Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

2012-12-13 Thread Sarah Maman 

Hi Daniel,

In fact, my version needs to be updated :

changeset:   6799:40f1816d6857
tag: tip
user:Greg Von Kuster 
date:Wed Mar 07 13:35:34 2012 -0500
summary: Fix for populating the tool panel and generating the  
integrated_tool_panel.xml file.


I try and let you know.
Sarah

Daniel Blankenberg  a écrit :


Hi Sarah,

This looks to be due to a non-unicode character in the dataset's  
info field. Are you using a Galaxy revision >= 7563:fca4e12478d6?



Thanks for using Galaxy,

Dan


On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote:


Hello,

One of my users gets the following message when he wishes to edit  
the attribute of a dataset which is generated by using a tool (same  
problem as it is a tool provided by Galaxy or a tool coded by us).


Do you have any idea?

Thanks in advance,
Sarah Maman

URL:  
http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in  
__call__

app_iter = self.application(environ, start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in  
__call__

environ, self.app)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in  
intercept_output

app_iter = application(environ, replacement_start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in  
__call__

return self.application(environ, start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in  
__call__

return self.app( environ, start_response )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in  
__call__

return self.application(environ, start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in  
__call__

body = method( trans, **kwargs )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in  
edit

refresh_frames=refresh_frames )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in  
fill_template

return self.fill_template_mako( filename, **kwargs )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in  
fill_template_mako

return template.render( **data )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in  
render

return runtime._render(self, self.callable_, args, data)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in  
_render

**_kwargs_for_callable(callable_, data))
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in  
_render_context

_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in  
_exec_template

callable_(context, *args, **kwargs)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in  
render_body

__M_writer(unicode(next.body()))
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in  
render_body

__M_writer(filters.html_escape(unicode(data.info )))
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in  
position 31: ordinal not in range(128)

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--
Sarah Maman
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53

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Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

2012-12-12 Thread Daniel Blankenberg 
Hi Sarah,

This looks to be due to a non-unicode character in the dataset's info field. 
Are you using a Galaxy revision >= 7563:fca4e12478d6? 


Thanks for using Galaxy,

Dan


On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote:

> Hello,
> 
> One of my users gets the following message when he wishes to edit the 
> attribute of a dataset which is generated by using a tool (same problem as it 
> is a tool provided by Galaxy or a tool coded by us).
> 
> Do you have any idea?
> 
> Thanks in advance,
> Sarah Maman
> 
> URL: 
> http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
>  line 143 in __call__
> app_iter = self.application(environ, start_response)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
>  line 98 in __call__
> environ, self.app)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
>  line 539 in intercept_output
> app_iter = application(environ, replacement_start_response)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
>  line 80 in __call__
> return self.application(environ, start_response)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>  line 111 in __call__
> return self.app( environ, start_response )
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>  line 632 in __call__
> return self.application(environ, start_response)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', 
> line 160 in __call__
> body = method( trans, **kwargs )
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py',
>  line 600 in edit
> refresh_frames=refresh_frames )
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>  line 722 in fill_template
> return self.fill_template_mako( filename, **kwargs )
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>  line 733 in fill_template_mako
> return template.render( **data )
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py',
>  line 296 in render
> return runtime._render(self, self.callable_, args, data)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py',
>  line 660 in _render
> **_kwargs_for_callable(callable_, data))
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py',
>  line 692 in _render_context
> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py',
>  line 718 in _exec_template
> callable_(context, *args, **kwargs)
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py',
>  line 42 in render_body
> __M_writer(unicode(next.body()))
> File 
> '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py',
>  line 95 in render_body
> __M_writer(filters.html_escape(unicode(data.info )))
> UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: 
> ordinal not in range(128)
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Re: [galaxy-dev] Server Error in history framer when debug = False

2012-09-11 Thread Nate Coraor 
On Aug 3, 2012, at 10:42 AM, David Roquis wrote:

