@quiltdata/benchling-webhook 0.8.0-20251118T054240Z → 0.8.2

package/README.md

@@ -1,146 +1,136 @@
 # Benchling Webhook Integration for Quilt
 
-Connects Benchling lab notebook entries to Quilt data packages via webhooks.
+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 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.
 
-> **⚠️ Breaking Change in v1.0.0**: Runtime CloudFormation dependencies removed. Service configuration now resolved at deployment time. See [MIGRATION.md](./spec/206-service-envars/MIGRATION.md) for upgrade instructions.
-## Prerequisites
+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).
 
-- Node.js 18+ with `npx` ([download](https://nodejs.org))
-- [AWS credentials](https://docs.aws.amazon.com/cli/v1/userguide/cli-configure-files.html) configured
-- Existing [Quilt deployment](https://www.quilt.bio/install)
-- Benchling tenant (need Admin permissions to install a Benchling app)
+## Availability
 
-## Quick Start
+It is available in the Quilt Platform (1.65 or later) or as a standalone CDK stack via the `@quiltdata/benchling-webhook` [npm package](https://www.npmjs.com/package/@quiltdata/benchling-webhook).
 
-### 1. Install the Benchling app
+## Functionality
 
-First create a manifest:
+### Auto-Packaging
 
-```bash
-npx @quiltdata/benchling-webhook@latest manifest
-```
+![Packaged Notebook](imgs/benchling-package.png)
 
-Then follow the instructions to [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) the app.
+When scientists create notebook entries in Benchling, this webhook automatically:
 
-This will give you an App Definition ID and Client ID,
-which --- along with the Client Secret must generate -- you will need later.
+- **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.
 
-### 2. Run the setup wizard
+### Package Linking
 
-```bash
-npx @quiltdata/benchling-webhook@latest
-```
+![experiment_id](imgs/benchling-link.png)
 
-The wizard will:
+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`.
 
-1. **Catalog Discovery** - Detect and confirm your Quilt catalog DNS
-2. **Stack Query** - Extract configuration from your CloudFormation stack
-3. **Parameter Collection** - Collect Benchling credentials and package settings
-4. **Validation** - Validate all parameters before proceeding
-5. **Deployment Mode** - Choose between integrated or standalone deployment:
-   - **Integrated Mode**: Updates the existing BenchlingSecret in your Quilt stack (recommended if you have one)
-   - **Standalone Mode**: Creates a dedicated secret and optionally deploys a separate webhook stack
+From inside the Quilt Catalog:
 
-#### Deployment Modes
+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'
 
-**Integrated Mode** (recommended if your Quilt stack has a BenchlingSecret):
-- Uses the existing BenchlingSecret from your Quilt CloudFormation stack
-- No separate deployment needed - the webhook URL is available from your Quilt stack outputs
-- Cleaner architecture with fewer AWS resources
+### Benchling App Canvas
 
-**Standalone Mode** (for separate deployments):
-- Creates a dedicated secret: `quiltdata/benchling-webhook/<profile>/<tenant>`
-- Prompts you to deploy a separate webhook stack to AWS
-- Useful for testing or isolated deployments
+![App Canvas - Home](imgs/benchling-canvas.png)
 
-It will list the webhook URL in the completion message or next steps.
+The webhook includes a Benchling App Canvas, which allows Benchling users to view, browse, and sync the associated Quilt packages.
 
-NOTE: This version no longer reads your `.env` file.
-Instead, it stores your results in the [XDG_CONFIG_HOME](https://wiki.archlinux.org/title/XDG_Base_Directory),
-where you can have more than one profile.
+- 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 refreshes the package, as Benchling only notifies Quilt of changes when the metadata fields are modified.
 
