diff --git a/README.md b/README.md
index 730f4a9..8974341 100644
--- a/README.md
+++ b/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.
diff --git a/cellxgene_gateway/cache_entry.py b/cellxgene_gateway/cache_entry.py
index a24fa70..ea12390 100644
--- a/cellxgene_gateway/cache_entry.py
+++ b/cellxgene_gateway/cache_entry.py
@@ -8,6 +8,8 @@
# the specific language governing permissions and limitations under the License.
import datetime
import logging
+from flask.helpers import url_for
+from flask.wrappers import Response
import psutil
from enum import Enum
@@ -120,7 +122,7 @@ class CacheEntry:
return gateway_content
def gateway_basepath(self):
- return f"{env.external_protocol}://{env.external_host}/view/{self.key.pathpart}/"
+ return url_for("do_view", path=self.key.pathpart) + "/"
def cellxgene_basepath(self):
return f"http://127.0.0.1:{self.port}"
@@ -130,7 +132,7 @@ class CacheEntry:
subpath = path[len(self.key.pathpart) :] # noqa: E203
if len(subpath) == 0:
- r = make_response(f"Redirect to {gateway_basepath}\n", 301)
+ r = make_response(f"Redirect to {gateway_basepath}\n", 302)
r.headers["location"] = gateway_basepath + querystring()
return r
elif self.status == CacheEntryStatus.loading:
diff --git a/cellxgene_gateway/env.py b/cellxgene_gateway/env.py
index 2fcae35..2cc491a 100644
--- a/cellxgene_gateway/env.py
+++ b/cellxgene_gateway/env.py
@@ -47,6 +47,12 @@ env_vars = {
"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 +64,11 @@ 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,
}
diff --git a/cellxgene_gateway/filecrawl.py b/cellxgene_gateway/filecrawl.py
index cf0b443..97c2126 100644
--- a/cellxgene_gateway/filecrawl.py
+++ b/cellxgene_gateway/filecrawl.py
@@ -14,6 +14,7 @@ from cellxgene_gateway.dir_util import (
make_annotations,
annotations_suffix,
)
+from flask import url_for
def recurse_dir(path):
@@ -91,7 +92,7 @@ def render_entries(entries):
def get_url(entry):
- return f"/view/{ entry['path'].lstrip('/') }/"
+ return url_for("do_view", path=entry["path"].lstrip("/") + "/")
def get_class(entry):
diff --git a/cellxgene_gateway/gateway.py b/cellxgene_gateway/gateway.py
index 723d488..12e9352 100644
--- a/cellxgene_gateway/gateway.py
+++ b/cellxgene_gateway/gateway.py
@@ -25,7 +25,7 @@ from flask import (
)
from flask_api import status
from werkzeug.utils import secure_filename
-
+from werkzeug.middleware.proxy_fix import ProxyFix
from cellxgene_gateway import env
from cellxgene_gateway.backend_cache import BackendCache
from cellxgene_gateway.cache_entry import CacheEntryStatus
@@ -50,9 +50,23 @@ def _force_https(app):
app.wsgi_app = _force_https(app.wsgi_app)
+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()
-location = f"{env.external_protocol}://{env.external_host}"
@app.errorhandler(CellxgeneException)
@@ -126,7 +140,7 @@ def make_user():
create_dir(env.cellxgene_data, dir_name)
- return redirect(location, code=302)
+ return redirect(url_for("index"), code=302)
def make_subdir():
@@ -135,7 +149,7 @@ def make_subdir():
create_dir(parent_path, dir_name)
- return redirect(location, code=302)
+ return redirect(url_for("index"), code=302)
def upload_file():
@@ -154,7 +168,7 @@ def upload_file():
full_upload_path, secure_filename(f.filename)
)
)
- return redirect("/filecrawl.html", code=302)
+ return redirect(url_for("filecrawl"), code=302)
else:
raise CellxgeneException(
"Uploaded file must be in anndata (.h5ad) format.",
@@ -170,7 +184,7 @@ def upload_file():
"Invalid directory.", status.HTTP_400_BAD_REQUEST
)
- return redirect(location, code=302)
+ return redirect(url_for("index"), code=302)
if env.enable_upload:
diff --git a/cellxgene_gateway/prune_process_cache.py b/cellxgene_gateway/prune_process_cache.py
index f332ffd..98126ec 100644
--- a/cellxgene_gateway/prune_process_cache.py
+++ b/cellxgene_gateway/prune_process_cache.py
@@ -10,14 +10,16 @@
import logging
import time
-from cellxgene_gateway.env import ttl
-from cellxgene_gateway.util import current_time_stamp
+from cellxgene_gateway import env
+from cellxgene_gateway import util
+
+logger = logging.getLogger(__name__)
class PruneProcessCache:
def __init__(self, cache):
self.cache = cache
- self.expire_seconds = 3600 if ttl is None else int(ttl)
+ self.expire_seconds = 3600 if env.ttl is None else int(env.ttl)
def __call__(self):
while True:
@@ -25,7 +27,7 @@ class PruneProcessCache:
self.prune()
def prune(self):
- timestamp = current_time_stamp()
+ timestamp = util.current_time_stamp()
cutoff = timestamp - self.expire_seconds
processes_to_delete = [
p for p in self.cache.entry_list if p.timestamp < cutoff
@@ -33,9 +35,9 @@ class PruneProcessCache:
processes_to_keep = [
p for p in self.cache.entry_list if not p.timestamp < cutoff
]
- logger = logging.getLogger("cellxgene_gateway")
+
logger.debug(
- f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}"
+ f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}, pruning {processes_to_delete}"
)
for process in processes_to_delete:
diff --git a/cellxgene_gateway/templates/cellxgene_error.html b/cellxgene_gateway/templates/cellxgene_error.html
index 908b5bf..aea6764 100644
--- a/cellxgene_gateway/templates/cellxgene_error.html
+++ b/cellxgene_gateway/templates/cellxgene_error.html
@@ -28,11 +28,11 @@
{{ message }}
-
+
Please click here to be redirected to the file directory.
-
+
Please click here to return to the homepage.
diff --git a/cellxgene_gateway/templates/filecrawl.html b/cellxgene_gateway/templates/filecrawl.html
index 7d59e34..e31f54d 100644
--- a/cellxgene_gateway/templates/filecrawl.html
+++ b/cellxgene_gateway/templates/filecrawl.html
@@ -36,10 +36,10 @@
Navigation: