renalware-core 2.0.75 → 2.0.76

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 7bd749bf8191908be7e9bc1d15e9f283eb70a5584dc53ebb45c94cda8afd2060
-  data.tar.gz: 56679014ae649da1baa18755117a23cc5f199542de3e6bb6d922499b444fec8e
+  metadata.gz: 644e883f0c733d49ad49139eb2118a2387f3378db8a6fc9eb5b20eaf5dad4db2
+  data.tar.gz: 71cd0139f74aa162bbaedb783d6ce450270de74a64b74751cf1873ead4b9829a
 SHA512:
-  metadata.gz: c23f24fd2a0694433493e02129fe01c3e13f1ebb785ed78291d08ffac9e6386eaa33f7b1a3f50f8b9a691749ff86ad447bef490bd89043e8891b1c8c39130f32
-  data.tar.gz: d5e83fd37cfc7bf6b1a573b30d550b69a7fa2ed9c3d89bdd41fba2935d3940d05574ce681982f5eaaf757f905490169fb49939204694082961ffcc63985725f4
+  metadata.gz: 6dfe27f438b2f56ecaec02bda8abce84f8015ca5054f05b7e76bf6c405e6a0632f60013287e913b7e03aa0bf0a7f7ad8127742253fdecba60f3ce5277269abf0
+  data.tar.gz: a007bf5ef7be7ee91722e27ac434ed7d49e8edf32cc6408dd048b613272f0938c7073dff9990419d201d711ef574433cfe3faac4835b53e78d8265d2f1f9353b

data/app/assets/javascripts/renalware/application.js.erb

@@ -39,7 +39,6 @@
 //= require cocoon
 //= require mousetrap
 //= require renalware/iframeResizer
-//= require chosen-jquery
 //= require clipboard
 //= require renalware/masonry.min
 //= require rails.validations

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

@@ -53,3 +53,8 @@ Renalware.PdRegimes = (function () {
 $(document).ready(Renalware.PdRegimes.init);
 $(document).ready(Renalware.PdRegimes.toggleAddRemoveBags);
 $(document).on('nested:fieldAdded:bags', Renalware.PdRegimes.toggleAddRemoveBags);
+
+
+$(document).on('ready ajaxSuccess', function(event, xhr, status) {
+  $("#peritonitis_episode_types .searchable_select").select2();
+});

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

@@ -10,7 +10,6 @@
 @import "font-awesome";
 @import "foundation-datepicker";
 @import "dataTables/jquery.dataTables.foundation";
-@import "chosen";
 @import "trix";
 @import "renalware/balloon";
 @import "./lib/foundation_and_overrides";

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

@@ -30,10 +30,6 @@ textarea.monospace {
   }
 }
 
-.chosen-container-multi {
-  margin-bottom: 0.5rem;
-}
-
 // Hide up down arrows on number inputs
 input[type="number"]::-webkit-inner-spin-button,
 input[type="number"]::-webkit-outer-spin-button {

data/app/models/renalware/pathology/observation_request.rb

@@ -23,6 +23,28 @@ module Renalware
       def requested_on
         requested_at.to_date
       end
+
+      # Exlucludes duplicate rows; there may be an original OBR and one or more updates (with more
+      # complete results) and we only want the last received one got any requestor_order_number
+      # (actually for any requestor_order_number + requested_at + description_id) combination
+      # because requestor_order_number is sometimes blank
+      # rubocop:disable Metrics/MethodLength
+      def self.distinct_for_patient_id(patient_id)
+        select(
+          Arel.sql(
+            "DISTINCT ON (patient_id, requestor_order_number, requested_at, description_id) id"
+          )
+        )
+        .where(patient_id: patient_id)
+        .order(
+          patient_id: :asc,
+          requestor_order_number: :asc,
+          requested_at: :asc,
+          description_id: :asc,
+          created_at: :desc
+        )
+      end
+      # rubocop:enable Metrics/MethodLength
     end
   end
 end

