NIHR Leicester BRC Uploads

Catalogue of phage and bacterial samples

Installation

Download Repository

Down this repository using the command:

gh repo clone LCBRU/lbrc_uploads

or

git clone https://github.com/LCBRU/lbrc_uploads.git

Prerequisites

To install the pre-requisites on Ubuntu, use the commands:

sudo apt install libldap2-dev
sudo apt install libsasl2-dev

Virtual Environment

Install the python requirements into a new virtual environment in the project directory and install the toolset:

cd lbrc_uploads
python3 -m venv .venv
. .venv/bin/activate
pip install --upgrade pip
pip install pip-tools
pip install -r requirements.txt

Python Requirements Management

Python requirements are stored in the requirements.in file. The locked versions of these requirements, and any sub-requirements, are stored in the requirements.txt file. The requirements.txt file is created from the requirements.in file by running the command:

pip-compile

This should be run whenever new requirements have been added to the requirements.in file or new requirement versions are being tested.

Both the requirements.in and requirements.txt files should be checked into git.

Parameters

Parameters used for running the application should be stored in the .env file. This should not be checked into git.

An example of what parameters are needed to run the application are contained within the example.env file.

Running the Application

1. Create an empty database using the parameters set in the .env file.
2. Create a test data by running the command python create_test_db.py
3. Run the application using the command python app.py

Database

Creating Migrations

Database changes are managed using the Alembic library.

The easiest way to make a change to the database is to amend the data objects in the application and then get Alembic to automatically create the migration using the following command:

alembic revision --autogenerate -m "{description}"

This creates a file in the alembic/versions directory that starts with a unique splat of random characters, followed by your {description} from above.

The file contains upgrade and downgrade functions that you will need to create. It also contains some variables:

• revision: the revision unique random code
• down_revision: the code of the previous revision's code. This is used to determine revision order.
• branch_labels: sutin else.

This file should be validated as the autogeneration function does not always work correctly. The Alembic documentations will help you validate the code or write custom code.

Running Migrations

Run the alembic upgrade sub-command to upgrade the database to the latest version:

alembic upgrade head

See the Alembic Tutorial for more information.

Asynchronous Processing

If configured correctly in the .env file, it is possible to run processes asynchronously (in the background) using Celery.

Redis

Celery uses a broker as a message queue. The easiest one to install and use for testimng is Redis. Use the instructions on the website to install it.

Then, follow the instructions from Celery using Redis, setting the configuration in the .env file for the BROKER_URL and CELERY_RESULT_BACKEND.

Running the Celery Worker Process

To run the celery worker process, run the command:

celery -A celery_worker.celery worker -l info -B