prompt: We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  Env value of TOIL_DOCKER_REGISTRY is not honored in the docker image
  When a docker image is build with a custom `TOIL_DOCKER_REGISTRY`, the built docker image still looks at `quay.io/ucsc_cgl` for pulling related images (e.g. `mtail`, `grafana`, etc). The fix is to put the actual registry in `version_template.py`.
  
  --- END ISSUE ---
  
  Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
  --- BEGIN FILES ---
  Path: `version_template.py`
  Content:
  ```
  1 # Copyright (C) 2015-2018 Regents of the University of California
  2 #
  3 # Licensed under the Apache License, Version 2.0 (the "License");
  4 # you may not use this file except in compliance with the License.
  5 # You may obtain a copy of the License at
  6 #
  7 #     http://www.apache.org/licenses/LICENSE-2.0
  8 #
  9 # Unless required by applicable law or agreed to in writing, software
  10 # distributed under the License is distributed on an "AS IS" BASIS,
  11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  12 # See the License for the specific language governing permissions and
  13 # limitations under the License.
  14 
  15 """This script is a template for src/toil/version.py. Running it without arguments echoes all
  16 globals, i.e. module attributes. Constant assignments will be echoed verbatim while callables
  17 will be invoked and their result echoed as an assignment using the function name as the left-hand
  18 side and the return value of the function as right-hand side. To prevent a module attribute from
  19 being echoed, start or end the attribute name with an underscore. To print the value of a single
  20 symbol, pass the name of that attribute to the script as a command line argument. You can also
  21 import the expand_ function and invoke it directly with either no or exactly one argument."""
  22 
  23 # Note to maintainers:
  24 #
  25 #  - don't import at module level unless you want the imported value to be included in the output
  26 #  - only import from the Python standard run-time library (you can't have any dependencies)
  27 
  28 
  29 baseVersion = '3.20.0a1'
  30 cgcloudVersion = '1.6.0a1.dev393'
  31 dockerRegistry = 'quay.io/ucsc_cgl'
  32 dockerName = 'toil'
  33 
  34 
  35 def version():
  36     """
  37     A version identifier that includes the full-legth commit SHA1 and an optional suffix to
  38     indicate that the working copy is dirty.
  39     """
  40     return _version()
  41 
  42 
  43 def shortVersion():
  44     """
  45     A version identifier that includes the abbreviated commit SHA1 and an optional suffix to
  46     indicate that the working copy is dirty.
  47     """
  48     return _version(shorten=True)
  49 
  50 
  51 def _version(shorten=False):
  52     return '-'.join(filter(None, [distVersion(),
  53                                   currentCommit()[:7 if shorten else None],
  54                                   ('dirty' if dirty() else None)]))
  55 
  56 
  57 def distVersion():
  58     """
  59     The distribution version identifying a published release on PyPI.
  60     """
  61     from pkg_resources import parse_version
  62     build_number = buildNumber()
  63     parsedBaseVersion = parse_version(baseVersion)
  64     if isinstance(parsedBaseVersion, tuple):
  65         raise RuntimeError("Setuptools version 8.0 or newer required. Update by running "
  66                            "'pip install setuptools --upgrade'")
  67 
  68     if build_number is not None and parsedBaseVersion.is_prerelease:
  69         return baseVersion + '.dev' + build_number
  70     else:
  71         return baseVersion
  72 
  73 
  74 def dockerTag():
  75     """
  76     The primary tag of the Docker image for the appliance. This uniquely identifies the appliance
  77     image.
  78     """
  79     return version()
  80 
  81 
  82 def dockerShortTag():
  83     """
  84     A secondary, shortened form of :func:`dockerTag` with which to tag the appliance image for
  85     convenience.
  86     """
  87     return shortVersion()
  88 
  89 
  90 def dockerMinimalTag():
  91     """
  92     A minimal tag with which to tag the appliance image for convenience. Does not include
  93     information about the git commit or working copy dirtyness.
  94     """
  95     return distVersion()
  96 
  97 
  98 def buildNumber():
  99     """
  100     The Jenkins build number, if defined, else None.
  101     """
  102     import os
  103     return os.getenv('BUILD_NUMBER')
  104 
  105 
  106 def currentCommit():
  107     from subprocess import check_output
  108     try:
  109         output = check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).decode('utf-8').split()[0]
  110     except:
  111         # Return this we are not in a git environment.
  112         return '000'
  113     if isinstance(output, bytes):
  114         return output.decode('utf-8')
  115     return str(output)
  116 
  117 
  118 def dirty():
  119     from subprocess import call
  120     try:
  121         return 0 != call('(git diff --exit-code '
  122                          '&& git diff --cached --exit-code) > /dev/null', shell=True)
  123     except:
  124         return False # In case the git call fails.
  125 
  126 
  127 def expand_(name=None):
  128     variables = {k: v for k, v in globals().items()
  129                  if not k.startswith('_') and not k.endswith('_')}
  130 
  131     def resolve(k):
  132         v = variables[k]
  133         if callable(v):
  134             v = v()
  135         return v
  136 
  137     if name is None:
  138         return ''.join("%s = %s\n" % (k, repr(resolve(k))) for k, v in variables.items())
  139     else:
  140         return resolve(name)
  141 
  142 
  143 def _main():
  144     import sys
  145     sys.stdout.write(expand_(*sys.argv[1:]))
  146 
  147 
  148 if __name__ == '__main__':
  149     _main()
  150
  ```
  --- END FILES ---
  
  Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.
  
  Here is an example:
  
  ```diff
  diff --git a/examples/server_async.py b/examples/server_async.py
  --- a/examples/server_async.py
  +++ b/examples/server_async.py
  @@ -313,4 +313,4 @@
   
   
   if __name__ == "__main__":
  -    asyncio.run(run_async_server("."), debug=True)
  +    asyncio.run(run_async_server(), debug=True)
  diff --git a/examples/server_sync.py b/examples/server_sync.py
  --- a/examples/server_sync.py
  +++ b/examples/server_sync.py
  @@ -313,5 +313,5 @@
   
   
   if __name__ == "__main__":
  -    server = run_sync_server(".")
  +    server = run_sync_server()
       server.shutdown()
  
  ```
  
golden_diff: diff --git a/version_template.py b/version_template.py
  --- a/version_template.py
  +++ b/version_template.py
  @@ -28,7 +28,6 @@
   
   baseVersion = '3.20.0a1'
   cgcloudVersion = '1.6.0a1.dev393'
  -dockerRegistry = 'quay.io/ucsc_cgl'
   dockerName = 'toil'
   
   
  @@ -115,6 +114,11 @@
       return str(output)
   
   
  +def dockerRegistry():
  +    import os
  +    return os.getenv('TOIL_DOCKER_REGISTRY', 'quay.io/ucsc_cgl')
  +
  +
   def dirty():
       from subprocess import call
       try:
  
