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feat: divert log to standard output for debugging #958

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merged 2 commits into from
Oct 14, 2024
Merged

feat: divert log to standard output for debugging #958

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2adb395
feat: divert log to standard output for debugging
bkieft-usa Oct 14, 2024
ee940e4
Merge branch 'main' into untargeted_dev
bkieft-usa Oct 14, 2024
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3 changes: 2 additions & 1 deletion metatlas/untargeted/run_untargeted_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def main():
step_bools = check_skipped_steps(args)

##### Configure logging
mzm.call_logger(log_filename=args.log_file, log_level=args.log_level, log_format=args.log_format)
mzm.call_logger(log_filename=args.log_file, log_level=args.log_level, log_format=args.log_format, log_to_stdout=args.log_to_stdout)

##### Kick off the script
start_message = mzm.start_script(script="run_untargeted_pipeline.py")
Expand Down Expand Up @@ -102,6 +102,7 @@ def add_arguments(parser):
parser.add_argument('--log_file', type=str, default='/global/cfs/cdirs/m2650/untargeted_logs/untargeted_pipeline.log', help='Log file name with full path')
parser.add_argument('--log_level', type=str, default='INFO', help='Logger level. One of [DEBUG, INFO, WARNING, ERROR, or CRITICAL]')
parser.add_argument('--log_format', type=str, default='%(asctime)s - %(levelname)s - %(message)s', help='Logger format')
parser.add_argument('--log_to_stdout', action='store_true', help='Log to stdout instead of a file')

def check_args(args):
##### Check if the input arguments are valid
Expand Down
8 changes: 7 additions & 1 deletion metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,12 @@
def call_logger(log_filename: str, log_level: str, log_format: str):
logging.basicConfig(filename=log_filename, level=log_level, format=log_format, filemode='a')

def call_logger(log_filename: str, log_level: str, log_format: str, log_to_stdout: bool):
if log_to_stdout:
logging.basicConfig(stream=sys.stdout, level=log_level, format=log_format)
else:
logging.basicConfig(filename=log_filename, level=log_level, format=log_format, filemode='a')

def start_script(script:str=None) -> str:
"""
Kick off script with a timestamp for log
Expand Down Expand Up @@ -1016,6 +1022,7 @@ def mirror_raw_data_to_gnps2(
if not os.path.exists(local_directory):
logging.error(f"Local directory for {project} raw data not found after trying several possible alternatives. Exiting.")
return
local_directory = Path(local_directory)
remote_subdir = local_directory.parent.name # Use the same subdir as on perlmutter instead of inferring from the project name directly
remote_directory = f"/raw_data/{remote_subdir}/{project}"
polarity_directory = f"{remote_directory}/{polarity}"
Expand All @@ -1042,7 +1049,6 @@ def mirror_raw_data_to_gnps2(
logging.error(f"Failed to create remote directory {polarity_directory} at GNPS2: {e}")

try:
local_directory = Path(local_directory)
logging.info("Walking through local directory %s and uploading mzML files to GNPS2..."%(local_directory))
for file_path in local_directory.rglob('*'):
if file_path.is_file() and file_path.suffix == '.mzML' and polarity_short in file_path.name:
Expand Down
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