renalware-core 2.0.0.pre.beta8 → 2.0.0.pre.beta9

data/db/views/reporting_anaemia_audit_v01.sql

@@ -0,0 +1,41 @@
+
+--explain analyze
+select
+  modality_desc       modality,
+  count(e1.patient_id)   count_patients,
+  round(avg(hgb),2)    avg_hgb,
+  round(count(hgb_gt_eq_10) / greatest(count(hgb), 1.0) * 100.0, 2) pct_hgb_gt_eq_10,
+  round(count(hgb_gt_eq_11) / greatest(count(hgb), 1.0) * 100.0, 2) pct_hgb_gt_eq_11,
+  round(count(hgb_gt_eq_13) / greatest(count(hgb), 1.0) * 100.0, 2) pct_hgb_gt_eq_13,
+  round(avg(fer),2) avg_fer,
+  round(count(fer_gt_eq_150) / greatest(count(fer), 1.0) * 100.0, 2) pct_fer_gt_eq_150,
+  coalesce(sum(immunosuppressants.ct), 0)::integer as count_epo,
+  coalesce(sum(mircer.ct), 0)::integer as count_mircer,
+  coalesce(sum(neo.ct), 0)::integer as count_neo,
+  coalesce(sum(ara.ct), 0)::integer as count_ara
+  from (
+    select
+    p.id patient_id,
+    md.name modality_desc
+    from patients p
+    inner join modality_modalities m on m.patient_id = p.id
+    inner join modality_descriptions md on m.description_id = md.id
+    where m.ended_on is null or m.ended_on > current_timestamp
+  ) e1
+  full join (select mcp.patient_id, count(distinct mcp.drug_id) as ct from medication_current_prescriptions mcp where drug_type_code = 'immunosuppressant' group by mcp.patient_id) as immunosuppressants
+  on e1.patient_id = immunosuppressants.patient_id
+  full join (select mcp.patient_id, count(distinct mcp.drug_id) as ct from medication_current_prescriptions mcp where drug_name like 'Mircer%' group by mcp.patient_id) as mircer
+  on e1.patient_id = mircer.patient_id
+  full join (select mcp.patient_id, count(distinct mcp.drug_id) as ct from medication_current_prescriptions mcp where drug_name like 'Neo%' group by mcp.patient_id) as neo
+  on e1.patient_id = neo.patient_id
+  full join (select mcp.patient_id, count(distinct mcp.drug_id) as ct from medication_current_prescriptions mcp where drug_name like 'Ara%' group by mcp.patient_id) as ara
+  on e1.patient_id = ara.patient_id
+
+  left join lateral (select result::decimal hgb from pathology_current_observations where description_code = 'HGB' and patient_id = e1.patient_id) e2 ON true
+  left join lateral (select result::decimal fer from pathology_current_observations where description_code = 'FER' and patient_id = e1.patient_id) e3 ON true
+  left join lateral (select hgb hgb_gt_eq_10 where hgb >= 10) e4 ON true
+  left join lateral (select hgb hgb_gt_eq_11 where hgb >= 11) e5 ON true
+  left join lateral (select hgb hgb_gt_eq_13 where hgb >= 13) e6 ON true
+  left join lateral (select fer fer_gt_eq_150 where fer >= 150) e7 ON true
+  where modality_desc in ('HD','PD','Transplant', 'LCC', 'Nephrology')
+  group by modality_desc

data/db/views/reporting_bone_audit_v01.sql

@@ -0,0 +1,32 @@
+-- Note that in the example of
+-- greatest(count(cca_2_1_to_2_4), 1) we default to a 1 if count is 0 which you think
+-- would ff
+select
+  modality_desc       modality,
+  count(patient_id)   patient_count,
+  round(avg(cca),2)   avg_cca,
+  round(count(cca_2_1_to_2_4) / greatest(count(cca), 1.0) * 100.0, 2) pct_cca_2_1_to_2_4,
+  round(count(pth_gt_300) / greatest(count(pth), 1.0) * 100.0, 2)         pct_pth_gt_300,
+  round(count(pth_gt_800) / greatest(count(pth), 1.0) * 100.0, 2)         pct_pth_gt_800_pct,
+  round(avg(phos),2)  avg_phos,
+  max(phos)           max_phos,
+  round(count(phos_lt_1_8)   / greatest(count(phos), 1.0) * 100.0, 2) pct_phos_lt_1_8
+
+  from (
+    select
+    p.id patient_id,
+    md.name modality_desc
+    from patients p
+    inner join modality_modalities m on m.patient_id = p.id
+    inner join modality_descriptions md on m.description_id = md.id
+  ) e1
+  left join lateral (select result::decimal pth  from pathology_current_observations where description_code = 'PTH'  and patient_id = e1.patient_id) e2 ON true
+  left join lateral (select result::decimal phos from pathology_current_observations where description_code = 'PHOS' and patient_id = e1.patient_id) e3 ON true
+  left join lateral (select result::decimal cca  from pathology_current_observations where description_code = 'CCA'  and patient_id = e1.patient_id) e4 ON true
+  left join lateral (select phos phos_lt_1_8 where phos < 1.8) e5 ON true
+  left join lateral (select pth pth_gt_800 where pth > 800) e6 ON true
+  left join lateral (select pth pth_gt_300 where pth > 300) e7 ON true
+  left join lateral (select cca cca_2_1_to_2_4 where cca between 2.1 and 2.4) e8 ON true
+  where modality_desc in ('HD','PD','Transplant', 'LCC')
+  group by modality_desc
+

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.beta8".freeze
+  VERSION = "2.0.0.pre.beta9".freeze
 end

data/spec/factories/deaths/cause.rb

@@ -1,5 +1,5 @@
 FactoryGirl.define do
-  factory :cause, class: "Renalware::Deaths::Cause" do
+  factory :cause_of_death, class: "Renalware::Deaths::Cause" do
     code "12"
     description "Hyperkalaemia"
   end

data/spec/factories/drugs/drug.rb

@@ -1,5 +1,11 @@
 FactoryGirl.define do
   factory :drug, class: "Renalware::Drugs::Drug" do
     name "Blue Pill"
+
+    trait :immunosuppressant do
+      after(:create) do |instance|
+        instance.drug_types << create(:drug_type, :immunosuppressant)
+      end
+    end
   end
 end

data/spec/factories/drugs/drug_types.rb

@@ -2,5 +2,10 @@ FactoryGirl.define do
   factory :drug_type, class: "Renalware::Drugs::Type" do
     code "immuno"
     name "Immunosuppressant"
+
+    trait :immunosuppressant do
+      code "immunosuppressant"
+      name "Immunosuppressant"
+    end
   end
 end

data/spec/factories/hospitals/wards.rb

@@ -0,0 +1,9 @@
+FactoryGirl.define do
+  factory :hospital_ward, class: "Renalware::Hospitals::Ward" do
+    initialize_with do
+      Renalware::Hospitals::Ward.find_or_create_by!(name: name, hospital_unit: hospital_unit)
+    end
+    hospital_unit
+    name "Ward A"
+  end
+end

data/spec/factories/modalities/modality_descriptions.rb

@@ -1,26 +1,22 @@
 FactoryGirl.define do
   factory :modality_description, class: "Renalware::Modalities::Description" do
-    name "CAPD (disconnect)"
+    name "unspecific modality description not set in factory"
 
     initialize_with { Renalware::Modalities::Description.find_or_create_by(name: name) }
 
-    trait :capd_standard do
-      name "CAPD (standard)"
-    end
-    trait :ccpd_6_nights do
-      name "CCPD (<6 nights/wk)"
-    end
-
     trait :pd do
       name "PD"
+      type "Renalware::PD::ModalityDescription"
     end
 
     trait :hd do
       name "HD"
+      type "Renalware::HD::ModalityDescription"
     end
 
     trait :transplant do
       name "Transplant"
+      type "Renalware::Transplants::RecipientModalityDescription"
     end
 
     trait :lcc do
@@ -29,6 +25,12 @@ FactoryGirl.define do
 
     trait :death do
       name "Death"
+      type "Renalware::Deaths::ModalityDescription"
+    end
+
+    trait :live_donor do
+      name "Live Donor"
+      type "Renalware::Transplants::DonorModalityDescription"
     end
   end
 end

data/spec/factories/patients/ethnicities.rb

@@ -2,5 +2,8 @@ FactoryGirl.define do
   factory :ethnicity, class: "Renalware::Patients::Ethnicity" do
     name "White - British"
     rr18_code "A"
+
+    trait :white_british do
+    end
   end
 end

