merging dev into master

argschema/argschema_parser.py

@@ -6,6 +6,7 @@
 import copy
 from . import schemas
 from . import utils
+from . import fields
 import marshmallow as mm
 
 
@@ -160,26 +161,20 @@ def __init__(self,
         self.logger.debug('argsdict is {}'.format(argsdict))
 
         if argsobj.input_json is not None:
-            result = self.schema.load(argsdict)
-            if 'input_json' in result.errors:
-                raise mm.ValidationError(result.errors['input_json'])
-            with open(result.data['input_json'], 'r') as j:
+            fields.files.validate_input_path(argsobj.input_json)
+            with open(argsobj.input_json, 'r') as j:
                 jsonargs = json.load(j)
         else:
             jsonargs = input_data if input_data else {}
 
-
         # merge the command line dictionary into the input json
         args = utils.smart_merge(jsonargs, argsdict)
         self.logger.debug('args after merge {}'.format(args))
 
         # validate with load!
         result = self.load_schema_with_defaults(self.schema, args)
-        if len(result.errors) > 0:
-            raise mm.ValidationError(json.dumps(result.errors, indent=2))
 
-        self.schema_args = result
-        self.args = result.data
+        self.args = result
         self.output_schema_type = output_schema_type
         self.logger = self.initialize_logger(
             logger_name, self.args.get('log_level'))
@@ -204,9 +199,7 @@ def get_output_json(self,d):
         """
         if self.output_schema_type is not None:
             schema = self.output_schema_type()
-            (output_json,errors)=schema.dump(d)
-            if len(errors)>0:
-                raise mm.ValidationError(json.dumps(errors))
+            output_json = utils.dump(schema,d)
         else:
             self.logger.warning("output_schema_type is not defined,\
                                  the output won't be validated")
@@ -278,7 +271,7 @@ def load_schema_with_defaults(self  ,schema, args):
                 'Recursive schemas need to subclass argschema.DefaultSchema else defaults will not work')
 
         # load the dictionary via the schema
-        result = schema.load(args)
+        result = utils.load(schema, args)
 
         return result
 

argschema/fields/files.py

@@ -113,6 +113,11 @@ def _validate(self, value):
         # use outputfile to test that a file in this location is a valid path
         validate_outpath(value)
 
+def validate_input_path(value):
+    if not os.path.isfile(value):
+        raise mm.ValidationError("%s is not a file" % value)
+    elif not os.access(value, os.R_OK):
+        raise mm.ValidationError("%s is not readable" % value)
 
 class InputDir(mm.fields.Str):
     """InputDir is  :class:`marshmallow.fields.Str` subclass which is a path to a
@@ -135,7 +140,4 @@ class InputFile(mm.fields.Str):
     """
 
     def _validate(self, value):
-        if not os.path.isfile(value):
-            raise mm.ValidationError("%s is not a file" % value)
-        elif not os.access(value, os.R_OK):
-            raise mm.ValidationError("%s is not readable" % value)
+        validate_input_path(value)

argschema/utils.py

@@ -371,11 +371,11 @@ def schema_argparser(schema):
 
     """
 
-    #build up a list of argument groups using recursive function
-    #to traverse the tree, root node gets the description given by doc string
-    #of the schema
+    # build up a list of argument groups using recursive function
+    # to traverse the tree, root node gets the description given by doc string
+    # of the schema
     arguments = build_schema_arguments(schema,description=schema.__doc__)
-    #make the root schema appeear first rather than last
+    # make the root schema appeear first rather than last
     arguments = [arguments[-1]]+arguments[0:-1]
 
     parser = argparse.ArgumentParser()
@@ -385,3 +385,64 @@ def schema_argparser(schema):
         for arg_name,arg in arg_group['args'].items():
             group.add_argument(arg_name, **arg)
     return parser
+
+def load(schema, d):
+    """ function to wrap marshmallow load to smooth 
+        differences from marshmallow 2 to 3 
+        
+    Parameters
+    ----------
+    schema: marshmallow.Schema
+        schema that you want to use to validate
+    d: dict
+        dictionary to validate and load
+    
+    Returns
+    -------
+    dict
+        deserialized and validated dictionary
+    
+    Raises
+    ------
+    marshmallow.ValidationError
+        if the dictionary does not conform to the schema
+    """
+
+    results = schema.load(d)
+    if isinstance(results, tuple):
+        (results, errors) = results
+        if len(errors) > 0:
+            raise mm.ValidationError(errors)
+
+    return results
+
+
+def dump(schema, d):
+    """ function to wrap marshmallow dump to smooth 
+        differences from marshmallow 2 to 3 
+        
+    Parameters
+    ----------
+    schema: marshmallow.Schema
+        schema that you want to use to validate and dump
+    d: dict
+        dictionary to validate and dump
+    
+    Returns
+    -------
+    dict
+        serialized and validated dictionary
+    
+    Raises
+    ------
+    marshmallow.ValidationError
+        if the dictionary does not conform to the schema
+    """
+
+    results = schema.dump(d)
+    if isinstance(results, tuple):
+        (results, errors) = results
+        if len(errors) > 0:
+            raise mm.ValidationError(errors)
+
+    return results

requirements.txt

@@ -1,2 +1,2 @@
 numpy
-marshmallow<=3.0.0
+marshmallow

setup.py

@@ -7,7 +7,7 @@
     test_required = f.read().splitlines()
 
 setup(name='argschema',
-      version='1.16.6',
+      version='1.17.1',
       description=' a wrapper for setting up modules that can have parameters specified by command line arguments,\
        json_files, or dictionary objects. Providing a common wrapper for data processing modules.',
       author='Forrest Collman,David Feng',

test/fields/test_numpyarray.py

@@ -1,6 +1,7 @@
 import pytest
 from argschema import ArgSchemaParser, ArgSchema
 from argschema.fields import NumpyArray
+from argschema.utils import load,dump
 import marshmallow as mm
 import numpy as np
 
@@ -46,7 +47,6 @@ def test_serialize():
     object_dict = {
         'a': np.array([1, 2])
     }
-    (json_dict, errors) = schema.dump(object_dict)
-    assert(len(errors) == 0)
+    json_dict = dump(schema, object_dict)
     assert(type(json_dict['a']) == list)
     assert(json_dict['a'] == object_dict['a'].tolist())

test/test_nested_examples.py

@@ -18,5 +18,4 @@ def test_nested_example():
 
 def test_nested_marshmallow_example():
     schema = MySchema()
-    (result,errors)=schema.load({})
-    assert(len(errors)==0)
+    argschema.utils.load(schema, {})