Merge pull request #26 from Novartis/feature/25

#25 added CELLXGENE_ARGS environment variable

README.md

@@ -39,7 +39,7 @@ Note: you may need to downgrade h5py with `pip install h5py==2.9.0` due to an [i
 
 ```bash
 mkdir ../cellxgene_data
-wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
+wget https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
 ```
 
 
@@ -61,6 +61,7 @@ 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}"
 * `EXTERNAL_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy that performs https termination. Default value "http"
 * `GATEWAY_IP` - ip addess of instance gateway is running on, mostly used to display SSH instructions. Defaults to `socket.gethostbyname(socket.gethostname())`

cellxgene_gateway/env.py

@@ -13,6 +13,7 @@ import socket
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
 cellxgene_data = os.environ.get("CELLXGENE_DATA")
+cellxgene_args = os.environ.get("CELLXGENE_ARGS", None)
 gateway_port = int(os.environ.get("GATEWAY_PORT", "5005"))
 external_host = os.environ.get(
     "EXTERNAL_HOST",
@@ -50,6 +51,7 @@ optional_env_vars = {
     "GATEWAY_ENABLE_UPLOAD": enable_upload,
     "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
     "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
+    "CELLXGENE_ARGS": cellxgene_args,
 }
 
 

cellxgene_gateway/subprocess_backend.py

@@ -11,7 +11,11 @@ import logging
 import subprocess
 
 from flask_api import status
-from cellxgene_gateway.env import enable_annotations, enable_backed_mode
+from cellxgene_gateway.env import (
+    enable_annotations,
+    enable_backed_mode,
+    cellxgene_args,
+)
 from cellxgene_gateway.process_exception import ProcessException
 from cellxgene_gateway.dir_util import make_annotations
 from cellxgene_gateway.path_util import get_file_path, get_annotation_file_path
@@ -35,6 +39,9 @@ class SubprocessBackend:
             extra_args = " --disable-annotations"
         if enable_backed_mode:
             extra_args += " --backed"
+        if not cellxgene_args is None:
+            extra_args += f" {cellxgene_args}"
+
         cmd = (
             f"yes | {cellxgene_loc} launch {file_path}"
             + " --port "

environment.yml

@@ -7,6 +7,7 @@ dependencies:
 - flask
 - psutil
 - black
+- pip
 - pip:
   - flask-api
   - cellxgene>=0.15