DataJoint pipeline: On-premises deployment#

This guide describes the processes and resources required to deploy the Aeon DataJoint pipeline on-premises.

Prerequisites#

To deploy and operate a DataJoint pipeline, you will need the following:

MySQL database server (version 8.0) configured to be DataJoint-compatible. To simplify the setup, we recommend using DataJoint’s pre-configured MySQL Docker image following the instructions below.
- Install Docker and run:
```
docker run -d \
   --name db \
   -p 3306:3306 \
   -e MYSQL_ROOT_PASSWORD=simple \
   -v ./mysql/data:/var/lib/mysql \
   datajoint/mysql:8.0 \
   mysqld --default-authentication-plugin=mysql_native_password
```
  The above command launches a new MySQL server in a Docker container with the following credentials:
  - Host: localhost
  - Username: root
  - Password: simple
- To stop the container, run:
```
docker stop db
```
- To restart the container after stopping it, run:
```
docker start db
```
aeon_mecha GitHub repository containing the codebase of the DataJoint pipeline.
- Install the codebase. No additional modifications are needed to deploy the pipeline locally.
File storage
- Provide a location for the pipeline to access/store the data files (e.g. a local directory or mounted network storage).
Compute environment
- Ensure you have a compute environment with the necessary software installed to run the pipeline (e.g. a laptop, local workstation, or an HPC cluster).
Data to be ingested and processed
- You can use the Single mouse in a foraging assay sample dataset as a starting point to test the pipeline. If you choose to use this sample dataset, ensure that you switch to the aeon_docs branch of the codebase.

DataJoint requires a configuration file named dj_local_conf.json. This file should be located in the root directory of the codebase.

Create the dj_local_conf.json file
- Copy the sample_dj_local_conf.json file and rename it to dj_local_conf.json.
- Update the file with your database credentials (username, password, and database host).
- Ensure the file is kept secure and not shared publicly.
Set database.prefix
- In the custom section, set database.prefix to your desired value, or keep the default aeon_.
Set the data directory (ceph_aeon)
- In the custom section, set the ceph_aeon value (under repository_config) to the root directory of your data (i.e. the directory containing aeon/data/raw/).
- For example, if aeon/data/raw/ is located at D:/data/project-aeon/aeon/data/raw/, set the ceph_aeon value to D:/data/project-aeon.

Now that the pipeline is installed and configured, you can start ingesting and processing your data.