renalware-core 2.0.0.pre.rc6 → 2.0.0.pre.rc7

data/config/routes.rb

@@ -308,6 +308,11 @@ Renalware::Engine.routes.draw do
               controller: "events/swabs",
               defaults: { slug: :swabs }
 
+    resources :investigations,
+              only: [:new, :create, :edit, :update],
+              controller: "events/investigations",
+              defaults: { slug: :investigations }
+
     # Here we could enable new event by any other slug
     # eg patient_new_specific_event(slug: "transplant_biopsies")
     # get "events/:slug/new",

data/db/migrate/20180119121243_create_trigger_to_preprocess_hl7_msg.rb

@@ -1,6 +1,8 @@
 class CreateTriggerToPreprocessHL7Msg < ActiveRecord::Migration[5.1]
   def up
-    sql = <<-SQL
+    # Note that we need to use a quoted heredoc ('SQL') here in order to preserve our
+    # SQL escaping e.g. E'\\S\\' which would otherwise be interpreted by Ruby as E'\S\'
+    sql = <<-'SQL'
       /* Create a function for the trigger to call */
       CREATE FUNCTION preprocess_hl7_message() RETURNS trigger AS
       $body$
@@ -17,11 +19,11 @@ class CreateTriggerToPreprocessHL7Msg < ActiveRecord::Migration[5.1]
         To get around this we need to convert instances of \S\ with another escape sequence eg «
         and manually map this back to a ^ in the job handler ruby code.
 
-        So here, if this delayed_job is destinated to be picked up by a Feed job handler
+        So here, if this delayed_job is destined to be picked up by a Feed job handler
         make sure we convert the Mirth escape sequence \S\ to \\S\\
         */
         IF position('Feed' in NEW.handler) > 0 THEN
-          NEW.handler = replace(NEW.handler, '\S\', '\\S\\');
+          NEW.handler = replace(NEW.handler, E'\\S\\', E'\\\\S\\\\');
         END IF;
 
         RETURN NEW;

data/db/migrate/20180125201356_make_obs_set_trigger_change_updated_at.rb

@@ -0,0 +1,191 @@
+class MakeObsSetTriggerChangeUpdatedAt < 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't exist yet
+            -- ignore the error if 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 updated_at = CURRENT_TIMESTAMP,
+                  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
+    SQL
+    ActiveRecord::Base.connection.execute(sql)
+  end
+
+  def down
+    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;
+    SQL
+    ActiveRecord::Base.connection.execute(sql)
+  end
+end

data/db/migrate/20180126142314_add_uuid_to_letters.rb

@@ -0,0 +1,6 @@
+class AddUuidToLetters < ActiveRecord::Migration[5.1]
+  def change
+    add_column :letter_letters, :uuid, :uuid, default: "uuid_generate_v4()", null: false
+    add_index :letter_letters, :uuid, using: :btree
+  end
+end

data/db/seeds/default/events/event_types.csv

@@ -4,3 +4,4 @@
 "Swab","Renalware::Events::Swab","swabs"
 "Plasma Exchange",,
 "PD Line Change",,"pd_line_changes"
+"Investigation","Renalware::Events::Investigation","investigations"

data/lib/renalware/configuration.rb

@@ -47,6 +47,7 @@ module Renalware
     config_accessor(:fallback_email_address_for_test_messages) do
       ENV["FALLBACK_EMAIL_ADDRESS_FOR_TEST_MESSAGES"]
     end
+    config_accessor(:ukrdc_sending_facility_name) { "NOT_CONFIGURED" }
   end
 
   def self.config

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.rc6".freeze
+  VERSION = "2.0.0.pre.rc7".freeze
 end

data/lib/test_support/text_editor_helpers.rb

@@ -3,4 +3,10 @@ module TextEditorHelpers
   def fill_in_trix_editor(id, value)
     find(:xpath, "//*[@id='#{id}']", visible: false).set(value)
   end
+
+  # A simplified version of the helper, requires JavaScript, and will end up
+  # having <div>value</div> in the trix-saved content, but that is normal
+  def fill_trix_editor(with:)
+    find("trix-editor").click.set(with)
+  end
 end

data/spec/factories/events/events.rb

@@ -2,7 +2,7 @@ FactoryBot.define do
   factory :event, class: "Renalware::Events::Event" do
     accountable
     patient
-    event_type factory: :events_type
+    event_type factory: :access_clinic_event_type
     date_time { Time.zone.now }
     description "Needs blood sample taken."
     notes "Would like son to accompany them on clinic visit."
@@ -20,5 +20,28 @@ FactoryBot.define do
         }
       }
     end
+
+    factory :investigation, class: "Renalware::Events::Investigation" do
+      event_type factory: :investigation_event_type
+      document {
+        {
+          modality: "other",
+          type: Renalware::Events::Investigation::Document.type.values.first,
+          result: "result"
+        }
+      }
+
+      trait :transplant_recipient do
+        before :create do |investigation|
+          investigation.document.modality = "transplant_recipient"
+        end
+      end
+
+      trait :transplant_donor do
+        before :create do |investigation|
+          investigation.document.modality = "transplant_donor"
+        end
+      end
+    end
   end
 end

data/spec/factories/events/events_types.rb

@@ -1,6 +1,10 @@
 FactoryBot.define do
-  factory :events_type, class: "Renalware::Events::Type" do
-    name "Access--Clinic"
+  factory :event_type, class: "Renalware::Events::Type" do
+    initialize_with { Renalware::Events::Type.find_or_create_by(name: name) }
+
+    factory :access_clinic_event_type do
+      name "Access--Clinic"
+    end
 
     factory :swab_event_type do
       name "Swab"
@@ -8,9 +12,20 @@ FactoryBot.define do
       slug "swabs"
     end
 
+    factory :biopsy_event_type do
+      name "Renal biopsy"
+      event_class_name "Renalware::Events::Biopsy"
+    end
+
     factory :pd_line_change_event_type do
       name "PD Line Change"
       slug "pd_line_changes"
     end
+
+    factory :investigation_event_type do
+      name "Investigation"
+      slug "investigations"
+      event_class_name "Renalware::Events::Investigation"
+    end
   end
 end

data/spec/support/database_functions_spec_helper.rb

@@ -0,0 +1,6 @@
+module DatabaseFunctionsSpecHelper
+  def toggle_all_triggers(option)
+    arg = (option == :off) ? "replica" : "DEFAULT"
+    ActiveRecord::Base.connection.execute("SET session_replication_role = #{arg};")
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.0.pre.rc6
+  version: 2.0.0.pre.rc7
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-01-25 00:00:00.000000000 Z
+date: 2018-01-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -1037,6 +1037,7 @@ files:
 - app/controllers/renalware/directory/people_controller.rb
 - app/controllers/renalware/drugs/drugs_controller.rb
 - app/controllers/renalware/events/events_controller.rb
+- app/controllers/renalware/events/investigations_controller.rb
 - app/controllers/renalware/events/swabs_controller.rb
 - app/controllers/renalware/events/types_controller.rb
 - app/controllers/renalware/hd/base_controller.rb
@@ -1322,6 +1323,7 @@ files:
 - app/models/renalware/events/biopsy.rb
 - app/models/renalware/events/event.rb
 - app/models/renalware/events/event_query.rb
+- app/models/renalware/events/investigation.rb
 - app/models/renalware/events/line_change_event_query.rb
 - app/models/renalware/events/patient_listener.rb
 - app/models/renalware/events/simple.rb
@@ -1492,7 +1494,7 @@ files:
 - app/models/renalware/pathology/all_observation_codes.rb
 - app/models/renalware/pathology/clinic.rb
 - app/models/renalware/pathology/consultant.rb
-- app/models/renalware/pathology/create_observations.rb
+- app/models/renalware/pathology/create_observation_requests.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
@@ -1501,7 +1503,6 @@ files:
 - app/models/renalware/pathology/lab.rb
 - app/models/renalware/pathology/measurement_unit.rb
 - app/models/renalware/pathology/message_listener.rb
-- app/models/renalware/pathology/message_param_parser.rb
 - app/models/renalware/pathology/observation.rb
 - app/models/renalware/pathology/observation_date_range.rb
 - app/models/renalware/pathology/observation_description.rb
@@ -1509,6 +1510,7 @@ files:
 - 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_jsonb_serializer.rb
 - app/models/renalware/pathology/observations_within_date_range_query.rb
@@ -1689,6 +1691,7 @@ files:
 - app/policies/renalware/drugs/drug_policy.rb
 - app/policies/renalware/events/biopsy_policy.rb
 - app/policies/renalware/events/event_policy.rb
+- app/policies/renalware/events/investigation_policy.rb
 - app/policies/renalware/events/simple_policy.rb
 - app/policies/renalware/events/swab_policy.rb
 - app/policies/renalware/feeds/file_policy.rb
@@ -1822,8 +1825,10 @@ files:
 - app/presenters/renalware/system/users_presenter.rb
 - app/presenters/renalware/time_of_day_presenter.rb
 - app/presenters/renalware/transplants/consent_presenter.rb
+- app/presenters/renalware/transplants/donor_dashboard_presenter.rb
 - app/presenters/renalware/transplants/mdm_presenter.rb
 - app/presenters/renalware/transplants/patient_presenter.rb
+- app/presenters/renalware/transplants/recipient_dashboard_presenter.rb
 - app/presenters/renalware/transplants/wait_list_registration_presenter.rb
 - app/presenters/renalware/ukrdc/pathology_observation_presenter.rb
 - app/presenters/renalware/ukrdc/patient_presenter.rb
@@ -2004,10 +2009,12 @@ files:
 - app/views/renalware/events/events/_list.html.slim
 - app/views/renalware/events/events/_table.html.slim
 - app/views/renalware/events/events/cell/_biopsy.html.slim
+- app/views/renalware/events/events/cell/_investigation.html.slim
 - app/views/renalware/events/events/cell/_simple.html.slim
 - app/views/renalware/events/events/cell/_swab.html.slim
 - app/views/renalware/events/events/index.html.slim
 - app/views/renalware/events/events/inputs/_biopsy.html.slim
+- app/views/renalware/events/events/inputs/_investigation.html.slim
 - app/views/renalware/events/events/inputs/_simple.html.slim
 - app/views/renalware/events/events/inputs/_swab.html.slim
 - app/views/renalware/events/events/new.html.slim
@@ -2016,8 +2023,11 @@ files:
 - app/views/renalware/events/events/simple/_list.html.slim
 - app/views/renalware/events/events/simple/_table.html.slim
 - app/views/renalware/events/events/toggled_cell/_biopsy.html.slim
+- app/views/renalware/events/events/toggled_cell/_investigation.html.slim
 - app/views/renalware/events/events/toggled_cell/_simple.html.slim
 - app/views/renalware/events/events/toggled_cell/_swab.html.slim
+- app/views/renalware/events/investigations/_list.html.slim
+- app/views/renalware/events/investigations/edit.html.slim
 - app/views/renalware/events/swabs/_list.html.slim
 - app/views/renalware/events/swabs/edit.html.slim
 - app/views/renalware/events/swabs/new.html.slim
@@ -2651,6 +2661,7 @@ files:
 - config/locales/renalware/errors.en.yml
 - config/locales/renalware/events/biopsy.en.yml
 - config/locales/renalware/events/events.yml
+- config/locales/renalware/events/investigation.en.yml
 - config/locales/renalware/events/swab.en.yml
 - config/locales/renalware/feeds/file.en.yml
 - config/locales/renalware/hd/accesses.en.yml
@@ -3055,6 +3066,8 @@ files:
 - db/migrate/20180112151706_create_low_clearance_profiles.rb
 - db/migrate/20180112151813_create_low_clearance_versions.rb
 - db/migrate/20180119121243_create_trigger_to_preprocess_hl7_msg.rb
+- db/migrate/20180125201356_make_obs_set_trigger_change_updated_at.rb
+- db/migrate/20180126142314_add_uuid_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
@@ -3350,6 +3363,7 @@ files:
 - spec/factories/transplants/registrations.rb
 - spec/support/capybara.rb
 - spec/support/capybara_helper.rb
+- spec/support/database_functions_spec_helper.rb
 - spec/support/date_helpers.rb
 - spec/support/devise_spec_helper.rb
 - spec/support/drugs_spec_helper.rb