renalware-core 2.0.161 → 2.0.166

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0bc096586b16fb31366d250f5e89808e021822a56fed19237530c6abd9cbf0dd
-  data.tar.gz: 61359de738b4d48c4c4e301d8ff7e5a421aad80258e26387b86bbd525ee62f2d
+  metadata.gz: ac2d49cbce8125bf334c28dce8c0363c766aa0b4951509bab613eaf3c6c8cc10
+  data.tar.gz: 795e74e0004088a1506766f9e468b1c67be68783c664ff228ff2bd6e98f0aca4
 SHA512:
-  metadata.gz: cafb016f3c443c10cddc2b1db2fd469f60b98bd0ad266350758e9e94127e9e8c036dcba451b415bb3497eb7eed28d12f848c2b153d4c2d6c1c42cc0bc78135df
-  data.tar.gz: 712f000b0e02727277097de9fa11f76966ca0163bcbf731e330dd4adee5a1d495044c2794a6a81defbdd44369e67c6ced3fc9b139bd920e3346017627ce59dcb
+  metadata.gz: 995cf6f9c31fc67b071e57a07f1235aeb2d86a357854a29bef6d794b9d2548a2ea485222af0bba4e6fae83cf0d8398f1b56026b9233a614c40c3a7d2e053ce3e
+  data.tar.gz: edbc6fdf11d7aad748f713669ccdf1a4c9a6fbe0ffc8f9f0cda3fec4e7a8c875593b4c98e9983e2db331bc617ab26bb5741d1de480bc761c43e1e68f4085f32d

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

@@ -141,6 +141,7 @@ article.clinical-allergies {
 .patient-alerts {
   color: $white;
   background-color: transparent;
+  padding-top: .1rem;
 
   @media print {
     display: none;
@@ -199,6 +200,33 @@ article.clinical-allergies {
           }
         }
 
+        &.vaccination {
+          background-color: $nhs-aqua-green;
+
+          &:hover {
+            background-color: darken($nhs-aqua-green, 4);
+          }
+
+          .title a,
+          i:before {
+            color: $white;
+          }
+        }
+
+        &.event {
+          background-color: $nhs-yellow;
+
+          &:hover {
+            background-color: darken($nhs-yellow, 7);
+          }
+
+          .title a,
+          .date,
+          i:before {
+            color: $dark-grey;
+          }
+        }
+
         &.research-study-participant {
           background-color: darken($nhs-green, 3);
           color: $white;

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

@@ -409,6 +409,12 @@ table {
   }
 }
 
+tr.deleted {
+  td {
+    background-color: lighten($nhs-red, 53);
+  }
+}
+
 table.report {
   table-layout: auto;
 

data/app/components/renalware/system/admin_menu_component.html.slim

@@ -24,6 +24,7 @@ ul.side-nav.side-nav--admin
   = super_admin_menu_item "Print batches", renalware.letters_batches_path, %r{letters/batches}
   = super_admin_menu_item "OBX", renalware.pathology_observation_descriptions_path, %r{admin/pathology_observation_descriptions}
   = super_admin_menu_item "Pathology Code Groups", renalware.pathology_code_groups_path, %r{pathology/code_groups}
+  = super_admin_menu_item "Virology Vaccination Types", renalware.virology_vaccination_types_path, %r{virology/vaccination_types}
   = admin_menu_item "Mailshots", renalware.letters_mailshots_path, %r{letters/mailshots}
   = super_admin_menu_item "Playground", renalware.admin_playground_path, %r{admin/playground}
   = developer_menu_item "HL7 Test", renalware.new_feeds_hl7_test_message_path, %r{admin/123}

