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updated arguments for cellxgene v 0.15. Added option for backed mode.

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This commit is contained in:
Fidel Ramírez
2020-05-04 13:49:09 +02:00
parent 11bbc1aba8
commit 9a130a8eb7
4 changed files with 13 additions and 7 deletions
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cellxgene_gateway/subprocess_backend.py
+8 -6
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@@ -11,30 +11,32 @@ import logging
import subprocess
from flask_api import status
from cellxgene_gateway.env import enable_annotations
from cellxgene_gateway.env import enable_annotations, enable_backed_mode
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
class SubprocessBackend:
def __init__(self):
pass
def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
if enable_annotations and not annotation_file_path is None:
annotation_args_prefix = " --experimental-annotations"
if annotation_file_path == "":
annotation_args = f"{annotation_args_prefix} --experimental-annotations-output-dir {make_annotations(file_path)}"
extra_args = f" --annotations-dir {make_annotations(file_path)}"
else:
annotation_args = f"{annotation_args_prefix} --experimental-annotations-file {annotation_file_path}"
extra_args = f" --annotations-file {annotation_file_path}"
else:
annotation_args = ""
extra_args = " --disable-annotations"
if enable_backed_mode:
extra_args += " --backed"
cmd = (
f"yes | {cellxgene_loc} launch {file_path}"
+ " --port "
+ str(port)
+ " --host 127.0.0.1"
+ annotation_args
+ extra_args
)
for s in scripts: