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ENH: Allow chained name_source #938

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Merged
merged 9 commits into from
Feb 15, 2015
Merged

ENH: Allow chained name_source #938

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d7f9186
[engine] Allow chained name_source
oesteban Oct 7, 2014
2b1d259
revert outdated changes to master
oesteban Oct 7, 2014
06c2298
use six.string_types
oesteban Oct 9, 2014
18973cd
Merge branch 'master' into enh/ChainedNameSource
oesteban Feb 11, 2015
5b6066c
add regression test for chained namesource
oesteban Feb 11, 2015
ebb46cd
update CHANGES
oesteban Feb 11, 2015
c9e7b09
added new tests, updated documentation
oesteban Feb 12, 2015
5f991fb
fixed regression tests
oesteban Feb 12, 2015
b43941c
Merge branch 'master' into enh/ChainedNameSource
oesteban Feb 15, 2015
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42 changes: 27 additions & 15 deletions nipype/interfaces/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1469,6 +1469,7 @@ def _format_arg(self, name, trait_spec, value):
def _filename_from_source(self, name):
trait_spec = self.inputs.trait(name)
retval = getattr(self.inputs, name)

if not isdefined(retval) or "%s" in retval:
if not trait_spec.name_source:
return retval
Expand All @@ -1478,26 +1479,37 @@ def _filename_from_source(self, name):
name_template = trait_spec.name_template
if not name_template:
name_template = "%s_generated"
if isinstance(trait_spec.name_source, list):
for ns in trait_spec.name_source:
if isdefined(getattr(self.inputs, ns)):
name_source = ns
break

ns = trait_spec.name_source
while isinstance(ns, list):
if len(ns) > 1:
iflogger.warn('Only one name_source per trait is allowed')
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why is only one allowed?

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well, we have a somewhat difficult decision here.

Former implementation iterated the name_source list until it found the first defined name_source.
Current implementation may accept undefined name_sources, but they must have a name_source as well.

In both implementations only one name_source is actually used, right?.

ns = ns[0]

if not isinstance(ns, basestring):
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replace with six.string_types

raise ValueError(('name_source of \'%s\' trait sould be an '
'input trait name') % name)

if isdefined(getattr(self.inputs, ns)):
name_source = ns
source = getattr(self.inputs, name_source)
while isinstance(source, list):
source = source[0]

# special treatment for files
try:
_, base, _ = split_filename(source)
except AttributeError:
base = source
else:
name_source = trait_spec.name_source
source = getattr(self.inputs, name_source)
while isinstance(source, list):
source = source[0]
#special treatment for files
try:
_, base, _ = split_filename(source)
except AttributeError:
base = source
base = self._filename_from_source(ns)

retval = name_template % base
_, _, ext = split_filename(retval)
if trait_spec.keep_extension and ext:
return retval
return self._overload_extension(retval, name)

return retval

def _gen_filename(self, name):
Expand All @@ -1513,7 +1525,7 @@ def _list_outputs(self):
outputs = self.output_spec().get()
for name, trait_spec in traits.iteritems():
out_name = name
if trait_spec.output_name != None:
if trait_spec.output_name is not None:
out_name = trait_spec.output_name
outputs[out_name] = \
os.path.abspath(self._filename_from_source(name))
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