def _report_crash(self, node, result=None):
if result and result['traceback']:
node._result = result['result']
node._traceback = result['traceback']
return report_crash(node,
traceback=result['traceback'])
else:
return report_crash(node)
def run(self, graph, config, updatehash=False):
"""Executes a pre-defined pipeline in a serial order.
Parameters
----------
graph : networkx digraph
defines order of execution
"""
import networkx as nx
try:
dfs_preorder = nx.dfs_preorder # type: ignore
except AttributeError:
dfs_preorder = nx.dfs_preorder_nodes
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, _ = topological_sort(graph)
for node in nodes:
endstatus = "end"
try:
if node in donotrun:
continue
if self._status_callback:
self._status_callback(node, "start")
node.run(updatehash=updatehash)
except Exception:
import pdb
pdb.post_mortem()
endstatus = "exception"
# bare except, but i really don't know where a
# node might fail
crashfile = report_crash(node)
if str2bool(config["execution"]["stop_on_first_crash"]):
raise
# remove dependencies from queue
subnodes = [s for s in dfs_preorder(graph, node)]
notrun.append({
"node": node,
"dependents": subnodes,
"crashfile": crashfile
})
donotrun.extend(subnodes)
# Delay raising the crash until we cleaned the house
if str2bool(config["execution"]["stop_on_first_crash"]):
os.chdir(old_wd) # Return wherever we were before
report_nodes_not_run(notrun) # report before raising
raise
finally:
if self._status_callback:
self._status_callback(node, endstatus)
os.chdir(old_wd) # Return wherever we were before
report_nodes_not_run(notrun)
def test_report_crash():
with mock.patch('pickle.dump', mock.MagicMock()) as mock_pickle_dump:
with mock.patch('nipype.pipeline.plugins.base.format_exception',
mock.MagicMock()): # see iss 1517
mock_pickle_dump.return_value = True
mock_node = mock.MagicMock(name='mock_node')
mock_node._id = 'an_id'
mock_node.config = {'execution': {'crashdump_dir': '.'}}
actual_crashfile = pb.report_crash(mock_node)
expected_crashfile = re.compile(
'.*/crash-.*-an_id-[0-9a-f\-]*.pklz')
yield assert_regexp_matches, actual_crashfile, expected_crashfile
yield assert_true, mock_pickle_dump.call_count == 1
def test_report_crash():
with mock.patch('pickle.dump', mock.MagicMock()) as mock_pickle_dump:
with mock.patch('nipype.pipeline.plugins.base.format_exception', mock.MagicMock()): # see iss 1517
mock_pickle_dump.return_value = True
mock_node = mock.MagicMock(name='mock_node')
mock_node._id = 'an_id'
mock_node.config = {
'execution' : {
'crashdump_dir' : '.'
}
}
actual_crashfile = pb.report_crash(mock_node)
expected_crashfile = re.compile('.*/crash-.*-an_id-[0-9a-f\-]*.pklz')
assert expected_crashfile.match(actual_crashfile).group() == actual_crashfile
assert mock_pickle_dump.call_count == 1
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)