def test_clean_and_reformat_mapping_allpgp(self):
"""Exercise the reformat mapping code, verify expected results"""
out = StringIO()
reformat_mapping_testdata.seek(0)
clean_and_reformat_mapping(reformat_mapping_testdata, out, 'body_site',
'test')
out.seek(0)
# verify the resulting header structure
test_mapping = [l.strip().split('\t') for l in out]
test_header = test_mapping[0]
self.assertEqual(test_header[-4:], ['SIMPLE_BODY_SITE',
'TITLE_ACRONYM', 'TITLE_BODY_SITE',
'HMP_SITE'])
self.assertEqual(test_mapping[1][:], ['A', 'w00t', '43.0',
'UBERON_mucosa_of_tongue', '5',
'ORAL', 'test', 'test-ORAL',
'ORAL'])
self.assertEqual(test_mapping[2][:], ['B', 'left', '51.0',
'UBERON:FECES', '10',
'FECAL', 'test', 'test-FECAL',
'FECAL'])
self.assertEqual(test_mapping[3][:], ['C', 'right', '12.0',
'UBERON_FECES', '15',
'FECAL', 'test', 'test-FECAL',
'FECAL'])
self.assertEqual(test_mapping[4][:], ['E', 'stuff', '56.0',
'UBERON:SKIN', '37',
'SKIN', 'test', 'test-SKIN',
'SKIN'])
def test_clean_and_reformat_mapping_allpgp(self):
"""Exercise the reformat mapping code, verify expected results"""
out = StringIO()
reformat_mapping_testdata.seek(0)
clean_and_reformat_mapping(reformat_mapping_testdata, out, 'body_site',
'test')
out.seek(0)
# verify the resulting header structure
test_mapping = [l.strip().split('\t') for l in out]
test_header = test_mapping[0]
self.assertEqual(test_header[-4:], [
'SIMPLE_BODY_SITE', 'TITLE_ACRONYM', 'TITLE_BODY_SITE', 'HMP_SITE'
])
self.assertEqual(test_mapping[1][:], [
'A', 'w00t', '43.0', 'UBERON_mucosa_of_tongue', '5', 'ORAL',
'test', 'test-ORAL', 'ORAL'
])
self.assertEqual(test_mapping[2][:], [
'B', 'left', '51.0', 'UBERON:FECES', '10', 'FECAL', 'test',
'test-FECAL', 'FECAL'
])
self.assertEqual(test_mapping[3][:], [
'C', 'right', '12.0', 'UBERON_FECES', '15', 'FECAL', 'test',
'test-FECAL', 'FECAL'
])
self.assertEqual(test_mapping[4][:], [
'E', 'stuff', '56.0', 'UBERON:SKIN', '37', 'SKIN', 'test',
'test-SKIN', 'SKIN'
])