Physiqual

Ruby Engine for merging multiple data sources with diary questionnaire data

Installation

Add Physiqual to your Gemfile. Currently Physiqual is not yet on RubyGems, this will happen after Physiqual is in a more stable beta state.

  gem 'physiqual', github: 'roqua/physiqual'

Install the dependencies by running:

  bundle

Initialize the database

  bundle exec rake db:setup

Mount the engine in the config/routes.rb file (in the Rails.application.routes.draw block)

  mount Physiqual::Engine => '/physiqual'

Configuration

First create your an application on Google and Fitbit with the correct access levels and copy the key and ID from those services. Create initializer in config/initializers/physiqual.rb and add the configuration as follows, using the ID and secret retrieved from the services:

Physiqual.configure do |config|
  # Google API tokens
  config.google_client_id     = ENV['GOOGLE_CLIENT_ID']
  config.google_client_secret = ENV['GOOGLE_CLIENT_SECRET']

  # Fitbit oauth tokens
  config.fitbit_client_id     = ENV['FITBIT_CLIENT_ID']
  config.fitbit_client_secret = ENV['FITBIT_CLIENT_SECRET']

  # Host settings
  config.host_url             = ENV['HOST_URL'] || 'physiqual.dev'
  config.host_protocol        = ENV['HOST_PROTOCOL'] || 'http'

  # EMA Settings
  config.measurements_per_day           = 3 # Number of measurements per day, from the end of day downwards
  config.interval                       = 6 # Number of hours between measurements
  config.hours_before_first_measurement = 6 # How many hours before the first measurement each day should be included

  # Imputation
  # List of imputers to use, prefix with Physiqual::Imputers::, choose from:
  # - CatMullImputer
  # - KNearestNeighborImputer
  # - LastObservationCarriedForwardImputer
  # - MeanImputer
  # - SplineImputer
  # - MockImputer (doesn't actually impute).
  config.imputers             = [Physiqual::Imputers::CatMullImputer]
end

Now you should be able to start your server.

Dummy

If you would like to run the dummy application, make a full checkout of Physiqual

  git clone git@github.com:roqua/physiqual.git --shallow
  bundle install
  bundle exec rake db:setup

And cd to spec/dummy. From this directory you can either run bundle exec rails s or create an apache v-host on passenger to run the server, for example:

  cd /etc/apache2/other
  touch physiqual.dev.vhost.conf

And add to this file a virtualhost configuration, for example:

<VirtualHost *:80>
  ServerName physiqual.dev
  ServerAdmin info@physiqual.dev
  DocumentRoot "<YOUR DIRECTORY>/physiqual/spec/dummy/public"
  RailsEnv development
  PassengerRuby /Users/frbl/.rvm/gems/ruby-2.2.1/wrappers/ruby
  <Directory "<YOUR DIRECTORY>/physiqual/spec/dummy/public">
    Options FollowSymLinks Multiviews
    MultiviewsMatch Any
    AllowOverride None
    Require all granted
  </Directory>
</VirtualHost>

you should now be able to surf to, for example: http://physiqual.dev/oauth_session/google/authorize?email=a

Troubleshooting

You might run into some issues with regards to SSL warnings and errors. In that case, add the curl ca certificates to the environment variables, e.g., in osx:

  SSL_CERT_FILE=/usr/lib/ssl/certs/ca-certificates.crt

If your system has no SSL_CERT_FILE, you can get one from http://curl.haxx.se/ca/cacert.pem