$ conda create --name onyx --channel conda-forge climb-onyx-client
$ pip install climb-onyx-client
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.