Created
March 26, 2018 22:46
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Update Airtable records from Excel metadata
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| import pandas as pd | |
| from airtable import airtable | |
| metadata = pd.read_table(metadata_path, sep=',', header=0, index_col=None) | |
| at = airtable.Airtable(base_id, api_key) | |
| ibd_records = at.get('sample', filter_by_formula='AND(project = "cho-ibd", phenotype = "")')['records'] | |
| for record in ibd_records: | |
| if (metadata.local_sample == record['fields']['sample_id']).sum() != 1: | |
| print(record) | |
| raise ValueError('Could not match records') | |
| for record in ibd_records: | |
| id_ = record['id'] | |
| fields = record['fields'] | |
| record_metadata = metadata[metadata.local_sample == fields['sample_id']].iloc[0] | |
| consortium_id = record_metadata.consortium_id | |
| local_pedigree = record_metadata.local_pedigree | |
| sex = record_metadata.sex.lower() | |
| if pd.isnull(record_metadata.diag): | |
| phenotype = ['unaffected'] | |
| elif 'Crohn' in record_metadata.diag: | |
| phenotype = ['crohns', 'ibd'] | |
| elif 'Ulcer' in record_metadata.diag: | |
| phenotype = ['uc', 'ibd'] | |
| else: | |
| raise ValueError('phenotype') | |
| age = record_metadata.age.tolist() | |
| notes = fields['Notes'] + f'\nconsortium_id: {consortium_id}\nlocal_pedigree: {local_pedigree}' | |
| update_data = { | |
| 'sex': sex, | |
| 'age': age, | |
| 'phenotype': phenotype, | |
| 'Notes': notes} | |
| ret = at.update('sample', id_, update_data) | |
| print(ret) | |
| # break |
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