renalware-core 2.0.39 → 2.0.40

checksums.yaml

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

@@ -1,8 +1,7 @@
 # Renalware
 
-[![Code Climate](https://codeclimate.com/repos/58beee3ed41d600266000147/badges/50451f89d7aad6c2d200/gpa.svg)](https://codeclimate.com/repos/58beee3ed41d600266000147/feed)
+[![Maintainability](https://api.codeclimate.com/v1/badges/644897239eebaf83f564/maintainability)](https://codeclimate.com/github/airslie/renalware-core/maintainability)
 [![Test Coverage](https://codeclimate.com/repos/58beee3ed41d600266000147/badges/50451f89d7aad6c2d200/coverage.svg)](https://codeclimate.com/repos/58beee3ed41d600266000147/coverage)
-[![Dependency Status](https://gemnasium.com/badges/github.com/airslie/renalware-core.svg)](https://gemnasium.com/github.com/airslie/renalware-core)
 [![Gem Version](https://badge.fury.io/rb/renalware-core.svg)](https://badge.fury.io/rb/renalware-core)
 
 Renalware uses demographic, clinical, pathology, and nephrology datasets to improve patient care,

data/app/assets/javascripts/renalware/clockpicker.js

@@ -24,7 +24,7 @@
 			supported = (el.firstChild && el.firstChild.namespaceURI) == svgNS;
 			el.innerHTML = '';
 			return supported;
-		})();
+		}());
 
 	// Can I use transition ?
 	var transitionSupported = (function(){
@@ -34,7 +34,7 @@
 			'MozTransition' in style ||
 			'msTransition' in style ||
 			'OTransition' in style;
-	})();
+	}());
 
 	// Listen touch events in touch screen device, instead of mouse events in desktop.
 	var touchSupported = 'ontouchstart' in window,

data/app/assets/javascripts/renalware/letters.js

@@ -104,6 +104,6 @@ Renalware.Letters = (function() {
       bindOnLetterAboutToPrint();
     }
   };
-})();
+}());
 
 $(document).ready(Renalware.Letters.init);

data/app/assets/javascripts/renalware/messaging.js

@@ -10,6 +10,6 @@ Renalware.Messaging = (function() {
       focusRecipientSearchInput()
     }
   };
-})();
+}());
 
 $(document).on('opened.fndtn.reveal', '#send-message-modal', Renalware.Messaging.init);

data/app/assets/javascripts/renalware/patient_ajax_search.js

@@ -40,7 +40,7 @@ Renalware.PatientSearch = (function() {
       initPatientSearch()
     }
   };
-})();
+}());
 
 $(document).ready(Renalware.PatientSearch.init);
 $(document).on('opened.fndtn.reveal', '[data-reveal]', function() {

data/app/assets/javascripts/renalware/pd.js

@@ -47,7 +47,7 @@ Renalware.PdRegimes = (function () {
       $('a.remove-bag').show();
     }
   }
-})();
+}());
 // Bind DOM ready and nested_form:fieldAdded events
 // so that buttons are toggled when JS is active.
 $(document).ready(Renalware.PdRegimes.init);

data/app/assets/javascripts/renalware/primary_care_physician_search.js

@@ -75,7 +75,6 @@ Renalware.PrimaryCarePhysicianSearch = (function() {
       initPracticeAutocomplete()
     }
   };
-})();
+}());
 
 $(document).on('opened.fndtn.reveal', '[data-reveal]', Renalware.PrimaryCarePhysicianSearch.init);
-

data/app/assets/javascripts/renalware/primary_care_physicians.js

@@ -20,6 +20,6 @@ Renalware.PrimaryCarePhysicians = (function () {
       bindAddressFormToggle();
     }
   }
-})();
+}());
 
 $(document).ready(Renalware.PrimaryCarePhysicians.init);

data/app/assets/javascripts/renalware/renal.js

@@ -29,6 +29,6 @@ Renalware.Renal = (function () {
       wireUpUseCurrentAddressButton();
     }
   }
-})();
+}());
 
 $(document).ready(Renalware.Renal.init);

data/app/assets/javascripts/renalware/research.js

@@ -13,6 +13,6 @@ Renalware.Research = (function() {
       focusPatientInput();
     }
   };
-})();
+}());
 
