#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Defines functionality for pipelined execution of interfaces
The `Workflow` class provides core functionality for batch processing.
"""
import os
import os.path as op
import sys
from datetime import datetime
from copy import deepcopy
import pickle
import shutil
import numpy as np
from ... import config, logging
from ...utils.misc import str2bool
from ...utils.functions import getsource, create_function_from_source
from ...interfaces.base import traits, TraitedSpec, TraitDictObject, TraitListObject
from ...utils.filemanip import save_json
from .utils import (
generate_expanded_graph,
export_graph,
write_workflow_prov,
write_workflow_resources,
format_dot,
topological_sort,
get_print_name,
merge_dict,
format_node,
)
from .base import EngineBase
from .nodes import MapNode
logger = logging.getLogger("nipype.workflow")
class Workflow(EngineBase):
"""Controls the setup and execution of a pipeline of processes."""
[docs] def __init__(self, name, base_dir=None):
"""Create a workflow object.
Parameters
----------
name : alphanumeric string
unique identifier for the workflow
base_dir : string, optional
path to workflow storage
"""
import networkx as nx
super(Workflow, self).__init__(name, base_dir)
self._graph = nx.DiGraph()
# PUBLIC API
[docs] def clone(self, name):
"""Clone a workflow
.. note::
Will reset attributes used for executing workflow. See
_init_runtime_fields.
Parameters
----------
name: alphanumeric name
unique name for the workflow
"""
clone = super(Workflow, self).clone(name)
clone._reset_hierarchy()
return clone
# Graph creation functions
[docs] def connect(self, *args, **kwargs):
"""Connect nodes in the pipeline.
This routine also checks if inputs and outputs are actually provided by
the nodes that are being connected.
Creates edges in the directed graph using the nodes and edges specified
in the `connection_list`. Uses the NetworkX method
DiGraph.add_edges_from.
Parameters
----------
args : list or a set of four positional arguments
Four positional arguments of the form::
connect(source, sourceoutput, dest, destinput)
source : nodewrapper node
sourceoutput : string (must be in source.outputs)
dest : nodewrapper node
destinput : string (must be in dest.inputs)
A list of 3-tuples of the following form::
[(source, target,
[('sourceoutput/attribute', 'targetinput'),
...]),
...]
Or::
[(source, target, [(('sourceoutput1', func, arg2, ...),
'targetinput'), ...]),
...]
sourceoutput1 will always be the first argument to func
and func will be evaluated and the results sent ot targetinput
currently func needs to define all its needed imports within the
function as we use the inspect module to get at the source code
and execute it remotely
"""
if len(args) == 1:
connection_list = args[0]
elif len(args) == 4:
connection_list = [(args[0], args[2], [(args[1], args[3])])]
else:
raise TypeError(
"connect() takes either 4 arguments, or 1 list of"
" connection tuples (%d args given)" % len(args)
)
disconnect = False
if kwargs:
disconnect = kwargs.get("disconnect", False)
if disconnect:
self.disconnect(connection_list)
return
newnodes = []
for srcnode, destnode, _ in connection_list:
if self in [srcnode, destnode]:
msg = (
"Workflow connect cannot contain itself as node:"
" src[%s] dest[%s] workflow[%s]"
) % (srcnode, destnode, self.name)
raise IOError(msg)
if (srcnode not in newnodes) and not self._has_node(srcnode):
newnodes.append(srcnode)
if (destnode not in newnodes) and not self._has_node(destnode):
newnodes.append(destnode)
if newnodes:
self._check_nodes(newnodes)
for node in newnodes:
if node._hierarchy is None:
node._hierarchy = self.name
not_found = []
connected_ports = {}
for srcnode, destnode, connects in connection_list:
if destnode not in connected_ports:
connected_ports[destnode] = []
# check to see which ports of destnode are already
# connected.
if not disconnect and (destnode in self._graph.nodes()):
for edge in self._graph.in_edges(destnode):
data = self._graph.get_edge_data(*edge)
for sourceinfo, destname in data["connect"]:
if destname not in connected_ports[destnode]:
connected_ports[destnode] += [destname]
for source, dest in connects:
# Currently datasource/sink/grabber.io modules
# determine their inputs/outputs depending on
# connection settings. Skip these modules in the check
if dest in connected_ports[destnode]:
raise Exception(
"""\
Trying to connect %s:%s to %s:%s but input '%s' of node '%s' is already
connected.
