renalware-core 2.0.78 → 2.0.79

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

@@ -1,23 +1,56 @@
+- compact = local_assigns.fetch(:compact, false)
+- allow_sorting = local_assigns[:query].present?
+
 .admissions-consults-table
   table
     thead
       tr
         th.col-width-medium.noprint
-        th.col-width-large
-          = sort_link(query, :patient, ["patient_family_name", "patient_given_name asc"], "Patient")
+        - unless compact
+          th.col-width-large
+            - if allow_sorting
+              = sort_link(query, :patient, ["patient_family_name", "patient_given_name asc"], "Patient")
+            - else
+              | Patient
         th.col-width-nhs-no.noprint NHS No.
         th.col-width-reference-no Hosp Nos.
-        th.col-width-medium= sort_link(query, :hospital_ward_name, "Ward")
+        th.col-width-medium
+          - if allow_sorting
+            = sort_link(query, :hospital_ward_name, "Ward")
+          - else
+            | Ward
         th.col-width-tiny RRT
-        th.col-width-date.noprint= sort_link(query, :started_on, "Started")
-        th.col-width-date.noprint= sort_link(query, :ended_on, "Ended")
-        th.col-width-small.show-for-large-up
-          = sort_link([:renalware, query], :modality_desc, "Modality")
-        th.col-width-tiny.show-for-large-up Sex
-        th.col-width-date.show-for-large-up= sort_link(query, :patient_born_on, "DOB")
-        th.col-width-tiny.show-for-large-up Age
-        th.col-width-tiny.noprint= sort_link(query, :aki_risk, "AKI Risk")
-
+        th.col-width-date.noprint
+          - if allow_sorting
+            = sort_link(query, :started_on, "Started")
+          - else
+            | Started
+        th.col-width-date.noprint
+          - if allow_sorting
+            = sort_link(query, :ended_on, "Ended")
+          - else
+            | Ended
+        - unless compact
+          th.col-width-small.show-for-large-up
+            - if allow_sorting
+              = sort_link([:renalware, query], :modality_desc, "Modality")
+            - else
+              | Modality
+        - unless compact
+          th.col-width-tiny.show-for-large-up Sex
+        - unless compact
+          th.col-width-date.show-for-large-up
+            - if allow_sorting
+              = sort_link(query, :patient_born_on, "DOB")
+            - else
+              | DOB
+        - unless compact
+          th.col-width-tiny.show-for-large-up Age
+        th.col-width-tiny.noprint
+          - if allow_sorting
+            = sort_link(query, :aki_risk, "AKI Risk")
+          - else
+            | AKI Risk
     tbody
       - consults.each do |consult|
         - uid = "consult-#{consult.id}"
@@ -54,22 +87,28 @@
             = link_to("Toggle",
                       "#consult-quick-preview-#{consult.id}",
                       data: { behaviour: "toggler" })
-          td= default_patient_link(consult.patient)
+          - unless compact
+            td= default_patient_link(consult.patient)
           td.noprint= consult.patient_nhs_number
           td= consult.patient_hospital_identifiers&.to_s_multiline
           td= consult.hospital_ward
           td= yes_no(consult.rrt?)
           td.noprint= l(consult.started_on)
           td.noprint= l(consult.ended_on)
-          td.show-for-large-up.col-width-medium-with-ellipsis= consult.patient_current_modality
-          td.show-for-large-up= consult.patient_sex
-          td.show-for-large-up= l(consult.patient.born_on)
-          td.show-for-large-up= consult.patient_age
+          - unless compact
+            td.show-for-large-up.col-width-medium-with-ellipsis= consult.patient_current_modality
+          - unless compact
+            td.show-for-large-up= consult.patient_sex
+          - unless compact
+            td.show-for-large-up= l(consult.patient.born_on)
+          - unless compact
+            td.show-for-large-up= consult.patient_age
           td.noprint= consult.aki_risk&.text
           /td.show-for-xlarge-up.consult-author.col-width-medium-with-ellipsis(title=consult.created_by)= consult.created_by
           /td.col-width-medium-with-ellipsis(title=consult.description)= consult.description
         = content_tag(:tr, id: "consult-quick-preview-#{consult.id}", style: "display: none")
-          td(colspan=11)
+          - colspan = compact ? 8 : 11
+          td(colspan=colspan)
             .quick-preview
               dl.dl-horizontal
                 dt Author
@@ -78,7 +117,7 @@
                 dd= consult.patient_current_modality
                 dt Description
                 dd= simple_format consult.description
-          td
+
         / When printing we just show the notes on the second row
         tr.print-only.child-row
           td(colspan=12)= simple_format consult.description

data/app/views/renalware/api/ukrdc/patients/_diagnoses.xml.builder

@@ -1,10 +1,8 @@
 # frozen_string_literal: true
 
 # https://github.com/renalreg/ukrdc/blob/6d95e364dd8de857839fe6cdbd4e7fc3fb4c1d42/Schema/Diagnoses/Diagnosis.xsd
-# This is snomed-based, so might not be possible?
 xml = builder
 xml.Diagnoses do
-  xml.Diagnosis
   if patient.dead? && patient.first_cause.present?
     # Only 1 CauseOfDeath element is allowed so we ignore patient.second_cause
     render(
@@ -13,5 +11,47 @@ xml.Diagnoses do
       cause: patient.first_cause
     )
   end
-  xml.RenalDiagnosis
+
+  patient.yes_comorbidities.each do |comorb|
+    xml.Diagnosis do
+      xml.Diagnosis do
+        xml.CodingStandard "SNOMED"
+        xml.Code comorb.code
+        xml.Description comorb.name
+      end
+
+      # See email from GS to TC 23/5/18 regarding dates.
+      # UKRDC would like to receive a date so if no onset date stored in RW for the comorbidity,
+      # send the esrf date as the identification date
+      if comorb.date.present?
+        xml.OnsetTime comorb.date
+      elsif patient.esrf_on.present?
+        xml.IdentificationTime patient.esrf_on
+      end
+    end
+  end
+
+  if patient.smoking_history?
+    xml.Diagnosis do
+      xml.Diagnosis do
+        xml.CodingStandard "SNOMED"
+        xml.Code patient.snomed_smoking_history.code
+        xml.Description "Smoking history: #{patient.snomed_smoking_history.description}"
+      end
+      # We don't store a smoking date (it doesn't make much sense to) but UKRDC
+      # would like a date so send th ESRF date. See email from GS to TC 23/5/18.
+      xml.IdentificationTime(patient.esrf_on) if patient.esrf_on.present?
+    end
+  end
+
+  if patient.prd_description_code.present?
+    xml.RenalDiagnosis do
+      xml.Diagnosis do
+        xml.CodingStandard "EDTA2"
+        xml.Code patient.prd_description_code
+        xml.Description patient.prd_description_term
+      end
+      xml.IdentificationTime(patient.first_seen_on) if patient.first_seen_on.present?
+    end
+  end
 end

data/app/views/renalware/api/ukrdc/patients/_medications.xml.builder

@@ -23,9 +23,29 @@ xml.Medications do
         # end
       end
       xml.Frequency prescription.frequency
-      xml.Comments prescription.notes
-      # xml.DoseUoM
-      # xml.Indication
+      xml.Comments [prescription.dose_amount,
+                    prescription.dose_unit&.text,
+                    prescription.frequency].compact.join(" ")
+
+
+      # rubocop:disable Style/RescueModifier
+      # Only output DoseQuantity is it is an integer or decimal
+      dose_amount_is_a_number = Float(prescription.dose_amount) rescue nil
+      # rubocop:enable Style/RescueModifier
+      if dose_amount_is_a_number
+        xml.DoseQuantity prescription.dose_amount
+      end
+
+      if prescription.dose_unit.present?
+        xml.DoseUoM do
+          prescription.dose_unit
+          xml.CodingStandard "LOCAL"
+          xml.Code prescription.dose_unit&.text
+          xml.Description prescription.dose_unit
+        end
+      end
+
+      xml.ExternalId prescription.id
     end
   end
 end

data/app/views/renalware/api/ukrdc/patients/_social_histories.xml.builder

@@ -4,11 +4,11 @@ xml = builder
 
 # Currently only used for smoking for which CodingStandard=RRSMOKE Code=YES/NO/EX
 xml.SocialHistories do
-  if patient.smoking_history.present?
+  if patient.smoking_history?
     xml.SocialHistory do
       xml.SocialHabit do
         xml.CodingStandard "RRSMOKE"
-        xml.Code patient.smoking_history
+        xml.Code patient.rr_smoking_history
       end
     end
   end

data/app/views/renalware/hd/protocols/_virology.html.slim

@@ -1,5 +1,7 @@
 - document = Renalware::Virology.cast_patient(protocol.patient).profile&.document || Renalware::NullObject.instance
 table(style="text-align: left;")
+  / Do not display hepatitis_b_core_anti_body in the HD protocol as that does not
+  / imply the patient is infectious
   - %i(hiv hepatitis_b hepatitis_c htlv).each do |attr|
     - if document.public_send(attr).status&.yes?
       tr

data/app/views/renalware/hd/sessions/_form.html.slim

@@ -83,6 +83,8 @@ ruby:
         = render_input fcm, :blood_pressure
         = fcm.input :temperature_measured, as: :inline_radio_buttons, wrapper: :horizontal_medium
         = fcm.input :temperature, wrapper: :horizontal_tiny
+        = fcm.input :respiratory_rate_measured, as: :inline_radio_buttons, wrapper: :horizontal_medium
+        = fcm.input :respiratory_rate, wrapper: :horizontal_tiny
         = fcm.input :bm_stix, wrapper: :horizontal_tiny
 