> Dear Galaxy community,
> 
> I have noticed on forums that some users are experiencing this problem too, 
> but no clues on how to fix it. When I set debug = false in universe.wsgi.ini, 
> I get a server error in the history frame (history works perfectly when debug 
> = true). Trying to create a new history, or to upload a saved one, doesn't 
> work either. I use postgresql and nginx, but I this problem also appears on a 
> freshly cloned instance of galaxy-dist. I tried on two machines with Fedora 
> 13 + python 2.6.4  and Fedora 17 + python 2.7.3. As my goal is to use Galaxy 
> in a production environment (with 2 webservers, 1 manager and 2 handlers), I 
> would really like to be able to turn off debug. Here is what I can find in my 
> paster.log when I turn off debug.
> 
> Thanks a lot if anyone has a solution!
> 
> David
> 
> Starting server in PID 4664.
> serving on 0.0.0.0:8081 view at http://127.0.0.1:8081
> 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET / HTTP/1.0" 200 - "-" 
> "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 Firefox/14.0.1"
> 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET /root/tool_menu HTTP/1.0" 200 
> - "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) 
> Gecko/20100101 Firefox/14.0.1"
> 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET /history HTTP/1.0" 200 - 
> "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) 
> Gecko/20100101 Firefox/14.0.1"
> 127.0.0.1 - - [03/Aug/2012:16:26:49 +0200] "GET /history HTTP/1.0" 500 - 
> "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Linux x86_64; rv:14.0) 
> Gecko/20100101 Firefox/14.0.1"
> Error - : 'NoneType' object is not callable
> URL: http://127.0.0.1/history
> File '/usr/lib/python2.7/site-packages/paste/exceptions/errormiddleware.py', 
> line 144 in __call__
>   app_iter = self.application(environ, sr_checker)
> File '/usr/lib/python2.7/site-packages/paste/recursive.py', line 84 in 
> __call__
>   return self.application(environ, start_response)
> File '/usr/lib/python2.7/site-packages/paste/httpexceptions.py', line 633 in 
> __call__
>   return self.application(environ, start_response)
> File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 
> in __call__
>   return body( environ, start_response )
> File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 
> 772 in render
>   template.render_context( context )
> File 
> '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', 
> line 319 in render_context
>   **kwargs)
> File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', 
> line 692 in _render_context
>   _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> File '/home/galaxy2ei/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', 
> line 718 in _exec_template
>   callable_(context, *args, **kwargs)
> File 
> '/home/galaxy2ei/galaxy-dist/database/compiled_templates/root/history.mako.py',
>  line 62 in render_body
>   __M_writer(u'\n\n')
> File '/home/galaxy2ei/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 
> 769 in write
>   response_write( d.encode( 'utf-8' ) )
> TypeError: 'NoneType' object is not callable

Hi David,

Sorry it took so long to get back to you.  The problem appears to be that 
Galaxy is using a version of Paste from your site-packages rather than the egg 
bundled with Galaxy.  A quick solution to this would be to set up a virtualenv 
as described in the production server documentation and run Galaxy under that 
interpreter.

--nate

> 
> 
> CGI Variables
> -
>   CONTENT_LENGTH: '0'
>   HTTP_ACCEPT: 
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>   HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>   HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5'
>   HTTP_CONNECTION: 'close'
>   HTTP_COOKIE: 
> 'galaxysession=c6ca0ddb55be603a1a924b5a883eb84f93f9e2c6424cabed485f00c49dc51dd6632e1e679e865175'
>   HTTP_HOST: '127.0.0.1'
>   HTTP_REFERER: 'http://127.0.0.1:8080/'
>   HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:14.0) Gecko/20100101 
> Firefox/14.0.1'
>   HTTP_X_FORWARDED_FOR: '127.0.0.1'
>   HTTP_X_FORWARDED_HOST: '127.0.0.1'
>   ORGINAL_HTTP_HOST: 'galaxy_app'
>   ORGINAL_REMOTE_ADDR: '127.0.0.1'
>   PATH_INFO: '/history'
>   REMOTE_ADDR: '127.0.0.1'
>   REQUEST_METHOD: 'GET'
>   SERVER_NAME: '0.0.0.0'
>   SERVER_PORT: '8081'
>   SERVER_PROTOCOL: 'HTTP/1.0'
> 
> 
> Configuration
> -
>   __file__: '/home/galaxy2ei/galaxy-dist/universe_wsgi.ini'
>   admin_users: 'david.roq...@yahoo.com, galaxyt...@2ei.com'
>   allow_library_path_paste: 'True'
>   allow_user_dataset_purge: 'True'
>   allow_user_deletion: 'True'
>   allow_user_impersonation: 'True'
>   database_connection: 
> 'postgres://galaxy2ei:galaxy2ei@localhost:5432/galaxyprod'
>   database_engine_option_server_side_cursors: 'True'
>   database_engine_option_strategy: 'threadlocal'
>   datatypes_config_file: 'datatypes_conf.xml'
>

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-07-03 Thread Iry Witham 
Thanks Dannon and Bjorn for the assistance.  I followed Dannon's
suggestion and that fixed my issue.

