added environment variables for ProxyFix

README.md

@@ -60,6 +60,7 @@ Here's what the environment variables mean:
 
 * `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`
 * `CELLXGENE_DATA` - a directory that can contain subdirectories with `.h5ad` data files, *without* trailing slash, e.g. `/mnt/cellxgene_data`
+
 Optional environment variables:
 * `CELLXGENE_ARGS` - catch-all variable that can be used to pass additional command line args to cellxgene server
 * `EXTERNAL_HOST` - the hostname and port from the perspective of the web browser, typically `localhost:5005` if running locally. Defaults to "localhost:{GATEWAY_PORT}"
@@ -69,7 +70,14 @@ 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.
 * `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
-* `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.  
+* `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.
+
+If any of the following optional variables are set, [ProxyFix](https://werkzeug.palletsprojects.com/en/1.0.x/middleware/proxy_fix/) will be used.
+* `PROXY_FIX_FOR` - Number of upstream proxies setting X-Forwarded-For
+* `PROXY_FIX_PROTO` - Number of upstream proxies setting X-Forwarded-Proto
+* `PROXY_FIX_HOST` - Number of upstream proxies setting X-Forwarded-Host
+* `PROXY_FIX_PORT` - Number of upstream proxies setting X-Forwarded-Port
+* `PROXY_FIX_PREFIX` - Number of upstream proxies setting X-Forwarded-Prefix
 
 The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 

cellxgene_gateway/cache_entry.py

@@ -171,15 +171,11 @@ class CacheEntry:
             cellxgene_response = get(full_path, headers=headers)
         elif request.method == "PUT":
             cellxgene_response = put(
-                full_path,
-                headers=headers,
-                data=request.data,
+                full_path, headers=headers, data=request.data,
             )
         elif request.method == "POST":
             cellxgene_response = post(
-                full_path,
-                headers=headers,
-                data=request.data,
+                full_path, headers=headers, data=request.data,
             )
         else:
             raise CellxgeneException(
@@ -199,9 +195,7 @@ class CacheEntry:
                 resp_headers[h] = cellxgene_response.headers[h]
 
         gateway_response = make_response(
-            gateway_content,
-            cellxgene_response.status_code,
-            resp_headers,
+            gateway_content, cellxgene_response.status_code, resp_headers,
         )
 
         return gateway_response

cellxgene_gateway/env.py

@@ -31,22 +31,22 @@ enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in [
 ]
 enable_annotations = os.environ.get(
     "GATEWAY_ENABLE_ANNOTATIONS", ""
-).lower() in [
-    "true",
-    "1",
-]
+).lower() in ["true", "1",]
 enable_backed_mode = os.environ.get(
     "GATEWAY_ENABLE_BACKED_MODE", ""
-).lower() in [
-    "true",
-    "1",
-]
+).lower() in ["true", "1",]
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
     "CELLXGENE_DATA": cellxgene_data,
 }
 
+proxy_fix_for = int(os.environ.get("PROXY_FIX_FOR", "0"))
+proxy_fix_proto = int(os.environ.get("PROXY_FIX_PROTO", "0"))
+proxy_fix_host = int(os.environ.get("PROXY_FIX_HOST", "0"))
+proxy_fix_port = int(os.environ.get("PROXY_FIX_PORT", "0"))
+proxy_fix_prefix = int(os.environ.get("PROXY_FIX_PREFIX", "0"))
+
 optional_env_vars = {
     "EXTERNAL_HOST": external_host,
     "EXTERNAL_PROTOCOL": external_protocol,
@@ -58,6 +58,11 @@ optional_env_vars = {
     "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
     "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
     "CELLXGENE_ARGS": cellxgene_args,
+    "PROXY_FIX_FOR": proxy_fix_for,
+    "PROXY_FIX_PROTO": proxy_fix_proto,
+    "PROXY_FIX_HOST": proxy_fix_host,
+    "PROXY_FIX_PORT": proxy_fix_port,
+    "PROXY_FIX_PREFIX": proxy_fix_prefix,
 }
 
 

cellxgene_gateway/filecrawl.py

@@ -92,7 +92,7 @@ def render_entries(entries):
 
 
 def get_url(entry):
-    return url_for("do_view", path=entry["path"].lstrip("/")) +"/""
+    return url_for("do_view", path=entry["path"].lstrip("/") + "/")
 
 
 def get_class(entry):

cellxgene_gateway/gateway.py

@@ -50,7 +50,21 @@ def _force_https(app):
 
 
 app.wsgi_app = _force_https(app.wsgi_app)
-app.wsgi_app = ProxyFix(app.wsgi_app, x_proto=1, x_host=1, x_prefix=1)
+if (
+    env.proxy_fix_for > 0
+    or env.proxy_fix_proto > 0
+    or env.proxy_fix_host > 0
+    or env.proxy_fix_port > 0
+    or env.proxy_fix_prefix > 0
+):
+    app.wsgi_app = ProxyFix(
+        app.wsgi_app,
+        x_for=env.proxy_fix_for,
+        x_proto=env.proxy_fix_proto,
+        x_host=env.proxy_fix_host,
+        x_port=env.proxy_fix_port,
+        x_prefix=env.proxy_fix_prefix,
+    )
 
 cache = BackendCache()