Merge pull request #1908 from satra/fix/clirun

MRG: allow more support for cli

Author: satra

nipype/scripts/utils.py

@@ -3,9 +3,12 @@
 Utilities for the CLI functions.
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-import re
 
+from builtins import bytes, str
+
+import re
 import click
+import json
 
 from .instance import import_module
 from ..interfaces.base import InputMultiPath, traits
@@ -16,7 +19,6 @@
 UNKNOWN_OPTIONS = dict(allow_extra_args=True,
                        ignore_unknown_options=True)
 
-
 # specification of existing ParamTypes
 ExistingDirPath  = click.Path(exists=True, file_okay=False, resolve_path=True)
 ExistingFilePath = click.Path(exists=True,  dir_okay=False, resolve_path=True)
@@ -63,18 +65,62 @@ def add_args_options(arg_parser, interface):
         # Escape any % signs with a %
         desc = desc.replace('%', '%%')
         args = {}
+        has_multiple_inner_traits = False
 
         if spec.is_trait_type(traits.Bool):
             args["default"] = getattr(inputs, name)
             args["action"] = 'store_true'
 
-        if hasattr(spec, "mandatory") and spec.mandatory:
+        print(name, spec.trait_type)
+        # current support is for simple trait types
+        if not spec.inner_traits:
+            if not spec.is_trait_type(traits.TraitCompound):
+                trait_type = type(spec.trait_type.default_value)
+            if trait_type in (bytes, str, int, float):
+                if trait_type == bytes:
+                    trait_type = str
+                args["type"] = trait_type
+        elif len(spec.inner_traits) == 1:
+            trait_type = type(spec.inner_traits[0].trait_type.default_value)
+            if trait_type == bytes:
+                trait_type = str
+            if trait_type in (bytes, bool, str, int, float):
+                args["type"] = trait_type
+        else:
+            if len(spec.inner_traits) > 1:
+                if not spec.is_trait_type(traits.Dict):
+                    has_multiple_inner_traits = True
+
+        if getattr(spec, "mandatory", False):
             if spec.is_trait_type(InputMultiPath):
                 args["nargs"] = "+"
+            elif spec.is_trait_type(traits.List):
+                if (spec.trait_type.minlen == spec.trait_type.maxlen) and \
+                        spec.trait_type.maxlen:
+                    args["nargs"] = spec.trait_type.maxlen
+                else:
+                    args["nargs"] = "+"
+            elif spec.is_trait_type(traits.Dict):
+                args["type"] = json.loads
+
+            if has_multiple_inner_traits:
+                raise NotImplementedError(
+                    ('This interface cannot be used. via the'
+                     ' command line as multiple inner traits'
+                     ' are currently not supported for mandatory'
+                     ' argument: {}.'.format(name)))
             arg_parser.add_argument(name, help=desc, **args)
         else:
             if spec.is_trait_type(InputMultiPath):
                 args["nargs"] = "*"
-            arg_parser.add_argument("--%s" % name, dest=name,
-                                    help=desc, **args)
+            elif spec.is_trait_type(traits.List):
+                if (spec.trait_type.minlen == spec.trait_type.maxlen) and \
+                        spec.trait_type.maxlen:
+                    args["nargs"] = spec.trait_type.maxlen
+                else:
+                    args["nargs"] = "*"
+            if not has_multiple_inner_traits:
+                arg_parser.add_argument("--%s" % name, dest=name,
+                                        help=desc, **args)
+
     return arg_parser

nipype/utils/nipype_cmd.py

@@ -50,19 +50,8 @@ def run_instance(interface, options):
     print("setting function inputs")
 
     for input_name, _ in list(interface.inputs.items()):
-        if getattr(options, input_name) != None:
+        if getattr(options, input_name) is not None:
             value = getattr(options, input_name)
-            if not isinstance(value, bool):
-                # traits cannot cast from string to float or int
-                try:
-                    value = float(value)
-                except:
-                    pass
-                # try to cast string input to boolean
-                try:
-                    value = str2bool(value)
-                except:
-                    pass
             try:
                 setattr(interface.inputs, input_name,
                         value)