API Reference

biokb_ipni.import_data

Import all data in database.

Parameters:

Name	Type	Description	Default
engine	Optional[Engine]	SQLAlchemy engine. Defaults to None.	None
force_download	bool	If True, will force download the data, even if files already exist. If False, it will skip the downloading part if files already exist locally. Defaults to False.	False
delete_files	bool	If True, downloaded files are deleted after import. Defaults to False.	False

Returns:

Type	Description
dict[str, int]	Dict[str, int]: table=key and number of inserted=value

Source code in biokb_ipni/db/manager.py

def import_data(
    engine: Optional[Engine] = None,
    force_download: bool = False,
    delete_files: bool = False,
) -> dict[str, int]:
    """Import all data in database.

    Args:
        engine (Optional[Engine]): SQLAlchemy engine. Defaults to None.
        force_download (bool, optional): If True, will force download the data, even if
            files already exist. If False, it will skip the downloading part if files
            already exist locally. Defaults to False.
        delete_files (bool, optional): If True, downloaded files are deleted after import.
            Defaults to False.

    Returns:
        Dict[str, int]: table=key and number of inserted=value
    """
    db_manager = DbManager(engine)
    return db_manager.import_data(
        force_download=force_download, delete_files=delete_files
    )

biokb_ipni.create_ttls

Create all turtle files.

If engine=None tries to get the settings from environment else uses the default engine.

If export_to_folder is provided, turtle files are exported to this folder. Otherwise, the default export folder (~/.biokb/ipni/data) is used.

Parameters:

Name	Type	Description	Default
engine	Engine | None	SQLAlchemy engine. Defaults to None.	None
export_to_folder	str | None	Folder to export ttl files. Defaults to None.	None

Returns:

Name	Type	Description
str	str	path zipped file with ttls.

Source code in biokb_ipni/rdf/turtle.py

def create_ttls(
    engine: Optional[Engine] = None,
    export_to_folder: Optional[str] = None,
) -> str:
    """Create all turtle files.

    If engine=None tries to get the settings from environment else uses the default engine.

    If export_to_folder is provided, turtle files are exported to this folder. Otherwise,
    the default export folder (~/.biokb/ipni/data) is used.

    Args:
        engine (Engine | None, optional): SQLAlchemy engine. Defaults to None.
        export_to_folder (str | None, optional): Folder to export ttl files.
            Defaults to None.

    Returns:
        str: path zipped file with ttls.
    """
    ttl_creator = TurtleCreator(engine=engine)
    if export_to_folder:
        ttl_creator._set_ttls_folder(export_to_folder)
    return ttl_creator.create_ttls()

biokb_ipni.import_ttls

Import data into Neo4J from zipped turtle files.

Parameters:

Name	Type	Description	Default
neo4j_uri	str | None	URI of the Neo4j database.	None
neo4j_user	str | None	Username for Neo4j.	None
neo4j_pwd	str | None	Password for Neo4j.	None
delete_existing_graph	bool	delete existing graph before import.	True

Returns: bool: True if import is successful.

Source code in biokb_ipni/rdf/neo4j_importer.py

def import_ttls(
    neo4j_uri: str | None = None,
    neo4j_user: str | None = None,
    neo4j_pwd: str | None = None,
    delete_existing_graph: bool = True,
) -> bool:
    """Import data into Neo4J from zipped turtle files.

    Args:
        neo4j_uri (str | None): URI of the Neo4j database.
        neo4j_user (str | None): Username for Neo4j.
        neo4j_pwd (str | None): Password for Neo4j.
        delete_existing_graph (bool): delete existing graph before import.
    Returns:
        bool: True if import is successful.
    """
    importer = Neo4jImporter(
        neo4j_uri=neo4j_uri, neo4j_user=neo4j_user, neo4j_pwd=neo4j_pwd
    )
    result: bool = importer.import_ttls(delete_existing_graph=delete_existing_graph)
    return result