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Do not write shed_tool_data_table_config in place
This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in #5031.
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Original file line number | Diff line number | Diff line change |
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"""Safely write file to temporary file and then move file into place.""" | ||
# Copied from https://stackoverflow.com/a/12007885. | ||
import os | ||
import tempfile | ||
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class RenamedTemporaryFile(object): | ||
""" | ||
A temporary file object which will be renamed to the specified | ||
path on exit. | ||
""" | ||
def __init__(self, final_path, **kwargs): | ||
tmpfile_dir = kwargs.pop('dir', None) | ||
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# Put temporary file in the same directory as the location for the | ||
# final file so that an atomic move into place can occur. | ||
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if tmpfile_dir is None: | ||
tmpfile_dir = os.path.dirname(final_path) | ||
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self.tmpfile = tempfile.NamedTemporaryFile(dir=tmpfile_dir, **kwargs) | ||
self.final_path = final_path | ||
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def __getattr__(self, attr): | ||
""" | ||
Delegate attribute access to the underlying temporary file object. | ||
""" | ||
return getattr(self.tmpfile, attr) | ||
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def __enter__(self): | ||
self.tmpfile.__enter__() | ||
return self | ||
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def __exit__(self, exc_type, exc_val, exc_tb): | ||
if exc_type is None: | ||
self.tmpfile.delete = False | ||
result = self.tmpfile.__exit__(exc_type, exc_val, exc_tb) | ||
os.rename(self.tmpfile.name, self.final_path) | ||
else: | ||
result = self.tmpfile.__exit__(exc_type, exc_val, exc_tb) | ||
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return result |