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

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/virology"
+
+module Renalware
+  module Virology
+    class VaccinationTypesController < BaseController
+      def index
+        types = VaccinationType.with_deleted.ordered
+        authorize types
+        render locals: { types: types }
+      end
+
+      def edit
+        type = find_and_authorise_type
+        render locals: { type: type }
+      end
+
+      def update
+        type = find_and_authorise_type
+        if type.update(type_params)
+          redirect_to virology_vaccination_types_path
+        else
+          render :edit, locals: { type: type }
+        end
+      end
+
+      def new
+        type = VaccinationType.new
+        authorize type
+        render locals: { type: type }
+      end
+
+      def create
+        type = VaccinationType.new(type_params)
+        authorize type
+        if type.save
+          redirect_to virology_vaccination_types_path
+        else
+          render :new, locals: { type: type }
+        end
+      end
+
+      def destroy
+        find_and_authorise_type.destroy!
+        redirect_to virology_vaccination_types_path
+      end
+
+      def sort
+        authorize VaccinationType, :sort?
+        ids = params[:virology_vaccination_type]
+        VaccinationType.sort(ids)
+        render json: ids
+      end
+
+      private
+
+      def find_and_authorise_type
+        VaccinationType.find(params[:id]).tap { |type| authorize type }
+      end
+
+      def type_params
+        params
+          .require("virology_vaccination_type")
+          .permit(:name, :code, :position)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/events"
+
+module Renalware
+  module Events
+    # Query object that returns, for a patient, the most recent matching event (if any) for each
+    # event_type_alert_trigger row in the databse. The results are used to display
+    # alerts in the UI.
+    # For example given a vaccination Event::Type and an EventTypeAlertTrigger
+    # which is configured to find any vaccination event with the word "covid" in
+    # anywhere in the document, this query will return the most matching event.
+    # It is possible to have mltiple triggers rows for the same event type, so for eample one
+    # could display triggers for the most recent covid vaccination, and the most recent HBV
+    # vaccination.
+    class AlertableEventsQuery
+      def self.call(patient:)
+        Event
+          .for_patient(patient)
+          .joins(event_type: :alert_triggers)
+          .select("DISTINCT ON (events.patient_id, event_type_alert_triggers.id) events.*")
+          .where("(events.document::text ilike '%' || when_event_document_contains || '%') or (events.description ilike '%' || when_event_description_contains || '%')")
+          .order("events.patient_id, event_type_alert_triggers.id, events.created_at desc")
+      end
+    end
+  end
+end

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

@@ -45,6 +45,10 @@ module Renalware
       end
       alias :to_input_partial_path :to_partial_path
 
+      def to_alert_partial_path
+        partial_for "alert"
+      end
+
       def to_cell_partial_path
         partial_for "cell"
       end

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

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/events"
+
+module Renalware
+  module Events
+    # Used to defines conditions where, for a particular event type, if the there is e.g. a case-
+    # insensitive text match against the contents of the event document (eg 'COVID')
+    # then an alert will be displayed in the UI (for the most recent match is there are > 1).
+    class EventTypeAlertTrigger < ApplicationRecord
+      belongs_to :event_type, class_name: "Events::Type"
+      validates :event_type, presence: true
+    end
+  end
+end

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

@@ -6,6 +6,13 @@ module Renalware
   module Events
     class Type < ApplicationRecord
       self.table_name = "event_types"
+      has_many(
+        :alert_triggers,
+        class_name: "EventTypeAlertTrigger",
+        foreign_key: :event_type_id,
+        dependent: :destroy
+      )
+
       DEFAULT_EVENT_CLASS_NAME = "Renalware::Events::Simple"
 
       acts_as_paranoid

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

@@ -40,7 +40,7 @@ module Renalware
         delegate :clear, to: :store
 
         def fetch(letter, **options)
-          store.fetch(cache_key_for(letter, **options)) { yield }
+          store.fetch(cache_key_for(letter, **options), expires_in: 4.weeks) { yield }
         end
 