verification_info: {"golden_diff": "diff --git a/version_template.py b/version_template.py\n--- a/version_template.py\n+++ b/version_template.py\n@@ -28,7 +28,6 @@\n \n baseVersion = '3.20.0a1'\n cgcloudVersion = '1.6.0a1.dev393'\n-dockerRegistry = 'quay.io/ucsc_cgl'\n dockerName = 'toil'\n \n \n@@ -115,6 +114,11 @@\n     return str(output)\n \n \n+def dockerRegistry():\n+    import os\n+    return os.getenv('TOIL_DOCKER_REGISTRY', 'quay.io/ucsc_cgl')\n+\n+\n def dirty():\n     from subprocess import call\n     try:\n", "issue": "Env value of TOIL_DOCKER_REGISTRY is not honored in the docker image\nWhen a docker image is build with a custom `TOIL_DOCKER_REGISTRY`, the built docker image still looks at `quay.io/ucsc_cgl` for pulling related images (e.g. `mtail`, `grafana`, etc). The fix is to put the actual registry in `version_template.py`.\n", "before_files": [{"content": "# Copyright (C) 2015-2018 Regents of the University of California\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\n\"\"\"This script is a template for src/toil/version.py. Running it without arguments echoes all\nglobals, i.e. module attributes. Constant assignments will be echoed verbatim while callables\nwill be invoked and their result echoed as an assignment using the function name as the left-hand\nside and the return value of the function as right-hand side. To prevent a module attribute from\nbeing echoed, start or end the attribute name with an underscore. To print the value of a single\nsymbol, pass the name of that attribute to the script as a command line argument. You can also\nimport the expand_ function and invoke it directly with either no or exactly one argument.\"\"\"\n\n# Note to maintainers:\n#\n#  - don't import at module level unless you want the imported value to be included in the output\n#  - only import from the Python standard run-time library (you can't have any dependencies)\n\n\nbaseVersion = '3.20.0a1'\ncgcloudVersion = '1.6.0a1.dev393'\ndockerRegistry = 'quay.io/ucsc_cgl'\ndockerName = 'toil'\n\n\ndef version():\n    \"\"\"\n    A version identifier that includes the full-legth commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version()\n\n\ndef shortVersion():\n    \"\"\"\n    A version identifier that includes the abbreviated commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version(shorten=True)\n\n\ndef _version(shorten=False):\n    return '-'.join(filter(None, [distVersion(),\n                                  currentCommit()[:7 if shorten else None],\n                                  ('dirty' if dirty() else None)]))\n\n\ndef distVersion():\n    \"\"\"\n    The distribution version identifying a published release on PyPI.\n    \"\"\"\n    from pkg_resources import parse_version\n    build_number = buildNumber()\n    parsedBaseVersion = parse_version(baseVersion)\n    if isinstance(parsedBaseVersion, tuple):\n        raise RuntimeError(\"Setuptools version 8.0 or newer required. Update by running \"\n                           \"'pip install setuptools --upgrade'\")\n\n    if build_number is not None and parsedBaseVersion.is_prerelease:\n        return baseVersion + '.dev' + build_number\n    else:\n        return baseVersion\n\n\ndef dockerTag():\n    \"\"\"\n    The primary tag of the Docker image for the appliance. This uniquely identifies the appliance\n    image.\n    \"\"\"\n    return version()\n\n\ndef dockerShortTag():\n    \"\"\"\n    A secondary, shortened form of :func:`dockerTag` with which to tag the appliance image for\n    convenience.\n    \"\"\"\n    return shortVersion()\n\n\ndef dockerMinimalTag():\n    \"\"\"\n    A minimal tag with which to tag the appliance image for convenience. Does not include\n    information about the git commit or working copy dirtyness.\n    \"\"\"\n    return distVersion()\n\n\ndef buildNumber():\n    \"\"\"\n    The Jenkins build number, if defined, else None.\n    \"\"\"\n    import os\n    return os.getenv('BUILD_NUMBER')\n\n\ndef currentCommit():\n    from subprocess import check_output\n    try:\n        output = check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).decode('utf-8').split()[0]\n    except:\n        # Return this we are not in a git environment.\n        return '000'\n    if isinstance(output, bytes):\n        return output.decode('utf-8')\n    return str(output)\n\n\ndef dirty():\n    from subprocess import call\n    try:\n        return 0 != call('(git diff --exit-code '\n                         '&& git diff --cached --exit-code) > /dev/null', shell=True)\n    except:\n        return False # In case the git call fails.