Merge pull request #938 from oesteban/enh/ChainedNameSource

ENH: Allow chained name_source

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
 * ENH: Improve JSON interfaces: default settings when reading and consistent output creation
        when writing (https://github.com/nipy/nipype/pull/1047)
 * FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)

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'
@@ -1510,9 +1516,13 @@ 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)
+
         if not isdefined(retval) or "%s" in retval:
             if not trait_spec.name_source:
                 return retval
@@ -1522,26 +1532,42 @@ 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')
+                ns = ns[0]
+
+            if not isinstance(ns, 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
+                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:
                 return retval
             return self._overload_extension(retval, name)
+
         return retval
 
     def _gen_filename(self, name):
@@ -1557,7 +1583,7 @@ 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))

nipype/interfaces/tests/test_base.py

@@ -172,11 +172,13 @@ class DeprecationSpec3(nib.TraitedSpec):
     yield assert_equal, spec_instance.foo, Undefined
     yield assert_equal, spec_instance.bar, 1
 
+
 def test_namesource():
     tmp_infile = setup_file()
     tmpd, nme, ext = split_filename(tmp_infile)
     pwd = os.getcwd()
     os.chdir(tmpd)
+
     class spec2(nib.CommandLineInputSpec):
         moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s",
                        position=2)
@@ -196,6 +198,104 @@ class TestName(nib.CommandLine):
     os.chdir(pwd)
     teardown_file(tmpd)
 
+
+def test_chained_namesource():
+    tmp_infile = setup_file()
+    tmpd, nme, ext = split_filename(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+
+    class spec2(nib.CommandLineInputSpec):
+        doo = nib.File(exists=True, argstr="%s", position=1)
+        moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s",
+                       position=2, name_template='%s_mootpl')
+        poo = nib.File(name_source=['moo'], hash_files=False,
+                       argstr="%s", position=3)
+
+    class TestName(nib.CommandLine):
+        _cmd = "mycommand"
+        input_spec = spec2
+
+    testobj = TestName()
+    testobj.inputs.doo = tmp_infile
+    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_namesource1():
+    tmp_infile = setup_file()
+    tmpd, nme, ext = split_filename(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+
+    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
+
+    # Check that an exception is raised
+    to0 = TestCycle()
+    not_raised = True
+    try:
+        to0.cmdline
+    except nib.NipypeInterfaceError:
+        not_raised = False
+    yield assert_false, not_raised
+
+    os.chdir(pwd)
+    teardown_file(tmpd)
+
+def test_cycle_namesource2():
+    tmp_infile = setup_file()
+    tmpd, nme, ext = split_filename(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+
+
+    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
+
+    # Check that loop can be broken by setting one of the inputs
+    to1 = TestCycle()
+    to1.inputs.poo = tmp_infile
+
+    not_raised = True
+    try:
+        res = to1.cmdline
+    except nib.NipypeInterfaceError:
+        not_raised = False
+    print res
+
+    yield assert_true, not_raised
+    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)
+
+
 def checknose():
     """check version of nose for known incompatability"""
     mod = __import__('nose')
@@ -536,4 +636,4 @@ def test_global_CommandLine_output():
     res = ci.run()
     yield assert_equal, res.runtime.stdout, ''
     os.chdir(pwd)
-    teardown_file(tmpd)
+    teardown_file(tmpd)