renalware-core 2.0.0.pre.rc10 → 2.0.0.pre.rc11

data/db/migrate/20180213125734_update_fn_update_current_obs_set_trgger.rb

@@ -0,0 +1,9 @@
+class UpdateFnUpdateCurrentObsSetTrgger < ActiveRecord::Migration[5.1]
+  def up
+    load_function("update_current_observation_set_from_trigger_v04.sql")
+  end
+
+  def down
+    load_function("update_current_observation_set_from_trigger_v03.sql")
+  end
+end

data/db/migrate/20180214124317_add_cols_to_aki_alerts.rb

@@ -0,0 +1,9 @@
+class AddColsToAKIAlerts < ActiveRecord::Migration[5.1]
+  def change
+    add_column :renal_aki_alerts, :max_cre, :integer
+    add_column :renal_aki_alerts, :cre_date, :date
+    add_column :renal_aki_alerts, :max_aki, :integer
+    add_column :renal_aki_alerts, :aki_date, :date
+    remove_column :renal_aki_alerts, :string, :string
+  end
+end

data/db/migrate/20180216132741_disable_some_audits.rb

@@ -0,0 +1,8 @@
+class DisableSomeAudits < ActiveRecord::Migration[5.1]
+  def change
+    add_column :reporting_audits, :enabled, :boolean, null: false, default: true
+    connection.execute(
+      "update reporting_audits set enabled = false where name in ('Bone', 'Anaemia');"
+    )
+  end
+end

data/db/seeds/default/transplants/transplant_donor_stages.rb

@@ -12,7 +12,7 @@ module Renalware
     ]
 
     names.each_with_index do |name, index|
-      Transplants::DonorStagePosition.find_or_create_by!(
+      Transplants::DonorStagePosition.find_or_create_by(
         name: name,
         position: index * 10
       )
@@ -30,7 +30,7 @@ module Renalware
     ]
 
     names.each_with_index do |name, index|
-      Transplants::DonorStageStatus.find_or_create_by!(
+      Transplants::DonorStageStatus.find_or_create_by(
         name: name,
         position: index * 10
       )

data/db/views/pathology_observation_digests_v01.sql

@@ -0,0 +1,20 @@
+/*
+Returns a jsonb hash of OBX results for each day a patient had an observation.
+
+Example output:
+
+patient_id  observation_date  observations
+------------------------------------------
+1           2018-02-02        {"CYA": "14"}
+1           2016-06-15        {"CMVDNA": "0.10"}
+1           2016-03-15        {"NA": "137", "TP": "74", "ALB": "48", "ALP": "71", ...
+1           2016-02-29        {"NA": "136", "TP": "78", "ALB": "47", "ALP": "71", ...
+*/
+
+select obs_req.patient_id, cast(observed_at as date) as observed_on,
+jsonb_object_agg(obs_desc.code, obs.result) results
+from pathology_observations obs
+inner join pathology_observation_requests obs_req on obs.request_id = obs_req.id
+inner join pathology_observation_descriptions obs_desc on obs.description_id = obs_desc.id
+group by patient_id, observed_on
+order by patient_id asc, observed_on desc;

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.rc10".freeze
+  VERSION = "2.0.0.pre.rc11".freeze
 end

data/spec/factories/pathology/observation_requests.rb

@@ -4,5 +4,36 @@ FactoryBot.define do
     requestor_order_number "123"
     requestor_name "Jane Doe"
     requested_at "2016-03-04 10:14:49"
+
+    trait :full_blood_count_with_observations do
+      association :description, factory: :pathology_request_description, code: "FBC"
+      after(:create) do |request|
+        %w(WBC HGB PLT).each do |obx_code|
+          desc = create(:pathology_observation_description, code: obx_code)
+          create(
+            :pathology_observation,
+            description: desc,
+            request: request,
+            observed_at: request.requested_at
+          )
+        end
+      end
+    end
+
+    trait :renal_live_urea_with_observations do
+      association :description, factory: :pathology_request_description, code: "RLU"
+      after(:create) do |request|
+        %w(NA POT URE).each do |obx_code|
+          desc = create(:pathology_observation_description, code: obx_code)
+          create(
+            :pathology_observation,
+            description: desc,
+            request: request,
+            observed_at: request.requested_at,
+            result: 1.0
+          )
+        end
+      end
+    end
   end
 end

data/spec/support/login_macros.rb

@@ -1,4 +1,8 @@
 module LoginMacros
+  def login_as_super_admin
+    login_user(:super_admin)
+  end
+
   def login_as_admin
     login_user(:admin)
   end
@@ -21,6 +25,4 @@ module LoginMacros
     end
     @current_user = user
   end
-
-  alias_method :login_as_super_admin, :login_user
 end

