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Update fix_pbmc_sample_participant.py script for multiple external ids #831

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Update fix_pbmc_sample_participant.py script for multiple external ids #831

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6 changes: 3 additions & 3 deletions scripts/fix_pbmc_sample_participant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,12 @@ def main():
)
)

sample_map_by_external_id = {s['external_id']: s for s in all_samples}
sample_map_by_external_id = {eid: s for s in all_samples for eid in s['external_ids'].values()}

pbmc_samples = [s for s in all_samples if '-PBMC' in s['external_id']]
pbmc_samples = [s for s in all_samples if any('-PBMC' in eid for eid in s['external_ids'].values())]

for sample in pbmc_samples:
external_id = sample['external_id']
external_id = next(eid for eid in sample['external_ids'].values() if '-PBMC' in eid)
non_pbmc_id = external_id.strip('-PBMC')
non_pbmc_sample = sample_map_by_external_id.get(non_pbmc_id)
pbmc_sample = sample_map_by_external_id.get(external_id)
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