Add URL prefix mounting for proxy deployments

README.md

@@ -26,7 +26,9 @@ python sample_registry/app.py
 
 How you want to deploy this will depend on your needs, facilities, and ability. We have it deployed by a Kubernetes cluster but you could also 1) just run it in development mode from a lab computer or 2) setup Nginx/Apache on a dedicated server or 3) run it serverlessly in the cloud (e.g. with [Zappa](https://github.com/zappa/Zappa) on AWS) or 4) do something else. There are lots of well documented examples of deploying Flask sites out there, look around and find what works best for you.
 
-When running, it will default to using a SQLite3 database located in the root of this repository (automatically created if it doesn't already exist). You can change to use a different backend by setting the `SAMPLE_REGISTRY_DB_URI` environment variable before running the app. For example, another sqlite database could be specified with a URI like this: `export SAMPLE_REGISTRY_DB_URI=sqlite:////path/to/db.sqlite`.
+When running, it will default to using a SQLite3 database located in the root of this repository (automatically created if it doesn't already exist). You can change to use a different backend by setting the `SAMPLE_REGISTRY_DB_URI` environment variable before running the app. For example, another sqlite database could be specified with a URI like this: `export SAMPLE_REGISTRY_DB_URI=sqlite:////path/to/db.sqlite`.
+
+If you're deploying behind a reverse proxy at a URL prefix, set `SAMPLE_REGISTRY_URL_PREFIX` (for example, `/sample_registry`). The WSGI entrypoint `sample_registry.app:application` will mount the Flask app at that prefix while leaving local development (`python sample_registry/app.py`) available at `/`.
 
 ## Using the library
 
@@ -36,4 +38,4 @@ The `sample_registry` library can be installed and run anywhere by following the
 
 If you want to iterate over a feature you can only test on the K8s deployment, you can manually build the Docker image instead of relying on the release workflow. Use `docker build -t ctbushman/sample_registry:latest -f Dockerfile .` to build the image and then `docker push ctbushman/sample_registry:latest` to push it to DockerHub. You can then trigger the K8s deployment to grab the new image.
 
-N.B. You might want to use a different tag than `latest` if you're testing something volatile so that if someone else is trying to use the image as you're developing, they won't pull your wonky changes.
+N.B. You might want to use a different tag than `latest` if you're testing something volatile so that if someone else is trying to use the image as you're developing, they won't pull your wonky changes.

sample_registry/app.py

@@ -19,29 +19,45 @@
 from pathlib import Path
 from sample_registry import ARCHIVE_ROOT, SQLALCHEMY_DATABASE_URI
 from sample_registry.models import Base, Annotation, Run, Sample
-from sample_registry.db import run_to_dataframe, query_tag_stats, STANDARD_TAGS
-from sample_registry.standards import STANDARD_HOST_SPECIES, STANDARD_SAMPLE_TYPES
-from werkzeug.middleware.proxy_fix import ProxyFix
-
-app = Flask(__name__)
-app.secret_key = os.urandom(12)
+from sample_registry.db import run_to_dataframe, query_tag_stats, STANDARD_TAGS
+from sample_registry.standards import STANDARD_HOST_SPECIES, STANDARD_SAMPLE_TYPES
+from werkzeug.middleware.dispatcher import DispatcherMiddleware
+from werkzeug.middleware.proxy_fix import ProxyFix
+
+app = Flask(__name__)
+app.secret_key = os.urandom(12)
 
 # This line is only used in production mode on a nginx server, follow instructions to setup forwarding for
 # whatever production server you are using instead. It's ok to leave this in when running the dev server.
 app.wsgi_app = ProxyFix(app.wsgi_app, x_for=1, x_proto=1, x_host=1, x_prefix=1)
 
-# Sanitize and RO db connection
-SQLALCHEMY_DATABASE_URI = f"{SQLALCHEMY_DATABASE_URI.split('?')[0]}?mode=ro"
-app.config["SQLALCHEMY_DATABASE_URI"] = SQLALCHEMY_DATABASE_URI
-print(SQLALCHEMY_DATABASE_URI)
+# Sanitize and RO db connection
+SQLALCHEMY_DATABASE_URI = f"{SQLALCHEMY_DATABASE_URI.split('?')[0]}?mode=ro"
+app.config["SQLALCHEMY_DATABASE_URI"] = SQLALCHEMY_DATABASE_URI
+print(SQLALCHEMY_DATABASE_URI)
 # Ensure SQLite explicitly opens in read-only mode
 app.config["SQLALCHEMY_ENGINE_OPTIONS"] = {"connect_args": {"uri": True}}
-db = SQLAlchemy(model_class=Base)
-db.init_app(app)
-
-
-@app.route("/favicon.ico")
-def favicon():
+db = SQLAlchemy(model_class=Base)
+db.init_app(app)
+
+def _normalize_url_prefix(raw_prefix: str) -> str:
+    prefix = (raw_prefix or "").strip()
+    if not prefix or prefix == "/":
+        return ""
+    if not prefix.startswith("/"):
+        prefix = f"/{prefix}"
+    return prefix.rstrip("/")
+
+
+URL_PREFIX = _normalize_url_prefix(os.getenv("SAMPLE_REGISTRY_URL_PREFIX"))
+if URL_PREFIX:
+    application = DispatcherMiddleware(Flask("dummy_root"), {URL_PREFIX: app})
+else:
+    application = app
+
+
+@app.route("/favicon.ico")
+def favicon():
     return send_from_directory(
         Path(app.root_path) / "static",
         "favicon.ico",