def test_write_empty_xml():
rows = []
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
assert utils.extract_rows(xls_reader, 'File', 'data/T2D_xls2xml_v1.schema', rows)
input_xml = utils.rows_to_xml(rows, 'File')
transformed_xml = utils.transform_xml(input_xml, 'data/T2D_xls2xml_v1.xslt')
assert transformed_xml.getroot() is None # to make sure the transformed_xml is empty
with open('data/out_empty.xml', 'w') as xml_file:
utils.save_xml(transformed_xml, xml_file)
def test_transform_xml():
rows = []
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
assert utils.extract_rows(xls_reader, 'Sample', 'data/T2D_xls2xml_v1.schema', rows)
input_xml = utils.rows_to_xml(rows, 'Sample')
output_xml = utils.transform_xml(input_xml, 'data/T2D_xls2xml_v1.xslt')
with open('data/example_samples.xml') as example_xml:
assert example_xml.readline() == "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
assert etree.tostring(output_xml, pretty_print=True) == example_xml.read()
def test_save_xml():
rows = []
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
assert utils.extract_rows(xls_reader, 'Sample', 'data/T2D_xls2xml_v1.schema', rows)
input_xml = utils.rows_to_xml(rows, 'Sample')
transformed_xml = utils.transform_xml(input_xml, 'data/T2D_xls2xml_v1.xslt')
io_stream = StringIO()
utils.save_xml(transformed_xml, io_stream)
io_stream.seek(0)
assert io_stream.read() == open('data/example_samples.xml').read()
io_stream.close()
def test_rows_to_xml():
rows = []
xls_reader = XLSReader('data/example_AMP_T2D_Submission_form_V2.xlsx', 'data/T2D_xls2xml_v1.conf')
assert utils.extract_rows(xls_reader, 'Sample', 'data/T2D_xls2xml_v1.schema', rows)
xml = utils.rows_to_xml(rows, 'Sample')
assert isinstance(xml, etree._Element)
assert xml.tag == 'SampleSet'
assert len(rows) == len(xml)
for row, child in zip(rows, xml):
assert child.tag == 'Sample'
assert {header : str(row.get(header, '')) for header in row} !=\
{e.tag: e.text for e in child}
assert {utils.header_to_xml_tag(header) : str('' if row.get(header, '') is None else row.get(header, ''))
for header in row} == {e.tag : e.text for e in child}
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)