bbconf
BEDBASE project configuration package (agent)
What is this?
bbconf is a configuration and data management library for the BEDbase platform. It serves as the central backbone for all BEDbase tools and pipelines by:
- Reading and validating YAML configuration files
- Setting up and managing connections to PostgreSQL, Qdrant, S3, and PEPHub
- Loading ML models (Region2Vec, text embedders, sparse encoders, UMAP) used for BED file search
- Providing high-level Python interfaces for querying and managing BED files and BED sets
- Exposing a unified
BedBaseAgentobject that all downstream tools use to interact with the platform
Documentation: https://docs.bedbase.org/bedboss
Source Code: https://github.com/databio/bbconf
Installation
To install bbclient use this command:
pip install bbconf
or install the latest version from the GitHub repository:
pip install git+https://github.com/databio/bbconf.git
Quick start
from bbconf import BedBaseAgent
agent = BedBaseAgent(config="config.yaml")
# Access submodules
agent.bed # BED file operations
agent.bedset # BED set operations
agent.objects # Generic object/file operations
# Get platform statistics
stats = agent.get_stats()
print(stats.bedfiles_number, stats.bedsets_number)
Database migrations
bbconf uses Alembic to version the database
schema. The migration scripts live in bbconf/alembic, and alembic.ini (repo
root) is used for local CLI work. The first (baseline) revision is
8b0b706d0827; it reproduces exactly the schema that Base.metadata.create_all()
builds, including the pg_trgm extension and the trigram / partial / expression
indexes.
To update schema for desirable database, use different database url in alembic.ini,
otherwise run test database
Creating a new revision
After changing the models in bbconf/db_utils.py:
alembic revision --autogenerate -m "Describe your change"
Review the generated file. Alembic cannot autogenerate a few constructs used by
bbconf — the pg_trgm extension and expression-based indexes may need a manual
op.execute(...) — so always check the diff before committing.
Applying migrations
alembic upgrade head # upgrade to the latest revision
alembic downgrade -1 # roll back one revision
alembic current # show the DB's current revision
Running migrations automatically
To upgrade the database to head automatically when bbconf starts, set
run_migrations: true under the database section of the config file:
database:
host: localhost
port: 5432
user: postgres
password: docker
database: bedbase
run_migrations: true
Note: enable this only after the database has been stamped/upgraded to a known revision. Turning it on against an un-stamped existing database will fail on startup, because the baseline revision creates tables that already exist.
3 maintainers
Metadata
3 maintainers
Release files for bbconf 0.16.0
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| File | Size | Uploaded | Provenance | |
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|---|---|---|---|---|
| bbconf-0.16.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 501.2 kB
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