renalware-core 2.0.0.pre.rc8 → 2.0.0.pre.rc9

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

@@ -6,7 +6,7 @@ xml.Observation do
 
   xml.ObservationCode do
     # xml.CodingStandard "2.16.840.1.113883.4.642.2.115"
-    xml.CodingStandard "LOCAL"
+    xml.CodingStandard "PV"
     xml.Code I18n.t("loinc.#{i18n_key}.code")
     xml.Description I18n.t("loinc.#{i18n_key}.description")
   end

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

@@ -1,8 +1,8 @@
 xml = builder
 
-xml.LabOrders(start: Time.zone.today.iso8601, stop: Time.zone.today.iso8601) do
-  # xml.comment! "TODO: start and stop date"
-
+# TODO: Implement start stop dates
+# xml.LabOrders (start: Time.zone.today.iso8601, stop: Time.zone.today.iso8601) do
+xml.LabOrders do
   render partial: "renalware/api/ukrdc/patients/lab_orders/lab_order",
          collection: patient.observation_requests.includes(
            :description,

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

@@ -4,7 +4,9 @@
 #   - bp
 xml = builder
 
-xml.Observations(start: Time.zone.today.iso8601, stop: Time.zone.today.iso8601) do
+# TODO: Implement start stop dates
+# xml.Observations do(start: Time.zone.today.iso8601, stop: Time.zone.today.iso8601) do
+xml.Observations do
   patient.clinic_visits.includes(:updated_by).each do |visit|
     render "clinic_visit_observation",
            visit: visit,

data/app/views/renalware/api/ukrdc/patients/lab_orders/_lab_order.xml.builder

@@ -20,7 +20,7 @@ xml.LabOrder do
   xml.OrderCategory do
     xml.Code request.description.code
   end
-  xml.SpecimenCollectedTime request.requested_at.iso8601
+  # xml.SpecimenCollectedTime request.requested_at.iso8601
   # xml.SpecimenReceivedTime "TODO"
   # xml.Priority do
   #   xml.Code "TODO: Probably n/a"
@@ -30,7 +30,7 @@ xml.LabOrder do
 
   xml.ResultItems do
     render partial: "renalware/api/ukrdc/patients/lab_orders/result_item",
-           collection: request.observations,
+           collection: request.observations.having_a_loinc_code,
            as: :observation,
            locals: { builder: builder, patient: patient }
   end

data/app/views/renalware/api/ukrdc/patients/lab_orders/_result_item.xml.builder

@@ -7,8 +7,13 @@ xml.ResultItem do
   xml.EnteredOn observation.updated_at&.iso8601
   xml.PrePost observation.pre_post(patient_is_on_hd: patient.current_modality_hd?)
   xml.ServiceId do
-    xml.CodingStandard "LOCAL"
-    xml.Code(observation.description_loinc_code || observation.description_code)
+    if observation.description_loinc_code.present?
+      xml.CodingStandard "PV"
+      xml.Code observation.description_loinc_code
+    else
+      xml.CodingStandard "LOCAL"
+      xml.Code observation.description_code
+    end
     xml.Description observation.description_name
   end
   # xml.SubId

data/app/views/renalware/clinical/_header.html.slim

@@ -0,0 +1,47 @@
+ruby:
+  header = local_assigns[:header] || Renalware::Clinical::HeaderPresenter.new(patient)
+  current_pathology = header.current_pathology
+
+.clinical-header.lozenge
+  ul
+    li
+      dl
+        dt= t(".blood_pressure")
+        - result = header.blood_pressure_measurement.compact.join("/")
+        - if result.present?
+          dd= result
+          dd.date= l(header.blood_pressure_date)
+        - else
+          dd.empty
+    li
+      dl
+        dt= t(".weight")
+        - result = header.weight_measurement
+        - if result.present?
+          dd= "#{result} kg"
+          dd.date= l(header.weight_date)
+        - else
+          dd.empty
+    li
+      dl
+        dt= t(".height")
+        - result = header.height_measurement
+        - if result.present?
+          dd= "#{result} m"
+        - else
+          dd.empty
+    li
+      dl
+        dt= t(".bmi")
+        dd= header.bmi_measurement
+
+    - %i(hgb cre pot egfr ure).each do |code|
+      li
+        dl
+          dt= t(".#{code}")
+          - result = current_pathology.send(:"#{code}_result")
+          - if result.present?
+            dd= result
+            dd.date= l(current_pathology.send(:"#{code}_observed_at"))
+          - else
+            dd.empty

