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
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>>>>>
>>>>> 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
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