> For the complete documentation index, see [llms.txt](https://docs.quilt.bio/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.quilt.bio/quilt-ecosystem-integrations/benchling.md).

# Benchling Packager

The Benchling Webhook creates a seamless connection between [Benchling](https://www.benchling.com)'s Electronic Lab Notebook (ELN) and [Quilt](https://www.quilt.bio)'s Scientific Data Management System (SDMS) for Amazon S3. It not only allows you to view Benchling metadata and attachments inside Quilt packages, but also enables users to browse Quilt package descriptions from inside Benchling notebooks.

The webhook works through a [Benchling App](https://docs.benchling.com/docs/getting-started-benchling-apps) that must be installed in your Organization by a Benchling Administrator and configured to call your stack's unique webhook (see Installation, below).

## Availability

It is available in the Quilt Platform (1.65 or later; Referenced Entities and bucketless deployments require 1.71.0 or later) or as a standalone CDK stack via the `@quiltdata/benchling-webhook` [npm package](https://www.npmjs.com/package/@quiltdata/benchling-webhook).

## Functionality

### Auto-Packaging

![Packaged Notebook](/files/DjDTIl9WxrxsPBifvzDB)

When scientists create notebook entries in Benchling, this webhook automatically:

* **Creates a dedicated Quilt package** for each notebook entry
* **Synchronizes metadata** from Benchling into that package, e.g.:
  * `authors` (list)
  * `created_at` (ISO timestamp)
  * `creator` (e.g. `"First Last <user_id@ent_XXXX>"`)
  * `display_id` (e.g. `"EXP0000XXXXXX"`)
  * `entry_id` (e.g. `"etr_XXXXXX"`)
  * `files` (list)
  * `links` (list of referenced Benchling objects — see [Referenced Entities](#referenced-entities))
  * `modified_at` (ISO timestamp)
  * `web_url` (URL string)
* **Copies attachments** from that notebook into Amazon S3 as part of the package.
* **Enables organizational data discovery** by making contents available in ElasticSearch, and metadata available in Amazon Athena.

### Bucketless Deployments

[Auto-Packaging](#auto-packaging) writes each entry's package to a configured **package bucket**. That bucket is now **optional** — you can run the webhook without one. This suits organizations that link Benchling entries to Quilt packages spread across many buckets rather than a single dedicated one.

When no package bucket is configured:

* **Setup omits the bucket.** The configuration wizard and secret creation no longer require a package bucket, so you can stand up the integration without dedicating one.
* **No default package is auto-created.** Entry and canvas events skip per-entry package creation and instead surface the Quilt packages that already reference the entry.
* **Discovery spans every bucket.** Linked-package search runs across all Quilt package-view buckets in the stack (via Amazon Athena) instead of a single bucket, and the source bucket is preserved when you browse a linked package's files or metadata from a Benchling canvas.

> **Note:** Requires Quilt Platform 1.71.0 or later (or standalone benchling-webhook v0.19.0 or later).

### Referenced Entities

When packaging a notebook entry, the webhook also discovers the Benchling objects that entry references — custom entities, sequences, results tables, and so on — and makes them **searchable by their human-readable name**. This answers questions like *"show me every experiment that referenced QB-2743.1."*

The package metadata gains a `links` array, one object per referenced entity, each with four fields:

```json
[
  {
    "type": "custom_entity",
    "id": "bfi_xCUXNVyG",
    "name": "QB-2743.1",
    "slug": "qb-2743-1"
  }
]
```

* **`type`** and **`id`** identify the referenced object.
* **`name`** is the authoritative Benchling display name, resolved via the Benchling API. It is the field you search on. It is `null` when the app lacks registry access for that object or the object type is unsupported.
* **`slug`** is a lossy token parsed from the object's URL, shown for reference only — it is **never** treated as a name or matched by name search.

To find packages that reference a given entity, search the Quilt Catalog for its name (e.g. `QB-2743.1`); matches are scoped to `links.name`.

The raw discovery is also written to a `links.json` file in each package for auditing and reprocessing.

> **Note:** This requires Quilt Platform 1.71.0 or later (or standalone benchling-webhook v0.18.0 or later). It is distinct from the manual [Package Linking](#package-linking) below, which tags packages by `experiment_id`.