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

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+require_dependency "renalware/ukrdc"
+require "attr_extras"
+
+module Renalware
+  module UKRDC
+    class PathologyObservationRequestsQuery
+      pattr_initialize [:patient_id!, :changes_since!]
+
+      def call
+        observation_requests
+      end
+
+      private
+
+      def observation_requests
+        Pathology::ObservationRequest
+          .where(id: Pathology::ObservationRequest.distinct_for_patient_id(patient_id))
+          .where("requested_at >= ?", changes_since)
+          .where("loinc_code is not null")
+          .eager_load(
+            :description,
+            observations: { description: :measurement_unit }
+          )
+      end
+    end
+  end
+end

data/app/policies/renalware/clinics/clinic_visit_policy.rb

@@ -8,7 +8,21 @@ module Renalware
       def destroy?
         return false unless record.persisted?
 
-        record.created_at > Renalware.config.new_clinic_visit_deletion_window.ago
+        record.created_at > Renalware.config.new_clinic_visit_deletion_window.ago &&
+          (user_created_record? || user_is_super_admin?)
+      end
+
+      def edit?
+        return false unless record.persisted?
+
+        record.created_at > Renalware.config.new_clinic_visit_edit_window.ago &&
+          (user_created_record? || user_is_super_admin?)
+      end
+
+      private
+
+      def user_created_record?
+        record.created_by_id == user.id
       end
     end
   end

data/app/presenters/renalware/ukrdc/pathology_observation_request_presenter.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module Renalware
+  module UKRDC
+    class PathologyObservationRequestPresenter < SimpleDelegator
+      # Note that we can't just use requestor_order_number as some OBR
+      # segments arrive with a blank one. We need put something in the XML
+      # that is unique per observation_request, but will still _be_ something
+      # when requestor_order is blank
+      def placer_id
+        [
+          requestor_order_number,
+          requested_at.strftime("%Y%m%d%H%M%S%L"),
+          description_id
+        ].reject(&:blank?).join("-")
+      end
+    end
+  end
+end

data/app/presenters/renalware/ukrdc/patient_presenter.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require_dependency "renalware"
+require_dependency "renalware/ukrdc"
 
 # rubocop:disable Metrics/ClassLength
 module Renalware
@@ -102,41 +102,12 @@ module Renalware
         __getobj__.prescriptions.current.includes(:termination, :medication_route, :drug)
       end
 
-      # We want to avoid returning duplicate pathology_observation_requests. We might have had
-      # and update to a pathology_observation_requests, adding a previously missing result,
-      # and the requestor_order_number is the same, so we have two rows with the same
-      # patient_id and requestor_order_number. We want to just select that latest one. We'll use
-      # created_at for this, even though it would be more accurate to look at the timestamp in the
-      # OBR or MSH segment (these not currently available).
-      # We use fully qualified column names here to prevent SQL errors when AR compiles the SQL.
-      def latest_observation_requests
-        Pathology::ObservationRequest
-          .select(<<-SELECT)
-          DISTINCT ON (
-            pathology_observation_requests.patient_id,
-            pathology_observation_requests.requestor_order_number,
-            pathology_observation_requests.requested_at,
-            pathology_observation_requests.description_id)
-          *
-          SELECT
-          .order(<<-ORDER)
-            pathology_observation_requests.patient_id ASC,
-            pathology_observation_requests.requestor_order_number ASC,
-            pathology_observation_requests.requested_at ASC,
-            pathology_observation_requests.description_id ASC,
-            pathology_observation_requests.created_at DESC
-          ORDER
-      end
-
       def observation_requests
-        latest_observation_requests
-          .where(patient_id: id)
-          .where("requested_at >= ?", changes_since)
-          .where("loinc_code is not null")
-          .eager_load(
-            :description,
-            observations: { description: :measurement_unit }
-          )
+        requests = UKRDC::PathologyObservationRequestsQuery.new(
+          patient_id: id,
+          changes_since: changes_since
+        ).call
+        CollectionPresenter.new(requests, UKRDC::PathologyObservationRequestPresenter)
       end
 
       private

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

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+return if visit.public_send(method).blank?
+
 xml = builder
 
 i18n_key ||= method

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

@@ -2,22 +2,6 @@
 
 # See HL7 spec http://pacs.hk/Doc/HL7/Hl7V231.pdf
 
-# A Note about PlacerId
-# ---------------------
-# In UKRDC terms an OBR equates to their LabOrder. Each LabOrder must have a unique
-# PlacerId. However an HL7 message (for example at KCH) can have multiple OBRs with the same
-# placer id (aka requester order number) thus causing duplicate placer ids to appear in the XML.
-# After email discussion with George and Nick at UKRDC it was decided that PlacerID could be
-# any value as long as it is unique and is persisted in Renalware (in case an update needs to be
-# sent, and the original LabOrder identified). To solve this we obfuscate the request.id (slightly)
-# by converting to base 16 (hex) and then append it to the original requester order number.
-# Its not good practice to expose a database id in this way though it is to an internal NHS consumer
-# and the hex obfuscation helps slightly.
-# A better approach might be to generate a GUID for each pathology_observation_request and pass
-# this as the placer id. However that would introduce more moving parts (calling the SQL function
-# to generate the uuid) and increases storage and XML file sizes.
-placer_id = "#{request.requestor_order_number}-#{request.id.to_s(16)}".upcase
-
 xml = builder
 
 xml.LabOrder do
@@ -25,7 +9,7 @@ xml.LabOrder do
   #   xml.Code ""
   #   xml.Description # request.pathology_lab.name
   # end
-  xml.PlacerId placer_id
+  xml.PlacerId request.placer_id
   # xml.FillerId "??ORC:3 Labs Order Id"
   # xml.OrderedBy do
   #   xml.Code "unknown"

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

@@ -1,7 +1,9 @@
 tr(class="#{'dna' if clinic_visit.did_not_attend?}")
   td
-    = link_to "Edit", edit_patient_clinic_visit_path(patient, clinic_visit)
-    = pipe_separator
+    - if policy(clinic_visit).edit?
+      = link_to "Edit",
+                edit_patient_clinic_visit_path(patient, clinic_visit)
+      = pipe_separator
     = link_to("Toggle",
               "#clinic_visit-quick-preview-#{clinic_visit.id}",
               data: { behaviour: "toggler" })

data/app/views/renalware/pd/peritonitis_episodes/_fields.html.slim

@@ -6,14 +6,17 @@
 .row
   .large-12.columns
     = field_set_tag t(".fieldsets.outcomes") do
-      = f.input :episode_types,
-                collection: Renalware::PD::PeritonitisEpisodeTypeDescription.pluck(:term, :id),
-                include_blank: t("collection.blank_option"),
-                input_html: { data: { placeholder: t("collection.blank_option_for_multiple") } },
-                as: :multiple_select,
-                include_hidden: false,
-                selected: f.object.episode_types.map(&:peritonitis_episode_type_description_id)
+      #peritonitis_episode_types
+        = f.input :episode_types,
+                  collection: Renalware::PD::PeritonitisEpisodeTypeDescription.pluck(:term, :id),
+                  include_blank: t("collection.blank_option"),
+                  input_html: { data: { placeholder: t("collection.blank_option_for_multiple") },
+                    class: "searchable_select",
+                    multiple: "multiple"},
+                  include_hidden: false,
+                  selected: f.object.episode_types.map(&:peritonitis_episode_type_description_id)
       = f.input :catheter_removed, as: :inline_radio_buttons
+
 .row
   .large-12.columns
     = field_set_tag t(".fieldsets.causes") do

data/config/locales/loinc_codes.yml

@@ -9,7 +9,7 @@ en:
       diastolic:
         # code: 76539-6
         code: bpdia
-        description: Blood pressure device Cuff pressure.systolic
+        description: Blood pressure device Cuff pressure.diastolic
         units: "mmHg"
     weight:
       # code: 3141-9
@@ -20,4 +20,3 @@ en:
       code: height
       description: Height Measured
       units: "m"
-

data/db/migrate/20190422095620_streamline_daily_summary_reports.rb

@@ -0,0 +1,11 @@
+class StreamlineDailySummaryReports < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view(
+        :reporting_daily_pathology,
+        version: 3,
+        revert_to_version: 2
+      )
+    end
+  end
+end

data/db/views/reporting_daily_pathology_v03.sql

@@ -0,0 +1,13 @@
+-- A pathology report to help identify any HL7/delayed_job issues
+-- the name of the view (the filename here) is significant as we'll compile all reporting_daily_*
+-- views into a daily digest email
+select
+  (select count(*) from delayed_jobs) as delayed_jobs_total,
+  (select count(*) from delayed_jobs where attempts = 0) as delayed_jobs_unprocessed,
+  (select count(*) from delayed_jobs where last_error is not null and failed_at is null ) as delayed_jobs_retrying,
+  (select count(*) from delayed_jobs where last_error is not null and failed_at is not null ) as delayed_jobs_failed,
+  (select max(created_at) from delayed_jobs) as delayed_jobs_latest_entry,
+  (select count(*) from delayed_jobs where created_at >= now()::date) as delayed_jobs_added_today,
+  (select json_object_agg(priority, count) from (select priority, count(*) from delayed_jobs group by priority ) query) as delayed_jobs_priority_counts,
+  (select json_object_agg(coalesce(queue, 'unset'), count) from (select queue, count(*) from delayed_jobs group by queue ) query) as delayed_jobs_queue_counts,
+  (select json_object_agg(attempts, count) from (select attempts, count(*) from delayed_jobs group by attempts ) query) as delayed_jobs_attempts_counts

data/lib/renalware/configuration.rb

@@ -25,6 +25,7 @@ module Renalware
     config_accessor(:hospital_name) { "KINGS COLLEGE HOSPITAL" }
     config_accessor(:delay_after_which_a_finished_session_becomes_immutable) { 6.hours }
     config_accessor(:new_clinic_visit_deletion_window) { 24.hours }
+    config_accessor(:new_clinic_visit_edit_window) { 7.days }
     config_accessor(:salutation_prefix) { "Dear" }
     config_accessor(:page_title_spearator) { " : " }
     config_accessor(:patient_hospital_identifiers) { {} }

data/lib/renalware/engine.rb

@@ -5,7 +5,6 @@ require "active_type"
 require "activerecord-import"
 require "ahoy"
 require "autoprefixer-rails"
-require "chosen-rails"
 require "simple_form"
 require "client_side_validations"
 require "client_side_validations/simple_form"

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.75"
+  VERSION = "2.0.76"
 end

