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

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