renalware-core 2.0.73 → 2.0.74

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: fa22b53287a50bfb41fc8de7c46fe936fe87387b2b209b46e34caee3e330ef5a
-  data.tar.gz: dfd75e90ef80382dccc2118e1c7983d1ac04f0dfcb94dbca78c89d12b85ad2ba
+  metadata.gz: ccdebf5655509330b7b4deb66b132a39080ed140451aefb122a556e0fb04fc82
+  data.tar.gz: 3903cfc62c753c5019d459a0d9363a57432ed9ba20b7b1e489b5203fafc51a2e
 SHA512:
-  metadata.gz: 71693a8d39c32435d5b2175341c9377bc472bcec42249e1fe8eb34f76f7144c02258af99c47c3cab2e47885e9af5e23777a8385508c7008b4d3b97d05d93b656
-  data.tar.gz: a5056e47da3cd879f1e6ec4836d7846448f76aee72c38881d9500876e06252bd2f561dec5efc84d60232f5ae079a7664bea493874f49513de3f2525ca24bcdc1
+  metadata.gz: df449f7e2014ec25ea0e12511c96d39177454bdbc9badd36dfef1beec7f57c8b8eb3b4f21baf95953088ca672db0e922bad0ee4a096ddaf410076313839276b7
+  data.tar.gz: c3c2066f6fa67117a6502073de4cc61f707631f7527c56308327034a3689242251fce6befed72dd713c4117f7c269aa126f760ea11526064e981e2b1aa350164

data/app/assets/stylesheets/renalware/base/_variables.scss

@@ -142,6 +142,13 @@ $large-range: (64.063em, 90em);
 $xlarge-range: (90.063em, 120em);
 $xxlarge-range: (120.063em, 99999999em);
 
+// Foundation defaults
+// $small-range: (0, 45.78570em);
+// $medium-range: (45.78571em, 73.21429em);
+// $large-range: (73.21423em, 102.92857em);
+// $xlarge-range: (102.9286em, 137.21429em)
+//
+
 $screen: "only screen";
 
 $landscape: "#{$screen} and (orientation: landscape)";

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

@@ -66,4 +66,61 @@
       margin: auto;
     }
   }
+
+  .wrapper.wrapper_style_horizontal {
+    @include grid-row($behavior: nest);
+
+    > .wrapper__label {
+      @media #{$small-only} {
+        @include grid-column(12);
+      }
+      @media #{$medium-only} {
+        @include grid-column(4);
+      }
+      @media #{$large-up} {
+        @include grid-column(3);
+      }
+
+      label {
+        margin: 0 0 0.85714rem 0;
+        padding: 0.5rem 0;
+        float: none !important;
+        text-align: right;
+        display: inline;
+      }
+    }
+
+    // Medium is the default style if no other wrapper name given
+    > .wrapper__input {
+      @media #{$small-only} {
+        @include grid-column(12);
+      }
+      @media #{$medium-up} {
+        @include grid-column(6, $last-column: false);
+      }
+
+      .datepicker-wrapper {
+        max-width: 12rem !important;
+      }
+    }
+
+    &.wrapper_size_large {
+      > .wrapper__input {
+        @media #{$medium-only} {
+          @include grid-column(8, $last-column: false);
+        }
+        @media #{$large-up} {
+          @include grid-column(9, $last-column: false);
+        }
+      }
+    }
+
+    &.wrapper_size_small {
+      > .wrapper__input {
+        @media #{$medium-up} {
+          @include grid-column(4, $last-column: false);
+        }
+      }
+    }
+  }
 }

