def test_sample_from_row_invalid(self):
samples_file = test_data.open_biobank_samples(111, 222, 333)
reader = csv.DictReader(samples_file, delimiter='\t')
row = reader.next()
row[biobank_samples_pipeline._Columns.CONFIRMED_DATE] = '2016 11 19'
with self.assertRaises(biobank_samples_pipeline.DataError):
biobank_samples_pipeline._create_sample_from_row(
row, get_biobank_id_prefix())
def test_sample_from_row_wrong_prefix(self):
samples_file = test_data.open_biobank_samples(111, 222, 333)
reader = csv.DictReader(samples_file, delimiter='\t')
row = reader.next()
row[biobank_samples_pipeline._Columns.CONFIRMED_DATE] = '2016 11 19'
self.assertIsNone(
biobank_samples_pipeline._create_sample_from_row(row, 'Q'))
def test_sample_from_row_old_test(self):
samples_file = test_data.open_biobank_samples(111, 222, 333)
reader = csv.DictReader(samples_file, delimiter='\t')
row = reader.next()
row[biobank_samples_pipeline._Columns.TEST_CODE] = '2PST8'
sample = biobank_samples_pipeline._create_sample_from_row(
row, get_biobank_id_prefix())
self.assertIsNotNone(sample)
cols = biobank_samples_pipeline._Columns
self.assertEquals(sample.biobankStoredSampleId, row[cols.SAMPLE_ID])
self.assertEquals(sample.test, row[cols.TEST_CODE])
def test_sample_from_row(self):
samples_file = test_data.open_biobank_samples(112, 222, 333)
reader = csv.DictReader(samples_file, delimiter='\t')
row = reader.next()
sample = biobank_samples_pipeline._create_sample_from_row(
row, get_biobank_id_prefix())
self.assertIsNotNone(sample)
cols = biobank_samples_pipeline._Columns
self.assertEquals(sample.biobankStoredSampleId, row[cols.SAMPLE_ID])
self.assertEquals(to_client_biobank_id(sample.biobankId),
row[cols.EXTERNAL_PARTICIPANT_ID])
self.assertEquals(sample.test, row[cols.TEST_CODE])
confirmed_date = self._naive_utc_to_naive_central(sample.confirmed)
self.assertEquals(
confirmed_date.strftime(
biobank_samples_pipeline._INPUT_TIMESTAMP_FORMAT),
row[cols.CONFIRMED_DATE])
received_date = self._naive_utc_to_naive_central(sample.created)
self.assertEquals(
received_date.strftime(
biobank_samples_pipeline._INPUT_TIMESTAMP_FORMAT),
row[cols.CREATE_DATE])
