def process_sample_sheet(sample_sheet):
"""Create a SequencingRun object for the specified sample sheet.
Arguments:
sample_sheet -- a `SampleSheet.csv` file that refers to an Illumina
MiSeq sequencing run.
Returns: an individual SequencingRun object for the sample sheet,
ready to be uploaded.
"""
try:
logging.info("going to parse metadata")
run_metadata = parse_metadata(sample_sheet)
logging.info("going to parse samples")
samples = complete_parse_samples(sample_sheet)
logging.info("going to build sequencing run")
sequencing_run = SequencingRun(run_metadata, samples, sample_sheet)
logging.info("going to validate sequencing run")
validate_run(sequencing_run)
send_message(DirectoryScannerTopics.run_discovered, run=sequencing_run)
return sequencing_run
except SampleSheetError, e:
logging.exception("Failed to parse sample sheet.")
send_message(DirectoryScannerTopics.garbled_sample_sheet,
sample_sheet=sample_sheet,
error=e)
def test_parse_metadata(self):
sheet_file = path.join(path_to_module, "fake_ngs_data",
"SampleSheet.csv")
meta_data = parse_metadata(sheet_file)
correct_metadata = {"readLengths": "251",
"assay": "Nextera XT",
"description": "Superbug",
"application": "FASTQ Only",
"investigatorName": "Some Guy",
"adapter": "AAAAGGGGAAAAGGGGAAA",
"workflow": "GenerateFASTQ",
"reversecomplement": "0",
"iemfileversion": "4",
"date": "10/15/2013",
"experimentName": "1",
"chemistry": "Amplicon",
"layoutType": "PAIRED_END"}
self.assertEqual(correct_metadata, meta_data)
def test_parse_metadata_extra_commas(self):
sheet_file = path.join(path_to_module, "testValidSheetTrailingCommas",
"SampleSheet.csv")
meta_data = parse_metadata(sheet_file)
correct_metadata = {"readLengths": "301",
"assay": "TruSeq HT",
"description": "252",
"application": "FASTQ Only",
"investigatorName": "Investigator",
"adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
"adapterread2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
"workflow": "GenerateFASTQ",
"reversecomplement": "0",
"iemfileversion": "4",
"date": "2015-11-12",
"experimentName": "252",
"chemistry": "Amplicon",
"layoutType": "PAIRED_END"}
self.assertEqual(correct_metadata, meta_data)
def test_parse_extra_metadata(self):
sample_sheet = path.join(path_to_module, 'extra-metadata', 'SampleSheet.csv')
# test that these parsers don't throw on unexpected sections or keys
metadata = parse_metadata(sample_sheet)
samples = complete_parse_samples(sample_sheet)
def test_super_invalid_sample_sheets(self):
with self.assertRaises(SampleSheetError):
parse_metadata(path.join(path_to_module, "super-invalid-sample-sheet", "SampleSheet.csv"))