data/spec/support/pathology_spec_helper.rb

@@ -19,6 +19,36 @@ module PathologySpecHelper
     end
   end
 
+  # rubocop:disable Metrics/ParameterLists, Metrics/MethodLength
+  def create_request_with_observations(requestor_order_number: "123",
+                                       obr_code: "OBR1",
+                                       obx_codes: ["OBX1"],
+                                       requested_at: 1.year.ago,
+                                       patient:,
+                                       created_at: nil)
+    request_desc = create(:pathology_request_description, code: obr_code)
+    create(
+      :pathology_observation_request,
+      patient: patient,
+      requestor_order_number: requestor_order_number,
+      requested_at: requested_at,
+      description: request_desc,
+      created_at: created_at
+    ).tap do |request|
+      obx_codes.each do |obx_code|
+        description = create(:pathology_observation_description, code: obx_code)
+        create(
+          :pathology_observation,
+          request: request,
+          description: description,
+          observed_at: 1.year.ago,
+          result: "1.1"
+        )
+      end
+    end
+  end
+  # rubocop:enable Metrics/ParameterLists, Metrics/MethodLength
+
   # name and code will be the same
   def create_observation_description(name)
     create(:pathology_observation_description, name: name, code: name)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.75
+  version: 2.0.76
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-11 00:00:00.000000000 Z
+date: 2019-05-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -80,20 +80,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 9.4.2
-- !ruby/object:Gem::Dependency
-  name: chosen-rails
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.8.3
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.8.3
 - !ruby/object:Gem::Dependency
   name: client_side_validations
   requirement: !ruby/object:Gem::Requirement
@@ -686,16 +672,16 @@ dependencies:
   name: rails-assets-select2
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: 4.0.2
+        version: 4.0.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: 4.0.2
+        version: 4.0.5
 - !ruby/object:Gem::Dependency
   name: ransack
   requirement: !ruby/object:Gem::Requirement
@@ -989,7 +975,6 @@ files:
 - app/assets/javascripts/renalware/appointments.js
 - app/assets/javascripts/renalware/auto_complete.js
 - app/assets/javascripts/renalware/behaviours.js
-- app/assets/javascripts/renalware/chosen.js
 - app/assets/javascripts/renalware/clipboard_setup.js
 - app/assets/javascripts/renalware/clockpicker.js
 - app/assets/javascripts/renalware/contacts.js
@@ -1337,7 +1322,6 @@ files:
 - app/inputs/datetime_picker_input.rb
 - app/inputs/hidden_array_input.rb
 - app/inputs/inline_radio_buttons_input.rb
-- app/inputs/multiple_select_input.rb
 - app/inputs/select_container_input.rb
 - app/inputs/simple_time_input.rb
 - app/inputs/user_picker_input.rb
@@ -1829,6 +1813,7 @@ files:
 - app/models/renalware/ukrdc/create_patient_xml_file.rb
 - app/models/renalware/ukrdc/export_summary.rb
 - app/models/renalware/ukrdc/filename.rb
+- app/models/renalware/ukrdc/pathology_observation_requests_query.rb
 - app/models/renalware/ukrdc/paths.rb
 - app/models/renalware/ukrdc/patients_query.rb
 - app/models/renalware/ukrdc/transmission_log.rb
@@ -2007,6 +1992,7 @@ files:
 - app/presenters/renalware/transplants/wait_list_registration_presenter.rb
 - app/presenters/renalware/ukrdc/modality_presenter.rb
 - app/presenters/renalware/ukrdc/pathology_observation_presenter.rb
+- app/presenters/renalware/ukrdc/pathology_observation_request_presenter.rb
 - app/presenters/renalware/ukrdc/patient_presenter.rb
 - app/presenters/string_presenter.rb
 - app/presenters/time_presenter.rb
@@ -3460,6 +3446,7 @@ files:
 - db/migrate/20190225103005_add_info_to_hospital_centres.rb
 - db/migrate/20190315125638_add_timestamps_to_pathology_description_tables.rb
 - db/migrate/20190401105149_create_function_for_hl7_insertion_from_mirth.rb
+- db/migrate/20190422095620_streamline_daily_summary_reports.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3564,6 +3551,7 @@ files:
 - db/views/reporting_daily_letters_v02.sql
 - db/views/reporting_daily_pathology_v01.sql
 - db/views/reporting_daily_pathology_v02.sql
+- db/views/reporting_daily_pathology_v03.sql
 - db/views/reporting_daily_ukrdc_v01.sql
 - db/views/reporting_hd_blood_pressures_audit_v01.sql
 - db/views/reporting_hd_overall_audit_v01.sql

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

@@ -1,7 +0,0 @@
-
-$(document).on('ready ajaxSuccess', function(event, xhr, status) {
-  $('.chosen-select').chosen({
-      allow_single_deselect: true,
-      no_results_text: 'No results matched',
-      width: '400px'})
-});

data/app/inputs/multiple_select_input.rb

@@ -1,15 +0,0 @@
-# frozen_string_literal: true
-
-class MultipleSelectInput < SimpleForm::Inputs::CollectionSelectInput
-  def input_type
-    :multiple_select
-  end
-
-  def input_html_options
-    options = super
-    klass = (options[:class] ||= [])
-    klass << "chosen-select"
-    options[:multiple] = "multiple"
-    options
-  end
-end