marc_db

A simple database and query interface for the microbial archive

Usage

CLI

pip install .
export MARC_DB_URL=sqlite:////path/to/db.sqlite  # optional environment variable
marc_db -h
marc_db --db sqlite:////path/to/db.sqlite ingest /path/to/data_anonymized.tsv
marc_db --db sqlite:////path/to/db.sqlite ingest_assembly /path/to/assembly.tsv /path/to/amr.tsv

This will create a new database at /path/to/db.sqlite and ingest the anonymized data from marc_honest at /path/to/data_anonymized.tsv.

Library

Import SQLAlchemy data models with from marc_db.models import Aliquot, Isolate. Either create your own database connection (e.g. with flask_sqlalchemy if using Flask) or import with from marc_db.db import get_session. Query the database or import and use the provided views:

from marc_db.db import get_session
from marc_db.models import Aliquot, Isolate
from marc_db.views import get_isolates

session = get_session()
print(session.query(Isolate).limit(10))
print(get_isolates(session, n = 10))

Database migrations

Schema changes are managed with Alembic. After installing the package, apply migrations with:

alembic upgrade head

By default the migration configuration uses the database URL from the MARC_DB_URL environment variable, falling back to an in-memory SQLite database.