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[GEN-1191] Add file logging #552

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merged 5 commits into from
Mar 13, 2024
Merged

[GEN-1191] Add file logging #552

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0833504
add logging for getting files
rxu17 Mar 6, 2024
7945ca6
explicitly set logging at INFO level
rxu17 Mar 6, 2024
0f5952d
add stream for logger
rxu17 Mar 6, 2024
32a1dac
add stream handler to write to stdout
rxu17 Mar 8, 2024
39b381f
add note
rxu17 Mar 8, 2024
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5 changes: 5 additions & 0 deletions genie/extract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
"""

import logging
import sys
from typing import List, Optional

import synapseclient
Expand All @@ -13,6 +14,9 @@
from genie import process_functions

logger = logging.getLogger(__name__)
stdout_handler = logging.StreamHandler(stream=sys.stdout)
stdout_handler.setLevel(logging.INFO)
logger.addHandler(stdout_handler)


def get_center_input_files(
Expand Down Expand Up @@ -54,6 +58,7 @@ def get_center_input_files(
if name.endswith(".vcf") and process != "mutation":
continue

logger.info(f"GETTING FILE {name} ({ent_synid})")
ent = syn.get(ent_synid, downloadFile=downloadFile)

# HACK: Clinical file can come as two files.
Expand Down
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