Hi Hans, thanks for your reply.
>
> - is your PostgreSQL database in sync with the database folder?
I'm sorry I'm not sure I get what you mean, what folder is it?
>
> - are you sure there is no second galaxy installation accessing the
> same PostgreSQL database?
Never been this sure of something before. :) I installed both galaxy and
postgresql myself so I can guarantee there's ony one galaxy install on
it.
>
> - you mention, that you have started with an empty PostgreSQL
> database, so this last question does probably not apply: make sure
> you have the right user names (you even run into trouble with case
> sensitivity) in your PostgreSQL database. We had troubles when we
> switched to external authentication: some users just couldn't work
> anymore, ie could not create new history items anymore. The problem
> was then solved by fixing their user names in the (MySQL) database.
Yes, the username is properly created in the database when I log in on
an empty database. We never used anything besides LDAP anyway.
>
> Regards, Hans
Cheers,
L-A
>
>
>
> >
> > On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote:
> >
> >> The thing is, we use LDAP logging so we can't even access the website
> >> without logging in.
> >> Moreover, when I logged in, I arrived on the data analysis page where the
> >> automatic "unnamed history" was obviously created in the history panel.
> >>
> >> I forgot to mention we have issues creating and deleting histories, like,
> >> we can't access some histories and everytime we delete histories, two extra
> >> unnamed histories are created. As I mentioned before, it is also impossible
> >> to load a dataset in any history, existing or not.
> >>
> >> Do you think it could be linked to our using LDAP?
> >>
> >> Thanks
> >> L-A
> >>
> >>
> >> On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kuster<g...@bx.psu.edu>
> >> wrote:
> >>> 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 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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>
> >>> Greg Von Kuster
> >>> Galaxy Development Team
> >>> g...@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/
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