"""
% (srcnode, source, destnode, dest, dest, destnode)
)
if not (
hasattr(destnode, "_interface")
and (
".io" in str(destnode._interface.__class__)
or any(
[
".io" in str(val)
for val in destnode._interface.__class__.__bases__
]
)
)
):
if not destnode._check_inputs(dest):
not_found.append(["in", destnode.name, dest])
if not (
hasattr(srcnode, "_interface")
and (
".io" in str(srcnode._interface.__class__)
or any(
[
".io" in str(val)
for val in srcnode._interface.__class__.__bases__
]
)
)
):
if isinstance(source, tuple):
# handles the case that source is specified
# with a function
sourcename = source[0]
elif isinstance(source, (str, bytes)):
sourcename = source
else:
raise Exception(
(
"Unknown source specification in "
"connection from output of %s"
)
% srcnode.name
)
if sourcename and not srcnode._check_outputs(sourcename):
not_found.append(["out", srcnode.name, sourcename])
connected_ports[destnode] += [dest]
infostr = []
for info in not_found:
infostr += [
"Module %s has no %sput called %s\n" % (info[1], info[0], info[2])
]
if not_found:
raise Exception("\n".join(["Some connections were not found"] + infostr))
# turn functions into strings
for srcnode, destnode, connects in connection_list:
for idx, (src, dest) in enumerate(connects):
if isinstance(src, tuple) and not isinstance(src[1], (str, bytes)):
function_source = getsource(src[1])
connects[idx] = ((src[0], function_source, src[2:]), dest)
# add connections
for srcnode, destnode, connects in connection_list:
edge_data = self._graph.get_edge_data(srcnode, destnode, None)
if edge_data:
logger.debug(
"(%s, %s): Edge data exists: %s", srcnode, destnode, str(edge_data)
)
for data in connects:
if data not in edge_data["connect"]:
edge_data["connect"].append(data)
if disconnect:
logger.debug("Removing connection: %s", str(data))
edge_data["connect"].remove(data)
if edge_data["connect"]:
self._graph.add_edges_from([(srcnode, destnode, edge_data)])
else:
# pass
logger.debug("Removing connection: %s->%s", srcnode, destnode)
self._graph.remove_edges_from([(srcnode, destnode)])
elif not disconnect:
logger.debug("(%s, %s): No edge data", srcnode, destnode)
self._graph.add_edges_from([(srcnode, destnode, {"connect": connects})])
edge_data = self._graph.get_edge_data(srcnode, destnode)
logger.debug(
"(%s, %s): new edge data: %s", srcnode, destnode, str(edge_data)
)
[docs] def disconnect(self, *args):
"""Disconnect nodes
See the docstring for connect for format.
"""
if len(args) == 1:
connection_list = args[0]
elif len(args) == 4:
connection_list = [(args[0], args[2], [(args[1], args[3])])]
else:
raise TypeError(
"disconnect() takes either 4 arguments, or 1 list "
"of connection tuples (%d args given)" % len(args)
)
for srcnode, dstnode, conn in connection_list:
logger.debug("disconnect(): %s->%s %s", srcnode, dstnode, str(conn))
if self in [srcnode, dstnode]:
raise IOError(
"Workflow connect cannot contain itself as node: src[%s] "
"dest[%s] workflow[%s]"
) % (srcnode, dstnode, self.name)
# If node is not in the graph, not connected
if not self._has_node(srcnode) or not self._has_node(dstnode):
continue
edge_data = self._graph.get_edge_data(srcnode, dstnode, {"connect": []})
ed_conns = [(c[0], c[1]) for c in edge_data["connect"]]
remove = []
for edge in conn:
if edge in ed_conns:
# idx = ed_conns.index(edge)
remove.append((edge[0], edge[1]))
logger.debug("disconnect(): remove list %s", str(remove))
for el in remove:
edge_data["connect"].remove(el)
logger.debug("disconnect(): removed connection %s", str(el))
if not edge_data["connect"]:
self._graph.remove_edge(srcnode, dstnode)
else:
self._graph.add_edges_from([(srcnode, dstnode, edge_data)])
[docs] def add_nodes(self, nodes):
""" Add nodes to a workflow
Parameters
----------
nodes : list
