climb-onyx-client 4.6.0

CLI and Python library for 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 ────────────────────────────────────────────────────────────────────────────────╮
│ auth        Authentication commands.                                                      │
│ admin       Admin commands.                                                               │
╰───────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Data ────────────────────────────────────────────────────────────────────────────────────╮
│ projects    View available projects.                                                      │
│ types       View available field types.                                                   │
│ lookups     View available lookups.                                                       │
│ fields      View the field specification for a project.                                   │
│ choices     View options for a choice field in a project.                                 │
│ get         Get a record from a project.                                                  │
│ filter      Filter multiple records from a project.                                       │
│ history     View the history of a record in a project.                                    │
│ identify    Get the anonymised identifier for a value on a field.                         │
│ create      Create a record in a project.                                                 │
│ update      Update a record in a project.                                                 │
│ delete      Delete a record in a project.                                                 │
╰───────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Accounts ────────────────────────────────────────────────────────────────────────────────╮
│ profile     View profile information.                                                     │
│ activity    View latest profile activity.                                                 │
│ siteusers   View users from the same site.                                                │
╰───────────────────────────────────────────────────────────────────────────────────────────╯

For more information, check out the documentation.