-#### Integrated Mode: BenchlingIntegration Parameter
+The canvas also allows you to browse package contents:
 
-When using integrated mode (built-in Quilt stack webhook), the setup wizard will:
+![App Canvas - Browse](imgs/benchling-browse.png)
 
-1. Check if `BenchlingIntegration` is enabled in your Quilt stack
-2. Offer to enable it automatically if disabled
-3. Provide a status command to monitor the stack update
+and view package metadata:
 
-**Checking Integration Status:**
+![App Canvas - Metadata](imgs/benchling-browse.png)
 
-```bash
-npx @quiltdata/benchling-webhook@latest status --profile myprofile
-```
-
-This shows:
+#### Inserting a Canvas
 
-- CloudFormation stack status
-- BenchlingIntegration parameter state
-- Last update timestamp
-- Direct link to CloudFormation console
+If the App Canvas is not already part of your standard notebook template, Benchling users can add it themselves:
 
-**Enabling BenchlingIntegration:**
+1. Create a notebook entry
+2. Select "Insert" → "Canvas"
+3. Choose "Quilt Package"
+4. After it is inserted, click the "Create" button
 
-If your Quilt stack has `BenchlingIntegration` set to `false`, the setup wizard will detect this and offer to enable it automatically. You can:
+![App Canvas - Insert](imgs/benchling-insert.png)
 
-- Let the wizard update the parameter (recommended)
-- Enable it manually through the AWS CloudFormation console
-- Use the `status` command to monitor the update progress
+## Installation
 
-### 3. Configure Webhook URL
+### 1. Installing the Benchling App
 
-After deployment, add the webhook URL to your [Benchling app settings](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app).
+This requires a Benchling admin to use `npx` from [NodeJS](https://nodejs.org) version 18 or later.
 
-### 4. Usage
+#### 1.1 Generate a manifest
 
-In Benchling:
+```bash
+npx @quiltdata/benchling-webhook@latest manifest
+```
 
-1. Create entry →
-2. Insert Canvas →
-3. Select "Quilt Package" →
-4. Click "Create"
+This will generate an `app-manifest.yaml` file in your local folder
 
-This will generate an App Canvas with a dedicated Quilt package for this notebook, as well as additional links and buttons.
+#### 1.2 Upload the manifest to Benchling
 
-## Other Commands
+- 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.
 
-### Deploy
+### 2. Configuring the Benchling App
 
-If necessary, you can manually deploy (without redoing setup) via:
+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 deploy
+npx @quiltdata/benchling-webhook@latest
 ```
 
-### Status
+The wizard will guide you through:
 
-Check the status of your Quilt stack and BenchlingIntegration parameter:
+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
 
-```bash
-npx @quiltdata/benchling-webhook@latest status [--profile <name>]
-```
+**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.
 
-This command displays:
-- CloudFormation stack status (CREATE_COMPLETE, UPDATE_IN_PROGRESS, etc.)
-- BenchlingIntegration parameter value (true/false)
-- Last update timestamp
-- Direct console link for manual updates
+### 3. Configure Webhook URL
 
-Useful for monitoring stack updates after enabling BenchlingIntegration.
+Add the webhook URL (displayed after setup) to your [Benchling app settings](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app).
 
-### Help
+### 4. Test Integration
 
-For more information, use:
+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](support@quilt.bio)
+
+## Additional Commands
 
 ```bash
-npx @quiltdata/benchling-webhook@latest --help    # Show all commands
-```
+# Deploy without re-running setup
+npx @quiltdata/benchling-webhook@latest deploy [--profile <name>]
 
-## Resources
+# Check CloudFormation stack status
+npx @quiltdata/benchling-webhook@latest status [--profile <name>]
 
-- [Changelog](./CHANGELOG.md) - Version history
-- [Report Issues](https://github.com/quiltdata/benchling-webhook/issues)
+# Show all available commands
+npx @quiltdata/benchling-webhook@latest --help
+```
 
