prompt: You will be provided with a partial code base and an issue statement explaining a problem to resolve.
  <issue>
  model: JSON to dict modified key values for transformation
  In ` Replace` transformation, you specify as a dict which variables to transform.
  
  e.g.:
  
  ```
  {'LIKELY': "5"}
  ```
  
  However, the parser from JSON to dict to convert BIDS Stats Models modifies keys to lower case, which in the case of specific case sensitive values modifies the transformation itself.
  
  </issue>
  <code>
  [start of bids/utils.py]
  1 """ Utility functions. """
  2 
  3 import re
  4 import os
  5 
  6 
  7 def listify(obj):
  8     ''' Wraps all non-list or tuple objects in a list; provides a simple way
  9     to accept flexible arguments. '''
  10     return obj if isinstance(obj, (list, tuple, type(None))) else [obj]
  11 
  12 
  13 def matches_entities(obj, entities, strict=False):
  14     ''' Checks whether an object's entities match the input. '''
  15     if strict and set(obj.entities.keys()) != set(entities.keys()):
  16         return False
  17 
  18     comm_ents = list(set(obj.entities.keys()) & set(entities.keys()))
  19     for k in comm_ents:
  20         current = obj.entities[k]
  21         target = entities[k]
  22         if isinstance(target, (list, tuple)):
  23             if current not in target:
  24                 return False
  25         elif current != target:
  26             return False
  27     return True
  28 
  29 
  30 def natural_sort(l, field=None):
  31     '''
  32     based on snippet found at http://stackoverflow.com/a/4836734/2445984
  33     '''
  34     convert = lambda text: int(text) if text.isdigit() else text.lower()
  35 
  36     def alphanum_key(key):
  37         if field is not None:
  38             key = getattr(key, field)
  39         if not isinstance(key, str):
  40             key = str(key)
  41         return [convert(c) for c in re.split('([0-9]+)', key)]
  42     return sorted(l, key=alphanum_key)
  43 
  44 
  45 def convert_JSON(j):
  46     """ Recursively convert CamelCase keys to snake_case.
  47     From: https://stackoverflow.com/questions/17156078/converting-identifier-naming-between-camelcase-and-underscores-during-json-seria
  48     """
  49 
  50     def camel_to_snake(s):
  51         a = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')
  52         return a.sub(r'_\1', s).lower()
  53 
  54     def convertArray(a):
  55         newArr = []
  56         for i in a:
  57             if isinstance(i,list):
  58                 newArr.append(convertArray(i))
  59             elif isinstance(i, dict):
  60                 newArr.append(convert_JSON(i))
  61             else:
  62                 newArr.append(i)
  63         return newArr
  64 
  65     out = {}
  66     for k, value in j.items():
  67         newK = camel_to_snake(k)
  68 
  69         if isinstance(value, dict):
  70             out[newK] = convert_JSON(value)
  71         elif isinstance(value, list):
  72             out[newK] = convertArray(value)
  73         else:
  74             out[newK] = value
  75 
  76     return out
  77 
  78 
  79 def splitext(path):
  80     """splitext for paths with directories that may contain dots.
  81     From https://stackoverflow.com/questions/5930036/separating-file-extensions-using-python-os-path-module"""
  82     li = []
  83     path_without_extensions = os.path.join(os.path.dirname(path),
  84         os.path.basename(path).split(os.extsep)[0])
  85     extensions = os.path.basename(path).split(os.extsep)[1:]
  86     li.append(path_without_extensions)
  87     # li.append(extensions) if you want extensions in another list inside the list that is returned.
  88     li.extend(extensions)
  89     return li
  90 
  91 
  92 def make_bidsfile(filename):
  93     """Create a BIDSFile instance of the appropriate class. """
  94     from .layout import models
  95 
  96     patt = re.compile("[._]*[a-zA-Z0-9]*?\\.([^/\\\\]+)$")
  97     m = re.search(patt, filename)
  98 
  99     ext = None if not m else m.group(1)
  100 
  101     if ext in ['nii', 'nii.gz']:
  102         cls = 'BIDSImageFile'
  103     elif ext in ['tsv', 'tsv.gz']:
  104         cls = 'BIDSDataFile'
  105     elif ext == 'json':
  106         cls = 'BIDSJSONFile'
  107     else:
  108         cls = 'BIDSFile'
  109 
  110     Cls = getattr(models, cls)
  111     return Cls(filename)
  112
  [end of bids/utils.py]
  </code>
  
