climb-onyx-client 4.2.0

Client program for interacting with Onyx.

onyx-client

Setup

Install from conda-forge

$ conda create --name onyx --channel conda-forge climb-onyx-client

Install from PyPI

$ 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 .venv
$ source .venv/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.                                │
│ choices        View options for a choice field.                                           │
│ get            Get a record from a project.                                               │
│ filter         Filter multiple records from a project.                                    │
│ identify       Get the anonymised identifier for a value on a 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.