Re: [galaxy-dev] Error when adding datasets

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=f2db... >>>> 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 >>> greg(a)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(a)bx.psu.edu > > > > > >