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=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
>
>
>
>
>
>