renalware-core 2.0.0.pre.rc13 → 2.0.0

data/app/views/renalware/research/_alert.html.slim

@@ -0,0 +1,6 @@
+li.patient-alert.research-study-participant
+  i.fa.fa-warning
+  span.title= link_to(participation.study.code, research_study_participants_path(participation.study))
+  span.body participant
+  span.date= l(participation.joined_on)
+

data/app/views/renalware/research/_alerts.html.slim

@@ -0,0 +1,6 @@
+/ Note the caching here relies on study_participant edit/create/destroy touching patient
+- cache(patient)
+  - participations = Renalware::Research::StudyParticipant.where(participant_id: patient.id).where("joined_on <= ?", Time.zone.now).where("left_on is null or left_on > ?", Time.zone.now)
+  = render partial: "renalware/research/alert",
+           collection: participations,
+           as: :participation

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

@@ -30,3 +30,5 @@
             = link_to "Edit", edit_research_study_path(study)
             = " | "
             = link_to "View Participants", research_study_participants_path(study)
+
+  = paginate studies

data/app/views/renalware/system/email_templates/index.html.slim

@@ -1,12 +1,11 @@
-.row
-  .large-12.columns
-    h2 System Email Templates
+ = within_admin_layout(title: "System Email Templates") do
 
+  .panel
     p Listed below are previews of the email templates sent by this application.
 
-    dl
-      dt= link_to "User Approval Email", "/rails/mailers/renalware/admin/user_mailer/approval"
-      dd Sent when an administrator approves a user's registration.
+  dl
+    dt= link_to "User Approval Email", "/rails/mailers/renalware/admin/user_mailer/approval"
+    dd Sent when an administrator approves a user's registration.
 
-      dt= link_to "User Reactivated Email", "/rails/mailers/renalware/admin/user_mailer/unexpiry"
-      dd Sent when an administrator reactivates a deactivated user.
+    dt= link_to "User Reactivated Email", "/rails/mailers/renalware/admin/user_mailer/unexpiry"
+    dd Sent when an administrator reactivates a deactivated user.

data/app/views/renalware/system/user_feedback/new.html.slim

@@ -1,13 +1,9 @@
 = within_admin_layout(title: "Send Us Feedback") do
-
   = simple_form_for(feedback, as: :feedback, wrapper: :horizontal_form) do |f|
-
+    .panel
+      | Please do not include any patient identifiable data
     = f.input :category, include_blank: false, as: :radio_buttons
     = f.input :comment, as: :text
-    .row
-      .small-3.columns
-        label.right.inline From
-      .small-9.columns
-        = current_user.username
+
     br
     = f.submit "Submit", class: :button

data/app/views/renalware/transplants/mdm/_pathology_cmvdna.html.slim

@@ -4,4 +4,3 @@ article
 
   = render "renalware/pathology/historical_observation_results/table",
            table: mdm.cmvdna_pathology
-  /= mdm.cmvdna_pathology.table.render(mdm.cmvdna_pathology.rows)

data/app/views/renalware/virology/vaccinations/_toggled_cell.html.slim

@@ -5,4 +5,4 @@ dl.dl-horizontal
   dt= attr_name(document, :type, suffix: ":")
   dd= document.type&.text || t("unspecified")
   dt= attr_name(event, :notes, suffix: ":")
-  dd= event.notes || t("unspecified")
+  dd= event.notes&.html_safe || t("unspecified")

data/config/initializers/ahoy.rb

@@ -0,0 +1,14 @@
+class Ahoy::Store < Ahoy::DatabaseStore
+  def visit_model
+    Renalware::System::Visit
+  end
+
+  def event_model
+    Renalware::System::Event
+  end
+end
+
+# set to true for JavaScript tracking
+Ahoy.api = false
+Ahoy.visit_duration = 30.minutes
+Ahoy.geocode = false

data/config/locales/renalware/events/investigation.en.yml

@@ -21,11 +21,13 @@ en:
         cardiac_24_hour_abpm: "Cardiac - 24 hour ABPM"
         cardiac_24_hour_ecg: "Cardiac - 24 hr ECG"
         cardiac_coronary_angio: "Cardiac - Coronary Angio"
+        cardiac_periph_angio: "Cardiac - Peripheral Angio"
         cardiac_cpet: "Cardiac - CPET"
         cardiac_ecg: "Cardiac - ECG"
         cardiac_echo: "Cardiac - Echo"
         cardiac_exercise_ecg: "Cardiac - Exercise ECG"
         cardiac_myoview_scan: "Cardiac - Myoview Scan"
+        cardiac_muga_scan: "Cardiac - MUGA Scan"
         cardiac_stress_echo: "Cardiac - Stress Echo"
         cervical_smear: "Cervical Smear"
         colonoscopy: "Colonoscopy"
@@ -37,19 +39,25 @@ en:
         dental_check: "Dental Check"
         psa: "PSA"
         isotopic_gfr: "Isotopic GFR"
+        lung_biopsy: "Lung Biopsy"
         lung_function_tests: "Lung Function Tests"
         imaging_bone Scan: "Imaging - Bone Scan"
         imaging_ct_abdomen: "Imaging - CT Abdomen"
         imaging_ct_chest: "Imaging - CT Chest"
+        imaging_ct_head: "Imaging - CT Head"
+        imaging_ct_kub: "Imaging - CT KUB"
         imaging_ct_pulm_angio: "Imaging - CT Pulm Angio"
         imaging_ct_renal_angio: "Imaging - CT Renal Angio"
+        imaging_ct_unspec: "Imaging - CT (Unspec)"
         imaging_cxr: "Imaging - CXR"
         imaging_doppler_carotids: "Imaging - Doppler Carotids"
+        imaging_doppler_carotids_legs: "Imaging - Doppler Carotids Legs"
         imaging_doppler_legs: "Imaging - Doppler Legs"
         imaging_liver_us: "Imaging - Liver US"
         imaging_mammography: "Imaging - Mammography"
         imaging_post_mict_bladder_us: "Imaging - Post mict bladder US"
         imaging_renal_us: "Imaging - Renal US"
+        imaging_us_unspec: "Imaging - US (Unspec)"
         imaging_static_dmsa: "Imaging - Static DMSA"
         imaging_mag3_scan: "Imaging - MAG3 Scan"
         opinion_cardiology: "Opinion - Cardiology"

data/config/locales/renalware/patients/side_menu.en.yml

@@ -14,7 +14,7 @@ en:
           clinic_visits: Clinic Visits (%{count})
           letters: Letters (%{count})
           events: Events (%{count})
-          access_profiles: Access Summary (%{count})
+          access_profiles: Access Summary
           prescriptions: Prescriptions (%{count})
           pathology: Pathology (%{count})
           virology: Virology

data/config/routes.rb

@@ -189,6 +189,7 @@ Renalware::Engine.routes.draw do
   end
 
   namespace :letters do
+    resource :pdf_letter_cache, only: [:destroy], controller: "pdf_letter_cache"
     resources :descriptions, only: :search do
       collection do
         get :search

data/db/migrate/20180307191650_add_dwell_time_to_pd_regime.rb

@@ -0,0 +1,5 @@
+class AddDwellTimeToPDRegime < ActiveRecord::Migration[5.1]
+  def change
+    add_column :pd_regimes, :dwell_time, :integer
+  end
+end

data/db/migrate/20180307223111_create_system_visits_and_events.rb

@@ -0,0 +1,44 @@
+class CreateSystemVisitsAndEvents < ActiveRecord::Migration[5.1]
+  def change
+   create_table :system_visits do |t|
+      t.string :visit_token
+      t.string :visitor_token
+
+      # the rest are recommended but optional
+      # simply remove any you don't want
+
+      # user
+      t.references :user, index: true
+
+      # standard
+      t.string :ip
+      t.text :user_agent
+      t.text :referrer
+      t.string :referring_domain
+      t.string :search_keyword
+      t.text :landing_page
+
+      # technology
+      t.string :browser
+      t.string :os
+      t.string :device_type
+
+      t.timestamp :started_at
+    end
+
+    add_index :system_visits, [:visit_token], unique: true
+
+    create_table :system_events do |t|
+      t.references :visit
+      t.references :user, index: true
+      t.timestamp :time
+
+      t.string :name
+      t.jsonb :properties
+    end
+
+    add_index :system_events, [:name, :time]
+    add_index :system_events, "properties jsonb_path_ops", using: "gin"
+  end
+end
+

data/db/migrate/20180309140316_add_unique_constraint_to_obr_requestor.rb

@@ -0,0 +1,5 @@
+class AddUniqueConstraintToObrRequestor < ActiveRecord::Migration[5.1]
+  def change
+    add_index :pathology_observation_requests, :requestor_order_number, unique: true
+  end
+end

data/db/migrate/20180311071146_update_patient_summaries_to_version6.rb

@@ -0,0 +1,5 @@
+class UpdatePatientSummariesToVersion6 < ActiveRecord::Migration[5.0]
+  def change
+    update_view :patient_summaries, version: 6, revert_to_version: 5
+  end
+end

data/db/views/patient_summaries_v06.sql

@@ -0,0 +1,16 @@
+SELECT
+patients.id as patient_id,
+(SELECT COUNT(*) FROM "events" WHERE "events"."patient_id" = patients.id) as events_count,
+(SELECT COUNT(*) FROM "clinic_visits" WHERE "clinic_visits"."patient_id" = patients.id) as clinic_visits_count,
+(SELECT COUNT(*) FROM "letter_letters" WHERE "letter_letters"."patient_id" = patients.id) as letters_count,
+(SELECT COUNT(*) FROM "modality_modalities" WHERE "modality_modalities"."patient_id" = patients.id) as modalities_count,
+(SELECT COUNT(*) FROM "problem_problems" WHERE "problem_problems"."deleted_at" IS NULL AND "problem_problems"."patient_id" = patients.id) as problems_count,
+(SELECT COUNT(*) FROM "pathology_observation_requests" WHERE "pathology_observation_requests"."patient_id" = patients.id) as observation_requests_count,
+(SELECT COUNT(*) FROM "medication_prescriptions" P
+  full outer join "medication_prescription_terminations" PT on PT.prescription_id = P.id
+  WHERE P."patient_id" = patients.id
+  AND (PT."terminated_on" IS NULL OR PT."terminated_on" > CURRENT_TIMESTAMP)) as prescriptions_count,
+(SELECT COUNT(*) FROM "letter_contacts" WHERE "letter_contacts"."patient_id" = patients.id) as contacts_count,
+(SELECT COUNT(*) FROM "transplant_recipient_operations" WHERE "transplant_recipient_operations"."patient_id" = patients.id) as recipient_operations_count,
+(SELECT COUNT(*) FROM "admission_admissions" WHERE "admission_admissions"."patient_id" = patients.id) as admissions_count
+FROM patients

data/lib/renalware/configuration.rb

@@ -37,6 +37,9 @@ module Renalware
     config_accessor(:letter_default_care_group_name) { "RenalCareGroup" }
     config_accessor(:default_from_email) { "dev@airslie.com" }
     config_accessor(:display_feedback_banner) { ENV.key?("DISPLAY_FEEDBACK_BANNER") }
+    config_accessor(:display_feedback_button_in_navbar) do
+      ENV.key?("DISPLAY_FEEDBACK_BUTTON_IN_NAVBAR")
+    end
     config_accessor(:default_from_email_address) { ENV["DEFAULT_FROM_EMAIL_ADDRESS"] }
     config_accessor(:phone_number_on_letters) { ENV["PHONE_NUMBER_ON_LETTERS"] }
     config_accessor(:renal_unit_on_letters) { ENV["RENAL_UNIT_ON_LETTERS"] }

data/lib/renalware/engine.rb

@@ -1,6 +1,7 @@
 require "rubygems"
 require "active_type"
 require "activerecord-import"
+require "ahoy"
 require "autoprefixer-rails"
 require "chosen-rails"
 require "simple_form"
@@ -112,7 +113,6 @@ 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.rc13".freeze
+  VERSION = "2.0.0".freeze
 end

data/spec/factories/pathology/observation_requests.rb

@@ -1,9 +1,11 @@
 # frozen_string_literal: true
 
 FactoryBot.define do
+  sequence(:requestor_order_number) { |n| "PlacerID-#{n}" }
+
   factory :pathology_observation_request, class: "Renalware::Pathology::ObservationRequest" do
     association :description, factory: :pathology_request_description
-    requestor_order_number "123"
+    requestor_order_number
     requestor_name "Jane Doe"
     requested_at { 1.year.ago }
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.0.pre.rc13
+  version: 2.0.0
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-03-06 00:00:00.000000000 Z
+date: 2018-03-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -52,6 +52,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.22.0
+- !ruby/object:Gem::Dependency
+  name: ahoy_matey
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.0.1
 - !ruby/object:Gem::Dependency
   name: attr_extras
   requirement: !ruby/object:Gem::Requirement
@@ -1011,7 +1025,6 @@ files:
 - app/assets/stylesheets/renalware/partials/_tooltip.scss
 - app/assets/stylesheets/renalware/partials/_typography.scss
 - app/assets/stylesheets/renalware/partials/_utilities.scss
-- app/assets/stylesheets/renalware/patient_pages.scss
 - app/assets/stylesheets/renalware/pdf.scss
 - app/assets/stylesheets/renalware/print/pathology_request_forms.scss
 - app/assets/stylesheets/renalware/protocol_pdf.scss
@@ -1089,6 +1102,7 @@ files:
 - app/controllers/renalware/letters/formatted_letters_controller.rb
 - app/controllers/renalware/letters/letters_controller.rb
 - app/controllers/renalware/letters/lists_controller.rb
+- app/controllers/renalware/letters/pdf_letter_cache_controller.rb
 - app/controllers/renalware/letters/pending_review_letters_controller.rb
 - app/controllers/renalware/letters/rejected_letters_controller.rb
 - app/controllers/renalware/low_clearance/base_controller.rb
@@ -1652,6 +1666,8 @@ files:
 - app/models/renalware/renal.rb
 - app/models/renalware/renal/aki_alert.rb
 - app/models/renalware/renal/aki_alert_action.rb
+- app/models/renalware/renal/aki_alert_query.rb
+- app/models/renalware/renal/aki_alert_search_form.rb
 - app/models/renalware/renal/patient.rb
 - app/models/renalware/renal/prd_description.rb
 - app/models/renalware/renal/prd_descriptions/search_query.rb
@@ -1674,10 +1690,12 @@ files:
 - app/models/renalware/snippets/user.rb
 - app/models/renalware/system.rb
 - app/models/renalware/system/country.rb
+- app/models/renalware/system/event.rb
 - app/models/renalware/system/render_liquid_template.rb
 - app/models/renalware/system/template.rb
 - app/models/renalware/system/update_user.rb
 - app/models/renalware/system/user_feedback.rb
+- app/models/renalware/system/visit.rb
 - app/models/renalware/system_user.rb
 - app/models/renalware/transplants.rb
 - app/models/renalware/transplants/create_donor_stage.rb
@@ -2037,6 +2055,7 @@ files:
 - app/views/renalware/devise/passwords/new.html.erb
 - app/views/renalware/devise/registrations/edit.html.slim
 - app/views/renalware/devise/registrations/new.html.slim
+- app/views/renalware/devise/sessions/_warning.html.slim
 - app/views/renalware/devise/sessions/new.html.slim
 - app/views/renalware/directory/people/_address_form.html.slim
 - app/views/renalware/directory/people/_filters.html.slim
@@ -2089,7 +2108,6 @@ files:
 - app/views/renalware/events/types/new.html.slim
 - app/views/renalware/hd/accesses/_summary.html.slim
 - app/views/renalware/hd/cannulation_types/_form.html.slim
-- app/views/renalware/hd/cannulation_types/_header.html.slim
 - app/views/renalware/hd/cannulation_types/edit.html.slim
 - app/views/renalware/hd/cannulation_types/index.html.slim
 - app/views/renalware/hd/cannulation_types/new.html.slim
@@ -2101,7 +2119,6 @@ files:
 - app/views/renalware/hd/dashboards/_page_actions.html.slim
 - app/views/renalware/hd/dashboards/show.html.slim
 - app/views/renalware/hd/dialysers/_form.html.slim
-- app/views/renalware/hd/dialysers/_header.html.slim
 - app/views/renalware/hd/dialysers/edit.html.slim
 - app/views/renalware/hd/dialysers/index.html.slim
 - app/views/renalware/hd/dialysers/new.html.slim
@@ -2322,6 +2339,7 @@ files:
 - app/views/renalware/navigation/_main.html.slim
 - app/views/renalware/navigation/_mdms.html.slim
 - app/views/renalware/navigation/_menu.html.slim
+- app/views/renalware/navigation/_more_help_items.html.slim
 - app/views/renalware/navigation/_patient_search.html.slim
 - app/views/renalware/navigation/_patients_admin.html.slim
 - app/views/renalware/navigation/_renal.html.slim
@@ -2400,7 +2418,6 @@ files:
 - app/views/renalware/patients/primary_care_physician/edit.html.slim
 - app/views/renalware/patients/primary_care_physician/edit.js.erb
 - app/views/renalware/patients/primary_care_physicians/_form.html.slim
-- app/views/renalware/patients/primary_care_physicians/_header.html.slim
 - app/views/renalware/patients/primary_care_physicians/_primary_care_physician.html.slim
 - app/views/renalware/patients/primary_care_physicians/edit.html.slim
 - app/views/renalware/patients/primary_care_physicians/index.html.slim
@@ -2423,6 +2440,7 @@ files:
 - app/views/renalware/pd/_exit_site_infections.html.slim
 - app/views/renalware/pd/_peritonitis_episodes.html.slim
 - app/views/renalware/pd/_pet_adequacies.html.slim
+- app/views/renalware/pd/_regimes.html.slim
 - app/views/renalware/pd/assessments/_form.html.slim
 - app/views/renalware/pd/assessments/_list.html.slim
 - app/views/renalware/pd/assessments/edit.html.slim
@@ -2528,6 +2546,8 @@ 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/research/_alert.html.slim
+- app/views/renalware/research/_alerts.html.slim
 - app/views/renalware/research/studies/_form.html.slim
 - app/views/renalware/research/studies/edit.html.slim
 - app/views/renalware/research/studies/index.html.slim
@@ -2669,6 +2689,7 @@ files:
 - config/autoprefixer.yml
 - config/cable.yml
 - config/cucumber.yml
+- config/initializers/ahoy.rb
 - config/initializers/backtrace_silencers.rb
 - config/initializers/client_side_validations.rb
 - config/initializers/core_extensions.rb
@@ -3167,6 +3188,10 @@ files:
 - db/migrate/20180305134959_add_display_group_to_observation_desriptions.rb
 - db/migrate/20180306071308_remove_rogue_aki_alerts_column.rb
 - db/migrate/20180306080518_add_state_tracking_cols_to_letters.rb
+- db/migrate/20180307191650_add_dwell_time_to_pd_regime.rb
+- db/migrate/20180307223111_create_system_visits_and_events.rb
+- db/migrate/20180309140316_add_unique_constraint_to_obr_requestor.rb
+- db/migrate/20180311071146_update_patient_summaries_to_version6.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3261,6 +3286,7 @@ files:
 - db/views/patient_summaries_v03.sql
 - db/views/patient_summaries_v04.sql
 - db/views/patient_summaries_v05.sql
+- db/views/patient_summaries_v06.sql
 - db/views/reporting_anaemia_audit_v01.sql
 - db/views/reporting_bone_audit_v01.sql
 - db/views/reporting_hd_blood_pressures_audit_v01.sql
@@ -3518,9 +3544,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.7.4