\n\n\ndef expand_(name=None):\n    variables = {k: v for k, v in globals().items()\n                 if not k.startswith('_') and not k.endswith('_')}\n\n    def resolve(k):\n        v = variables[k]\n        if callable(v):\n            v = v()\n        return v\n\n    if name is None:\n        return ''.join(\"%s = %s\\n\" % (k, repr(resolve(k))) for k, v in variables.items())\n    else:\n        return resolve(name)\n\n\ndef _main():\n    import sys\n    sys.stdout.write(expand_(*sys.argv[1:]))\n\n\nif __name__ == '__main__':\n    _main()\n", "path": "version_template.py"}], "after_files": [{"content": "# Copyright (C) 2015-2018 Regents of the University of California\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n#     http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, software\n# distributed under the License is distributed on an \"AS IS\" BASIS,\n# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n\n\"\"\"This script is a template for src/toil/version.py. Running it without arguments echoes all\nglobals, i.e. module attributes. Constant assignments will be echoed verbatim while callables\nwill be invoked and their result echoed as an assignment using the function name as the left-hand\nside and the return value of the function as right-hand side. To prevent a module attribute from\nbeing echoed, start or end the attribute name with an underscore. To print the value of a single\nsymbol, pass the name of that attribute to the script as a command line argument. You can also\nimport the expand_ function and invoke it directly with either no or exactly one argument.\"\"\"\n\n# Note to maintainers:\n#\n#  - don't import at module level unless you want the imported value to be included in the output\n#  - only import from the Python standard run-time library (you can't have any dependencies)\n\n\nbaseVersion = '3.20.0a1'\ncgcloudVersion = '1.6.0a1.dev393'\ndockerName = 'toil'\n\n\ndef version():\n    \"\"\"\n    A version identifier that includes the full-legth commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version()\n\n\ndef shortVersion():\n    \"\"\"\n    A version identifier that includes the abbreviated commit SHA1 and an optional suffix to\n    indicate that the working copy is dirty.\n    \"\"\"\n    return _version(shorten=True)\n\n\ndef _version(shorten=False):\n    return '-'.join(filter(None, [distVersion(),\n                                  currentCommit()[:7 if shorten else None],\n                                  ('dirty' if dirty() else None)]))\n\n\ndef distVersion():\n    \"\"\"\n    The distribution version identifying a published release on PyPI.\n    \"\"\"\n    from pkg_resources import parse_version\n    build_number = buildNumber()\n    parsedBaseVersion = parse_version(baseVersion)\n    if isinstance(parsedBaseVersion, tuple):\n        raise RuntimeError(\"Setuptools version 8.0 or newer required. Update by running \"\n                           \"'pip install setuptools --upgrade'\")\n\n    if build_number is not None and parsedBaseVersion.is_prerelease:\n        return baseVersion + '.dev' + build_number\n    else:\n        return baseVersion\n\n\ndef dockerTag():\n    \"\"\"\n    The primary tag of the Docker image for the appliance. This uniquely identifies the appliance\n    image.\n    \"\"\"\n    return version()\n\n\ndef dockerShortTag():\n    \"\"\"\n    A secondary, shortened form of :func:`dockerTag` with which to tag the appliance image for\n    convenience.\n    \"\"\"\n    return shortVersion()\n\n\ndef dockerMinimalTag():\n    \"\"\"\n    A minimal tag with which to tag the appliance image for convenience. Does not include\n    information about the git commit or working copy dirtyness.\n    \"\"\"\n    return distVersion()\n\n\ndef buildNumber():\n    \"\"\"\n    The Jenkins build number, if defined, else None.\n    \"\"\"\n    import os\n    return os.getenv('BUILD_NUMBER')\n\n\ndef currentCommit():\n    from subprocess import check_output\n    try:\n        output = check_output('git log --pretty=oneline -n 1 -- $(pwd)', shell=True).decode('utf-8').split()[0]\n    except:\n        # Return this we are not in a git environment.\n        return '000'\n    if isinstance(output, bytes):\n        return output.decode('utf-8')\n    return str(output)\n\n\ndef dockerRegistry():\n    import os\n    return os.getenv('TOIL_DOCKER_REGISTRY', 'quay.io/ucsc_cgl')\n\n\ndef dirty():\n    from subprocess import call\n    try:\n        return 0 != call('(git diff --exit-code '\n                         '&& git diff --cached --exit-code) > /dev/null', shell=True)\n    except:\n        return False # In case the git call fails.\n\n\ndef expand_(name=None):\n    variables = {k: v for k, v in globals().items()\n                 if not k.startswith('_') and not k.endswith('_')}\n\n    def resolve(k):\n        v = variables[k]\n        if callable(v):\n            v = v()\n        return v\n\n    if name is None:\n        return ''.join(\"%s = %s\\n\" % (k, repr(resolve(k))) for k, v in variables.items())\n    else:\n        return resolve(name)\n\n\ndef _main():\n    import sys\n    sys.stdout.write(expand_(*sys.argv[1:]))\n\n\nif __name__ == '__main__':\n    _main()\n", "path": "version_template.py"}]}