Command Line Interface

biolookup automatically installs the command biolookup. See biolookup --help for usage details.

biolookup

CLI for the Biolookup Service.

biolookup [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

load

Load the SQL database.

biolookup load [OPTIONS]

Options

--uri <uri>

The database URL.

Default:

<function get_sqlalchemy_uri at 0x769b3a62df80>

--refs-table <refs_table>

Default:

'obo_reference'

--refs-path <refs_path>

By default, load from Zenodo

Default:

<function ensure_ooh_na_na at 0x769b31fbb560>

--alts-table <alts_table>

Default:

'obo_alt'

--alts-path <alts_path>

By default, load from Zenodo

Default:

<function ensure_alts at 0x769b31fbb060>

--defs-table <defs_table>

Default:

'obo_def'

--defs-path <defs_path>

By default, load from Zenodo

Default:

<function ensure_definitions at 0x769b31fbade0>

--xrefs-table <xrefs_table>

Default:

'xrefs'

--xrefs-path <xrefs_path>

By default, load from Zenodo

Default:

<function ensure_inspector_javert at 0x769b31fbb420>

--test

Test run with a small test subset

-v, --verbose

Enable verbose mode. More -v’s means more verbose.

--date <date>

Required

lookup

Look up a CURIE.

biolookup lookup [OPTIONS] CURIE

Arguments

CURIE

Required argument

web

Run the Biolookup Service.

biolookup web [OPTIONS]

Options

--port <port>

Flask port.

Default:

5000

--host <host>

Flask host.

Default:

'0.0.0.0'

--name-data <name_data>

local 3-column gzipped TSV as database

--alts-data <alts_data>

local 3-column gzipped TSV as database

--defs-data <defs_data>

local 3-column gzipped TSV as database

--sql

Use a sql database backend. If not used, defaults to in memory dictionaries

--uri <uri>

SQL URI string when using –sql

--sql-refs-table <sql_refs_table>

use preloaded SQL database as backend

--sql-alts-table <sql_alts_table>

use preloaded SQL database as backend

--sql-defs-table <sql_defs_table>

use preloaded SQL database as backend

--lazy

do no load full cache into memory automatically

--test

run in test mode with only a few datasets

--workers <workers>

number of workers to use in –gunicorn mode

-v, --verbose

Enable verbose mode. More -v’s means more verbose.