  I need you to solve this issue by generating a single patch file that I can apply directly to this repository using git apply. Please respond with a single patch file in the following format.
  <patch>
  diff --git a/file.py b/file.py
  --- a/file.py
  +++ b/file.py
  @@ -1,27 +1,35 @@
   def euclidean(a, b):
  -    while b:
  -        a, b = b, a % b
  -    return a
  +    if b == 0:
  +        return a
  +    return euclidean(b, a % b)
   
   
   def bresenham(x0, y0, x1, y1):
       points = []
       dx = abs(x1 - x0)
       dy = abs(y1 - y0)
  -    sx = 1 if x0 < x1 else -1
  -    sy = 1 if y0 < y1 else -1
  -    err = dx - dy
  +    x, y = x0, y0
  +    sx = -1 if x0 > x1 else 1
  +    sy = -1 if y0 > y1 else 1
   
  -    while True:
  -        points.append((x0, y0))
  -        if x0 == x1 and y0 == y1:
  -            break
  -        e2 = 2 * err
  -        if e2 > -dy:
  -            err -= dy
  -            x0 += sx
  -        if e2 < dx:
  -            err += dx
  -            y0 += sy
  +    if dx > dy:
  +        err = dx / 2.0
  +        while x != x1:
  +            points.append((x, y))
  +            err -= dy
  +            if err < 0:
  +                y += sy
  +                err += dx
  +            x += sx
  +    else:
  +        err = dy / 2.0
  +        while y != y1:
  +            points.append((x, y))
  +            err -= dx
  +            if err < 0:
  +                x += sx
  +                err += dy
  +            y += sy
  +
  +    points.append((x, y))
       return points
  
  </patch>
golden_diff: diff --git a/bids/utils.py b/bids/utils.py
  --- a/bids/utils.py
  +++ b/bids/utils.py
  @@ -44,9 +44,10 @@
   
   def convert_JSON(j):
       """ Recursively convert CamelCase keys to snake_case.
  -    From: https://stackoverflow.com/questions/17156078/converting-identifier-naming-between-camelcase-and-underscores-during-json-seria
  +    From: https://stackoverflow.com/questions/17156078/
  +    converting-identifier-naming-between-camelcase-and-
  +    underscores-during-json-seria
       """
  -
       def camel_to_snake(s):
           a = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')
           return a.sub(r'_\1', s).lower()
  @@ -54,7 +55,7 @@
       def convertArray(a):
           newArr = []
           for i in a:
  -            if isinstance(i,list):
  +            if isinstance(i, list):
                   newArr.append(convertArray(i))
               elif isinstance(i, dict):
                   newArr.append(convert_JSON(i))
  @@ -66,7 +67,8 @@
       for k, value in j.items():
           newK = camel_to_snake(k)
   
  -        if isinstance(value, dict):
  +        # Replace transformation uses a dict, so skip lower-casing
  +        if isinstance(value, dict) and k != 'Replace':
               out[newK] = convert_JSON(value)
           elif isinstance(value, list):
               out[newK] = convertArray(value)
  
