API¶
A kmviz instance can host a REST API that allows querying the underlying databases. When enabled, the available features are:
- Information query, which return info about the instance: list of databases, parameters, etc.
- Metadata query, which return a TSV file per query containing the hits and associated metadata.
- Session query, which return a JSON file that can be explored in any other kmviz instance running in session mode.
Note that kmviz provides CLI tools to simplify the execution of these queries, avoiding the need to make raw 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...
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.
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.
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.