def test_translate_ids_with_sample_id(self):
# Tests sample_id_to_specimen_id and specimen_id_to_sample_id when
# there is no specimen identifier set for the study
s = Study(1)
obs = s.sample_id_to_specimen_id('1.SKM4.640180')
self.assertEqual(obs, '1.SKM4.640180')
# doesn't even need to be a valid sample id
obs = s.sample_id_to_specimen_id('SKM3')
self.assertEqual(obs, 'SKM3')
with self.assertRaisesRegex(ValueError, 'Could not find "SKM4"'):
s.specimen_id_to_sample_id('SKM4')
with self.assertRaisesRegex(ValueError, 'Could not find "SSSS"'):
s.specimen_id_to_sample_id('SSSS')
def test_translate_ids_with_specimen_id(self):
s = Study(1)
# HACK: the Study object in labman can't modify specimen_id_column
# hence we do this directly in SQL, if a test fails the transaction
# will rollback, otherwise we reset the column to NULL.
sql = """UPDATE qiita.study
SET specimen_id_column = %s
WHERE study_id = 1"""
with sql_connection.TRN as TRN:
TRN.add(sql, ['anonymized_name'])
obs = s.sample_id_to_specimen_id('1.SKM4.640180')
self.assertEqual(obs, 'SKM4')
obs = s.specimen_id_to_sample_id('SKM4')
self.assertEqual(obs, '1.SKM4.640180')
# should be an exact match
with self.assertRaisesRegex(ValueError,
'Could not find \"1\.skm4\.640180\"'):
s.sample_id_to_specimen_id('1.skm4.640180')
with self.assertRaisesRegex(ValueError, 'Could not find \"skm4\"'):
s.specimen_id_to_sample_id('skm4')
# raise an error in the rare case that the specimen_id_column was
# set to something that's not unique (this could only accidentally
# happen)
TRN.add(sql, ['taxon_id'])
with self.assertRaisesRegex(
RuntimeError, 'There are several '
'matches found for "1118232"; there is'
' a problem with the specimen id '
'column'):
s.specimen_id_to_sample_id('1118232')
TRN.add(sql, [None])