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Open Source Clinical Content Analysis and Management System

Features

• Configurable forms with version tagging
• Study visit matrix configuration
• Direct data entry instead of using paper forms
• Data export tools
• Immutable data auditing
• Data workflow captured by the system design, but flexible enough to work for multiple use-cases
• Secure, role-based data access control

System Requirements

• Python 2.7+

• npm

  • bower
  • lessc (must be installed globally, i.e. with "-g" option)

• redis
• PostgreSQL 9.6+

Development

This application uses Docker to setup a development environment with dummy user accounts. It is recommended you familiarize yourself with some basic knowledge of how it works.

VirtualBox

If you are using macOS or Windows, you must install Virtualbox:

https://www.virtualbox.org/wiki/Downloads

This is required to install boot2docker on containers.

Machine and Compose

You will neeed to install Docker Compose and Machine in order so setup your environment. To do so, follow the instructions the following instructions based on your host environment:

• macOS: https://docs.docker.com/docker-for-mac/
• Windows: https://docs.docker.com/docker-for-windows/
• Linux: https://docs.docker.com/engine/installation/linux/

Installation

1. Provision a new Docker machine called "occams-develop" by running the following command:

   > docker-machine create -d virtualbox occams-develop
   

2. Point Docker to the development machine:

   > eval $(docker-machine env occams-develop)
   > docker-machine ls
   NAME             ACTIVE   DRIVER       STATE     URL                         SWARM   DOCKER    ERRORS
   occams-develop   *        virtualbox   Running   tcp://192.168.99.100:2376           v1.12.2
   

   Note the asterisk in the "ACTIVE" column.

3. Clone the application and build the containers:

   > git clone https://github.com/razorlabs/occams
   > cd occams
   > docker-compose build
   

   This will take a moment, so it's a good idea to refill on coffee at this time.

4. Back? Ok, spin up the containers, there will some additional building for dependencies, this is normal:

   > docker-compose up -d
   

5. Get the IP address of the machine and use it to navigate to http://the.ip.addr.es:3000/

   > docker-machine ip occams-develop
   

You now should have a working OCCAMS instance.

Common Tasks

How do I add more users?

Modify the data setting in the [plugin:dev_users] section of the develop.ini file. There is already a test user there for you, so use that a template.

How do I run the tests?

Create a test user and database to run the tests.

> psql -U occams -h `docker-machine ip occams-develop` -c "CREATE USER test"
> psql -U occams -h `docker-machine ip occams-develop` -c "CREATE DATABASE test OWNER test"
> docker-compose run app py.test --db postgresql://test@postgres/test --redis redis://redis/9

How do I check the logs?

> docker-compose logs -f

How do I access the database?

Install the Postgres client on the host machine and run:

> psql -U occams -h `docker-machine ip occams-develop`

How do I restart the application?

> docker-compose restart app

How do I reset the database and start over again?

> docker-compose down
> docker volume rm postgres
> docker-compose up -d
> docker-compose run app occams_initdb develop.ini