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Open Source Clinical Content Analysis and Management System

• 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

• Python 2.7+

• npm

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

• redis
• PostgreSQL 9.6+

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.

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.

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/

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.

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.

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

> docker-compose logs -f

Install the Postgres client on the host machine and run:

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

> docker-compose restart app

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