renalware-core 2.0.44 → 2.0.45

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

@@ -1,4 +1,4 @@
 = link_to "#",
         "aria-label" => "Close",
         class: "reveal-modal-close" do
-  i.fa.fa-close
+  i.fas.fa-window-close

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

@@ -9,11 +9,11 @@
   ul.tabs
     li(class= "#{'active' if author == :me}")
       = link_to snippets_path, remote: remote do
-        i.fa.fa-user
+        i.fas.fa-user
         | Mine
     li(class= "#{'active' if author == :anyone}")
       = link_to snippets_path(author: :anyone), remote: remote do
-        i.fa.fa-users
+        i.fas.fa-users
         | Everyone's
 
   = render "search_form", search: search, author: author, remote: remote

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

@@ -12,4 +12,4 @@
                          class: "radius radius-left"
     .columns.small-2.large-1
       = f.button class: "button tiny postfix radius radius-right" do
-        i.fa.fa-search
+        i.fas.fa-search

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

@@ -12,7 +12,7 @@
 
     .columns.small-6.medium-4.end
       = f.button class: "button", name: nil do
-        i.fa.fa-search
+        i.fas.fa-search
         |   Filter
       = " or "
       = link_to "reset", transplants_live_donors_path

data/app/views/renalware/transplants/recipient_dashboards/_modality_missing_warning.html.slim

@@ -1,3 +1,3 @@
 li.missing-modality-warning
-  i.fa.fa-info
+  i.fas.fa-info
   span= message

data/app/views/renalware/transplants/recipient_dashboards/_page_actions.html.slim

@@ -1,6 +1,6 @@
 - if patient.ever_been_a_recipient?
   = link_to(patient_transplants_mdm_path(patient), class: "button with-icon secondary") do
-    i.fa.fa-group
+    i.fas.fa-group
     = t(".mdm")
 
 a.button.dropdown(href="#"

data/config/initializers/ransack.rb

@@ -7,7 +7,7 @@ Ransack.configure do |config|
 
   # Raise errors if a query contains an unknown predicate or attribute.
   # Default is true (do not raise error on unknown conditions).
-  config.ignore_unknown_conditions = !Rails.env.development?
+  config.ignore_unknown_conditions = !(Rails.env.development? || Rails.env.test?)
 
   # Globally display sort links without the order indicator arrow.
   # Default is false (sort order indicators are displayed).

data/config/initializers/renalware.rb

@@ -2,8 +2,26 @@
 
 require_dependency "renalware"
 
-# New subscription registry - previous implementation does not work across threads
-
+# New subscription registry - previous implementation does not work across threads.
+# Each key in the map (hash) is the name of a class that broadacasts/publishes messages.
+# Entries in the array (value) for that key are classes which subscribe to events in the
+# publishing class. If you want a subscriber to listen asynchronously for events via ActiveJob,
+# use an Subscriber instance like so
+# "Renalware::Modalities::ChangePatientModality" => [
+#   Renalware::Broadcasting::Subscriber.new("Renalware::Patients::DummyListener", async: true),
+#   ...
+# ]
+# TODO: Ideally we would like an API something like this:
+#   Renalware.configure do |config|
+#     config.broadcast_subscription_map.configure do |publishers|
+#       publishers[Renalware::Modalities::ChangePatientModality] do |publisher|
+#         publisher.add_subscriber(Renalware::X)
+#         publisher.add_subscriber(Renalware::y, async: true)
+#       end
+#     end
+#   end
+# As it stands its a bit too easy for the exposed subscription map hash to be overwritten by a host
+# application with confusing and undesirable outcomes.
 Renalware.configure do |config|
   config.broadcast_subscription_map = {
     "Renalware::Modalities::ChangePatientModality" => [

data/config/locales/renalware/reporting/reporting_daily.en.yml

@@ -0,0 +1,7 @@
+en:
+  renalware:
+    reporting:
+      reporting_daily_pathology:
+        title: Pathology
+      reporting_daily_letters:
+        title: Letters

data/config/locales/renalware/virology/virology.en.yml

@@ -23,3 +23,4 @@ en:
         hbv3: HBV Vaccination 3
         hbv4: HBV Vaccination 4
         hbv_booster: HBV Booster
+        patient_refused: Patient Refused

data/db/migrate/20180831134606_add_reporting_indexes.rb

@@ -0,0 +1,13 @@
+class AddReportingIndexes < ActiveRecord::Migration[5.1]
+  def up
+    connection.execute(<<-SQL)
+      CREATE INDEX pathology_observations_created_on ON pathology_observations USING btree ((created_at::date));
+    SQL
+  end
+
+  def down
+    connection.execute(<<-SQL)
+      DROP INDEX pathology_observations_created_on;
+    SQL
+  end
+end

data/db/migrate/20180831134926_create_daily_reports.rb

@@ -0,0 +1,6 @@
+class CreateDailyReports < ActiveRecord::Migration[5.1]
+  def change
+    create_view :reporting_daily_pathology
+    create_view :reporting_daily_letters
+  end
+end

data/db/seeds/default/reporting/audits.yml

@@ -1,6 +1,6 @@
 -
   name: Main Authors
-  description: A list of authors with their letter statistics.
+  description: A list of authors with statistics across the last 3 months of letters.
   view_name: reporting_main_authors_audit
   materialized: true
   refresh_schedule: "1 0 * * *"
@@ -329,4 +329,3 @@
         }
       ]
     }
-

data/db/views/reporting_daily_letters_v01.sql

@@ -0,0 +1,3 @@
+select
+  (select count(*) from letter_letters where created_at::date = now()::date) as letters_created_today,
+  (select count(*) from letter_letters where completed_at::date = now()::date) as letters_printed_today;

data/db/views/reporting_daily_pathology_v01.sql

@@ -0,0 +1,16 @@
+-- A pathology report to help identify any HL7/delayed_job issues
+-- the name of the view (the filename here) is significant as we'll compile all reporting_daily_*
+-- views into a daily digest email
+select
+  (select count(*) from delayed_jobs) as delayed_jobs_total,
+  (select count(*) from delayed_jobs where attempts = 0) as delayed_jobs_unprocessed,
+  (select count(*) from delayed_jobs where last_error is not null and failed_at is null ) as delayed_jobs_retrying,
+  (select count(*) from delayed_jobs where last_error is not null and failed_at is null ) as delayed_jobs_failed,
+  (select max(created_at) from delayed_jobs) as delayed_jobs_latest_entry,
+  (select count(*) from delayed_jobs where created_at >= now()::date) as delayed_jobs_added_today,
+  (select jsonb_agg(query) from (select priority, count(*) from delayed_jobs group by priority ) query) as delayed_jobs_priority_counts,
+  (select count(*) from feed_messages) as feed_messages_total,
+  (select count(*) from feed_messages where created_at >= now()::date) as feed_messages_added_today,
+  (select max(created_at) from feed_messages) as feed_messages_added_latest_entry, -- will be slow, needs index on feed_messages.created_at
+  (select count(*) from pathology_observations where created_at::date >= now()::date) as pathology_observations_added_today,
+  (select max(observed_at) from pathology_observations) as pathology_observations_latest_observed_at;

data/lib/gpg_encrypt_folder.rb

@@ -0,0 +1,74 @@
+# frozen_string_literal: true
+
+require "attr_extras"
+
+# Shell out to gpg with a a command like this
+# gpg --armor --no-default-keyring --keyring keyring.gpg
+#     --trust-model always -r 'renalware_test'
+#     --output output.xml.enc
+#     --encrypt input.xml
+#
+# Note if you want to see a more verbose output you can add -vv but don't do this here
+# as it outputs info to stderr and causes an error to be raised.
+#
+# Some options may be omitted optional depending on how GPG is set up however as we may use
+# more than 1 GPG key on thie server, we are explicitly setting the
+# Recipient may be optional e.g. --recipient 'patient view'
+class GpgEncryptFolder
+  pattr_initialize [:folder!, :options!]
+
+  def call
+    Dir.glob(folder.join("xml", "*.xml")) do |file|
+      GpgEncryptFile.new(file: file, options: options).call
+    end
+  end
+end
+
+class GpgOptions
+  attr_reader_initialize [:recipient, :keyring, :homedir, :filename_transform]
+end
+
+class GpgEncryptFile
+  pattr_initialize [:file!, :options!]
+
+  def call
+    err = Open3.popen3(gpg_command) do |_stdin, _stdout, stderr|
+      stderr.read
+    end
+    raise "Error encrypting UKRDC files: #{err}" unless err.empty?
+  end
+
+  private
+
+  def gpg_command
+    GpgCommand.new(file: file, options: options).to_s
+  end
+end
+
+class GpgCommand
+  pattr_initialize [:file!, :options!]
+
+  def to_s
+    "gpg --armor --no-default-keyring --trust-model always "\
+      "#{keyring} #{homedir} #{recipient} "\
+      "-o #{encrypted_filename} "\
+      "--encrypt #{file}"
+  end
+
+  def recipient
+    options.recipient && "--recipient #{options.recipient}"
+  end
+
+  def homedir
+    options.homedir && "--homedir #{options.homedir}"
+  end
+
+  def keyring
+    "--keyring #{options.keyring}"
+  end
+
+  # Calls a proc to transform the in file name into an out file name
+  def encrypted_filename
+    options.filename_transform.call(file)
+  end
+end

data/lib/renalware/configuration.rb

@@ -56,6 +56,11 @@ module Renalware
     config_accessor(:ukrdc_default_changes_since_date) {
       Date.parse(ENV.fetch("UKRDC_DEFAULT_CHANGES_SINCE_DATE", "2018-01-01"))
     }
+    config_accessor(:ukrdc_gpg_recipient) { ENV.fetch("UKRDC_GPG_RECIPIENT", "renalware_test") }
+    config_accessor(:ukrdc_gpg_homedir) { ENV["UKRDC_GPG_HOMEDIR"] }
+    config_accessor(:ukrdc_gpg_keyring) do
+      ENV.fetch("UKRDC_GPG_KEYRING", Engine.root.join("config", "gpg", "renalware_test.gpg"))
+    end
 
     # We override this in some tests as a means of getting wicked_Pdf to generate an HTML version
     # of the PDF so we can examine its content

data/lib/renalware/engine.rb

@@ -18,7 +18,7 @@ require "dotenv-rails"
 require "dumb_delegator"
 require "email_validator"
 require "enumerize"
-require "font-awesome-rails"
+require "font-awesome-sass"
 require "foundation-rails"
 require "friendly_id"
 require "hashdiff"
@@ -51,6 +51,7 @@ require "validates_timeliness"
 require "virtus"
 require "wicked_pdf"
 require "wisper"
+require "wisper/activejob"
 require "rails-assets-foundation-datepicker"
 require "rails-assets-select2"
 if ENV["RAILS_ENV"] == "development"
@@ -79,9 +80,9 @@ module Renalware
     config.autoload_paths += Dir["#{config.root}/lib/**/"]
     config.autoload_paths += %W(#{config.root}/app/validators/concerns)
 
-    config.generators do |g|
-      g.test_framework :rspec
-      g.fixture_replacement :factory_girl, dir: "../../spec/factories"
+    config.generators do |gens|
+      gens.test_framework :rspec
+      gens.fixture_replacement :factory_girl, dir: "../../spec/factories"
     end
 
     initializer :add_locales do |app|

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.44"
+  VERSION = "2.0.45"
 end

data/lib/tasks/audit.rake

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 begin
   namespace :audit do
     desc <<-DESC
@@ -23,6 +25,9 @@ begin
         month: ENV["month"],
         year: ENV["year"]
       ).call
+
+      # Refresh the materialized view which will aggregate the monthly hd_patient_statistics data
+      RefreshMaterializedViewJob.perform_later(view_name: "renalware.reporting_hd_overall_audit")
     end
   end
 end

data/lib/tasks/reporting.rake

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+namespace :reporting do
+  desc "Send a daily system report email to confguired recpients"
+  task send_daily_summary_email: :environment do
+    recipents = Array(ENV.fetch("DAILY_REPORT_EMAIL_RECIPIENTS", "dev@airslie.com").split(","))
+    Renalware::Reporting::ReportMailer.daily_summary(to: recipents)
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.44
+  version: 2.0.45
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-29 00:00:00.000000000 Z
+date: 2018-09-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -212,14 +212,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.4.0
+        version: 4.5.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.4.0
+        version: 4.5.0
 - !ruby/object:Gem::Dependency
   name: dotenv-rails
   requirement: !ruby/object:Gem::Requirement
@@ -277,19 +277,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 2.2.2
 - !ruby/object:Gem::Dependency
-  name: font-awesome-rails
+  name: font-awesome-sass
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.7.0.3
+        version: 5.3.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.7.0.3
+        version: 5.3.1
 - !ruby/object:Gem::Dependency
   name: foundation-rails
   requirement: !ruby/object:Gem::Requirement
@@ -548,14 +548,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.1.3
 - !ruby/object:Gem::Dependency
   name: puma
   requirement: !ruby/object:Gem::Requirement
@@ -576,14 +576,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: rack-attack
   requirement: !ruby/object:Gem::Requirement
@@ -646,14 +646,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.7
+        version: 2.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.7
+        version: 2.0.1
 - !ruby/object:Gem::Dependency
   name: record_tag_helper
   requirement: !ruby/object:Gem::Requirement
@@ -683,19 +683,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 1.2.0
 - !ruby/object:Gem::Dependency
-  name: sass-rails
+  name: sassc-rails
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.0.7
+        version: 1.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.0.7
+        version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: scenic
   requirement: !ruby/object:Gem::Requirement
@@ -864,6 +864,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
+- !ruby/object:Gem::Dependency
+  name: wisper-activejob
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: wkhtmltopdf-binary
   requirement: !ruby/object:Gem::Requirement
@@ -1284,6 +1298,7 @@ files:
 - app/jobs/application_job.rb
 - app/jobs/feed_job.rb
 - app/jobs/hl7_message_example.yml
+- app/jobs/refresh_materialized_view_job.rb
 - app/jobs/renalware/hd/generate_monthly_statistics.rb
 - app/jobs/renalware/hd/generate_monthly_statistics_for_patient_job.rb
 - app/jobs/renalware/hd/update_rolling_patient_statistics_job.rb
@@ -1292,7 +1307,9 @@ files:
 - app/mailers/renalware/admin/user_mailer.rb
 - app/mailers/renalware/letters/delivery/errors.rb
 - app/mailers/renalware/letters/delivery/practice_mailer.rb
+- app/mailers/renalware/previews/report_preview.rb
 - app/mailers/renalware/previews/user_mailer_preview.rb
+- app/mailers/renalware/reporting/report_mailer.rb
 - app/models/application_record.rb
 - app/models/concerns/renalware/accountable.rb
 - app/models/concerns/renalware/broadcasting.rb
@@ -2602,6 +2619,8 @@ files:
 - app/views/renalware/reporting/audits/edit.html.slim
 - app/views/renalware/reporting/audits/index.html.slim
 - app/views/renalware/reporting/audits/show.html.slim
+- app/views/renalware/reporting/report_mailer/daily_summary.html.slim
+- app/views/renalware/reporting/report_mailer/daily_summary.text.erb
 - app/views/renalware/research/_alert.html.slim
 - app/views/renalware/research/_alerts.html.slim
 - app/views/renalware/research/studies/_form.html.slim
@@ -2761,6 +2780,7 @@ files:
 - config/autoprefixer.yml
 - config/cable.yml
 - config/cucumber.yml
+- config/gpg/renalware_test.gpg
 - config/initializers/ahoy.rb
 - config/initializers/backtrace_silencers.rb
 - config/initializers/client_side_validations.rb
@@ -2867,6 +2887,7 @@ files:
 - config/locales/renalware/renal/profile.en.yml
 - config/locales/renalware/renal/registry.en.yml
 - config/locales/renalware/reporting/audit.en.yml
+- config/locales/renalware/reporting/reporting_daily.en.yml
 - config/locales/renalware/research/study_participant.en.yml
 - config/locales/renalware/shared.yml
 - config/locales/renalware/snippets/snippets.en.yml
@@ -3308,6 +3329,8 @@ files:
 - db/migrate/20180803131157_add_uuid_to_hd_transmission_logs.rb
 - db/migrate/20180814103916_create_index_on_lower_patient_family_name.rb
 - db/migrate/20180815144429_update_hd_overall_audit_to_version_8.rb
+- db/migrate/20180831134606_add_reporting_indexes.rb
+- db/migrate/20180831134926_create_daily_reports.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3407,6 +3430,8 @@ files:
 - db/views/patient_summaries_v06.sql
 - db/views/reporting_anaemia_audit_v01.sql
 - db/views/reporting_bone_audit_v01.sql
+- db/views/reporting_daily_letters_v01.sql
+- db/views/reporting_daily_pathology_v01.sql
 - db/views/reporting_hd_blood_pressures_audit_v01.sql
 - db/views/reporting_hd_overall_audit_v01.sql
 - db/views/reporting_hd_overall_audit_v02.sql
@@ -3442,6 +3467,7 @@ files:
 - lib/dropdown_button_item.rb
 - lib/duration_calculator.rb
 - lib/git_commit_sha.rb
+- lib/gpg_encrypt_folder.rb
 - lib/hash_collection.rb
 - lib/inline_image.rb
 - lib/numeric_inclusion_validator.rb
@@ -3468,6 +3494,7 @@ files:
 - lib/tasks/feeds/files.rake
 - lib/tasks/hd.rake
 - lib/tasks/pathology.rake
+- lib/tasks/reporting.rake
 - lib/tasks/ukrdc.rake
 - lib/templates/slim/scaffold/_form.html.slim
 - lib/test_support/ajax_helpers.rb