data/app/jobs/hl7_message_example.txt

@@ -0,0 +1,22 @@
+MSH|^~\&|HM|LBE|SCM||20191112164645||ORU^R01|1258271|P|2.3.1|||AL||||
+PID|||Z100002^^^PAS Number||RABBIT^JESSICA^^^MS||19880924|F|||18 RABBITHOLE ROAD^LONDON^^^SE8 8JR|||||||||||||||||||
+PV1||Inpatient|NIBC^^^^^^^^|||||MID^KINGS MIDWIVES||||||||||NHS|HXF888888^^^Visit Number|||||||||
+ORC|RE|^PCS|09B0099478^LA||CM||||201911111841|||MID^KINGS MIDWIVES|||||||
+OBR|1|^PCS|09B0099478^LA|FBC^FULL BLOOD COUNT^MB||201911111841|201911111841|||||||201911111841|B^Blood|MID^KINGS MIDWIVES||09B0099478||||201911121646||HM|F||||||||||||||||||
+OBX|1|TX|WBC^WBC^MB||9.99||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|2|TX|RBC^RBC^MB||9.99||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|3|TX|HGB^Hb^MB||9.99||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|4|TX|PCV^PCV^MB||0.344||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|5|TX|MCV^MCV^MB||85.9||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|6|TX|MCH^MCH^MB||29.5||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|7|TX|MCHC^MCHC^MB||34.4||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|8|TX|RDW^RDW^MB||13.3||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|9|TX|PLT^PLT^MB||259||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|10|TX|MPV^Mean Platelet Volume^MB||8.3||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|11|TX|NRBC^Machine NRBC^MB||<0.2%||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|12|TX|HYPO^% HYPO^MB||0.2||||||F|||201911112026||BBKA^Donald DUCK|
+OBX|13|TX|NEUT^Neutrophil Count^MB||  3.16||||||F|||201911121646||BHISVC01^BHI Authchecker|
+OBX|14|TX|LYM^Lymphocyte Count^MB||  2.32||||||F|||201911121646||BHISVC01^BHI Authchecker|
+OBX|15|TX|MON^Monocyte Count^MB||  0.44||||||F|||201911121646||BHISVC01^BHI Authchecker|
+OBX|16|TX|EOS^Eosinophil Count^MB||  0.15||||||F|||201911121646||BHISVC01^BHI Authchecker|
+OBX|17|TX|BASO^Basophils^MB||  0.02||||||F|||201911121646||BHISVC01^BHI Authchecker|

data/app/models/renalware/feeds/hl7_message.rb

@@ -27,13 +27,17 @@ module Renalware
           universal_service_id.split("^").first
         end
 
+        def name
+          universal_service_id.split("^")[1]
+        end
+
         # Select only OBX children. OBR can have other types of child
         # segments but we want to ignore those.
         def observations
           @observations ||= begin
             children
-              .select{ |segment| segment.is_a? HL7::Message::Segment::OBX }
-              .map{ |obx_segment| Observation.new(obx_segment) }
+              .select { |segment| segment.is_a? HL7::Message::Segment::OBX }
+              .map { |obx_segment| Observation.new(obx_segment) }
           end
         end
 
@@ -61,6 +65,10 @@ module Renalware
           observation_id.split("^").first
         end
 
+        def name
+          observation_id.split("^")[1]
+        end
+
         # TODO: Implement comment extraction
         def comment
           @comment || ""
@@ -102,7 +110,7 @@ module Renalware
       # There is a problem here is there are < 1 OBR
       # i.e. self[:OBR] could be an array
       def observation_requests
-        Array(self[:OBR]).map{ |obr| ObservationRequest.new(obr) }
+        Array(self[:OBR]).map { |obr| ObservationRequest.new(obr) }
       end
 
       class PatientIdentification < SimpleDelegator

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

@@ -56,7 +56,10 @@ module Renalware
       # rubocop:disable Metrics/MethodLength
       def build_observation_request_params
         requests.each_with_object([]) do |request, arr|
-          request_description = find_request_description(request.identifier)
+          request_description = find_request_description(
+            code: request.identifier,
+            name: request.name
+          )
           hash = {
             observation_request: {
               description_id: request_description.id,
@@ -71,9 +74,13 @@ module Renalware
       end
       # rubocop:enable Metrics/MethodLength
 
+      # rubocop:disable Metrics/MethodLength
       def build_observations_params(request)
         request.observations.map do |observation|
-          observation_description = find_observation_description(observation.identifier)
+          observation_description = find_observation_description(
+            code: observation.identifier,
+            name: observation.name
+          )
           next unless validate_observation(observation, observation_description)
 
           {
@@ -85,18 +92,19 @@ module Renalware
           }
         end.compact
       end
+      # rubocop:enable Metrics/MethodLength
 
-      def find_request_description(code)
+      def find_request_description(code:, name:)
         RequestDescription.find_or_create_by!(code: code) do |desc|
-          desc.name = code
+          desc.name = name || code
           desc.lab = Lab.unknown
         end
       rescue ActiveRecord::RecordNotFound
         raise MissingRequestDescriptionError, code
       end
 
