On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote:
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
This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you.
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 importingdatasets 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 importingdatasets 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=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.
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu