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Add boolean for using polarity subdirectory during raw data mirror to GNPS2 #993

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merged 2 commits into from
Nov 20, 2024
Merged

Add boolean for using polarity subdirectory during raw data mirror to GNPS2 #993

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016bdf3
Add boolean for using polarity subdirectory during raw data mirror to…
bkieft-usa Nov 20, 2024
8d84848
Merge branch 'main' into untargeted_mirror
bkieft-usa Nov 20, 2024
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32 changes: 22 additions & 10 deletions metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -995,6 +995,7 @@ def mirror_raw_data_to_gnps2(
project: str,
username: str,
raw_data_dir: str,
overwrite_existing_dir: bool = False,
polarity: Optional[str] = None,
raw_data_subdir: Optional[str] = None,
use_polarity_subdir: Optional[bool] = False
Expand Down Expand Up @@ -1097,35 +1098,46 @@ def mirror_raw_data_to_gnps2(
logging.error(tab_print(f"Failed to connect to GNPS2 again. Skipping mirror with error: {e}", 4))
return "Failed"

if use_polarity_subdir is True:
try:
sftp.mkdir(remote_directory)
except Exception as e:
if "mkdir file exists" in str(e).lower():
if overwrite_existing_dir is False:
logging.info(tab_print(f"Found existing directory {remote_directory} at GNPS2 and overwrite_existing_dir is False. Exiting.", 3))
return "Failed"
else:
logging.warning(tab_print(f"Notice! Did not create {remote_directory} at GNPS2 for reason: {e}", 3))
return "Failed"

if use_polarity_subdir is True and polarity is not None:
polarity_short = f"_{polarity[:3].upper()}_"
try:
sftp.mkdir(remote_directory)
except Exception as e:
if "mkdir file exists" not in str(e).lower():
logging.warning(tab_print(f"Notice! Did not create {remote_directory} at GNPS2 for reason: {e}", 3))
try:
sftp.mkdir(polarity_directory)
except Exception as e:
if "mkdir file exists" not in str(e).lower():
if "mkdir file exists" in str(e).lower():
if overwrite_existing_dir is False:
logging.info(tab_print(f"Found existing directory {polarity_directory} at GNPS2 and overwrite_existing_dir is False. Exiting.", 3))
return "Failed"
else:
logging.warning(tab_print(f"Notice! Did not create {polarity_directory} at GNPS2 for reason: {e}", 3))

return "Failed"
try:
for file_path in local_directory.rglob('*'):
if use_polarity_subdir is True:
polarity_short = f"_{polarity[:3].upper()}_"
if file_path.is_file() and file_path.suffix == '.mzML' and polarity_short in file_path.name:
#logging.info("Uploading %s to GNPS2..." % file_path.name)
local_path = str(file_path)
remote_path = f"{polarity_directory}/{file_path.name}"
sftp.put(local_path, remote_path)
logging.info(tab_print(f"Uploaded {file_path.name} to GNPS2...", 3))
logging.info(tab_print(f"Uploaded {file_path.name} to {remote_path} at GNPS2...", 3))
if use_polarity_subdir is False:
if file_path.is_file() and file_path.suffix == '.mzML' in file_path.name:
#logging.info("Uploading %s to GNPS2..." % file_path.name)
local_path = str(file_path)
remote_path = f"{remote_directory}/{file_path.name}"
sftp.put(local_path, remote_path)
logging.info(tab_print(f"Uploaded {file_path.name} to GNPS2...", 3))
logging.info(tab_print(f"Uploaded {file_path.name} to {remote_path} at GNPS2...", 3))

sftp.close()
transport.close()
Expand Down
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