kmviz api¶
The kmviz api command group contains utilities to request the kmviz API without making manuel HTTP requests.
python -m kmviz api --help
Usage: python -m kmviz api [OPTIONS] COMMAND [ARGS]...
Query kmviz REST API
Options:
-u, --url <str> Host [default: http://localhost]
-p, --port <int> Port
-a, --auth <user>:<password> HTTP BasicAuth credentials
--help Show this message and exit.
Commands:
infos Get databases information
metadata Make queries and get results as a tsv dataframe
query Make queries and get results as a json session file, viewable...
Usage: python -m kmviz api [OPTIONS] COMMAND [ARGS]...
Query kmviz REST API
Options:
-u, --url <str> Host [default: http://localhost]
-p, --port <int> Port
-a, --auth <user>:<password> HTTP BasicAuth credentials
--help Show this message and exit.
Commands:
infos Get databases information
metadata Make queries and get results as a tsv dataframe
query Make queries and get results as a json session file, viewable...
kmviz api infos retrieves instance information in JSON format. This information includes registered databases and their options, making it useful for constructing API requests.
python -m kmviz api infos --help
Usage: python -m kmviz api infos [OPTIONS]
Get databases information
Options:
-r, --route <str> Route [default: /api]
-o, --output <path> Output file [default: stdout]
--help Show this message and exit.
Usage: python -m kmviz api infos [OPTIONS]
Get databases information
Options:
-r, --route <str> Route [default: /api]
-o, --output <path> Output file [default: stdout]
--help Show this message and exit.
kmviz api metadata command allows you to query a database and obtain a zip archive of results, with one TSV file per query sequence. Note that the archive name is a session-id, which can be used to reload the result on the interface associated with the API endpoint, if it exists.
python -m kmviz api metadata --help
Usage: python -m kmviz api metadata [OPTIONS]
Make queries and get results as a tsv dataframe
Options:
-r, --route <str> Query route [default: /api/query]
-o, --output <dir> Output directory [default: .]
-d, --database <str> Database to query [required]
-x, --opt <opt_name> <value> Database option, -x <opt_name> <value>
-f, --fastx <path> Path to fastx query file [required]
--help Show this message and exit.
Usage: python -m kmviz api metadata [OPTIONS]
Make queries and get results as a tsv dataframe
Options:
-r, --route <str> Query route [default: /api/query]
-o, --output <dir> Output directory [default: .]
-d, --database <str> Database to query [required]
-x, --opt <opt_name> <value> Database option, -x <opt_name> <value>
-f, --fastx <path> Path to fastx query file [required]
--help Show this message and exit.
kmviz api query allows you to query an instance to obtain a JSON session file, which can then be reloaded into a kmviz instance in session mode.
python -m kmviz api query --help
Usage: python -m kmviz api query [OPTIONS]
Make queries and get results as a json session file, viewable using a local
kmviz instance. See kmviz app start session
Options:
-r, --route <str> Query route [default: /api/query]
-o, --output <path> Output file [default: stdout]
-d, --database <str> Database to query [required]
-x, --opt <db_name> <opt_name> <value>
Database options
-f, --fastx <path> Path to fastx query file [required]
--help Show this message and exit.
Usage: python -m kmviz api query [OPTIONS]
Make queries and get results as a json session file, viewable using a local
kmviz instance. See kmviz app start session
Options:
-r, --route <str> Query route [default: /api/query]
-o, --output <path> Output file [default: stdout]
-d, --database <str> Database to query [required]
-x, --opt <db_name> <opt_name> <value>
Database options
-f, --fastx <path> Path to fastx query file [required]
--help Show this message and exit.