A list of EngineBase-based objects
"""
newnodes = []
all_nodes = self._get_all_nodes()
for node in nodes:
if self._has_node(node):
raise IOError("Node %s already exists in the workflow" % node)
if isinstance(node, Workflow):
for subnode in node._get_all_nodes():
if subnode in all_nodes:
raise IOError(
("Subnode %s of node %s already exists " "in the workflow")
% (subnode, node)
)
newnodes.append(node)
if not newnodes:
logger.debug("no new nodes to add")
return
for node in newnodes:
if not issubclass(node.__class__, EngineBase):
raise Exception("Node %s must be a subclass of EngineBase", node)
self._check_nodes(newnodes)
for node in newnodes:
if node._hierarchy is None:
node._hierarchy = self.name
self._graph.add_nodes_from(newnodes)
[docs] def remove_nodes(self, nodes):
""" Remove nodes from a workflow
Parameters
----------
nodes : list
A list of EngineBase-based objects
"""
self._graph.remove_nodes_from(nodes)
# Input-Output access
@property
def inputs(self):
return self._get_inputs()
@property
def outputs(self):
return self._get_outputs()
[docs] def get_node(self, name):
"""Return an internal node by name
"""
nodenames = name.split(".")
nodename = nodenames[0]
outnode = [
node for node in self._graph.nodes() if str(node).endswith("." + nodename)
]
if outnode:
outnode = outnode[0]
if nodenames[1:] and issubclass(outnode.__class__, Workflow):
outnode = outnode.get_node(".".join(nodenames[1:]))
else:
outnode = None
return outnode
[docs] def list_node_names(self):
"""List names of all nodes in a workflow
"""
import networkx as nx
outlist = []
for node in nx.topological_sort(self._graph):
if isinstance(node, Workflow):
outlist.extend(
[
".".join((node.name, nodename))
for nodename in node.list_node_names()
]
)
else:
outlist.append(node.name)
return sorted(outlist)
[docs] def write_graph(
self,
dotfilename="graph.dot",
graph2use="hierarchical",
format="png",
simple_form=True,
):
"""Generates a graphviz dot file and a png file
Parameters
----------
graph2use: 'orig', 'hierarchical' (default), 'flat', 'exec', 'colored'
orig - creates a top level graph without expanding internal
workflow nodes;
flat - expands workflow nodes recursively;
hierarchical - expands workflow nodes recursively with a
notion on hierarchy;
colored - expands workflow nodes recursively with a
notion on hierarchy in color;
exec - expands workflows to depict iterables
format: 'png', 'svg'
simple_form: boolean (default: True)
Determines if the node name used in the graph should be of the form
'nodename (package)' when True or 'nodename.Class.package' when
False.
"""
graphtypes = ["orig", "flat", "hierarchical", "exec", "colored"]
if graph2use not in graphtypes:
raise ValueError(
"Unknown graph2use keyword. Must be one of: " + str(graphtypes)
)
base_dir, dotfilename = op.split(dotfilename)
if base_dir == "":
if self.base_dir:
base_dir = self.base_dir
if self.name:
base_dir = op.join(base_dir, self.name)
else:
base_dir = os.getcwd()
os.makedirs(base_dir, exist_ok=True)
if graph2use in ["hierarchical", "colored"]:
if self.name[:1].isdigit(): # these graphs break if int
raise ValueError(
"{} graph failed, workflow name cannot begin "
"with a number".format(graph2use)
)
dotfilename = op.join(base_dir, dotfilename)
self.write_hierarchical_dotfile(
dotfilename=dotfilename,
colored=graph2use == "colored",
simple_form=simple_form,
)
outfname = format_dot(dotfilename, format=format)
else:
graph = self._graph
if graph2use in ["flat", "exec"]:
graph = self._create_flat_graph()
if graph2use == "exec":
graph = generate_expanded_graph(deepcopy(graph))
outfname = export_graph(
graph,
base_dir,
dotfilename=dotfilename,
format=format,
simple_form=simple_form,
)
logger.info(
"Generated workflow graph: %s (graph2use=%s, simple_form=%s)."
