renalware-core 2.0.0.pre.beta4

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data/README.md

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+# Renalware
+
+[![Code Climate](https://codeclimate.com/repos/58beee3ed41d600266000147/badges/50451f89d7aad6c2d200/gpa.svg)](https://codeclimate.com/repos/58beee3ed41d600266000147/feed)
+[![Test Coverage](https://codeclimate.com/repos/58beee3ed41d600266000147/badges/50451f89d7aad6c2d200/coverage.svg)](https://codeclimate.com/repos/58beee3ed41d600266000147/coverage)
+[![Dependency Status](https://gemnasium.com/badges/github.com/airslie/renalware-core.svg)](https://gemnasium.com/github.com/airslie/renalware-core)
+
+Renalware uses demographic, clinical, pathology, and nephrology datasets to improve patient care,
+undertake clinical and administrative audits and share data with external systems.
+
+## Technical Overview
+
+renalware-core is a Ruby On Rails [engine](http://guides.rubyonrails.org/engines.html) intended to encapsulate the majority of Renalware's
+features in a re-usable [gem](http://guides.rubygems.org/what-is-a-gem/). When a renal unit deploys Renalware, it will create its own _host_
+Rails application, and configure it to include the Renalware engine. The host application may be
+extremely thin, adding no custom features other than site-specific configuration, or it may include
+Ruby, HTML and JavaScript to override or augment renalware-core's features.
+
+While the engine is indented to be deployed inside a host application in production, it can be run
+stand-alone in a local development environment (or indeed deployed  in a limited way to somewhere like Heroku) by employing
+the _dummy_ host application that ships inside the engine. This dummy app (in `./spec/dummy`)
+allows a developer to quickly mount the engine, and is used also used Rails integration tests (which is why
+it is in the `./spec` folder)
+
+There are other optional renalware gems which can also be included in the host application,
+for example `renalware-ukrdc` which enables sending data to the UKRDC.
+
+### Stack
+
+- Ruby 2.4.1
+- Ruby on Rails 5
+- Postgres 9.6+
+
+## Get up and running locally
+
+> An alternative Docker approach will be available shortly
+
+As a Rails developer we assume you are using OS X or Linux (natively or inside a [VM](https://www.virtualbox.org/wiki/Downloads) on Windows),
+and have the following installed:
+
+* Git
+* Postgres 9.6
+* a ruby version manager (e.g. [rbenv](https://github.com/rbenv/rbenv) or [RVM](https://rvm.io/))
+* NodeJS required by the [uglifier gem](https://github.com/lautis/uglifier#installation)
+
+### Postgres setup
+
+Set up Postgres user with a password - for development purposes this can be your system login.
+
+```bash
+sudo su - postgres
+psql template1
+```
+
+At the psql prompt run the following (replacing `<username>` and `<password>` accordingly):
+
+```sql
+CREATE USER <username> WITH PASSWORD '<password>';
+ALTER USER <username> SUPERUSER;
+```
+
+### Configure Ruby
+
+Check the `ruby` declaration at the top of the Gemfile to see which version of Ruby to install
+using your preferred Ruby version manager.
+If using rbenv for example:
+```bash
+rbenv install 2.4.1
+cd renalware-core
+rbenv local 2.4.1
+```
+
+### Install app dependencies and seed the database with demo data
+
+```bash
+gem install bundler --conservative
+bundle exec rake db:setup
+```
+
+### Run the server
+
+```
+$ bin/web
+```
+
+> Note `bin/web` starts a sever in the spec/dummy directory. Just executing `rails server` will not work.
+
+Visit [http://localhost:3000](http://localhost:3000)
+
+Login in one of the demo users (in order of role permissiveness):
+- superkch
+- kchdoc
+- kchnurse
+- kchguest
+
+They all share the password `renalware`
+
+> Alternatively you can use foreman to start to the web server and the background workers all together
+(see the Procfile) and tail the development log to see the output:
+
+    bundle exec foreman start
+    tail -f spec/dummy/log/developments.log
+
+## Running tests
+
+Install PhantomJS if you don't have it already (check with `phantomjs -v`):
+
+    wget -O /tmp/phantomjs.tar.bz2 http://airslie-public.s3.amazonaws.com/phantomjs-2.1.1-linux-x86_64.tar.bz2
+    tar -xjf /tmp/phantomjs.tar.bz2 -C /tmp
+    mv /tmp/phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin/phantomjs
+
+### RSpec unit and integration tests
+
+    bundle exec rspec
+
+### Cucumber acceptance tests
+
+Run domain tests which bypass the UI:
+
+    bundle exec cucumber
+
+Run web tests exercising the UI:
+
+    bundle exec cucumber TEST_DEPTH=web --profile rake_web
+
+> Test coverage reports can be found in `coverage/`
+
+## Code Quality
+
+Code quality can be analyzed using by running `codeclimate analyze`. To setup
+CodeClimate locally read the setup instructions:
+
+    https://github.com/codeclimate/codeclimate
+
+### Deploying
+
+#### To a server
+
+> Please note the deployment scripts are under development
+
+Please see the [renalware-provisioning](https://github.com/airslie/renalware-provisioning) repo.
+
+#### To a Vagrant VM
+
+Follow [these instructions](https://github.com/airslie/renalware-provisioning#vagrant)
+and deploy using capistrano:
+
+```
+cap vagrant deploy
+```
+
+#### Heroku
+
+Just push `app.json` in the project root defines the deployment steps for Heroku so you should be able
+to just create
+
+## General notes
+
+#### Engine migrations
+
+`config.active_record.schema_format = :sql` in `application.rb` is used the engine
+uses postgres views and functions which are not properly supported in a `schema.rb`
+
+#### Throttling login attempts
+
+[rack-attack](https://github.com/kickstarter/rack-attack) is configured to throttle login attempts.
+Only 10 attempts per username as permitted in any one minute in an attempt to thwaght login attacks.
+
+#### Test Configuration
+
+RSpec is configured to silence backtrace from third-party gems. This can be
+configured in `.rspec` with `--backtrace` which will display the full backtrace.
+
+#### Debugging
+
+The [awesome_print](https://github.com/awesome-print/awesome_print) gem is available
+for improved inspection formatting, for example:
+
+    Rails.logger.ap @variable
+
+To make awesome_print the default formatter in irb, add the following to `~/.irbrc`
+
+    require "awesome_print"
+    AwesomePrint.irb!

data/Rakefile

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+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+puts "Loading engine rake tasks"
+
+begin
+  require "bundler/setup"
+rescue LoadError
+  puts "You must `gem install bundler` and `bundle install` to run rake tasks"
+end
+
+# We can use rake tasks like app:db:reset when APP_RAKEFILE set
+unless defined?(APP_RAKEFILE)
+  APP_RAKEFILE = File.expand_path("../spec/dummy/Rakefile", __FILE__)
+end
+
+load "rails/tasks/engine.rake"
+load "rails/tasks/statistics.rake"
+
+require "bundler/gem_tasks"
+
+# Bundler::GemHelper.install_tasks
+
+# assets:* tasks for For Heroku only
+# When deploying the engine to Heroku, we are actually deployment the spec/dummy app.
+# Heroku however loads this Rakefile first hunting for an assets:precompile task to indicate
+# it should compile the assets. If not found it won't compile assets and we won't have any styling.
+namespace :assets do
+  desc "Clean any assets within dummy app"
+  task :clean do
+    Rake::Task["app:assets:clean"].invoke
+  end
+
+  desc "Precompile assets within dummy app"
+  task :precompile do
+    Rake::Task["app:assets:precompile"].invoke
+  end
+
+  desc "Clobbers assets within dummy app"
+  task :clobber do
+    Rake::Task["app:assets:clobber"].invoke
+  end
+end

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data/app/assets/images/renalware/favicon/browserconfig.xml

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+<?xml version="1.0" encoding="utf-8"?>
+<browserconfig>
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+        <tile>
+            <square150x150logo src="/mstile-150x150.png"/>
+            <TileColor>#da532c</TileColor>
+        </tile>
+    </msapplication>
+</browserconfig>

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+Note that favicons are generated using http://realfavicongenerator.net/
+and the resulting files places here.

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data/app/assets/javascripts/renalware/ajax_errors.js

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+$(document).ajaxError(function (e, xhr, settings) {
+  switch(xhr.status) {
+    // For 401 Unathorised responses, for example trying to making a
+    // js request after a session timeout, reloading the current page
+    // will redirect the user to the login page.
+    case 401:
+      location.reload();
+      break;
+    case 500:
+      alert("Your request has unexpectedly failed (" + xhr.statusText + ").  Please try again.");
+  }
+});

data/app/assets/javascripts/renalware/application.js.erb

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+// This is a manifest file that'll be compiled into application.js, which will include all the files
+// listed below.
+//
+// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
+// or vendor/assets/javascripts of plugins, if any, can be referenced here using a relative path.
+//
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// compiled file.
+//
+// Read Sprockets README (https://github.com/sstephenson/sprockets#sprockets-directives) for details
+// about supported directives.
+//
+// Not that jquery3 is not currently compatible for foundation 5
+//= require jquery2
+//= require jquery-readyselector
+//= require jquery_ujs
+//= require jquery-ui/core
+//= require jquery-ui/widgets/autocomplete
+//= require jquery-ui/widgets/sortable
+//= require jquery-ui/effects/effect-highlight
+//= require dataTables/jquery.dataTables
+//= require dataTables/jquery.dataTables.foundation
+//= require trix
+//= require foundation/foundation
+//= require foundation/foundation.accordion
+//= require foundation/foundation.alert
+//= require foundation/foundation.dropdown
+//= require foundation/foundation.magellan
+//= require foundation/foundation.reveal
+//= require foundation/foundation.tab
+//= require foundation/foundation.tooltip
+//= require foundation/foundation.topbar
+//= require underscore
+//= require select2
+//= require jquery_nested_form
+//= require foundation-datepicker
+//= require renalware/clockpicker
+//= require cocoon
+//= require renalware/mousetrap
+//= require renalware/iframeResizer
+//= require chosen-jquery
+//= require clipboard
+//= require renalware/masonry.min
+//= require rails.validations
+//= require rails.validations.simple_form
+//= require renalware/print.min
+//= require_tree .
+//
+
+// Disabled jQuery animations during tests to speed things up a little
+<% if Rails.env.test? %>
+  $.fx.off = true;
+<% end %>