Thanks,
Iry

On 7/3/12 1:15 PM, "Dannon Baker"  wrote:

>It looks like what happened is that you've updated the instance that was
>originally connected to this database from galaxy-central at some point
>recently.  The current tip of galaxy-central is at database version 103.
>
>The first two options that come to mind are:
>
>1)  Hook a fresh galaxy-central clone up to this database and
>`manage_db.sh downgrade 97` which should set your database back to the
>version appropriate for galaxy-dist.
>2)  Swap to galaxy-central instead of -dist
>
>Taking a brief look at the migrations, #1 looks fairly safe, but as
>always -- back up the database first.
>
>-Dannon
>
>
>
>On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:
>
>> I am still experiencing issues getting my galaxy server to start since
>>the upgrade.  The logs are all getting this type of error:
>> 
>> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat
>>runner0.log 
>> python path is: 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linu
>>x-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10
>>f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-
>>linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.eg
>>g, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-l
>>inux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
>>tatic-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
>>194725-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
>>g, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
>>6498-py2.6.egg, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-
>>linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.e
>>gg, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6
>>-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.eg
>>g, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
>>0316-py2.6.egg, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg
>>, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
>> 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.eg
>>g, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
>>nux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
>>6.egg, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.
>>6.egg, 
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib,
>>/usr/lib/python26.zip, /usr/lib64/python2.6,
>>/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
>>/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
>>/usr/lib64/python2.6/site-packages/Numeric,
>>/usr/lib64/python2.6/site-packages/gtk-2.0,
>>/usr/local/lib64/python2.6/site-packages,
>>/usr/lib64/python2.6/site-packages
>> galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
>>successfully loaded for postgres dialect
>> Traceback (most recent call last):
>>   File 
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py
>>", line 82, in app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>>   File 
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line
>>35, in __init__
>> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
>>).get( '__file__', None ), self.config.database_engine_options, app=self
>>)
>>   File 
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/c
>>heck.py", line 103, in create_or_verify_database
>> % ( db_schema.version, migrate_repository.versions.latest,
>>config_arg ) )
>> Exception: Your database has version '101' but this code expects
>>version '97'.  Please backup your database and then migrate the schema
>>by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
>> Removing PID file runner0.pid
>> 
>> I have not dropped my database and built it fresh.  However, I have
>>attempted the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini
>>upgrade' for both the runner and web app ini files wit

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-07-03 Thread Björn Grüning 
Hi Iry,


> 
> Exception: Your database has version '101' but this code expects
> version '97'.  Please backup your database and then migrate the schema
> by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
> Removing PID file runner0.pid

Your galaxy version seems to be older than your database. It seems you
run galaxy-central and afterwards starting galaxy-dist with the same
database. That does not work. With your database you should run a newer
version of galaxy, e.g. the newest galaxy-central.

Hope that helps,
Bjoern

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-07-03 Thread Dannon Baker 
It looks like what happened is that you've updated the instance that was 
originally connected to this database from galaxy-central at some point 
recently.  The current tip of galaxy-central is at database version 103.

The first two options that come to mind are:

1)  Hook a fresh galaxy-central clone up to this database and `manage_db.sh 
downgrade 97` which should set your database back to the version appropriate 
for galaxy-dist.
2)  Swap to galaxy-central instead of -dist

Taking a brief look at the migrations, #1 looks fairly safe, but as always -- 
back up the database first.

-Dannon



On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:

> I am still experiencing issues getting my galaxy server to start since the 
> upgrade.  The logs are all getting this type of error:
> 
> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log 
> python path is: 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
>  
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
>  /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg, 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
>  /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
>  
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
>  
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
>  /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchem!
 y-0.5.6_dev_r6498-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDe!
 ploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy!
 -dist/eg
gs/PasteScript-1.7.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, 
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, 
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, 
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric, 
/usr/lib64/python2.6/site-packages/gtk-2.0, 
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
> galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg 
> successfully loaded for postgres dialect
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py", 
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", 
> line 35, in __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
> '__file__', None ), self.config.database_engine_options, app=self )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py",
>  line 103, in create_or_verify_database
> % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
> Exception: Your database has version '101' but this code expects version 
> '97'.  Please backup your database and then migrate the schema by running 'sh 
> manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
> Removing PID file runner0.pid
> 
> I have not dropped my database and built it fresh.  However, I have attempted 
> the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for 
> both the runner and web app ini files with the following error:
> 
> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh 
> -c ./universe_wsgi.webapp.ini upgrade
> Traceback (most recent call last):
>   File "./scripts/manage_db.py", line 63, in 
> main( repository=repo, url=

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-07-03 Thread Iry Witham 
I am still experiencing issues getting my galaxy server to start since the 
upgrade.  The logs are all getting this type of error:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log
python path is: 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
 /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, 
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, 
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, 
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, 
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric, 
/usr/lib64/python2.6/site-packages/gtk-2.0, 
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg 
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py", 
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 
35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( 
'__file__', None ), self.config.database_engine_options, app=self )
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py",
 line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '101' but this code expects version '97'.  
Please backup your database and then migrate the schema by running 'sh 
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid

I have not dropped my database and built it fresh.  However, I have attempted 
the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for 
both the runner and web app ini files with the following error:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh 
-c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in 
main( repository=repo, url=db_url )
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
 line 150, in main
ret = command_func(**kwargs)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
 line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
 line 327, in _migrate
changeset = schema.changeset(version)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
 line 173, in changeset
chang

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-06-27 Thread Iry Witham 
Hi Nate,

I removed to previous instillation just to be safe and performed a new
clone.  This time it appears to be less problematic.  I am no longer
getting all of the errors.  However, I am getting an error due to my
database version.  The error is:

galaxy.model.migrate.check DEBUG 2012-06-27 12:39:11,843 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py",
 line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py",
line 35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/che
ck.py", line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg
) )
Exception: Your database has version '101' but this code expects version
'97'.  Please backup your database and then migrate the schema by running
'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.



I have attempted to run sh manage_db.sh -c ./universe_wsgi.runner.ini
upgrade and that fails with the following error:

galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in 
main( repository=repo, url=db_url )
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
ret = command_func(**kwargs)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err,
**opts)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py", line 327, in _migrate
changeset = schema.changeset(version)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/schema.py", line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py", line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py", line 145, in version
return self.versions.version(*p, **k)
  File 
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/version.py", line 125, in version
return self.versions[VerNum(vernum)]
KeyError: 



It is getting closer, but I am not quite there yet.

Thanks,
Iry

On 6/22/12 11:50 AM, "Nate Coraor"  wrote:

>On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:
>
>> I have recently performed a fresh installation of Galaxy utilizing the
>>latest distribution and am getting a sizable number of errors when
>>attempting to start the server.  The issue started when I performed a
>>merge so I decided to do the clean install as a test.  The server
>>appears to start just fine, but with errors reported in the logs.  The
>>web0.log gives the following errors and warnings (I am truncating the
>>file for space):
>> 
>> galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg
>>successfully loaded for postgres dialect
>> galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database
>>version 97
>> galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2
>>egg successfully loaded for postgres dialect
>> galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At
>>migrate_tools version 2
>> galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg
>>successfully loaded for postgres dialect
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loading references to tool sheds from tool_sheds_conf.xml
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loaded reference to tool shed: Galaxy main tool shed
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loaded reference to tool shed: Galaxy test tool shed
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading
>>datatypes from datatypes_conf.xml
>> galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding
>>conflicting datatype with extension 'coverage', using datatype from
>>datatypes_conf.xml.
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
>>for datatype 'galaxy.datatypes.binary:Bam'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:2

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-06-25 Thread Iry Witham 
I used changeset:   7148:17d57db9a7c0 for the clone.  I don't recall
making any changes, but have removed it and am about to start fresh and
see if the issue still exists.

Iry


On 6/22/12 11:50 AM, "Nate Coraor"  wrote:

>On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:
>
>> I have recently performed a fresh installation of Galaxy utilizing the
>>latest distribution and am getting a sizable number of errors when
>>attempting to start the server.  The issue started when I performed a
>>merge so I decided to do the clean install as a test.  The server
>>appears to start just fine, but with errors reported in the logs.  The
>>web0.log gives the following errors and warnings (I am truncating the
>>file for space):
>> 
>> galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg
>>successfully loaded for postgres dialect
>> galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database
>>version 97
>> galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2
>>egg successfully loaded for postgres dialect
>> galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At
>>migrate_tools version 2
>> galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg
>>successfully loaded for postgres dialect
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loading references to tool sheds from tool_sheds_conf.xml
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loaded reference to tool shed: Galaxy main tool shed
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loaded reference to tool shed: Galaxy test tool shed
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading
>>datatypes from datatypes_conf.xml
>> galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding
>>conflicting datatype with extension 'coverage', using datatype from
>>datatypes_conf.xml.
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
>>for datatype 'galaxy.datatypes.binary:Bam'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
>>for datatype 'galaxy.datatypes.binary:Sff'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
>>for datatype 'galaxy.datatypes.xml:BlastXml'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.sequence:Maf'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.sequence:Lav'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.sequence:csFasta'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.sequence:Fasta'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer
>>for datatype 'galaxy.datatypes.sequence:Fastq'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:Wiggle'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer
>>for datatype 'galaxy.datatypes.images:Html'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer
>>for datatype 'galaxy.datatypes.images:Pdf'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer
>>for datatype 'galaxy.datatypes.sequence:Axt'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:Bed'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:CustomTrack'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:Gtf'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:Gff'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:Gff3'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer
>>for datatype 'galaxy.datatypes.tabular:Pileup'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer
>>for datatype 'galaxy.datatypes.interval:Interval'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer
>>for datatype 'galaxy.datatypes.tabular:Sam'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer
>>for datatype 'galaxy.datatypes.tabular:Vcf'
>> galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table
>>'all_fasta'
>> galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table
>>'bfast_indexes'
>> galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table
>>'blastdb'
>>

