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Add new raw data subdirectories to mirror walk #977

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merged 2 commits into from
Nov 12, 2024
Merged

Add new raw data subdirectories to mirror walk #977

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816dc8b
Add new raw data subdirectories to mirror walk
bkieft-usa Nov 12, 2024
34bb916
Merge branch 'main' into untargeted_dev
bkieft-usa Nov 12, 2024
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8 changes: 4 additions & 4 deletions metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -961,7 +961,7 @@ def mirror_mzmine_results_to_gnps2(
logging.info("Walking through local directory %s and uploading mzmine results to GNPS2..."%(local_directory))
for file_path in local_directory.rglob('*'):
if file_path.is_file() and file_path.suffix in ('.mgf', '.csv', '.tab'):
logging.info("Uploading %s to GNPS2..." % 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)
Expand Down Expand Up @@ -1021,7 +1021,7 @@ def mirror_raw_data_to_gnps2(
if os.path.exists(check_project_raw_dir):
local_directory = check_project_raw_dir
else:
possible_subdirs = ["jgi", "egsb", "akuftin", "agolini", "kblouie"]
possible_subdirs = ["jgi", "egsb", "akuftin", "agolini", "kblouie", "lzhan", "smkosina", "jsjordan", "mtvu", "tharwood"]
for subdir in possible_subdirs:
check_project_raw_dir = os.path.join(raw_data_dir, subdir, project)
if os.path.exists(check_project_raw_dir):
Expand Down Expand Up @@ -1069,7 +1069,7 @@ def mirror_raw_data_to_gnps2(
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:
logging.info("Uploading %s to GNPS2..." % 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)
Expand Down Expand Up @@ -1781,7 +1781,7 @@ def write_metadata_per_new_project(
if os.path.exists(check_project_raw_dir):
full_mzml_path = check_project_raw_dir
else:
possible_subdirs = ["jgi", "egsb", "akuftin", "agolini", "kblouie"]
possible_subdirs = ["jgi", "egsb", "akuftin", "agolini", "kblouie", "lzhan", "smkosina", "jsjordan", "mtvu", "tharwood"]
for subdir in possible_subdirs:
check_project_raw_dir = os.path.join(raw_data_dir, subdir, parent_dir)
if os.path.exists(check_project_raw_dir):
Expand Down
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