On 04/14/2011 07:36 PM, Greg Von Kuster wrote:
Hello Louise,

I've CC'd Nate on this as he may be able to help - although no guarantees.  I'm 
not expert enough in this area to know where to look for the cause.  Perhaps 
someone in the community can help as well.

It is likely that LDAP is playing a role in this behavior.



Hi

I am sure you have tested everything, but just to double check

 - is your PostgreSQL database in sync with the database folder?

 - are you sure there is no second galaxy installation accessing the
   same PostgreSQL database?

 - 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.


Regards, Hans




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

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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu





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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




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