ENH: Add resolve/rebase BasePath traits methods & tests

Two new methods ``resolve_path_traits`` and ``rebase_path_traits`` are
being included.

They take trait instances from a spec (selected via
``spec.trait('traitname')``, the value and a base path.

These two functions will be usefull to progress towards #2944.

Author: oesteban

nipype/interfaces/base/tests/test_traits_extension.py

@@ -0,0 +1,152 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+from __future__ import print_function, unicode_literals
+
+from ... import base as nib
+from ..traits_extension import rebase_path_traits, resolve_path_traits, Path
+
+
+class _test_spec(nib.TraitedSpec):
+    a = nib.traits.File()
+    b = nib.traits.Tuple(nib.File(),
+                         nib.File())
+    c = nib.traits.List(nib.File())
+    d = nib.traits.Either(nib.File(), nib.traits.Float())
+    e = nib.OutputMultiObject(nib.File())
+    f = nib.traits.Dict(nib.Str, nib.File())
+    g = nib.traits.Either(nib.File, nib.Str)
+    h = nib.Str
+    ee = nib.OutputMultiObject(nib.Str)
+
+
+def test_rebase_path_traits():
+    """Check rebase_path_traits."""
+    spec = _test_spec()
+
+    a = rebase_path_traits(
+        spec.trait('a'), '/some/path/f1.txt', '/some/path')
+    assert '%s' % a == 'f1.txt'
+
+    b = rebase_path_traits(
+        spec.trait('b'), ('/some/path/f1.txt', '/some/path/f2.txt'), '/some/path')
+    assert b == (Path('f1.txt'), Path('f2.txt'))
+
+    c = rebase_path_traits(
+        spec.trait('c'), ['/some/path/f1.txt', '/some/path/f2.txt', '/some/path/f3.txt'],
+        '/some/path')
+    assert c == [Path('f1.txt'), Path('f2.txt'), Path('f3.txt')]
+
+    d = rebase_path_traits(
+        spec.trait('d'), 2.0, '/some/path')
+    assert d == 2.0
+
+    d = rebase_path_traits(
+        spec.trait('d'), '/some/path/either.txt', '/some/path')
+    assert '%s' % d == 'either.txt'
+
+    e = rebase_path_traits(
+        spec.trait('e'), ['/some/path/f1.txt', '/some/path/f2.txt', '/some/path/f3.txt'],
+        '/some/path')
+    assert e == [Path('f1.txt'), Path('f2.txt'), Path('f3.txt')]
+
+    e = rebase_path_traits(
+        spec.trait('e'), [['/some/path/f1.txt', '/some/path/f2.txt'], [['/some/path/f3.txt']]],
+        '/some/path')
+    assert e == [[Path('f1.txt'), Path('f2.txt')], [[Path('f3.txt')]]]
+
+    f = rebase_path_traits(
+        spec.trait('f'), {'1': '/some/path/f1.txt'}, '/some/path')
+    assert f == {'1': Path('f1.txt')}
+
+    g = rebase_path_traits(
+        spec.trait('g'), 'some/path/either.txt', '/some/path')
+    assert '%s' % g == 'some/path/either.txt'
+
+    g = rebase_path_traits(
+        spec.trait('g'), '/some/path/either.txt', '/some')
+    assert '%s' % g == 'path/either.txt'
+
+    g = rebase_path_traits(spec.trait('g'), 'string', '/some')
+    assert '%s' % g == 'string'
+
+    g = rebase_path_traits(spec.trait('g'), '2', '/some/path')
+    assert g == '2'  # You dont want this one to be a Path