         # Note the letter must be a LetterPresenter which has a #to_html method

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

@@ -5,12 +5,34 @@ require_dependency "renalware/virology"
 module Renalware
   module Virology
     class VaccinationType < ApplicationRecord
-      validates :name, presence: true, uniqueness: true
-      validates :code, presence: true, uniqueness: true
+      include Sortable
+
+      class UniquenessIncludingDeletedValidator < ActiveModel::EachValidator
+        def validate_each(record, attribute, value)
+          return unless record.send(:"#{attribute}_changed?")
+
+          if record.class.with_deleted.exists?(attribute => value)
+            record.errors.add attribute, (options[:message] || "already used")
+          end
+        end
+      end
+      validates :name, presence: true, uniqueness_including_deleted: true
+      validates :code, presence: true, uniqueness_including_deleted: true
+      before_create :underscore_code
 
       acts_as_paranoid
 
-      scope :ordered, -> { order(position: :asc, name: :asc) }
+      scope :ordered, -> { order(deleted_at: :desc, position: :asc, name: :asc) }
+
+      def self.policy_class
+        BasePolicy
+      end
+
+      def underscore_code
+        return if code.blank?
+
+        self.code = code.downcase.tr("  ", " ").tr(" ", "_")
+      end
     end
   end
 end

data/app/views/renalware/admin/cache/show.html.slim

@@ -42,39 +42,3 @@
             method: :delete,
             data: { confirm: "Are you sure you want to clear the PDF letter cache?\n" },
             class: "button alert"
-
-  <label class="block">
-    <span class="text-gray-700">Name</span>
-    <input class="form-input mt-1 block w-full" placeholder="Jane Doe">
-  </label>
-
-  <div class="mt-4">
-    <span class="text-gray-700">Account Type</span>
-    <div class="mt-2">
-      <label class="inline-flex items-center">
-        <input type="radio" class="form-radio" name="accountType" value="personal">
-        <span class="ml-2">Personal</span>
-      </label>
-      <label class="inline-flex items-center ml-6">
-        <input type="radio" class="form-radio" name="accountType" value="busines">
-        <span class="ml-2">Business</span>
-      </label>
-    </div>
-  </div>
-
-  <label class="block mt-4">
-    <span class="text-gray-700">Requested Limit</span>
-    <select class="form-select mt-1 block w-full">
-      <option>$1,000</option>
-      <option>$5,000</option>
-      <option>$10,000</option>
-      <option>$25,000</option>
-    </select>
-  </label>
-
-  <div class="flex mt-6">
-    <label class="flex items-center">
-      <input type="checkbox" class="form-checkbox">
-      <span class="ml-2">I agree to the <span class="underline">privacy policy</span></span>
-    </label>
-  </div>

data/app/views/renalware/events/events/_alerts.html.slim

@@ -0,0 +1,3 @@
+- events = Renalware::Events::AlertableEventsQuery.call(patient: patient)
+- events.each do |event|
+  = render event.to_alert_partial_path, event: event

data/app/views/renalware/events/events/alert/_simple.html.slim

@@ -0,0 +1,5 @@
+/ The default markup for an alertable event
+li.patient-alert.event
+  i.fas.fa-exclamation-triangle
+  span.title= link_to event.description&.truncate(12), patient_events_path
+  span.date= l(event.date_time.to_date)

data/app/views/renalware/events/events/toggled_cell/_swab.html.slim

@@ -1,6 +1,6 @@
 - document = event.document
 dl.dl-horizontal
   dt= attr_name(document, :location, suffix: ":")
-  dd= document.location.present? ? document.location : t("unspecified")
+  dd= document.location.presence || t("unspecified")
   dt= attr_name(event, :notes, suffix: ":")
   dd== event.notes

data/app/views/renalware/hd/dashboards/_page_actions.html.slim

@@ -1,7 +1,10 @@
 = link_to(patient_hd_mdm_path(patient), class: "button with-icon secondary") do
   i.fas.fa-users
   = t(".mdm")
-= link_to(patient_hd_protocol_path(patient), class: "button with-icon secondary", target: "_blank") do
+= link_to(patient_hd_protocol_path(patient),
+         class: "button with-icon secondary",
+         target: "_blank",
+         rel: "noopener") do
   i.fas.fa-print
   = t(".protocol")
 

