16 Apr 00:52

6720457

Release v0.17.2 Latest

Latest

@quiltdata/benchling-webhook@0.17.2 deploy:notes
bash scripts/release-notes.sh 0.17.2 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.2 false @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The Benchling Webhook creates a seamless connection between Benchling's Electronic Lab Notebook (ELN) and Quilt's Scientific Data Managements 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 notebookes.

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

If your integration reads or writes within a specific Benchling project, share that project with the service account behind the Benchling App Client ID. This integration uses the app/service-account identity, not an end-user OAuth session. If project access appears broken, verify the service account can perform a simple read or list API call for the target project.

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.2

View on npmjs.com: @quiltdata/benchling-webhook@0.17.2

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.2

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.2

Changes

Fixed

Canvas during entry export now shows the full navigation layout (Browse/Update buttons, package header, and footer reading "Updating...") instead of a bare "Processing..." placeholder. Update Package is disabled while the export runs; Browse Package stays enabled so the previous package version remains reachable on re-exports
Packaging requests are now sequenced per entry through a FIFO SQS queue, so entry.created and canvas.created events for the same entry can no longer race and drop canvas_id from entry.json

Removed

.canvas_id S3 sidecar is no longer read or written — per-entry FIFO ordering makes it unnecessary. Existing sideca...

Contributors

drernie

Assets 3

15 Apr 21:57

github-actions

v0.17.1-20260415T215352Z

4e31324

Release v0.17.1-20260415T215352Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.17.1 deploy:notes
bash scripts/release-notes.sh 0.17.1-20260415T215352Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.1-20260415T215352Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.1-20260415T215352Z

View on npmjs.com: @quiltdata/benchling-webhook@0.17.1-20260415T215352Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.1-20260415T215352Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.1-20260415T215352Z

Resources

Full Changelog: v0.17.1-20260415T202609Z...v0.17.1-20260415T215352Z

Assets 3

15 Apr 20:29

github-actions

v0.17.1-20260415T202609Z

beb3b3c

Release v0.17.1-20260415T202609Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.17.1 deploy:notes
bash scripts/release-notes.sh 0.17.1-20260415T202609Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.1-20260415T202609Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.1-20260415T202609Z

View on npmjs.com: @quiltdata/benchling-webhook@0.17.1-20260415T202609Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.1-20260415T202609Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.1-20260415T202609Z

Resources

Full Changelog: v0.17.0-20260415T153833Z...v0.17.1-20260415T202609Z

Assets 3

15 Apr 04:50

github-actions

v0.17.0

2eae1d1

Release v0.17.0

@quiltdata/benchling-webhook@0.17.0 deploy:notes
bash scripts/release-notes.sh 0.17.0 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0 false @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.0

View on npmjs.com: @quiltdata/benchling-webhook@0.17.0

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0

Changes

Changed

Package events via SQS — EventBridge now routes package-revision events through an SQS queue to a dedicated ECS sidecar consumer, replacing the API Gateway /package-event route
Secrets fetching uses a TTL cache with background refresh (prevents 504 on cache miss)
Dev deploy is hardcoded to standalone
Integrated-stack deploy now prompts instead of blocking outright
Dependency updates (#380, #381)

Added

SQS dead-letter queue (14-day retention) for failed package events
Deployment plan displays workflow, Benchling tenant and masked client ID from the secret

Removed

--stage CLI option — all deployments use a single `p...

Contributors

drernie and renovate

Assets 3

15 Apr 15:42

github-actions

v0.17.0-20260415T153833Z

ddf648f

Release v0.17.0-20260415T153833Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.17.0 deploy:notes
bash scripts/release-notes.sh 0.17.0-20260415T153833Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260415T153833Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.0-20260415T153833Z

View on npmjs.com: @quiltdata/benchling-webhook@0.17.0-20260415T153833Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260415T153833Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260415T153833Z

Resources

Full Changelog: v0.17.0...v0.17.0-20260415T153833Z

Assets 3

15 Apr 02:46

github-actions

v0.17.0-20260415T024257Z

81e1c37

Release v0.17.0-20260415T024257Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.17.0 deploy:notes
bash scripts/release-notes.sh 0.17.0-20260415T024257Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260415T024257Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.0-20260415T024257Z

View on npmjs.com: @quiltdata/benchling-webhook@0.17.0-20260415T024257Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260415T024257Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260415T024257Z

Resources

Full Changelog: v0.17.0-20260414T232113Z...v0.17.0-20260415T024257Z

Assets 3

14 Apr 23:24

github-actions

v0.17.0-20260414T232113Z

f09cdcf

Release v0.17.0-20260414T232113Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.17.0 deploy:notes
bash scripts/release-notes.sh 0.17.0-20260414T232113Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260414T232113Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.0-20260414T232113Z

View on npmjs.com: @quiltdata/benchling-webhook@0.17.0-20260414T232113Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260414T232113Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260414T232113Z

Resources

Full Changelog: v0.17.0-20260414T022608Z...v0.17.0-20260414T232113Z

Assets 3

14 Apr 02:30

github-actions

v0.17.0-20260414T022608Z

5b03a3d

Release v0.17.0-20260414T022608Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.17.0 deploy:notes
bash scripts/release-notes.sh 0.17.0-20260414T022608Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260414T022608Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.17.0-20260414T022608Z

View on npmjs.com: @quiltdata/benchling-webhook@0.17.0-20260414T022608Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260414T022608Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.17.0-20260414T022608Z

Resources

What's Changed

chore(deps): update softprops/action-gh-release action to v3 by @renovate[bot] in #380
fix(deps): update all minor and patch up...

Contributors

renovate

Assets 3

12 Apr 06:22

github-actions

v0.16.0

772762a

Release v0.16.0

@quiltdata/benchling-webhook@0.16.0 deploy:notes
bash scripts/release-notes.sh 0.16.0 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.16.0 false @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.16.0

View on npmjs.com: @quiltdata/benchling-webhook@0.16.0

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.16.0

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.16.0

Resources

What's Changed

fix(deps): update all minor and patch updates by @renovate[bot] in #378
fix: EventBridge runtime filtering + remove pending canvas by @drernie in #379

Full Changelog: https://github.com/qu...

Contributors

drernie and renovate

Assets 3

11 Apr 22:43

github-actions

v0.16.0-20260411T224037Z

32e21ac

Release v0.16.0-20260411T224037Z Pre-release

Pre-release

@quiltdata/benchling-webhook@0.16.0 deploy:notes
bash scripts/release-notes.sh 0.16.0-20260411T224037Z 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.16.0-20260411T224037Z true @quiltdata/benchling-webhook

Benchling Webhook Integration for Quilt

The webhook works through a Benchling App 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) or as a standalone CDK stack via the @quiltdata/benchling-webhook npm package.

Functionality

Auto-Packaging

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

Creates a dedicated Quilt package for each notebook entry
Synchronizes metadata from Benchling (experiment IDs, authors, etc.) into that package
Copies attachments from that notebook into Amazon S3 as part of the package.
Enables orgnizational data discovery by making contents available in ElasticSearch, and metadata available in Amazon Athena.

Package Linking

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

From inside the Quilt Catalog:

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

Benchling App Canvas

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, if you have it installed.
The Update button refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.

The canvas also allows you to browse package contents:

and view package metadata:

Inserting a Canvas

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

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

Security Features

Single Authentication Layer:

FastAPI HMAC Verification - All webhook requests verified against Benchling secret
Signatures computed over raw request body
Invalid signatures return 403 Forbidden

Optional Network Filtering:

Resource Policy IP Filtering - Free alternative to AWS WAF ($7/month saved)
Blocks unknown IPs at API Gateway edge (applies to all endpoints)
BREAKING CHANGE (v1.1.0+): Health endpoints NO LONGER exempt from IP filtering
External monitoring services must be added to allowlist or IP filtering disabled
NLB health checks unaffected (bypass API Gateway)
IP filtering does NOT replace authentication (it's defense-in-depth)

Infrastructure Security:

Private network (ECS in private subnets, no public IPs)
VPC Link encrypted connection between API Gateway and NLB
TLS 1.2+ encryption on all API Gateway endpoints
CloudWatch audit trail for HMAC verification and resource policy decisions
Least-privilege IAM roles

Installation

1. Installing the Benchling App

This requires a Benchling admin to use npx from NodeJS version 18 or later.

1.1 Get the app manifest

Download app-manifest.yaml from the
latest GitHub release,
or generate one locally:

npx @quiltdata/benchling-webhook@latest manifest

1.2 Upload the manifest to Benchling

Follow Benchling's create and install 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:

npx @quiltdata/benchling-webhook@latest

If you need to choose AWS credentials explicitly, prefer --aws-profile:

npx @quiltdata/benchling-webhook@latest --aws-profile myaws

You can also use AWS_PROFILE:

AWS_PROFILE=myaws npx @quiltdata/benchling-webhook@latest

--profile is different: it selects a local benchling-webhook config profile under ~/.config/benchling-webhook/, not your AWS credential profile.