data/app/views/renalware/clinics/clinic_visits/_table.html.slim

@@ -15,7 +15,6 @@ table.clinics.auto-layout
       th.col-width-tiny Urine blood
       th.col-width-tiny Urine protein
       th.col-width-medium Created by
-
   tbody
     = render partial: "renalware/clinics/clinic_visits/table_row",
              collection: clinic_visits,

data/app/views/renalware/clinics/visits/_table.html.slim

@@ -8,13 +8,16 @@ table.global-clinic-visits
       th.col-width-nhs-no NHS Number
       th.col-width-tiny Sex
       th.col-width-tiny Age
-      th.col-width-small Modality
+      th.col-width-medium Modality
       th.col-width-medium Clinic Type
       th.col-width-tiny BMI
       th.col-width-tiny BP
       th.no-print
       th.col-width-medium Created by
   tbody
+    / Note we can't use cached: true yet when rendering the events collection, as each row is
+    / used in a different context and displays there slightly differently, for example showing
+    / an Edit link or Type column in certain circumstances.
     = render partial: "table_row",
              collection: clinic_visits,
              as: :clinic_visit

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

@@ -9,7 +9,7 @@ tr
       = link_to("Edit", edit_proc.call(event))
 
   td.nowrap= l event.created_at.to_date
-  - unless local_assigns.fetch(:exclude_type_column, false)
+  - unless local_assigns[:exclude_type_column] == true
     td= event.event_type
   td.col-width-medium-with-ellipsis
     = render partial: "renalware/events/events/cell/#{event.to_partial_path}",

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

@@ -11,6 +11,9 @@ table.has-togglable-rows.events-table
       th.created_at.col-width-date-time= t(".date_time")
       th.created_by.col-width-medium= t(".created_by")
   tbody
+    / Note we can't use cached: true yet when rendering the events collection, as each row is
+    / used in a different context and displays there slightly differently, for example showing
+    / an Edit link or Type column in certain circumstances.
     = render partial: "renalware/events/events/event",
              collection: events,
              locals: { exclude_type_column: local_assigns[:exclude_type_column],

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

@@ -8,6 +8,7 @@
   .patient-content.full-screenable
     .layout-wrapper
       = render "renalware/patients/mini_profile", patient: current_patient
+      = render "renalware/clinical/header", patient: current_patient
       = render "renalware/patients/alerts/list", patient: current_patient
       .row.collapse
         - if local_assigns[:title].present?

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

@@ -29,7 +29,7 @@ ruby:
               }
     = hidden_field_tag "description_id"
     = f.input :clinical, as: :hidden
-    = f.input :issued_on, as: :date_picker
+    = f.input :issued_on, as: :date_picker, wrapper: :horizontal_datepicker
     = f.association :author,
         as: :user_picker,
         collection: Renalware::System::UsersPresenter.new.list_for_dropdown( \

data/app/views/renalware/letters/letters/_pathology.html.slim

@@ -5,7 +5,6 @@ ruby:
     observation_set_b: letter.patient.current_observation_set&.values,
     descriptions: Renalware::Letters::RelevantObservationDescription.all
   )
-
 - if letter.clinical?
   article.letter-pathology
     header

