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FIX: Serialize all interface arguments when exporting workflows #3240

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Merged
merged 4 commits into from
Aug 16, 2020
Merged

FIX: Serialize all interface arguments when exporting workflows #3240

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14a304a
TEST: Reproduce gh-3230
effigies Aug 15, 2020
6566e6e
Removed line that excluded fields parameter during export.
matteomancini Aug 3, 2020
7df2d62
Added if statement to correctly handle strings and list during export.
matteomancini Aug 3, 2020
fc8e991
RF: Simplify serialization
effigies Aug 15, 2020
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15 changes: 14 additions & 1 deletion nipype/pipeline/engine/tests/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,12 @@
from ....interfaces import base as nib
from ....interfaces import utility as niu
from .... import config
from ..utils import clean_working_directory, write_workflow_prov, load_resultfile
from ..utils import (
clean_working_directory,
write_workflow_prov,
load_resultfile,
format_node,
)


class InputSpec(nib.TraitedSpec):
Expand Down Expand Up @@ -327,3 +332,11 @@ def test_save_load_resultfile(tmpdir, use_relative):
)

config.set("execution", "use_relative_paths", old_use_relative)


def test_format_node():
node = pe.Node(niu.IdentityInterface(fields=["a", "b"]), name="node")
serialized = format_node(node)
workspace = {"Node": pe.Node}
exec("\n".join(serialized), workspace)
assert workspace["node"].interface._fields == node.interface._fields
18 changes: 6 additions & 12 deletions nipype/pipeline/engine/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -364,18 +364,12 @@ def format_node(node, format="python", include_config=False):
importline = "from %s import %s" % (klass.__module__, klass.__class__.__name__)
comment = "# Node: %s" % node.fullname
spec = signature(node.interface.__init__)
args = [p.name for p in list(spec.parameters.values())]
args = args[1:]
if args:
filled_args = []
for arg in args:
if hasattr(node.interface, "_%s" % arg):
filled_args.append(
"%s=%s" % (arg, getattr(node.interface, "_%s" % arg))
)
args = ", ".join(filled_args)
else:
args = ""
filled_args = []
for param in spec.parameters.values():
val = getattr(node.interface, f"_{param.name}", None)
if val is not None:
filled_args.append(f"{param.name}={val!r}")
args = ", ".join(filled_args)
klass_name = klass.__class__.__name__
if isinstance(node, MapNode):
nodedef = '%s = MapNode(%s(%s), iterfield=%s, name="%s")' % (
Expand Down