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pydantic model udpates #217

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Merged
lopierra merged 1 commit into from
Dec 4, 2024
Merged

pydantic model udpates #217

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4 changes: 2 additions & 2 deletions src/data_validation/validate_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ def validate_dataset_entry(row):
expectedNumberOfFiles=handle_nan(row['expected number of files']),
dataCollectionStartYear=handle_nan(row['data collection start year']),
dataCollectionEndYear=handle_nan(row['data collection end year']),
dataCategory=row['data category'],
dataType=handle_nan(row['data type']),
dataCategory=row['data category'].split('|') if handle_nan(row['data category']) else [],
dataType=row['data type'].split('|') if handle_nan(row['data type']) else [],
experimentalStrategy=row['experimental strategy'].split('|') if handle_nan(row['experimental strategy']) else [],
experimentalPlatform=row['experimental platform'].split('|') if handle_nan(row['experimental platform']) else [],
publication=row['publication'].split('|') if handle_nan(row['publication']) else [],
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1 change: 1 addition & 0 deletions src/data_validation/validate_study.py
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Expand Up @@ -28,6 +28,7 @@ def validate_study_entry(row):
publication = str(row['publication']).split('|') if handle_nan(row['publication']) else [],
expectedNumberOfParticipants = handle_nan(row['expected number of participants']),
guidType = row['guid type'],
guidMapped = bool(row['guids mapped?']),
acknowledgments = row['acknowledgments'].split('|') if handle_nan(row['acknowledgments']) else [],
citationStatement = row['citation statement'].split('|') if handle_nan(row['citation statement']) else []
)
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4 changes: 2 additions & 2 deletions src/data_validation/validation.py
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Expand Up @@ -10,7 +10,7 @@

def validate_study(file_path, output_path='.'):
string_columns = ['study code', 'program', 'research domain', 'participant lifespan stage',
'clinical data source type', 'data category', 'guid type']
'study design', 'clinical data source type', 'data category', 'guid type']
return validate_data(file_path, string_columns, validate_study_entry, output_path)


Expand All @@ -36,7 +36,7 @@ def validate_datafile(file_path, output_path='.'):


def validate_dataset(file_path, output_path='.'):
string_columns = ['study code', 'data category', 'data access']
string_columns = ['study code', 'data category']
return validate_data(file_path, string_columns, validate_dataset_entry, output_path)


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