% (outfname, graph2use, simple_form)
)
return outfname
def write_hierarchical_dotfile(
self, dotfilename=None, colored=False, simple_form=True
):
dotlist = ["digraph %s{" % self.name]
dotlist.append(
self._get_dot(prefix=" ", colored=colored, simple_form=simple_form)
)
dotlist.append("}")
dotstr = "\n".join(dotlist)
if dotfilename:
fp = open(dotfilename, "wt")
fp.writelines(dotstr)
fp.close()
else:
logger.info(dotstr)
[docs] def export(
self, filename=None, prefix="output", format="python", include_config=False
):
"""Export object into a different format
Parameters
----------
filename: string
file to save the code to; overrides prefix
prefix: string
prefix to use for output file
format: string
one of "python"
include_config: boolean
whether to include node and workflow config values
"""
import networkx as nx
formats = ["python"]
if format not in formats:
raise ValueError("format must be one of: %s" % "|".join(formats))
flatgraph = self._create_flat_graph()
nodes = nx.topological_sort(flatgraph)
all_lines = None
lines = ["# Workflow"]
importlines = ["from nipype.pipeline.engine import Workflow, " "Node, MapNode"]
functions = {}
if format == "python":
connect_template = '%s.connect(%%s, %%s, %%s, "%%s")' % self.name
connect_template2 = '%s.connect(%%s, "%%s", %%s, "%%s")' % self.name
wfdef = '%s = Workflow("%s")' % (self.name, self.name)
lines.append(wfdef)
if include_config:
lines.append("%s.config = %s" % (self.name, self.config))
for idx, node in enumerate(nodes):
nodename = node.fullname.replace(".", "_")
# write nodes
nodelines = format_node(
node, format="python", include_config=include_config
)
for line in nodelines:
if line.startswith("from"):
if line not in importlines:
importlines.append(line)
else:
lines.append(line)
# write connections
for u, _, d in flatgraph.in_edges(nbunch=node, data=True):
for cd in d["connect"]:
if isinstance(cd[0], tuple):
args = list(cd[0])
if args[1] in functions:
funcname = functions[args[1]]
else:
func = create_function_from_source(args[1])
funcname = [
name
for name in func.__globals__
if name != "__builtins__"
][0]
functions[args[1]] = funcname
args[1] = funcname
args = tuple([arg for arg in args if arg])
line_args = (
u.fullname.replace(".", "_"),
args,
nodename,
cd[1],
)
line = connect_template % line_args
line = line.replace("'%s'" % funcname, funcname)
lines.append(line)
else:
line_args = (
u.fullname.replace(".", "_"),
cd[0],
nodename,
cd[1],
)
lines.append(connect_template2 % line_args)
functionlines = ["# Functions"]
for function in functions:
functionlines.append(pickle.loads(function).rstrip())
all_lines = importlines + functionlines + lines
if not filename:
filename = "%s%s.py" % (prefix, self.name)
with open(filename, "wt") as fp:
fp.writelines("\n".join(all_lines))
return all_lines
[docs] def run(self, plugin=None, plugin_args=None, updatehash=False):
""" Execute the workflow
Parameters
----------
plugin: plugin name or object
Plugin to use for execution. You can create your own plugins for
execution.
plugin_args : dictionary containing arguments to be sent to plugin
constructor. see individual plugin doc strings for details.
