Пример #1
0
    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')
Пример #2
0
    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])