+
+    h = rebase_path_traits(spec.trait('h'), '2', '/some/path')
+    assert h == '2'
+
+    ee = rebase_path_traits(
+        spec.trait('ee'), [['/some/path/f1.txt', '/some/path/f2.txt'], [['/some/path/f3.txt']]],
+        '/some/path')
+    assert ee == [['/some/path/f1.txt', '/some/path/f2.txt'], [['/some/path/f3.txt']]]
+
+
+def test_resolve_path_traits():
+    """Check resolve_path_traits."""
+    spec = _test_spec()
+
+    a = resolve_path_traits(
+        spec.trait('a'), 'f1.txt', '/some/path')
+    assert a == Path('/some/path/f1.txt')
+
+    b = resolve_path_traits(
+        spec.trait('b'), ('f1.txt', 'f2.txt'), '/some/path')
+    assert b == (Path('/some/path/f1.txt'), Path('/some/path/f2.txt'))
+
+    c = resolve_path_traits(
+        spec.trait('c'), ['f1.txt', 'f2.txt', 'f3.txt'],
+        '/some/path')
+    assert c == [Path('/some/path/f1.txt'), Path('/some/path/f2.txt'), Path('/some/path/f3.txt')]
+
+    d = resolve_path_traits(
+        spec.trait('d'), 2.0, '/some/path')
+    assert d == 2.0
+
+    d = resolve_path_traits(
+        spec.trait('d'), 'either.txt', '/some/path')
+    assert '%s' % d == '/some/path/either.txt'
+
+    e = resolve_path_traits(
+        spec.trait('e'), ['f1.txt', 'f2.txt', 'f3.txt'],
+        '/some/path')
+    assert e == [Path('/some/path/f1.txt'), Path('/some/path/f2.txt'), Path('/some/path/f3.txt')]
+
+    e = resolve_path_traits(
+        spec.trait('e'), [['f1.txt', 'f2.txt'], [['f3.txt']]],
+        '/some/path')
+    assert e == [[Path('/some/path/f1.txt'), Path('/some/path/f2.txt')],
+                 [[Path('/some/path/f3.txt')]]]
+
+    f = resolve_path_traits(
+        spec.trait('f'), {'1': 'path/f1.txt'}, '/some')
+    assert f == {'1': Path('/some/path/f1.txt')}
+
+    g = resolve_path_traits(
+        spec.trait('g'), '/either.txt', '/some/path')
+    assert g == Path('/either.txt')
+
+    # This is a problematic case, it is impossible to know whether this
+    # was meant to be a string or a file.
+    # Commented out because in this implementation, strings take precedence
+    # g = resolve_path_traits(
+    #     spec.trait('g'), 'path/either.txt', '/some')
+    # assert g == Path('/some/path/either.txt')
+
+    # This is a problematic case, it is impossible to know whether this
+    # was meant to be a string or a file.
+    g = resolve_path_traits(spec.trait('g'), 'string', '/some')
+    assert g == 'string'
+
+    # This is a problematic case, it is impossible to know whether this
+    # was meant to be a string or a file.
+    g = resolve_path_traits(spec.trait('g'), '2', '/some/path')
+    assert g == '2'  # You dont want this one to be a Path
+
+    h = resolve_path_traits(spec.trait('h'), '2', '/some/path')
+    assert h == '2'
+
+    ee = resolve_path_traits(
+        spec.trait('ee'), [['f1.txt', 'f2.txt'], [['f3.txt']]],
+        '/some/path')
+    assert ee == [['f1.txt', 'f2.txt'], [['f3.txt']]]

nipype/interfaces/base/traits_extension.py

@@ -30,6 +30,7 @@
 import traits.api as traits
 from traits.trait_handlers import TraitType, NoDefaultSpecified
 from traits.trait_base import _Undefined
+from traits.traits import _TraitMaker, trait_from
 
 from traits.api import Unicode
 from future import standard_library
@@ -307,6 +308,11 @@ def validate(self, objekt, name, value, return_pathlike=False):
         return value
 
 
+# Patch in traits these two new
+traits.File = File
+traits.Directory = Directory
+
+
 class ImageFile(File):
     """Defines a trait whose value must be a known neuroimaging file."""
 
@@ -468,3 +474,120 @@ class InputMultiObject(MultiObject):
 
 InputMultiPath = InputMultiObject
 OutputMultiPath = OutputMultiObject
+
+
+class Tuple(traits.BaseTuple):
+    """Defines a new type of Tuple trait that reports inner types."""
+
+    def init_fast_validator(self, *args):
+        """Set up the C-level fast validator."""
+        super(Tuple, self).init_fast_validator(*args)
+        self.fast_validate = args
+
+    def inner_traits(self):
+        """Return the *inner trait* (or traits) for this trait."""
+        return self.types
+
+
+class PatchedEither(TraitType):
+    """Defines a trait whose value can be any of of a specified list of traits."""
+
+    def __init__(self, *traits, **metadata):
+        """Create a trait whose value can be any of of a specified list of traits."""
+        metadata['alternatives'] = tuple(trait_from(t) for t in traits)
+        self.trait_maker = _TraitMaker(
+            metadata.pop("default", None), *traits, **metadata)
+
+    def as_ctrait(self):
+        """Return a CTrait corresponding to the trait defined by this class."""
+        return self.trait_maker.as_ctrait()
+
+
+traits.Tuple = Tuple
+traits.Either = PatchedEither
+
+
+def _rebase_path(value, cwd):
+    if isinstance(value, list):
+        return [_rebase_path(v, cwd) for v in value]
+
+    try:
+        value = Path(value)
+    except TypeError:
+        pass
+    else:
+        try:
+            value = Path(value).relative_to(cwd)
+        except ValueError:
+            pass
+    return value
+
+
+def rebase_path_traits(thistrait, value, cwd):
+    """Rebase a BasePath-derived trait given an interface spec."""
+    if thistrait.is_trait_type(BasePath):
+        value = _rebase_path(value, cwd)
+    elif thistrait.is_trait_type(traits.List):
+        innertrait, = thistrait.inner_traits
+        if not isinstance(value, (list, tuple)):
+            value = rebase_path_traits(innertrait, value, cwd)
+        else:
+            value = [rebase_path_traits(innertrait, v, cwd)
+                     for v in value]
+    elif thistrait.is_trait_type(traits.Dict):
+        _, innertrait = thistrait.inner_traits
+        value = {k: rebase_path_traits(innertrait, v, cwd)
+                 for k, v in value.items()}
+    elif thistrait.is_trait_type(Tuple):
+        value = tuple([rebase_path_traits(subtrait, v, cwd)
+                       for subtrait, v in zip(thistrait.inner_traits, value)])
+    elif thistrait.alternatives:
+        is_str = [f.is_trait_type((traits.String, traits.BaseStr, traits.BaseBytes, Str))
+                  for f in thistrait.alternatives]
+        if any(is_str) and isinstance(value, (bytes, str)) and not value.startswith('/'):
+            return value
+        for subtrait in thistrait.alternatives:
+            value = rebase_path_traits(subtrait, value, cwd)
+    return value
+
+
+def _resolve_path(value, cwd):
+    if isinstance(value, list):
+        return [_resolve_path(v, cwd) for v in value]
+
+    try:
+        value = Path(value)
+    except TypeError:
+        pass
+    else:
+        if not value.is_absolute():
+            value = Path(cwd) / value
+    return value
+
+
+def resolve_path_traits(thistrait, value, cwd):
+    """Resolve a BasePath-derived trait given an interface spec."""
+    if thistrait.is_trait_type(BasePath):
+        value = _resolve_path(value, cwd)
+    elif thistrait.is_trait_type(traits.List):
+        innertrait, = thistrait.inner_traits
+        if not isinstance(value, (list, tuple)):
+            value = resolve_path_traits(innertrait, value, cwd)
+        else:
+            value = [resolve_path_traits(innertrait, v, cwd)
+                     for v in value]
+    elif thistrait.is_trait_type(traits.Dict):
+        _, innertrait = thistrait.inner_traits
+        value = {k: resolve_path_traits(innertrait, v, cwd)
+                 for k, v in value.items()}
+    elif thistrait.is_trait_type(Tuple):
+        value = tuple([resolve_path_traits(subtrait, v, cwd)
+                       for subtrait, v in zip(thistrait.inner_traits, value)])
+    elif thistrait.alternatives:
+        is_str = [f.is_trait_type((traits.String, traits.BaseStr, traits.BaseBytes, Str))
+                  for f in thistrait.alternatives]
+        if any(is_str) and isinstance(value, (bytes, str)) and not value.startswith('/'):
+            return value
+        for subtrait in thistrait.alternatives:
+            value = resolve_path_traits(subtrait, value, cwd)
+    return value