Hi,
Me again. I don't know why I've suddenly got all these errors. Updates aren't normally this problematic.
This time I've got a huge amount of these errors in my paster.log: galaxy.tools ERROR 2010-03-09 14:12:46,128 error in help for tool Upload File Traceback (most recent call last): File "/homes/www-galaxy/galaxy_live/lib/galaxy/tools/__init__.py", line 489, in parse_help self.help = util.rst_to_html(self.help.text) File "/homes/www-galaxy/galaxy_live/lib/galaxy/util/__init__.py", line 232, in rst_to_html return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) ) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string enable_exit_status=enable_exit_status) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 607, in publish_programmatically pub.set_components(reader_name, parser_name, writer_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 92, in set_components self.set_reader(reader_name, self.parser, parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 82, in set_reader self.reader = reader_class(parser, parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 51, in __init__ self.set_parser(parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 62, in set_parser parser_class = parsers.get_parser_class(parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/__init__.py", line 48, in get_parser_class module = __import__(parser_name, globals(), locals()) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/__init__.py", line 77, in <module> from docutils.parsers.rst import states File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 110, in <module> import roman ImportError: No module named roman
As far as I can see there's an error (like above) for every tool and the help text for the tools is no longer displayed within Galaxy. Has something changed in how the XML files should be formatted or is it something in the egg that's not right?
Thanks again for any help. Cheers,
Chris
Chris Cole wrote:
Hi,
Me again. I don't know why I've suddenly got all these errors. Updates aren't normally this problematic.
A recent update included a nearly complete rewrite of egg support and a rebuild of all the eggs. I tested pretty extensively, but it wasn't possible to test every case.
This time I've got a huge amount of these errors in my paster.log: "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 110, in <module> import roman ImportError: No module named roman
As far as I can see there's an error (like above) for every tool and the help text for the tools is no longer displayed within Galaxy. Has something changed in how the XML files should be formatted or is it something in the egg that's not right?
The Python 2.6 docutils egg needed to be rebuilt due to this missing dependent extra module. If you remove eggs/docutils-0.4-py2.6.egg and then start up Galaxy, it'll fetch the new docutils egg and this should be fixed.
--nate
Thanks again for any help. Cheers,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On 10/03/10 14:27, Nate Coraor wrote:
Chris Cole wrote:
Hi,
Me again. I don't know why I've suddenly got all these errors. Updates aren't normally this problematic.
A recent update included a nearly complete rewrite of egg support and a rebuild of all the eggs. I tested pretty extensively, but it wasn't possible to test every case.
OK. I didn't realise.
This time I've got a huge amount of these errors in my paster.log: "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 110, in <module> import roman ImportError: No module named roman
As far as I can see there's an error (like above) for every tool and the help text for the tools is no longer displayed within Galaxy. Has something changed in how the XML files should be formatted or is it something in the egg that's not right?
The Python 2.6 docutils egg needed to be rebuilt due to this missing dependent extra module. If you remove eggs/docutils-0.4-py2.6.egg and then start up Galaxy, it'll fetch the new docutils egg and this should be fixed.
Perfect. That fixed it. Thanks very much.
Chris
galaxy-dev@lists.galaxyproject.org
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Chris Cole -
Nate Coraor