metadata

@@ -1,27 +1,27 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.0.pre.rc10
+  version: 2.0.0.pre.rc11
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-02-14 00:00:00.000000000 Z
+date: 2018-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
         version: 5.1.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
         version: 5.1.4
 - !ruby/object:Gem::Dependency
@@ -686,14 +686,14 @@ dependencies:
   name: simple_form
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
         version: 3.5.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
         version: 3.5.0
 - !ruby/object:Gem::Dependency
@@ -702,14 +702,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 2.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 2.0.1
 - !ruby/object:Gem::Dependency
   name: slim-rails
   requirement: !ruby/object:Gem::Requirement
@@ -965,6 +965,7 @@ files:
 - app/assets/stylesheets/renalware/modules/_reporting.scss
 - app/assets/stylesheets/renalware/modules/_snippets.scss
 - app/assets/stylesheets/renalware/modules/_transplants.scss
+- app/assets/stylesheets/renalware/modules/_users.scss
 - app/assets/stylesheets/renalware/partials/_animation.scss
 - app/assets/stylesheets/renalware/partials/_animations.scss
 - app/assets/stylesheets/renalware/partials/_autocomplete.scss
@@ -1006,13 +1007,16 @@ files:
 - app/controllers/renalware/accesses/plans_controller.rb
 - app/controllers/renalware/accesses/procedures_controller.rb
 - app/controllers/renalware/accesses/profiles_controller.rb
+- app/controllers/renalware/admin/cache_controller.rb
 - app/controllers/renalware/admin/feeds/files_controller.rb
 - app/controllers/renalware/admin/users_controller.rb
 - app/controllers/renalware/admissions/admissions_controller.rb
 - app/controllers/renalware/admissions/consults_controller.rb
 - app/controllers/renalware/admissions/patient_admissions_controller.rb
 - app/controllers/renalware/admissions/requests_controller.rb
+- app/controllers/renalware/api/token_authenticated_api_controller.rb
 - app/controllers/renalware/api/ukrdc/patients_controller.rb
+- app/controllers/renalware/api/v1/patients/patients_controller.rb
 - app/controllers/renalware/application_controller.rb
 - app/controllers/renalware/base_controller.rb
 - app/controllers/renalware/clinical/allergies_controller.rb
@@ -1281,6 +1285,7 @@ files:
 - app/models/renalware/accesses/site.rb
 - app/models/renalware/accesses/type.rb
 - app/models/renalware/accesses/version.rb
+- app/models/renalware/admin.rb
 - app/models/renalware/admissions.rb
 - app/models/renalware/admissions/admission.rb
 - app/models/renalware/admissions/admission_query.rb
@@ -1290,6 +1295,7 @@ files:
 - app/models/renalware/admissions/consult_site.rb
 - app/models/renalware/admissions/request.rb
 - app/models/renalware/admissions/request_reason.rb
+- app/models/renalware/api.rb
 - app/models/renalware/clinical.rb
 - app/models/renalware/clinical/allergy.rb
 - app/models/renalware/clinical/allergy_status_form.rb
@@ -1500,6 +1506,7 @@ files:
 - app/models/renalware/pathology/clinic.rb
 - app/models/renalware/pathology/consultant.rb
 - app/models/renalware/pathology/create_observation_requests.rb
+- app/models/renalware/pathology/create_observations_grouped_by_date_table.rb
 - app/models/renalware/pathology/current_observation.rb
 - app/models/renalware/pathology/current_observation_set.rb
 - app/models/renalware/pathology/current_observations_for_descriptions_query.rb
@@ -1511,11 +1518,14 @@ files:
 - app/models/renalware/pathology/observation_date_range.rb
 - app/models/renalware/pathology/observation_description.rb
 - app/models/renalware/pathology/observation_descriptions_by_code_query.rb
+- app/models/renalware/pathology/observation_digest.rb
 - app/models/renalware/pathology/observation_for_patient_observation_description_query.rb
 - app/models/renalware/pathology/observation_for_patient_request_description_query.rb
 - app/models/renalware/pathology/observation_request.rb
 - app/models/renalware/pathology/observation_requests_attributes_builder.rb
 - app/models/renalware/pathology/observations_for_descriptions_query.rb
+- app/models/renalware/pathology/observations_grouped_by_date_query.rb
+- app/models/renalware/pathology/observations_grouped_by_date_table.rb
 - app/models/renalware/pathology/observations_jsonb_serializer.rb
 - app/models/renalware/pathology/observations_within_date_range_query.rb
 - app/models/renalware/pathology/ordered_patient_query.rb
@@ -1685,6 +1695,7 @@ files:
 - app/models/renalware/virology/vaccination.rb
 - app/models/renalware/zip_archive.rb
 - app/policies/application_policy.rb
+- app/policies/renalware/admin/cache_policy.rb
 - app/policies/renalware/admissions/admission_policy.rb
 - app/policies/renalware/admissions/consult_policy.rb
 - app/policies/renalware/admissions/request_policy.rb
@@ -1758,6 +1769,7 @@ files:
 - app/presenters/renalware/address_presenter/block.rb