"""
if plugin is None:
plugin = config.get("execution", "plugin")
if not isinstance(plugin, (str, bytes)):
runner = plugin
plugin = runner.__class__.__name__[: -len("Plugin")]
plugin_args = runner.plugin_args
else:
name = ".".join(__name__.split(".")[:-2] + ["plugins"])
try:
__import__(name)
except ImportError:
msg = "Could not import plugin module: %s" % name
logger.error(msg)
raise ImportError(msg)
else:
plugin_mod = getattr(sys.modules[name], "%sPlugin" % plugin)
runner = plugin_mod(plugin_args=plugin_args)
flatgraph = self._create_flat_graph()
self.config = merge_dict(deepcopy(config._sections), self.config)
logger.info("Workflow %s settings: %s", self.name, str(sorted(self.config)))
self._set_needed_outputs(flatgraph)
execgraph = generate_expanded_graph(deepcopy(flatgraph))
for index, node in enumerate(execgraph.nodes()):
node.config = merge_dict(deepcopy(self.config), node.config)
node.base_dir = self.base_dir
node.index = index
if isinstance(node, MapNode):
node.use_plugin = (plugin, plugin_args)
self._configure_exec_nodes(execgraph)
if str2bool(self.config["execution"]["create_report"]):
self._write_report_info(self.base_dir, self.name, execgraph)
runner.run(execgraph, updatehash=updatehash, config=self.config)
datestr = datetime.utcnow().strftime("%Y%m%dT%H%M%S")
if str2bool(self.config["execution"]["write_provenance"]):
prov_base = op.join(self.base_dir, "workflow_provenance_%s" % datestr)
logger.info("Provenance file prefix: %s" % prov_base)
write_workflow_prov(execgraph, prov_base, format="all")
if config.resource_monitor:
base_dir = self.base_dir or os.getcwd()
write_workflow_resources(
execgraph,
filename=op.join(base_dir, self.name, "resource_monitor.json"),
)
return execgraph
# PRIVATE API AND FUNCTIONS
def _write_report_info(self, workingdir, name, graph):
if workingdir is None:
workingdir = os.getcwd()
report_dir = op.join(workingdir, name)
os.makedirs(report_dir, exist_ok=True)
shutil.copyfile(
op.join(op.dirname(__file__), "report_template.html"),
op.join(report_dir, "index.html"),
)
shutil.copyfile(
op.join(op.dirname(__file__), "..", "..", "external", "d3.js"),
op.join(report_dir, "d3.js"),
)
nodes, groups = topological_sort(graph, depth_first=True)
graph_file = op.join(report_dir, "graph1.json")
json_dict = {"nodes": [], "links": [], "groups": [], "maxN": 0}
for i, node in enumerate(nodes):
report_file = "%s/_report/report.rst" % node.output_dir().replace(
report_dir, ""
)
result_file = "%s/result_%s.pklz" % (
node.output_dir().replace(report_dir, ""),
node.name,
)
json_dict["nodes"].append(
dict(
name="%d_%s" % (i, node.name),
report=report_file,
result=result_file,
group=groups[i],
)
)
maxN = 0
for gid in np.unique(groups):
procs = [i for i, val in enumerate(groups) if val == gid]
N = len(procs)
if N > maxN:
maxN = N
json_dict["groups"].append(
dict(procs=procs, total=N, name="Group_%05d" % gid)
)
json_dict["maxN"] = maxN
for u, v in graph.in_edges():
json_dict["links"].append(
dict(source=nodes.index(u), target=nodes.index(v), value=1)
)
save_json(graph_file, json_dict)
graph_file = op.join(report_dir, "graph.json")
# Avoid RuntimeWarning: divide by zero encountered in log10
num_nodes = len(nodes)
if num_nodes > 0:
index_name = np.ceil(np.log10(num_nodes)).astype(int)
else:
index_name = 0
template = "%%0%dd_" % index_name
def getname(u, i):
name_parts = u.fullname.split(".")
# return '.'.join(name_parts[:-1] + [template % i + name_parts[-1]])
return template % i + name_parts[-1]
json_dict = []
for i, node in enumerate(nodes):
imports = []
for u, v in graph.in_edges(nbunch=node):
imports.append(getname(u, nodes.index(u)))
json_dict.append(
dict(name=getname(node, i), size=1, group=groups[i], imports=imports)
)
save_json(graph_file, json_dict)
def _set_needed_outputs(self, graph):
"""Initialize node with list of which outputs are needed."""
