[galaxy-dev] error when try to add datafiles

Edward Kirton edward.kirton at gmail.com
Sat May 29 02:38:45 EDT 2010


hello folks,

i had little difficulty setting up the balanced proxies and ldap auth,
thanks to your wiki and mailing list.  but now i'm running into an odd
problem i'm hope you fellas can help shine some light on...

i set up multiple galaxy sites running as different users (in the same
group), with each site submitting to a different sge cluster (based on
users sge env vars), but all use the same postgresql db and a common
database/ folder.

i get an error when i try to add a dataset in the library admin view.
however i can add folders, no problem.

Error - <class 'sqlalchemy.orm.exc.UnmappedInstanceError'>: Class
'__builtin__.NoneType' is not mapped
URL: https://galaxy.jgi-psf.org/main/library_common/upload_library_dataset?library_id=da9f6461ccaabf51&show_deleted=False&cntrller=library_admin&folder_id=a675b834218c0399&use_panels=False
File '/house/tooldirs/galaxy/galaxy-main/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
File '/house/tooldirs/galaxy/galaxy-main/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
File '/house/tooldirs/galaxy/galaxy-main/lib/galaxy/web/framework/middleware/remoteuser.py',
line 102 in __call__
File '/house/tooldirs/galaxy/galaxy-main/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
File '/house/tooldirs/galaxy/galaxy-main/lib/galaxy/web/framework/base.py',
line 126 in __call__
File '/house/tooldirs/galaxy/galaxy-main/lib/galaxy/web/controllers/library_common.py',
line 803 in upload_library_dataset
File '/house/tooldirs/galaxy/galaxy-main/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py',
line 127 in do
File '/house/tooldirs/galaxy/galaxy-main/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py',
line 925 in refresh
UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped

when i use the upload tool, it submits without error ("Your upload has
been queued..."), the files appears in the database/files folder
(permissions okay), but no history item is created and no error
message appears in the logs.

any hints or suggestions would be greatly appreciated!

thanks again,
ed

p.s.
do you foresee any problems with the setup i'm trying?  what about
collisions of job ids since all sites use a common db and each site
uses a different sge cluster?

p.p.s.
does this part of my universe_wsgi.ini.main.job look right?  i'm not
sure what the implications of these settings are.

[filter:proxy-prefix]

use = egg:PasteDeploy#prefix
prefix = /main

[app:main]

filter-with = proxy-prefix
cookie_path = /main
cookie_prefix = main

i have similar files for other sites besides 'main' (e.g. test, etc.)


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