renalware-core 2.0.0.pre.rc1 → 2.0.0.pre.rc3

data/db/migrate/20171214141335_create_trigger_to_update_current_observation_sets.rb

@@ -0,0 +1,111 @@
+class CreateTriggerToUpdateCurrentObservationSets < ActiveRecord::Migration[5.1]
+  def up
+    sql = <<-SQL
+      CREATE OR REPLACE FUNCTION update_current_observation_set_from_trigger() RETURNS TRIGGER AS $body$
+        -- TC 14/12/2017
+        -- This function is called by a trigger when a row is inserted or updated in
+        -- pathology_observations. Its purpose is to keep current_observation_sets up to date
+        -- with the latest observations for any patient.
+        -- The current_observation_sets table maintains a jsonb hash into which we insert or replace
+        -- the observation, keyed by OBX code.
+        -- e.g.  .. {"HGB": { "result": 123.1, "observed_at": '2017-12-12-01:01:01'}, ..
+        DECLARE
+          a_patient_id bigint;
+          a_code text;
+          current_observed_at timestamp;
+          current_result text;
+          new_observed_at timestamp;
+        BEGIN
+          RAISE NOTICE 'TRIGGER called on %',TG_TABLE_NAME ;
+
+          /*
+          If inserting or updating, we _could_ assume the last observation to be inserted is
+          the most 'recent' one (with the latest observed_at date).
+          However the order of incoming messages is not guaranteed, so we have two options:
+          1. Refresh the entire current_observation_set for the patient
+          2. Check the current observed_at date in the jsonb and only update if we have a more
+             recent one
+          We have gone for 2.
+          */
+
+          IF (TG_OP = 'INSERT' OR TG_OP = 'UPDATE') THEN
+
+            -- Note we could re-generate the entire current pathology for the patient using
+            --  select refresh_current_observation_set(a_patient_id);
+            -- which is safer but uses more resources, so avoiding this for now.
+
+            -- Find and store patient_id into local variable
+            select request.patient_id into a_patient_id
+              from pathology_observation_requests request
+              where request.id = NEW.request_id;
+
+            -- Find and store the obx code into local variable
+            select description.code into a_code
+              from pathology_observation_descriptions description
+              where description.id = NEW.description_id;
+
+            -- Important! Create the observation_set if it doesn exist yet
+            -- ignore the error id the row already exists
+            insert into pathology_current_observation_sets (patient_id)
+            values (a_patient_id)
+            ON CONFLICT DO NOTHING;
+
+            -- We are going to compare the current and new observed_at dates
+            -- so need to cast them  to a timestamp
+            select cast(New.observed_at as timestamp) into new_observed_at;
+
+            -- Get the most recent date and value for this observation
+            -- and store to variables.
+            select
+            cast(values -> a_code ->> 'observed_at' as timestamp),
+            values -> a_code ->> 'result'
+            into current_observed_at, current_result from
+            pathology_current_observation_sets
+            where patient_id = a_patient_id;
+
+            -- Output some info to helps us debug. This can be removed later.
+            RAISE NOTICE '  Request id % Patient id % Code %', NEW.request_id, a_patient_id, a_code;
+            RAISE NOTICE '  Last %: % at %', a_code, current_result, current_observed_at;
+            RAISE NOTICE '  New  %: % at %', a_code, NEW.result, new_observed_at;
+
+            IF current_observed_at IS NULL OR new_observed_at >= current_observed_at THEN
+              -- The new pathology_observation row contain a more recent result that the old one.
+              -- (note there may not be an old one if the patient has neve had this obs before).
+
+              RAISE NOTICE '  Updating pathology_current_observation_sets..';
+
+              -- Update the values jsonb column with the new hash for this code, e.g.
+              -- .. {"HGB": { "result": 123.1, "observed_at": '2017-12-12-01:01:01'}, ..
+                    -- Note the `set values` below actually reads in the jsonb, updates it,
+                    -- and wites the whole thing back.
+              update pathology_current_observation_sets
+                set values = jsonb_set(
+                  values,
+                  ('{'||a_code||'}')::text[], -- defined in the fn path::text[]
+                  jsonb_build_object('result', NEW.result, 'observed_at', new_observed_at),
+                  true)
+                where patient_id = a_patient_id;
+            END IF;
+          END IF;
+          RETURN NULL ;
+        END $body$ LANGUAGE plpgsql VOLATILE COST 100;
+      -- End function
+
+      -- Create the trigger which will call out function every time a row in pathology_observations
+      -- is inserted or updated
+      DROP TRIGGER IF EXISTS update_current_observation_set_trigger ON pathology_observations;
+      CREATE TRIGGER update_current_observation_set_trigger
+        AFTER INSERT OR UPDATE
+        ON pathology_observations
+        FOR EACH ROW EXECUTE PROCEDURE update_current_observation_set_from_trigger();
+    SQL
+    ActiveRecord::Base.connection.execute(sql)
+  end
+
+  def down
+    ActiveRecord::Base.connection.execute("
+      DROP TRIGGER IF EXISTS update_current_observation_set_trigger ON pathology_observations;
+      DROP FUNCTION IF EXISTS update_current_observation_set_from_trigger();
+    ")
+  end
+end