 - app/presenters/renalware/address_presenter/short.rb
 - app/presenters/renalware/address_presenter/single_line.rb
+- app/presenters/renalware/admin/users/summary_part.rb
 - app/presenters/renalware/admissions/admission_presenter.rb
 - app/presenters/renalware/admissions/consult_presenter.rb
 - app/presenters/renalware/admissions/summary_part.rb
@@ -1899,10 +1911,12 @@ files:
 - app/views/renalware/addresses/_address.html.slim
 - app/views/renalware/addresses/_contact_info.html.slim
 - app/views/renalware/addresses/_form.html.slim
+- app/views/renalware/admin/cache/show.html.slim
 - app/views/renalware/admin/feeds/files/index.html.slim
 - app/views/renalware/admin/user_mailer/approval.text.erb
 - app/views/renalware/admin/user_mailer/unexpiry.text.erb
 - app/views/renalware/admin/users/_filters.html.slim
+- app/views/renalware/admin/users/_summary_part.html.slim
 - app/views/renalware/admin/users/edit.html.slim
 - app/views/renalware/admin/users/index.html.slim
 - app/views/renalware/admissions/_summary_part.html.slim
@@ -1957,6 +1971,7 @@ files:
 - app/views/renalware/api/ukrdc/patients/observations/_standing_blood_pressure.xml.builder
 - app/views/renalware/api/ukrdc/patients/observations/_weight.xml.builder
 - app/views/renalware/api/ukrdc/patients/show.xml.builder
+- app/views/renalware/api/v1/patients/patients/show.json.jbuilder
 - app/views/renalware/base/_black_hole.html.slim
 - app/views/renalware/base/_modality_missing_warning.html.slim
 - app/views/renalware/clinical/_header.html.slim
@@ -2295,6 +2310,7 @@ files:
 - app/views/renalware/pathology/_navigation.html.slim
 - app/views/renalware/pathology/_observations_definition_list.html.slim
 - app/views/renalware/pathology/current_observation_results/index.html.slim
+- app/views/renalware/pathology/historical_observation_results/_table.html.slim
 - app/views/renalware/pathology/historical_observation_results/index.html.slim
 - app/views/renalware/pathology/observation_requests/_table.html.slim
 - app/views/renalware/pathology/observation_requests/index.html.slim
@@ -2306,6 +2322,7 @@ files:
 - app/views/renalware/pathology/patient_rules/_form.html.slim
 - app/views/renalware/pathology/patient_rules/edit.html.slim
 - app/views/renalware/pathology/patient_rules/new.html.slim
+- app/views/renalware/pathology/recent_observation_results/_table.html.slim
 - app/views/renalware/pathology/recent_observation_results/index.html.slim
 - app/views/renalware/pathology/requests/requests/_pdf_header.html.slim
 - app/views/renalware/pathology/requests/requests/create.pdf.slim
@@ -2467,6 +2484,7 @@ files:
 - app/views/renalware/problems/problems/_current_table.html.slim
 - app/views/renalware/problems/problems/_details.html.slim
 - app/views/renalware/problems/problems/_history.html.slim
+- app/views/renalware/problems/problems/_problem.html.slim
 - app/views/renalware/problems/problems/_summary_part.html.slim
 - app/views/renalware/problems/problems/edit.html.slim
 - app/views/renalware/problems/problems/index.html.slim
@@ -2754,7 +2772,7 @@ files:
 - config/locales/validates_timeliness.en.yml
 - config/permissions.yml
 - config/routes.rb
-- config/schedule.rb
+- config/schedule.rb.example
 - config/spring.rb
 - db/functions/audit_view_as_json_v01.sql
 - db/functions/count_estimate_v01.sql
@@ -2769,6 +2787,8 @@ files:
 - db/functions/refresh_current_observation_set_v01.sql
 - db/functions/update_current_observation_set_from_trigger_v01.sql
 - db/functions/update_current_observation_set_from_trigger_v02.sql
+- db/functions/update_current_observation_set_from_trigger_v03.sql
+- db/functions/update_current_observation_set_from_trigger_v04.sql
 - db/migrate/20141004150240_create_ethnicities.rb
 - db/migrate/20141010170329_create_death_causes.rb
 - db/migrate/20141020170329_create_patients.rb
@@ -3106,8 +3126,15 @@ files:
 - db/migrate/20180126142314_add_uuid_to_letters.rb
 - db/migrate/20180130165803_add_deleted_at_indexes.rb
 - db/migrate/20180201090444_add_created_at_to_delayed_jobs_in_hl7_trig_fn.rb
+- db/migrate/20180202184954_create_view_pathology_observation_digests.rb
+- db/migrate/20180206225525_update_fn_update_current_observation_set_from_trigger.rb
 - db/migrate/20180207082540_create_count_estimate_function.rb
+- db/migrate/20180208150629_add_authentication_token_to_users.rb
+- db/migrate/20180213124203_add_cancelled_to_pathology_observations.rb
+- db/migrate/20180213125734_update_fn_update_current_obs_set_trgger.rb
 - db/migrate/20180213171805_add_display_order_cols_to_observation_descriptions.rb
+- db/migrate/20180214124317_add_cols_to_aki_alerts.rb
+- db/migrate/20180216132741_disable_some_audits.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3196,6 +3223,7 @@ files:
 - 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
+- db/views/pathology_observation_digests_v01.sql
 - db/views/patient_summaries_v01.sql
 - db/views/patient_summaries_v02.sql
 - db/views/patient_summaries_v03.sql