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Merge pull request #26 from Novartis/feature/25

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#25 added CELLXGENE_ARGS environment variable
This commit is contained in:
Alokito
2020-08-18 19:45:31 -04:00
committed by GitHub
parent 61c7c43da7 0f8092e07a
commit 13802b72b9
4 changed files with 13 additions and 2 deletions
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cellxgene_gateway/env.py
+2
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@@ -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
+8 -1
View File
@@ -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 "