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biocypher/_config/biocypher_config.yaml

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+Title: BioCypher python module configuration file
+
+## Some options are not used by default. Uncomment them to use them.
+
+biocypher:
+  ### Required parameters ###
+  ## DBMS type
+
+  dbms: neo4j
+
+  ## Schema configuration
+
+  # schema_config_path: config/schema_config.yaml
+
+  ## Offline mode: do not connect to a running DBMS instance
+  ## Can be used e.g. for writing batch import files
+
+  offline: true
+
+  ## Strict mode: do not allow to create new nodes or relationships without
+  ## specifying source, version, and license parameters
+
+  strict_mode: false
+
+  ## Ontology configuration
+
+  head_ontology:
+    url: https://github.com/biolink/biolink-model/raw/v3.2.1/biolink-model.owl.ttl
+    root_node: entity
+    # switch_label_and_id: true
+
+  ### Optional parameters ###
+
+  ## Logging
+  # Write log to disk
+  log_to_disk: true
+
+  # Activate more granular logging
+  debug: true
+
+  # Change the log directory
+  # log_directory: biocypher-log
+
+  ## Data output directory
+  # output_directory: biocypher-out
+
+  ## Resource cache directory
+  # cache_directory: .cache
+
+  ## Optional tail ontologies
+
+  # tail_ontologies:
+  #   so:
+  #     url: test/ontologies/so.owl
+  #     head_join_node: sequence variant
+  #     tail_join_node: sequence_variant
+  #     switch_label_and_id: true
+  #   mondo:
+  #     url: test/ontologies/mondo.owl
+  #     head_join_node: disease
+  #     tail_join_node: disease
+  #     switch_label_and_id: true
+
+### DBMS configuration ###
+
+neo4j:
+  ### Neo4j configuration ###
+  ## Database name
+
+  database_name: neo4j
+
+  ## Wipe DB before import (offline mode: --force)
+
+  wipe: true
+
+  ## Neo4j authentication
+
+  uri: neo4j://localhost:7687
+  user: neo4j
+  password: neo4j
+
+  ## Neo4j admin import batch writer settings
+
+  delimiter: ";"
+  array_delimiter: "|"
+  quote_character: "'"
+
+  ## MultiDB functionality
+  ## Set to false for using community edition or older versions of Neo4j
+
+  multi_db: true
+
+  ## Import options
+
+  skip_duplicate_nodes: false
+  skip_bad_relationships: false
+
+  ## Import call prefixes
+
+  # import_call_bin_prefix: bin/
+  # import_call_file_prefix: path/to/files/
+
+postgresql:
+  ### PostgreSQL configuration ###
+
+  # PostgreSQL connection credentials
+  database_name: postgres # DB name
+  user: postgres # user name
+  password: postgres # password
+  host: localhost # host
+  port: 5432 # port
+
+  # PostgreSQL import batch writer settings
+  quote_character: '"'
+  delimiter: '\t'
+  # import_call_bin_prefix: '' # path to "psql"
+  # import_call_file_prefix: '/path/to/files'
+
+rdf:
+  ### RDF configuration ###
+  rdf_format: turtle
+
+sqlite:
+  ### SQLite configuration ###
+
+  # SQLite connection credentials
+  database_name: sqlite.db # DB name
+
+  # SQLite import batch writer settings
+  quote_character: '"'
+  delimiter: '\t'
+  # import_call_bin_prefix: '' # path to "sqlite3"
+  # import_call_file_prefix: '/path/to/files'
+
+csv:
+  ### CSV/Pandas configuration ###
+  delimiter: ","
+
+networkx:
+  ### NetworkX configuration ###
+  some_config: some_value # placeholder for technical reasons TODO