 $(document).on('opened.fndtn.reveal', '#study-participant-modal', Renalware.Research.init);

data/app/assets/javascripts/renalware/select2-ajax-search.js

@@ -78,7 +78,7 @@ Renalware.AjaxSearch = (function() {
       initAjaxSearch()
     }
   };
-})();
+}());
 
 $(document).ready(Renalware.AjaxSearch.init);
 $(document).on('opened.fndtn.reveal', '[data-reveal]', function() {

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

@@ -83,3 +83,11 @@
     }
   }
 }
+
+ul.indented {
+  li {
+    text-indent: -1.5em;
+    list-style-position: outside;
+    padding-left: 1.5em;
+  }
+}

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

@@ -26,25 +26,16 @@
   }
 }
 
-.mdm-page {
-  article {
-    &.events {
-      .created_at,
-      .created_by {
-
-      }
-    }
-  }
-
-  .expandable {
-    clear: both;
-    height: 0;
-    opacity: 0;
-
-    &.expanded {
-      height: auto;
-      opacity: 1;
-      transition: all .3s ease .15s;
-    }
+.expandable {
+  clear: both;
+  height: 0;
+  opacity: 0;
+  float: left;
+  width: 100%;
+
+  &.expanded {
+    height: auto;
+    opacity: 1;
+    transition: all .2s; // ease .15s;
   }
 }

data/app/assets/stylesheets/renalware/protocol_pdf.scss

@@ -134,13 +134,8 @@ h1 {
           }
 
           &.col-width-date {
-            min-width: 5.6rem;
-            width: 5.6px;
-          }
-
-          &.col-width-date {
-            min-width: 5.6rem;
-            width: 5.6rem;
+            min-width: 6rem;
+            width: 6rem;
           }
 
           &.col-width-time {

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

@@ -183,3 +183,4 @@ module Renalware
     end
   end
 end
+# rubocop:enable Metrics/ClassLength

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

@@ -171,3 +171,4 @@ module Renalware
     end
   end
 end
+# rubocop:enable Metrics/ClassLength

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

@@ -6,11 +6,14 @@ module Renalware
   module HD
     class MDMPatientsController < Renalware::MDMPatientsController
       def index
+        filter_form = HD::MDMPatientsForm.new(filter_form_params)
+
         query = HD::MDMPatientsQuery.new(
-          relation: HD::Patient.eager_load(hd_profile: [:hospital_unit]),
-          q: params[:q]
+          params: filter_form.ransacked_parameters.merge(query_params).with_indifferent_access
         )
-        render_index(query: query,
+
+        render_index(filter_form: filter_form,
+                     query: query,
                      page_title: t(".page_title"),
                      view_proc: ->(patient) { patient_hd_mdm_path(patient) },
                      patient_presenter_class: HD::PatientPresenter)
@@ -18,10 +21,21 @@ module Renalware
 
       private
 
-      def render_index(**args)
+      def filter_form_params
+        params.fetch(:filter, {}).permit!
+      end
+
+      def query_params
+        params.fetch(:q, {}).permit!
+      end
+
+      def render_index(filter_form:, **args)
         presenter = build_presenter(params: params, **args)
         authorize presenter.patients
-        render :index, locals: { presenter: presenter }
+        render(
+          :index,
+          locals: { presenter: presenter, filter_form: filter_form }
+        )
       end
     end
   end

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

@@ -224,3 +224,4 @@ module Renalware
     end
   end
 end
+# rubocop:enable Metrics/ClassLength

data/app/controllers/renalware/mdm_patients_controller.rb

@@ -23,7 +23,7 @@ module Renalware
       query = args.fetch(:query)
 
       MDMPatientsPresenter.new(
-        patients: query.call.page(page),
+        patients: query.call.page(page).per(per_page),
         page_title: args.fetch(:page_title),
         view_proc: args.fetch(:view_proc),
         q: query.search,

data/app/controllers/renalware/modalities/modalities_controller.rb

@@ -65,6 +65,7 @@ module Renalware
             notice: t(".success", model_name: "modality")
         end
       end
+      # rubocop:enable Metrics/MethodLength
     end
   end
 end

