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BioPack Retriever

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Intermediary between Knowledge Providers and Shepherd, deduplicating subquery operations, cache layer, centralized normalization calls.

Installation

For a more detailed overview, see the Installation Documentation.

Note

Requires Docker and Python ~3.13

Quick setup for local workspace:

git clone https://github.com/BioPack-team/retriever
cd retriever
pip install uv # If you don't have uv installed
uv sync

Usage

Quick start:

Note

Retriever uses external database backends for its data. These backends do not currently have public access. If you wish to test Retriever, you'll either need to be granted access (Translator devs only), or stand up your own backends.

# Get into the Virtual Environment.
# Otherwise, add `uv run` in front of the following commands
source .venv/bin/activate
task start # or `task dev` if you want some useful options (tracelogs, single worker, etc.)

Shut down the database containers when you're done (warning, wipes the containers):

task dbs:stop

Configuration

See the Configuration Documentation.