Re: [galaxy-dev] Server Error after fresh installation of Galaxy

2012-06-22 Thread Nate Coraor 
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:

> I have recently performed a fresh installation of Galaxy utilizing the latest 
> distribution and am getting a sizable number of errors when attempting to 
> start the server.  The issue started when I performed a merge so I decided to 
> do the clean install as a test.  The server appears to start just fine, but 
> with errors reported in the logs.  The web0.log gives the following errors 
> and warnings (I am truncating the file for space):
> 
> galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg 
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database version 97
> galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 egg 
> successfully loaded for postgres dialect
> galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At migrate_tools 
> version 2
> galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg 
> successfully loaded for postgres dialect
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loading 
> references to tool sheds from tool_sheds_conf.xml
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded 
> reference to tool shed: Galaxy main tool shed
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded 
> reference to tool shed: Galaxy test tool shed
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading datatypes 
> from datatypes_conf.xml
> galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding 
> conflicting datatype with extension 'coverage', using datatype from 
> datatypes_conf.xml.
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for 
> datatype 'galaxy.datatypes.binary:Bam'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for 
> datatype 'galaxy.datatypes.binary:Sff'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for 
> datatype 'galaxy.datatypes.xml:BlastXml'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Maf'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Lav'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:csFasta'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.qualityscore:QualityScore454'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Fasta'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Fastq'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Wiggle'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.images:Html'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.images:Pdf'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Axt'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Bed'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:CustomTrack'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Gtf'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Gff'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Gff3'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.tabular:Pileup'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Interval'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.tabular:Sam'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.tabular:Vcf'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table 
> 'all_fasta'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table 
> 'bfast_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table 
> 'blastdb'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,062 Loaded tool data table 
> 'blastdb_p'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,065 Loaded tool data table 
> 'bowtie_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,06

Re: [galaxy-dev] Server Error when downloading files from history

2012-05-10 Thread Dannon Baker 
This was a temporary issue with the public server that has been fixed.  Let me 
know if you still have issues.  Also, for future reference, galaxy-bugs would 
be the correct list to send this type of problem to.

Thanks!

Dannon


On May 9, 2012, at 7:55 PM, "Rathi D. Thiagarajan"  
wrote:

> Hi there,
> 
> I received the following error when trying to download/save my tabular files 
> with 5k lines:
> 
> Server Error
> 
> An error occurred. See the error logs for more information. (Turn debug on to 
> display exception reports here)
> 
> Please help!
> 
> Thanks in advance.
> 
> Cheers,
> Rathi
> 
> -- 
> Rathi D. Thiagarajan, PhD
> Professional Scientific Collaborator
> UCSD Research Scholar
> Dept. of Chemical Physiology
> Center for Regenerative Medicine
> The Scripps Research Institute
> 3030 Science Park Rd,
> La Jolla, CA 92035, USA
> 
> Mail:SP30-3021
> W: 858.784.7753
> E: ra...@scripps.edu
> E: rthiagara...@ucsd.edu
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Re: [galaxy-dev] server error

2012-05-09 Thread Langhorst, Brad 
Ashley:

I think he was joking around.
Essentially - to provide any help, people here need to know much more detail 
about what kind of server error occurred,
and what input was provided so that the problem can be reproduced or a helpful 
suggestion can be made.

This guide to asking good questions might be of some help to you:
http://catb.org/~esr/faqs/smart-questions.html

I probably can't help you with your actual problem, but if you can provide more 
information maybe somebody else can.

some examples that might help.

if you were running on the public galaxy server or not
what you were trying to do
what kind of data you where trying to analyze
the contents of /var/log/galaxy/galaxy.log (or wherever the log is on your 
local installation)
the results you see when you click on the "bug" icon in your failing history 
step

Brad
On May 9, 2012, at 6:51 PM, Ashley Tehranchi wrote:


I'm not sure what that means.



From: Bob Harris mailto:rshar...@bx.psu.edu>>
Date: Wednesday, May 9, 2012 1:49 PM
To: Ashley Tehranchi mailto:a...@stanford.edu>>
Cc: mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] server error

Given the information supplied, I suggest a spatula.  Many servers are quite 
adept with a spatula.

Your results may vary.

Bob H


On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote:

Hi,
I have run into a server error, how can I fix it?

Thanks,
Ashley
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--
Brad Langhorst
langho...@neb.com<mailto:langho...@neb.com>
978-380-7564




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Re: [galaxy-dev] server error

2012-05-09 Thread Ashley Tehranchi 

I'm not sure what that means.



