def test_valid_data():
validator = MetadataValidator('data/T2D_xls2xml_v1.schema')
reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx',
'data/T2D_xls2xml_v1.conf')
reader.active_worksheet = 'Sample'
row = reader.next()
assert validator.validate_data(row, 'Sample')
reader.active_worksheet = 'Analysis'
row = reader.next()
assert validator.validate_data(row, 'Analysis')
reader = TSVReader('data/example_samples.tsv', 'data/T2D_xls2xml_v1.conf',
'Sample')
row = reader.next()
assert validator.validate_data(row, 'Sample')
def test_next_row():
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx',
'data/T2D_xls2xml_v1.conf')
xls_reader.set_current_conf_key('Sample')
row = xls_reader.next()
assert isinstance(row, dict)
assert 0 == cmp(
row, {
'Hispanic or Latino; of Spanish origin': None,
'Phenotype': 'MeSH:D006262',
'row_num': 2,
'Description': 'Male normal',
'Center_name': 'WTGC cambridge',
'Case_Control': 'Control',
'T2D': 0L,
'Analysis_alias': 'AN001',
'Geno_ID': None,
'Year of first visit': None,
'Cell Type': 'Blood',
'Maternal_id': 'SAM111113',
'Gender': 'male',
'Subject_ID': 'SAM111111',
'Paternal_id': 'SAM111115',
'Cohort ID': 'CO1111',
'Novel Attributes': None,
'Ethnicity Description': None,
'Year of Birth': 1986L,
'Sample_ID': 'SAM111111',
'Age': 31L,
'Ethnicity': 'EUWH'
})
