biocypher.BioCypher

class biocypher.BioCypher(dbms: Optional[str] = None, offline: Optional[bool] = None, strict_mode: Optional[bool] = None, biocypher_config_path: Optional[str] = None, schema_config_path: Optional[str] = None, head_ontology: Optional[dict] = None, tail_ontologies: Optional[dict] = None, output_directory: Optional[str] = None, cache_directory: Optional[str] = None, db_name: Optional[str] = None)

Orchestration of BioCypher operations. Instantiate this class to interact with BioCypher.

Parameters:

• dbms (str) – The database management system to use. For supported systems see SUPPORTED_DBMS.

• offline (bool) – Whether to run in offline mode. If True, no connection to the database will be made.

• strict_mode (bool) – Whether to run in strict mode. If True, the translator will raise an error if a node or edge does not provide source, version, and licence information.

• biocypher_config_path (str) – Path to the BioCypher config file.

• schema_config_path (str) – Path to the user schema config file.

• head_ontology (dict) – The head ontology defined by URL (‘url’) and root node (‘root_node’).

• tail_ontologies (dict) – The tail ontologies defined by URL and join nodes for both head and tail ontology.

• output_directory (str) – Path to the output directory. If not provided, the default value ‘biocypher-out’ will be used.

__init__(dbms: Optional[str] = None, offline: Optional[bool] = None, strict_mode: Optional[bool] = None, biocypher_config_path: Optional[str] = None, schema_config_path: Optional[str] = None, head_ontology: Optional[dict] = None, tail_ontologies: Optional[dict] = None, output_directory: Optional[str] = None, cache_directory: Optional[str] = None, db_name: Optional[str] = None)

Methods

__init__([dbms, offline, strict_mode, ...])
add(entities)	Function to add entities to the in-memory database.
add_edges(edges)	Wrapper for add() to add edges to the in-memory database.
add_nodes(nodes)	Wrapper for add() to add nodes to the in-memory database.
download(*resources)	Use the Downloader class to download or load from cache the resources given by the adapter.
log_duplicates()	Get the set of duplicate nodes and edges encountered and print them to the logger.
log_missing_input_labels()	Get the set of input labels encountered without an entry in the schema_config.yaml and print them to the logger.
merge_edges(edges)	Merge edges into database.
merge_nodes(nodes)	Merge nodes into database.
reverse_translate_query(query)	Reverse translate a query from its BioCypher equivalent.
reverse_translate_term(term)	Reverse translate a term from its BioCypher equivalent.
show_ontology_structure(**kwargs)	Show the ontology structure using treelib or write to GRAPHML file.
summary()	Wrapper for showing ontology structure and logging duplicates and missing input types.
to_df()	Convert entities to a pandas DataFrame for each entity type and return a list.
translate_query(query)	Translate a query to its BioCypher equivalent.
translate_term(term)	Translate a term to its BioCypher equivalent.
write_edges(edges[, batch_size])	Write edges to database.
write_import_call()	Write a shell script to import the database depending on the chosen DBMS.
write_nodes(nodes[, batch_size, force])	Write nodes to database.
write_schema_info([as_node])	Write an extended schema info YAML file that extends the schema_config.yaml with run-time information of the built KG.