From:  Bob Harris 
Date:  Wednesday, May 9, 2012 1:49 PM
To:  Ashley Tehranchi 
Cc:  
Subject:  Re: [galaxy-dev] server error

Given the information supplied, I suggest a spatula.  Many servers are quite
adept with a spatula.

Your results may vary.

Bob H


On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote:

> Hi, 
> I have run into a server error, how can I fix it?
> 
> Thanks,
> Ashley 
>  ___
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Re: [galaxy-dev] server error

2012-05-09 Thread Bob Harris 
Given the information supplied, I suggest a spatula.  Many servers are  
quite adept with a spatula.


Your results may vary.

Bob H


On May 9, 2012, at 4:43 PM, Ashley Tehranchi wrote:


Hi,
I have run into a server error, how can I fix it?

Thanks,
Ashley
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Re: [galaxy-dev] Server Error after Update

2011-11-07 Thread Nate Coraor 
On Oct 27, 2011, at 8:23 AM, SHAUN WEBB wrote:

> 
> Hi, I updated my test server today and everything seemed fine. I added a new 
> library item via a URL. After that my history panel displays "Internal Server 
> Error" and I am getting the error below in paster.log:
> 
> Any ideas how this has occurred and if there is a fix?

Hi Shaun,

If you set 'debug = True', you should get a more helpful error message in the 
log.

--nate

> 
> Shaun
> 
> 
> Exception happened during processing of request from ('2.218.9.31', 63227)
> Traceback (most recent call last):
>  File 
> "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 1053, in process_request_in_thread
>self.finish_request(request, client_address)
>  File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request
>self.RequestHandlerClass(request, client_address, self)
>  File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__
>self.handle()
>  File 
> "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 432, in handle
>BaseHTTPRequestHandler.handle(self)
>  File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle
>self.handle_one_request()
>  File 
> "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 427, in handle_one_request
>self.wsgi_execute()
>  File 
> "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 290, in wsgi_execute
>self.wsgi_write_chunk(chunk)
>  File 
> "/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 125, in wsgi_write_chunk
>"Content returned before start_response called")
> RuntimeError: Content returned before start_response called
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
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Re: [galaxy-dev] Server Error when trying to upload repository.

2011-10-27 Thread David Murphy 
Just realized I didn't reply to all, so the list didn't see this.

No problem at all, it would be much appreciated in fact.

Is there anything I need to do to do so you can do that?

Cheers
David

On Wed, Oct 26, 2011 at 9:28 PM, Greg Von Kuster  wrote:

> Hello David,
>
> I'm not sure why you're seeing this - do you mind if I try to delete all of
> the files in your repository whose name ends in '~'?  That may help me track
> down the problem.
>
> Greg Von Kuster
>
> On Oct 26, 2011, at 3:09 PM, David Murphy wrote:
>
> > Hi
> >
> > I've been trying to create a repository for a small tool called CodonLogo
> at
> > http://toolshed.g2.bx.psu.edu/.
> >
> > The problem is that the first zip I uploaded contained a few backup
> copies of
> > some text files ending with a "~".
> > It now won't allow me to delete them by checking them and clicking
> "delete
> > selected files" it then simply gives the error
> >
> > "The selected files were deleted from the repository.
> > Change set revision '7ff079013d98' includes no tools or exported
> workflows for
> > which metadata can be set."
> >
> > but the selected files are not deleted.
> >
> > When I try to upload a new zip without the older files it gives an error
> >
> > "Server Error
> > An error occurred. See the error logs for more information. (Turn debug
> on to
> > display exception reports here) "
> >
> > Am I doing something foolish or is this a bug?
> >
> > Cheers
> > David
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>
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Re: [galaxy-dev] Server Error when trying to upload repository.

2011-10-27 Thread Greg Von Kuster 
David,

I looked into this for some time, and although I found strange behavior in the 
mercurial environment, it is impossible to determine what caused it.  Your 
repository was definitely corrupted in some way, perhaps by a network problem 
that occurred when you were transferring files, or some other indeterminate 
issue.  In any case, I have recreated your repository from scratch so it is 
ready for you to upload your files once again.  From your change log, it was 
clear that you had deleted all files in the repository anyway.

I'll keep a watch on this.  Please let us know if you encounter further 
problems.  Sorry for the inconvenience with this.