### Package Linking

![experiment\_id](/files/r4dwfcjNdskQMrFN5psB)

In addition, Quilt users can 'tag' additional packages by setting the `experiment_id` (or a custom metadata key) to the display ID of a Benchling notebook, e.g., `EXP00001234`.

From inside the Quilt Catalog:

1. Navigate to the package of interest
2. Click 'Revise Package'
3. Go the metadata editor in the bottom left
4. In the bottom row, enter `experiment_id` as key and the display ID as the value.
5. Set the commit message and click 'Save'

### Benchling App Canvas

![App Canvas - Home](/files/9Pc5vhODt5sR3dwhvnpD)

The webhook includes a Benchling App Canvas, which allows Benchling users to view, browse, and sync the associated Quilt packages.

* Clicking the package name opens it in the Quilt Catalog
* The `sync` button will open the package or file in [QuiltSync](https://www.quilt.bio/quiltsync), if you have it installed.
* The `Update` button manually refreshes the package. The canvas stays browsable while Quilt re-exports in the background, showing a "pending" badge that flips to "complete" when the new revision is ready.
* Package updates also happen automatically: any metadata change to the linked entry triggers a refresh, as does a Benchling `reviewRecord` event (e.g. when a notebook entry is submitted for review).

![App Canvas - Updated](/files/ZbJjX2ALOreMHBDUKdSR)

The canvas also allows you to browse package contents:

![App Canvas - Browse](/files/3qfhiWkSh27GTbWT8KT5)

and view package metadata:

![App Canvas - Metadata](/files/1eqIiZCQLWtc77TRCgoV)

#### Inserting a Canvas

If the App Canvas is not already part of your standard notebook template, Benchling users can add it themselves:

1. Create a notebook entry
2. Select "Insert" → "Canvas"
3. Choose "Quilt Package"
4. After it is inserted, click the "Create" button

![App Canvas - Insert](/files/bJcs2F10Mbf6rgHCJygo)

## Installation

### 1. Installing the Benchling App

This requires a Benchling admin to use `npx` from [NodeJS](https://nodejs.org) version 18 or later.

#### 1.1 Generate a manifest

```bash
npx @quiltdata/benchling-webhook@latest manifest
```

This will generate an `app-manifest.yaml` file in your local folder

#### 1.2 Upload the manifest to Benchling

Follow Benchling's [create](https://docs.benchling.com/docs/getting-started-benchling-apps#creating-an-app-from-a-manifest) and [install](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app) instructions. Save the **App Definition ID**, **Client ID**, and **Client Secret** for the next step.

### 2. Configuring the Benchling App

Your command-line environment must have AWS credentials for the account containing your Quilt stack. All you need to do is use `npx` to run the package:

```bash
npx @quiltdata/benchling-webhook@latest
```

The wizard will guide you through:

1. **Catalog discovery** - Detect your Quilt catalog configuration
2. **Stack validation** - Extract settings from your CloudFormation stack
3. **Credential collection** - Enter Benchling app credentials
4. **Deployment mode selection**:
   * **Integrated**: Uses your Quilt stack's built-in webhook, if any
   * **Standalone**: Deploys a separate webhook stack for testing

**Note**: Configuration is stored in `~/.config/benchling-webhook/` using the [XDG Base Directory](https://wiki.archlinux.org/title/XDG_Base_Directory) standard, supporting multiple profiles.

### 3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your [Benchling app settings](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app).

In the Benchling **Webhook Setup** dialog, set **Webhook Routing Setting** to **Suffixed**. Benchling then appends a path suffix based on the kind of event (`/lifecycle`, `/event`, or `/canvas`) to your configured webhook URL, which is what the Quilt webhook expects.

![Webhook Routing Setting](/files/rtBr66WZ3aHcGm0YJxft)

> **Important:** Do **not** select **Stable**. It posts every event to the bare webhook URL with no suffix, which the Quilt webhook does not handle — requests return `404 Endpoint not found`.

### 4. Test Integration

In Benchling:

1. Create a notebook entry
2. Insert Canvas → Select "Quilt Package"
3. Click "Create"

A Quilt package will be automatically created and linked to your notebook entry. If you run into problems, contact [Quilt Support](mailto:support@quilt.bio)


---

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