Louise-Amélie Schmitt wrote:
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=f2db41e... 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.
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