this MDM Base class i.e. subclasses (e.g.
 # HD::MDMPatientsController) can override templates and partials (e.g. add a _filters partial

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

@@ -22,7 +22,7 @@ module Renalware
         else
           skip_authorization
         end
-        fallback_location = patient.present? ? patient : root_path
+        fallback_location = patient.presence || root_path
         redirect_back(fallback_location: patient_path(fallback_location),
                       notice: success_msg_for("bookmark"))
       end

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

@@ -8,7 +8,7 @@ module Renalware
 
       def show
         clinical_summary = Renal::ClinicalSummaryPresenter.new(patient)
-        render :show, locals: { clinical_summary: clinical_summary }
+        render :show, locals: { clinical_summary: clinical_summary, patient: patient }
       end
     end
   end

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

@@ -1,11 +1,10 @@
-require_dependency "renalware/hd/base_controller"
+require_dependency "renalware/pd"
 
 module Renalware
   module PD
     class MDMController < Renalware::MDMController
-      before_action :load_patient
-
       def show
+        authorize patient
         mdm_presenter = PD::MDMPresenter.new(patient: patient, view_context: view_context)
         render_show(mdm_presenter: mdm_presenter)
       end

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

@@ -1,3 +1,5 @@
+require "renalware/pd"
+
 module Renalware
   module PD
     class MDMPatientsController < Renalware::MDMPatientsController

data/app/controllers/renalware/renal/low_clearance/mdm_controller.rb

@@ -0,0 +1,15 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    module LowClearance
+      class MDMController < Renalware::MDMController
+        def show
+          authorize patient
+          presenter = LowClearance::MDMPresenter.new(patient: patient, view_context: view_context)
+          render_show(mdm_presenter: presenter)
+        end
+      end
+    end
+  end
+end

data/app/controllers/renalware/renal/low_clearance/mdm_patients_controller.rb

@@ -0,0 +1,29 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    module LowClearance
+      class MDMPatientsController < Renalware::MDMPatientsController
+        def index
+          render_index(query: query,
+                       page_title: t(".page_title"),
+                       view_proc: ->(patient) { patient_renal_low_clearance_mdm_path(patient) })
+        end
+
+        private
+
+        def query
+          LowClearance::MDMPatientsQuery.new(query: q, named_filter: named_filter)
+        end
+
+        def named_filter
+          params[:named_filter]
+        end
+
+        def q
+          params[:q]
+        end
+      end
+    end
+  end
+end

data/app/controllers/renalware/session_timeout_controller.rb

@@ -17,6 +17,7 @@ module Renalware
     # We could return the amount of time remaining before the session expires like so
     #   time_left = Devise.timeout_in - (Time.now - user_session["last_request_at"]).round
     # and display this to the user if required.
+    # rubocop :disable Naming/PredicateName
     def has_user_timed_out
       skip_authorization
       if referrer_is_a_devise_url? || !current_users_session_has_timed_out?
@@ -26,6 +27,7 @@ module Renalware
         head :unauthorized
       end
     end
+    # rubocop :enable Naming/PredicateName
 
     # A user could invoke this action to keep their session alive, by for example
     # clicking on a "Keep my session active" button which makes an ajax call to this action.

data/app/controllers/renalware/system/user_feedback_controller.rb

@@ -0,0 +1,35 @@
+module Renalware
+  module System
+    class UserFeedbackController < BaseController
+      def new
+        feedback = UserFeedback.new
+        authorize feedback
+        render_new(feedback)
+      end
+
+      def create
+        feedback = UserFeedback.new(user_feedback_params)
+        feedback.author = current_user
+        authorize feedback
+
+        if feedback.save
+          redirect_to root_url, notice: "Feedback registered, thank you"
+        else
+          render_new(feedback)
+        end
+      end
+
+      private
+
+      def render_new(feedback)
+        render :new, locals: { feedback: feedback }
+      end
+
+      def user_feedback_params
+        params
+          .require(:feedback)
+          .permit(:comment, :category)
+      end
+    end
+  end
+end

data/app/controllers/renalware/transplants/mdm_controller.rb

@@ -1,12 +1,10 @@
-require_dependency "renalware/hd/base_controller"
 require_dependency "renalware/transplants"
 
 module Renalware
   module Transplants
     class MDMController < Renalware::MDMController
-      before_action :load_patient
-
       def show
+        authorize patient
         mdm_presenter = Transplants::MDMPresenter.new(patient: patient, view_context: view_context)
         render_show(mdm_presenter: mdm_presenter)
       end

data/app/controllers/renalware/transplants/mdm_patients_controller.rb

@@ -1,3 +1,5 @@
+require_dependency "renalware/transplants"
+
 module Renalware
   module Transplants
     class MDMPatientsController < Renalware::MDMPatientsController

data/app/helpers/renalware/application_helper.rb

@@ -65,7 +65,7 @@ module Renalware
     end
 
     def default_for_blank(val, msg)
-      val.blank? ? msg : val
+      val.presence || msg
     end
 
     def default_for_blank_date(date, msg)
@@ -76,46 +76,6 @@ module Renalware
       val.blank? ? msg : "#{val} #{unit}"
     end
 
-    def medication_and_route(med_route)
-      if med_route.blank?
-        "No medication prescribed"
-      else
-        other_route = "Route: Other (Please specify in notes)"
-        safe_join(
-          med_route.map do |m|
-            route = if m.medication_route.name == other_route
-                      m.medication_route.full_name
-                    else
-                      m.medication_route.name
-                    end
-            "<li>
-                #{m.drug.name} - #{route}
-            </li>".html_safe
-          end
-        )
-      end
-    end
-
-    def organisms_and_sensitivities(infection_organisms)
-      if infection_organisms.blank?
-        "Unknown"
-      else
-        safe_join(
-          infection_organisms.map do |io|
-            "<li>#{io.organism_code.name} - #{io.sensitivity}</li>".html_safe
-          end
-        )
-      end
-    end
-
-    def organisms(infection_organisms)
-      if infection_organisms.blank?
-        "Unknown"
-      else
-        safe_join(infection_organisms.map { |io| "<li>#{io.organism_code.name}</li>".html_safe })
-      end
-    end
-
     def pipe_separator
       "&nbsp;|&nbsp;".html_safe
     end
@@ -130,7 +90,6 @@ module Renalware
     end
 
     def inline_image(file_path)
-      # InlineImage.new("/app/assets/images/#{file_path}")
       InlineImage.new(asset_path(file_path))
     end
 

data/app/helpers/renalware/clinic_helper.rb

@@ -7,7 +7,9 @@ module Renalware
       else
         link_to("Draft Letter", new_patient_letters_letter_path(
           patient,
-          event_type: Renalware::Clinics::ClinicVisit.name.to_s, event_id: clinic_visit.id
+          event_type: Renalware::Clinics::ClinicVisit.name.to_s,
+          event_id: clinic_visit.id,
+          clinical: true
         ))
       end
     end

data/app/helpers/renalware/infection_organisms_helper.rb

@@ -7,5 +7,25 @@ module Renalware
     def new_pd_infection_organism_path(infectable)
       super(infectable_type: infectable.class.to_s, infectable_id: infectable.id)
     end
+
+    def organisms_and_sensitivities(infection_organisms)
+      if infection_organisms.blank?
+        "Unknown"
+      else
+        safe_join(
+          infection_organisms.map do |io|
+            "<li>#{io.organism_code.name} - #{io.sensitivity}</li>".html_safe
+          end
+        )
+      end
+    end
+
+    def organisms(infection_organisms)
+      if infection_organisms.blank?
+        "Unknown"
+      else
+        safe_join(infection_organisms.map { |io| "<li>#{io.organism_code.name}</li>".html_safe })
+      end
+    end
   end
 end

data/app/helpers/renalware/mdm_helper.rb

@@ -17,11 +17,12 @@ module Renalware
 
       def path
         @path ||= begin
-          case modality_description_name&.downcase&.to_sym
+          return if modality_description.type.blank?
+          case modality_description_symbol
           when :pd then patient_pd_mdm_path(patient)
           when :hd then patient_hd_mdm_path(patient)
           when :transplant then patient_transplants_mdm_path(patient)
-          when :lcc then nil # patient_low_clearance_mdm_path(patient)
+          when :low_clearance then patient_renal_low_clearance_mdm_path(patient)
           end
         end
       end
@@ -32,11 +33,8 @@ module Renalware
 
       private
 
-      attr_reader :patient, :modality_description_name
-
-      def modality_description_name
-        modality_description.name
-      end
+      attr_reader :patient
+      delegate :name, to: :modality_description, prefix: true, allow_nil: true
 
       def modality_description
         current_modality = patient.current_modality || NullObject.instance
@@ -46,6 +44,10 @@ module Renalware
       def mdm_name
         "#{modality_description_name} MDM"
       end
+
+      def modality_description_symbol
+        modality_description.becomes(modality_description.type.constantize).to_sym
+      end
     end
   end
 end