data/spec/factories/patients/languages.rb

@@ -1,5 +1,16 @@
 FactoryGirl.define do
-  factory :patients_language, class: "Renalware::Patients::Language" do
+  factory :language, class: "Renalware::Patients::Language" do
     name "English"
+    code "en"
+
+    trait :english do
+      name "English"
+      code "en"
+    end
+
+    trait :aftrikaans do
+      name "Afrikaans"
+      code "af"
+    end
   end
 end

data/spec/factories/renal/aki_alert_actions.rb

@@ -0,0 +1,5 @@
+FactoryGirl.define do
+  factory :aki_alert_action, class: "Renalware::Renal::AKIAlertAction" do
+    name "IP Review"
+  end
+end

data/spec/factories/renal/aki_alerts.rb

@@ -0,0 +1,9 @@
+FactoryGirl.define do
+  factory :aki_alert, class: "Renalware::Renal::AKIAlert" do
+    accountable
+    notes "Some notes"
+    hotlist false
+    association :action, factory: :aki_alert_action
+    hospital_ward
+  end
+end

data/spec/factories/reporting/audits.rb

@@ -1,7 +1,7 @@
 FactoryGirl.define do
   factory :audit, class: "Renalware::Reporting::Audit" do
     name "Letters Authors"
-    materialized_view_name "audit_letter_authors"
+    view_name "audit_letter_authors"
     refresh_schedule "1 0 * * *"
     display_configuration "{}"
   end

data/spec/factories/system/addresses.rb

@@ -5,7 +5,7 @@ FactoryGirl.define do
     street_3 "Brownswater"
     town "Windsor"
     county "Berkshire"
-    country "England"
+    country { Renalware::System::Country.find_by(alpha2: "GB") }
     postcode "NW1 6BB"
   end
 end

