Merge remote-tracking branch 'upstream/master' into maint/strip-help-from-interfaces

Author: oesteban

nipype/interfaces/base/core.py

@@ -39,7 +39,9 @@
 
 from .traits_extension import traits, isdefined, TraitError
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
-                    StdOutCommandLineInputSpec, MpiCommandLineInputSpec)
+                    StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
+                    get_filecopy_info)
+
 from .support import (Bunch, InterfaceResult, NipypeInterfaceError,
                       format_help)
 
@@ -116,11 +118,15 @@ def _list_outputs(self):
         """ List expected outputs"""
         raise NotImplementedError
 
-    def _get_filecopy_info(self):
-        """ Provides information about file inputs to copy or link to cwd.
-            Necessary for pipeline operation
+    @classmethod
+    def _get_filecopy_info(cls):
+        """Provides information about file inputs to copy or link to cwd.
+        Necessary for pipeline operation
         """
-        raise NotImplementedError
+        iflogger.warning(
+            '_get_filecopy_info member of Interface was deprecated '
+            'in nipype-1.1.6 and will be removed in 1.2.0')
+        return get_filecopy_info(cls)
 
 
 class BaseInterface(Interface):
@@ -188,19 +194,6 @@ def _outputs(self):
 
         return outputs
 
-    @classmethod
-    def _get_filecopy_info(cls):
-        """ Provides information about file inputs to copy or link to cwd.
-            Necessary for pipeline operation
-        """
-        info = []
-        if cls.input_spec is None:
-            return info
-        metadata = dict(copyfile=lambda t: t is not None)
-        for name, spec in sorted(cls.input_spec().traits(**metadata).items()):
-            info.append(dict(key=name, copy=spec.copyfile))
-        return info
-
     def _check_requires(self, spec, name, value):
         """ check if required inputs are satisfied
         """

nipype/interfaces/base/specs.py

@@ -13,6 +13,7 @@
                         absolute_import)
 
 import os
+from inspect import isclass
 from copy import deepcopy
 from warnings import warn
 from builtins import str, bytes
@@ -375,3 +376,21 @@ class MpiCommandLineInputSpec(CommandLineInputSpec):
     n_procs = traits.Int(desc="Num processors to specify to mpiexec. Do not "
                          "specify if this is managed externally (e.g. through "
                          "SGE)")
+
+
+def get_filecopy_info(cls):
+    """Provides information about file inputs to copy or link to cwd.
+    Necessary for pipeline operation
+    """
+    if cls.input_spec is None:
+        return None
+
+    # normalize_filenames is not a classmethod, hence check first
+    if not isclass(cls) and hasattr(cls, 'normalize_filenames'):
+        cls.normalize_filenames()
+    info = []
+    inputs = cls.input_spec() if isclass(cls) else cls.inputs
+    metadata = dict(copyfile=lambda t: t is not None)
+    for name, spec in sorted(inputs.traits(**metadata).items()):
+        info.append(dict(key=name, copy=spec.copyfile))
+    return info

nipype/interfaces/base/tests/test_core.py

@@ -55,15 +55,12 @@ def __init__(self):
         nif.aggregate_outputs()
     with pytest.raises(NotImplementedError):
         nif._list_outputs()
-    with pytest.raises(NotImplementedError):
-        nif._get_filecopy_info()
 
 
 def test_BaseInterface():
     config.set('monitoring', 'enable', '0')
 
     assert nib.BaseInterface.help() is None
-    assert nib.BaseInterface._get_filecopy_info() == []
 
     class InputSpec(nib.TraitedSpec):
         foo = nib.traits.Int(desc='a random int')
@@ -83,10 +80,6 @@ class DerivedInterface(nib.BaseInterface):
     assert DerivedInterface.help() is None
     assert 'moo' in ''.join(_inputs_help(DerivedInterface))
     assert DerivedInterface()._outputs() is None
-    assert DerivedInterface._get_filecopy_info()[0]['key'] == 'woo'
-    assert DerivedInterface._get_filecopy_info()[0]['copy']
-    assert DerivedInterface._get_filecopy_info()[1]['key'] == 'zoo'
-    assert not DerivedInterface._get_filecopy_info()[1]['copy']
     assert DerivedInterface().inputs.foo == nib.Undefined
     with pytest.raises(ValueError):
         DerivedInterface()._check_mandatory_inputs()

nipype/interfaces/base/tests/test_specs.py

@@ -14,7 +14,7 @@
 from ....interfaces import fsl
 from ...utility.wrappers import Function
 from ....pipeline import Node
-
+from ..specs import get_filecopy_info
 
 standard_library.install_aliases()
 
