TheJacksonLaboratory / geneweaver-db

The GeneWeaver database interaction code.

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