Greg Von Kuster

On Oct 27, 2011, at 9:52 AM, David Murphy wrote:

> Just realized I didn't reply to all, so the list didn't see this.
> 
> No problem at all, it would be much appreciated in fact.
> 
> Is there anything I need to do to do so you can do that?
> 
> Cheers
> David
> 
> On Wed, Oct 26, 2011 at 9:28 PM, Greg Von Kuster  wrote:
> Hello David,
> 
> I'm not sure why you're seeing this - do you mind if I try to delete all of 
> the files in your repository whose name ends in '~'?  That may help me track 
> down the problem.
> 
> Greg Von Kuster
> 
> On Oct 26, 2011, at 3:09 PM, David Murphy wrote:
> 
> > Hi
> >
> > I've been trying to create a repository for a small tool called CodonLogo at
> > http://toolshed.g2.bx.psu.edu/.
> >
> > The problem is that the first zip I uploaded contained a few backup copies 
> > of
> > some text files ending with a "~".
> > It now won't allow me to delete them by checking them and clicking "delete
> > selected files" it then simply gives the error
> >
> > "The selected files were deleted from the repository.
> > Change set revision '7ff079013d98' includes no tools or exported workflows 
> > for
> > which metadata can be set."
> >
> > but the selected files are not deleted.
> >
> > When I try to upload a new zip without the older files it gives an error
> >
> > "Server Error
> > An error occurred. See the error logs for more information. (Turn debug on 
> > to
> > display exception reports here) "
> >
> > Am I doing something foolish or is this a bug?
> >
> > Cheers
> > David
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
> 
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
> 
> 
> 
> 

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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Re: [galaxy-dev] Server Error when trying to upload repository.

2011-10-26 Thread Greg Von Kuster 
Hello David,

I'm not sure why you're seeing this - do you mind if I try to delete all of the 
files in your repository whose name ends in '~'?  That may help me track down 
the problem.

Greg Von Kuster

On Oct 26, 2011, at 3:09 PM, David Murphy wrote:

> Hi
> 
> I've been trying to create a repository for a small tool called CodonLogo at
> http://toolshed.g2.bx.psu.edu/.
> 
> The problem is that the first zip I uploaded contained a few backup copies of
> some text files ending with a "~".
> It now won't allow me to delete them by checking them and clicking "delete
> selected files" it then simply gives the error 
> 
> "The selected files were deleted from the repository.
> Change set revision '7ff079013d98' includes no tools or exported workflows for
> which metadata can be set."
> 
> but the selected files are not deleted.
> 
> When I try to upload a new zip without the older files it gives an error 
> 
> "Server Error
> An error occurred. See the error logs for more information. (Turn debug on to
> display exception reports here) "
> 
> Am I doing something foolish or is this a bug?
> 
> Cheers
> David
> 
> ___
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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Re: [galaxy-dev] Server Error

2011-09-09 Thread Greg Von Kuster 
Hello Alex,

This issue was the result of a configuration error that should now be 
corrected.  Please let us know if you encounter further issues.

thanks for reporting this,

Greg Von Kuster


On Sep 9, 2011, at 12:41 PM, Alex R Bigelow wrote:

> Hi,
> I am a new developer interested in writing tools for Galaxy, but when I try 
> to use the tool shed (http://toolshed.g2.bx.psu.edu), every link I click on 
> gives me a Server Error. I have tried in both Google Chrome and Safari; does 
> anyone know what is going on?
> 
> Thanks,
> Alex Bigelow
> ___
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Re: [galaxy-dev] Server error from history view

2011-04-04 Thread Nate Coraor 
Hi Sarah,

Does this occur with all histories?  Does it change if you create a new
history?