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

@@ -37,6 +37,7 @@ module Renalware
         document.hiv = YearDatedDiagnosis.new(document_params[:hiv])
         document.hepatitis_b = YearDatedDiagnosis.new(document_params[:hepatitis_b])
         document.hepatitis_c = YearDatedDiagnosis.new(document_params[:hepatitis_c])
+        document.htlv = YearDatedDiagnosis.new(document_params[:htlv])
         profile.save_by(current_user)
       end
 

data/app/documents/renalware/hd/profile_document.rb

@@ -77,3 +77,4 @@ module Renalware
     end
   end
 end
+# rubocop:enable Layout/EmptyLineBetweenDefs, Style/SingleLineMethods

data/app/documents/renalware/virology/profile_document.rb

@@ -9,6 +9,7 @@ module Renalware
       attribute :hiv, YearDatedDiagnosis
       attribute :hepatitis_b, YearDatedDiagnosis
       attribute :hepatitis_c, YearDatedDiagnosis
+      attribute :htlv, YearDatedDiagnosis
     end
   end
 end

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

@@ -5,10 +5,10 @@ require_dependency "renalware/accesses"
 module Renalware
   module Accesses
     class Patient < ActiveType::Record[Renalware::Patient]
-      has_many :profiles
-      has_many :plans
-      has_many :procedures
-      has_many :assessments
+      has_many :profiles, dependent: :destroy
+      has_many :plans, dependent: :destroy
+      has_many :procedures, dependent: :destroy
+      has_many :assessments, dependent: :destroy
 
       def current_profile
         profiles.current.first
@@ -17,6 +17,24 @@ module Renalware
       def current_plan
         plans.current.first
       end
+
+      scope :with_current_plan, lambda {
+        joins(<<-SQL)
+          left outer join access_plans on access_plans.patient_id = patients.id
+            and access_plans.terminated_at is null
+          left outer join access_plan_types
+            on access_plans.plan_type_id = access_plan_types.id
+        SQL
+      }
+
+      scope :with_profile, lambda {
+        joins(<<-SQL)
+          left outer join access_profiles on (access_profiles.patient_id = patients.id
+            and access_profiles.terminated_on is not null
+            and access_profiles.started_on <= current_date)
+          left outer join access_types on access_types.id = access_profiles.type_id
+        SQL
+      }
     end
   end
 end

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

@@ -5,7 +5,7 @@ require_dependency "renalware/clinical"
 module Renalware
   module Clinical
     class Patient < ActiveType::Record[Renalware::Patient]
-      has_many :allergies
+      has_many :allergies, dependent: :restrict_with_exception
 
       # These statuses match NHS standards for the display of recorded allergy status.
       # Note that

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

@@ -9,7 +9,7 @@ module Renalware
       validates :description, presence: true
       validates :prompt, presence: true
 
-      has_many :files
+      has_many :files, dependent: :destroy
     end
   end
 end

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

@@ -144,7 +144,8 @@ module Renalware
 
           class CountryNotFoundError < StandardError; end
         end
-        # rubocop:enable Metrics/MethodLength, Metrics/AbcSize
+        # rubocop:enable Metrics/MethodLength, Metrics/AbcSize, Metrics/PerceivedComplexity
+        # rubocop:enable Metrics/CyclomaticComplexity
       end
     end
   end

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

@@ -96,3 +96,5 @@ module Renalware
     end
   end
 end
+# rubocop:enable Metrics/PerceivedComplexity
+# rubocop:enable Metrics/AbcSize

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

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+module Renalware
+  module HD
+    # Form object to help us map chosen input values in the HD MDM patient list filters form
+    # into ransack predicates. Used in this instance because mapping the form's
+    # schedule_definition_ids dropdown value in the format of e.g "[1, 3, 6]" into the
+    # integer arry [1, 3, 6] is not something Ransack can do - hence this intermediate form object
+    # to do the mapping.
+    class MDMPatientsForm
+      include ActiveModel::Model
+      include Virtus::Model
+
+      attribute :hospital_unit_id, Integer
+      attribute :schedule_definition_ids, String # an Integer array in string form e.g. "[1 ,2]"
+
+      # The hash returned here is passed into the Ransack #search method later i the ouery object.
+      def ransacked_parameters
+        {
+          hd_profile_hospital_unit_id_eq: hospital_unit_id,
+          hd_profile_schedule_definition_id_in: schedule_definition_ids_array
+        }
+      end
+
+      private
+
+      # Convert e.g. "[1,2,3]" to [1,2,3]
+      def schedule_definition_ids_array
+        return if schedule_definition_ids.blank?
+        schedule_definition_ids.scan(/\d+/).map(&:to_i)
+      end
+    end
+  end
+end

