renalware-core 2.0.0.pre.rc8 → 2.0.0.pre.rc9

data/db/migrate/20180130165803_add_deleted_at_indexes.rb

@@ -0,0 +1,16 @@
+class AddDeletedAtIndexes < ActiveRecord::Migration[5.1]
+  def change
+    add_index :research_studies, :deleted_at
+    add_index :research_study_participants, :deleted_at
+    add_index :admission_consults, :deleted_at
+    add_index :clinical_allergies, :deleted_at
+    add_index :patient_alerts, :deleted_at
+    add_index :access_plan_types, :deleted_at
+    add_index :drugs, :deleted_at
+    add_index :event_types, :deleted_at
+    add_index :hd_cannulation_types, :deleted_at
+    add_index :modality_descriptions, :deleted_at
+    add_index :pd_systems, :deleted_at
+    add_index :hd_profiles, :deactivated_at
+  end
+end

data/db/migrate/20180201090444_add_created_at_to_delayed_jobs_in_hl7_trig_fn.rb

@@ -0,0 +1,9 @@
+class AddCreatedAtToDelayedJobsInHL7TrigFn < ActiveRecord::Migration[5.1]
+  def up
+    load_function("preprocess_hl7_message_v02.sql")
+  end
+
+  def down
+    load_function("preprocess_hl7_message_v01.sql")
+  end
+end

data/db/migrate/20180207082540_create_count_estimate_function.rb

@@ -0,0 +1,9 @@
+class CreateCountEstimateFunction < ActiveRecord::Migration[5.1]
+  def up
+    load_function "count_estimate_v01.sql"
+  end
+
+  def down
+    connection.execute("DROP FUNCTION count_estimate(text);")
+  end
+end

data/db/triggers/feed_messages_preprocessing_trigger_v01.sql

@@ -0,0 +1,5 @@
+CREATE TRIGGER feed_messages_preprocessing_trigger
+  BEFORE INSERT
+  ON delayed_jobs
+  FOR EACH ROW
+  EXECUTE PROCEDURE preprocess_hl7_message();

data/db/triggers/update_current_observation_set_trigger_v01.sql

@@ -0,0 +1,7 @@
+-- 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();

data/lib/core_extensions/active_record/migration_helpers.rb

@@ -0,0 +1,43 @@
+module CoreExtensions
+  module ActiveRecord
+    module MigrationHelpers
+      # Can be called from a migration to load in a function from a sql file
+      # at e.g. db/functions/my_function_v01.sql
+      #
+      # Example usage:
+      #  load_function("my_function_v01.sql")
+      #
+      def load_function(filename)
+        load_sql_file(DatabaseObjectPaths.functions, filename)
+      end
+
+      # Can be called from a migration to load in a trigger from a sql file
+      # at e.g. db/functions/my_trigger_v01.sql
+      #
+      # Example usage:
+      #  load_trigger("my_trigger_v01.sql")
+      #
+      def load_trigger(filename)
+        load_sql_file(DatabaseObjectPaths.triggers, filename)
+      end
+
+      def load_sql_file(path, filename)
+        connection.execute(File.read(path.join(filename)))
+      end
+
+      class DatabaseObjectPaths
+        class << self
+          def triggers
+            Renalware::Engine.root.join("db", "triggers")
+          end
+
+          def functions
+            Renalware::Engine.root.join("db", "functions")
+          end
+        end
+      end
+    end
+  end
+end
+
+ActiveRecord::Migration[5.1].send(:prepend, CoreExtensions::ActiveRecord::MigrationHelpers)

data/lib/renalware/engine.rb

@@ -152,12 +152,14 @@ module Renalware
     end
 
     initializer :resolve_scenic_views_inside_engine do |app|
-      # Set app.config.paths["db/views"] to the engine's db/views path so (out monkey-patched)
-      # scenic will load views from the engine (otherwise not supported un;es manually copies in
+      # Set app.config.paths["db/views"] to the engine's db/views path so (our monkey-patched)
+      # scenic will load views from the engine (otherwise not supported unless manually copies in
       # a rake task, which I am keen to avoid)
       # See lib/core_extensions/scenic.rb
-      view_dir = Rails.root.join(config.root, "db", "views")
-      app.config.paths.add("db/views", with: view_dir)
+      %w(views functions triggers).each do |db_thing|
+        dir = Rails.root.join(config.root, "db", db_thing)
+        app.config.paths.add("db/#{db_thing}", with: dir)
+      end
     end
 
     initializer :general do |app|

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.rc8".freeze
+  VERSION = "2.0.0.pre.rc9".freeze
 end

data/spec/factories/pathology/observation_descriptions.rb

@@ -1,6 +1,12 @@
 FactoryBot.define do
   factory :pathology_observation_description,
-      class: "Renalware::Pathology::ObservationDescription" do
+          class: "Renalware::Pathology::ObservationDescription" do
+    initialize_with do
+      Renalware::Pathology::ObservationDescription.find_or_create_by!(code: code)
+    end
+
+    before(:create){ |desc| desc.loinc_code ||= desc.code.downcase }
+
     code "WBR"
     association :measurement_unit, factory: :pathology_measurement_unit
   end

data/spec/support/shared_examples/accountable_examples.rb

@@ -0,0 +1,6 @@
+shared_examples_for "an Accountable model" do
+  it { is_expected.to respond_to(:by=) }
+  it { is_expected.to respond_to(:save_by!) }
+  it { is_expected.to have_db_index(:created_by_id) }
+  it { is_expected.to have_db_index(:updated_by_id) }
+end

data/spec/support/shared_examples/supersedable_examples.rb

@@ -0,0 +1,12 @@
+shared_examples_for "a Supersedable model" do
+  it { is_expected.to have_db_column(:deactivated_at) }
+  it { is_expected.to have_db_index(:deactivated_at) }
+
+  it "adds a deactivated_at where clause" do
+    expect(described_class.all.where_sql).to include(".\"deactivated_at\" IS NULL")
+  end
+
+  it "skips adding the deactivated_at where clause when unscoped" do
+    expect(described_class.unscoped.where_sql.to_s).not_to include("\"deactivated_at\"")
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.0.pre.rc8
+  version: 2.0.0.pre.rc9
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-01-30 00:00:00.000000000 Z
+date: 2018-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -1248,6 +1248,7 @@ files:
 - app/models/application_record.rb
 - app/models/concerns/renalware/accountable.rb
 - app/models/concerns/renalware/broadcasting.rb
+- app/models/concerns/renalware/clinics/most_recent_measurement_scopes.rb.dead
 - app/models/concerns/renalware/deviseable.rb
 - app/models/concerns/renalware/explicit_state_model.rb
 - app/models/concerns/renalware/feeds/job.rb
@@ -1305,6 +1306,7 @@ files:
 - app/models/renalware/clinics/clinic_visit.rb
 - app/models/renalware/clinics/consultant.rb
 - app/models/renalware/clinics/create_clinic_visit.rb
+- app/models/renalware/clinics/current_observations.rb
 - app/models/renalware/clinics/patient.rb
 - app/models/renalware/clinics/remembered_clinic_visit_preferences.rb
 - app/models/renalware/clinics/version.rb
@@ -1410,7 +1412,6 @@ files:
 - app/models/renalware/letters/complete_letter.rb
 - app/models/renalware/letters/contact.rb
 - app/models/renalware/letters/contact_description.rb
-- app/models/renalware/letters/delivery/deliver_letter.rb.dead
 - app/models/renalware/letters/delivery/delivery_policy.rb
 - app/models/renalware/letters/delivery/email_letter_to_practice.rb
 - app/models/renalware/letters/delivery/practice_email.rb
@@ -1496,7 +1497,6 @@ 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/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
@@ -1557,8 +1557,7 @@ 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_current_observation_results.rb.dead
 - app/models/renalware/pathology/view_observation_results.rb
 - app/models/renalware/patient.rb
 - app/models/renalware/patients.rb
@@ -1757,6 +1756,7 @@ files:
 - app/presenters/renalware/clinical/body_composition_presenter.rb
 - app/presenters/renalware/clinical/dry_weight_presenter.rb
 - app/presenters/renalware/clinical/dry_weights_presenter.rb
+- app/presenters/renalware/clinical/header_presenter.rb
 - app/presenters/renalware/clinical/profile_presenter.rb
 - app/presenters/renalware/country_presenter.rb
 - app/presenters/renalware/dashboard/dashboard_presenter.rb
@@ -1784,6 +1784,7 @@ files:
 - app/presenters/renalware/letters/letter_form_presenter.rb
 - app/presenters/renalware/letters/letter_presenter.rb
 - app/presenters/renalware/letters/letter_presenter_factory.rb
+- app/presenters/renalware/letters/part_class_filter.rb
 - app/presenters/renalware/letters/practice_email_meta_data.rb
 - app/presenters/renalware/letters/recipient_presenter.rb
 - app/presenters/renalware/low_clearance/dashboard_presenter.rb
@@ -1798,7 +1799,6 @@ files:
 - app/presenters/renalware/messaging/internal/message_presenter.rb
 - app/presenters/renalware/messaging/internal/receipt_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
@@ -1850,6 +1850,7 @@ files:
 - app/validators/renalware/patients/temperature_validator.rb
 - app/validators/renalware/patients/weight_validator.rb
 - app/values/renalware/address.rb
+- app/values/renalware/bmi.rb
 - app/values/renalware/duration.rb
 - app/values/renalware/gender.rb
 - app/values/renalware/time_of_day.rb
@@ -1945,6 +1946,7 @@ files:
 - app/views/renalware/api/ukrdc/patients/show.xml.builder
 - app/views/renalware/base/_black_hole.html.slim
 - app/views/renalware/base/_modality_missing_warning.html.slim
+- app/views/renalware/clinical/_header.html.slim
 - app/views/renalware/clinical/allergies/_list.html.slim
 - app/views/renalware/clinical/allergies/_mini.html.slim
 - app/views/renalware/clinical/allergies/_new.html.slim
@@ -2166,7 +2168,6 @@ files:
 - app/views/renalware/letters/formatted_letters/show.html.slim
 - app/views/renalware/letters/formatted_letters/show.inlinepdf.slim
 - app/views/renalware/letters/formatted_letters/show.pdf.slim
-- app/views/renalware/letters/formatted_letters/show.rtf.slim.ol
 - app/views/renalware/letters/letters/_actions.html.slim
 - app/views/renalware/letters/letters/_add_contact.html.slim
 - app/views/renalware/letters/letters/_additional_ccs.html.slim
@@ -2311,7 +2312,6 @@ files:
 - app/views/renalware/patients/_layout.html.slim
 - app/views/renalware/patients/_mini_profile.html.slim
 - app/views/renalware/patients/_person_form_fields.html.slim
-- app/views/renalware/patients/_prescriptions.html.slim.dead
 - app/views/renalware/patients/_search_form.html.slim
 - app/views/renalware/patients/_side_menu.html.slim
 - app/views/renalware/patients/alerts/_alert.html.slim
@@ -2654,7 +2654,8 @@ files:
 - config/locales/renalware/blood_pressure.en.yml
 - config/locales/renalware/clinical/allergies.en.yml
 - config/locales/renalware/clinical/body_composition.yml
-- config/locales/renalware/clinical/dry_weight.yml
+- config/locales/renalware/clinical/dry_weight.en.yml
+- config/locales/renalware/clinical/header.en.yml
 - config/locales/renalware/clinics/visit.yml
 - config/locales/renalware/dashboard/dashboard.yml
 - config/locales/renalware/dates_test.yml
@@ -2736,6 +2737,19 @@ files:
 - config/routes.rb
 - config/schedule.rb
 - config/spring.rb
+- db/functions/audit_view_as_json_v01.sql
+- db/functions/count_estimate_v01.sql
+- db/functions/generate_patient_secure_id_v01.sql
+- db/functions/generate_secure_id_v01.sql
+- db/functions/import_gps_csv_v01.sql
+- db/functions/import_practice_memberships_csv_v01.sql
+- db/functions/import_practices_csv_v01.sql
+- db/functions/preprocess_hl7_message_v01.sql
+- db/functions/preprocess_hl7_message_v02.sql
+- db/functions/refresh_all_matierialized_views_v01.sql
+- 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/migrate/20141004150240_create_ethnicities.rb
 - db/migrate/20141010170329_create_death_causes.rb
 - db/migrate/20141020170329_create_patients.rb
@@ -3067,8 +3081,12 @@ 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/20180121115246_add_include_pathology_in_letter_to_letters_letterheads.rb
 - db/migrate/20180125201356_make_obs_set_trigger_change_updated_at.rb
 - 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/20180207082540_create_count_estimate_function.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3151,6 +3169,8 @@ files:
 - db/seeds/default/transplants/transplant_registration_statuses.rb
 - db/seeds/seeds_helper.rb
 - db/static.obsolete/medication_routes.yml
+- db/triggers/feed_messages_preprocessing_trigger_v01.sql
+- db/triggers/update_current_observation_set_trigger_v01.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
@@ -3174,6 +3194,7 @@ files:
 - lib/array_stringifier.rb
 - lib/breadcrumb.rb
 - lib/collection_presenter.rb
+- lib/core_extensions/active_record/migration_helpers.rb
 - lib/core_extensions/active_record/sort.rb
 - lib/core_extensions/active_support/duration.rb
 - lib/core_extensions/date.rb
@@ -3381,7 +3402,9 @@ files:
 - spec/support/select2_spec_helper.rb
 - spec/support/select_date_spec_helper.rb
 - spec/support/shared_contexts/a_global_rule_set.rb
+- spec/support/shared_examples/accountable_examples.rb
 - spec/support/shared_examples/paranoia_examples.rb
+- spec/support/shared_examples/supersedable_examples.rb
 - spec/support/translations.rb
 - spec/support/travel.rb
 - spec/support/webmock.rb

data/app/models/renalware/letters/delivery/deliver_letter.rb.dead

@@ -1,41 +0,0 @@
-require "renalware/letters"
-require "attr_extras"
-
-module Renalware
-  module Letters
-    module Delivery
-      # Responsible for delivering the letter according to the recipient's preferred method:
-      # - Email letter to practice if GP is a recipient and the practice has an email address;
-      # - Currently no other action taken, but this class could be extended to for example to
-      #   email the letter contacts who wanted it delivered that way etc.
-      class DeliverLetter
-        pattr_initialize [:letter!]
-        delegate :email_letter_to_practice?, :gp_recipient, to: :policy
-
-        def call
-          if email_letter_to_practice?
-            email_letter_to_the_patients_practice_and_flag_as_sent
-          end
-        end
-
-        private
-
-        def email_letter_to_the_patients_practice_and_flag_as_sent
-          Letter.transaction do
-            mail = PracticeMailer.patient_letter(letter: letter, to: practice_email_address)
-            mail.deliver_later
-            gp_recipient.update(emailed_at: Time.zone.now)
-          end
-        end
-
-        def practice_email_address
-          PracticeEmail.new(letter).address
-        end
-
-        def policy
-          @policy ||= DeliveryPolicy.new(letter)
-        end
-      end
-    end
-  end
-end

data/app/models/renalware/pathology/current_key_observation_set.rb.dead

@@ -1,10 +0,0 @@
-require_dependency "renalware/pathology"
-
-module Renalware
-  module Pathology
-    class CurrentKeyObservationSet < ApplicationRecord
-      belongs_to :patient, class_name: "Renalware::Pathology::Patient"
-      self.primary_key = :patient_id
-    end
-  end
-end

data/app/models/renalware/pathology/update_current_observations.rb.dead

@@ -1,25 +0,0 @@
-require_dependency "renalware/pathology"
-
-module Renalware
-  module Pathology
-    class UpdateCurrentObservations
-      def call(params)
-        patient = find_patient(params[:patient_id])
-        set = patient.fetch_current_observation_set
-
-        params[:observation_request][:observations_attributes].each do |new_obs|
-          description = ObservationDescription.select(:code).find(new_obs[:description_id])
-          set.values[description.code] = new_obs.slice(:result, :observed_at)
-        end
-
-        set.save!
-      end
-
-      private
-
-      def find_patient(id)
-        Pathology::Patient.find_by(id: id)
-      end
-    end
-  end
-end

data/app/presenters/renalware/pathology/current_observation_results.dead/presenter.rb.dead

@@ -1,54 +0,0 @@
-require_dependency "renalware/pathology"
-
-module Renalware
-  module Pathology
-    class CurrentObservationResults::Presenter
-      attr_reader :view_model
-
-      def present(results)
-        @view_model = [build_header] + build_body(results)
-      end
-
-      private
-
-      def build_header
-        %w(description result date)
-      end
-
-      def build_body(results)
-        results.map do |result|
-          [build_description(result), ObservationPresenter.new(result), format_date(result)]
-        end
-      end
-
-      def build_description(result)
-        description = ObservationDescription.new(
-          code: result.description_code, name: result.description_name)
-        ResultPresenter.new(description)
-      end
-
-      def format_date(result)
-        date = I18n.l(result.observed_at.try(:to_date))
-        DatePresenter.new(date)
-      end
-
-      class DatePresenter < SimpleDelegator
-        def content
-          to_s
-        end
-      end
-
-      class ResultPresenter < SimpleDelegator
-        def content
-          name
-        end
-      end
-
-      class ObservationPresenter < SimpleDelegator
-        def content
-          to_s
-        end
-      end
-    end
-  end
-end