Here is the result I got from the debug statements:

galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
history: None
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans: <galaxy.web.framework.GalaxyWebUITransaction object at
0x29f40950>
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
trans.sa_session: <sqlalchemy.orm.scoping.ScopedSession object at
0x19ab21d0>

Thanks again
L-A


Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit :
> I assume when you dropped the old database and recreated the new,
> empty database, you made sure the database connection string in
> universe_wsgi.ini was correctly set.  if so, when you started up
> Galaxy, it would have created all of the required tables in the new
> database, and they would all be empty.  When you first registered as
> the admin user, it would have automatically populated several tables
> with data, including the history table.  One or more of these things
> must not have been successful.
> 
> 
> To attempt to narrow down the problem, I'll need you to do the
> following.  Here are lines # 905 - 907 in
> ~/lib/galaxy/web/controllers/library-common.py
> 
> 
>         # Send the current history to the form to enable importing
> datasets from history to library
>         history = trans.get_history()
>         trans.sa_session.refresh( history )
> 
> 
> Please add the following debug statements:
> 
> 
>         # Send the current history to the form to enable importing
> datasets from history to library
>         history = trans.get_history()
>         log.debug("### history: %s" % str( history ))
>         log.debug("### trans: %s" % str( trans ))
>         log.debug("### trans.sa_session: %s" %
> str( trans.sa_session ))
>         trans.sa_session.refresh( history )
> 
> 
> Stop and restart your Galaxy server after making the above changes,
> and reply back with the output of the debug statements.  Assuming you
> start your Galaxy instance with:
> 
> 
> sh run.sh
> 
> 
> you'll see the results of the debug statements in the log scrolling in
> the window in which you started Galaxy.
> 
> 
> Thanks
> 
> 
> On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote:
> 
> > Hello Greg
> > 
> > Thank you for answering. Please find the answers after each
> > question.
> > 
> > 
> > Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit :
> > > Hello Louise,
> > > 
> > > I do not think this issue is related to the Galaxy eggs, but
> > > instead looks like a data issue of some kind.  Please replly back
> > > with answers to the following questions.
> > > 
> > > How did you create your database?  
> > 
> > Couldn't have done it more simply ^^:
> > CREATE DATABASE "galaxy_db";
> > GRANT ALL ON DATABASE "galaxy_db" TO "galaxy";
> > executed in psql.
> > The very same way I did for the one that's still working fine.
> > 
> > > Did you populate it with any data exported from another database?
> > >  
> > 
> > In the beginning yes but when I saw that error I dropped the
> > database
> > and re-created it again, to start anew and test on an empty
> > database. I
> > even created a brand new test database to see if the issue wasn't
> > related to stuff remaining after dropping the database, but it
> > turned
> > out badly too.
> > 
> > > What version of Galaxy are you using?  
> > 
> > The latest dist, cause when I saw how things were turning out I hg
> > pulled and updated hoping it would fix the issue. I did that this
> > morning.
> > 
> > > What database are you using?
> > 
> > PostgreSQL, as recommended in the doc.
> > 
> > > 
> > > Greg Von Kuster
> > 
> > Cheers,
> > L-A
> > 
> > > 
> > > On Apr 14, 2011, at 5:38 AM, 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.
> > > > 
> > > > Cheers,
> > > > L-A
> > > > 
> > > > ___________________________________________________________
> > > > 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
> > > 
> > > 
> > > 
> > 
> > 
> > ___________________________________________________________
> > 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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