def runfile(script=None,
raw_args='',
wdir='.',
code=None,
kernel=None,
**kwargs):
# this has something to do with Prefix matching rule of parse_known_args
#
# That is to say
#
# --rep 3
#
# would be parsed as
#
# args.workflow=3, unknown --rep
#
# instead of
#
# args.workflow=None, unknown --rep 3
#
# we then have to change the parse to disable args.workflow when
# there is no workflow option.
raw_args = shlex.split(raw_args) if isinstance(raw_args, str) else raw_args
if (script is None and code is None) or '-h' in raw_args:
parser = get_run_parser(interactive=True, with_workflow=True)
parser.print_help()
return
if raw_args and raw_args[0].lstrip().startswith('-'):
parser = get_run_parser(interactive=True, with_workflow=False)
parser.error = _parse_error
args, workflow_args = parser.parse_known_args(raw_args)
args.workflow = None
else:
parser = get_run_parser(interactive=True, with_workflow=True)
parser.error = _parse_error
args, workflow_args = parser.parse_known_args(raw_args)
# for reporting purpose
sys.argv = ['%run'] + raw_args
env.verbosity = args.verbosity
if kernel and not isinstance(env.logger.handlers[0],
NotebookLoggingHandler):
env.logger.handlers = []
levels = {
0: logging.ERROR,
1: logging.WARNING,
2: logging.INFO,
3: logging.DEBUG,
4: logging.TRACE,
None: logging.INFO
}
env.logger.addHandler(
NotebookLoggingHandler(levels[env.verbosity],
kernel,
title=' '.join(sys.argv)))
else:
env.logger.handers[0].setTitle(' '.join(sys.argv))
dt = datetime.datetime.now().strftime('%m%d%y_%H%M')
if args.__dag__ is None:
args.__dag__ = f'workflow_{dt}.dot'
elif args.__dag__ == '':
args.__dag__ = None
if args.__report__ is None:
args.__report__ = f'workflow_{dt}.html'
elif args.__report__ == '':
args.__report__ = None
if args.__remote__:
from sos.utils import load_config_files
cfg = load_config_files(args.__config__)
env.sos_dict.set('CONFIG', cfg)
# if executing on a remote host...
from sos.hosts import Host
host = Host(args.__remote__)
#
if script is None:
if not code.strip():
return
script = os.path.join('.sos', '__interactive__.sos')
with open(script, 'w') as s:
s.write(code)
# copy script to remote host...
host.send_to_host(script)
from sos.utils import remove_arg
argv = shlex.split(raw_args) if isinstance(raw_args, str) else raw_args
argv = remove_arg(argv, '-r')
argv = remove_arg(argv, '-c')
# execute the command on remote host
try:
with kernel.redirect_sos_io():
ret = host._host_agent.run_command(['sos', 'run', script] +
argv,
wait_for_task=True,
realtime=True)
if ret:
kernel.send_response(
kernel.iopub_socket, 'stream',
dict(name='stderr',
text=
f'remote execution of workflow exited with code {ret}'
))
except Exception as e:
if kernel:
kernel.send_response(kernel.iopub_socket, 'stream', {
'name': 'stdout',
'text': str(e)
})
return
if args.__bin_dirs__:
for d in args.__bin_dirs__:
if d == '~/.sos/bin' and not os.path.isdir(os.path.expanduser(d)):
os.makedirs(os.path.expanduser(d), exist_ok=True)
os.environ['PATH'] = os.pathsep.join(
[os.path.expanduser(x)
for x in args.__bin_dirs__]) + os.pathsep + os.environ['PATH']
# clear __step_input__, __step_output__ etc because there is
# no concept of passing input/outputs across cells.
env.sos_dict.set('__step_output__', sos_targets([]))
for k in [
'__step_input__', '__default_output__', 'step_input',
'step_output', 'step_depends', '_input', '_output', '_depends'
]:
env.sos_dict.pop(k, None)
try:
if script is None:
if not code.strip():
return
if kernel is None:
script = SoS_Script(content=code)
else:
if kernel._workflow_mode:
# in workflow mode, the content is sent by magics %run and %sosrun
script = SoS_Script(content=code)
else:
# this is a scratch step...
# if there is no section header, add a header so that the block
# appears to be a SoS script with one section
if not any([
SOS_SECTION_HEADER.match(line)
or line.startswith('%from')
or line.startswith('%include')
for line in code.splitlines()
]):
code = '[scratch_0]\n' + code
script = SoS_Script(content=code)
else:
#kernel.send_frontend_msg('stream',
# {'name': 'stdout', 'text': 'Workflow cell can only be executed with magic %run or %sosrun.'},
# title='# SoS warning')
return
else:
script = SoS_Script(filename=script)
workflow = script.workflow(args.workflow,
use_default=not args.__targets__)
env.config: DefaultDict[str, Union[None, bool, str]] = defaultdict(str)
executor = Interactive_Executor(
workflow,
args=workflow_args,
config={
'config_file':
args.__config__,
'output_dag':
args.__dag__,
'output_report':
args.__report__,
'sig_mode':
'ignore' if args.dryrun else args.__sig_mode__,
'default_queue':
'' if args.__queue__ is None else args.__queue__,
'wait_for_task':
True if args.__wait__ is True or args.dryrun else
(False if args.__no_wait__ else None),
'resume_mode':
kernel is not None and kernel._resume_execution,
'run_mode':
'dryrun' if args.dryrun else 'interactive',
'verbosity':
args.verbosity,
# wait if -w or in dryrun mode, not wait if -W, otherwise use queue default
'max_procs':
args.__max_procs__,
'max_running_jobs':
args.__max_running_jobs__,
# for infomration and resume only
'workdir':
os.getcwd(),
'script':
"interactive",
'workflow':
args.workflow,
'targets':
args.__targets__,
'bin_dirs':
args.__bin_dirs__,
'workflow_args':
workflow_args
})
return executor.run(args.__targets__)['__last_res__']
except PendingTasks:
raise
except SystemExit:
# this happens because the executor is in resume mode but nothing
# needs to be resumed, we simply pass
return
except Exception:
if args.verbosity and args.verbosity > 2:
sys.stderr.write(get_traceback())
raise
finally:
env.config['sig_mode'] = 'ignore'
env.verbosity = 2
def runfile(script=None,
raw_args='',
wdir='.',
code=None,
kernel=None,
**kwargs):
# this has something to do with Prefix matching rule of parse_known_args
#
# That is to say
#
# --rep 3
#
# would be parsed as
#
# args.workflow=3, unknown --rep
#
# instead of
#
# args.workflow=None, unknown --rep 3
#
# we then have to change the parse to disable args.workflow when
# there is no workflow option.
args = shlex.split(raw_args) if isinstance(raw_args, str) else raw_args
if (script is None and code is None) or '-h' in args:
parser = get_run_parser(interactive=True, with_workflow=True)
parser.print_help()
return
if args and args[0].lstrip().startswith('-'):
parser = get_run_parser(interactive=True, with_workflow=False)
parser.error = _parse_error
args, workflow_args = parser.parse_known_args(args)
args.workflow = None
else:
parser = get_run_parser(interactive=True, with_workflow=True)
parser.error = _parse_error
args, workflow_args = parser.parse_known_args(args)
# no multi-processing in interactive mode
env.max_jobs = 1
env.verbosity = args.verbosity
if args.__queue__ == '':
from sos.hosts import list_queues
list_queues(args.__config__, args.verbosity)
return
if args.__remote__:
from sos.utils import load_config_files
cfg = load_config_files(args.__config__)
env.sos_dict.set('CONFIG', cfg)
if args.__remote__ == '':
from .hosts import list_queues
list_queues(cfg, args.verbosity)
return
# if executing on a remote host...
from sos.hosts import Host
host = Host(args.__remote__)
#
if script is None:
if not code.strip():
return
script = os.path.join('.sos', '__interactive__.sos')
with open(script, 'w') as s:
s.write(code)
# copy script to remote host...
host.send_to_host(script)
from sos.utils import remove_arg
argv = shlex.split(raw_args) if isinstance(raw_args, str) else raw_args
argv = remove_arg(argv, '-r')
argv = remove_arg(argv, '-c')
# execute the command on remote host
try:
with kernel.redirect_sos_io():
ret = host._host_agent.run_command(['sos', 'run', script] +
argv,
wait_for_task=True,
realtime=True)
if ret:
kernel.send_response(
kernel.iopub_socket, 'stream',
dict(name='stderr',
text=
f'remote execution of workflow exited with code {ret}'
))
except Exception as e:
if kernel:
kernel.send_response(kernel.iopub_socket, 'stream', {
'name': 'stdout',
'text': str(e)
})
return
if args.__bin_dirs__:
import fasteners
for d in args.__bin_dirs__:
if d == '~/.sos/bin' and not os.path.isdir(os.path.expanduser(d)):
with fasteners.InterProcessLock(
os.path.join(tempfile.gettempdir(), 'sos_lock_bin')):
os.makedirs(os.path.expanduser(d))
elif not os.path.isdir(os.path.expanduser(d)):
raise ValueError(f'directory does not exist: {d}')
os.environ['PATH'] = os.pathsep.join(
[os.path.expanduser(x)
for x in args.__bin_dirs__]) + os.pathsep + os.environ['PATH']
# clear __step_input__, __step_output__ etc because there is
# no concept of passing input/outputs across cells.
env.sos_dict.set('__step_output__', [])
for k in ['__step_input__', '__default_output__', 'input', 'output', \
'depends', '_input', '_output', '_depends']:
env.sos_dict.pop(k, None)
try:
if script is None:
if not code.strip():
return
if kernel is None:
script = SoS_Script(content=code)
else:
if kernel._workflow_mode:
# in workflow mode, the content is sent by magics %run and %sosrun
script = SoS_Script(content=code)
else:
# this is a scratch step...
# if there is no section header, add a header so that the block
# appears to be a SoS script with one section
if not any([
SOS_SECTION_HEADER.match(line)
or line.startswith('%from')
or line.startswith('%include')
for line in code.splitlines()
]):
code = '[scratch_0]\n' + code
script = SoS_Script(content=code)
else:
if kernel.cell_idx == -1:
kernel.send_frontend_msg(
'stream', {
'name':
'stdout',
'text':
'Workflow can only be executed with magic %run or %sosrun.'
})
return
else:
script = SoS_Script(filename=script)
workflow = script.workflow(args.workflow)
executor = Interactive_Executor(
workflow,
args=workflow_args,
config={
'config_file':
args.__config__,
'output_dag':
args.__dag__,
'sig_mode':
args.__sig_mode__,
'default_queue':
'' if args.__queue__ is None else args.__queue__,
'wait_for_task':
True if args.__wait__ is True or args.dryrun else
(False if args.__no_wait__ else None),
'resume_mode':
kernel is not None and kernel._resume_execution,
'run_mode':
'dryrun' if args.dryrun else 'interactive',
'verbosity':
args.verbosity,
# wait if -w or in dryrun mode, not wait if -W, otherwise use queue default
'max_procs':
1,
'max_running_jobs':
args.__max_running_jobs__,
# for infomration and resume only
'workdir':
os.getcwd(),
'script':
"interactive",
'workflow':
args.workflow,
'targets':
args.__targets__,
'bin_dirs':
args.__bin_dirs__,
'workflow_args':
workflow_args
})
return executor.run(args.__targets__)
except PendingTasks:
raise
except SystemExit:
# this happens because the executor is in resume mode but nothing
# needs to be resumed, we simply pass
return
except Exception:
if args.verbosity and args.verbosity > 2:
sys.stderr.write(get_traceback())
raise
finally:
env.config['sig_mode'] = 'ignore'
env.verbosity = 2
