def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.3',
# only '.txt' files are considered as valid input
input_filename_pattern = '*.ini',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__,
application=gimc_preprocessingApplication,
stats_only_for=gimc_preprocessingApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.3',
# only '.txt' files are considered as valid input
input_filename_pattern = '*.ini',
)
def __init__(self):
SessionBasedScript.__init__(
self,
usage="%(prog)s [options] FLAGSFILE INPUT ... [: OUTPUT ...]",
version=__version__, # module version == script version
application=RosettaApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__,
application=GbidsApplication,
stats_only_for=GbidsApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
application=GParseURLApplication,
stats_only_for=GParseURLApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__,
application = Gfit3C_ABC_uml_Application,
input_filename_pattern = '*.d',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__,
application=Gfit3C_ABC_uml_Application,
input_filename_pattern='*.d',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__,
application=gsentitweetApplication,
stats_only_for=gsentitweetApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
application=BidsWrappsApplication,
stats_only_for=BidsWrappsApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
application = GreductionApplication,
stats_only_for = GreductionApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__,
application = GpartialequilibriumApplication,
stats_only_for = GpartialequilibriumApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__,
application=GpartialequilibriumApplication,
stats_only_for=GpartialequilibriumApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__,
application = GpfiApplication,
stats_only_for = GpfiApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.2',
# TURBOMOLE's "coord" files are input
input_filename_pattern = 'coord',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.2',
# TURBOMOLE's "coord" files are input
input_filename_pattern = 'coord',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
# application = GATKStagedTaskCollection,
application=Application,
stats_only_for=Application)
def __init__(self):
SessionBasedScript.__init__(
self,
usage = "%(prog)s [options] FLAGSFILE INPUT ... [: OUTPUT ...]",
version = __version__, # module version == script version
application = RosettaApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
# application = GATKStagedTaskCollection,
application = Application,
stats_only_for = Application
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.2',
# only '.loop' files are considered as valid input
input_filename_pattern = '*.loop',
)
forwardPremium.paraLoop_fp.__init__(self, verbosity = 'INFO')
def __init__(self):
self.bids_app_execution = DEFAULT_DOCKER_BIDS_APP
SessionBasedScript.__init__(
self,
version=__version__,
application=GbidsApplication,
stats_only_for=GbidsApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.2',
# only '.loop' files are considered as valid input
input_filename_pattern = '*.loop',
)
paraLoop.__init__(self, 'INFO')
def __init__(self):
SessionBasedScript.__init__(
self,
version='0.2',
# only '.loop' files are considered as valid input
input_filename_pattern='*.loop',
)
forwardPremium.paraLoop_fp.__init__(self, verbosity='INFO')
def __init__(self):
SessionBasedScript.__init__(
self,
version = '1.0',
input_filename_pattern = '*.loop',
stats_only_for = Application,
)
paraLoop.__init__(self, 'INFO')
def __init__(self):
SessionBasedScript.__init__(
self,
version='1.0',
input_filename_pattern='*.loop',
stats_only_for=Application,
)
paraLoop.__init__(self, 'INFO')
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.2',
# only '.loop' files are considered as valid input
input_filename_pattern = '*.loop',
)
paraLoop.__init__(self, 'INFO')
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
input_filename_pattern = '*.csv',
application = GmbsimApplication,
# only display stats for the top-level policy objects
#stats_only_for = GmbsimApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
input_filename_pattern='*.csv',
application=GmbsimApplication,
# only display stats for the top-level policy objects
#stats_only_for = GmbsimApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
# `CodemlRetryPolicy` is the top-level object here,
# so only print information about it.
# stats_only_for = CodemlRetryPolicy,
stats_only_for = gc3libs.application.codeml.CodemlApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
# `CodemlRetryPolicy` is the top-level object here,
# so only print information about it.
# stats_only_for = CodemlRetryPolicy,
stats_only_for = gc3libs.application.codeml.CodemlApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
# Use fully-qualified name for class,
# to allow GC3Utils to unpickle job instances
# see: https://github.com/uzh/gc3pie/issues/95
application=GDockingApplication,
input_filename_pattern='*.pdb')
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
# only display stats for the top-level policy objects
# (which correspond to the processed files) omit counting
# actual applications because their number varies over
# time as checkpointing and re-submission takes place.
stats_only_for=GsnowpackApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
# only display stats for the top-level policy objects
# (which correspond to the processed files) omit counting
# actual applications because their number varies over
# time as checkpointing and re-submission takes place.
stats_only_for = GsnowpackApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
application = ggamess_retry.GamessRetryPolicy,
input_filename_pattern = '*.inp',
# `GamessRetryPolicy` is the top-level object now,
# so only print information about it.
stats_only_for = ggamess_retry.GamessRetryPolicy,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
application = ggamess_retry.GamessRetryPolicy,
input_filename_pattern = '*.inp',
# `GamessRetryPolicy` is the top-level object now,
# so only print information about it.
stats_only_for = ggamess_retry.GamessRetryPolicy,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
# Use fully-qualified name for class,
# to allow GC3Utils to unpickle job instances
# see: https://github.com/uzh/gc3pie/issues/95
application = GDockingApplication,
input_filename_pattern = '*.pdb'
)
def __init__(self):
SessionBasedScript.__init__(
self,
version="0.2",
# only '.loop' files are considered as valid input
input_filename_pattern="*.loop",
stats_only_for=Application
# idRiskApppotApplication
# idRiskApplication,
)
paraLoop.__init__(self, "INFO")
def __init__(self):
SessionBasedScript.__init__(
self,
version='0.2',
# only '.loop' files are considered as valid input
input_filename_pattern='*.loop',
stats_only_for=Application
#idRiskApppotApplication
#idRiskApplication,
)
paraLoop.__init__(self, 'INFO')
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
input_filename_pattern='MHC_coev_*',
application=GMhcCoevTask,
# only display stats for the top-level policy objects
# (which correspond to the processed files) omit counting
# actual applications because their number varies over
# time as checkpointing and re-submission takes place.
stats_only_for=GMhcCoevTask,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
input_filename_pattern = 'MHC_coev_*',
application = GMhcCoevTask,
# only display stats for the top-level policy objects
# (which correspond to the processed files) omit counting
# actual applications because their number varies over
# time as checkpointing and re-submission takes place.
stats_only_for = GMhcCoevTask,
)
def _main_loop_exitcode(self, stats):
"""
This works in daemon mode;
Thus do not end if all simulations have been
processed. Continue and wait for new models to be uploaded.
"""
if self.extra['is_daemon']:
return 4
else:
return SessionBasedScript._main_loop_exitcode(self, stats)
def _main_loop_exitcode(self, stats):
"""
This works in daemon mode;
Thus do not end if all simulations have been
processed. Continue and wait for new models to be uploaded.
"""
if self.extra['is_daemon']:
return 4
else:
return SessionBasedScript._main_loop_exitcode(self, stats)
def pre_run(self):
"""
- If instance_type or image_id are specified in the command line,
override config file settings.
- write session path to log path for check logs
"""
SessionBasedScript.pre_run(self)
if self.params.instance_type:
self._core.resources[
'S3ITSC'].bidswrapps_instance_type = self.params.instance_type
if self.params.image_id:
self._core.resources[
'S3ITSC'].bidswrapps_image_id = self.params.image_id
# create link to session path in output path
out_path = self.params.output.replace("NAME", "")
if not os.path.isdir(out_path):
os.makedirs(out_path)
info_file = os.path.join(out_path, ".session_path")
with open(info_file, "w") as fi:
fi.write(os.path.abspath(self.params.session))
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
input_filename_pattern = '*.inp'
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__,
)
def process_args(self):
from time import localtime, strftime
# set timestamp
self.time_stamp = strftime("%Y-%m-%d-%H%M", localtime())
SessionBasedScript.process_args(self)
def __init__(self):
SessionBasedScript.__init__(
self,
version='0.0.1',
)
def __init__(self):
SessionBasedScript.__init__(self,
version='0.2',
stats_only_for=Application)
def process_args(self):
from time import localtime, strftime
# set timestamp
self.time_stamp = strftime("%Y-%m-%d-%H%M", localtime())
SessionBasedScript.process_args(self)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.2',
stats_only_for = Application
)
def __init__(self):
SessionBasedScript.__init__(
self,
version='0.2',
input_filename_pattern='*.ini',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version=__version__, # module version == script version
application=FunctionalDiversityApplication,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = '0.3',
# input_filename_pattern = '*.ini',
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
stats_only_for = CryptoApplication,
)
def __init__(self):
SessionBasedScript.__init__(self, version="1.0", input_filename_pattern="*.loop", stats_only_for=Application)
paraLoop.__init__(self, "INFO")
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__,
)
def __init__(self):
SessionBasedScript.__init__(
self,
version = __version__, # module version == script version
application = FunctionalDiversityApplication,
)
