Command Line Interface Reference
This page provides documentation for the e(BE:L) command line interface (CLI).
main
BEL test framework Command Line Utilities on /home/docs/checkouts/readthedocs.org/user_builds/ebel/envs/latest/bin/python
Usage:
main [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
enrich
Trigger the enrichment step for a database.
Parameters
skip : str Comma-separated list of databases to skip during enrichment. include : str Comma-separated list of databases to include during enrichment. skip_drugbank : bool Boolean flag to disable DrugBank enrichment. Useful if you do not have valid DrugBank credentials drugbank_user: str (optional) DrugBank user name. drugbank_password: str (optional) DrugBank password. odb_name: str OrientDB database name odb_user: str OrientDB user (with admin rights) odb_password: str OrientDB user (with admin rights) password odb_server: str OrientDB server name or URI odb_port: int OrientDB server port odb_user_reader: str OrientDB user with only read rights odb_user_reader_password: OrientDB user with only read rights password odb_root_password: str OrientDB root user password (only first database setup needed) kegg_species: str KEGG species 3-4 letter code https://www.genome.jp/kegg/catalog/org_list4.html sqlalchemy_connection_string: SQL Alchemy connection string schema: user:passwd@server/database snp_related_traits: str SNP related traits
Usage:
main enrich [OPTIONS]
Options:
-s, --skip TEXT Comma-separated list of databases to skip
during enrichment
-i, --include TEXT Comma-separated list of databases to include
during enrichment
--skip_drugbank Flag to disable DrugBank
--drugbank_user TEXT Valid username for DrugBank
--drugbank_password TEXT Valid username for DrugBank
-n, --odb_name TEXT OrientDB database name
-u, --odb_user TEXT OrientDB user (with admin rights)
-p, --odb_password TEXT OrientDB user (with admin rights) password
-h, --odb_server TEXT OrientDB server name or URI
-o, --odb_port TEXT OrientDB server port
--odb_user_reader TEXT OrientDB user with only read rights
--odb_user_reader_password TEXT
OrientDB user with only read rights password
--odb_root_password TEXT OrientDB root user password (only during
database setup)
--kegg_species TEXT KEGG species
--sqlalchemy_connection_string TEXT
schema is user:password@server/database
--snp_related_traits TEXT key of SNP related traits in GWAS catalog
and ClinVar
--help Show this message and exit.
import-json
Import JSON into OrientDB.
Parameters
json_file_path : str Path to a BEL JSON file, list of BEL JSON files (separated by ","), or a directory containing BEL JSON files. extend : bool Boolean flag to disable network extension by e(BE:L) p2g : bool Boolean flag to disable adding genes and RNA to proteins in network skip_drugbank : bool Boolean flag to disable DrugBank enrichment. Useful if you do not have valid DrugBank credentials drugbank_user: str (optional) DrugBank user name. drugbank_password: str (optional) DrugBank password. include_subfolders: bool (optional) Boolean flag to enable walking through subdirectories during import. odb_name: str OrientDB database name odb_user: OrientDB user (with admin rights) odb_password: OrientDB user (with admin rights) password odb_server: OrientDB server name or URI odb_port: OrientDB server port odb_user_reader: OrientDB user with only read rights odb_user_reader_password: OrientDB user with only read rights password odb_root_password: OrientDB root user password (only first database setup needed) kegg_species: KEGG species 3-4 letter code https://www.genome.jp/kegg/catalog/org_list4.html sqlalchemy_connection_string: SQL Alchemy connection string schema: user:passwd@server/database snp_related_traits: SNP related traits
Returns
type returns True if imported.
Usage:
main import-json [OPTIONS] JSON_FILE_PATH
Options:
-e, --extend Flag to disable "extension" during import
-g, --p2g Flag to disable "protein2gene" during import
-s, --skip_drugbank Flag to disable DrugBank
-i, --include_subfolders Flag to enable directory walking
--drugbank_user TEXT Valid username for DrugBank
--drugbank_password TEXT Valid username for DrugBank
-n, --odb_name TEXT OrientDB database name
-u, --odb_user TEXT OrientDB user (with admin rights)
-p, --odb_password TEXT OrientDB user (with admin rights) password
-h, --odb_server TEXT OrientDB server name or URI
-o, --odb_port TEXT OrientDB server port
--odb_user_reader TEXT OrientDB user with only read rights
--odb_user_reader_password TEXT
OrientDB user with only read rights password
--odb_root_password TEXT OrientDB root user password (only during
database setup)
--kegg_species TEXT KEGG species
--sqlalchemy_connection_string TEXT
schema is user:password@server/database
--snp_related_traits TEXT key of SNP related traits in GWAS catalog
--drugbank_user TEXT Drugbank user
--drugbank_password TEXT DrugBank password
--help Show this message and exit.
repair
Repair the BEL file for common delimiters and line separations.
Usage:
main repair [OPTIONS] BEL_SCRIPT_PATH REPAIRED_FILE_PATH
Options:
-d, --diff Also export a file showing the differences between the original
and repaired file.
--help Show this message and exit.
serve
Start the API RESTful server.
Usage:
main serve [OPTIONS]
Options:
-h, --host TEXT Server or host name
-p, --port TEXT server port [5000]
-d, --debug_mode debug mode
-o, --open_browser open browser
--help Show this message and exit.
set-connection
Set the SQLAlchemy connection string.
:param connection: An existing RDBMS connection.
Usage:
main set-connection [OPTIONS] CONNECTION
Options:
--help Show this message and exit.
set-mysql
Set the SQLAlchemy connection string with MySQL settings.
Usage:
main set-mysql [OPTIONS]
Options:
-h, --host TEXT MySQL server
-u, --user TEXT MySQL username
-p, --password TEXT MySQL password
-d, --database TEXT MySQL database name
-i, --interactive Enable interactive mode
--help Show this message and exit.
settings
Interactive method to create a configuration file.
Usage:
main settings [OPTIONS]
Options:
--help Show this message and exit.
validate
Validate a BEL file using the defined grammar.
Usage:
main validate [OPTIONS] BEL_SCRIPT_PATH
Options:
-l, --line_by_line check script line by line
-r, --reports TEXT path(s) to report file(s) seperated by comma
with suffix (.md, .txt, .csv, .tsv, .json,
.html)
-v, --bel_version TEXT stores a report in a file
-t, --tree shows tree
-s, --sqlalchemy_connection_str TEXT
SQLAlchmy connection string
-j, --json_file Create json file
-f, --force_json Force the creation of a JSON file
--help Show this message and exit.