def test_validate_file():
validation_schema = 'data/T2D_xls2xml_v1.schema'
tsv_reader = TSVReader('data/example_samples.tsv', 'data/T2D_xls2xml_v1.conf', 'Sample')
assert utils.validate_file(tsv_reader, validation_schema)
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
xls_reader.set_current_conf_key('Sample')
assert utils.validate_file(xls_reader, validation_schema)
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'
})
def test_set_current_conf_key():
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx',
'data/T2D_xls2xml_v1.conf')
active_worksheet = xls_reader.active_worksheet
assert active_worksheet is None
xls_reader.set_current_conf_key('Sample')
active_worksheet = xls_reader.active_worksheet
assert active_worksheet == 'Sample'
xls_reader.set_current_conf_key('Analysis')
active_worksheet = xls_reader.active_worksheet
assert active_worksheet == 'Analysis'
def test_get_current_headers():
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx',
'data/T2D_xls2xml_v1.conf')
xls_reader.set_current_conf_key('Sample')
headers = xls_reader.get_current_headers()
assert isinstance(headers, list)
assert set(headers) == {
u'Sample_ID', u'Subject_ID', u'Geno_ID', u'Phenotype', u'Gender',
u'Analysis_alias', u'Cohort ID', u'Ethnicity',
u'Ethnicity Description', u'T2D', u'Case_Control', u'Description',
u'Center_name', u'Hispanic or Latino; of Spanish origin', u'Age',
u'Year of Birth', u'Year of first visit', u'Cell Type', u'Maternal_id',
u'Paternal_id', u'Novel Attributes'
}
xls_reader.set_current_conf_key('Analysis')
headers = xls_reader.get_current_headers()
assert isinstance(headers, list)
assert set(headers) == {
u'Analysis_name', u'Analysis_alias', u'Title', u'Description',
u'Project_name', u'Experiment_type', u'Platform',
u'Standard_refname or Sequence_accession', u'Imputation',
u'Sequence_accession_label', u'External_link', u'Software',
u'Pipeline Description', u'Run Accession(s)', u'Center_name',
u'Analysis_date'
}
xls_reader.set_current_conf_key('ExceptionExpected')
with pytest.raises(Exception):
xls_reader.get_current_headers()
def test_extract_rows():
validation_schema = 'data/T2D_xls2xml_v1.schema'
rows = []
tsv_reader = TSVReader('data/example_samples.tsv', 'data/T2D_xls2xml_v1.conf', 'Sample')
assert utils.extract_rows(tsv_reader, 'Sample', validation_schema, rows)
assert isinstance(rows, list)
assert 6 == len(rows)
tsv_reader = TSVReader('data/example_samples.tsv', 'data/T2D_xls2xml_v1.conf', 'Sample')
for a, b in zip(rows, tsv_reader):
assert 0 == cmp(a, b)
rows = []
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
assert utils.extract_rows(xls_reader, 'Sample', validation_schema, rows)
assert isinstance(rows, list)
assert 6 == len(rows)
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
xls_reader.set_current_conf_key('Sample')
for a, b in zip(rows, xls_reader):
assert 0 == cmp(a, b)
rows = []
assert not utils.extract_rows(xls_reader, 'FalseExpected', validation_schema, rows)
