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 0x7f5b5ef875e0>

--refs-table <refs_table>
Default

obo_reference

--refs-path <refs_path>

By default, load from Zenodo

Default

<function ensure_ooh_na_na at 0x7f5b5ef859d0>

--alts-table <alts_table>
Default

obo_alt

--alts-path <alts_path>

By default, load from Zenodo

Default

<function ensure_alts at 0x7f5b5ef85c10>

--defs-table <defs_table>
Default

obo_def

--defs-path <defs_path>

By default, load from Zenodo

Default

<function ensure_definitions at 0x7f5b5ef85d30>

--xrefs-table <xrefs_table>
Default

xrefs

--xrefs-path <xrefs_path>

By default, load from Zenodo

Default

<function ensure_inspector_javert at 0x7f5b5ef85a60>

--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

--with-gunicorn

Use gunicorn instead of flask dev server

-v, --verbose

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

--debug