@@ -55,8 +55,8 @@ def test_TraitedSpec_tab_completion():
     bet_nd = Node(fsl.BET(), name='bet')
     bet_interface = fsl.BET()
     bet_inputs = bet_nd.inputs.class_editable_traits()
-    bet_outputs = bet_nd.outputs.class_editable_traits() 
-    
+    bet_outputs = bet_nd.outputs.class_editable_traits()
+
     # Check __all__ for bet node and interface inputs
     assert set(bet_nd.inputs.__all__) == set(bet_inputs)
     assert set(bet_interface.inputs.__all__) == set(bet_inputs)
@@ -433,3 +433,45 @@ def test_ImageFile():
     with pytest.raises(nib.TraitError):
         x.nocompress = 'test.nii.gz'
     x.nocompress = 'test.mgh'
+
+
+def test_filecopy_info():
+    class InputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int')
+        goo = nib.traits.Int(desc='a random int', mandatory=True)
+        moo = nib.traits.Int(desc='a random int', mandatory=False)
+        hoo = nib.traits.Int(desc='a random int', usedefault=True)
+        zoo = nib.File(desc='a file', copyfile=False)
+        woo = nib.File(desc='a file', copyfile=True)
+
+    class DerivedInterface(nib.BaseInterface):
+        input_spec = InputSpec
+        resource_monitor = False
+
+        def normalize_filenames(self):
+            """A mock normalize_filenames for freesurfer interfaces that have one"""
+            self.inputs.zoo = 'normalized_filename.ext'
+
+    assert get_filecopy_info(nib.BaseInterface) == []
+
+    # Test on interface class, not instantiated
+    info = get_filecopy_info(DerivedInterface)
+    assert info[0]['key'] == 'woo'
+    assert info[0]['copy']
+    assert info[1]['key'] == 'zoo'
+    assert not info[1]['copy']
+    info = None
+
+    # Test with instantiated interface
+    derived = DerivedInterface()
+    # First check that zoo is not defined
+    assert derived.inputs.zoo == Undefined
+    # After the first call to get_filecopy_info zoo is defined
+    info = get_filecopy_info(derived)
+    # Ensure that normalize_filenames was called
+    assert derived.inputs.zoo == 'normalized_filename.ext'
+    # Check the results are consistent
+    assert info[0]['key'] == 'woo'
+    assert info[0]['copy']
+    assert info[1]['key'] == 'zoo'
+    assert not info[1]['copy']

nipype/interfaces/freesurfer/base.py

@@ -189,16 +189,6 @@ class FSSurfaceCommand(FSCommand):
     including the full path in the filename, we can also avoid this behavior.
     """
 
-    def _get_filecopy_info(self):
-        self._normalize_filenames()
-        return super(FSSurfaceCommand, self)._get_filecopy_info()
-
-    def _normalize_filenames(self):
-        """Filename normalization routine to perform only when run in Node
-        context
-        """
-        pass
-
     @staticmethod
     def _associated_file(in_file, out_name):
         """Based on MRIsBuildFileName in freesurfer/utils/mrisurf.c

nipype/interfaces/freesurfer/utils.py

@@ -1289,9 +1289,11 @@ def _list_outputs(self):
 
         return outputs
 
-    def _normalize_filenames(self):
-        """ In a Node context, interpret out_file as a literal path to
-        reduce surprise.
+    def normalize_filenames(self):
+        """
+        Filename normalization routine to perform only when run in Node
+        context.
+        Interpret out_file as a literal path to reduce surprise.
         """
         if isdefined(self.inputs.out_file):
             self.inputs.out_file = os.path.abspath(self.inputs.out_file)
@@ -3837,8 +3839,11 @@ def _list_outputs(self):
                                                     self.inputs.out_name)
         return outputs
 
-    def _normalize_filenames(self):
-        """ Find full paths for pial, thickness and sphere files for copying
+    def normalize_filenames(self):
+        """
+        Filename normalization routine to perform only when run in Node
+        context.
+        Find full paths for pial, thickness and sphere files for copying.
         """
         in_file = self.inputs.in_file
 

nipype/pipeline/engine/nodes.py

@@ -32,6 +32,8 @@
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
                                 DynamicTraitedSpec, Bunch, InterfaceResult,
                                 Interface, isdefined)
+from ...interfaces.base.specs import get_filecopy_info
+
 from .utils import (
     _parameterization_dir, save_hashfile as _save_hashfile, load_resultfile as
     _load_resultfile, save_resultfile as _save_resultfile, nodelist_runner as
@@ -656,7 +658,8 @@ def _run_command(self, execute, copyfiles=True):
 
     def _copyfiles_to_wd(self, execute=True, linksonly=False):
         """copy files over and change the inputs"""
-        if not hasattr(self._interface, '_get_filecopy_info'):
+        filecopy_info = get_filecopy_info(self.interface)
+        if not filecopy_info:
             # Nothing to be done
             return
 
@@ -669,7 +672,7 @@ def _copyfiles_to_wd(self, execute=True, linksonly=False):
             outdir = op.join(outdir, '_tempinput')
             makedirs(outdir, exist_ok=True)
 
-        for info in self._interface._get_filecopy_info():
+        for info in filecopy_info:
             files = self.inputs.trait_get().get(info['key'])
             if not isdefined(files) or not files:
                 continue