data/app/views/renalware/hd/mdm_patients/_patient.html.slim

@@ -4,7 +4,7 @@
 
 tr
   td.actions
-    = link_to view_proc.call(patient), target: "_blank" do
+    = link_to view_proc.call(patient), target: "_blank", rel: "noopener" do
       i.fa.fa-external-link-square-alt
       |   
       = t(".view")

data/app/views/renalware/hd/transmission_logs/index.html.slim

@@ -30,7 +30,8 @@
                 = link_to "...",
                         hd_transmission_log_path(log, format: :xml),
                         class: "button small_ellipsis_button",
-                        target: "_blank"
+                        target: "_blank",
+                        rel: "noopener"
             td
               span(title=log.filepath)
                 - filename = log.filepath && Pathname(log.filepath).basename

data/app/views/renalware/layouts/_patient.html.slim

@@ -17,6 +17,7 @@ nav.patient-side-nav.full-screenable
       ul
         = render "renalware/patients/alerts/list", patient: current_patient
         = render "renalware/research/alerts", patient: current_patient
+        = render "renalware/events/events/alerts", patient: current_patient
     = render "renalware/clinical/header", patient: current_patient
     .row.collapse
       - if local_assigns[:title].present?

data/app/views/renalware/letters/batches/_create.html.slim

@@ -4,14 +4,14 @@
     .percent_complete
   .modal__body
     .content
-      .batch_results_container(data={"poll-url" => renalware.letters_batch_status_path(batch)})
+      .batch_results_container(data={ "poll-url" => renalware.letters_batch_status_path(batch) })
         .preparing
           = image_tag("renalware/loading-gears-animation.gif", height: "116")
 
-
         .generated-batch-print-pdf-container(style="display:none")
           = link_to letters_batch_path(batch, format: :pdf),
                     target: "_blank",
+                    rel: "noopener",
                     class: "print-batch-letter",
                     data: { "modal-url" => new_letters_batch_completion_path(batch) } do
             i.far.fa-check-circle

data/app/views/renalware/system/downloads/index.html.slim

@@ -22,7 +22,7 @@
     - items.each do |item|
       .download
         .file
-          = link_to(system_download_path(item), target: "_blank") do
+          = link_to(system_download_path(item), target: "_blank", rel: "noopener") do
             i.far.fa-file-alt
         .details
           h3= link_to(item.name, system_download_path(item), target: "_blank")

data/app/views/renalware/system/messages/_form.html.slim

@@ -1,4 +1,4 @@
-- severities = Renalware::System::Message.severity.values.map{|val| [val&.humanize, val] }
+- severities = Renalware::System::Message.severity.values.map{ |val| [val&.humanize, val] }
 = simple_form_for(message,
                   as: :message,
                   html: { autocomplete: "off" }) do |f|

data/app/views/renalware/virology/vaccination_types/_form.html.slim

@@ -0,0 +1,10 @@
+= simple_form_for type do |f|
+  = f.input :name
+  - if type.new_record?
+    = f.input :code, hint: "Will be converted to lower case with underscores"
+  - else
+    p.px-0.mb-5
+      ' Code:
+      code= type.code
+
+  = f.submit class: :button

data/app/views/renalware/virology/vaccination_types/edit.html.slim

@@ -0,0 +1,3 @@
+= within_new_admin_layout(title: "Edit",
+                          breadcrumbs: breadcrumb_for("Virology Vaccination Types", virology_vaccination_types_path)) do
+  = render "form", type: type

data/app/views/renalware/virology/vaccination_types/index.html.slim

@@ -0,0 +1,42 @@
+= content_for(:actions) do
+  = link_to t("new_record.link_title"),
+            new_virology_vaccination_type_path,
+            class: "button"
+
+= within_new_admin_layout(title: "Virology Vaccination Types") do
+  .rounded-md.bg-blue-100.px-3.py-2.flex.items-start.shadow.mb-5
+    i.fas.fa-info-circle.mr-2.mt-1.text-blue-500
+    ' Deleting a type sets the 'deleted at' date, preventing the type from
+    ' being used prospectively.
+    br
+    ' The type's code cannot be edited once set, just in case it has already been used.
+    br
+    ' Drag and drop the icon to change the sort order.
+
+  table.vaccination_types
+    thead
+      tr
+        th.actions.col-width-small
+        th Name
+        th Code
+        th.text-center Sort order
+        th.col-width-date-time Created at
+        th.col-width-date-time Deleted at
+    tbody.sortables(data-rel=sort_virology_vaccination_types_path)
+      - types.each do |type|
+        = content_tag_for(:tr, type, class: "sortable #{type.deleted? ? 'deleted' : ''}") do
+          td.actions
+            - unless type.deleted?
+              =link_to "Edit", edit_virology_vaccination_type_path(type)
+              =link_to "Delete",
+                        virology_vaccination_type_path(type),
+                        method: :delete,
+                        data: { confirm: "Are you sure you want to delete this type? Doing so will prevent it from being used prospectively."}
+
+          td= type.name
+          td= type.code
+          td.handle
+            - unless type.deleted?
+              i.fas.fa-bars
+          td= l(type.created_at)
+          td= l(type.deleted_at)

data/app/views/renalware/virology/vaccination_types/new.html.slim

@@ -0,0 +1,3 @@
+= within_new_admin_layout(title: "New",
+                          breadcrumbs: breadcrumb_for("Virology Vaccination Types", virology_vaccination_types_path)) do
+  = render "form", type: type

data/app/views/renalware/virology/vaccinations/_alert.html.slim

@@ -0,0 +1,11 @@
+ruby:
+  # Its possible the vaccination type has been soft-deleted so we need to use the
+  # #with_deleted scope. Its also possible the vaccination type row was hard deleted, so be
+  # sure to revert to just displaying the code from the document if this is the case.
+  code = event.document&.type
+  type = Renalware::Virology::VaccinationType.with_deleted.find_by(code: code)
+  title = type&.name || code&.titleize
+li.patient-alert.vaccination
+    i.fas.fa-syringe
+    span.title= link_to title, renalware.patient_virology_dashboard_path(event.patient)
+    span.date= l(event.date_time.to_date)

data/config/permissions.yml

@@ -8,6 +8,7 @@ super_admin:
   - Renalware::HD::CannulationType
   - Renalware::System::Download
   - Renalware::Pathology::ObservationDescription
+  - Renalware::Virology::VaccinationType
 admin:
   - Renalware::User
   - Renalware::BagType

data/config/routes/virology.rb

@@ -10,3 +10,9 @@ resources :patients, only: [] do
               defaults: { slug: :vaccinations }
   end
 end
+
+namespace :virology do
+  resources :vaccination_types do
+    post :sort, on: :collection
+  end
+end

data/db/migrate/20210115181817_create_event_type_alert_triggers.rb

@@ -0,0 +1,15 @@
+class CreateEventTypeAlertTriggers < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table(
+        :event_type_alert_triggers,
+        comment: "Matching alerts are displayed on patient pages"
+      ) do |t|
+        t.references :event_type, foreign_key: true, null: false
+        t.text :when_event_document_contains
+        t.text :when_event_description_contains
+        t.timestamps null: false
+      end
+    end
+  end
+end

