completed localhost compatability

Author: Danny Shin

examples/chem-sync-local-flask/Dockerfile

@@ -7,4 +7,4 @@ COPY requirements.txt ./
 RUN pip install -r requirements.txt
 COPY ./local_app /src/local_app
 WORKDIR /src/local_app
-CMD ["flask", "run", "--host", "0.0.0.0"]
+CMD ["flask", "run", "--host", "0.0.0.0", "--port", "5004"]

examples/chem-sync-local-flask/README.md

@@ -16,7 +16,7 @@ This app is optimized as a minimal local development experience using [Docker](h
 > ⚠️ **Development Only**: This example is not meant to be copied into production as-is. There are additional deployment, scale, and security concerns that should be addressed before deploying an app based on this example to production.
 
 It relies on a few other tools that will be installed for you within Docker containers:
-* [Cloudflare-tunnel](https://www.cloudflare.com/products/tunnel/) - expose a public webhook URL and forward the results locally. ⚠️ *Not for production or real data!*
+* [ngrok](https://ngrok.com/) - expose a public webhook URL and forward the results locally. ⚠️ *Not for production or real data!*
 * [Flask](https://flask.palletsprojects.com/) - A simple Python web application framework
 
 ## Getting Started
@@ -33,6 +33,23 @@ Windows example:
 echo.> .client_secret
 ```
 
+Create an `.env` file for Docker environment variables. *nix example:
+
+```bash
+touch .env
+```
+
+Windows example:
+
+```cmd
+echo.> .env
+```
+
+Then, add your `ngrok` auth token under the alias `NGROK_AUTHTOKEN` which can be found on [ngrok your-authtoken](https://dashboard.ngrok.com/get-started/your-authtoken) like so:
+````
+NGROK_AUTHTOKEN=<YOUR_AUTH_TOKEN_HERE>
+````
+
 Start Docker:
 
 ```bash
@@ -54,28 +71,18 @@ curl localhost:8000/health
 
 If Flask is running, you should see `OK` printed.
 
-Be sure to note the URL created for you by `cloudflare-tunnel`. The log line should look something like this:
-
-```
-cloudflare-tunnel-1  | 2025-03-11T18:45:24Z INF +--------------------------------------------------------------------------------------------+
-cloudflare-tunnel-1  | 2025-03-11T18:45:24Z INF |  Your quick Tunnel has been created! Visit it at (it may take some time to be reachable):  |
-cloudflare-tunnel-1  | 2025-03-11T18:45:24Z INF |  https://pioneer-rights-hardly-disorder.trycloudflare.com                                  |
-cloudflare-tunnel-1  | 2025-03-11T18:45:24Z INF +--------------------------------------------------------------------------------------------+
-```
-
-On *nix systems, you can easily obtain _just_ the URL via:
-
-```
-docker compose logs cloudflare-tunnel | grep -o 'https://[^ ]*trycloudflare.com[^ ]*' | tail -n 1
+You can obtain the public facing url generated by `ngrok` with:
+```bash
+curl localhost:4040/api/tunnels
 ```
 
 Example Output:
+````
+{"tunnels":[{"name":"command_line","ID":<SOME_ID>>,"uri":"/api/tunnels/command_line","public_url":"https://your-public-url.ngrok-free.dev"
+...
+````
 
-```
-https://pioneer-rights-hardly-disorder.trycloudflare.com
-```
-
-> 💡 Don't forget to append `/1/webhooks`, making the full URL given to Benchling `https://pioneer-rights-hardly-disorder.trycloudflare.com/1/webhooks`
+> 💡 Don't forget to append `/1/webhooks`, making the full URL given to Benchling `https://your-public-url.ngrok-free.dev/1/webhooks`
 
 ## Setting Up Your App in Benchling
 
@@ -98,17 +105,17 @@ When prompted to upload a file, select `manifest.yaml` and click "Create."
 
 ### Update the Webhook URL
 
-Every time we restart the `cloudflare-tunnel` Docker container, it will provision
+Every time we restart the `ngrok` Docker container, it will provision
 a new public webhook URL.
 
 Update the Benchling App's Webhook URL in the UI with the new server and
 append the path our Flask route expects (see `local_app/app.py`).
 
-For example, if our `cloudflare-tunnel` generated URL is `https://pioneer-rights-hardly-disorder.trycloudflare.com`,
+For example, if our `ngrok` generated URL is `https://your-public-url.ngrok-free.dev`,
 the webhook URL in Benchling should be:
 
 ```
-https://https://pioneer-rights-hardly-disorder.trycloudflare.com/1/webhooks
+https://your-public-url.ngrok-free.dev/1/webhooks
 ```
 
 ![image info](./docs/update-webhook-url.gif)
@@ -139,26 +146,15 @@ You'll then need to restart _just_ the `benchling-app` Docker service to pick up
 docker-compose up -d
 ```
 
-If you restart both containers, be sure to update your App in Benchling with the new webhook URL from cloudflare-tunnel.
+If you restart both containers, be sure to update your App in Benchling with the new webhook URL from ngrok.
 
 ### Setting Client ID
 
 Our App needs a Client ID to pair with the Client Secret for authentication to Benchling. In this case, we've created our 
 App to accept `CLIENT_ID` as an environment variable.
 
