def test_no_reverse_read(self):
"""
The file list in the sample sheet is invalid
:return:
"""
directory = path.join(path_to_module, "fake_dir_data")
file_path = path.join(directory, "list_no_reverse.csv")
with self.assertRaises(SampleSheetError):
res = sample_parser.parse_sample_list(file_path, directory)
def test_no_forward_read(self):
"""
No Valid files were found with names given in sample sheet
:return:
"""
directory = path.join(path_to_module, "fake_dir_data")
file_path = path.join(directory, "list_no_forward.csv")
with self.assertRaises(SampleSheetError):
res = sample_parser.parse_sample_list(file_path, directory)
def get_sequencing_run(sample_sheet, run_data_directory_file_list=None):
"""
Does local validation on the integrity of the run directory / sample sheet
Throws a ValidationError with a validation result attached if it cannot make a sequencing run
:param sample_sheet:
:return: SequencingRun
"""
# get file list
validation_result = model.ValidationResult()
try:
if run_data_directory_file_list is None:
data_dir = os.path.dirname(sample_sheet)
run_data_directory_file_list = common.get_file_list(data_dir)
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 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_file_list)
run_metadata = sample_parser.parse_metadata(sample_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
def test_valid_full_file_path(self, mock_parse_samples):
"""
Given a valid sample sheet with full file paths, parse correctly
:return:
"""
sheet_file = path.join(path_to_module, "fake_dir_data",
"SampleList_simple.csv")
file_path_1 = path.join(path_to_module,
"fake_dir_data", "file_1.fastq.gz")
file_path_2 = path.join(path_to_module,
"fake_dir_data", "file_2.fastq.gz")
sample_list = [
model.Sample(
sample_name='my-sample-1',
description="",
sample_number=0,
samp_dict={
('sample_project', '75'),
('File_Forward', path.abspath(file_path_1)),
('File_Reverse', path.abspath(file_path_2))
}
)
]
mock_parse_samples.return_value = sample_list
run_data_directory_file_list = ["file_1.fastq.gz", "file_2.fastq.gz"]
res = sample_parser.parse_sample_list(sheet_file, run_data_directory_file_list)
mock_parse_samples.assert_called_with(sheet_file)
# Check we have 1 sample
self.assertEqual(len(res), 1)
# Check if data is correct
self.assertEqual(res[0].sample_name, "my-sample-1")
self.assertEqual(res[0].get_uploadable_dict()["sample_project"], "75")
self.assertEqual(res[0].get_uploadable_dict()["File_Forward"], path.abspath(file_path_1))
self.assertEqual(res[0].get_uploadable_dict()["File_Reverse"], path.abspath(file_path_2))
def test_valid(self):
"""
Given a valid sample sheet, parse correctly
:return:
"""
sheet_file = path.join(path_to_module, "fake_dir_data",
"SampleList_simple.csv")
file_path_1 = path.join(path_to_module,
"fake_dir_data", "file_1.fastq.gz")
file_path_2 = path.join(path_to_module,
"fake_dir_data", "file_2.fastq.gz")
run_data_directory_file_list = ["file_1.fastq.gz", "file_2.fastq.gz"]
res = sample_parser.parse_sample_list(sheet_file, run_data_directory_file_list)
# Check we have 1 sample
self.assertEqual(len(res), 1)
# Check if data is correct
self.assertEqual(res[0].sample_name, "my-sample-1")
self.assertEqual(res[0].get_uploadable_dict()["sample_project"], "75")
self.assertEqual(res[0].get_uploadable_dict()["File_Forward"], "file_1.fastq.gz")
self.assertEqual(res[0].get_uploadable_dict()["File_Reverse"], "file_2.fastq.gz")
def test_mixed_paired_and_single_reads(self):
directory = path.join(path_to_module, "fake_dir_data")
file_path = path.join(directory, "list_mixed.csv")
with self.assertRaises(SampleSheetError):
res = sample_parser.parse_sample_list(file_path, directory)