[galaxy-dev] Error when adding datasets

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Hello everyone
> 
> I have an issue when trying to import new datasets or when putting a
> dataset into a history. I saw Edward Kirton had the same problem but he
> got no answer:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html
> 
> Here is the error message I get when clicking the "Add datasets" button
> in a library, in the admin's "Manage data libraries" panel:
> 
> 
> UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped
> 
> URL:
> http://manni/galaxy/library_common/upload_library_dataset?library_id=f2db41e1fa331b3e&show_deleted=False&cntrller=library_admin&folder_id=f2db41e1fa331b3e&use_panels=False
> File
> '/g/funcgen/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
>   app_iter = self.application(environ, detect_start_response)
> File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
> line 98 in __call__
>   environ, self.app)
> File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line
> 539 in intercept_output
>   app_iter = application(environ, replacement_start_response)
> File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File
> '/g/funcgen/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 109 in __call__
>   return self.app( environ, start_response )
> File
> '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File '/g/funcgen/galaxy/lib/galaxy/web/framework/base.py', line 145 in
> __call__
>   body = method( trans, **kwargs )
> File '/g/funcgen/galaxy/lib/galaxy/web/controllers/library_common.py',
> line 907 in upload_library_dataset
>   trans.sa_session.refresh( history )
> File
> '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py', line 127 in do
>   return getattr(self.registry(), name)(*args, **kwargs)
> File
> '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py', line 925 in refresh
>   raise exc.UnmappedInstanceError(instance)
> UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped
> 
> 
> Now when does it occur:
> 
> I have two databases. One test database I created a month ago which
> works fine, even now. The other one I created recently which is supposed
> to be the final database. But the latter keeps triggering the above
> message, even when I drop it and create it all over again. I even tried
> to create a third one, all clean and new but the problem remains. I
> tried to trash all the eggs so Galaxy gets fresh new eggs, with no
> effect at all. The error's still there.
> 
> If you have any clue, I'll be forever grateful.

Okay, the problem is that the exact process you're taking after
recreating the database is resulting in your user not having a history.
This is pretty rare, but does occasionally happen.  I just committed a
fix for it in 5616:1f2870dc3ab0 and 5617:83103cff8757, but you can work
around it without these changes pretty easily by hitting the Analysis
view before uploading to make sure you have a history.

--nate

> 
> Cheers,
> L-A
> 
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