On Mon, Feb 8, 2010 at 12:37 PM,
<galaxy-dev-request@lists.bx.psu.edu> wrote:
Message: 1
Date: Fri, 5 Feb 2010 18:13:05 -0500
From: Kanwei Li <kanwei@gmail.com>
To: Juan Perin <juanperin@gmail.com>, James Taylor
<james.taylor@emory.edu>
Cc: galaxy-dev@bx.psu.edu
Subject: Re: [galaxy-dev] Python problems
Message-ID:
<1469e4b41002051513o5a21793an348c37646724cb3e@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Juan,
After some searching it seems that it is an issue with python2.4 and
hashlib. We recently introduced a change that might be responsible for
this (commit 3311) and we'll look into it.
Thanks,
Kanwei
On Fri, Feb 5, 2010 at 12:47 PM, Juan Perin <juanperin@gmail.com> wrote:
> I've been working with a much older release of galaxy for a while, and it
> has worked great for the last few months. ?I noticed some progress with the
> NGS tools, so decided to attempt updating. ?My first mistake was in not
> knowing how to do so, so I essentially decided to start from the hg clone
> step and rebuild galaxy entirely in a new place on the same machine. ? ?I
> stupidly ran the database update script without listening to the warning
> about backing up the original galaxy db. ?So, my original instance won't
> work now...
> So, i'm trying to get the new instance working. ?Copied over my universe
> file and the custom .loc files from tool-data/ . ?everything seems to be ok,
> however I'm getting a python error that essentially repeats for anything I
> try to do, I'll paste the full output below for reference. ?I'm using python
> 2.4
> Any ideas?
> Thanks in advance.
> URL: http://variome.chop.edu:8082/tool_runner?tool_id=bowtie_wrapper File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py',
> line 364 in respond app_iter = self.application(environ,
> detect_start_response) File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/debug/prints.py',
> line 97 in __call__ status, headers, body = wsgilib.intercept_output( File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/wsgilib.py',
> line 539 in intercept_output app_iter = application(environ,
> replacement_start_response) File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/recursive.py',
> line 80 in __call__ return self.application(environ, start_response) File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/httpexceptions.py',
> line 632 in __call__ return self.application(environ, start_response) File
> '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__
> body = method( trans, **kwargs ) File
> '/opt/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 61 in
> index return trans.fill_template( template, history=history,
> toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) File
> '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 602 in
> fill_template return self.fill_template_mako( filename, **kwargs ) File
> '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 613 in
> fill_template_mako return template.render( **data ) File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/template.py',
> line 133 in render return runtime._render(self, self.callable_, args, data)
> File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.py',
> line 364 in _render _render_context(template, callable_, context, *args,
> **_kwargs_for_callable(callable_, data)) File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.py',
> line 381 in _render_context _exec_template(inherit, lclcontext, args=args,
> kwargs=kwargs) File
> '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.py',
> line 414 in _exec_template callable_(context, *args, **kwargs) File
> '/opt/galaxy-dist/database/compiled_templates/tool_form.mako.py', line 103
> in render_body __M_writer(unicode(util.object_to_string( tool_state.encode(
> tool, app ) ))) File '/opt/galaxy-dist/lib/galaxy/tools/__init__.py', line
> 216 in encode a = hmac_new( app.config.tool_secret, value ) File
> '/opt/galaxy-dist/lib/galaxy/util/hash_util.py', line 33 in hmac_new return
> hmac.new( key, value, sha1 ).hexdigest() File
> '/usr/lib64/python2.4/hmac.py', line 107 in new return HMAC(key, msg,
> digestmod) File '/usr/lib64/python2.4/hmac.py', line 42 in __init__
> self.outer = digestmod.new() AttributeError: 'builtin_function_or_method'
> object has no attribute 'new'