renalware-core 2.0.89 → 2.0.90

data/app/views/renalware/api/ukrdc/patients/procedures/_dialysis_session.xml.builder

@@ -32,7 +32,7 @@ xml.DialysisSession(
   xml.Attributes do
     xml.QHD19 session.had_intradialytic_hypotension?
     xml.QHD20 session.access_rr02_code
-    xml.QHD21 session.access_side_rr40_code
+    xml.QHD21 session.access_rr41_code
     xml.QHD22 "N" # Access in two sites simultaneously
     xml.QHD30 session.blood_flow
     xml.QHD31 session.duration_in_minutes # Time Dialysed in Minutes

data/app/views/renalware/api/ukrdc/patients/treatments/_generic.xml.builder

@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+
+xml = builder
+
+xml.Treatment do
+  xml.EncounterNumber treatment.modality_id
+  xml.EncounterType "N"
+  xml.FromTime treatment.started_on&.iso8601
+  xml.ToTime(treatment.ended_on&.iso8601) if treatment.ended_on.present?
+
+  xml.AdmitReason do
+    xml.CodingStandard "CF_RR7_TREATMENT"
+    xml.Code treatment.modality_code.txt_code
+  end
+end

data/app/views/renalware/api/ukrdc/patients/treatments/_hd.xml.builder

@@ -0,0 +1,30 @@
+# frozen_string_literal: true
+
+xml = builder
+
+xml.Treatment do
+  xml.EncounterNumber [treatment.modality_id, treatment.hd_profile_id].compact.join("-")
+  xml.EncounterType "N"
+  xml.FromTime treatment.started_on&.iso8601
+  xml.ToTime(treatment.ended_on&.iso8601) if treatment.ended_on.present?
+
+  if treatment.hospital_unit.present?
+    xml.HealthCareFacility do
+      xml.CodingStandard "ODS"
+      xml.Code treatment.hospital_unit.unit_code
+    end
+  end
+
+  xml.AdmitReason do
+    xml.CodingStandard "CF_RR7_TREATMENT"
+    xml.Code treatment.modality_code.txt_code
+  end
+
+  # HD
+  rr8 = treatment.hospital_unit&.unit_type_rr8
+  if rr8.present?
+    xml.Attributes do
+      xml.QBL05 rr8 # eg HOME
+    end
+  end
+end

data/app/views/renalware/api/ukrdc/patients/treatments/_pd.xml.builder

@@ -0,0 +1,13 @@
+xml = builder
+
+xml.Treatment do
+  xml.EncounterNumber [treatment.modality_id,treatment.pd_regime_id].compact.join("-")
+  xml.EncounterType "N"
+  xml.FromTime treatment.started_on&.iso8601
+  xml.ToTime(treatment.ended_on&.iso8601) if treatment.ended_on.present?
+
+  xml.AdmitReason do
+    xml.CodingStandard "CF_RR7_TREATMENT"
+    xml.Code treatment.modality_code.txt_code
+  end
+end

data/db/migrate/20190705083727_alter_ukrdc_treatments.rb

@@ -0,0 +1,8 @@
+class AlterUKRDCTreatments < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_reference :ukrdc_treatments, :hd_profile, index: true, foreign_key: true
+      add_reference :ukrdc_treatments, :pd_regime, index: true, foreign_key: true
+    end
+  end
+end

data/db/migrate/20190705105921_create_hd_profile_for_modalites.rb

@@ -0,0 +1,7 @@
+class CreateHDProfileForModalites < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_view :hd_profile_for_modalities
+    end
+  end
+end

data/db/migrate/20190709101610_create_pd_regime_for_modalities.rb

@@ -0,0 +1,7 @@
+class CreatePDRegimeForModalities < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_view :pd_regime_for_modalities
+    end
+  end
+end

