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