added new tests, updated documentation

Author: oesteban

doc/devel/interface_specs.rst

@@ -358,6 +358,9 @@ CommandLine
 ``name_source``
     Indicates the list of input fields from which the value of the current File
     output variable will be drawn. This input field must be the name of a File.
+    Chaining is allowed, meaning that an input field can point to another as
+    ``name_source``, which also points as ``name_source`` to a third field.
+    In this situation, the templates for substitutions are also accumulated.
 
 ``name_template``
     By default a ``%s_generated`` template is used to create the output

nipype/interfaces/base.py

@@ -47,6 +47,12 @@
 
 __docformat__ = 'restructuredtext'
 
+class NipypeInterfaceError(Exception):
+    def __init__(self, value):
+        self.value = value
+    def __str__(self):
+        return repr(self.value)
+
 def _lock_files():
     tmpdir = '/tmp'
     pattern = '.X*-lock'
@@ -1510,7 +1516,10 @@ def _format_arg(self, name, trait_spec, value):
             # Append options using format string.
             return argstr % value
 
-    def _filename_from_source(self, name):
+    def _filename_from_source(self, name, chain=None):
+        if chain is None:
+            chain = []
+
         trait_spec = self.inputs.trait(name)
         retval = getattr(self.inputs, name)
 
@@ -1546,8 +1555,13 @@ def _filename_from_source(self, name):
                 except AttributeError:
                     base = source
             else:
-                base = self._filename_from_source(ns)
+                if name in chain:
+                    raise NipypeInterfaceError('Mutually pointing name_sources')
+
+                chain.append(name)
+                base = self._filename_from_source(ns, chain)
 
+            chain = None
             retval = name_template % base
             _, _, ext = split_filename(retval)
             if trait_spec.keep_extension and ext:

nipype/interfaces/tests/test_base.py

@@ -218,8 +218,49 @@ class TestName(nib.CommandLine):
 
     testobj = TestName()
     testobj.inputs.doo = tmp_infile
-    yield assert_true, '%s_mootpl' % nme in testobj.cmdline
-    yield assert_true, '%s_mootpl_generated' % nme in testobj.cmdline
+    res = testobj.cmdline
+    yield assert_true, '%s' % tmp_infile in res
+    yield assert_true, '%s_mootpl ' % nme in res
+    yield assert_true, '%s_mootpl_generated' % nme in res
+
+    os.chdir(pwd)
+    teardown_file(tmpd)
+
+
+def test_cycle_namesource():
+    tmp_infile = setup_file()
+    tmpd, nme, ext = split_filename(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+
+    from unittest import TestCase
+
+    class spec3(nib.CommandLineInputSpec):
+        moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s",
+                       position=1, name_template='%s_mootpl')
+        poo = nib.File(name_source=['moo'], hash_files=False,
+                       argstr="%s", position=2)
+        doo = nib.File(name_source=['poo'], hash_files=False,
+                       argstr="%s", position=3)
+
+    class TestCycle(nib.CommandLine):
+        _cmd = "mycommand"
+        input_spec = spec3
+
+        def get_cmd(self):
+            return self.cmdline
+
+    # Check that an exception is raised
+    to0 = TestCycle()
+    yield assert_raises, nib.NipypeInterfaceError, to0.get_cmd
+
+    # Check that loop can be broken by setting one of the inputs
+    to1 = TestCycle()
+    to1.inputs.poo = tmp_infile
+    res = to1.cmdline
+    yield assert_true, '%s' % tmp_infile in res
+    yield assert_true, '%s_generated ' % nme in res
+    yield assert_true, '%s_generated_mootpl' % nme in res
 
     os.chdir(pwd)
     teardown_file(tmpd)