renalware-core 2.0.146 → 2.0.147

data/app/models/renalware/patient.rb

@@ -73,6 +73,10 @@ module Renalware
             -> { order(started_on: :desc).where(state: "current") },
             class_name: "Modalities::Modality"
 
+    has_one :previous_modality,
+            -> { order(ended_on: :desc, created_at: :desc).where.not(ended_on: nil) },
+            class_name: "Modalities::Modality"
+
     has_one :modality_description,
             through: :current_modality,
             class_name: "Modalities::Description",

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Renalware
+  module Patients
+    # Finds patients with a death modality or who have a died_on date
+    class DeceasedPatientsQuery
+      attr_reader :query_params
+
+      def initialize(query_params)
+        @query_params = query_params || {}
+        @query_params[:s] = "family_name ASC" if @query_params[:s].blank?
+      end
+
+      def call
+        search.result.where(id: ids_of_deceased_patients)
+      end
+
+      def search
+        Patient
+          .includes(:first_cause, current_modality: :description)
+          .ransack(query_params)
+      end
+
+      private
+
+      def ids_of_deceased_patients
+        (ids_of_patients_with_death_modality + ids_of_patients_with_died_on_date).uniq
+      end
+
+      def ids_of_patients_with_death_modality
+        Patient
+          .extending(ModalityScopes)
+          .with_current_modality_of_class(Renalware::Deaths::ModalityDescription)
+          .pluck(:id)
+      end
+
+      def ids_of_patients_with_died_on_date
+        Patient.where.not(died_on: nil).pluck(:id)
+      end
+    end
+  end
+end

data/app/models/renalware/ukrdc/create_encrypted_patient_xml_files.rb

@@ -66,31 +66,59 @@ module Renalware
         end
       end
 
-      # rubocop:disable Metrics/MethodLength
+      # If UKRDC_THREADS is set to a nonzero value (eg 4 but depending on CPUs/cores),
+      # a threadpool containing that number of threads is created and XML creation
+      # (including PDF letter rendering) for that patient happens in a separate thread.
+      # The performance increase in doing it this way is marginal unless there are
+      # PDFs to be rendered, which can introduce significant IO wait. As PDFs are cached
+      # by the PDFLetterCache, using threads may have limited benefit but
+      # rubocop:disable Metrics/MethodLength, Metrics/AbcSize
       def create_patient_xml_files
         count = 0
         patients = ukrdc_patients_who_have_changed_since_last_send
         summary.num_changed_patients = patients.count
         schema = UKRDC::XsdSchema.new
-        patients.find_each do |patient|
+        thread_count = ENV["UKRDC_THREADS"].to_i
+        use_threads = thread_count.nonzero?
+
+        if use_threads
+          thread_pool = Concurrent::ThreadPoolExecutor.new(max_threads: thread_count)
+        end
+
+        patients.map do |patient|
           count += 1
           Rails.logger.info count
-          CreatePatientXMLFile.new(
-            patient: patient,
-            dir: paths.timestamped_xml_folder,
-            changes_since: changed_since,
-            request_uuid: request_uuid,
-            batch_number: batch_number,
-            logger: logger,
-            force_send: force_send,
-            schema: schema
-          ).call
-
-          # Every n patients, force the garbage collector to kick in
-          # GC.start if (count % 10).zero?
+          if use_threads
+            thread_pool.post do
+              Rails.logger.info "Thread #{Thread.current.object_id}"
+              ActiveRecord::Base.connection_pool.with_connection do
+                create_xml_file(patient: patient, schema: schema)
+              end
+            end
+          else
+            create_xml_file(patient: patient, schema: schema)
+          end
+        end
+      ensure
+        if use_threads
+          thread_pool.shutdown
+          thread_pool.wait_for_termination
         end
       end
-      # rubocop:enable Metrics/MethodLength
+      # rubocop:enable Metrics/MethodLength, Metrics/AbcSize
+
+      def create_xml_file(patient:, schema:)
+        CreatePatientXMLFile.new(
+          patient: patient,
+          dir: paths.timestamped_xml_folder,
+          changes_since: changed_since,
+          request_uuid: request_uuid,
+          batch_number: batch_number,
+          logger: logger,
+          force_send: force_send,
+          schema: schema
+        ).call
+      end
 
       def build_summary
         summary.count_of_files_in_outgoing_folder = count_of_files_in_outgoing_folder

data/app/models/renalware/ukrdc/create_patient_xml_file.rb

@@ -86,7 +86,7 @@ module Renalware
           nil
         else
           Payload.new(result.xml).tap do |payload|
-            log.payload = payload.to_s
+            # log.payload = payload.to_s
             log.payload_hash = payload.to_md5_hash
           end
         end

data/app/views/renalware/accesses/assessments/_form.html.slim

@@ -4,7 +4,7 @@ ruby:
 .row.top
   .medium-6.columns
     = f.button :submit
-    span= " or "
+    '  or
     = link_to "cancel", back_path
 
 .form-content
@@ -39,5 +39,5 @@ ruby:
   .row
     .large-12.columns
       = f.button :submit
-      span= " or "
+      '  or
       = link_to "cancel", back_path

data/app/views/renalware/accesses/plans/new.html.slim

@@ -18,5 +18,5 @@
                       wrapper: :horizontal_medium
 
       = f.submit "Save", class: "button"
-      span= " or "
+      '  or
       = link_to "cancel", patient_accesses_dashboard_path(patient)

data/app/views/renalware/accesses/procedures/_form.html.slim

@@ -4,7 +4,7 @@ ruby:
 .row.top
   .medium-6.columns
     = f.button :submit
-    span= " or "
+    '  or
     = link_to "cancel", back_path
 
 .form-content
@@ -41,5 +41,5 @@ ruby:
 .row
   .large-12.columns
     = f.button :submit
-    span= " or "
+    '  or
     = link_to "cancel", back_path

data/app/views/renalware/accesses/profiles/_form.html.slim

@@ -4,7 +4,7 @@ ruby:
 .row.top
   .medium-6.columns
     = f.button :submit
-    span= " or "
+    '  or
     = link_to "cancel", back_path
 
 .form-content
@@ -31,5 +31,5 @@ ruby:
 .row
   .large-12.columns
     = f.button :submit
-    span= " or "
+    '  or
     = link_to "cancel", back_path

data/app/views/renalware/admin/playgrounds/pathology_chart_data.js.erb

@@ -0,0 +1 @@
+console.log("as")

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

@@ -0,0 +1,59 @@
+css:
+  .chart {
+    width: 500px;
+    height: 200px;
+  }
+  #patient_id {
+    width:300px;
+    display: block
+  }
+  #patient_id input {
+    width:200px;
+    display:inline;
+  }
+
+  #patient_id a {
+    width: 90px;
+    display:inline;
+    padding: 5px;
+    margin-left: 5px;
+  }
+
+= within_new_admin_layout(title: "Admin Playground") do
+
+  article
+    header
+      h2 Pathology Charts
+    span A testbed for trying out highchart linecharts
+    br
+    br
+
+    .chart-container(data-controller="charts"
+                    data-charts-url=pathology_chart_data_admin_playground_path)
+      .row
+        .columns.small-12.medium-6.large-4
+          = simple_form_for(form,
+                            remote: true,
+                            as: :chart,
+                            url: pathology_chart_data_admin_playground_path,
+                            wrapper: nil,
+                            method: :get,
+                            data: { target: "charts.form", action: "ajax:success->charts#redisplay" }) do |f|
+
+            = f.input :patient_id,
+                      collection: [[form.patient_id, form.patient_id]],
+                      selected: 1,
+                      input_html: { \
+                        class: "patient-id-select2 patient-ajax-search",
+                        data: { "ajax--url" => search_patients_path(format: :json),
+                                placeholder: "Search by patient name or hospital/NHS no." } \
+                      }
+            = f.input :obx_code,
+                      collection: Renalware::Pathology::ObservationDescription.order(:code).pluck(:code),
+                      input_html: {  class: "searchable_select" }
+            = f.input :period,
+                      collection: %w(all yr 6m 3m 1m wk),
+                      include_blank: false
+            = f.submit "Refresh", class: :button
+
+      #chart1 style="height: 300px; width: 500px" data-target="charts.chart"

data/app/views/renalware/admin/users/_filters.html.slim

@@ -7,5 +7,5 @@
           = f.search_field :family_name_or_given_name_or_username_or_email_cont
         .small-3.large-4.columns.actions.end
           = f.submit t("helpers.submit.filter"), class: "button"
-          span= " or "
+          '  or
           = link_to t("helpers.reset"), admin_users_path

data/app/views/renalware/admissions/admissions/index.html.slim

@@ -6,9 +6,9 @@
 
 = within_admin_layout(title: "Inpatient Admissions") do
   .panel.radius.compact
-    | If the patient is not on Renalware yet, please 
+    ' If the patient is not on Renalware yet, please
     = link_to("add them", new_patient_path)
-    |  first
+    |  first
 
   = render "table", admissions: admissions
   = paginate admissions

data/app/views/renalware/admissions/consults/_form.html.slim

@@ -53,5 +53,5 @@
   = f.input :description, wrapper: :horizontal_large, input_html: { rows: 10 }
 
   = f.submit class: :button
-  span= " or "
+  '  or
   = link_to "Cancel", admissions_consults_path

data/app/views/renalware/admissions/consults/index.html.slim

@@ -15,9 +15,9 @@
   = render "renalware/admissions/requests/modal_dialog_placeholder"
 
   .panel.radius.compact
-    | If the patient is not on Renalware yet, please 
+    ' If the patient is not on Renalware yet, please
     = link_to("add them", new_patient_path)
-    |  first
+    |  first
 
   = render "table", consults: consults, query: query
   = paginate consults

data/app/views/renalware/deaths/index.html.slim

@@ -9,28 +9,36 @@
   table#patients-deceased
     thead
       tr
-        th Name
+        th
+        th.col-width-mediumish= sort_link([:renalware, q], :family_name, "Name")
         th.col-width-nhs-no NHS No.
         th.col-width-reference-no Hosp No.
         th.col-width-tiny Sex
-        th.col-width-date= sort_link([:renalware, q], :born_on, "Date of Birth")
-        th.col-width-date-time= sort_link([:renalware, q], :died_on, "Date of Death")
         th.col-width-tiny Age
-        th.col-width-medium
+        th.col-width-date= sort_link([:renalware, q], :born_on, "Date of Birth")
+        th.col-width-date= sort_link([:renalware, q], :died_on, "Date of Death")
+        th First cause
+        th Current Modality
+        th Previous Modality
 
     tbody
       - patients.each do |patient|
         tr
+          td.actions
+            = link_to edit_patient_death_path(patient),
+                      title: "Edit death details" do
+              i.fas.fa-edit
+              span.show-for-large-up
+                |  Death details
           td= default_patient_link(patient)
           td= patient.nhs_number
           td= patient.hospital_identifier
           td= patient.sex
+          td= patient.age
           td= l patient.born_on
           td= l patient.died_on
-          td= patient.age
-          td.actions
-            = link_to "Edit death details",
-                      edit_patient_death_path(patient),
-                      title: "Edit death details"
+          td= patient.first_cause&.description
+          td= patient.current_modality
+          td= patient.previous_modality
 
-  = paginate patients
+  == pagy_foundation_nav pagy

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

@@ -6,4 +6,4 @@ dl.dl-horizontal
   dt= attr_name(document, :result2, suffix: ":")
   dd= document.result2&.text || t("unspecified")
   dt= attr_name(event, :notes, suffix: ":")
-  dd= event.notes&.html_safe
+  dd== event.notes

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

@@ -2,4 +2,4 @@ dl.dl-horizontal
   dt= attr_name(event, :description, suffix: ":")
   dd= event.description
   dt= attr_name(event, :notes, suffix: ":")
-  dd= event.notes&.html_safe
+  dd== event.notes

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

@@ -3,4 +3,4 @@ dl.dl-horizontal
   dt= attr_name(document, :location, suffix: ":")
   dd= document.location.present? ? document.location : t("unspecified")
   dt= attr_name(event, :notes, suffix: ":")
-  dd= event.notes&.html_safe
+  dd== event.notes

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

@@ -36,8 +36,7 @@
                 - filename = log.filepath && Pathname(log.filepath).basename
                 - if filename.present?
                   i.fas.fa-file
-                  |  
-                  = filename
+                  => filename
             td= log.patient && link_to(log.patient, patient_hd_sessions_path(log.patient))
             td
               - if log.parent_id.present?

data/app/views/renalware/letters/mailshots/mailshots/_form.html.slim

@@ -4,7 +4,8 @@
                     url: letters_mailshots_path,
                     html: { id: "mailshot-form" }) do |form|
     .columns.small-12
-      = form.input :description, placeholder: "A description of the mailshot purpose."
+      = form.input(:description,
+        placeholder: "The patient will see this at the top of letter. A description of the letter's purpose.")
     .columns.small-12
       = form.input(:sql_view_name,
         collection: Renalware::Letters::Mailshots::DataSource.all.map(&:viewname),

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

@@ -4,8 +4,7 @@ tr
   td.actions
     = link_to view_proc.call(patient), target: "_blank" do
       i.fa.fa-external-link-square-alt
-      |   
-      = t(".view")
+      =< t(".view")
   td.full-name= link_to patient.to_s(:default), view_proc.call(patient)
   td.nowrap= patient.nhs_number
   td.nowrap= patient.hospital_identifier

data/app/views/renalware/medications/drug_types/prescriptions/_filters.html.slim

@@ -18,8 +18,6 @@
                 label: "Provider"
     .small-3.columns.actions.end
       = f.submit "Search", class: "button"
-      |  
-      span or
-      |  
+      '  or
       = link_to "Reset", medications_esa_prescriptions_path
       /class: "cancel-link #{'disabled' unless searching}"

data/app/views/renalware/medications/home_delivery/prescriptions/index.html.slim

@@ -0,0 +1,51 @@
+- content_for(:filters) do
+  .panel
+    | Prescriptions with a next home prescription date within the last 4 weeks or the next 2 weeks.
+
+  .row
+    .columns.small-12.medium-6
+      = simple_form_for(form,
+                        as: :search,
+                        url: renalware.medications_home_delivery_prescriptions_path(named_filter: params[:named_filter]),
+                        method: :get) do |f|
+        = f.input :modality_description_id,
+                  collection: Renalware::Modalities::Description.order(:name),
+                  input_html: { onchange: "this.form.submit();" }
+  br
+
+- content_for(:tabs) do
+ dl.sub-nav
+    dd
+      = link_to "ESA",
+                renalware.medications_home_delivery_prescriptions_path(named_filter: "esa")
+    dd
+      = link_to "Immunosuppressant",
+                renalware.medications_home_delivery_prescriptions_path(named_filter: "immunosuppressant")
+
+= within_admin_layout(title: "Home Delivery Prescriptions") do
+  table
+    thead
+      tr
+        th.col-width-large= sort_link(query, :patient_family_name, "Patient")
+        th.col-width-nhs-no NHS number
+        th.col-width-medium Drug Type
+        th.col-width-large= sort_link(query, :drug_name, "Drug")
+        th.col-width-date= sort_link(query, :prescribed_on, "Prescribed on")
+        th.col-width-date-time= sort_link(query, :last_delivery_date, "Last home prescription date")
+        th.col-width-date-time= sort_link(query, :next_delivery_date, "Next home prescription date")
+        th.col-width-medium Modality
+        th
+    tbody
+      - prescriptions.each do |prescription|
+        tr
+          td= default_patient_link(prescription.patient)
+          td= prescription.patient.nhs_number
+          td= prescription.drug.drug_types.first&.name
+          td= prescription.drug.name
+          td= l(prescription.prescribed_on)
+          td= l(prescription.last_delivery_date)
+          td= l(prescription.next_delivery_date)
+          td= prescription.patient.current_modality
+          td
+
+  == pagy_foundation_nav pagy