biocypher.output.connect._neo4j_driver._Neo4jDriver

class biocypher.output.connect._neo4j_driver._Neo4jDriver(database_name: str, uri: str, user: str, password: str, multi_db: bool, translator: Translator, wipe: bool = False, fetch_size: int = 1000, increment_version: bool = True)

Manages a BioCypher connection to a Neo4j database using the neo4j_utils.Driver class.

Parameters:

  • database_name (str) – The name of the database to connect to.

  • wipe (bool) – Whether to wipe the database before importing.

  • uri (str) – The URI of the database.

  • user (str) – The username to use for authentication.

  • password (str) – The password to use for authentication.

  • multi_db (bool) – Whether to use multi-database mode.

  • fetch_size (int) – The number of records to fetch at a time.

  • increment_version (bool) – Whether to increment the version number.

  • translator (Translator) – The translator to use for mapping.

__init__(database_name: str, uri: str, user: str, password: str, multi_db: bool, translator: Translator, wipe: bool = False, fetch_size: int = 1000, increment_version: bool = True)

Methods

__init__(database_name, uri, user, password, ...)

add_biocypher_edges(edges[, explain, profile])

Accepts an edge type handoff class (biocypher.create.BioCypherEdge) with source and target ids, label, and a dict of properties (passing on the type of property, ie, int, string ...).

add_biocypher_nodes(nodes[, explain, profile])

Accepts a node type handoff class (biocypher.create.BioCypherNode) with id, label, and a dict of properties (passing on the type of property, ie, int, str, ...).

add_edges(id_src_tar_type_tuples)

Generic edge adder method to add any kind of input to the graph via the biocypher.create.BioCypherEdge class.

add_nodes(id_type_tuples)

Generic node adder method to add any kind of input to the graph via the biocypher.create.BioCypherNode class.

init_db()

Used to initialise a property graph database by setting up new constraints.