climb-onyx-client 2.4.0

Client program for interacting with Onyx.

onyx-client

Setup

Install via pip

$ pip install climb-onyx-client

Build from source

Download and install the client into a Python virtual environment:

$ git clone https://github.com/CLIMB-COVID/onyx-client.git
$ cd onyx-client/
$ python -m venv env
$ source env/bin/activate
$ pip install .

Check it works:

$ onyx
                                                                                             
 Usage: onyx [OPTIONS] COMMAND [ARGS]...                                                     
                                                                                             
 API for pathogen metadata.                                                                  
                                                                                             
╭─ Options ─────────────────────────────────────────────────────────────────────────────────╮
│ --domain    -d      TEXT  Domain name for connecting to Onyx. [env var: ONYX_DOMAIN]      │
│                           [default: None]                                                 │
│ --token     -t      TEXT  Token for authenticating with Onyx. [env var: ONYX_TOKEN]       │
│                           [default: None]                                                 │
│ --username  -u      TEXT  Username for authenticating with Onyx. [env var: ONYX_USERNAME] │
│                           [default: None]                                                 │
│ --password  -p      TEXT  Password for authenticating with Onyx. [env var: ONYX_PASSWORD] │
│                           [default: None]                                                 │
│ --version   -v            Show the client version number and exit.                        │
│ --help      -h            Show this message and exit.                                     │
╰───────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ────────────────────────────────────────────────────────────────────────────────╮
│ projects          View available projects.                                                │
│ fields            View the field specification for a project.                             │
│ get               Get a record from a project.                                            │
│ filter            Filter multiple records from a project.                                 │
│ choices           View options for a choice field.                                        │
│ profile           View profile information.                                               │
│ siteusers         View users from the same site.                                          │
│ auth              Authentication commands.                                                │
│ admin             Admin commands.                                                         │
╰───────────────────────────────────────────────────────────────────────────────────────────╯

For more information, check out the documentation.