data/db/views/hd_profile_for_modalities_v01.sql

@@ -0,0 +1,63 @@
+-- This view is HD-specific, but really serevers to make UKRDC export easier.
+-- It attempts to solve the gnarly problem of finding the hd profile associated with the start
+-- of an HD modality. For example if a patient goes on to HD, an HD modality row is created.
+-- However it could be a couple of weeks before they have an HD profile setup. This view
+-- attempts to find that association.
+-- We need to know the association so when we export the modality as a UKRDC
+-- Treatment, we can pull in the site, hd_type etc from the hd profile.
+-- Sometimes we will not be able to resolve a profile for the patient however.
+WITH hd_modalities AS (
+    SELECT
+        m.patient_id,
+        m.id AS modality_id,
+        m.started_on,
+        m.ended_on
+    FROM
+        modality_modalities m
+        INNER JOIN modality_descriptions md ON md.id = m.description_id
+    WHERE
+        md.name = 'HD'
+),
+distinct_hd_profiles AS (
+    -- selects the last profile created for a patient on any one day as there can be
+    -- many iterations of a profile as it is refined/edited by the clinician.
+    -- We can assume the final iteration on that day is the final one.
+    -- If it was changed the next day then no bother
+    SELECT DISTINCT ON (patient_id, created_at::date)
+        id AS hd_profile_id,
+        patient_id,
+        COALESCE(prescribed_on, created_at)::date AS effective_prescribed_on,
+        prescribed_on,
+        created_at::date AS created_on,
+        created_at,
+        deactivated_at,
+        active
+    FROM
+        hd_profiles
+    ORDER BY
+        -- Note the last order by (created_at) is required otherwsie we are only ordering by
+        -- date - and since there might be several on the same day, the order is undefined.
+        -- Note we cannot use created_at as the 2nd sort as its type has to match the distinct on..
+        -- so we have to cast it to a date here. Feel free to run just this select statmment to
+        -- understand the limitations
+        patient_id, created_at::date, created_at desc
+)
+-- Note in this last select we select the earlist hd profile we find that matches
+-- as sometimes there can be > 1 hd profile returned from distinct_hd_profiles
+SELECT
+    m.*,
+    (
+        SELECT
+            hd_profile_id
+        FROM
+            distinct_hd_profiles hp
+        WHERE
+            hp.patient_id = m.patient_id
+            AND(hp.deactivated_at IS NULL OR deactivated_at > m.started_on)
+            -- No longer limiting the look ahead to 2 weeks - there is now no future limit
+            -- AND hp.created_on <= (started_on + interval '2 weeks')
+        ORDER BY
+            created_at ASC
+        LIMIT 1) AS hd_profile_id
+FROM
+    hd_modalities m;

data/db/views/pd_regime_for_modalities_v01.sql

@@ -0,0 +1,60 @@
+-- This view is PD-specific, but really serevers to make UKRDC export easier.
+-- It attempts to solve the gnarly problem of finding the pd regime associated with the start
+-- of a PD modality. For example if a patient goes on to PD, a PD regime row is created.
+-- However it could be a couple of weeks before they have a the PD regime setup. This view
+-- attempts to find that association.
+-- We need to know this association so when we export the modality as a UKRDC
+-- Treatment, we can pull in the pd type (CAPD etc) from the regime.
+-- Sometimes we will not be able to resolve a regime for the patient however.
+
+WITH pd_modalities AS (
+    SELECT
+        m.patient_id,
+        m.id AS modality_id,
+        m.started_on,
+        m.ended_on
+    FROM
+        modality_modalities m
+        INNER JOIN modality_descriptions md ON md.id = m.description_id
+    WHERE
+        md.name = 'PD'
+),
+distinct_pd_regimes AS (
+    -- selects the last regime created for a patient on any one day as there can be
+    -- many iterations of a regime as it is refined/edited by the clinician.
+    -- We can assume the final iteration on that day is the final one.
+    -- If it was changed the next day then no bother
+    SELECT DISTINCT ON (patient_id, start_date)
+        id AS pd_regime_id,
+        patient_id,
+        start_date,
+        end_date,
+        created_at
+    FROM
+        pd_regimes
+    ORDER BY
+        -- Note the last order by (created_at) is required otherwsie we are only ordering by
+        -- date - and since there might be several on the same day, the order is undefined.
+        -- Feel free to run just this select statmment to understand the limitations
+        patient_id, start_date asc, created_at desc
+)
+-- Note in this last select we select the earlist pd regime we find that matches
+-- as sometimes there can be > 1 regime returned from distinct_pd_regimes
+SELECT
+    m.*,
+    (
+        SELECT
+            pd_regime_id
+        FROM
+            distinct_pd_regimes pdr
+        WHERE
+            pdr.patient_id = m.patient_id
+            AND (pdr.end_date IS NULL OR pdr.end_date > m.started_on)
+            -- No longer limiting our look-ahead search for a regime to a specific time limit -
+            -- instead we just keep looking til we find the first regime
+            -- AND pdr.start_date <= (m.started_on + interval '2 weeks')::date
+        ORDER BY
+            created_at ASC
+        LIMIT 1) AS pd_regime_id
+FROM
+    pd_modalities m order by m.patient_id;

