About occams

Open Source Clinical Content Analysis and Management System

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README.md

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O\ pen Source C\ linical C\ ontent A\ nalysis and M\ anagement S\ ystem

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.

.. _Docker: https://www.docker.com/

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 ++++++++++++

. 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.

. Back? Ok, spin up the containers, there will some additional building for

dependencies, this is normal::

  > docker-compose up -d

. 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

occams