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
manage¶
Manage the database.
compath manage [OPTIONS] COMMAND [ARGS]...
Options
-
-c
,
--connection
<connection>
¶ Cache connection. Defaults to sqlite:////home/docs/.pybel/bio2bel/bio2bel.db
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