Post-installation: AttributeError: 'builtin_function_or_method' object has no attribute 'body'
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Hi all,
I'm trying out Galaxy. Installation went fine, but most links other than those under Tools (Workflow, Libraries, Help, User, etc.) return a python traceback (included below) relating to AttributeError.
I'm pretty new to Python and the egg system, so I am having a hard time figuring out the problem. I've tested this with the generic release tarball, mercurial checkout, and latest 3851029eda94 revision.
I'm running this on Ubuntu 9.04 x86_64 with Python 2.6.2 (but already tested with 2.4 and 2.5 as well -- both fail to start the server).
I've a server running at http://dzlab.pmb.berkeley.edu:8081/, in case it helps.
Thanks for your help. The software looks pretty sweet in any case.
Pedro
Traceback: - --- URL: http://dzlab.pmb.berkeley.edu:8081/workflow/list File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/debug/prints.py', line 98 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Beaker-0.5-py2.6.egg/beaker/session.py', line 103 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/recursive.py', line 80 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 74 in decorator % ( url_for( controller='user', action='login' ), verb ) ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 542 in show_error_message return self.show_message( message, 'error', refresh_frames ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 537 in show_message return self.fill_template( "message.mako", message_type=type, message=message, refresh_frames=refresh_frames, cont=cont ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 567 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 578 in fill_template_mako return template.render( **data ) File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/template.py', line 114 in render File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 287 in _render File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 304 in _render_context File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 337 in _exec_template File '/home/psilva/src/galaxy_dist/database/compiled_templates/base.mako.py', line 33 in render_body context.write(unicode(next.body())) AttributeError: 'builtin_function_or_method' object has no attribute 'body'
Hello Pedro,
We have built the eggs for Python 2.6 as the first step toward supporting that Python version, but we have yet to thoroughly test the Galaxy distribution with it, so some things may not be functionally correct. However, Python 2.4 and 2.5 are definitely supported, and I would suggest using Python 2.5.
If you can get your path set to point to that version of Python, and send the stack trace if you still get one, that would better help us determine the cause of the problem.
Thanks,
Greg Von Kuster Galaxy Development Team
Pedro Silva wrote:
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Hi all,
I'm trying out Galaxy. Installation went fine, but most links other than those under Tools (Workflow, Libraries, Help, User, etc.) return a python traceback (included below) relating to AttributeError.
I'm pretty new to Python and the egg system, so I am having a hard time figuring out the problem. I've tested this with the generic release tarball, mercurial checkout, and latest 3851029eda94 revision.
I'm running this on Ubuntu 9.04 x86_64 with Python 2.6.2 (but already tested with 2.4 and 2.5 as well -- both fail to start the server).
I've a server running at http://dzlab.pmb.berkeley.edu:8081/, in case it helps.
Thanks for your help. The software looks pretty sweet in any case.
Pedro
Traceback:
URL: http://dzlab.pmb.berkeley.edu:8081/workflow/list File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/debug/prints.py', line 98 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Beaker-0.5-py2.6.egg/beaker/session.py', line 103 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/recursive.py', line 80 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 74 in decorator % ( url_for( controller='user', action='login' ), verb ) ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 542 in show_error_message return self.show_message( message, 'error', refresh_frames ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 537 in show_message return self.fill_template( "message.mako", message_type=type, message=message, refresh_frames=refresh_frames, cont=cont ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 567 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 578 in fill_template_mako return template.render( **data ) File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/template.py', line 114 in render File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 287 in _render File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 304 in _render_context File '/home/psilva/src/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 337 in _exec_template File '/home/psilva/src/galaxy_dist/database/compiled_templates/base.mako.py', line 33 in render_body context.write(unicode(next.body())) AttributeError: 'builtin_function_or_method' object has no attribute 'body' -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
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galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
On Thu, 2009-07-23 at 16:15 -0400, Greg Von Kuster wrote:
Hello Pedro,
We have built the eggs for Python 2.6 as the first step toward supporting that Python version, but we have yet to thoroughly test
the
Galaxy distribution with it, so some things may not be functionally correct. However, Python 2.4 and 2.5 are definitely supported, and I would suggest using Python 2.5.
If you can get your path set to point to that version of Python, and send the stack trace if you still get one, that would better help us determine the cause of the problem.
Thanks,
Greg Von Kuster Galaxy Development Team
[cut]
Hello Greg,
Python 2.4.6 gives up with 'RuntimeError: maximum recursion depth exceeded' when starting server.
And here is a trace with python 2.5.4:
URL: http://192.168.0.101:8081/workflow/list File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/debug/prints.py', line 98 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Beaker-0.5-py2.5.egg/beaker/session.py', line 103 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py', line 80 in __call__ File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 74 in decorator % ( url_for( controller='user', action='login' ), verb ) ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 542 in show_error_message return self.show_message( message, 'error', refresh_frames ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 537 in show_message return self.fill_template( "message.mako", message_type=type, message=message, refresh_frames=refresh_frames, cont=cont ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 567 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/psilva/src/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 578 in fill_template_mako return template.render( **data ) File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Mako-0.1.10-py2.5.egg/mako/template.py', line 114 in render File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Mako-0.1.10-py2.5.egg/mako/runtime.py', line 287 in _render File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Mako-0.1.10-py2.5.egg/mako/runtime.py', line 304 in _render_context File '/home/psilva/src/galaxy_dist/eggs/py2.5-noplatform/Mako-0.1.10-py2.5.egg/mako/runtime.py', line 337 in _exec_template File '/home/psilva/src/galaxy_dist/database/compiled_templates/base.mako.py', line 33 in render_body context.write(unicode(next.body())) NameError: global name 'next' is not defined
Pedro Silva wrote:
Python 2.4.6 gives up with 'RuntimeError: maximum recursion depth exceeded' when starting server.
Hi Pedro,
A copy of the traceback here would help (although 2.5 is recommended anyway).
And here is a trace with python 2.5.4:
Can you try removing the contents of:
galaxy_dist/database/compiled_templates/
? Thanks.
--nate
On Mon, 2009-07-27 at 14:50 -0400, Nate Coraor wrote: [cut]
Can you try removing the contents of:
galaxy_dist/database/compiled_templates/
? Thanks.
--nate
Hi Nate,
Didn't work with python 2.6, giving out the same stack trace.
However, it did work with python 2.5, as far as I can tell. Thanks for your help! I guess it had something to do with certain python bytecode pre-compiled for a different architecture/machine/etc.?
I will starting testing now, and hope to be able to contribute something in the future.
Pedro
Pedro Silva wrote:
Didn't work with python 2.6, giving out the same stack trace.
We're still working on 2.6 support, so I can't guarantee that the eggs we built for 2.6 are functional. Best to stick with 2.5 for now.
However, it did work with python 2.5, as far as I can tell. Thanks for your help! I guess it had something to do with certain python bytecode pre-compiled for a different architecture/machine/etc.?
If built on the same platform, the bytecode would be the same, but built with 2.6 it could've been different (and it appears that was the case).
I will starting testing now, and hope to be able to contribute something in the future.
Great, thanks!
--nate
galaxy-dev@lists.galaxyproject.org
-
Greg Von Kuster -
Nate Coraor -
Pedro Silva