def _dispatch(modules, arguments):
try:
command, args = _parse_command_line_args(modules, arguments)
execution_context = _get_execution_context(arguments)
logger.initialize_logger(args)
logger.debug("Jacquard run begins")
logger.debug("cwd|{}", os.getcwd())
logger.debug("command|{}", " ".join(arguments))
command_validator.preflight(command, args)
logger.info("Jacquard begins (v{})", __version__)
logger.info("Saving log to [{}]",
os.path.basename(logger.log_filename))
logger.debug("Writing output to tmp directory [{}]",
args.temp_working_dir)
command.execute(args, execution_context)
_move_tmp_contents_to_original(args)
if logger.WARNING_OCCURRED:
logger.info("Done. (See warnings above)")
else:
logger.info("Done")
except utils.UsageError as usage_error:
message = "Jacquard usage problem: {}".format(str(usage_error))
logger.debug(message)
print(message, file=sys.stderr)
try:
print("See 'jacquard {} --help'.".format(args.subparser_name),
file=sys.stderr)
except NameError: #could not determine the command
print("See 'jacquard --help'.", file=sys.stderr)
sys.exit(1)
except Exception as exception: #pylint: disable=broad-except
logger.error(str(exception))
logger.error("Jacquard encountered an unanticipated problem. "
"Please review log file and contact your sysadmin "
"or Jacquard support for assistance.")
logger.debug(traceback.format_exc())
sys.exit(1)
finally:
try:
_cleanup(args.temp_working_dir)
except Exception: #pylint: disable=broad-except
pass #we tried
def _dispatch(modules, arguments):
try:
command, args = _parse_command_line_args(modules, arguments)
execution_context = _get_execution_context(arguments)
logger.initialize_logger(args)
logger.debug("Jacquard run begins")
logger.debug("cwd|{}", os.getcwd())
logger.debug("command|{}", " ".join(arguments))
command_validator.preflight(command, args)
logger.info("Jacquard begins (v{})", __version__)
logger.info("Saving log to [{}]",
os.path.basename(logger.log_filename))
logger.debug("Writing output to tmp directory [{}]",
args.temp_working_dir)
command.execute(args, execution_context)
_move_tmp_contents_to_original(args)
if logger.WARNING_OCCURRED:
logger.info("Done. (See warnings above)")
else:
logger.info("Done")
except utils.UsageError as usage_error:
message = "Jacquard usage problem: {}".format(str(usage_error))
logger.debug(message)
print(message, file=sys.stderr)
try:
print("See 'jacquard {} --help'.".format(args.subparser_name),
file=sys.stderr)
except NameError: #could not determine the command
print("See 'jacquard --help'.", file=sys.stderr)
sys.exit(1)
except Exception as exception: #pylint: disable=broad-except
logger.error(str(exception))
logger.error("Jacquard encountered an unanticipated problem. "
"Please review log file and contact your sysadmin "
"or Jacquard support for assistance.")
logger.debug(traceback.format_exc())
sys.exit(1)
finally:
try:
_cleanup(args.temp_working_dir)
except Exception: #pylint: disable=broad-except
pass #we tried
def _check_snp_indel_pairings(altered_file_names, args):
if not set([len(i) for i in altered_file_names.values()]) == set([1]):
if not args.allow_inconsistent_sample_sets:
error = 0
for file_names in altered_file_names.values():
if len(file_names) % 2 != 0:
message = ("File {} was missing a "
"corresponding snp/indel file.")
logger.error(message, file_names)
error = 1
if error:
message = ("Not all patients were represented by the same set "
"of caller-VCFs. Review inputs/command options to "
"align file pairings or use the flag "
"--allow_inconsistent_sample_sets.")
raise utils.UsageError(message)
def _check_snp_indel_pairings(altered_file_names, args):
if not set([len(i) for i in altered_file_names.values()]) == set([1]):
if not args.allow_inconsistent_sample_sets:
error = 0
for file_names in altered_file_names.values():
if len(file_names) % 2 != 0:
message = ("File {} was missing a "
"corresponding snp/indel file.")
logger.error(message, file_names)
error = 1
if error:
message = ("Not all patients were represented by the same set "
"of caller-VCFs. Review inputs/command options to "
"align file pairings or use the flag "
"--allow_inconsistent_sample_sets.")
raise utils.UsageError(message)
def test_error(self):
tool = "foo"
args = Namespace(subparser_name=tool, log_file=None, verbose=None)
logger.initialize_logger(args)
logger.error("bar")
root_logger = logger.logging.getLogger()
current_time = datetime.now().strftime('%Y-%m-%d')
output_lines = self.output.getvalue().rstrip().split("\n")
##nosetests overwrites logger.FileHandler
self.assertEquals(["root: ERROR: bar"], root_logger.handlers[0].buffer)
self.assertRegexpMatches(output_lines[0],
"" + current_time + r".*\|ERROR\|foo\|bar")
def _validate_vcf_readers(prefix_by_patients):
number_of_files = set()
for file_names in prefix_by_patients.values():
if len(file_names) == 1:
for file_name in file_names:
if re.search("snp", file_name):
msg = "VarScan VCF [{}] has no indel file."
logger.error(msg, file_name)
elif re.search("indel", file_name):
msg = "VarScan VCF [{}] has no snp file."
logger.error(msg, file_name)
number_of_files.add(len(file_names))
if len(number_of_files) > 1:
msg = ("Some Varscan VCFs were missing either a snp or indel file. "
"Review inputs/command options and try again.")
raise utils.JQException(msg)
def test_error(self):
tool = "foo"
args = Namespace(subparser_name=tool,
log_file=None,
verbose=None)
logger.initialize_logger(args)
logger.error("bar")
root_logger = logger.logging.getLogger()
current_time = datetime.now().strftime('%Y-%m-%d')
output_lines = self.output.getvalue().rstrip().split("\n")
##nosetests overwrites logger.FileHandler
self.assertEquals(["root: ERROR: bar"], root_logger.handlers[0].buffer)
self.assertRegexpMatches(output_lines[0], ""+current_time+r".*\|ERROR\|foo\|bar")
def _validate_vcf_readers(prefix_by_patients):
number_of_files = set()
for file_names in prefix_by_patients.values():
if len(file_names) == 1:
for file_name in file_names:
if re.search("snvs", file_name):
msg = "Strelka VCF [{}] has no indels file."
logger.error(msg, file_name)
elif re.search("indels", file_name):
msg = "Strelka VCF [{}] has no snvs file."
logger.error(msg, file_name)
number_of_files.add(len(file_names))
if len(number_of_files) > 1:
msg = ("Some Strelka VCFs were missing either a snvs or indels "
"file. Review inputs/command options and try again.")
raise utils.JQException(msg)