data/lib/renalware/version_number.rb

@@ -5,6 +5,6 @@ module Renalware
   # to creat that class even though its not used. If we don't do this zeitwerk
   # complains that version.rb does export a constant called Version.
   class VersionNumber
-    VERSION = "2.0.161"
+    VERSION = "2.0.166"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.161
+  version: 2.0.166
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-01-06 00:00:00.000000000 Z
+date: 2021-01-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord-import
@@ -310,14 +310,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.3.1
+        version: 2.4.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.3.1
+        version: 2.4.0
 - !ruby/object:Gem::Dependency
   name: font-awesome-sass
   requirement: !ruby/object:Gem::Requirement
@@ -664,14 +664,14 @@ dependencies:
   name: puma
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: '4.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: '4.3'
 - !ruby/object:Gem::Dependency
@@ -1455,6 +1455,7 @@ files:
 - app/controllers/renalware/virology/base_controller.rb
 - app/controllers/renalware/virology/dashboards_controller.rb
 - app/controllers/renalware/virology/profiles_controller.rb
+- app/controllers/renalware/virology/vaccination_types_controller.rb
 - app/controllers/renalware/virology/vaccinations_controller.rb
 - app/documents/document/attribute_initializer.rb
 - app/documents/document/attribute_initializer/active_model.rb
@@ -1677,12 +1678,14 @@ files:
 - app/models/renalware/drugs/type.rb
 - app/models/renalware/events.rb
 - app/models/renalware/events/advanced_care_plan.rb
+- app/models/renalware/events/alertable_events_query.rb
 - app/models/renalware/events/biopsy.rb
 - app/models/renalware/events/clinical_frailty_score.rb
 - app/models/renalware/events/create_event.rb
 - app/models/renalware/events/event.rb
 - app/models/renalware/events/event_list_query.rb
 - app/models/renalware/events/event_query.rb
+- app/models/renalware/events/event_type_alert_trigger.rb
 - app/models/renalware/events/investigation.rb
 - app/models/renalware/events/line_change_event_query.rb
 - app/models/renalware/events/lists/form.rb
@@ -2573,12 +2576,14 @@ files:
 - app/views/renalware/events/clinical_frailty_score/_cell.html.slim
 - app/views/renalware/events/clinical_frailty_score/_inputs.html.slim
 - app/views/renalware/events/clinical_frailty_score/_toggled_cell.html.slim
+- app/views/renalware/events/events/_alerts.html.slim
 - app/views/renalware/events/events/_event.html.slim
 - app/views/renalware/events/events/_filters.html.slim
 - app/views/renalware/events/events/_form.html.slim
 - app/views/renalware/events/events/_list.html.slim
 - app/views/renalware/events/events/_summary_part.html.slim
 - app/views/renalware/events/events/_table.html.slim
+- app/views/renalware/events/events/alert/_simple.html.slim
 - app/views/renalware/events/events/cell/_biopsy.html.slim
 - app/views/renalware/events/events/cell/_investigation.html.slim
 - app/views/renalware/events/events/cell/_simple.html.slim
@@ -3326,6 +3331,11 @@ files:
 - app/views/renalware/virology/dashboards/show.html.slim
 - app/views/renalware/virology/profiles/_summary.html.slim
 - app/views/renalware/virology/profiles/edit.html.slim
+- app/views/renalware/virology/vaccination_types/_form.html.slim
+- app/views/renalware/virology/vaccination_types/edit.html.slim
+- app/views/renalware/virology/vaccination_types/index.html.slim
+- app/views/renalware/virology/vaccination_types/new.html.slim
+- app/views/renalware/virology/vaccinations/_alert.html.slim
 - app/views/renalware/virology/vaccinations/_cell.html.slim
 - app/views/renalware/virology/vaccinations/_inputs.html.slim
 - app/views/renalware/virology/vaccinations/_list.html.slim
@@ -4078,6 +4088,7 @@ files:
 - db/migrate/20201105153422_update_medication_current_prescriptions_view.rb
 - db/migrate/20201112152752_update_pd_mdm_patients_view1.rb
 - db/migrate/20210105163944_create_virology_vaccination_types.rb
+- db/migrate/20210115181817_create_event_type_alert_triggers.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb