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Case management and instrument administration for NCS Navigator
Ruby JavaScript Other
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README.md

NCS Navigator Cases (formerly known as NCS Navigator Core)

NCS Navigator Cases (formerly NCS Navigator Core) manages participant activity and records interactions between Study Center personnel and participants. It can be used as a way to administer instruments to a participant for any event in the participant cycle. Also it is used to synchronize data between the NCS Navigator Offline field][] application and the NCS Navigator Core application.

Cases extensively uses Patient Study Calendar PSC to not only determine the participant schedule but also to inform Cases of the structure of the National Children's Study NCS.

The data schema is based on the Master Data Element Specification (MDES) of the National Children Study, versions 2.0-2.2.

It is a Ruby on Rails application which uses Rails 3 and a PostgreSQL database.

Prerequisites

On the deployment workstation:

  • Ruby 1.9.3
  • RubyGems
  • Bundler (install as a gem)
  • A git client

On the application server:

  • Ruby 1.9.3
  • RubyGems
  • Bundler (install as a gem)
  • Passenger
  • A git client
  • Access to a PostgreSQL server

Setup

Configuration on the application server

Database setup

Cases uses bcdatabase to discover the database configuration to use. Bcdatabase looks for a YAML file with a particular structure under /etc/nubic/db.

  • For a staging deployment, the file name should be /etc/nubic/db/ncsdb_staging.yml
  • For production, it should be /etc/nubic/db/ncsdb_prod.yml

Example:

defaults:
  adapter: postgresql
  host: ncsdb-staging
  port: 5432
ncs_navigator_core:
  database: ncs_navigator_core_staging   # database name
  username: ncs_navigator_core
  password: ncs_navigator_core

Authentication setup

Cases uses Aker-Rails and Aker for authentication.

First, create a file under /etc/nubic/ncs for the the central authentication parameters. These parameters will be used for all NCS Navigator applications on the same server.

  • In staging, the file name should be aker-staging.yml
  • In production, the file name should be aker-prod.yml

Contents:

cas:
  base_url: https://cas.myinst.edu/

Second, define a bootstrap user in /etc/nubic/ncs/navigator.ini. (See [NCS Staff Portal][] setup.)

Finally, Cases (and most of the applications in the NCS Navigator suite) use the ncs_navigator_authority gem for authentication, which requires a running instance of NCS Staff Portal ncs_staff_portal setup with Staff having particular roles.

Center-specific setup

Cases uses ncs_navigator_configuration for shared configuration of the NCS Navigator suite applications. Most configuration properties are documented in its sample configuration. Cases looks for the configuration in its default location, /etc/nubic/ncs/navigator.ini.

To further customize Cases for your center, add one or more of the following configuration elements to the [Core] section of the configuration file.

# Configuration options which are used by or which describe NCS
# Navigator Cases in this instance of the suite.

# The root URI for NCS Navigator Cases.
uri = "https://ncsnavigator.ncsstudycenter.org/"

# The Name and Phone number of the Study Center
study_center_name = "NCS Study Center"
study_center_phone_number = "123-555-1234"
toll_free_number = "800-555-1234"

# Whether or not the Study Center collects specimens and samples
with_specimens = "true"

# The identifier of the specimen/sample shipper
shipper_id = "shipper_id"

# The email addresses used in the application
mail_from = "ncs_navigator@greaterchicagoncs.org"
email_exception_recipients = "dev@greaterchicagoncs.org pm@greaterchicagoncs.org"

Deployment

Cases is deployed with capistrano from a workstation. On the workstation, you need to create a configuration file /etc/nubic/db/ncs_deploy.yml to describe where it should be deployed to.

Example:

ncs_navigator_core:
  # Repository for cases. This will always be this value
  # unless you wish to deploy your own fork.
  repo: "git://github.com/NUBIC/ncs_navigator_core.git"
  # path on the server where application will be deployed
  deploy_to: "/www/apps/ncs_navigator_core"
  # staging server hostname
  staging_app_server: "staging.server"
  # production server hostname
  production_app_server: "production.server"

After you check out the code, run bundle install to install the gems you'll need. The first time you deploy, capistrano needs to set up the directory layout it expects:

$ bundle exec cap production deploy:setup

Then deploy to the configured server:

$ bundle exec cap production deploy:migrations

(This deploys to your production server; to deploy to staging instead, substitute "staging" for "production".)

After the first deployment, you should only need to run deploy:migrations to get new versions. You can also use deploy:pending to see what would be deployed.

If you have problems deploying, you can run this:

$ bundle exec cap production deploy:check

and capistrano will try to tell you why it cannot deploy.

if you make changes to the footer logo paths in navigator.ini in between deploys, you have to run rake task to copy images

$ bundle exec cap production config:images

Deployment user

As currently configured, Cases will be deployed as the user you use to connect to the application server. The target directory must be writable by that user, and (by way of Passenger) the software will be executed with that users' permissions.

Most likely, the use account you use to connect to the application server will be your personal account. We may add specific support for deploying using a different account from the login account, but an option for now is to use an alias defined in .ssh/config on the workstation. See issue 1622 for a more detailed discussion of this option.

Initialization

Cases relies on many lists of data as determined by the MDES (see Code lists below). It ships with rake tasks which will populate these lists from outside sources.

All the tasks should be executed from the application root on the server where the application is deployed. Each one will need to be run at least once for each environment in which Cases is deployed.

RAILS_ENV needs to be set to the appropriate value (production, staging) when running the various setup rake tasks for production or staging environment. e.g bundle exec rake db:seed RAILS_ENV=production

Code lists

Initialize the code lists from the MDES using ncs_mdes:

$ bundle exec rake db:seed

Instruments

Cases uses surveyor to create the instruments used by the NCS. These surveys are proprietary and not currently available to the public. They are packaged as a separate ncs-instruments gem. Follow the instructions there to copy the instruments into a directory named surveys at the root of the deployed application.

Once the instruments are in the surveys directory, Cases is shipped with a rake task that will parse the survey syntax and load the surveys into the database.

$ bundle exec rake setup:surveys
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