def validate_file_of_sample_dirs(sample_dirs_file):
"""Verify each of the sample directories in the sample directory file is not empty and contains fastq's.
Parameters
----------
sample_dirs_file : str
Path to the file of sample directories
"""
found_error = False
with open(sample_dirs_file) as f:
for directory in f:
directory = directory.strip()
if not utils.verify_non_empty_directory("Sample directory", directory):
found_error = True
else:
files = fastq.list_fastq_files(directory)
if len(files) == 0:
utils.report_error("Sample directory %s does not contain any fastq files." % directory)
found_error = True
if found_error:
if os.environ.get("StopOnSampleError") == "true":
sys.exit(1)
else:
log_error("================================================================================")
def validate_file_of_sample_dirs(sample_dirs_file):
"""Verify each of the sample directories in the sample directory file is not empty and contains fastq's.
Parameters
----------
sample_dirs_file : str
Path to the file of sample directories
"""
found_error = False
with open(sample_dirs_file) as f:
for directory in f:
directory = directory.strip()
if not utils.verify_non_empty_directory("Sample directory",
directory):
found_error = True
else:
files = fastq.list_fastq_files(directory)
if len(files) == 0:
utils.report_error(
"Sample directory %s does not contain any fastq files."
% directory)
found_error = True
if found_error:
if os.environ.get("StopOnSampleError") == "true":
sys.exit(1)
else:
log_error(
"================================================================================"
)
def handle_called_process_exception(exc_type, exc_value, exc_traceback):
"""This function handles exceptions in the child processes executed by
the snp-pipeline.
It Logs the error and exits the SNP Pipeline if configured to do so.
"""
global log_dir
external_program_command = exc_value.cmd
error_code = exc_value.returncode
trace_entries = traceback.extract_tb(exc_traceback)
file_name, line_number, function_name, code_text = trace_entries[-1]
exc_type_name = exc_type.__name__
stop_on_error_env = os.environ.get("StopOnSampleError")
stop_on_error = stop_on_error_env is None or stop_on_error_env == "true"
error_output_file = os.environ.get("errorOutputFile")
# Error code 98 indicates an error affecting a single sample when the pipeline is configured to ignore such errors.
# This error has already been reported, but it should not stop execution.
if error_code == 98 and not stop_on_error:
return
# When configured to ignore single-sample errors, try to continue execution if
# xargs returns 123 when executing an array of jobs, one per sample
if error_code == 123 and not stop_on_error:
return
# A subprocess failed and was already trapped.
# Actually, we cannot be 100% certain the error was trapped if the error code is 123. This
# indicates an error in an array of sample jobs launched in parallel by xargs; but since
# StopOnSampleError is true, we will assume the error was already trapped.
if error_code == 100 or (stop_on_error and error_code == 123):
log_error("See also the log files in directory " + log_dir)
log_error("Shutting down the SNP Pipeline.")
log_error("================================================================================")
# Send the error log contents to stderr
if error_output_file:
with open(error_output_file, "r") as err_log:
shutil.copyfileobj(err_log, sys.stderr)
sys.exit(1)
# An error occured and was not already trapped.
# Error code 98 indicates an already handled error affecting a single sample when the pipeline is configured to ignore such errors
if error_code != 98:
external_program_command = external_program_command.replace("set -o pipefail; ", "")
log_error("Error detected while running " + utils.program_name_with_command())
log_error("")
log_error("The error occured while running:")
log_error(" %s" % external_program_command)
log_error("")
log_error("Shutting down the SNP Pipeline.")
log_error("================================================================================")
# Send the error log contents to stderr
if error_output_file:
with open(error_output_file, "r") as err_log:
shutil.copyfileobj(err_log, sys.stderr)
sys.exit(1)
def handle_called_process_exception(exc_type, exc_value, exc_traceback):
"""This function handles exceptions in the child processes executed by
the snp-pipeline.
It Logs the error and exits the SNP Pipeline if configured to do so.
"""
global log_dir
external_program_command = exc_value.cmd
error_code = exc_value.returncode
trace_entries = traceback.extract_tb(exc_traceback)
file_name, line_number, function_name, code_text = trace_entries[-1]
exc_type_name = exc_type.__name__
stop_on_error_env = os.environ.get("StopOnSampleError")
stop_on_error = stop_on_error_env is None or stop_on_error_env == "true"
error_output_file = os.environ.get("errorOutputFile")
# Error code 98 indicates an error affecting a single sample when the pipeline is configured to ignore such errors.
# This error has already been reported, but it should not stop execution.
if error_code == 98 and not stop_on_error:
return
# When configured to ignore single-sample errors, try to continue execution if
# xargs returns 123 when executing an array of jobs, one per sample
if error_code == 123 and not stop_on_error:
return
# A subprocess failed and was already trapped.
# Actually, we cannot be 100% certain the error was trapped if the error code is 123. This
# indicates an error in an array of sample jobs launched in parallel by xargs; but since
# StopOnSampleError is true, we will assume the error was already trapped.
if error_code == 100 or (stop_on_error and error_code == 123):
log_error("See also the log files in directory " + log_dir)
log_error("Shutting down the SNP Pipeline.")
log_error(
"================================================================================"
)
# Send the error log contents to stderr
if error_output_file:
with open(error_output_file, "r") as err_log:
shutil.copyfileobj(err_log, sys.stderr)
sys.exit(1)
# An error occured and was not already trapped.
# Error code 98 indicates an already handled error affecting a single sample when the pipeline is configured to ignore such errors
if error_code != 98:
external_program_command = external_program_command.replace(
"set -o pipefail; ", "")
log_error("Error detected while running " +
utils.program_name_with_command())
log_error("")
log_error("The error occured while running:")
log_error(" %s" % external_program_command)
log_error("")
log_error("Shutting down the SNP Pipeline.")
log_error(
"================================================================================"
)
# Send the error log contents to stderr
if error_output_file:
with open(error_output_file, "r") as err_log:
shutil.copyfileobj(err_log, sys.stderr)
sys.exit(1)