data/app/helpers/renalware/prescriptions_helper.rb

@@ -35,5 +35,25 @@ module Renalware
     def default_provider(provider)
       provider == "gp" ? "checked" : nil
     end
+
+    def medication_and_route(med_route)
+      if med_route.blank?
+        "No medication prescribed"
+      else
+        other_route = "Route: Other (Please specify in notes)"
+        safe_join(
+          med_route.map do |m|
+            route = if m.medication_route.name == other_route
+                      m.medication_route.full_name
+                    else
+                      m.medication_route.name
+                    end
+            "<li>
+                #{m.drug.name} - #{route}
+            </li>".html_safe
+          end
+        )
+      end
+    end
   end
 end

data/app/helpers/renalware/side_nav_helper.rb

@@ -2,14 +2,6 @@ require_dependency "renalware/patients"
 
 module Renalware
   module SideNavHelper
-    def display_pd_menu?(patient)
-      true
-    end
-
-    def display_hd_menu?(patient)
-      true
-    end
-
     def find_user_bookmark_for_patient(patient)
       user = Renalware::Patients.cast_user(current_user)
       user.bookmark_for_patient(patient)

data/app/jobs/application_job.rb

@@ -1,2 +1,4 @@
 class ApplicationJob < ActiveJob::Base
+  # :nocov:
+  # :nocov:
 end

data/app/models/concerns/renalware/explicit_state_model.rb

@@ -51,6 +51,7 @@ module Renalware
     module ClassMethods
       # Adds a ActiveRecord scopes for each state defined; e.g. `Letter.draft`
       #
+      # rubocop :disable Naming/PredicateName
       def has_states(*states)
         states.each do |state|
           state_scope(state, state)
@@ -64,6 +65,7 @@ module Renalware
           states
         end
       end
+      # rubocop :enable Naming/PredicateName
 
       # Allows for custom scope names, example:
       #

data/app/models/concerns/renalware/patient_pathology_scopes.rb

@@ -0,0 +1,39 @@
+require_dependency "renalware"
+
+# Mix this module into a Patient Query object for example in order to include the patient's
+# current key pathology and enable sorting on pathology date and value fields using
+# ransack's sort_link helper in the view.
+#
+module Renalware
+  module PatientPathologyScopes
+    def with_current_key_pathology
+      includes(:current_key_observation_set).joins(:current_key_observation_set)
+    end
+
+    # Define some ransackers to make it easier to sort the table (using sort_link)
+    # on pathology dates and values. Note it wasn't possible just to use say
+    # = sort_link(.., "pathology_current_key_observation_sets.cre_observed_at", ..)
+    # or
+    # = sort_link(.., :pathology_current_key_observation_set_cre_observed_at", ..)
+    # as ransack wasn't happy and discarded the sort predicate.
+    # So here we mix in useful ransackers as short cut to use in sort_link
+    #
+    # Example usage:
+    #   = sort_link(<url>, :cre_observed_at, "CRE date")
+    #
+    def self.extended(base)
+      %i(hgb ure cre).each do |code|
+        base.ransacker(code) { pathology_sort_predicate("#{code}_result") }
+        base.ransacker(:"#{code}_date") { pathology_sort_predicate("#{code}_observed_at") }
+      end
+
+      %i(mdrd).each do |code|
+        base.ransacker(code) { pathology_sort_predicate("#{code}_result") }
+      end
+    end
+
+    def self.pathology_sort_predicate(column)
+      Arel.sql("pathology_current_key_observation_sets.#{column}")
+    end
+  end
+end

data/app/models/concerns/renalware/personable.rb

@@ -4,7 +4,8 @@ module Renalware
 
     included do
       class_eval do
-        validates_presence_of :given_name, :family_name
+        validates :given_name, presence: true
+        validates :family_name, presence: true
       end
 
       def full_name
@@ -22,7 +23,7 @@ module Renalware
 
       def salutation
         parts = [Renalware.config.salutation_prefix]
-        parts << (title.present? ? title : given_name)
+        parts << (title.presence || given_name)
         parts << family_name
         parts.compact.join(" ")
       end

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

@@ -7,10 +7,10 @@ module Renalware
       belongs_to :clinic
       belongs_to :user
 
-      validates_presence_of :starts_at
-      validates_presence_of :patient
-      validates_presence_of :clinic
-      validates_presence_of :user
+      validates :starts_at, presence: true
+      validates :patient, presence: true
+      validates :clinic, presence: true
+      validates :user, presence: true
 
       validates :starts_at, timeliness: { type: :datetime }
 

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

@@ -15,8 +15,8 @@ module Renalware
       belongs_to :clinic
       has_many :clinic_letters
 
-      validates_presence_of :date
-      validates_presence_of :clinic
+      validates :date, presence: true
+      validates :clinic, presence: true
 
       validates :date, timeliness: { type: :date }
       validates :time, timeliness: { type: :time, allow_blank: true }