-      def find_observation_description(code)
-        ObservationDescription.find_or_create_by!(code: code) { |desc| desc.name = code }
+      def find_observation_description(code:, name:)
+        ObservationDescription.find_or_create_by!(code: code) { |desc| desc.name = name || code }
       rescue ActiveRecord::RecordNotFound
         raise MissingObservationDescriptionError, code
       end

data/app/models/renalware/transplants/registration.rb

@@ -50,6 +50,9 @@ module Renalware
 
       private
 
+      # Set the most recent status terminated_on to nil (so it is active)
+      # and then walk back across all other statuses and set the terminated_on
+      # to be started_on of the next status. Allow for > 1 status created on the same day.
       def recompute_termination_dates!
         previous_started_on = nil
         statuses.reversed.each do |status|

data/app/models/renalware/transplants/registration_status.rb

@@ -10,8 +10,8 @@ module Renalware
       belongs_to :description, class_name: "RegistrationStatusDescription"
       belongs_to :registration, touch: true
 
-      scope :ordered, -> { order(started_on: :asc) }
-      scope :reversed, -> { order(started_on: :desc) }
+      scope :ordered, -> { order(started_on: :asc, created_at: :asc) }
+      scope :reversed, -> { order(started_on: :desc, created_at: :desc) }
 
       validates :description_id, presence: true
       validates :started_on, timeliness: { type: :date, allow_blank: false }

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

@@ -97,22 +97,42 @@ module Renalware
           .includes(:updated_by)
       end
 
+      # We always send the patients current prescriptions.
       def prescriptions
-        __getobj__.prescriptions
-          .includes(:termination, :medication_route, :drug)
-          .where("updated_at > ?", changes_since)
+        __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)
+          *
+          SELECT
+          .order(<<-ORDER)
+            pathology_observation_requests.patient_id ASC,
+            pathology_observation_requests.requestor_order_number ASC,
+            pathology_observation_requests.created_at DESC
+          ORDER
       end
 
       def observation_requests
-        pathology_patient
-          .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 }
           )
-          .where(patient_id: id)
-          .where("requested_at >= ?", changes_since)
-          .where("loinc_code is not null")
       end
 
       private

data/app/views/renalware/transplants/registration_statuses/_list.html.slim

@@ -41,4 +41,3 @@ article.status-history.secondary
               dl.dl-horizontal
                 dt Notes
                 dd= simple_format status.notes
-

data/config/initializers/simple_form_wrappers.rb

@@ -0,0 +1,57 @@
+SimpleForm.setup do |config|
+  def configure_label(b)
+    b.use :html5
+    b.use :placeholder
+    b.optional :maxlength
+    b.optional :pattern
+    b.optional :min_max
+    b.optional :readonly
+
+    b.wrapper :label_wrapper, tag: :div, class: "wrapper__label" do |ba|
+      ba.use :label
+    end
+  end
+
+  def configure_input(b)
+    b.wrapper :right_input_wrapper, tag: :div, class: "wrapper__input" do |ba|
+      ba.use :input
+      ba.use :error, wrap_with: { tag: :small, class: ["error"] }
+      ba.use :hint,  wrap_with: { tag: :span, class: ["hint"] }
+    end
+  end
+
+  # Configure various sized wrappers. We use CSS to style the label and inputs within the top div
+  # with classes of e.g. "row wrapper-medium"
+  %i(tiny small medium large).each do |size|
+    config.wrappers(
+      :"hz_#{size}", # eg hz_medium
+      tag: "div",
+      class: "row wrapper wrapper_style_horizontal wrapper_size_#{size}",
+      hint_class: :field_with_hint,
+      error_class: :error
+    ) do |b|
+      configure_label(b)
+      configure_input(b)
+    end
+  end
+
+  config.wrappers(
+    :hz_datepicker,
+    tag: :div,
+    class: "row wrapper wrapper_style_horizontal wrapper_size_datepicker",
+    hint_class: :field_with_hint,
+    error_class: :error
+  ) do |b|
+
+    configure_label(b)
+
+    b.wrapper :right_input_wrapper, tag: :div, class: "wrapper__input" do |ba|
+      ba.wrapper :x, tag: :div, class: "row collapse datepicker-wrapper" do |bc|
+        bc.use :prefix_column
+        bc.use :input_column
+        bc.use :error, wrap_with: { tag: :small, class: [:error, :datepicker_error] }
+        bc.use :hint,  wrap_with: { tag: :span, class: :hint }
+      end
+    end
+  end
+end

