> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/command-line-interface/reference/workbench/samples-attributes-set.md).

# samples attributes set

Replace a sample's custom attributes

## Synopsis

```shell
omics workbench samples attributes set SAMPLE_ID (JSON | @FILE | -)
  [--namespace=STRING]
```

## Description

Replace one sample's custom attributes. The attributes can be given as a JSON literal, read from a file with `@`, or read from standard input with `-`.

{% hint style="warning" %}
This replaces the whole set. Attributes the document omits are deleted, so include everything you want to keep. There is no per-key update.
{% endhint %}

### The document shape

This command takes the attributes **on their own**, because the sample is already named by `SAMPLE_ID`:

```json
{"kit_lot": "A7-2291", "passed_qc": true}
```

That is not the same shape as the bulk upload document, which is keyed by sample ID. Passing a `*.attributes.json` file here is rejected with a pointer to the bulk command, because that document would otherwise be stored nested under a single sample.

To set attributes on many samples at once, use [samples metadata upload](/products/command-line-interface/reference/workbench/samples-metadata-upload.md) with a file named `*.attributes.json`.

## Examples

Set attributes from a JSON literal:

```shell
omics workbench samples attributes set HG002 '{"kit_lot": "A7-2291", "passed_qc": true}'
```

Set attributes from a file, using the `@` prefix:

```shell
omics workbench samples attributes set HG002 @bag.json
```

Set attributes from standard input:

```shell
cat bag.json | omics workbench samples attributes set HG002 -
```

Add an attribute to a sample that already has some, by reading the current set first:

```shell
omics workbench samples attributes get HG002 \
  | jq '. + {"run_id": "R-42"}' \
  | omics workbench samples attributes set HG002 -
```

## Positional Arguments

### `SAMPLE_ID`

The ID of the sample. Sample IDs can be retrieved from the [samples list](/products/command-line-interface/reference/workbench/samples-list.md) command.

### `JSON` | `@FILE` | `-`

The attributes to store, as a JSON object. The `@` prefix is required to read from a file; a bare path is rejected. Use `-` to read the document from standard input.

## Flags

### `--namespace`=`STRING`

An optional flag to define the namespace to connect to. By default, the namespace is extracted from the user's credentials.


---

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