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