def validate_run(sequencing_run):
"""Do the validation on a run, its samples, and files.
This function is kinda yucky because the validators should be raising
exceptions instead of returning validation objects...
Arguments:
sequencing_run -- the run to validate
"""
sample_sheet = sequencing_run.sample_sheet
validation = validate_sample_sheet(sequencing_run.sample_sheet)
if not validation.is_valid():
send_message(sequencing_run.offline_validation_topic,
run=sequencing_run,
errors=validation.get_errors())
raise SampleSheetError(
'Sample sheet {} is invalid. Reason:\n {}'.format(
sample_sheet, validation.get_errors()),
validation.error_list())
validation = validate_sample_list(sequencing_run.sample_list)
if not validation.is_valid():
raise SampleError(
'Sample sheet {} is invalid. Reason:\n {}'.format(
sample_sheet, validation.get_errors()),
validation.error_list())
def test_validateSampleList_invalid_empty(self):
sample_list = []
self.assertEqual(len(sample_list), 0)
v_res = validate_sample_list(sample_list)
self.assertFalse(v_res.is_valid())
self.assertEqual(v_res.error_count(), 1)
self.assertTrue(
"The given list of samples is empty" in v_res.get_errors())
def test_validate_sample_list_valid(self):
sample1 = Sample({
"sequencerSampleId": "01-1111",
"sampleName": "01-1111",
"Sample_Plate": "1",
"Sample_Well": "01",
"I7_Index_ID": "N01",
"index": "AAAAAAAA",
"I5_Index_ID": "S01",
"index2": "TTTTTTTT",
"sampleProject": "6",
"description": "Super bug"
})
sample2 = Sample({
"sequencerSampleId": "02-2222",
"sampleName": "02-2222",
"Sample_Plate": "2",
"Sample_Well": "02",
"I7_Index_ID": "N02",
"index": "GGGGGGGG",
"I5_Index_ID": "S02",
"index2": "CCCCCCCC",
"sampleProject": "6",
"description": "Scary bug"
})
sample3 = Sample({
"sequencerSampleId": "03-3333",
"sampleName": "03-3333",
"Sample_Plate": "3",
"Sample_Well": "03",
"I7_Index_ID": "N03",
"index": "CCCCCCCC",
"I5_Index_ID": "S03",
"index2": "GGGGGGGG",
"sampleProject": "6",
"description": "Deadly bug"
})
sample_list = [sample1, sample2, sample3]
v_res = validate_sample_list(sample_list)
self.assertTrue(v_res.is_valid())
self.assertEqual(v_res.error_count(), 0)
self.assertTrue("No error messages" in v_res.get_errors())
def test_validateSampleList_invalid_missing_req_values(self):
sample1 = Sample({
"sequencerSampleId": "01-1111",
"sampleName": "01-1111",
"Sample_Plate": "1",
"Sample_Well": "01",
"I7_Index_ID": "N01",
"index": "AAAAAAAA",
"I5_Index_ID": "S01",
"index2": "TTTTTTTT",
"sampleProject": "",
"description": "Super bug"
})
sample2 = Sample({
"sequencerSampleId": "02-2222",
"sampleName": "",
"Sample_Plate": "2",
"Sample_Well": "02",
"I7_Index_ID": "N02",
"index": "GGGGGGGG",
"I5_Index_ID": "S02",
"index2": "CCCCCCCC",
"sampleProject": "6",
"description": "Scary bug"
})
sample_list = [sample1, sample2]
v_res = validate_sample_list(sample_list)
self.assertFalse(v_res.is_valid())
self.assertEqual(v_res.error_count(), 2)
expected_err_msg1 = ("{sid} missing Project ID").format(
sid=sample1.get_id())
self.assertIn(expected_err_msg1, v_res.get_errors())
expected_err_msg2 = ("{sid} missing Sample Name").format(
sid=sample2.get_id())
self.assertIn(expected_err_msg2, v_res.get_errors())
def test_validate_sample_list_valid_empty_description(self):
sample = Sample({
"Sample_Well": "03",
"index": "CCCCCCCC",
"Sample_Plate": "3",
"I7_Index_ID": "N03",
"sampleName": "03-3333",
"sampleProject": "6",
"sequencerSampleId": "03-3333",
"I5_Index_ID": "S03",
"index2": "GGGGGGGG",
"description": ""
})
sample_list = [sample]
v_res = validate_sample_list(sample_list)
self.assertTrue(v_res.is_valid())
self.assertEqual(v_res.error_count(), 0)
self.assertTrue("No error messages" in v_res.get_errors())