class WorkflowLevelOptions(collections.Sized):
ATTR_TO_ID = {
'chunk_mode': to_workflow_option_ns('chunk_mode'),
'max_nchunks': to_workflow_option_ns('max_nchunks'),
'max_nproc': to_workflow_option_ns('max_nproc'),
'total_max_nproc': to_workflow_option_ns("max_total_nproc"),
'max_nworkers': to_workflow_option_ns('max_nworkers'),
"distributed_mode": to_workflow_option_ns("distributed_mode"),
"cluster_manager_path": to_workflow_option_ns("cluster_manager"),
"tmp_dir": to_workflow_option_ns("tmp_dir"),
"progress_status_url": to_workflow_option_ns("progress_status_url"),
"exit_on_failure": to_workflow_option_ns("exit_on_failure")
}
def __init__(self, chunk_mode, max_nchunks, max_nproc, total_max_nproc,
max_nworkers, distributed_mode, cluster_manager_path, tmp_dir,
progress_status_url, exit_on_failure):
""" Container for the known workflow options"""
self.chunk_mode = chunk_mode
self.max_nchunks = max_nchunks
self.max_nproc = max_nproc
self.total_max_nproc = total_max_nproc
self.max_nworkers = max_nworkers
self.distributed_mode = distributed_mode
# This can be given as an abspath to a dir,
# or "pbsmrtpipe.cluster_templates.sge"
self.cluster_manager_path = cluster_manager_path
self.tmp_dir = tmp_dir
self.progress_status_url = progress_status_url
self.exit_on_failure = exit_on_failure
@staticmethod
def from_defaults():
return WorkflowLevelOptions.from_id_dict({})
def __repr__(self):
_d = dict(k=self.__class__.__name__,
h=self.max_nchunks,
n=self.max_nproc,
w=self.max_nworkers,
c=self.cluster_manager_path)
return "<{k} chunk:{h} nproc:{n} workers:{w} cluster:{c}>".format(**_d)
def __len__(self):
return len(self.to_dict())
@staticmethod
def from_id_dict(d):
"""
Create an instance from a id dict of options (pbsmrtpipe.options.x:value}
"""
from pbsmrtpipe.pb_io import REGISTERED_WORKFLOW_OPTIONS
import pbsmrtpipe.schema_opt_utils as OP
adict = {}
for opt_id, schema in REGISTERED_WORKFLOW_OPTIONS.iteritems():
if opt_id in d:
v = d[opt_id]
OP.validate_value(schema, {opt_id: v})
adict[opt_id] = v
else:
value = OP.get_default_from_schema(schema)
d[opt_id] = value
# build map to instance var names
adict = {
k: d[v]
for k, v in WorkflowLevelOptions.ATTR_TO_ID.iteritems()
}
return WorkflowLevelOptions(**adict)
def to_dict(self):
return {v: getattr(self, k) for k, v in self.ATTR_TO_ID.iteritems()}
def _to_wopt_id(s):
"""Workflow Level Options"""
from pbsmrtpipe.constants import to_workflow_option_ns
return to_workflow_option_ns(s)
def _to_wopt_id(s):
"""Workflow Level Options"""
from pbsmrtpipe.constants import to_workflow_option_ns
return to_workflow_option_ns(s)