verification_info: {"golden_diff": "diff --git a/bids/utils.py b/bids/utils.py\n--- a/bids/utils.py\n+++ b/bids/utils.py\n@@ -44,9 +44,10 @@\n \n def convert_JSON(j):\n     \"\"\" Recursively convert CamelCase keys to snake_case.\n-    From: https://stackoverflow.com/questions/17156078/converting-identifier-naming-between-camelcase-and-underscores-during-json-seria\n+    From: https://stackoverflow.com/questions/17156078/\n+    converting-identifier-naming-between-camelcase-and-\n+    underscores-during-json-seria\n     \"\"\"\n-\n     def camel_to_snake(s):\n         a = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')\n         return a.sub(r'_\\1', s).lower()\n@@ -54,7 +55,7 @@\n     def convertArray(a):\n         newArr = []\n         for i in a:\n-            if isinstance(i,list):\n+            if isinstance(i, list):\n                 newArr.append(convertArray(i))\n             elif isinstance(i, dict):\n                 newArr.append(convert_JSON(i))\n@@ -66,7 +67,8 @@\n     for k, value in j.items():\n         newK = camel_to_snake(k)\n \n-        if isinstance(value, dict):\n+        # Replace transformation uses a dict, so skip lower-casing\n+        if isinstance(value, dict) and k != 'Replace':\n             out[newK] = convert_JSON(value)\n         elif isinstance(value, list):\n             out[newK] = convertArray(value)\n", "issue": "model: JSON to dict modified key values for transformation\nIn ` Replace` transformation, you specify as a dict which variables to transform.\r\n\r\ne.g.:\r\n\r\n```\r\n{'LIKELY': \"5\"}\r\n```\r\n\r\nHowever, the parser from JSON to dict to convert BIDS Stats Models modifies keys to lower case, which in the case of specific case sensitive values modifies the transformation itself.\n", "before_files": [{"content": "\"\"\" Utility functions. \"\"\"\n\nimport re\nimport os\n\n\ndef listify(obj):\n    ''' Wraps all non-list or tuple objects in a list; provides a simple way\n    to accept flexible arguments. '''\n    return obj if isinstance(obj, (list, tuple, type(None))) else [obj]\n\n\ndef matches_entities(obj, entities, strict=False):\n    ''' Checks whether an object's entities match the input. '''\n    if strict and set(obj.entities.keys()) != set(entities.keys()):\n        return False\n\n    comm_ents = list(set(obj.entities.keys()) & set(entities.keys()))\n    for k in comm_ents:\n        current = obj.entities[k]\n        target = entities[k]\n        if isinstance(target, (list, tuple)):\n            if current not in target:\n                return False\n        elif current != target:\n            return False\n    return True\n\n\ndef natural_sort(l, field=None):\n    '''\n    based on snippet found at http://stackoverflow.com/a/4836734/2445984\n    '''\n    convert = lambda text: int(text) if text.isdigit() else text.lower()\n\n    def alphanum_key(key):\n        if field is not None:\n            key = getattr(key, field)\n        if not isinstance(key, str):\n            key = str(key)\n        return [convert(c) for c in re.split('([0-9]+)', key)]\n    return sorted(l, key=alphanum_key)\n\n\ndef convert_JSON(j):\n    \"\"\" Recursively convert CamelCase keys to snake_case.\n    From: https://stackoverflow.com/questions/17156078/converting-identifier-naming-between-camelcase-and-underscores-during-json-seria\n    \"\"\"\n\n    def camel_to_snake(s):\n        a = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')\n        return a.sub(r'_\\1', s).lower()\n\n    def convertArray(a):\n        newArr = []\n        for i in a:\n            if isinstance(i,list):\n                newArr.append(convertArray(i))\n            elif isinstance(i, dict):\n                newArr.append(convert_JSON(i))\n            else:\n                newArr.append(i)\n        return newArr\n\n    out = {}\n    for k, value in j.items():\n        newK = camel_to_snake(k)\n\n        if isinstance(value, dict):\n            out[newK] = convert_JSON(value)\n        elif isinstance(value, list):\n            out[newK] = convertArray(value)\n        else:\n            out[newK] = value\n\n    return out\n\n\ndef splitext(path):\n    \"\"\"splitext for paths with directories that may contain dots.\n    From https://stackoverflow.com/questions/5930036/separating-file-extensions-using-python-os-path-module\"\"\"\n    li = []\n    path_without_extensions = os.path.join(os.path.dirname(path),\n        os.path.basename(path).split(os.extsep)[0])\n    extensions = os.path.basename(path).split(os.extsep)[1:]\n    li.append(path_without_extensions)\n    # li.append(extensions) if you want extensions in another list inside the list that is returned.\n    li.extend(extensions)\n    return li\n\n\ndef make_bidsfile(filename):\n    \"\"\"Create a BIDSFile instance of the appropriate class. \"\"\"\n    from .layout import models\n\n    patt = re.compile(\"[._]*[a-zA-Z0-9]*?\\\\.([^/\\\\\\\\]+)$\")\n    m = re.search(patt, filename)\n\n    ext = None if not m else m.group(1)\n\n    if ext in ['nii', 'nii.gz']:\n        cls = 'BIDSImageFile'\n    elif ext in ['tsv', 'tsv.gz']:\n        cls = 'BIDSDataFile'\n    elif ext == 'json':\n        cls = 'BIDSJSONFile'\n    else:\n        cls = 'BIDSFile'\n\n    Cls = getattr(models, cls)\n    return Cls(filename)\n", "path": "bids/utils.py"}]}