--nate

Sarah Diehl wrote:
> Hi all,
> 
> I encounter the same error that was already mentioned in this list
> (with the same email title). For me it also does only happen when
> debug is set to false. However I could not find a solution to it in
> the archive of the mailing list. I tried it with both galaxy-dist
> and galaxy-central, newest version.
> 
> The error is as follows:
> 
> 10.1.5.190 - - [10/Mar/2011:11:41:20 +0200] "GET /history HTTP/1.1"
> 500 - "http://solweb2/"; "Mozilla/5.0 (X11; U; Linux x86_64; en-US;
> rv:1.9.2.14) Gecko/20110301 Fedora/3.6.14-1.fc14 Firefox/3.6.14"
> Error - : 'NoneType' object is not callable
> URL: http://solweb2/history
> File '/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py',
> line 144 in __call__
>   app_iter = self.application(environ, sr_checker)
> File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80
> in __call__
>   return self.application(environ, start_response)
> File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py',
> line 633 in __call__
>   return self.application(environ, start_response)
> File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line
> 154 in __call__
>   return body( environ, start_response )
> File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
> line 676 in render
>   template.render_context( context )
> File
> '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py',
> line 146 in render_context
>   runtime._render_context(self, self.callable_, context, *args, **kwargs)
> File
> '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py',
> line 381 in _render_context
>   _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> File
> '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py',
> line 414 in _exec_template
>   callable_(context, *args, **kwargs)
> File '/galaxy/galaxy_server/database/compiled_templates/root/history.mako.py',
> line 55 in render_body
>   __M_writer(u'\n Transitional//EN" 
> "http://www.w3.org/TR/html4/loose.dtd";>\n\n\n\n\n')
> File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
> line 673 in write
>   response_write( d.encode( 'utf-8' ) )
> TypeError: 'NoneType' object is not callable
> 
> 
> CGI Variables
> -
>   CONTENT_LENGTH: '0'
>   HTTP_ACCEPT:
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>   HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7'
>   HTTP_ACCEPT_ENCODING: 'gzip,deflate'
>   HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5'
>   HTTP_CONNECTION: 'Keep-Alive'
>   HTTP_COOKIE: 
> 'galaxysession=f611411aa8a0c665eb9e71b6b35ec98d69a19a7826eff47d201855aea491539e3c45f483349e57b4'
>   HTTP_HOST: 'solweb2'
>   HTTP_REFERER: 'http://solweb2/'
>   HTTP_USER_AGENT: 'Mozilla/5.0 (X11; U; Linux x86_64; en-US;
> rv:1.9.2.14) Gecko/20110301 Fedora/3.6.14-1.fc14 Firefox/3.6.14'
>   HTTP_X_FORWARDED_FOR: '10.1.5.190'
>   HTTP_X_FORWARDED_HOST: 'solweb2'
>   HTTP_X_FORWARDED_SERVER: 'solweb2'
>   ORGINAL_HTTP_HOST: 'localhost:8080'
>   ORGINAL_REMOTE_ADDR: '127.0.0.1'
>   PATH_INFO: '/history'
>   REMOTE_ADDR: '10.1.5.190'
>   REQUEST_METHOD: 'GET'
>   SERVER_NAME: '0.0.0.0'
>   SERVER_PORT: '8080'
>   SERVER_PROTOCOL: 'HTTP/1.1'
> 
> 
> Configuration
> -
>   __file__: '/galaxy/galaxy_server/universe_wsgi.ini'
>   admin_users: 'di...@immunbio.mpg.de,lims...@solweb1.immunbio.mpg.de'
>   allow_library_path_paste: 'True'
>   allow_user_creation: 'True'
>   allow_user_deletion: 'False'
>   cookie_path: '/'
>   database_connection: 'postgres://galaxy:galaxy@localhost/galaxy'
>   database_engine_option_server_side_cursors: 'True'
>   database_engine_option_strategy: 'threadlocal'
>   datatypes_config_file: 'datatypes_conf.xml'
>   debug: 'False'
>   enable_api: 'True'
>   enable_sequencer_communication: 'True'
>   file_path: 'database/files'
>   gbrowse_display_sites: 'wormbase,tair,modencode_worm,modencode_fly'
>   genetrack_display_sites: 'main,test'
>   here: '/galaxy/galaxy_server'
>   id_secret: 'MPI IMMUNBIOLOGIE'
>   library_import_dir: '/galaxy/galaxy_server/data'
>   log_actions: 'True'
>   log_events: 'True'
>   log_level: 'DEBUG'
>   new_file_path: 'database/tmp'
>   new_user_dataset_access_role_default_private: 'True'
>   require_login: 'False'
>   static_cache_time: '360'
>   static_dir: '/galaxy/galaxy_server/static/'
>   static_enabled: 'True'
>   static_favicon_dir: '/galaxy/galaxy_server/static/favicon.ico'
>   static_images_dir: '/galaxy/galaxy_server/static/images'
>   static_scripts_dir: '/galaxy/galaxy_server/static/scripts/'
>   static_style_dir: '/galaxy/galaxy_server/static/june_2007_style/blue'
>   tool_config_file: 'tool_conf.xml'
>   tool_data_path: 'tool-data'
>   tool_path: 'tools'
>   ucsc_display_sites: 'main,test,archaea,ucla'
>   use_interactive: 'False'
>   use_lint: 'False'
>   use_profile: 'False'
> 
> 
> WSGI Variables
> --

Re: [galaxy-dev] Server error from history view

2011-03-11 Thread Sarah Diehl 

Hi Isabelle,

thank you for your help. However filter-with=gzip is disabled in our 
configuration. I set everything according to the guide on 
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer. The 
gzip option you see in my log is from the Apache server.


Sarah


On 03/10/2011 07:08 PM, Isabelle Phan wrote:

Hello Sarah,

(my galaxy-dev account is broken, read your post on nabble)

You need to disable filter-with=gzip in order to set debug=False

But in any case, I have not seen a difference in the log, so my take is that 
galaxy only ever runs in debug mode.

Isabelle


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Re: [galaxy-dev] Server error from history view

2011-03-10 Thread Isabelle Phan 
Hello Sarah,

(my galaxy-dev account is broken, read your post on nabble)

You need to disable filter-with=gzip in order to set debug=False

But in any case, I have not seen a difference in the log, so my take is that 
galaxy only ever runs in debug mode.

Isabelle


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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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