def test_parse_metadata_paired_valid(self, mock_csv_reader):
"""
When given a valid directory, ensure valid metadata is built
paired end reads
:return:
"""
h_field_values = ("IEMFileVersion,4\n"
"Investigator Name,Test Name\n"
"Experiment Name,Some_Test_Data\n"
"Date,2015-05-14\n"
"Workflow,GenerateFASTQ\n"
"Application,FASTQ Only\n"
"Assay,ASDF\n"
"Description,12-34\n"
"Chemistry,Yes\n")
reads = ("251\n" "251\n")
d_headers = ("Sample_ID,Sample_Name,Sample_Plate,Sample_Well,"
"I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,"
"Description")
d_field_values = (
"15-0318,,2015-08-05-SE,A01,N701,TAAGGCGA,S502,CTCTCTAT,203\n"
"15-0455,,2015-08-05-SE,B01,N701,TAAGGCGA,S503,TATCCTCT,203\n"
"15-0462,,2015-08-05-SE,C01,N701,TAAGGCGA,S505,GTAAGGAG,203\n")
file_contents_str = ("[Header]\n"
"{h_field_values}\n"
"[Reads]\n"
"{reads}\n"
"[Data]\n"
"{d_headers}\n"
"{d_field_values}").format(
h_field_values=h_field_values,
reads=reads,
d_headers=d_headers,
d_field_values=d_field_values)
# converts string as a pseudo file / memory file
sample_sheet_file = StringIO(file_contents_str)
# the call to get_csv_reader() inside parse_samples() will return
# items inside side_effect
mock_csv_reader.side_effect = [reader(sample_sheet_file)]
metadata = sample_parser.parse_metadata(None)
# The meta data we care about the most
self.assertEqual(metadata['readLengths'], "251")
self.assertEqual(metadata['layoutType'], "PAIRED_END")
# Other meta data should also be here
self.assertEqual(metadata['iemfileversion'], "4")
self.assertEqual(metadata['investigatorName'], "Test Name")
self.assertEqual(metadata['experimentName'], "Some_Test_Data")
self.assertEqual(metadata['date'], "2015-05-14")
self.assertEqual(metadata['workflow'], "GenerateFASTQ")
self.assertEqual(metadata['application'], "FASTQ Only")
self.assertEqual(metadata['assay'], "ASDF")
self.assertEqual(metadata['description'], "12-34")
self.assertEqual(metadata['chemistry'], "Yes")
def test_parse_metadata(self):
"""
Testing the parsing meta data with actual files, instead of mocked files
:return:
"""
sheet_file = path.join(path_to_module, "fake_ngs_data",
"SampleSheet.csv")
meta_data = sample_parser.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):
"""
Tests parsing meta data when extra commas are in the file
Testing the parsing meta data with actual files, instead of mocked files
:return:
"""
sheet_file = path.join(path_to_module, "testValidSheetTrailingCommas",
"SampleSheet.csv")
meta_data = sample_parser.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 get_sequencing_run(sample_sheet,
run_data_directory=None,
run_data_directory_file_list=None):
"""
Does local validation on the integrety of the run directory / sample sheet
Throws a ValidationError with a valadation result attached if it cannot make a sequencing run
:param sample_sheet: Sample Sheet File
:param run_data_directory: Optional: Directory (including run directory) to data files.
Can be provided for bypassing os calls when developing on cloud systems
:param run_data_directory_file_list: Optional: List of files in data directory.
Can be provided for bypassing os calls when developing on cloud systems
:return: SequencingRun
"""
# get data directory and file list
validation_result = model.ValidationResult()
try:
if run_data_directory is None:
run_data_directory = Parser.get_full_data_directory(
sample_sheet)
if run_data_directory_file_list is None:
run_data_directory_file_list = common.get_file_list(
run_data_directory)
except exceptions.DirectoryError as error:
validation_result.add_error(error)
logging.error("Errors occurred while parsing files")
raise exceptions.ValidationError(
"Errors occurred while parsing files", validation_result)
# Try to get the sample sheet, validate that the sample sheet is valid
validation_result = validation.validate_sample_sheet(sample_sheet)
if not validation_result.is_valid():
logging.error("Errors occurred while getting sample sheet")
raise exceptions.ValidationError(
"Errors occurred while getting sample sheet",
validation_result)
# Try to parse the meta data from the sample sheet, throw validation error if errors occur
validation_result = model.ValidationResult()
try:
run_metadata = sample_parser.parse_metadata(sample_sheet)
except exceptions.SampleSheetError as error:
validation_result.add_error(error)
logging.error("Errors occurred while parsing metadata")
raise exceptions.ValidationError(
"Errors occurred while parsing metadata", validation_result)
# Try to build sequencing run from sample sheet & meta data, raise validation error if errors occur
try:
sample_list = sample_parser.parse_sample_list(
sample_sheet, run_data_directory, run_data_directory_file_list)
sequencing_run = common.build_sequencing_run_from_samples(
sample_list, run_metadata)
except exceptions.SequenceFileError as error:
validation_result.add_error(error)
logging.error(
"Errors occurred while building sequence run from sample sheet"
)
raise exceptions.ValidationError(
"Errors occurred while building sequence run from sample sheet",
validation_result)
return sequencing_run