Cogat-Docker

Django application and containers for Spark and Neo4j to serve the Cognitive Atlas and manage development.

Caveats regarding the ASSERTS relationship and use of the Assertion node:

The ASSERTS relationship was created for the special situation where a task has no contrasts but still asserts a concept.

In the old database theories would refer to a relationship between a task, contrast, and concept. Neo4j can't make a relationship from a node to another relationship so a new node type was created so that theories could relate to these assertions. These types of assertion nodes are automatically generated for every group of task-contrast-concept applicable on import. Outside of that migration assertion nodes are only generated when a assertion relationship is added to a theory. The caveat being queries against assertion nodes do not necessarily cover all implied assertions. The correct way to figure all assertions is to look directly at the task - hascontrast -> contrast <- measuredby - concept relationships.

Getting started

This project uses docker and docker-compose:

Docker: https://docs.docker.com/installation/
Docker Compose: https://docs.docker.com/compose/install/

Docker file for neo4j taken from https://github.com/kbastani/docker-neo4j and modified to do some data imports.

Create default user

Add MAKE_DEFAULT_USER=True to the .env file in the root of the project. The user specificed in scripts/create_superuser.py will then be created on startup of the uwsgi container.

Old users

The import contianer looks for an environment variable named MYSQL_DUMP and uses its value as the sql dump file to import into mysql. This variable should be defined in .env. The users will be imported when the import container is started. It should be started with docker-compose using the docker-compose-import.yml config file.