def run_task_manifest_on_cluster(path):
"""
Run the Task on the queue (of possible)
:param path:
:return:
"""
output_dir = os.path.dirname(path)
os.chdir(output_dir)
rt = RunnableTask.from_manifest_json(path)
# this needs to be updated to have explicit paths to stderr, stdout
rcode, err_msg, run_time = run_task_on_cluster(rt, path, output_dir, True)
state = TaskStates.from_int(rcode)
return state, err_msg, run_time
def run_task_manifest_on_cluster(path):
"""
Run the Task on the queue (of possible)
:param path:
:return:
"""
output_dir = os.path.dirname(path)
os.chdir(output_dir)
rt = RunnableTask.from_manifest_json(path)
# this needs to be updated to have explicit paths to stderr, stdout
rcode, err_msg, run_time = run_task_on_cluster(rt, path, output_dir, True)
state = TaskStates.from_int(rcode)
return state, err_msg, run_time
def run_task_manifest(path):
output_dir = os.path.dirname(path)
os.chdir(output_dir)
stderr = os.path.join(output_dir, 'stderr')
stdout = os.path.join(output_dir, 'stdout')
try:
rt = RunnableTask.from_manifest_json(path)
except KeyError:
emsg = "Unable to deserialize RunnableTask from manifest {p}".format(p=path)
log.error(emsg)
raise
# blocking call
rcode, err_msg, run_time = run_task(rt, output_dir, stdout, stderr, True)
state = TaskStates.from_int(rcode)
return state, err_msg, run_time
def run_task_manifest(path):
output_dir = os.path.dirname(path)
os.chdir(output_dir)
stderr = os.path.join(output_dir, 'stderr')
stdout = os.path.join(output_dir, 'stdout')
try:
rt = RunnableTask.from_manifest_json(path)
except KeyError:
emsg = "Unable to deserialize RunnableTask from manifest {p}".format(p=path)
log.error(emsg)
raise
# blocking call
rcode, err_msg, run_time = run_task(rt, output_dir, stdout, stderr, True)
state = TaskStates.from_int(rcode)
return state, err_msg, run_time
def to_binding_graph_summary(bg):
"""
General func for getting a summary of BindingGraph instance
"""
header = "Binding Graph Status Summary"
_n = 80
sp = "-" * _n
ssp = "*" * _n
outs = []
_add = outs.append
_add_sp = functools.partial(_add, sp)
_add_ssp = functools.partial(_add, ssp)
_add_ssp()
_add(header)
_add_sp()
_add("Workflow complete? {c}".format(c=bg.is_workflow_complete()))
tn_states = {s: bg.get_tasks_by_state(s) for s in TaskStates.ALL_STATES()}
tn_s = " ".join([":".join([k, str(v)]) for k, v in tn_states.iteritems()])
_add_sp()
_add("Task Summary {n} tasks ({s})".format(n=len(bg.task_nodes()), s=str(tn_s)))
_add_sp()
sorted_nodes = nx.topological_sort(bg)
_add(" ".join(["resolved inputs".ljust(20), "resolved outputs".ljust(20), "state".ljust(12), "NodeType".ljust(30), "N inputs".ljust(12), "N outputs".ljust(12), "run time".ljust(12), "Id".ljust(60), ]))
_add_sp()
for tnode in sorted_nodes:
if isinstance(tnode, VALID_TASK_NODE_CLASSES):
state = bg.node[tnode]['state']
_is_resolved = lambda it: all(bg.node[n][ConstantsNodes.FILE_ATTR_IS_RESOLVED] for n in it)
inputs_resolved = _is_resolved(bg.predecessors(tnode))
outputs_resolved = _is_resolved(bg.successors(tnode))
ninputs = len(bg.predecessors(tnode))
noutputs = len(bg.successors(tnode))
run_time = bg.node[tnode]['run_time']
s = str(inputs_resolved).ljust(20), str(outputs_resolved).ljust(20), state.ljust(12), tnode.__class__.__name__.ljust(30), str(ninputs).ljust(12), str(noutputs).ljust(12), str(run_time).ljust(12), str(tnode).ljust(60)
_add(" ".join(s))
# File-esque summary
def _to_summary(fnode_):
# print type(fnode_), fnode_
s = bg.node[fnode_][ConstantsNodes.FILE_ATTR_IS_RESOLVED]
p = bg.node[fnode_][ConstantsNodes.FILE_ATTR_PATH]
if p is None:
ppath = str(None)
else:
ppath = '... ' + str(p)[-35:]
_add(" ".join([str(s).ljust(10), fnode.__class__.__name__.ljust(18), ppath.ljust(40), str(fnode)]))
_add("")
_add_sp()
_add("File Summary ({n}) files".format(n=len(bg.file_nodes())))
_add_sp()
_add(" ".join(["resolved".ljust(10), "NodeType".ljust(18), "Path".ljust(40), "Id"]))
_add_sp()
for fnode in sorted_nodes:
if isinstance(fnode, VALID_FILE_NODE_CLASSES):
_to_summary(fnode)
_add("")
_add_sp()
_add("Entry Point Node Summary ({n})".format(n=len(bg.entry_point_nodes())))
_add_sp()
_add(" ".join(["resolved".ljust(10), "NodeType".ljust(18), "Path".ljust(40), "Id"]))
_add_sp()
for x in bg.entry_point_nodes():
_to_summary(x)
_add_sp()
return "\n".join(outs)