renalware-core 2.0.0.pre.beta11 → 2.0.0.pre.beta12

data/app/views/renalware/pd/regimes/edit.html.slim

@@ -10,7 +10,7 @@
                           html: { class: "pd-form" },
                           method: :put do |f|
 
-    = render partial: "renalware/pd/regimes/form",  locals: local_assigns.merge!(f: f)
+    = render partial: "renalware/pd/regimes/form", locals: local_assigns.merge!(f: f)
 
     .row
       .large-12.columns

data/app/views/renalware/pd/regimes/show.html.slim

@@ -20,7 +20,7 @@
               = render("renalware/pd/regimes/assistance_type", regime: regime)
             dt On additional HD?:
             dd= yes_no(regime.add_hd)
-            = render"renalware/pd/regimes/glucose", regime: regime
+            = render "renalware/pd/regimes/glucose", regime: regime
 
     - if regime.apd?
       = render "renalware/pd/regimes/apd_regime_show", regime: regime

data/app/views/renalware/pd/training_sessions/_form.html.slim

@@ -15,7 +15,7 @@
       collection: Renalware::PD::TrainingType.ordered,
       wrapper: :horizontal_medium
 
-  = f.simple_fields_for :document, training_session.document  do |fdoc|
+  = f.simple_fields_for :document, training_session.document do |fdoc|
     = fdoc.input :started_on, as: :date_picker, wrapper: :horizontal_datepicker
     = fdoc.input :trainer, wrapper: :horizontal_medium
     = fdoc.input :training_duration,

data/app/views/renalware/renal/registry_preflight_checks/_table.html.slim

@@ -4,7 +4,11 @@ table.renal-registry-preflight-checks
       th.col-width-large Patient
       td.col-width-nhs-no NHS No.
       td.col-width-reference-no Hospital Nos.
-      td.col-width-reference-no Modality
+      td.col-width-reference-no
+        = sort_link([:renalware, query],
+                     :modality_descriptions_name,
+                      "Modality",
+                      default_order: :asc)
       td.col-width-small HD Site
       td Missing data
   tbody

data/app/views/renalware/renal/registry_preflight_checks/deaths.html.slim

@@ -1,4 +1,4 @@
 = within_admin_layout(title: "Renal Registry Return: Preflight Checks") do
   = render "navigation"
-  = render "table", patients: patients
+  = render "table", patients: patients, query: query
   = paginate patients

data/app/views/renalware/renal/registry_preflight_checks/patients.html.slim

@@ -1,4 +1,4 @@
 = within_admin_layout(title: "Renal Registry Return: Preflight Checks") do
   = render "navigation"
-  = render "table", patients: patients
+  = render "table", patients: patients, query: query
   = paginate patients

data/app/views/renalware/research/studies/_form.html.slim

@@ -6,4 +6,3 @@
   = f.input :terminated_on, as: :date_picker, wrapper: :horizontal_datepicker
   = f.input :notes, as: :text, wrapper: :horizontal_large, input_html: { rows: 6 }
   = save_or_cancel(form: f, back_path: research_studies_path)
-

data/app/views/renalware/research/studies/show.html.slim

@@ -16,4 +16,3 @@
       - study.participants.each do |participant|
         tr
           td= participant
-

data/app/views/renalware/research/study_participants/_form.html.slim

@@ -15,7 +15,7 @@ ruby:
     = simple_form_for(participant,
                       url: url,
                       remote: true,
-                      html: { autocomplete: "off"},
+                      html: { autocomplete: "off" },
                       wrapper: :horizontal_form) do |f|
       - if participant.persisted?
         h5= participant.patient.to_s(:long)
@@ -42,4 +42,3 @@ ruby:
 
 javascript:
   $(document).ready(Renalware.Research.init);
-

data/app/views/renalware/shared/_last_update.html.slim

@@ -1,4 +1,5 @@
 - if record.persisted?
+  / TODO: Bug here with assignment?
   - if version = record.versions.last
     span.note
       | Last update: 

