def get_sample_sheet(directory):
"""
gets the sample sheet file path from a given run directory
:param directory:
:return:
"""
logging.info("Looking for sample sheet in {}".format(directory))
# Checks if we can access to the given directory, return empty and log a warning if we cannot.
if not os.access(directory, os.W_OK):
logging.error((
"The directory is not accessible, can not parse samples from this directory {}"
"".format(directory), directory))
raise exceptions.DirectoryError(
"The directory is not accessible, "
"can not parse samples from this directory {}".format(
directory), directory)
sample_sheet_file_name = Parser.SAMPLE_SHEET_FILE_NAME
file_list = common.get_file_list(directory)
if sample_sheet_file_name not in file_list:
logging.error(
"No sample sheet file in the Directory Upload format found")
raise exceptions.DirectoryError(
"The directory {} has no sample sheet file in the Directory Upload format "
"with the name {}"
"".format(directory, sample_sheet_file_name), directory)
else:
logging.debug("Sample sheet found")
return os.path.join(directory, sample_sheet_file_name)
def build_sample_list_from_sample_sheet_with_abs_path(sample_sheet_file):
"""
Create a list of Sample objects, where each SequenceFile object has an absolute file path
:param sample_sheet_file:
:return:
"""
sample_list = _parse_samples(sample_sheet_file)
# Data directory is used if file names on sample sheet are not absolute paths (in directory files)
data_dir = path.dirname(sample_sheet_file)
sample_sheet_dir_file_list = common.get_file_list(data_dir)
for sample in sample_list:
sample_dict = sample.get_uploadable_dict()
paired_end_read = len(sample_dict['File_Reverse']) > 0
# create file list of full paths
file_list = []
# If file is not an abspath already, make it an abspath from filename + data dir
if path.isabs(sample_dict['File_Forward']):
file_list.append(sample_dict['File_Forward'])
elif sample_dict['File_Forward'] in sample_sheet_dir_file_list:
sample_dict['File_Forward'] = path.join(
path.abspath(data_dir), sample_dict['File_Forward'])
file_list.append(sample_dict['File_Forward'])
else:
raise exceptions.SampleSheetError((
"Your sample sheet is malformed. {} Does not match any file in the directory {}"
"".format(sample_dict['File_Forward'], data_dir)),
sample_sheet_file)
# reverse file is same as for forward file
if paired_end_read:
if path.isabs(sample_dict['File_Reverse']):
file_list.append(sample_dict['File_Reverse'])
elif sample_dict['File_Reverse'] in sample_sheet_dir_file_list:
sample_dict['File_Reverse'] = path.join(
path.abspath(data_dir), sample_dict['File_Reverse'])
file_list.append(sample_dict['File_Reverse'])
else:
raise exceptions.SampleSheetError((
"Your sample sheet is malformed. {} Does not match any file in the directory {}"
"".format(sample_dict['File_Reverse'], data_dir)),
sample_sheet_file)
# Create sequence file object and attach to sample
sq = model.SequenceFile(file_list=file_list)
sample.sequence_file = deepcopy(sq)
return sample_list
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 get_sequencing_run(self,
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, self.get_parser_type_name())
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