data/db/migrate/20171214190849_enforce_request_id_on_observations.rb

@@ -0,0 +1,5 @@
+class EnforceRequestIdOnObservations < ActiveRecord::Migration[5.1]
+  def change
+    change_column_null :pathology_observations, :request_id, false
+  end
+end

data/db/migrate/20171215122454_add_pathology_observation_set_to_letters.rb

@@ -0,0 +1,10 @@
+class AddPathologyObservationSetToLetters < ActiveRecord::Migration[5.1]
+  def change
+    add_column :letter_letters,
+               :pathology_snapshot,
+               :jsonb,
+               index: { using: :gin },
+               default: {},
+               null: false
+  end
+end

data/lib/core_extensions/hash.rb

@@ -0,0 +1,11 @@
+# Recursively covert a nested hash into nested OpenStructs
+# See https://coderwall.com/p/74rajw/convert-a-complex-nested-hash-to-an-object
+module CoreExtensions
+  module Hash
+    module OpenStructConversion
+      def to_o
+        JSON.parse to_json, object_class: OpenStruct
+      end
+    end
+  end
+end

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.rc1".freeze
+  VERSION = "2.0.0.pre.rc3".freeze
 end

data/spec/factories/admissions/consult_sites.rb

@@ -0,0 +1,6 @@
+FactoryBot.define do
+  factory :admissions_consult_site, class: "Renalware::Admissions::ConsultSite" do
+    # accountable
+    name { Faker::Company.name }
+  end
+end

data/spec/factories/admissions/consults.rb

@@ -2,6 +2,6 @@ FactoryBot.define do
   factory :admissions_consult, class: "Renalware::Admissions::Consult" do
     accountable
     patient { create(:patient, by: accountable_actor) }
-    hospital_unit
+    association :consult_site, factory: :admissions_consult_site
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.0.pre.rc1
+  version: 2.0.0.pre.rc3
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-13 00:00:00.000000000 Z
+date: 2017-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -1152,6 +1152,7 @@ files:
 - app/helpers/renalware/clinic_helper.rb
 - app/helpers/renalware/clinical_helper.rb
 - app/helpers/renalware/clipboard_helper.rb
+- app/helpers/renalware/dashboards_helper.rb
 - app/helpers/renalware/definition_list_helper.rb
 - app/helpers/renalware/devise_helper.rb
 - app/helpers/renalware/dropdown_button_helper.rb
@@ -1207,6 +1208,7 @@ files:
 - app/models/concerns/renalware/deviseable.rb
 - app/models/concerns/renalware/explicit_state_model.rb
 - app/models/concerns/renalware/hd/session_scopes.rb
+- app/models/concerns/renalware/letters/letter_pathology.rb
 - app/models/concerns/renalware/modality_scopes.rb
 - app/models/concerns/renalware/ordered_scope.rb
 - app/models/concerns/renalware/ordered_set_scope.rb
@@ -1233,6 +1235,7 @@ files:
 - app/models/renalware/admissions.rb
 - app/models/renalware/admissions/consult.rb
 - app/models/renalware/admissions/consult_query.rb
+- app/models/renalware/admissions/consult_site.rb
 - app/models/renalware/admissions/request.rb
 - app/models/renalware/admissions/request_reason.rb
 - app/models/renalware/clinical.rb
@@ -1414,8 +1417,9 @@ files:
 - app/models/renalware/pathology/clinic.rb
 - app/models/renalware/pathology/consultant.rb
 - app/models/renalware/pathology/create_observations.rb
-- app/models/renalware/pathology/current_key_observation_set.rb
+- app/models/renalware/pathology/current_key_observation_set.rb.dead
 - 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
 - app/models/renalware/pathology/determine_observation_date_series.rb
 - app/models/renalware/pathology/lab.rb
@@ -1430,6 +1434,7 @@ files:
 - app/models/renalware/pathology/observation_for_patient_request_description_query.rb
 - app/models/renalware/pathology/observation_request.rb
 - app/models/renalware/pathology/observations_for_descriptions_query.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
 - app/models/renalware/pathology/patient.rb
@@ -1473,6 +1478,7 @@ files:
 - app/models/renalware/pathology/requests/request_query.rb
 - app/models/renalware/pathology/requests/requests_factory.rb
 - app/models/renalware/pathology/results.rb
+- app/models/renalware/pathology/update_current_observations.rb.dead
 - app/models/renalware/pathology/view_current_observation_results.rb
 - app/models/renalware/pathology/view_observation_results.rb
 - app/models/renalware/patient.rb
@@ -1704,11 +1710,12 @@ files:
 - app/presenters/renalware/medications/treatable_presenter.rb
 - app/presenters/renalware/messaging/internal/message_presenter.rb
 - app/presenters/renalware/messaging/internal/receipt_presenter.rb
-- app/presenters/renalware/pathology/current_observation_results/html_table_view.rb
-- app/presenters/renalware/pathology/current_observation_results/presenter.rb
+- app/presenters/renalware/pathology/current_observation_results.dead/html_table_view.rb.dead
+- app/presenters/renalware/pathology/current_observation_results.dead/presenter.rb.dead
 - app/presenters/renalware/pathology/historical_observation_results/html_table_view.rb
 - app/presenters/renalware/pathology/historical_observation_results/presenter.rb
 - app/presenters/renalware/pathology/observation_presenter.rb
+- app/presenters/renalware/pathology/observation_set_presenter.rb
 - app/presenters/renalware/pathology/observations_diff.rb
 - app/presenters/renalware/pathology/observations_for_codes_presenter.rb
 - app/presenters/renalware/pathology/patient_presenter.rb
@@ -1792,6 +1799,7 @@ files:
 - app/views/renalware/addresses/_form.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/edit.html.slim
 - app/views/renalware/admin/users/index.html.slim
 - app/views/renalware/admissions/consults/_filters.html.slim
@@ -2912,9 +2920,15 @@ files:
 - db/migrate/20171123143534_add_pk_to_drug_types_drugs.rb
 - db/migrate/20171123154116_create_renal_versions.rb
 - db/migrate/20171128163543_add_more_missing_indexes.rb
+- db/migrate/20171204112150_create_consult_sites.rb
 - db/migrate/20171206121652_add_loinc_code_to_observation_descriptions.rb
 - db/migrate/20171208211206_create_user_feedback.rb
 - db/migrate/20171211130716_remove_unused_patients_cols.rb
+- db/migrate/20171211161400_create_pathology_current_table.rb
+- db/migrate/20171213111513_create_fn_to_refresh_current_obs.rb
+- db/migrate/20171214141335_create_trigger_to_update_current_observation_sets.rb
+- db/migrate/20171214190849_enforce_request_id_on_observations.rb
+- db/migrate/20171215122454_add_pathology_observation_set_to_letters.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3023,6 +3037,7 @@ files:
 - lib/core_extensions/active_support/duration.rb
 - lib/core_extensions/date.rb
 - lib/core_extensions/dumb_delegator.rb
+- lib/core_extensions/hash.rb
 - lib/core_extensions/i18n/always_cascade.rb
 - lib/core_extensions/i18n/handle_blank_value.rb
 - lib/core_extensions/scenic.rb
@@ -3069,6 +3084,7 @@ files:
 - spec/factories/accesses/profiles.rb
 - spec/factories/accesses/sites.rb
 - spec/factories/accesses/types.rb
+- spec/factories/admissions/consult_sites.rb
 - spec/factories/admissions/consults.rb
 - spec/factories/admissions/request_reasons.rb
 - spec/factories/admissions/requests.rb