rm_outputs = self.config["execution"]["remove_unnecessary_outputs"]
if not str2bool(rm_outputs):
return
for node in graph.nodes():
node.needed_outputs = []
for edge in graph.out_edges(node):
data = graph.get_edge_data(*edge)
sourceinfo = [
v1[0] if isinstance(v1, tuple) else v1 for v1, v2 in data["connect"]
]
node.needed_outputs += [
v for v in sourceinfo if v not in node.needed_outputs
]
if node.needed_outputs:
node.needed_outputs = sorted(node.needed_outputs)
def _configure_exec_nodes(self, graph):
"""Ensure that each node knows where to get inputs from
"""
for node in graph.nodes():
node.input_source = {}
for edge in graph.in_edges(node):
data = graph.get_edge_data(*edge)
for sourceinfo, field in data["connect"]:
node.input_source[field] = (
op.join(edge[0].output_dir(), "result_%s.pklz" % edge[0].name),
sourceinfo,
)
def _check_nodes(self, nodes):
"""Checks if any of the nodes are already in the graph
"""
node_names = [node.name for node in self._graph.nodes()]
node_lineage = [node._hierarchy for node in self._graph.nodes()]
for node in nodes:
if node.name in node_names:
idx = node_names.index(node.name)
try:
this_node_lineage = node_lineage[idx]
except IndexError:
raise IOError('Duplicate node name "%s" found.' % node.name)
else:
if this_node_lineage in [node._hierarchy, self.name]:
raise IOError('Duplicate node name "%s" found.' % node.name)
else:
node_names.append(node.name)
def _has_attr(self, parameter, subtype="in"):
"""Checks if a parameter is available as an input or output
"""
hierarchy = parameter.split(".")
# Connecting to a workflow needs at least two values,
# the name of the child node and the name of the input/output
if len(hierarchy) < 2:
return False
attrname = hierarchy.pop()
nodename = hierarchy.pop()
def _check_is_already_connected(workflow, node, attrname):
for _, _, d in workflow._graph.in_edges(nbunch=node, data=True):
for cd in d["connect"]:
if attrname == cd[1]:
return False
return True
targetworkflow = self
while hierarchy:
workflowname = hierarchy.pop(0)
workflow = None
for node in targetworkflow._graph.nodes():
if node.name == workflowname:
if isinstance(node, Workflow):
workflow = node
break
if workflow is None:
return False
# Verify input does not already have an incoming connection
# in the hierarchy of workflows
if subtype == "in":
hierattrname = ".".join(hierarchy + [nodename, attrname])
if not _check_is_already_connected(
targetworkflow, workflow, hierattrname
):
return False
targetworkflow = workflow
targetnode = None
for node in targetworkflow._graph.nodes():
if node.name == nodename:
if isinstance(node, Workflow):
return False
else:
targetnode = node
break
if targetnode is None:
return False
if subtype == "in":
if not hasattr(targetnode.inputs, attrname):
return False
else:
if not hasattr(targetnode.outputs, attrname):
return False
# Verify input does not already have an incoming connection
# in the target workflow
if subtype == "in":
if not _check_is_already_connected(targetworkflow, targetnode, attrname):
return False
return True
def _get_parameter_node(self, parameter, subtype="in"):
"""Returns the underlying node corresponding to an input or
output parameter
"""
if subtype == "in":
subobject = self.inputs
else:
subobject = self.outputs
attrlist = parameter.split(".")
cur_out = subobject
for attr in attrlist[:-1]:
cur_out = getattr(cur_out, attr)
return cur_out.traits()[attrlist[-1]].node
def _check_outputs(self, parameter):
return self._has_attr(parameter, subtype="out")
def _check_inputs(self, parameter):
return self._has_attr(parameter, subtype="in")
def _get_inputs(self):
"""Returns the inputs of a workflow
This function does not return any input ports that are already
connected
"""
inputdict = TraitedSpec()
for node in self._graph.nodes():
inputdict.add_trait(node.name, traits.Instance(TraitedSpec))
if isinstance(node, Workflow):
setattr(inputdict, node.name, node.inputs)
else:
taken_inputs = []
for _, _, d in self._graph.in_edges(nbunch=node, data=True):
