Getting started¶
This guide walks through getting started with the Onyx-client CLI.
The guide assumes an environment where authentication credentials are pre-configured.
Profile information¶
Available projects¶
If you cannot see the project(s) that you require access to, contact an admin.
Project fields¶
This returns the fields specification for the given PROJECT.
Project data¶
This returns all records from the given PROJECT.
The data can be exported to various file formats:
$ onyx filter PROJECT --format json > data.json
$ onyx filter PROJECT --format csv > data.csv
$ onyx filter PROJECT --format tsv > data.tsv
Filtering¶
A project's data can be filtered to return records that match certain conditions.
Filtering on the CLI uses a field=value syntax, where field is the name of a field in the project, and value is the value you want to match.
Multiple filters can be provided, and only the records that satisfy all these filters will be returned.
Lookups¶
The data can be filtered in more complex ways using lookups. These use a field.lookup=value syntax (or alternatively, field__lookup=value), and different ones are available depending on a field's data type (e.g. text, integer). There are lookups for searching between a range of values on a field (range), whether a field's value is empty (isnull), whether a field case-insensitively contains some text (icontains), and more.
Examples¶
To filter for all records in a PROJECT published on a specific date (e.g. 2023-09-18):
To filter for all records in a PROJECT published on the current date, a special today keyword can be used:
To filter for all records in a PROJECT with a published_date from 2023-09-01 to 2023-09-18, the range lookup can be used:
Assuming that PROJECT has a sample_type field, then all records with sample_type = "swab" that were published from 2023-09-01 to 2023-09-18 can be obtained with:
Further guidance¶
For further guidance using Onyx-client, use the --help option.