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' })