for cd in d["connect"]:
taken_inputs.append(cd[1])
unconnectedinputs = TraitedSpec()
for key, trait in list(node.inputs.items()):
if key not in taken_inputs:
unconnectedinputs.add_trait(key, traits.Trait(trait, node=node))
value = getattr(node.inputs, key)
setattr(unconnectedinputs, key, value)
setattr(inputdict, node.name, unconnectedinputs)
getattr(inputdict, node.name).on_trait_change(self._set_input)
return inputdict
def _get_outputs(self):
"""Returns all possible output ports that are not already connected
"""
outputdict = TraitedSpec()
for node in self._graph.nodes():
outputdict.add_trait(node.name, traits.Instance(TraitedSpec))
if isinstance(node, Workflow):
setattr(outputdict, node.name, node.outputs)
elif node.outputs:
outputs = TraitedSpec()
for key, _ in list(node.outputs.items()):
outputs.add_trait(key, traits.Any(node=node))
setattr(outputs, key, None)
setattr(outputdict, node.name, outputs)
return outputdict
def _set_input(self, objekt, name, newvalue):
"""Trait callback function to update a node input
"""
objekt.traits()[name].node.set_input(name, newvalue)
def _set_node_input(self, node, param, source, sourceinfo):
"""Set inputs of a node given the edge connection"""
if isinstance(sourceinfo, (str, bytes)):
val = source.get_output(sourceinfo)
elif isinstance(sourceinfo, tuple):
if callable(sourceinfo[1]):
val = sourceinfo[1](source.get_output(sourceinfo[0]), *sourceinfo[2:])
newval = val
if isinstance(val, TraitDictObject):
newval = dict(val)
if isinstance(val, TraitListObject):
newval = val[:]
logger.debug("setting node input: %s->%s", param, str(newval))
node.set_input(param, deepcopy(newval))
def _get_all_nodes(self):
allnodes = []
for node in self._graph.nodes():
if isinstance(node, Workflow):
allnodes.extend(node._get_all_nodes())
else:
allnodes.append(node)
return allnodes
def _has_node(self, wanted_node):
for node in self._graph.nodes():
if wanted_node == node:
return True
if isinstance(node, Workflow):
if node._has_node(wanted_node):
return True
return False
def _create_flat_graph(self):
"""Make a simple DAG where no node is a workflow."""
logger.debug("Creating flat graph for workflow: %s", self.name)
workflowcopy = deepcopy(self)
workflowcopy._generate_flatgraph()
return workflowcopy._graph
def _reset_hierarchy(self):
"""Reset the hierarchy on a graph
"""
for node in self._graph.nodes():
if isinstance(node, Workflow):
node._reset_hierarchy()
for innernode in node._graph.nodes():
innernode._hierarchy = ".".join((self.name, innernode._hierarchy))
else:
node._hierarchy = self.name
def _generate_flatgraph(self):
"""Generate a graph containing only Nodes or MapNodes
"""
import networkx as nx
logger.debug("expanding workflow: %s", self)
nodes2remove = []
if not nx.is_directed_acyclic_graph(self._graph):
raise Exception(
("Workflow: %s is not a directed acyclic graph " "(DAG)") % self.name
)
nodes = list(nx.topological_sort(self._graph))
for node in nodes:
logger.debug("processing node: %s", node)
if isinstance(node, Workflow):
nodes2remove.append(node)
# use in_edges instead of in_edges_iter to allow
# disconnections to take place properly. otherwise, the
# edge dict is modified.
# dj: added list() for networkx ver.2
for u, _, d in list(self._graph.in_edges(nbunch=node, data=True)):
logger.debug("in: connections-> %s", str(d["connect"]))
for cd in deepcopy(d["connect"]):
logger.debug("in: %s", str(cd))
dstnode = node._get_parameter_node(cd[1], subtype="in")
srcnode = u
srcout = cd[0]
dstin = cd[1].split(".")[-1]
logger.debug(
"in edges: %s %s %s %s", srcnode, srcout, dstnode, dstin
)
self.disconnect(u, cd[0], node, cd[1])
self.connect(srcnode, srcout, dstnode, dstin)
# do not use out_edges_iter for reasons stated in in_edges
# dj: for ver 2 use list(out_edges)
for _, v, d in list(self._graph.out_edges(nbunch=node, data=True)):
logger.debug("out: connections-> %s", str(d["connect"]))
for cd in deepcopy(d["connect"]):
logger.debug("out: %s", str(cd))
dstnode = v
if isinstance(cd[0], tuple):
parameter = cd[0][0]