     = render layout: "renalware/shared/fieldset",
@@ -94,6 +96,8 @@ ruby:
         = render_input fcm, :blood_pressure
         = fcm.input :temperature_measured, as: :inline_radio_buttons, wrapper: :horizontal_medium
         = fcm.input :temperature, wrapper: :horizontal_tiny
+        = fcm.input :respiratory_rate_measured, as: :inline_radio_buttons, wrapper: :horizontal_medium
+        = fcm.input :respiratory_rate, wrapper: :horizontal_tiny
         = fcm.input :bm_stix, wrapper: :horizontal_tiny
 
     = render layout: "renalware/shared/fieldset",

data/app/views/renalware/pathology/historical_observation_results/index.html.slim

@@ -3,8 +3,8 @@
   - if table.rows.empty?
     p No results available for this patient.
   - else
-    .embedded-scroll.pathology
-      p.hint Hover over table then scroll horizontally to view more results.
+    p.hint Hover over table then scroll horizontally to view more results.
+    .double-scroll.embedded-scroll.pathology
       = render "table", table: table
 
     = paginate(table)

data/app/views/renalware/virology/dashboards/_latest_hep_b_antibody_statuses.html.slim

@@ -0,0 +1,5 @@
+article.hep_b_antibody_path_results
+  h2 Latest Hep B Surface Antibody Titre
+  - if dashboard.latest_hep_b_antibody_statuses?
+    = render "renalware/pathology/historical_observation_results/table",
+             table: dashboard.latest_hep_b_antibody_statuses

data/app/views/renalware/virology/dashboards/show.html.slim

@@ -1,6 +1,9 @@
 = content_for(:actions) do
-  = render "actions", patient: patient
+  = render "actions", patient: dashboard.patient
 
 = within_patient_layout(title: "Virology") do
-  = render "renalware/virology/profiles/summary", patient: patient
-  = render "renalware/virology/vaccinations/list", vaccinations: vaccinations, patient: patient
+  = render "renalware/virology/profiles/summary", patient: dashboard.patient
+  = render "renalware/virology/vaccinations/list",
+           vaccinations: dashboard.vaccinations,
+           patient: dashboard.patient
+  = render "latest_hep_b_antibody_statuses", dashboard: dashboard

data/app/views/renalware/virology/profiles/_summary.html.slim

@@ -9,8 +9,8 @@ article
     ul.noprint
       li= link_to "Edit", edit_patient_virology_profile_path(patient), class: "button"
 
-  dl.dl-horizontal.medium
-    - %i(hiv hepatitis_b hepatitis_c htlv).each do |attr_name|
+  dl.dl-horizontal.xlarge
+    - %i(hiv hepatitis_b hepatitis_b_core_antibody hepatitis_c htlv).each do |attr_name|
       - status = document.public_send(attr_name).status
       - next if positive_results_only && !status&.yes?
       dt= attr_name(document, attr_name)

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

@@ -11,6 +11,7 @@
       .hint If YES, enter year of diagnosis
       = render_input fd, :hiv
       = render_input fd, :hepatitis_b
+      = render_input fd, :hepatitis_b_core_antibody
       = render_input fd, :hepatitis_c
       = render_input fd, :htlv
 

data/config/locales/renalware/hd/session.en.yml

@@ -33,6 +33,8 @@ en:
         blood_pressure: Blood Pressure
         temperature_measured: Temperature taken
         temperature: Temperature
+        respiratory_rate_measured: Respiratory rate taken
+        respiratory_rate: Respiratory rate
         bm_stix: BM Stix
       renalware/hd/session_document/dialysis:
         arterial_pressure: Arterial Pressure
@@ -90,6 +92,8 @@ en:
             bm_stix:
               out_of_range: Please enter a value between 0.5 and 50.0
               invalid_number: Please enter a number with up to 1 decimal place, for example 20 or 20.1
+            respiratory_rate:
+              out_of_range: Please enter a value between 4 and 40
 
   enumerize:
     renalware/hd/session_document/observations:

data/config/locales/renalware/virology/virology.en.yml

@@ -13,6 +13,7 @@ en:
       renalware/virology/profile_document:
         hiv: HIV
         hepatitis_b: Hepatitis B
+        hepatitis_b_core_antibody: Hepatitis B Core Antibody
         hepatitis_c: Hepatitis C
         htlv: HTLV
   enumerize:

