#6 add GATEWAY_ENABLE_UPLOAD environment variable

routes that modify disk are not added unless the env variable is set.

Readme.md

@@ -65,7 +65,10 @@ Here's what the environment variables mean:
 * `CELLXGENE_DATA` - a directory that can contain subdirectories with `.h5ad` data files, *without* trailing slash, e.g. `/mnt/cellxgene_data`
 * `GATEWAY_HOST` - the hostname and port that the gateway will run on, typically `localhost:5005` if running locally
 * `GATEWAY_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.
-* `GATEWAY_EXTRA_SCRIPTS` - (optional) JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
+* `GATEWAY_IP` - ip addess of instance gateway is running on, mostly used to display SSH instructions
+Optional environment variables:
+* `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
+* `GATEWAY_ENABLE_UPLOAD` - Set to `true` or `1` to enable HTTP uploads. This is not recommended for a public server.
 
 The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 

cellxgene_gateway/env.py

@@ -16,6 +16,7 @@ gateway_protocol = os.environ.get("GATEWAY_PROTOCOL")
 ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 ttl = os.environ.get("GATEWAY_TTL")
+enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,

cellxgene_gateway/gateway.py

@@ -99,10 +99,9 @@ def index():
         cellxgene_data=env.cellxgene_data,
         extra_scripts=get_extra_scripts(),
         users=users,
+        enable_upload=env.enable_upload,
     )
 
-
-@app.route("/make_user", methods=["POST"])
 def make_user():
     dir_name = request.form["directory"]
 
@@ -111,7 +110,6 @@ def make_user():
     return redirect(location, code=302)
 
 
-@app.route("/make_subdir", methods=["POST"])
 def make_subdir():
     parent_path = os.path.join(env.cellxgene_data, request.form["usernames"])
     dir_name = request.form["directory"]
@@ -121,7 +119,6 @@ def make_subdir():
     return redirect(location, code=302)
 
 
-@app.route("/upload_file", methods=["POST"])
 def upload_file():
     upload_dir = request.form["path"]
 
@@ -153,6 +150,11 @@ def upload_file():
     return redirect(env.location, code=302)
 
 
+if env.enable_upload:
+    app.add_url_rule('/make_user', 'make_user', make_user, methods=["POST"])
+    app.add_url_rule('/make_subdir', 'make_subdir', make_subdir, methods=["POST"])
+    app.add_url_rule('/upload_file', 'upload_file', upload_file, methods=["POST"])
+
 @app.route("/filecrawl.html")
 def filecrawl():
 

cellxgene_gateway/templates/index.html

@@ -44,10 +44,10 @@
 			<u>Cache Status: view status of launched cellxgene servers.</u></a>
 	</div>
 	
+	{% if enable_upload %}
 	<br>
-
 	<h1 style="padding-left:35px">
-		How To Upload Data:	
+		How To Upload Data via HTTP:
 	</h1>
 	<ol style="padding-left:85px;">
 		<li>
@@ -83,12 +83,12 @@
 		<br>
 		<li>Take a look at your data using the file crawler link above</li>
 	</ol>
-
+	{% endif %}
 
 	<br>
 
 	<h1 style="padding-left:35px">
-		How To Upload Data via SSH and SCP (Linux):	
+		How To Upload Data via SSH and SCP:
 	</h1>
 	<ol style="padding-left:85px;">
 		<li>