def run_wrapper(run, input, output, params, wildcards, threads, resources, log, linemaps):
"""
Wrapper around the run method that handles directory creation and
output file deletion on error.
Arguments
run -- the run method
input -- list of input files
output -- list of output files
wildcards -- so far processed wildcards
threads -- usable threads
log -- path to log file
"""
if log is None:
log = Unformattable(errormsg="log used but undefined")
try:
# execute the actual run method.
run(input, output, params, wildcards, threads, resources, log)
except (Exception, BaseException) as ex:
# this ensures that exception can be re-raised in the parent thread
lineno, file = get_exception_origin(ex, linemaps)
raise RuleException(format_error(
ex, lineno, linemaps=linemaps, snakefile=file,
show_traceback=True))
def run_wrapper(run, input, output, params, wildcards, threads, resources, log,
version, benchmark, benchmark_repeats, rule, conda_env, linemaps, debug=False,
shadow_dir=None):
"""
Wrapper around the run method that handles exceptions and benchmarking.
Arguments
run -- the run method
input -- list of input files
output -- list of output files
wildcards -- so far processed wildcards
threads -- usable threads
log -- list of log files
rule (str) -- rule name
shadow_dir -- optional shadow directory root
"""
if os.name == "posix" and debug:
sys.stdin = open('/dev/stdin')
try:
runs = 1 if benchmark is None else benchmark_repeats
wallclock = []
for i in range(runs):
w = time.time()
# execute the actual run method.
with change_working_directory(shadow_dir):
run(input, output, params, wildcards, threads, resources, log,
version, rule, conda_env)
w = time.time() - w
wallclock.append(w)
except (KeyboardInterrupt, SystemExit) as e:
# re-raise the keyboard interrupt in order to record an error in the scheduler but ignore it
raise e
except (Exception, BaseException) as ex:
log_verbose_traceback(ex)
# this ensures that exception can be re-raised in the parent thread
lineno, file = get_exception_origin(ex, linemaps)
raise RuleException(format_error(ex, lineno,
linemaps=linemaps,
snakefile=file,
show_traceback=True))
if benchmark is not None:
try:
with open(benchmark, "w") as f:
print("s", "h:m:s", sep="\t", file=f)
for t in wallclock:
print(t, str(datetime.timedelta(seconds=t)), sep="\t", file=f)
except (Exception, BaseException) as ex:
raise WorkflowError(ex)
def run_wrapper(run, input, output, params, wildcards, threads, resources, log,
version, benchmark, benchmark_repeats, linemaps, debug=False,
shadow_dir=None):
"""
Wrapper around the run method that handles exceptions and benchmarking.
Arguments
run -- the run method
input -- list of input files
output -- list of output files
wildcards -- so far processed wildcards
threads -- usable threads
log -- list of log files
shadow_dir -- optional shadow directory root
"""
if os.name == "posix" and debug:
sys.stdin = open('/dev/stdin')
try:
runs = 1 if benchmark is None else benchmark_repeats
wallclock = []
for i in range(runs):
w = time.time()
# execute the actual run method.
with change_working_directory(shadow_dir):
run(input, output, params, wildcards, threads, resources, log,
version)
w = time.time() - w
wallclock.append(w)
except (KeyboardInterrupt, SystemExit) as e:
# re-raise the keyboard interrupt in order to record an error in the scheduler but ignore it
raise e
except (Exception, BaseException) as ex:
log_verbose_traceback(ex)
# this ensures that exception can be re-raised in the parent thread
lineno, file = get_exception_origin(ex, linemaps)
raise RuleException(format_error(ex, lineno,
linemaps=linemaps,
snakefile=file,
show_traceback=True))
if benchmark is not None:
try:
with open(benchmark, "w") as f:
print("s", "h:m:s", sep="\t", file=f)
for t in wallclock:
print(t, str(datetime.timedelta(seconds=t)), sep="\t", file=f)
except (Exception, BaseException) as ex:
raise WorkflowError(ex)