data/db/functions/import_practice_memberships_csv_v03.sql

@@ -0,0 +1,65 @@
+CREATE OR REPLACE FUNCTION renalware.import_practice_memberships_csv(file text) RETURNS void
+  AS $$
+  BEGIN
+
+  DROP TABLE IF EXISTS copied_memberships;
+  CREATE TEMP TABLE copied_memberships (
+    gp_code text NOT NULL,
+    practice_code text NOT NULL,
+    unused3 text,
+    joined_on text,
+    left_on text,
+    unused7 text
+  );
+
+  -- Import the CSV file into copied_memberships - note there is no CSV header in this file
+  EXECUTE format ('COPY copied_memberships FROM %L DELIMITER %L CSV ', file, ',');
+
+  DROP TABLE IF EXISTS tmp_memberships;
+  CREATE TEMP TABLE tmp_memberships AS
+    SELECT
+      C.gp_code,
+      C.practice_code,
+      case C.joined_on when '' then NULL else C.joined_on::date end,
+      case C.left_on when '' then NULL else C.left_on::date end,
+      patient_primary_care_physicians.id primary_care_physician_id,
+      patient_practices.id as practice_id
+      from copied_memberships C
+      INNER JOIN patient_practices on patient_practices.code = C.practice_code
+      INNER JOIN patient_primary_care_physicians on patient_primary_care_physicians.code = C.gp_code;
+
+  -- Insert any new memberships, ignoring any conflicts where the
+  -- practice_id + primary_care_physician_id already exists
+  INSERT INTO renalware.patient_practice_memberships
+    (practice_id, primary_care_physician_id, joined_on, left_on, active, created_at, updated_at)
+  SELECT
+    practice_id,
+    primary_care_physician_id,
+    joined_on,
+    left_on,
+    case when left_on is null then true else false end,
+    CURRENT_TIMESTAMP,
+    CURRENT_TIMESTAMP
+  FROM tmp_memberships
+  ON CONFLICT (practice_id, primary_care_physician_id) DO NOTHING;
+
+  -- However we need to ensure the joined_on left_on and active columns are up to date as these
+  -- were recently added
+  UPDATE renalware.patient_practice_memberships AS M
+  SET
+    joined_on = T.joined_on,
+    left_on = T.left_on,
+    active = case when T.left_on is null then true else false end
+  FROM tmp_memberships T
+  WHERE T.practice_id = M.practice_id  AND T.primary_care_physician_id = M.primary_care_physician_id;
+
+  -- Mark as deleted any memberships not in the latest uploaded data set - ie those gps have retired or moved on
+  UPDATE patient_practice_memberships mem
+    SET deleted_at = CURRENT_TIMESTAMP
+    WHERE NOT EXISTS (select 1 FROM tmp_memberships tmem
+    WHERE tmem.practice_id = mem.practice_id AND tmem.primary_care_physician_id = mem.primary_care_physician_id);
+
+  DROP TABLE IF EXISTS copied_memberships;
+  DROP TABLE IF EXISTS tmp_memberships;
+END;
+$$ LANGUAGE plpgsql;

data/db/migrate/20190531172829_add_last_change_date_to_patient_practices.rb

@@ -0,0 +1,26 @@
+class AddLastChangeDateToPatientPractices < ActiveRecord::Migration[5.2]
+  def change
+    add_column :patient_practices, :last_change_date, :date
+
+    # Here we are moving away from using a deleted_at/acts_as_paranoid approach to hiding practices
+    # to just having an #active boolean flag - this more closely emulates the output of the NHS
+    # Organisation Data Service (ODS) API which returns Status = Active ot Status = Inactive.
+    # Because we are doing some data migration here also, we need to manually handle the rollback.
+    reversible do |direction|
+      direction.up do
+        add_column :patient_practices, :active, :boolean, default: true, index: true
+        connection.execute(
+          "update renalware.patient_practices set active = false where deleted_at is not null;"
+        )
+        remove_column :patient_practices, :deleted_at, :datetime
+      end
+      direction.down do
+        add_column :patient_practices, :deleted_at, :datetime, index: true
+        connection.execute(
+          "update renalware.patient_practices set deleted_at = '2000-01-01' where active = false;"
+        )
+        remove_column :patient_practices, :active, :boolean
+      end
+    end
+  end
+end

data/db/migrate/20190602114659_create_system_api_logs.rb

@@ -0,0 +1,15 @@
+class CreateSystemAPILogs < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :system_api_logs do |t|
+        t.string :identifier, null: false, index: true
+        t.string :status, null: false, index: true
+        t.integer :records_added, null: false, default: 0
+        t.integer :records_updated, null: false, default: 0
+        t.boolean :dry_run, null: false, default: false
+        t.text :error
+        t.timestamps null: false
+      end
+    end
+  end
+end

data/db/migrate/20190603084428_add_pages_to_system_api_logs.rb

@@ -0,0 +1,5 @@
+class AddPagesToSystemAPILogs < ActiveRecord::Migration[5.2]
+  def change
+    add_column :system_api_logs, :pages, :integer, null: false, default: 0
+  end
+end