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#68 read process output until it exits

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This commit is contained in:
Alok Saldanha
2022-06-20 21:46:19 -04:00
parent 0cd551382e
commit d32a31e855
1 changed files with 6 additions and 3 deletions
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cellxgene_gateway/subprocess_backend.py
+6 -3
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@@ -17,6 +17,8 @@ from cellxgene_gateway.dir_util import make_annotations
from cellxgene_gateway.env import cellxgene_args, enable_annotations, enable_backed_mode from cellxgene_gateway.env import cellxgene_args, enable_annotations, enable_backed_mode
from cellxgene_gateway.process_exception import ProcessException from cellxgene_gateway.process_exception import ProcessException
logger = logging.getLogger(__name__)
class SubprocessBackend: class SubprocessBackend:
def __init__(self): def __init__(self):
@@ -55,7 +57,7 @@ class SubprocessBackend:
scripts, scripts,
cache_entry.key.annotation_file_path, cache_entry.key.annotation_file_path,
) )
logging.getLogger("cellxgene_gateway").info(f"launching {cmd}") logger.info(f"launching {cmd}")
process = subprocess.Popen( process = subprocess.Popen(
[cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True [cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
) )
@@ -84,5 +86,6 @@ class SubprocessBackend:
cache_entry.append_output(output) cache_entry.append_output(output)
cache_entry.set_loaded(process.pid) cache_entry.set_loaded(process.pid)
for output in process.communicate():
return logger.debug(f"cellxgene:{output}")
logger.info(f"exiting {cmd}")