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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 3.7+

• npm 10

  • 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.

• 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. 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.

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

   > docker-compose up -d
   

3. Navigate to http://localhost:3000/

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.

> docker-compose run --rm app pytest --db "postgresql://test:test@postgres-test/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 localhost

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