 ## License
 

package/dist/bin/cli.js

@@ -87,7 +87,7 @@ program
     .option("--benchling-secret <name>", "Name or ARN of Benchling secret in Secrets Manager")
     .option("--env-file <path>", "Path to .env file", ".env")
     // Multi-environment options (v0.7.0)
-    .option("--profile <name>", "Configuration profile to use (default: default)")
+    .option("--profile, --config <name>", "Configuration profile to use (default: default)")
     .option("--stage <name>", "API Gateway stage: dev or prod (default: prod)")
     // Common options
     .option("--no-bootstrap-check", "Skip CDK bootstrap verification")
@@ -125,7 +125,7 @@ For more information: https://github.com/quiltdata/benchling-webhook#deployment
 program
     .command("setup")
     .description("Run setup wizard only (without deployment)")
-    .option("--profile <name>", "Configuration profile to use (default: default)")
+    .option("--profile, --config <name>", "Configuration profile to use (default: default)")
     .option("--inherit-from <name>", "Base profile to inherit from")
     .option("--region <region>", "AWS region")
     .option("--aws-profile <name>", "AWS credentials profile")
@@ -143,7 +143,7 @@ program
 program
     .command("status")
     .description("Check CloudFormation stack status and BenchlingIntegration parameter")
-    .option("--profile <name>", "Configuration profile to check (default: default)")
+    .option("--profile, --config <name>", "Configuration profile to check (default: default)")
     .option("--aws-profile <name>", "AWS credentials profile")
     .option("--detailed", "Show detailed stack events")
     .option("--timer <seconds>", "Auto-refresh interval in seconds (default: 10, use 0 or non-numeric to disable)", "10")
@@ -183,14 +183,13 @@ Use --no-exit to keep monitoring indefinitely.
 program
     .command("logs")
     .description("View CloudWatch logs from deployed webhook integration")
-    .option("--profile <name>", "Configuration profile to use (default: default)")
-    .option("--stage <name>", "Deployment stage: dev or prod (default: prod)")
+    .option("--profile, --config <name>", "Configuration profile to use (default: default)")
     .option("--aws-profile <name>", "AWS credentials profile")
     .option("--type <type>", "Log group to view: all (default), ecs, api, api-exec", "all")
     .option("--since <time>", "Time period to fetch logs (examples: 5m, 1h, 2d)", "5m")
     .option("--filter <pattern>", "Filter logs by pattern (example: ERROR)")
-    .option("--follow, -f", "Follow log output in real-time (not available with --type=all)")
-    .option("--tail <n>", "Number of lines to show (default: 100, only without --follow)", "100")
+    .option("--limit <n>", "Number of log entries to show per log group (default: 5)", "5")
+    .option("--timer <seconds>", "Auto-refresh interval in seconds (default: 10, use 0 to disable)", "10")
     .addHelpText("after", `
 
 Log Types:
@@ -200,25 +199,35 @@ Log Types:
   api-exec  API Gateway execution logs (detailed debugging)
 
 Examples:
-  View all logs from prod deployment:
+  View all logs (auto-refreshes every 10 seconds):
     $ npx @quiltdata/benchling-webhook logs --profile sales
 
-  View ECS logs from dev stage:
-    $ npx @quiltdata/benchling-webhook logs --profile sales --stage dev --type ecs
+  View only ECS logs:
+    $ npx @quiltdata/benchling-webhook logs --profile sales --type ecs
 
-  Follow ECS logs in real-time:
-    $ npx @quiltdata/benchling-webhook logs --profile sales --type ecs --follow
+  Show last 10 entries per log group:
+    $ npx @quiltdata/benchling-webhook logs --profile sales --limit 10
+
+  Disable auto-refresh (single snapshot):
+    $ npx @quiltdata/benchling-webhook logs --profile sales --timer 0
+
+  Auto-refresh every 5 seconds:
+    $ npx @quiltdata/benchling-webhook logs --profile sales --timer 5
 
   Filter for errors in last hour:
     $ npx @quiltdata/benchling-webhook logs --profile sales --since 1h --filter ERROR
 
-  View API Gateway execution logs:
-    $ npx @quiltdata/benchling-webhook logs --profile sales --type api-exec --tail 50
+  View last 2 days of API Gateway logs:
+    $ npx @quiltdata/benchling-webhook logs --profile sales --type api --since 2d
 