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

@@ -7,7 +7,7 @@ table#patients.mdm-patients.columns
       th.col-width-reference-no= t(".hosp_no")
       th.col-width-tiny= t(".sex")
       th.col-width-tiny= t(".age")
-      th.col-width-small= t(".modality")
+      th.col-width-medium= t(".modality")
       - %i(hgb ure cre).each do |code|
         th.col-width-tiny= sort_link(path, code, t(".#{code}"))
         th.col-width-date= sort_link(path, :"#{code}_date", t(".#{code}_date"))

data/app/views/renalware/pathology/_navigation.html.slim

@@ -1,7 +1,7 @@
 dl.sub-nav
   dd= link_to "Historical", patient_pathology_historical_observations_path(@patient)
   dd= link_to "Current", patient_pathology_current_observations_path(@patient)
-  dd= link_to "Recent", patient_pathology_recent_observations_path(@patient)
+  / dd= link_to "Recent", patient_pathology_recent_observations_path(@patient)
   dd= link_to "Investigations", patient_pathology_observation_requests_path(@patient)
   dd= link_to "Required Observations", patient_pathology_required_observations_path(@patient)
   dd= link_to "New Patient Rule", new_patient_pathology_patient_rule_path(@patient)

data/app/views/renalware/patients/patients/_table.html.slim

@@ -1,7 +1,7 @@
 table#patients
   thead
     tr
-      th.col-width-medium= attr_name(Renalware::Patient, :name)
+      th.col-width-large= attr_name(Renalware::Patient, :name)
       th.col-width-nhs-no NHS Number
       - Renalware.config.patient_hospital_identifiers.each_key do |key|
         th.col-width-reference-without-prefix="#{key} No"
@@ -10,7 +10,7 @@ table#patients
       th.col-width-tiny= attr_name(Renalware::Patient, :age)
       th.col-width-tiny= sort_link(search, :send_to_rpv, "RPV")
       th.col-width-tiny= sort_link(search, :send_to_renalreg, "RReg")
-      th.col-width-small Modality
+      th.col-width-medium Modality
 
   tbody
     = render partial: "patient", collection: patients

data/config/initializers/core_extensions.rb

@@ -1,6 +1,7 @@
 require "core_extensions/i18n/handle_blank_value"
 require "core_extensions/i18n/always_cascade"
 require "core_extensions/dumb_delegator"
+require "core_extensions/active_record/migration_helpers"
 require "core_extensions/active_record/sort"
 require "core_extensions/date"
 require "core_extensions/active_support/duration"

data/config/initializers/inflections.rb

@@ -15,6 +15,7 @@ ActiveSupport::Inflector.inflections(:en) do |inflect|
   inflect.acronym "AKI"
   inflect.acronym "APD"
   inflect.acronym "API"
+  inflect.acronym "BMI"
   inflect.acronym "CAPD"
   inflect.acronym "CC"
   inflect.acronym "CCs"

data/config/locales/renalware/clinical/allergies.en.yml

@@ -10,8 +10,6 @@ en:
           delete: Delete
           edit: Edit
 
-
-
         new:
           title: Add allergy
           description: Description

data/config/locales/renalware/clinical/header.en.yml

@@ -0,0 +1,14 @@
+en:
+  renalware:
+    clinical:
+      header:
+        blood_pressure: "BP:"
+        weight: "Wt:"
+        height: "Ht:"
+        bmi: "BMI:"
+        hgb: "HGB:"
+        cre: "Creat:"
+        pot: "Potass:"
+        egfr: "eGFR:"
+        ure: "Urea:"
+        cockroft_gault: "Cockr-Glt"

data/db/functions/audit_view_as_json_v01.sql

@@ -0,0 +1,25 @@
+CREATE OR REPLACE FUNCTION audit_view_as_json(view_name text)
+  /*
+  Converts the specified view into its json representation suitable for feeding for example
+  into jQuery datatables plugin, or creating a historical snapshot.
+  Example usage:
+    select audit_view_as_json('reporting_bone_audit')
+  TC 1.11.2017
+  */
+  RETURNS json
+  LANGUAGE 'plpgsql'
+  as $$
+  DECLARE result json;
+  BEGIN
+  EXECUTE format('
+  select row_to_json(t)
+    from (
+      select
+        current_timestamp as runat,
+        (select array_to_json(array_agg(row_to_json(d))
+      )
+    from (select * from %s) d) as data) t;
+    ', quote_ident(view_name)) into result;
+  return result;
+END
+$$;

