Command Line Interface¶

compath¶

ComPath at sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

compath [OPTIONS] COMMAND [ARGS]...

drop¶

Drop ComPath DB.

compath drop [OPTIONS]

Options

-v, --debug¶: Turn on debugging.

-y, --yes¶

-c, --connection <connection>¶: Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

drop-databases¶

Drop all databases.

compath drop-databases [OPTIONS]

Options

-v, --debug¶: Turn on debugging.

-y, --yes¶

-c, --connection <connection>¶: Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

load-hierarchies¶

Load pathway databases with hierarchies.

compath load-hierarchies [OPTIONS]

Options

-c, --connection <connection>¶: Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

-e, --email <email>¶: Default curator: daniel.domingo.fernandez@scai.fraunhofer.de

load-mappings¶

Load mappings from template.

compath load-mappings [OPTIONS]

Options

-c, --connection <connection>¶: Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

ls¶

Display registered Bio2BEL pathway managers.

compath ls [OPTIONS]

manage¶

Manage the database.

compath manage [OPTIONS] COMMAND [ARGS]...

Options

-c, --connection <connection>¶: Cache connection. Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

users¶

User group.

compath manage users [OPTIONS] COMMAND [ARGS]...

ls¶

List all users.

compath manage users ls [OPTIONS]

make-admin¶

Make a pre-existing user an admin.

compath manage users make-admin [OPTIONS] EMAIL

Arguments

EMAIL¶: Required argument

make-user¶

Create a pre-existing user an admin.

compath manage users make-user [OPTIONS] EMAIL PASSWORD

Arguments

EMAIL¶: Required argument

PASSWORD¶: Required argument

populate¶

Populate all registered Bio2BEL pathway packages.

compath populate [OPTIONS]

Options

-v, --debug¶: Turn on debugging.

-c, --connection <connection>¶: Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db

-d, --delete-first¶

web¶

Run web service.

compath web [OPTIONS]

Options

--host <host>¶: Flask host. Defaults to 0.0.0.0

--port <port>¶: Flask port. Defaults to 5000

--template-folder <template_folder>¶: Template folder. Defaults to ‘templates’

--static-folder <static_folder>¶: Template folder. Defaults to ‘static’

-v, --debug¶: Turn on debugging.

-c, --connection <connection>¶: Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db