 For more information: https://github.com/quiltdata/benchling-webhook#viewing-logs
 `)
     .action(async (options) => {
     try {
+        // Parse limit as integer
+        if (options.limit) {
+            options.limit = parseInt(options.limit, 10);
+        }
         await (0, logs_1.logsCommand)(options);
     }
     catch (error) {
@@ -243,7 +252,7 @@ program
 program
     .command("validate")
     .description("Validate configuration without deploying")
-    .option("--profile <name>", "Configuration profile to validate", "default")
+    .option("--profile, --config <name>", "Configuration profile to validate", "default")
     .option("--verbose", "Show detailed validation information")
     .action(async (options) => {
     try {
@@ -284,7 +293,7 @@ program
     .command("manifest")
     .description("Generate Benchling app manifest file")
     .option("--output <path>", "Output file path", "app-manifest.yaml")
-    .option("--profile <name>", "Configuration profile to use (optional)")
+    .option("--profile, --config <name>", "Configuration profile to use (optional)")
     .option("--catalog <url>", "Catalog URL to use (optional, overrides profile)")
     .action(async (options) => {
     try {
@@ -340,7 +349,7 @@ For more information: https://github.com/quiltdata/benchling-webhook#multi-envir
 program
     .command("health-check")
     .description("Check configuration health and secrets sync status")
-    .option("--profile <name>", "Configuration profile to check", "default")
+    .option("--profile, --config <name>", "Configuration profile to check", "default")
     .option("--json", "Output in JSON format")
     .action(async (options) => {
     try {
@@ -355,7 +364,7 @@ program
 program
     .command("config")
     .description("Show configuration for a profile as JSON")
-    .option("--profile <name>", "Configuration profile to show", "default")
+    .option("--profile, --config-name <name>", "Configuration profile to show", "default")
     .action(async (options) => {
     try {
         await (0, config_show_1.configShowCommand)(options);
@@ -379,7 +388,7 @@ if (!args.length ||
         else if (args[i] === "--setup-only") {
             options.setupOnly = true;
         }
-        else if (args[i] === "--profile" && i + 1 < args.length) {
+        else if ((args[i] === "--profile" || args[i] === "--config") && i + 1 < args.length) {
             options.profile = args[i + 1];
             i++;
         }

package/dist/bin/cli.js.map

@@ -1 +1 @@
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package/dist/bin/commands/infer-quilt-config.js

@@ -173,7 +173,7 @@ async function findQuiltStacks(region = "us-east-1", profile, targetCatalog) {
                 // Query stack resources for additional data - FAIL LOUDLY on errors
                 try {
                     const resources = await (0, stack_inference_1.getStackResources)(region, stack.StackName);
-                    const discovered = (0, stack_inference_1.extractQuiltResources)(resources);
+                    const discovered = (0, stack_inference_1.extractQuiltResources)(resources, stackInfo.account, region);
                     // Destructure discovered resources and assign to stackInfo
                     const { athenaUserWorkgroup, athenaUserPolicy, icebergWorkgroup, icebergDatabase, athenaResultsBucket, athenaResultsBucketPolicy, readRoleArn, writeRoleArn, } = discovered;
                     Object.assign(stackInfo, {

package/dist/bin/commands/infer-quilt-config.js.map

@@ -1 +1 @@
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package/dist/bin/commands/logs.d.ts

@@ -7,6 +7,7 @@
  *
  * @module commands/logs
  */
+import { type FilteredLogEvent } from "@aws-sdk/client-cloudwatch-logs";
 import type { XDGBase } from "../../lib/xdg-base";
 export interface LogsCommandOptions {
     profile?: string;
@@ -18,10 +19,18 @@ export interface LogsCommandOptions {
     follow?: boolean;
     tail?: number;
     configStorage?: XDGBase;
+    timer?: string | number;
+    limit?: number;
 }
 export interface LogsResult {
     success: boolean;
     error?: string;
+    logGroups?: LogGroupInfo[];
+}
+export interface LogGroupInfo {
+    name: string;
+    displayName: string;
+    entries: FilteredLogEvent[];
 }
 /**
  * Logs command implementation

package/dist/bin/commands/logs.d.ts.map

@@ -1 +1 @@
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