data/db/functions/count_estimate_v01.sql

@@ -0,0 +1,20 @@
+/*
+A plpgsql function by Michael Fuhr for faster counting.
+See https://wiki.postgresql.org/wiki/Count_estimate
+Normal count(*) can be slow where that are millions of rows.
+This is a faster way to count filtered rows by parsing the output of an explain query.
+*/
+CREATE FUNCTION count_estimate(query text) RETURNS INTEGER AS
+$func$
+DECLARE
+    rec   record;
+    ROWS  INTEGER;
+BEGIN
+    FOR rec IN EXECUTE 'EXPLAIN ' || query LOOP
+        ROWS := SUBSTRING(rec."QUERY PLAN" FROM ' rows=([[:digit:]]+)');
+        EXIT WHEN ROWS IS NOT NULL;
+    END LOOP;
+
+    RETURN ROWS;
+END
+$func$ LANGUAGE plpgsql;

data/db/functions/generate_patient_secure_id_v01.sql

@@ -0,0 +1,21 @@
+CREATE OR REPLACE FUNCTION generate_patient_secure_id()
+  /*
+    Generates and returns a unique base 58 token 24 characters long for use as a secure_id on
+    the Renalware patients table. If the generated token is in use already (very unlikely) it
+    retries until a unique one is generated.
+    Example usage:
+      select generate_patient_secure_id #=> 0KPNXf4X5x1o6O4mXWE5MC9H
+    TC 8.6.2017
+  */
+  RETURNS varchar AS $$
+  DECLARE
+  new_secure_id varchar;
+  BEGIN
+  LOOP
+    new_secure_id := generate_secure_id(24);
+    EXIT WHEN NOT EXISTS(select 1 from patients where 'secure_id' = new_secure_id);
+    RAISE NOTICE 'The generated secure_id % was already in use - now generating another', new_secure_id;
+  END LOOP;
+  RETURN new_secure_id;
+  END
+  $$ LANGUAGE plpgsql;

data/db/functions/generate_secure_id_v01.sql

@@ -0,0 +1,18 @@
+CREATE OR REPLACE FUNCTION generate_secure_id(length integer default 24)
+  /*
+  Generates and returns a unique base 58 token of <length> length for use in for example
+  the obfuscation of database ids in URLs.
+  Note base58 tokens are case sensitive.
+  Example usage:
+    select generate_secure_id(24) #=> 0KPNXf4X5x1o6O4mXWE5MC9H
+  TC 8.6.2017
+  */
+  RETURNS text AS
+  $body$
+  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789',
+                     ceil (random() * 62)::integer,
+                     1), '')
+  FROM   generate_series(1, length)
+  ;
+  $body$
+  LANGUAGE sql;

data/db/functions/import_gps_csv_v01.sql

@@ -0,0 +1,129 @@
+CREATE OR REPLACE FUNCTION renalware.import_gps_csv(file text) RETURNS void
+  AS $$
+  BEGIN
+  -- Imports a egpcur.csv.csv file created from ODS.
+  -- Returns counts of changed (insert/updated) and (soft) deleted rows.
+
+  DROP TABLE IF EXISTS tmp_gps_copy;
+
+  -- Create a tmp table to hold the ODS-defined standard 27 field format into which we will insert out CSV data
+  CREATE TEMP TABLE tmp_gps_copy (
+  code text NOT NULL,
+  name text NOT NULL,
+  unused3 text,
+  unused4 text,
+  street_1 text,
+  street_2 text,
+  street_3 text,
+  town text,
+  county text,
+  postcode text,
+  unused11 text,
+  unused12 text,
+  status text, -- A = Active B = Retired C = Closed P = Proposed
+  unused14 text,
+  unused15 text,
+  unused16 text,
+  unused17 text,
+  telephone text,
+  unused19 text,
+  unused20 text,
+  unused21 text,
+  amended_record_indicator text,
+  unused23 text,
+  unused24 text,
+  unused25 text,
+  unused26 text,
+  unused27 text,
+  CONSTRAINT tmp_gps_pkey PRIMARY KEY (code)
+  );
+
+  -- Import the CSV file into tmp_practices - note there is no CSV header in this file
+  EXECUTE format ('COPY tmp_gps_copy FROM %L DELIMITER %L CSV ', file, ',');
+
+  DROP TABLE IF EXISTS tmp_gps;
+  CREATE TEMP TABLE tmp_gps AS SELECT
+    code,
+    name,
+    telephone,
+    street_1,
+    street_2,
+    street_3,
+    town,
+    county,
+    postcode,
+    left(status,1) as status from tmp_gps_copy ;
+  ALTER TABLE tmp_gps ADD PRIMARY KEY (code);
+
+RAISE NOTICE 'Calling cs_create_job(%)', (select status from tmp_gps limit 1);
+
+  -- Upsert GPs
+  WITH
+   data AS (select * from  tmp_gps),
+   gp_changes AS (
+    INSERT INTO renalware.patient_primary_care_physicians (code, name, telephone, practitioner_type, created_at, updated_at)
+    SELECT code, name, telephone, 'GP', clock_timestamp(), clock_timestamp()
+    FROM data
+    ON CONFLICT (code) DO UPDATE
+      SET
+       telephone = excluded.telephone,
+       name = excluded.name,
+       updated_at = excluded.updated_at
+      where (patient_primary_care_physicians.telephone) is distinct from (excluded.telephone)
+      RETURNING code, id
+     )
+
+  -- Upsert GP addresses
+  INSERT INTO renalware.addresses (
+    addressable_type,
+    addressable_id,
+    street_1,
+    street_2,
+    street_3,
+    town,
+    county,
+    postcode,
+    created_at,
+    updated_at)
+  SELECT
+    'Renalware::Patients::PrimaryCarePhysician' as addressable_type,
+    gps.id as addressable_id,
+    street_1,
+    street_2,
+    street_3,
+    town,
+    county,
+    postcode,
+    CURRENT_TIMESTAMP as created_at,
+    CURRENT_TIMESTAMP as updated_at
+    FROM data join patient_primary_care_physicians gps using(code)
+  ON CONFLICT (addressable_type, addressable_id) DO UPDATE
+    SET
+    street_1 = excluded.street_1,
+    street_2 = excluded.street_2,
+    street_3 = excluded.street_3,
+    town = excluded.town,
+    county = excluded.county,
+    postcode = excluded.postcode,
+    updated_at = clock_timestamp()
+    where (addresses.street_1, addresses.street_2, addresses.street_3)
+    is distinct from (excluded.street_1, excluded.street_2, excluded.street_3);
+
+  --GET DIAGNOSTICS changed_count = ROW_COUNT;
+
+  -- Update the deleted_at column of any gps which do not have an Active status_code
+  UPDATE renalware.patient_primary_care_physicians AS p
+  SET deleted_at = CURRENT_TIMESTAMP
+  FROM tmp_gps AS tp
+  WHERE p.code = tp.code AND tp.status IN ('C', 'P', 'B');
+
+  -- Un-delete any previously deleted GPs
+  UPDATE renalware.patient_primary_care_physicians AS gp
+  SET deleted_at = NULL
+  FROM tmp_gps
+  WHERE gp.code = tmp_gps.code AND tmp_gps.status IN ('A') AND gp.code NOT IN ('A');
+
+  --GET DIAGNOSTICS deleted_count = ROW_COUNT;
+  --select changed_count, deleted_count;
+  END;
+ $$ LANGUAGE plpgsql;