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.89"
+  VERSION = "2.0.90"
 end

data/lib/tasks/ukrdc.rake

@@ -28,10 +28,11 @@ namespace :ukrdc do
 
          bundle exec rake ukrdc:export changed_since=2018-02-23 patient_ids=1,2
   DESC
-  task :export => :environment do |_task, args|
+  task export: :environment do |_task, _args|
     logger           = ActiveSupport::TaggedLogging.new(Logger.new(STDOUT))
     logger.level     = Logger::INFO
     Rails.logger     = logger
+    # Renalware::UKRDC::TreatmentTimeline::GenerateTreatments.call
     Renalware::UKRDC::CreateEncryptedPatientXMLFiles.new(
       changed_since: ENV["changed_since"],
       patient_ids: ENV.fetch("patient_ids", "").split(",").map(&:to_i),

data/spec/factories/hd/profiles.rb

@@ -16,5 +16,29 @@ FactoryBot.define do
         }
       }
     }
+
+    trait :hd do
+      # noop
+    end
+
+    trait :hdf_pre do
+      document {
+        {
+          dialysis: {
+            hd_type: :hdf_pre
+          }
+        }
+      }
+    end
+
+    trait :hdf_post do
+      document {
+        {
+          dialysis: {
+            hd_type: :hdf_post
+          }
+        }
+      }
+    end
   end
 end

data/spec/factories/pd/pd_regimes.rb

@@ -13,6 +13,10 @@ FactoryBot.define do
     amino_acid_volume { 40 }
     icodextrin_volume { 50 }
     add_hd { false }
+
+    factory :capd_assisted_regime do
+      treatment { "CAPD Dry Day Assisted" }
+    end
   end
 
   factory :apd_regime, class: "Renalware::PD::APDRegime" do
@@ -33,5 +37,9 @@ FactoryBot.define do
     no_cycles_per_apd { 7 }
     overnight_volume { 5100 }
     apd_machine_pac { "123-4567-890" }
+
+    factory :apd_assisted_regime do
+      treatment { "APD Dry Day Assisted" }
+    end
   end
 end

