class RealExecutor(AbstractExecutor):
def __init__(
self, workflow, dag,
printreason=False, quiet=False, printshellcmds=False, output_wait=3):
super().__init__(
workflow, dag, printreason=printreason,
quiet=quiet, printshellcmds=printshellcmds,
output_wait=output_wait)
self.stats = Stats()
def _run(self, job, callback=None, error_callback=None):
super()._run(job)
self.stats.report_job_start(job)
try:
self.workflow.persistence.started(job)
except IOError as e:
logger.warning("Failed to set marker file for job started ({}). "
"Snakemake will work, but cannot ensure that output files "
"are complete in case of a kill signal or power loss. "
"Please ensure write permissions for the "
"directory {}".format(
e, self.workflow.persistence.path))
def finish_job(self, job):
super().finish_job(job)
self.stats.report_job_end(job)
try:
self.workflow.persistence.finished(job)
except IOError as e:
logger.warning("Failed to remove marker file for job started "
"({}). Please ensure write permissions for the "
"directory {}".format(
e, self.workflow.persistence.path))
def __init__(
self, workflow, dag,
printreason=False, quiet=False, printshellcmds=False, output_wait=3):
super().__init__(
workflow, dag, printreason=printreason,
quiet=quiet, printshellcmds=printshellcmds,
output_wait=output_wait)
self.stats = Stats()
def __init__(self, workflow, dag,
printreason=False,
quiet=False,
printshellcmds=False,
latency_wait=3,
benchmark_repeats=1):
super().__init__(workflow, dag,
printreason=printreason,
quiet=quiet,
printshellcmds=printshellcmds,
latency_wait=latency_wait,
benchmark_repeats=benchmark_repeats)
self.stats = Stats()
def __init__(self, workflow, dag,
printreason=False,
quiet=False,
printshellcmds=False,
latency_wait=3,
benchmark_repeats=1):
super().__init__(workflow, dag,
printreason=printreason,
quiet=quiet,
printshellcmds=printshellcmds,
latency_wait=latency_wait,
benchmark_repeats=benchmark_repeats)
self.stats = Stats()
class RealExecutor(AbstractExecutor):
def __init__(self, workflow, dag,
printreason=False,
quiet=False,
printshellcmds=False,
latency_wait=3,
benchmark_repeats=1):
super().__init__(workflow, dag,
printreason=printreason,
quiet=quiet,
printshellcmds=printshellcmds,
latency_wait=latency_wait,
benchmark_repeats=benchmark_repeats)
self.stats = Stats()
def _run(self, job, callback=None, error_callback=None):
super()._run(job)
self.stats.report_job_start(job)
try:
self.workflow.persistence.started(job)
except IOError as e:
logger.info(
"Failed to set marker file for job started ({}). "
"Snakemake will work, but cannot ensure that output files "
"are complete in case of a kill signal or power loss. "
"Please ensure write permissions for the "
"directory {}".format(e, self.workflow.persistence.path))
def finish_job(self, job, upload_remote=True):
super().finish_job(job, upload_remote=upload_remote)
self.stats.report_job_end(job)
try:
self.workflow.persistence.finished(job)
except IOError as e:
logger.info("Failed to remove marker file for job started "
"({}). Please ensure write permissions for the "
"directory {}".format(e,
self.workflow.persistence.path))
def format_job_pattern(self, pattern, job=None, **kwargs):
overwrite_workdir = []
if self.workflow.overwrite_workdir:
overwrite_workdir.extend(("--directory", self.workflow.overwrite_workdir))
overwrite_config = []
if self.workflow.overwrite_configfile:
overwrite_config.extend(("--configfile", self.workflow.overwrite_configfile))
if self.workflow.config_args:
overwrite_config.append("--config")
overwrite_config.extend(self.workflow.config_args)
printshellcmds = ""
if self.workflow.printshellcmds:
printshellcmds = "-p"
target = job.output if job.output else job.rule.name
return format(pattern,
job=job,
overwrite_workdir=overwrite_workdir,
overwrite_config=overwrite_config,
printshellcmds=printshellcmds,
workflow=self.workflow,
cores=self.cores,
benchmark_repeats=self.benchmark_repeats,
target=target,
**kwargs)