Hi Tony,

this is side-effect of tool migration and should not effect how Galaxy runs
in any way. Please ignore it for now, we will fix it later. :)

thanks

Martin


On Wed, Apr 23, 2014 at 5:55 PM, Tony Kusalik <kusa...@cs.usask.ca> wrote:

> Hi,
>
> On April 16th, I did an
>    hg incoming
> command to update my local version of Galaxy.  Once I restarted my server,
> I was told to do
>    sh ./scripts/migrate_tools/0010_tools.sh
> take care of tools which had been migrated to the tool shed.
>
> Ever since the two changes above, I am seeing strange errors in paster.log
> that I do not understand.  Here are some samples:
> (Note that Galaxy is installed in directory /birl2/Galaxy.)
>
> -- begin paste --
> galaxy.tools ERROR 2014-04-23 12:29:48,869 Error reading tool from path:
> data_source/bx_browser.xml
> Traceback (most recent call last):
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544,
> in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid,
> repository_id=repository_id )
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658,
> in load_tool
>     tree = load_tool( config_file )
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in
> load_tool
>     tree = parse_xml(path)
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154,
> in parse_xml
>     tree = ElementTree.parse(fname)
>   File
> "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
> line 859, in parse
>     tree.parse(source, parser)
>   File
> "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
> line 576, in parse
>     source = open(source, "rb")
> IOError: [Errno 2] No such file or directory:
> './tools/data_source/bx_browser.xml'
> galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path:
> data_source/flymine.xml
> Traceback (most recent call last):
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544,
> in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid,
> repository_id=repository_id )
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658,
> in load_tool
>     tree = load_tool( config_file )
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in
> load_tool
>     tree = parse_xml(path)
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154,
> in parse_xml
>     tree = ElementTree.parse(fname)
>   File
> "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
> line 859, in parse
>     tree.parse(source, parser)
>   File
> "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
> line 576, in parse
>     source = open(source, "rb")
> IOError: [Errno 2] No such file or directory:
> './tools/data_source/flymine.xml'
> galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path:
> data_source/flymine_test.xml
> Traceback (most recent call last):
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544,
> in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid,
> repository_id=repository_id )
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658,
> in load_tool
>     tree = load_tool( config_file )
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in
> load_tool
>     tree = parse_xml(path)
>   File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154,
> in parse_xml
>     tree = ElementTree.parse(fname)
>   File
> "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
> line 859, in parse
>     tree.parse(source, parser)
>   File
> "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
> line 576, in parse
>     source = open(source, "rb")
> -- end paste --
>
> This pattern of error messages continues for/from flymine_test.xml,
> mousemine.xml, ratmine.xml, yeastmine.xml, metabolicmine.xml,
> encode_db.xml, epigraph_import.xml, epigraph_import_test.xml, epigraph.xml,
> epigraph_test.xml, gencode_partition.xml, random_intervals.xml,
> column_join.xml, wiggle_to_simple, phastOdds_tool.xml.  The general theme
> is the constant reference to "elementtree-1.2.6_20050316-py2.7.egg".  Also
> of note is that an ls command says that
> /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg is a
> regular file, and not a directory.
>
> Within the Galaxy Admin window, I tried to search for tools (either
> installed or available) matching "ElementTree" but couldn't find anything.
>  Further, checking paster.log files from prior to having given the
>   sh ./scripts/migrate_tools/0009_tools.sh
> command, I see
> /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg
> mentioned in the python path given at the beginning of paster.log, but no
> error messages involving "ElementTree" or "elementtree".
>
> How do I deal with this problem, and get the server to come up error free?
>  Any suggestions would be welcome.
>
>
>
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