factory

ensembl.io.genomio.database.factory

Generates one JSON file per metadata type inside manifest, including the manifest itself.

format_db_data(server_url, dbs, brc_mode=False)

Returns a metadata list from the given databases on a server.

Parameters:

Name	Type	Description	Default
server_url	URL	Server URL where all the databases are hosted.	required
dbs	list[str]	List of database names.	required
brc_mode	bool	If true, assign BRC4.organism_abbrev as the species, and BRC4.component as the division. Otherwise, the species will be species.production_name and the division will be species.division.	False

Returns:

Type	Description
list[dict]	List of dictionaries with 3 keys: "database", "species" and "division".

Source code in src/python/ensembl/io/genomio/database/factory.py

def format_db_data(server_url: URL, dbs: list[str], brc_mode: bool = False) -> list[dict]:
    """Returns a metadata list from the given databases on a server.

    Args:
        server_url: Server URL where all the databases are hosted.
        dbs: List of database names.
        brc_mode: If true, assign ``BRC4.organism_abbrev`` as the species, and ``BRC4.component`` as the
            division. Otherwise, the species will be ``species.production_name`` and the division will be
            ``species.division``.

    Returns:
        List of dictionaries with 3 keys: "database", "species" and "division".
    """
    databases_data = []
    for db_name in dbs:
        logging.debug(f"Get metadata for {db_name}")
        db_url = server_url.set(database=db_name)
        core_db = DBConnectionLite(db_url)

        prod_name = core_db.get_meta_value("species.production_name")
        species = prod_name
        division = core_db.get_meta_value("species.division")
        accession = core_db.get_meta_value("assembly.accession")
        project_release = core_db.get_project_release()

        if brc_mode:
            brc_organism = core_db.get_meta_value("BRC4.organism_abbrev")
            brc_component = core_db.get_meta_value("BRC4.component")
            if brc_organism is not None:
                species = brc_organism
            if brc_component is not None:
                division = brc_component

        if not division:
            division = "all"

        server_data = {
            "host": db_url.host,
            "user": db_url.username,
            "port": db_url.port,
            "password": db_url.password,
            "database": db_url.database,
        }
        db_data = {
            "server": server_data,
            "production_name": prod_name,
            "species": species,
            "division": division,
            "accession": accession,
            "release": project_release,
        }

        databases_data.append(db_data)
    return databases_data

get_core_dbs_metadata(server_url, *, prefix='', build=None, version=None, db_regex='', db_list=None, brc_mode=False)

Returns all the metadata fetched for the selected core databases.

Parameters:

Name	Type	Description	Default
server_url	URL	Server URL where the core databases are stored.	required
prefix	str	Filter by prefix (no "_" is added automatically).	''
build	int | None	Filter by VEuPathDB build number.	None
version	int | None	Filter by Ensembl version.	None
db_regex	str	Filter by dbname regular expression.	''
db_list	Path | None	Explicit list of database names.	None
brc_mode	bool	Enable BRC mode.	False

Returns:

Type	Description
list[dict]	List of dictionaries with 3 keys: "database", "species" and "division".

Source code in src/python/ensembl/io/genomio/database/factory.py

def get_core_dbs_metadata(
    server_url: URL,
    *,
    prefix: str = "",
    build: int | None = None,
    version: int | None = None,
    db_regex: str = "",
    db_list: Path | None = None,
    brc_mode: bool = False,
) -> list[dict]:
    """Returns all the metadata fetched for the selected core databases.

    Args:
        server_url: Server URL where the core databases are stored.
        prefix: Filter by prefix (no "_" is added automatically).
        build: Filter by VEuPathDB build number.
        version: Filter by Ensembl version.
        db_regex: Filter by dbname regular expression.
        db_list: Explicit list of database names.
        brc_mode: Enable BRC mode.

    Returns:
        List of dictionaries with 3 keys: "database", "species" and "division".
    """
    db_list_file = None
    if db_list:
        with db_list.open("r") as infile_fh:
            db_list_file = [line.strip() for line in infile_fh]
    # Get all database names
    server = CoreServer(server_url)
    logging.debug("Fetching databases...")
    databases = server.get_cores(
        prefix=prefix, build=build, version=version, dbname_re=db_regex, db_list=db_list_file
    )
    logging.info(f"Got {len(databases)} databases")
    logging.debug("\n".join(databases))
    return format_db_data(server_url, databases, brc_mode)

main(arg_list=None)

Main script entry-point.

Parameters:

Name	Type	Description	Default
arg_list	list[str] | None	Arguments to parse passing list to parse_args().	None

Source code in src/python/ensembl/io/genomio/database/factory.py

def main(arg_list: list[str] | None = None) -> None:
    """Main script entry-point.

    Args:
        arg_list: Arguments to parse passing list to parse_args().

    """
    args = parse_args(arg_list)
    init_logging_with_args(args)

    databases_data = get_core_dbs_metadata(
        server_url=args.url,
        prefix=args.prefix,
        build=args.build,
        version=args.release,
        db_regex=args.db_regex,
        db_list=args.db_list,
        brc_mode=args.brc_mode,
    )
    print(json.dumps(databases_data, sort_keys=True, indent=4))

parse_args(arg_list)

Return a populated namespace with the arguments parsed from a list or from the command line.

Parameters:

Name	Type	Description	Default
arg_list	list[str] | None	List of arguments to parse. If None, grab them from the command line.	required

Source code in src/python/ensembl/io/genomio/database/factory.py

def parse_args(arg_list: list[str] | None) -> argparse.Namespace:
    """Return a populated namespace with the arguments parsed from a list or from the command line.

    Args:
        arg_list: List of arguments to parse. If `None`, grab them from the command line.

    """
    parser = ArgumentParser(description=__doc__)
    parser.add_server_arguments()
    # Add filter arguments
    parser.add_argument("--prefix", default="", help="Prefix to filter the databases")
    parser.add_argument("--build", type=int, default=None, help="Build to filter the databases")
    parser.add_argument("--release", type=int, default=None, help="EnsEMBL release to filter the databases")
    parser.add_argument("--db_regex", default="", help="Regular expression to match database names against")
    parser.add_argument_src_path("--db_list", help="File with one database per line to load")
    # Add flags
    parser.add_argument(
        "--brc_mode",
        action="store_true",
        help="Enable BRC mode, i.e. use organism_abbrev for species, component for division",
    )
    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
    parser.add_log_arguments()
    return parser.parse_args(arg_list)