The wizard will guide you through:

Catalog discovery - Detect your Quilt catalog configuration
Stack validation - Extract settings from your CloudFormation stack
Credential collection - Enter Benchling app credentials
Package settings - Configure bucket, metadata key, and optional Quilt workflow
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 standard, supporting multiple profiles.

3. Configure Webhook URL

Add the webhook URL (displayed after setup) to your Benchling app settings.

Important: The endpoint URL format is https://{api-id}.execute-api.{region}.amazonaws.com/{stage}/webhook (includes stage prefix like /prod/webhook or /dev/webhook).

4. Test Integration

In Benchling:

Create a notebook entry
Insert Canvas → Select "Quilt Package"
Click "Create"

A Quilt package will be automatically created and linked to your notebook entry.
If you run into problems, contact Quilt Support

Multi-Stack Deployments (v0.9.8+)

Starting with version 0.9.8, you can deploy multiple webhook stacks in the same AWS account/region. This is useful for:

Multi-tenant deployments - Separate stacks for each customer
Environment isolation - Dev, staging, prod in same account
A/B testing - Parallel stacks with different configurations

Profile-Based Stack Names

Each profile automatically gets its own CloudFormation stack:

# Default profile uses legacy name (backwards compatible)
npx @quiltdata/benchling-webhook@latest deploy --profile default
# Creates: BenchlingWebhookStack

# Other profiles get unique names
npx @quiltdata/benchling-webhook@latest deploy --profile sales
# Creates: BenchlingWebhookStack-sales

npx @quiltdata/benchling-webhook@latest deploy --profile customer-acme
# Creates: BenchlingWebhookStack-customer-acme

Custom Stack Names

You can also specify a custom stack name in your profile configuration:

{
  "deployment": {
    "stackName": "MyCustomWebhookStack",
    ...
  }
}

Managing Multiple Stacks

All commands support the --profile flag:

# Deploy a specific profile
npx @quiltdata/benchling-webhook@latest deploy --profile sales

# Check status
npx @quiltdata/benchling-webhook@latest status --profile sales

# View logs
npx @quiltdata/benchling-webhook@latest logs --profile sales

# Destroy stack
npx @quiltdata/benchling-webhook@latest destroy --profile sales

NPM Package

npm install @quiltdata/benchling-webhook@0.16.0-20260411T224037Z

View on npmjs.com: @quiltdata/benchling-webhook@0.16.0-20260411T224037Z

Docker Image

For custom deployments, use the following Docker image:

712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.16.0-20260411T224037Z

Pull and run:

docker pull 712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:0.16.0-20260411T224037Z

Resources

What's Changed

fix(deps): update all minor and patch updates by @renovate[bot] in #378

Full Changelog: https://github.com/quiltdata/benchl...

Contributors

renovate

Assets 3

Releases: quiltdata/benchling-webhook

Release v0.17.2

Benchling Webhook Integration for Quilt

Availability

Functionality

Auto-Packaging

Package Linking

Benchling App Canvas

Inserting a Canvas

Security Features

Installation

1. Installing the Benchling App

1.1 Get the app manifest

1.2 Upload the manifest to Benchling

2. Configuring the Benchling App

3. Configure Webhook URL

4. Test Integration

Multi-Stack Deployments (v0.9.8+)

Profile-Based Stack Names

Custom Stack Names

Managing Multiple Stacks

NPM Package

Docker Image

Changes

Fixed

Removed

Contributors

Uh oh!

Release v0.17.1-20260415T215352Z

Benchling Webhook Integration for Quilt

Availability

Functionality

Auto-Packaging

Package Linking

Benchling App Canvas

Inserting a Canvas

Security Features

Installation

1. Installing the Benchling App

1.1 Get the app manifest

1.2 Upload the manifest to Benchling

2. Configuring the Benchling App

3. Configure Webhook URL

4. Test Integration

Multi-Stack Deployments (v0.9.8+)

Profile-Based Stack Names

Custom Stack Names

Managing Multiple Stacks

NPM Package

Docker Image

Resources

Uh oh!

Release v0.17.1-20260415T202609Z

Benchling Webhook Integration for Quilt

Availability

Functionality

Auto-Packaging

Package Linking

Benchling App Canvas

Inserting a Canvas

Security Features

Installation

1. Installing the Benchling App

1.1 Get the app manifest

1.2 Upload the manifest to Benchling

2. Configuring the Benchling App

3. Configure Webhook URL

4. Test Integration

Multi-Stack Deployments (v0.9.8+)

Profile-Based Stack Names

Custom Stack Names

Managing Multiple Stacks

NPM Package

Docker Image

Resources

Uh oh!

Release v0.17.0

Benchling Webhook Integration for Quilt

Availability

Functionality