data/app/views/renalware/shared/documents/_attributes_group.html.slim

@@ -3,7 +3,7 @@ ruby:
   attributes = group.class.attributes_list
 
 = render "renalware/shared/attributes_group",
-          local_assigns.merge!({ models: { model => attributes }} )
+          local_assigns.merge!({ models: { model => attributes } })
           / destination: local_assigns[:destination],
           / legend: legend,
           / size:

data/app/views/renalware/shared/documents/_dated_result.html.slim

@@ -1 +1 @@
-= dated_result.to_s
+= dated_result.to_s

data/app/views/renalware/snippets/snippets/_row.html.slim

@@ -25,7 +25,7 @@ tr(data={ "snippet-id" => snippet.id, invocation_url: snippet_invocations_path(s
     td.col-width-medium.author= snippet.author
   -unless remote
     td.last_used_on
-      = "#{snippet.last_used_on? ? l(snippet.last_used_on) : "Never"} (#{snippet.times_used})"
+      = "#{snippet.last_used_on? ? l(snippet.last_used_on) : 'Never'} (#{snippet.times_used})"
     td.updated_at= l(snippet.updated_at)
     td.actions
 

data/app/views/renalware/transplants/donations/edit.html.slim

@@ -1,5 +1,5 @@
 = within_patient_layout(title: "Edit",
-                        breadcrumbs: [ donor_summary_breadcrumb(patient),
+                        breadcrumbs: [donor_summary_breadcrumb(patient),
                                       donor_donation_breadcrumb(patient, donation)]) do
   .document
     = simple_form_for donation,

data/app/views/renalware/transplants/donor_followups/edit.html.slim

@@ -1,4 +1,3 @@
-
 = within_patient_layout(title: "Follow-up / Edit",
     breadcrumbs: [donor_summary_breadcrumb(patient)]) do
 

data/app/views/renalware/transplants/donor_followups/show.html.slim

@@ -1,4 +1,3 @@
-
 = content_for(:actions) do
   = link_to t("edit_record.link_title"),
             edit_patient_transplants_donor_operation_followup_path(patient,

data/app/views/renalware/transplants/live_donors/_index.html.slim

@@ -1,4 +1,3 @@
-
 = render_if_exists "filters", search: q
 
 table#patients.live-donors.columns

data/app/views/renalware/transplants/recipient_operations/_sections_nav.html.slim

@@ -11,4 +11,4 @@ ruby:
 dl.sub-nav data-magellan-expedition="fixed"
   - sections.each do |title, target|
     dd data-magellan-arrival="#{target}"
-      = link_to title, "#"+target
+      = link_to title, "#" + target

data/app/views/renalware/transplants/recipient_workups/_sections_nav.html.slim

@@ -12,4 +12,4 @@ ruby:
 dl.sub-nav data-magellan-expedition="fixed"
   - sections.each do |title, target|
     dd data-magellan-arrival="#{target}"
-      = link_to title, "#"+target
+      = link_to title, "#" + target

data/config/initializers/delayed_job.rb

@@ -0,0 +1 @@
+Delayed::Worker.logger = Logger.new(Rails.root.join("log", "delayed_job.log"))

data/config/initializers/ransack.rb

@@ -1,5 +1,4 @@
 Ransack.configure do |config|
-
   # Change default search parameter key name.
   # Default key name is :q
   # config.search_key = :query

data/config/initializers/simple_form.rb

@@ -5,8 +5,10 @@ SimpleForm.setup do |config|
   # wrapper, change the order or even add your own to the
   # stack. The options given below are used to wrap the
   # whole input.
-  config.wrappers :default, class: :input,
-    hint_class: :field_with_hint, error_class: :field_with_errors do |b|
+  config.wrappers(:default,
+                  class: :input,
+                  hint_class: :field_with_hint,
+                  error_class: :field_with_errors) do |b|
     ## Extensions enabled by default
     # Any of these extensions can be disabled for a
     # given input by passing: `f.input EXTENSION_NAME => false`.

data/config/initializers/simple_form_foundation.rb

@@ -138,8 +138,11 @@ SimpleForm.setup do |config|
     end
   end
 
-  config.wrappers :horizontal_form, tag: "div", class: "row",
-    hint_class: :field_with_hint, error_class: :error do |b|
+  config.wrappers(:horizontal_form,
+                  tag: "div",
+                  class: "row",
+                  hint_class: :field_with_hint,
+                  error_class: :error) do |b|
     b.use :html5
     b.use :placeholder
     b.optional :maxlength
@@ -228,8 +231,9 @@ SimpleForm.setup do |config|
   # The default wrapper to be used by the FormBuilder.
   config.default_wrapper = :vertical_form
 
-  config.wrappers :two_columns_table_row, tag: "tr",
-    hint_class: :field_with_hint, error_class: :error do |b|
+  config.wrappers(:two_columns_table_row,
+                  tag: "tr",
+                  hint_class: :field_with_hint, error_class: :error) do |b|
     b.use :html5
     b.use :placeholder
     b.optional :maxlength

data/config/locales/renalware/dashboard/dashboard.yml

@@ -23,5 +23,6 @@ en:
           age: Age
           sex: Sex
           notes: Notes
+          tags: Tags
           modality: Modality
           bookmarked_on: Bookmarked

data/config/locales/renalware/renal/profile.en.yml

@@ -59,13 +59,16 @@ en:
         capd_la: CAPD LA
         capd_ga: CAPD GA
         capd_ga_avf: CAPD GA + AVF
+        capd_ga_hernia: CAPD GA + Hernia Repair
+        capd_la_avf: CAPD LA + AVF
         capd_la_sedation: CAPD LA with sedation
+        capd_not_yet_assessed: CAPD not yet assessed by CAPD Team
         hd_via_avf: HD via AVF
         hd_via_ptfe_graft: HD via PTFE Graft
         hd_via_line: HD via line
         pre_emptive_lrd: pre-emptive LRD
         not_for_dial_patient_choice: Not for dialysis--patient choice
-        not_for_dial_concensus: Not for dialysis--consensus
+        not_for_dial_consensus: Not for dialysis--consensus
         refuse_to_plan_for_dial: Refusing to plan for RTT--In Denial
         home_hd: Home HD
         self_care_hd: Self Care HD

data/config/routes.rb

@@ -1,6 +1,5 @@
 # rubocop:disable Style/FormatStringToken
 Renalware::Engine.routes.draw do
-
   match "/404", to: "system/errors#not_found", via: :all
   match "/500", to: "system/errors#internal_server_error", via: :all
   match "/generate_test_internal_server_error",

data/db/migrate/20141004150240_create_ethnicities.rb

@@ -1,6 +1,6 @@
 class CreateEthnicities < ActiveRecord::Migration[4.2]
   def change
-    create_table :patient_ethnicities do |t|
+    create_table "patient_ethnicities" do |t|
       t.string :name
       t.timestamps null: false
     end

data/db/migrate/20171113120217_add_uuid_to_hd_sessions.rb

@@ -0,0 +1,6 @@
+class AddUuidToHDSessions < ActiveRecord::Migration[5.1]
+  def change
+    add_column :hd_sessions, :uuid, :uuid, default: 'uuid_generate_v4()', null: false
+    add_index :hd_sessions, :uuid
+  end
+end

data/db/migrate/20171116103230_move_objects_to_renalware_schema.rb

@@ -0,0 +1,63 @@
+# This migration moves all engine-specific objects into the renalware schema.
+# See also
+#   schema_search_path: "renalware,public"
+# in database.yml - we look for objects in the renalware schema first.
+#
+# Someone developing a host application can create custom tables, views etc in the
+# public schema and these will be found provided either
+# - their name is unique and does not clash with a name in the renalware schema, or
+# - they specify the schema in the model. For example if they are creating their own Patient model
+#   and `patients` table, they will need to use
+#     self.table_name = "public.patients"
+#   in order to avoid a clash with renalware.patients, which is the first entry
+#   in schema_search_path.
+# - . This lets us ring fence renalware db objects and prevent
+# name clashes as long as if for instance a host app defines a patients table in the public schema
+# they reference it as public.patients otherwise renalware.patients will be used.
+#
+class MoveObjectsToRenalwareSchema < ActiveRecord::Migration[5.1]
+  FUNCTIONS = [
+    "refresh_all_matierialized_views(text, boolean)",
+    "audit_view_as_json(text)"
+  ]
+
+  def db_objects_of_type(type:, in_schema:)
+    results = execute "SELECT table_name FROM information_schema.tables "\
+                      "WHERE table_schema='#{in_schema}' AND table_type='#{type}' " \
+                      "and table_name not in ('schema_migrations','ar_internal_metadata')"
+    results.map{ |obj| obj["table_name"] }
+  end
+
+  def views(in_schema:)
+    db_objects_of_type(type: "VIEW", in_schema: in_schema)
+  end
+
+  def materialized_views(in_schema:)
+    results = execute(
+      "SELECT oid::regclass::text as table_name FROM pg_class WHERE  relkind = 'm';"
+    )
+    results.map{ |obj| obj["table_name"] }
+  end
+
+  def tables(in_schema:)
+    db_objects_of_type(type: "BASE TABLE", in_schema: in_schema)
+  end
+
+  def up
+    execute "CREATE SCHEMA IF NOT EXISTS renalware"
+
+    tables(in_schema: "public").each{ |table| execute("ALTER TABLE #{table} SET SCHEMA renalware") }
+    views(in_schema: "public").each{ |view| execute("ALTER VIEW #{view} SET SCHEMA renalware") }
+    materialized_views(in_schema: "public").each{ |view| execute("ALTER MATERIALIZED VIEW #{view} SET SCHEMA renalware") }
+    FUNCTIONS.each{ |fn| execute "ALTER FUNCTION #{fn} SET SCHEMA renalware" }
+    # This causes an error on Heroku
+    # execute "ALTER EXTENSION \"uuid-ossp\" SET SCHEMA public;"
+  end
+
+  def down
+    tables(in_schema: "renalware").each{ |table| execute("ALTER TABLE #{table} SET SCHEMA public") }
+    views(in_schema: "renalware").each{ |view| execute("ALTER VIEW #{view} SET SCHEMA public") }
+    materialized_views(in_schema: "renalware").each{ |view| execute("ALTER MATERIALIZED VIEW #{view} SET SCHEMA public") }
+    FUNCTIONS.each{ |fn| execute "ALTER FUNCTION #{fn} SET SCHEMA public" }
+  end
+end

data/db/migrate/20171118160030_add_tags_to_patient_bookmarks.rb

@@ -0,0 +1,5 @@
+class AddTagsToPatientBookmarks < ActiveRecord::Migration[5.1]
+  def change
+    add_column :patient_bookmarks, :tags, :string
+  end
+end

data/lib/collection_presenter.rb

@@ -33,9 +33,7 @@ class CollectionPresenter
     @decorated_collection.to_a
   end
 
-  def size
-    to_ary.size
-  end
+  delegate :size, to: :to_ary
 
   def to_json
     @decorated_collection.map(&:to_hash).to_json

data/lib/document/attribute_initializer.rb

@@ -4,7 +4,6 @@ require "document/attribute_initializer/enum"
 
 module Document
   module AttributeInitializer
-
     def self.determine_initializer(klass, name, type, options)
       initializer_class = build_class(type)
       initializer_class.new(klass, name, type, options)

data/lib/document/base.rb

@@ -28,7 +28,7 @@ module Document
       end
 
       def document=(attributes)
-        return unless attributes.present?
+        return if attributes.blank?
         filtered_attributes = filter_date_params(attributes)
         @document = document_class.new(filtered_attributes)
         serialize_document

data/lib/renalware/configuration.rb

@@ -22,7 +22,7 @@ module Renalware
     config_accessor(:salutation_prefix) { "Dear" }
     config_accessor(:page_title_spearator) { " : " }
     config_accessor(:patient_hospital_identifiers) { {} }
-    config_accessor(:session_timeout_polling_frequency) { 15.seconds }
+    config_accessor(:session_timeout_polling_frequency) { 1.minute }
     config_accessor(:duration_of_last_url_memory_after_session_expiry) { 30.minutes }
     config_accessor(:broadcast_subscription_map) { {} }
     config_accessor(:include_sunday_on_hd_diaries) { false }

data/lib/renalware/engine.rb

@@ -54,7 +54,6 @@ if ENV["RAILS_ENV"] == "development"
 end
 
 module Renalware
-
   # Don't have prefix method return anything.
   # This will keep Rails Engine from generating all table prefixes with the engines name
   def self.table_name_prefix; end
@@ -80,6 +79,26 @@ module Renalware
       app.config.i18n.fallbacks = [:en]
     end
 
+    # In production use lograge to help us tame a verbose logs/production.log.
+    # Note that the timestamp will be added before the lograge output by whatever Rails
+    # LogFormatter is being used (see the app's production.rb) e.g.
+    #   config.log_formatter = ::Logger::Formatter.new
+    # So bear in mind both log_formatter and lograge are involved in logging.
+    # Note exceptions will still be logged including the stacktrace.
+    initializer :use_lograge_in_production do |app|
+      unless Rails.env.development?
+        require "lograge"
+        app.config.lograge.enabled = true
+
+        # Ignore session expiry JS polling as these calls fill up the log and we don't
+        # need to see them. 100 users with an active session polling every minute will add
+        # up to fair number of log entries.
+        app.config.lograge.ignore_actions = [
+          "Renalware::SessionTimeoutController#has_user_timed_out"
+        ]
+      end
+    end
+
     config.middleware.use Rack::Attack
     initializer :rack_attack do
       # Throttle login attempts for a given username parameter to 10 reqs/minute
@@ -141,6 +160,7 @@ module Renalware
     initializer :general do |app|
       app.config.time_zone = "London"
       app.config.active_record.time_zone_aware_types = [:datetime]
+      app.config.active_record.dump_schemas = :all
       unless Rails.env.development?
         app.config.exceptions_app = Engine.routes
       end

data/lib/renalware/version.rb

@@ -1,3 +1,3 @@
 module Renalware
-  VERSION = "2.0.0.pre.beta11".freeze
+  VERSION = "2.0.0.pre.beta12".freeze
 end

data/lib/smart_delegator.rb

@@ -19,7 +19,6 @@
 #           invokes `mymessage` returning self ->
 #             returns SmartDelegator decorating OriginalObject
 class SmartDelegator
-
   attr_reader :object
 
   def initialize(object)

data/lib/test_support/autocomplete_helpers.rb

@@ -2,11 +2,11 @@ module AutocompleteHelpers
   def fill_autocomplete(form, field, options = {})
     fill_in field, with: options[:with]
 
-    page.execute_script %Q{ $('#{form}').find('[name=#{field}]').trigger('focus') }
-    page.execute_script %Q{ $('#{form}').find('[name=#{field}]').trigger('keydown') }
+    page.execute_script " $('#{form}').find('[name=#{field}]').trigger('focus') "
+    page.execute_script " $('#{form}').find('[name=#{field}]').trigger('keydown') "
     selector = %Q{ul.ui-autocomplete li.ui-menu-item:contains("#{options[:select]}")}
 
     expect(page).to have_selector("ul.ui-autocomplete li.ui-menu-item")
-    page.execute_script %Q{ $('#{selector}').trigger('mouseenter').click() }
+    page.execute_script " $('#{selector}').trigger('mouseenter').click() "
   end
 end

data/spec/factories/clinical/body_compositions.rb

@@ -2,7 +2,7 @@ FactoryBot.define do
   factory :body_composition, class: "Renalware::Clinical::BodyComposition" do
     accountable
     patient
-    assessed_on 1.week.ago
+    assessed_on { 1.week.ago }
     overhydration "19.1"
     volume_of_distribution "52.1"
     total_body_water "23.1"