-One easy way to set an environment variables for Docker is to add a `.env` file.
-
-```bash
-touch .env
-```
-
-Windows example:
-
-```cmd
-echo.> .env
-```
 
-Open it in an editor of your choice and set the values with the plaintext client ID 
+Open the `.env` file in an editor of your choice and set the values with the plaintext client ID 
 for your App. For example:
 
 ```

examples/chem-sync-local-flask/docker-compose.yaml

@@ -1,8 +1,6 @@
 services:
   benchling-app:
     build: .
-    ports:
-      - "8000:5000"
     volumes:
       - type: bind
         source: .
@@ -21,16 +19,29 @@ services:
       - CLIENT_SECRET_FILE=/run/secrets/app_client_secret
     secrets:
       - app_client_secret
+    network_mode: host
+
 
   # FOR LOCAL DEVELOPMENT ONLY!
   # Free tool for providing a public URL to forward webhooks to our Benchling App running locally
   # Do not do this in production or use with any sensitive data.
   # Benchling has not vetted this tool for use in production or in sensitive systems.
   # Conduct your own due diligence before choosing a tool for production use.
-  cloudflare-tunnel:
-    image: cloudflare/cloudflared
+  tunnel:
+    image: ngrok/ngrok:3.7.0-alpine
     restart: unless-stopped
-    command: tunnel --url http://benchling-app:5000
+    command: "http localhost:5004"
+    volumes:
+      # For Mac and Linux
+      - type: bind
+        source: /run/host-services/ssh-auth.sock
+        target: /run/host-services/ssh-auth.sock
+    environment:
+      # For Mac and Linux
+      - SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock
+      # Note: You'll need to set NGROK_AUTHTOKEN as an environment variable, for example in .env
+      - NGROK_AUTHTOKEN
+    network_mode: host
 
 secrets:
   app_client_secret:

examples/chem-sync-local-flask/local_app/app.py

@@ -1,10 +1,10 @@
 from threading import Thread
 
-from benchling_sdk.apps.helpers.webhook_helpers import verify
 from flask import Flask, request
 
 from local_app.benchling_app.handler import handle_webhook
-from local_app.benchling_app.setup import app_definition_id
+
+# from local_app.benchling_app.setup import app_definition_id # noqa: ERA001
 from local_app.lib.logger import get_logger
 
 logger = get_logger()
@@ -21,11 +21,12 @@ def health_check() -> tuple[str, int]:
     @app.route("/1/webhooks/<path:target>", methods=["POST"])
     def receive_webhooks(target: str) -> tuple[str, int]:  # noqa: ARG001
         # For security, don't do anything else without first verifying the webhook
-        app_def_id = app_definition_id()
+        # app_def_id = app_definition_id() # noqa: ERA001
 
         # Important! To verify webhooks, we need to pass the body as an unmodified string
         # Flask's request.data is bytes, so decode to string. Passing bytes or JSON won't work
-        verify(app_def_id, request.data.decode("utf-8"), request.headers)
+        # Disable when using local instance of Benchling Monolith
+        # verify(app_def_id, request.data.decode("utf-8"), request.headers) # noqa: ERA001
 
         logger.debug("Received webhook message: %s", request.json)
         # Dispatch work and ACK webhook as quickly as possible

examples/chem-sync-local-flask/local_app/benchling_app/setup.py

@@ -6,6 +6,7 @@
 from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2
 from benchling_sdk.benchling import Benchling
 from benchling_sdk.models.webhooks.v0 import WebhookEnvelopeV0
+from httpx import Client
 
 
 def init_app_from_webhook(webhook: WebhookEnvelopeV0) -> App:
@@ -27,19 +28,21 @@ def app_definition_id() -> str:
 
 
 def _benchling_from_webhook(webhook: WebhookEnvelopeV0) -> Benchling:
-    return Benchling(webhook.base_url, _auth_method())
+    client = Client(verify=False)  # noqa: S501
+    return Benchling(webhook.base_url, _auth_method(), httpx_client=client)
 
 
 @cache
 def _auth_method() -> ClientCredentialsOAuth2:
     client_id = os.environ.get("CLIENT_ID")
     assert client_id is not None, "Missing CLIENT_ID from environment"
     client_secret = _client_secret_from_file()
-    return ClientCredentialsOAuth2(client_id, client_secret)
+    client = Client(verify=False)  # noqa: S501
+    return ClientCredentialsOAuth2(client_id, client_secret, httpx_client=client)
 
 
 def _client_secret_from_file() -> str:
     file_path = os.environ.get("CLIENT_SECRET_FILE")
     assert file_path is not None, "Missing CLIENT_SECRET_FILE from environment"
     with Path(file_path).open() as f:
-        return f.read()
+        return f.read().strip()

examples/chem-sync-local-flask/tests/unit/local_app/test_app.py

@@ -28,14 +28,8 @@ def client(app: Flask) -> FlaskClient:
 class TestApp:
 
     @patch("local_app.app._enqueue_work")
-    @patch("local_app.app.app_definition_id")
-    @patch("local_app.app.verify")
-    def test_app_receive_webhook(
-            self, mock_verify, mock_app_definition_id, mock_enqueue_work, client,
-    ) -> None:
+    def test_app_receive_webhook(self, mock_verify_app_installation, client) -> None:
         webhook = load_webhook_json(_TEST_FILES_PATH / "canvas_initialize_webhook.json")
         response = client.post("1/webhooks/canvas", json=webhook.to_dict())
         assert response.status_code == 200
-        mock_verify.assert_called_once()
-        mock_app_definition_id.assert_called_once()
-        mock_enqueue_work.assert_called_once()
+        mock_verify_app_installation.assert_called_once()