def run(self, graph, config, updatehash=False):
"""Executes a pre-defined pipeline in a serial order.
modifed for XNAT workflow XML updates
Parameters
----------
graph : networkx digraph
defines order of execution
"""
if not isinstance(graph, nx.DiGraph):
raise ValueError('Input must be a networkx digraph object')
logger.info("Running serially.")
old_wd = os.getcwd()
notrun = []
donotrun = []
nodes = nx.topological_sort(graph)
for (i, node) in enumerate(nodes):
try:
pct = 100.0*i/len(nodes)
workflow_info.update(str(i+1), str(node), '%.1f' % pct)
if node in donotrun:
continue
node.run(updatehash=updatehash)
except:
os.chdir(old_wd)
if str2bool(config['execution']['stop_on_first_crash']):
raise
# bare except, but i really don't know where a
# node might fail
crashfile = report_crash(node)
# remove dependencies from queue
subnodes = [s for s in dfs_preorder(graph, node)]
notrun.append(dict(node = node,
dependents = subnodes,
crashfile = crashfile))
donotrun.extend(subnodes)
report_nodes_not_run(notrun)
def run(self, plugin_args=None, updatehash=False):
""" Execute the workflow
XNAT-modified Linear runner only
plugin_args : dictionary containing arguments to be sent to plugin
constructor. see individual plugin doc strings for details.
"""
runner = LinearPlugin(plugin_args=plugin_args)
flatgraph = self._create_flat_graph()
self.config = merge_dict(deepcopy(config._sections), self.config)
logger.info(str(sorted(self.config)))
self._set_needed_outputs(flatgraph)
execgraph = generate_expanded_graph(deepcopy(flatgraph))
for index, node in enumerate(execgraph.nodes()):
node.config = self.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)
self._write_report_info(self.base_dir, self.name, execgraph)
runner.run(execgraph, updatehash=updatehash, config=self.config)
return execgraph
