DEMO of the bbconf module

bbconf is a configuration and management tool for BEDbase, facilitating the reading of configuration file, setting up connections to PostgreSQL, PEPhub, S3, and Qdrant databases, managing file paths, and storing transformer models.

Introduction

bbconf is divided into 2 main modules:

• bbconf.config_parser - reads the configuration file and sets up connections to databases. BedBaseConfig class is used to store the passwords, configuration, connection objects, and other information.

• bbconf.modules - contains modules for managing bed_files, bedsets, and other common functionalities. Users will mainly use this module because it provides classes with methods for managing the database.

Example:

1) Init the BedBaseAgent class

from bbconf.bbagent import BedBaseAgent

bbagent = BedBaseAgent(bbconf_file_path)

Where bbconf_file_path is the path to the configuration file. How to create a configuration file is described in the configuration section.

Upload a bedfile to the database

bbagent.bed.add(
    identifier=bed_metadata.bed_digest,
    stats=stats.model_dump(exclude_unset=True),
    metadata=other_metadata,
    plots=plots.model_dump(exclude_unset=True),
    files=files.model_dump(exclude_unset=True),
    classification=classification.model_dump(exclude_unset=True),
    upload_qdrant=upload_qdrant,
    upload_pephub=upload_pephub,
    upload_s3=upload_s3,
    local_path=outfolder,
    overwrite=force_overwrite,
    nofail=True,
)

Get a bedfile from the database

bed = bbagent.bed.get(
    identifier=bed_id,
    full=True,
)

Get a bedset from the database

bedset = bbagent.bedset.get(
    identifier=bedset_id,
    full=True,
)

User can access credentials and other configurations from the BedBaseConfig class

e.g. to get pephub namespace used in config you can use the following code:

bbagent.config._config["pephub"]["namespace"]

Full API of bbconf can be found here