data/spec/factories/system/countries.rb

@@ -0,0 +1,15 @@
+FactoryGirl.define do
+  factory :country, class: "Renalware::System::Country" do
+    factory :united_kingdom do
+      name "United Kingdom"
+      alpha2 "GB"
+      alpha3 "GBR"
+    end
+
+    factory :algeria do
+      name "Algeria"
+      alpha2 "DZ"
+      alpha3 "DZA"
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.0.pre.beta8
+  version: 2.0.0.pre.beta9
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-09-25 00:00:00.000000000 Z
+date: 2017-10-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -1080,14 +1080,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.49.0
+        version: 0.50.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.49.0
+        version: 0.50.0
 - !ruby/object:Gem::Dependency
   name: shoulda-matchers
   requirement: !ruby/object:Gem::Requirement
@@ -1374,6 +1374,7 @@ files:
 - app/controllers/renalware/pd/training_sessions_controller.rb
 - app/controllers/renalware/problems/notes_controller.rb
 - app/controllers/renalware/problems/problems_controller.rb
+- app/controllers/renalware/renal/aki_alerts_controller.rb
 - app/controllers/renalware/renal/base_controller.rb
 - app/controllers/renalware/renal/prd_descriptions_controller.rb
 - app/controllers/renalware/renal/profiles_controller.rb
@@ -1605,6 +1606,7 @@ files:
 - app/models/renalware/hospitals.rb
 - app/models/renalware/hospitals/centre.rb
 - app/models/renalware/hospitals/unit.rb
+- app/models/renalware/hospitals/ward.rb
 - app/models/renalware/letters.rb
 - app/models/renalware/letters/approve_letter.rb
 - app/models/renalware/letters/archive.rb
@@ -1811,6 +1813,8 @@ files:
 - app/models/renalware/problems/problem.rb
 - app/models/renalware/problems/version.rb
 - app/models/renalware/renal.rb
+- app/models/renalware/renal/aki_alert.rb
+- app/models/renalware/renal/aki_alert_action.rb
 - app/models/renalware/renal/patient.rb
 - app/models/renalware/renal/prd_description.rb
 - app/models/renalware/renal/prd_descriptions/search_query.rb
@@ -1825,6 +1829,7 @@ files:
 - app/models/renalware/snippets/snippet_query.rb
 - app/models/renalware/snippets/user.rb
 - app/models/renalware/system.rb
+- app/models/renalware/system/country.rb
 - app/models/renalware/system/render_liquid_template.rb
 - app/models/renalware/system/template.rb
 - app/models/renalware/system/update_user.rb
@@ -1895,6 +1900,7 @@ files:
 - app/policies/renalware/pd/regime_policy.rb
 - app/policies/renalware/pd/training_session_policy.rb
 - app/policies/renalware/problems/problem_policy.rb
+- app/policies/renalware/renal/aki_alert_policy.rb
 - app/policies/renalware/reporting/audit_policy.rb
 - app/policies/renalware/snippets/snippet_policy.rb
 - app/policies/renalware/transplants/donor_stage_policy.rb
@@ -2001,7 +2007,6 @@ files:
 - app/validators/renalware/patients/temperature_validator.rb
 - app/validators/renalware/patients/weight_validator.rb
 - app/values/renalware/address.rb
-- app/values/renalware/country.rb
 - app/values/renalware/duration.rb
 - app/values/renalware/gender.rb
 - app/values/renalware/time_of_day.rb
@@ -2064,6 +2069,7 @@ files:
 - app/views/renalware/api/ukrdc/patients/_encounters.xml.builder
 - app/views/renalware/api/ukrdc/patients/_family_histories.xml.builder
 - app/views/renalware/api/ukrdc/patients/_lab_orders.xml.builder
+- app/views/renalware/api/ukrdc/patients/_medications.xml.builder
 - app/views/renalware/api/ukrdc/patients/_name.xml.builder
 - app/views/renalware/api/ukrdc/patients/_observations.xml.builder
 - app/views/renalware/api/ukrdc/patients/_patient.xml.builder
@@ -2071,6 +2077,8 @@ files:
 - app/views/renalware/api/ukrdc/patients/_sending_facility.xml.builder
 - app/views/renalware/api/ukrdc/patients/_social_histories.xml.builder
 - app/views/renalware/api/ukrdc/patients/_surveys.xml.builder
+- app/views/renalware/api/ukrdc/patients/diagnoses/_cause_of_death.xml.builder
+- app/views/renalware/api/ukrdc/patients/encounters/_hd_session.xml.builder
 - app/views/renalware/api/ukrdc/patients/lab_orders/_lab_order.xml.builder
 - app/views/renalware/api/ukrdc/patients/lab_orders/_result_item.xml.builder
 - app/views/renalware/api/ukrdc/patients/observations/_blood_pressure.xml.builder
@@ -2563,6 +2571,9 @@ files:
 - app/views/renalware/problems/problems/index.html.slim
 - app/views/renalware/problems/problems/new.html.slim
 - app/views/renalware/problems/problems/show.html.slim
+- app/views/renalware/renal/aki_alerts/_filters.html.slim
+- app/views/renalware/renal/aki_alerts/edit.html.slim
+- app/views/renalware/renal/aki_alerts/index.html.slim
 - app/views/renalware/renal/prd_descriptions/search.json.jbuilder
 - app/views/renalware/renal/profiles/_form.html.slim
 - app/views/renalware/renal/profiles/_mini.html.slim
@@ -2692,7 +2703,6 @@ files:
 - app/views/renalware/transplants/wait_lists/show.html.slim
