Hi all,
Running galaxy-central default branch, I've seen a couple of cases where
what otherwise appears to be a successful job has failed with:
Traceback (most recent call last):
File "./scripts/set_metadata.py", line 122, in <module>
__main__()
File "./scripts/set_metadata.py", line 72, in __main__
datatypes_registry.load_datatypes( root_dir=config_root,
config=datatypes_config )
File "/mnt/galaxy/galaxy-central/lib/galaxy/datatypes/registry.py",
line 67, in load_datatypes
tree = galaxy.util.parse_xml( config )
File "/mnt/galaxy/galaxy-central/lib/galaxy/util/__init__.py", line
135, in parse_xml
tree = ElementTree.parse(fname)
File
"/mnt/galaxy/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 859, in parse
File
"/mnt/galaxy/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 576, in parse
IOError: [Errno 2] No such file or directory:
'/mnt/galaxy/galaxy-central/database/tmp/tmpWJZ1Aw'
I'm not quite sure what was in the temporary XML file which
no longer exists, perhaps there is a race condition with the
removal of the temporary files?
Has anyone else observed this?
Thanks,
Peter
One minor change which might help give a clearer error message
here (and in related issues like the functional tests where not all
the tools listed in tool_conf.xml.sample always exists on disk) is:
$ hg diff /mnt/galaxy/galaxy-central/lib/galaxy/util/__init__.py
diff -r 01b94ad2c377 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py Tue Oct 15 00:12:08 2013 -0400
+++ b/lib/galaxy/util/__init__.py Tue Oct 15 14:20:01 2013 +0100
@@ -132,6 +132,8 @@
def parse_xml(fname):
"""Returns a parsed xml tree"""
+ if not os.path.isfile(fname):
+ raise IOError("Asked to parse non-existant XML file %r" % fname)
tree = ElementTree.parse(fname)
root = tree.getroot()
ElementInclude.include(root)
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