else:
parameter = cd[0]
srcnode = node._get_parameter_node(parameter, subtype="out")
if isinstance(cd[0], tuple):
srcout = list(cd[0])
srcout[0] = parameter.split(".")[-1]
srcout = tuple(srcout)
else:
srcout = parameter.split(".")[-1]
dstin = cd[1]
logger.debug(
"out edges: %s %s %s %s", srcnode, srcout, dstnode, dstin
)
self.disconnect(node, cd[0], v, cd[1])
self.connect(srcnode, srcout, dstnode, dstin)
# expand the workflow node
# logger.debug('expanding workflow: %s', node)
node._generate_flatgraph()
for innernode in node._graph.nodes():
innernode._hierarchy = ".".join((self.name, innernode._hierarchy))
self._graph.add_nodes_from(node._graph.nodes())
self._graph.add_edges_from(node._graph.edges(data=True))
if nodes2remove:
self._graph.remove_nodes_from(nodes2remove)
logger.debug("finished expanding workflow: %s", self)
def _get_dot(
self, prefix=None, hierarchy=None, colored=False, simple_form=True, level=0
):
"""Create a dot file with connection info
"""
import networkx as nx
if prefix is None:
prefix = " "
if hierarchy is None:
hierarchy = []
colorset = [
"#FFFFC8", # Y
"#0000FF",
"#B4B4FF",
"#E6E6FF", # B
"#FF0000",
"#FFB4B4",
"#FFE6E6", # R
"#00A300",
"#B4FFB4",
"#E6FFE6", # G
"#0000FF",
"#B4B4FF",
] # loop B
if level > len(colorset) - 2:
level = 3 # Loop back to blue
dotlist = ['%slabel="%s";' % (prefix, self.name)]
for node in nx.topological_sort(self._graph):
fullname = ".".join(hierarchy + [node.fullname])
nodename = fullname.replace(".", "_")
if not isinstance(node, Workflow):
node_class_name = get_print_name(node, simple_form=simple_form)
if not simple_form:
node_class_name = ".".join(node_class_name.split(".")[1:])
if hasattr(node, "iterables") and node.iterables:
dotlist.append(
(
'%s[label="%s", shape=box3d,'
"style=filled, color=black, colorscheme"
"=greys7 fillcolor=2];"
)
% (nodename, node_class_name)
)
else:
if colored:
dotlist.append(
('%s[label="%s", style=filled,' ' fillcolor="%s"];')
% (nodename, node_class_name, colorset[level])
)
else:
dotlist.append(
('%s[label="%s"];') % (nodename, node_class_name)
)
for node in nx.topological_sort(self._graph):
if isinstance(node, Workflow):
fullname = ".".join(hierarchy + [node.fullname])
nodename = fullname.replace(".", "_")
dotlist.append("subgraph cluster_%s {" % nodename)
if colored:
dotlist.append(
prefix + prefix + 'edge [color="%s"];' % (colorset[level + 1])
)
dotlist.append(prefix + prefix + "style=filled;")
dotlist.append(
prefix + prefix + 'fillcolor="%s";' % (colorset[level + 2])
)
dotlist.append(
node._get_dot(
prefix=prefix + prefix,
hierarchy=hierarchy + [self.name],
colored=colored,
simple_form=simple_form,
level=level + 3,
)
)
dotlist.append("}")
else:
for subnode in self._graph.successors(node):
if node._hierarchy != subnode._hierarchy:
continue
if not isinstance(subnode, Workflow):
nodefullname = ".".join(hierarchy + [node.fullname])
subnodefullname = ".".join(hierarchy + [subnode.fullname])
nodename = nodefullname.replace(".", "_")
subnodename = subnodefullname.replace(".", "_")
for _ in self._graph.get_edge_data(node, subnode)["connect"]:
dotlist.append("%s -> %s;" % (nodename, subnodename))
logger.debug("connection: %s", dotlist[-1])
# add between workflow connections
for u, v, d in self._graph.edges(data=True):
uname = ".".join(hierarchy + [u.fullname])
vname = ".".join(hierarchy + [v.fullname])
for src, dest in d["connect"]:
uname1 = uname
vname1 = vname
if isinstance(src, tuple):
srcname = src[0]
else:
srcname = src
if "." in srcname:
uname1 += "." + ".".join(srcname.split(".")[:-1])
if "." in dest and "@" not in dest:
if not isinstance(v, Workflow):
if "datasink" not in str(v._interface.__class__).lower():
vname1 += "." + ".".join(dest.split(".")[:-1])
else:
vname1 += "." + ".".join(dest.split(".")[:-1])
if uname1.split(".")[:-1] != vname1.split(".")[:-1]:
dotlist.append(
"%s -> %s;"
% (uname1.replace(".", "_"), vname1.replace(".", "_"))
)
logger.debug("cross connection: %s", dotlist[-1])
return ("\n" + prefix).join(dotlist)