 - config/autoprefixer.yml
 - config/cable.yml
-- config/countries.csv
 - config/cucumber.yml
 - config/initializers/application_controller_renderer.rb
 - config/initializers/assets.rb
@@ -2788,7 +2798,8 @@ files:
 - config/locales/renalware/pd/training_sessions.en.yml
 - config/locales/renalware/pd/treatments.en.yml
 - config/locales/renalware/problems/note.yml
-- config/locales/renalware/renal/profile.yml
+- config/locales/renalware/renal/aki_alerts.en.yml
+- config/locales/renalware/renal/profile.en.yml
 - config/locales/renalware/reporting/audit.en.yml
 - config/locales/renalware/shared.yml
 - config/locales/renalware/snippets/snippets.en.yml
@@ -3052,7 +3063,6 @@ files:
 - db/migrate/20170705135512_create_reporting_hd_blood_pressures_audit.rb
 - db/migrate/20170705150913_create_reporting_hd_overall_audit.rb
 - db/migrate/20170705160726_add_descriptions_to_reporting_audits.rb
-- db/migrate/20170706120643_create_reporting_data_sources.rb
 - db/migrate/20170707110155_rename_access_plans_to_access_plan_types.rb
 - db/migrate/20170711140607_update_audit_letters_authors_to_version2.rb
 - db/migrate/20170711140926_update_hd_overall_audit_to_version2.rb
@@ -3072,6 +3082,19 @@ files:
 - db/migrate/20170911133224_add_type_to_messaging_messages.rb
 - db/migrate/20170912092135_create_letters_electronic_receipts.rb
 - db/migrate/20170920113628_create_admissions_requests.rb
+- db/migrate/20170925161033_add_code_to_patient_langauges.rb
+- db/migrate/20170925182738_add_rr_code_to_medication_routes.rb
+- db/migrate/20170926081426_create_countries.rb
+- db/migrate/20170926132845_add_country_of_birth_to_patients.rb
+- db/migrate/20171002175804_add_rr_columns_to_transplant_registration_status_descriptions.rb
+- db/migrate/20171003093347_create_hospital_wards.rb
+- db/migrate/20171003111228_create_aki_alert_actions.rb
+- db/migrate/20171003122425_create_renal_aki_alerts.rb
+- db/migrate/20171005081224_create_reporting_bone_audit.rb
+- db/migrate/20171005091202_reporting_audit_changes.rb
+- db/migrate/20171005130109_create_medication_current_prescriptions.rb
+- db/migrate/20171005144505_create_reporting_anaemia_audit.rb
+- db/migrate/20171009104106_add_legacy_patient_id_to_patients.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3092,10 +3115,8 @@ files:
 - db/seeds/default/drugs/drug_drug_types.csv
 - db/seeds/default/drugs/drugs.csv
 - db/seeds/default/drugs/seeds.rb
-- db/seeds/default/events/event_types_blt.csv
-- db/seeds/default/events/event_types_local.rb
-- db/seeds/default/events/event_types_required.csv
-- db/seeds/default/events/event_types_required.rb
+- db/seeds/default/events/event_types.csv
+- db/seeds/default/events/event_types.rb
 - db/seeds/default/events/seeds.rb
 - db/seeds/default/hd/cannulation_types.rb
 - db/seeds/default/hd/dialysers.rb
@@ -3155,6 +3176,8 @@ files:
 - db/seeds/default/reporting/audits.yml
 - db/seeds/default/reporting/seeds.rb
 - db/seeds/default/seeds.rb
+- db/seeds/default/system/countries.csv
+- db/seeds/default/system/countries.rb
 - db/seeds/default/system/roles.rb
 - db/seeds/default/system/seeds.rb
 - db/seeds/default/system/users.rb
@@ -3166,6 +3189,7 @@ files:
 - db/seeds/seeds_helper.rb
 - db/static.obsolete/medication_routes.yml
 - db/structure.sql
+- db/views/medication_current_prescriptions_v01.sql
 - db/views/pathology_current_key_observation_sets_v01.sql
 - db/views/pathology_current_key_observation_sets_v02.sql
 - db/views/pathology_current_observations_v01.sql
@@ -3173,7 +3197,8 @@ files:
 - db/views/patient_summaries_v02.sql
 - db/views/patient_summaries_v03.sql
 - db/views/patient_summaries_v04.sql
-- db/views/reporting_data_sources_v01.sql
+- db/views/reporting_anaemia_audit_v01.sql
+- db/views/reporting_bone_audit_v01.sql
 - db/views/reporting_hd_blood_pressures_audit_v01.sql
 - db/views/reporting_hd_overall_audit_v01.sql
 - db/views/reporting_hd_overall_audit_v02.sql
@@ -3260,6 +3285,7 @@ files:
 - spec/factories/hd/stations.rb
 - spec/factories/hospitals/centres.rb
 - spec/factories/hospitals/units.rb
+- spec/factories/hospitals/wards.rb
 - spec/factories/letters/archives.rb
 - spec/factories/letters/contact_descriptions.rb
 - spec/factories/letters/contacts.rb
@@ -3323,6 +3349,8 @@ files:
 - spec/factories/pd/training_sites.rb
 - spec/factories/pd/training_types.rb
 - spec/factories/problems/problems.rb
+- spec/factories/renal/aki_alert_actions.rb
+- spec/factories/renal/aki_alerts.rb
 - spec/factories/renal/patients.rb
 - spec/factories/renal/prd_description.rb
 - spec/factories/renal/profiles.rb
@@ -3331,6 +3359,7 @@ files:
 - spec/factories/snippets/snippets.rb
 - spec/factories/snippets/users.rb
 - spec/factories/system/addresses.rb
+- spec/factories/system/countries.rb
 - spec/factories/system/roles.rb
 - spec/factories/system/templates.rb
 - spec/factories/system/users.rb