data/spec/factories/ukrdc/modality_codes.rb

@@ -13,5 +13,35 @@ FactoryBot.define do
       txt_code { 3 }
       qbl_code { 3 }
     end
+
+    trait :pd do
+      description { "Peritoneal dialysis – type unknown" }
+      txt_code { 19 }
+      qbl_code { 19 }
+    end
+
+    trait :apd do
+      description { "APD" }
+      txt_code { 12 }
+      qbl_code { 12 }
+    end
+
+    trait :apd_assisted do
+      description { "Assisted APD" }
+      txt_code { 121 }
+      qbl_code { 121 }
+    end
+
+    trait :capd do
+      description { "CAPD" }
+      txt_code { 11 }
+      qbl_code { 11 }
+    end
+
+    trait :capd_assisted do
+      description { "Assisted CAPD" }
+      txt_code { 111 }
+      qbl_code { 111 }
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.89
+  version: 2.0.90
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-04 00:00:00.000000000 Z
+date: 2019-07-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -1497,6 +1497,8 @@ files:
 - app/models/renalware/hd/preference_set.rb
 - app/models/renalware/hd/prescription_administration.rb
 - app/models/renalware/hd/profile.rb
+- app/models/renalware/hd/profile_for_modality.rb
+- app/models/renalware/hd/profiles_in_date_range_query.rb
 - app/models/renalware/hd/provider.rb
 - app/models/renalware/hd/provider_unit.rb
 - app/models/renalware/hd/revise_hd_profile.rb
@@ -1753,7 +1755,9 @@ files:
 - app/models/renalware/pd/pet_adequacy_result.rb
 - app/models/renalware/pd/regime.rb
 - app/models/renalware/pd/regime_bag.rb
+- app/models/renalware/pd/regime_for_modality.rb
 - app/models/renalware/pd/regime_termination.rb
+- app/models/renalware/pd/regimes_in_date_range_query.rb
 - app/models/renalware/pd/revise_regime.rb
 - app/models/renalware/pd/save_peritonitis_episode.rb
 - app/models/renalware/pd/system.rb
@@ -1845,13 +1849,13 @@ files:
 - app/models/renalware/ukrdc/treatment_timeline/generate_timeline.rb
 - app/models/renalware/ukrdc/treatment_timeline/generate_treatments.rb
 - app/models/renalware/ukrdc/treatment_timeline/generator_factory.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/deaths_timeline.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/generic_timeline.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/hd_timeline.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/low_clearance_timelinex.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/pd_timeline.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/transplants_donor_timeline.rb
-- app/models/renalware/ukrdc/treatment_timeline/generators/transplants_recipient_timeline.rb
+- app/models/renalware/ukrdc/treatment_timeline/generic/generator.rb
+- app/models/renalware/ukrdc/treatment_timeline/hd/generator.rb
+- app/models/renalware/ukrdc/treatment_timeline/hd/modality_code_map.rb
+- app/models/renalware/ukrdc/treatment_timeline/hd/profile_decorator.rb
+- app/models/renalware/ukrdc/treatment_timeline/pd/generator.rb
+- app/models/renalware/ukrdc/treatment_timeline/pd/modality_code_map.rb
+- app/models/renalware/ukrdc/treatment_timeline/pd/regime_decorator.rb
 - app/models/renalware/ukrdc/treatment_timeline/prepare_tables.rb
 - app/models/renalware/ukrdc/treatment_timeline/remap_model_table_names_to_their_prepared_equivalents.rb
 - app/models/renalware/ukrdc/xml_renderer.rb
@@ -2161,6 +2165,9 @@ files:
 - app/views/renalware/api/ukrdc/patients/procedures/_dialysis_session.xml.builder
 - app/views/renalware/api/ukrdc/patients/procedures/_transplant_operation.xml.builder
 - app/views/renalware/api/ukrdc/patients/show.xml.builder
+- app/views/renalware/api/ukrdc/patients/treatments/_generic.xml.builder
+- app/views/renalware/api/ukrdc/patients/treatments/_hd.xml.builder
+- app/views/renalware/api/ukrdc/patients/treatments/_pd.xml.builder
 - app/views/renalware/api/v1/medications/prescriptions/index.json.jbuilder
 - app/views/renalware/api/v1/patients/patients/index.json.jbuilder
 - app/views/renalware/api/v1/patients/patients/show.json.jbuilder
@@ -3520,6 +3527,9 @@ files:
 - db/migrate/20190611152859_add_fields_to_transplant_recipient_workup.rb
 - db/migrate/20190612124015_create_transplant_rejection_episodes.rb
 - db/migrate/20190617121528_create_transplant_rejection_treatments.rb
+- db/migrate/20190705083727_alter_ukrdc_treatments.rb
+- db/migrate/20190705105921_create_hd_profile_for_modalites.rb
+- db/migrate/20190709101610_create_pd_regime_for_modalities.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3607,6 +3617,7 @@ files:
 - db/triggers/update_current_observation_set_trigger_v01.sql
 - db/triggers/update_research_study_participants_trigger_v01.sql
 - db/views/hd_grouped_transmission_logs_v01.sql
+- db/views/hd_profile_for_modalities_v01.sql
 - db/views/hd_schedule_definition_filters_v01.sql
 - db/views/medication_current_prescriptions_v01.sql
 - db/views/pathology_current_key_observation_sets_v01.sql
@@ -3620,6 +3631,7 @@ files:
 - db/views/patient_summaries_v04.sql
 - db/views/patient_summaries_v05.sql
 - db/views/patient_summaries_v06.sql
+- db/views/pd_regime_for_modalities_v01.sql
 - db/views/reporting_anaemia_audit_v01.sql
 - db/views/reporting_bone_audit_v01.sql
 - db/views/reporting_daily_letters_v01.sql

data/app/models/renalware/ukrdc/treatment_timeline/generators/deaths_timeline.rb

@@ -1,17 +0,0 @@
-# frozen_string_literal: true
-
-require_dependency "renalware/ukrdc"
-
-module Renalware
-  module UKRDC
-    module TreatmentTimeline
-      module Generators
-        class DeathsTimeline
-          pattr_initialize :modality
-
-          def call; end
-        end
-      end
-    end
-  end
-end

data/app/models/renalware/ukrdc/treatment_timeline/generators/generic_timeline.rb

@@ -1,17 +0,0 @@
-# frozen_string_literal: true
-
-require_dependency "renalware/ukrdc"
-
-module Renalware
-  module UKRDC
-    module TreatmentTimeline
-      module Generators
-        class GenericTimeline
-          pattr_initialize :modality
-
-          def call; end
-        end
-      end
-    end
-  end
-end