Geneweaver DB

The Geneweaver DB library provides database access functionality for the Geneweaver project. The library contains SQL queries wrapped in standard python functions, as well as a database connection manager.

Installation

To install the Geneweaver DB library, run one of the following commands:

Using Pip

pip install geneweaver-db

Using Poetry

poetry add geneweaver-db

Usage

The Geneweaver DB library is intended to be used as a dependency for other Geneweaver packages, but can also be used as a stand-alone pacakge.

The package has three main sections:

• geneweaver.db - contains non-async database functions.
• geneweaver.db.aio - contains async database functions.
• geneweaver.db.query - contains SQL queries and SQL generation functions.

Database functions usually take a Cursor or AsyncCursor object as their first argument.

Non-Async Functions

import psycopg
import geneweaver
from geneweaver.db.core.settings import settings

def get_my_gene():
    with psycopg.connect(settings.URI) as conn:
            with conn.cursor() as cur:
                result = geneweaver.db.gene.get(cur, 'my_gene')
    return result

Async Functions

import psycopg
import geneweaver
from geneweaver.db.core.settings import settings

async def get_my_gene():
    async with psycopg.AsyncConnection.connect(settings.URI) as conn:
            async with conn.cursor() as cur:
                result = await geneweaver.db.aio.gene.get(cur, 'my_gene')
    return result