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Fix ingest_eeg_bids_datasets.py #1275

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Merged
merged 2 commits into from
Apr 17, 2025
Merged

Fix ingest_eeg_bids_datasets.py #1275

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f284dda
Fix subject ID derived from PSCID + Use valid eeg_uploader.Status values
jeffersoncasimir Apr 17, 2025
9b094f6
Satisfy linter
jeffersoncasimir Apr 17, 2025
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11 changes: 6 additions & 5 deletions python/scripts/ingest_eeg_bids_datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,13 +127,13 @@ def main():
if os.path.isdir(
os.path.join(assembly_bids_path, 'sub-' + str(candid))
):
subjectid = str(candid)
subjectid = f'sub-{candid}'

# Try the pscid, case insensitive
if not subjectid:
gen = (
dir for dir in os.listdir(assembly_bids_path)
if dir.lower() == 'sub-' + pscid.lower()
if dir.lower() == ('sub-' + pscid.lower())
)
subjectid = next(gen, None)

Expand All @@ -143,7 +143,8 @@ def main():
continue

# Visit
path = os.path.join(assembly_bids_path, 'sub-' + subjectid, 'ses-' + visit)
path = os.path.join(assembly_bids_path, subjectid, 'ses-' + visit)

if not os.path.isdir(path):
print(f'No BIDS dataset matching visit {visit} for candidate {pscid} {candid} found.')
continue
Expand Down Expand Up @@ -174,7 +175,7 @@ def main():

if result.returncode == 0:
db.update(
"UPDATE electrophysiology_uploader SET Status = 'Ingested' WHERE UploadID = %s",
"UPDATE electrophysiology_uploader SET Status = 'Complete' WHERE UploadID = %s",
(uploadid,)
)
print('EEG Dataset with uploadID ' + uploadid + ' successfully ingested')
Expand All @@ -185,7 +186,7 @@ def main():
print('ERROR: error while executing bids_import.py')

db.update(
"UPDATE electrophysiology_uploader SET Status = 'Failed Ingestion' WHERE UploadID = %s",
"UPDATE electrophysiology_uploader SET Status = 'Failed' WHERE UploadID = %s",
(uploadid,)
)

Expand Down
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