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

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+# TODO: code here bleeds across modules
+
 module Renalware
   module HD
     class MDMPatientsQuery
@@ -7,27 +9,60 @@ module Renalware
       include PatientPathologyScopes
       MODALITY_NAMES = "HD"
       DEFAULT_SEARCH_PREDICATE = "hgb_date desc"
-      attr_reader :q, :relation
+      attr_reader :params
 
-      def initialize(relation: HD::Patient.all, q:)
-        @q = q || {}
-        @q[:s] = DEFAULT_SEARCH_PREDICATE if @q[:s].blank?
-        @relation = relation
+      def initialize(params:)
+        @params = params || {}
+        @params[:s] = DEFAULT_SEARCH_PREDICATE if @params[:s].blank?
       end
 
       def call
         search.result
       end
 
+      # rubocop:disable Metrics/MethodLength
       def search
         @search ||= begin
-          relation
-            .includes(:hd_profile)
+          HD::Patient
+            .include(QueryablePatient)
+            .merge(Accesses::Patient.with_current_plan)
+            .merge(Accesses::Patient.with_profile)
+            .merge(Transplants::Patient.with_registration_statuses)
+            .eager_load(hd_profile: [:hospital_unit])
             .extending(ModalityScopes)
             .extending(PatientPathologyScopes)
             .with_current_pathology
             .with_current_modality_matching(MODALITY_NAMES)
-            .search(q)
+            .search(params)
+        end
+      end
+      # rubocop:enable Metrics/MethodLength
+
+      # Module to allow us to mixin ransackers
+      module QueryablePatient
+        extend ActiveSupport::Concern
+        included do
+          # Using a custom ransacker to be able to order by access plan create_at
+          # becuase I believe using an implcit :access_plan_create_at in the sort_link
+          # will not work because there is no belongs_to access_plan on HD::Patient
+          # and even adding a custom join to access_plans as we do, Ransack will not resolve
+          # :access_plans_created_at. Still this seens a reasonable solution.
+          # We mix this module into HD::Patient at runtime.
+          ransacker :access_plan_date, type: :date do
+            Arel.sql("coalesce(access_plans.created_at, '1900-01-01'::timestamp)")
+          end
+
+          ransacker :access_plan_type, type: :string do
+            Arel.sql("coalesce(access_plan_types.name, '')")
+          end
+
+          ransacker :current_access, type: :string do
+            Arel.sql("access_types.name")
+          end
+
+          ransacker :transplant_registration_status do
+            Arel.sql("transplant_registration_status_descriptions.name")
+          end
         end
       end
     end

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

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/hd"
+
+module Renalware
+  module HD
+    # Backed by a Postgres view which defines all the possible permutations of
+    # filter that can be selected in a schedule definition filter dropdown, for example
+    #  days: "Mon Wed Fri", ids: [1,3,4]
+    #  days: "Mon Wed Fri PM", ids: [3]
+    # See also HD::MDMPatientsForm and db/views/hd_schedule_definition_filters_*.sql
+    class ScheduleDefinitionFilter < ApplicationRecord
+    end
+  end
+end

data/app/models/renalware/hd/sessions/auditable_session_collection.rb

@@ -204,3 +204,4 @@ module Renalware
     end
   end
 end
+# rubocop:enable Metrics/ClassLength

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

@@ -5,7 +5,7 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class Author < ActiveType::Record[Renalware::User]
-      has_many :letters
+      has_many :letters, dependent: :restrict_with_exception
     end
   end
 end

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

@@ -7,7 +7,7 @@ module Renalware
     class Description < ApplicationRecord
       validates :text, presence: true
 
-      has_many :letters
+      has_many :letters, dependent: :restrict_with_exception
     end
   end
 end

data/app/models/renalware/letters/part/problems.rb

@@ -10,6 +10,11 @@ module Renalware
         super(patient.problems.includes(:notes))
       end
 
+      # If you are wondering why #to_partial_path is not getting called when doing 'render part'
+      # in a view, note this object is array-like so Rails' render only looks for #to_partial_path
+      # on the array elements, not the top level arrary object. To render a single instance of
+      # this part class, wrap it in an array like so:
+      #   = render [part]
       def to_partial_path
         "renalware/letters/parts/problems"
       end

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

@@ -5,8 +5,8 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class Patient < ActiveType::Record[Renalware::Patient]
-      has_many :letters
-      has_many :contacts
+      has_many :letters, dependent: :restrict_with_exception
+      has_many :contacts, dependent: :restrict_with_exception
       belongs_to :primary_care_physician, class_name: "Renalware::Letters::PrimaryCarePhysician"
 
       def cc_on_letter?(letter)

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

@@ -5,7 +5,7 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class PrimaryCarePhysician < ActiveType::Record[Renalware::Patients::PrimaryCarePhysician]
-      has_many :patients
+      has_many :patients, dependent: :restrict_with_exception
       has_many :letters, through: :patients
 
       def cc_on_letter?(letter)

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

@@ -9,7 +9,7 @@ module Renalware
       DEFAULT_SEARCH_PREDICATE = "hgb_date DESC"
       attr_reader :query, :relation, :named_filter
 
-      def initialize(relation: Patient.all, query: nil, named_filter: nil)
+      def initialize(relation: LowClearance::Patient.all, query: nil, named_filter: nil)
         @query = query || {}
         @named_filter = named_filter || :none
         @query[:s] = DEFAULT_SEARCH_PREDICATE if @query[:s].blank?
@@ -39,6 +39,11 @@ module Renalware
           self # NOOP
         end
 
+        def supportive_care
+          joins(:profile)
+          .where("low_clearance_profiles.document ->> 'dialysis_plan' LIKE 'not_for_dial%'")
+        end
+
         def on_worryboard
           joins("RIGHT OUTER JOIN patient_worries ON patient_worries.patient_id = patients.id")
         end

data/app/models/renalware/low_clearance.rb

@@ -4,7 +4,7 @@ require_dependency "renalware"
 
 module Renalware
   module LowClearance
-    MDM_FILTERS = %w(urea hgb_low hgb_high on_worryboard).freeze # tx_candidates
+    MDM_FILTERS = %w(urea hgb_low hgb_high on_worryboard supportive_care).freeze
 
     def self.table_name_prefix
       "low_clearance_"

data/app/models/renalware/medications/medication_route.rb

@@ -9,7 +9,7 @@ module Renalware
         "medication_routes"
       end
 
-      has_many :prescriptions
+      has_many :prescriptions, dependent: :restrict_with_exception
       has_many :patients, through: :prescriptions
       has_many :exit_site_infections,
                through: :prescriptions,

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

@@ -7,7 +7,7 @@ module Renalware
     # TODO: Document the Internal module
     module Internal
       class Author < ActiveType::Record[Renalware::User]
-        has_many :messages
+        has_many :messages, dependent: :destroy
       end
     end
   end

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

@@ -7,7 +7,7 @@ module Renalware
     module Internal
       class Message < Renalware::Messaging::Message
         belongs_to :author, class_name: "Internal::Author"
-        has_many :receipts
+        has_many :receipts, dependent: :destroy
         has_many :recipients, through: :receipts
         belongs_to :replying_to_message, class_name: name
         scope :ordered, ->{ order(sent_at: :desc) }

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

@@ -6,7 +6,7 @@ module Renalware
   module Messaging
     module Internal
       class Recipient < ActiveType::Record[Renalware::User]
-        has_many :receipts
+        has_many :receipts, dependent: :destroy
         has_many :messages, through: :receipts
       end
     end

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

@@ -5,7 +5,7 @@ require_dependency "renalware/messaging"
 module Renalware
   module Messaging
     class Patient < ActiveType::Record[Renalware::Patient]
-      has_many :messages
+      has_many :messages, dependent: :restrict_with_exception
 
       def to_s(format = :long)
         super(format)