data/db/functions/new_hl7_message_v01.sql

@@ -0,0 +1,29 @@
+CREATE OR REPLACE FUNCTION renalware.new_hl7_message(message text) RETURNS void AS $$
+BEGIN
+/*
+  This fn is called by the Mirth integration engine to add an HL7 message to Renalware.
+  Mirth used to insert data directly into the delayed_jobs table but we are moving away from
+  that approach as it tightly couples Mirth to our internal implementation and prevents us
+  from easily moving to another background processing library eg que.
+
+  When using delayed_jobs
+  -----------------------
+  1. We craft a yml string and translate line endings.
+  2. The trigger function preprocess_hl7_message fires when a row is added to delayed_jobs.
+     It handles escaping odd characters eg 10^12 in the message. See that function for details.
+     Once we have migrated Mirth to use this function and are happy it is working we can
+     move that logic from preprocess_hl7_message into here and drop that function and its trigger.
+
+  When using que
+  ------------------
+  # TODO: psuedo SQL
+*/
+insert into renalware.delayed_jobs(handler, run_at, created_at, updated_at)
+values(
+  E'--- !ruby/struct:FeedJob\nraw_message: |\n  ' || REPLACE(message, E'\r', E'\n  '),
+  NOW() AT TIME ZONE 'UTC',
+  NOW() AT TIME ZONE 'UTC',
+  NOW() AT TIME ZONE 'UTC'
+);
+END;
+$$ LANGUAGE plpgsql;

data/db/migrate/20190401105149_create_function_for_hl7_insertion_from_mirth.rb

@@ -0,0 +1,13 @@
+class CreateFunctionForHL7InsertionFromMirth < ActiveRecord::Migration[5.2]
+  def up
+    within_renalware_schema do
+      load_function "new_hl7_message_v01.sql"
+    end
+  end
+
+  def down
+    within_renalware_schema do
+      connection.execute("DROP FUNCTION new_hl7_message(text);")
+    end
+  end
+end

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.73"
+  VERSION = "2.0.74"
 end

data/lib/tasks/pathology.rake

@@ -25,5 +25,26 @@ namespace :pathology do
       hash = YAML.safe_load(*raw_message).symbolize_keys
       FeedJob.new(hash[:raw_message]).perform
     end
+
+    desc "In development only, enqueue a test HL7 message"
+    task enqueue_one: :environment do
+      raise NotImplementedError unless Rails.env.development?
+
+      # Load the example HL7 file.
+      path = Renalware::Engine.root.join("app", "jobs", "hl7_message_example.txt")
+      raw_message = File.read(path)
+
+      # Make sure line endings are \r and not \n or as that is how the HL7 looks
+      raw_message = raw_message.gsub /\n/, "\r"
+
+      # Replace the MSH date with now() to guarantee a unique message. not doing so results in
+      # an index violation becuase we calc am MD5 hash of the message and this has to be unique -
+      # this prevents us importing the same message twice.
+      raw_message = raw_message.gsub("20091112164645", Time.zone.now.strftime("%Y%m%d%H%M%S"))
+
+      ActiveRecord::Base.connection.execute(
+        "select renalware.new_hl7_message('#{raw_message}'::text);"
+      )
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.73
+  version: 2.0.74
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-28 00:00:00.000000000 Z
+date: 2019-04-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1343,6 +1343,7 @@ files:
 - app/inputs/user_picker_input.rb
 - app/jobs/application_job.rb
 - app/jobs/feed_job.rb
+- app/jobs/hl7_message_example.txt
 - app/jobs/hl7_message_example.yml
 - app/jobs/refresh_materialized_view_job.rb
 - app/jobs/renalware/events/save_pdf_event_to_file_job.rb
@@ -2884,6 +2885,7 @@ files:
 - config/initializers/simple_form_clock_picker.rb
 - config/initializers/simple_form_datepicker.rb
 - config/initializers/simple_form_foundation.rb
+- config/initializers/simple_form_wrappers.rb
 - config/initializers/validates_timeliness.rb
 - config/initializers/wicked_pdf.rb
 - config/initializers/wrap_parameters.rb
@@ -3028,6 +3030,7 @@ files:
 - db/functions/import_practice_memberships_csv_v01.sql
 - db/functions/import_practice_memberships_csv_v02.sql
 - db/functions/import_practices_csv_v01.sql
+- db/functions/new_hl7_message_v01.sql
 - db/functions/preprocess_hl7_message_v01.sql
 - db/functions/preprocess_hl7_message_v02.sql
 - db/functions/pseudo_encrypt_v01.sql
@@ -3456,6 +3459,7 @@ files:
 - db/migrate/20190218142207_add_filename_prefix_to_event_types.rb
 - 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/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb