renalware-core 2.0.0.pre.rc11 → 2.0.0.pre.rc13

data/config/initializers/wicked_pdf.rb

@@ -14,7 +14,6 @@ WickedPdf.config = {
   # exe_path: '/usr/local/bin/wkhtmltopdf',
   #   or
   # exe_path: Gem.bin_path('wkhtmltopdf-binary', 'wkhtmltopdf')
-
   # Layout file to be used for all PDFs
   # (but can be overridden in `render :pdf` calls)
   # layout: 'pdf.html',

data/config/locales/en.yml

@@ -23,6 +23,12 @@ en:
         pending_review: Pending Review
         approved: Approved
         completed: Completed
+      for_receptionists:
+        state:
+          draft: Draft
+          pending_review: Pending Review
+          approved: Approved (Ready to Print)
+          completed: Completed (Printed)
     provider:
       gp: GP
       hospital: Hospital

data/config/locales/renalware/hd/mdm_patients.yml

@@ -25,6 +25,12 @@ en:
           hgb_date: HGB Date
           ure: URE
           ure_date: URE Date
+          urr: URR
+          urr_date: URR Date
+          phos: PO4
+          phos_date: PO4 Date
+          pth: PTH
+          pth_date: PTH Date
           cre: CRE
           cre_date: CRE Date
           egfr: EGFR

data/config/routes.rb

@@ -82,9 +82,7 @@ Renalware::Engine.routes.draw do
     # The JSON API
     namespace :v1, constraints: { format: :json }, defaults: { format: :json } do
       resources :patients, only: :show, controller: "patients/patients" do
-        namespace :medications do
-          resources :prescriptions, only: :index
-        end
+        resources :prescriptions, controller: "medications/prescriptions", only: [:index]
         namespace :hd do
           resource :current_profile,
                    only: :show,
@@ -369,7 +367,7 @@ Renalware::Engine.routes.draw do
         resource :pending_review, controller: "pending_review_letters", only: :create
         resource :rejected, controller: "rejected_letters", only: :create
         resource :approved, controller: "approved_letters", only: :create
-        resource :completed, controller: "completed_letters", only: :create
+        resource :completed, controller: "completed_letters", only: [:new, :create]
         resource :formatted, controller: "formatted_letters", only: :show
         collection do
           get :contact_added

data/db/functions/import_practice_memberships_csv_v02.sql

@@ -0,0 +1,50 @@
+CREATE OR REPLACE FUNCTION renalware.import_practice_memberships_csv(file text) RETURNS void
+  AS $$
+  BEGIN
+
+  DROP TABLE IF EXISTS copied_memberships;
+  CREATE TEMP TABLE copied_memberships (
+    gp_code text NOT NULL,
+    practice_code text NOT NULL,
+    unused3 text,
+    unused4 text,
+    unused5 text,
+    unused7 text
+  );
+
+  -- Import the CSV file into copied_memberships - note there is no CSV header in this file
+  EXECUTE format ('COPY copied_memberships FROM %L DELIMITER %L CSV ', file, ',');
+
+  DROP TABLE IF EXISTS tmp_memberships;
+  CREATE TEMP TABLE tmp_memberships AS
+    SELECT
+      gp_code,
+      practice_code,
+      patient_primary_care_physicians.id primary_care_physician_id,
+      patient_practices.id as practice_id
+      from copied_memberships
+      INNER JOIN patient_practices on patient_practices.code = practice_code
+      INNER JOIN patient_primary_care_physicians on patient_primary_care_physicians.code = gp_code;
+
+  -- Insert any new memberships, ignoring any conflicts where the
+  -- practice_id + primary_care_physician_id already exists
+  INSERT INTO renalware.patient_practice_memberships
+    (practice_id, primary_care_physician_id, created_at, updated_at)
+  SELECT
+    practice_id,
+    primary_care_physician_id,
+    CURRENT_TIMESTAMP,
+    CURRENT_TIMESTAMP
+  FROM tmp_memberships
+  ON CONFLICT (practice_id, primary_care_physician_id) DO NOTHING;
+
+  -- Mark as deleted any memberships not in the latest uploaded data set - ie those gps have retired or moved on
+  UPDATE patient_practice_memberships mem
+    SET deleted_at = CURRENT_TIMESTAMP
+    WHERE NOT EXISTS (select 1 FROM tmp_memberships tmem
+    WHERE tmem.practice_id = mem.practice_id AND tmem.primary_care_physician_id = mem.primary_care_physician_id);
+
+  DROP TABLE IF EXISTS copied_memberships;
+  DROP TABLE IF EXISTS tmp_memberships;
+END;
+$$ LANGUAGE plpgsql;

data/db/migrate/20180221210458_add_state_index_on_modalities.rb

@@ -0,0 +1,5 @@
+class AddStateIndexOnModalities < ActiveRecord::Migration[5.1]
+  def change
+    add_index :modality_modalities, :state
+  end
+end

data/db/migrate/20180222090501_add_partial_index_to_bookmarks.rb

@@ -0,0 +1,6 @@
+class AddPartialIndexToBookmarks < ActiveRecord::Migration[5.1]
+  def change
+    remove_index :patient_bookmarks, :deleted_at
+    add_index :patient_bookmarks, :deleted_at, where: "deleted_at IS NULL"
+  end
+end

data/db/migrate/20180223100420_add_sent_to_ukrdc_at_to_patients.rb

@@ -0,0 +1,5 @@
+class AddSentToUKRDCAtToPatients < ActiveRecord::Migration[5.1]
+  def change
+    add_column :patients, :sent_to_ukrdc_at, :datetime, index: true, null: true
+  end
+end

data/db/migrate/20180226124724_add_patient_id_to_virology_profile.rb

@@ -0,0 +1,9 @@
+class AddPatientIdToVirologyProfile < ActiveRecord::Migration[5.1]
+  def change
+    add_reference :virology_profiles,
+                  :patient,
+                  foreign_key: true,
+                  index: { unique: true },
+                  null: false
+  end
+end

data/db/migrate/20180226132410_create_ukrdc_transmission_logs.rb

@@ -0,0 +1,15 @@
+class CreateUKRDCTransmissionLogs < ActiveRecord::Migration[5.1]
+  def change
+    create_table :ukrdc_transmission_logs do |t|
+      t.references :patient, foreign_key: true, index: true, null: false
+      t.datetime :sent_at, null: false
+      t.integer :status, null: false
+      t.uuid :request_uuid, null: false, index: true
+      t.text :payload_hash
+      t.xml :payload
+      t.text :error
+      t.string :file_path
+      t.timestamps null: false
+    end
+  end
+end

data/db/migrate/20180301095040_update_fn_to_upsert_gp_practive_memberships.rb

@@ -0,0 +1,9 @@
+class UpdateFnToUpsertGPPractiveMemberships < ActiveRecord::Migration[5.1]
+  def up
+    load_function("import_practice_memberships_csv_v02.sql")
+  end
+
+   def down
+    load_function("import_practice_memberships_csv_v01.sql")
+  end
+end

data/db/migrate/20180305134959_add_display_group_to_observation_desriptions.rb

@@ -0,0 +1,32 @@
+class AddDisplayGroupToObservationDesriptions < ActiveRecord::Migration[5.1]
+  def change
+
+    remove_column :pathology_observation_descriptions, :display_order, :integer
+    remove_column :pathology_observation_descriptions, :display_order_letters, :integer
+
+    add_column :pathology_observation_descriptions,
+               :display_group,
+               :integer
+
+    add_column :pathology_observation_descriptions,
+               :display_order,
+               :integer
+
+    add_column :pathology_observation_descriptions,
+               :letter_group,
+               :integer
+
+    add_column :pathology_observation_descriptions,
+               :letter_order,
+               :integer
+
+    # Only allow an obs desc to be in a group exactly once
+    add_index :pathology_observation_descriptions,
+              [:display_group, :display_order],
+              name: :obx_unique_display_grouping
+
+    add_index :pathology_observation_descriptions,
+              [:letter_group, :letter_order],
+              name: :obx_unique_letter_grouping
+  end
+end

data/db/migrate/20180306071308_remove_rogue_aki_alerts_column.rb

@@ -0,0 +1,5 @@
+class RemoveRogueAKIAlertsColumn < ActiveRecord::Migration[5.1]
+  def change
+    remove_column :renal_aki_alerts, :renal_aki_alerts, :string
+  end
+end

data/db/migrate/20180306080518_add_state_tracking_cols_to_letters.rb

@@ -0,0 +1,19 @@
+class AddStateTrackingColsToLetters < ActiveRecord::Migration[5.1]
+  def change
+    add_column :letter_letters, :submitted_for_approval_at, :datetime
+    add_reference :letter_letters,
+                  :submitted_for_approval_by,
+                  foreign_key: { to_table: :users },
+                  index: true
+    add_column :letter_letters, :approved_at, :datetime
+    add_reference :letter_letters,
+                  :approved_by,
+                  foreign_key: { to_table: :users },
+                  index: true
+    add_column :letter_letters, :completed_at, :datetime
+    add_reference :letter_letters,
+                  :completed_by,
+                  foreign_key: { to_table: :users },
+                  index: true
+  end
+end

data/lib/renalware/engine.rb

@@ -112,6 +112,7 @@ module Renalware
       app.config.assets.precompile += %w(renalware/pdf.css renalware/watermark.css)
       app.config.assets.precompile += %w(renalware/protocol_pdf.css)
       app.config.assets.precompile += %w(renalware/hd_diary_pdf.css)
+      app.config.assets.precompile += %w(renalware/patient_pages.css)
       app.config.assets.precompile += %w(
         renalware/nhs_a4_letter_logo_blue.png
         renalware/nhs_a4_letter_logo_black.png

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.rc11".freeze
+  VERSION = "2.0.0.pre.rc13".freeze
 end

data/lib/tasks/ukrdc.rake

@@ -0,0 +1,16 @@
+require "fileutils"
+require "gpgme"
+
+# Need to bear in mind we if we find a patient with changes, we still don't take everything
+# the patient has but only those bits modified since the last export or :since_date
+#
+namespace :ukrdc do
+  desc "Creates a folder of UKRDC XML files containing any changes to PV patients since "\
+       "their last export"
+  task :export, [:changed_since, :patient_ids] => [:environment] do |t, args|
+    logger           = Logger.new(STDOUT)
+    logger.level     = Logger::INFO
+    Rails.logger     = logger
+    Renalware::UKRDC::SendPatients.new(**args.to_h).call
+  end
+end

data/lib/test_support/ajax_helpers.rb

@@ -1,6 +1,6 @@
 module AjaxHelpers
-  def wait_for_ajax
-    Timeout.timeout(Capybara.default_max_wait_time) do
+  def wait_for_ajax(timeout = Capybara.default_max_wait_time)
+    Timeout.timeout(timeout) do
       loop until finished_all_ajax_requests?
     end
   end

data/spec/factories/accesses/patients.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :accesses_patient, class: "Renalware::Accesses::Patient", parent: :patient
 end

data/spec/factories/accesses/plans.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :access_plan, class: Renalware::Accesses::Plan do
     accountable

data/spec/factories/accesses/plans_types.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :access_plan_type, class: Renalware::Accesses::PlanType do
     name "Continue"

data/spec/factories/accesses/procedures.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :access_procedure, class: Renalware::Accesses::Procedure do
     type { create(:access_type) }

data/spec/factories/accesses/profiles.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :access_profile, class: Renalware::Accesses::Profile do
     accountable

data/spec/factories/accesses/sites.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :access_site, class: Renalware::Accesses::Site do
     name "Femoral vein line"

data/spec/factories/accesses/types.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :access_type, class: Renalware::Accesses::Type do
     name "Tunnelled subclav"

data/spec/factories/admissions/admissions.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :admissions_admission, class: "Renalware::Admissions::Admission" do
     accountable

data/spec/factories/admissions/consult_sites.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :admissions_consult_site, class: "Renalware::Admissions::ConsultSite" do
     # accountable

data/spec/factories/admissions/consults.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :admissions_consult, class: "Renalware::Admissions::Consult" do
     accountable

data/spec/factories/admissions/request_reasons.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :admissions_request_reason, class: "Renalware::Admissions::RequestReason" do
     initialize_with do

data/spec/factories/admissions/requests.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 
 FactoryBot.define do
   factory :admissions_request, class: "Renalware::Admissions::Request" do

data/spec/factories/clinical/allergies.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :allergy, class: "Renalware::Clinical::Allergy" do
     patient

data/spec/factories/clinical/body_compositions.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :body_composition, class: "Renalware::Clinical::BodyComposition" do
     accountable

data/spec/factories/clinical/dry_weights.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :dry_weight, class: "Renalware::Clinical::DryWeight" do
     accountable

data/spec/factories/clinical/patients.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :clinical_patient, class: "Renalware::Clinical::Patient", parent: :patient
 end

data/spec/factories/clinics/appointments.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :appointment, class: "Renalware::Clinics::Appointment" do
     patient

data/spec/factories/clinics/clinic_visits.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :clinic_visit, class: "Renalware::Clinics::ClinicVisit" do
     accountable

data/spec/factories/clinics/clinics.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :clinic, class: "Renalware::Clinics::Clinic" do
     name "Access"

data/spec/factories/deaths/cause.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :cause_of_death, class: "Renalware::Deaths::Cause" do
     code "12"

data/spec/factories/deaths/modality_descriptions.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :death_modality_description, class: "Renalware::Deaths::ModalityDescription" do
     initialize_with { Renalware::Deaths::ModalityDescription.find_or_create_by(name: "Death") }

data/spec/factories/directory/people.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :directory_person, class: "Renalware::Directory::Person" do
     accountable

data/spec/factories/drugs/drug.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :drug, class: "Renalware::Drugs::Drug" do
     name "Blue Pill"

data/spec/factories/drugs/drug_types.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :drug_type, class: "Renalware::Drugs::Type" do
     code "immuno"
@@ -7,5 +9,10 @@ FactoryBot.define do
       code "immunosuppressant"
       name "Immunosuppressant"
     end
+
+    trait :esa do
+      code "esa"
+      name "ESA"
+    end
   end
 end