Wehrlab Datajoint Models

Running SQL docker

Create an .env file in whatever directory you're running this from with MYSQL_ROOT_PASSWORD=<some password>, or else pass it explicitly like -e MYSQL_ROOT_PASSWORD=tutorial (not recommended since stdin is not encrypted lol)

docker-compose -f ./wehrlab-datajoint/config/dj_docker.yaml --project-directory ./ up -d

Python

Connect to database

Use the wehrdj.connect.connect() function to open a database connection. It will prompt you for connection information when first run, and then will stash those credentials in ~/.djcredentials.json

>>> from wehrdj import connect
>>> connect()
host ip and port: 127.0.0.1:3307
username: root
password: <password>
Connecting root@127.0.0.1:3307
>>> 

Activate schema

This part is in flux. Now we need to register all the schema objects that we'll use. For now, this is done with wehrdj.elements.activate, but as we make our own schema we'll have to adapt this to include the rest of our own.

from wehrdj.elements import activate
activate()

Reference

workflow-session

Examples of ingesting data and basic usage of session information

• https://github.com/datajoint/workflow-session/blob/main/notebooks/1_Explore_Workflow.ipynb
• https://github.com/datajoint/workflow-session/blob/main/workflow_session/ingest.py