#3351 should fix this - Juan, can you please try pulling the current code to see if it works for you? Also, some notes on how to maintain a local code repository have also been added to section 6 of http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy - no need to do a fresh clone each time you want to update your local copy. Fixes and comments on the updated notes welcomed... 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
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
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
On Fri, Feb 5, 2010 at 12:47 PM, Juan Perin <juanperin@gmail.com> wrote: the python
2.4 Any ideas? Thanks in advance. URL: http://variome.chop.edu:8082/tool_runner?tool_id=bowtie_wrapperFile
'/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
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',
'/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.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'