Ooops, this is very right, I totally forgot about that. It woud have
become problematic at some point I guess. Thank you for pointing this
out!
I changed it so the new database is associated with brand new
appropriate directories. (and dropped and re-created the db again) But I
keep getting the same error message with supposedly nonexistent
histories.
Thanks again
L-A
Le vendredi 15 avril 2011 à 13:47 +0200, Hans-Rudolf Hotz a écrit :
On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote:
> 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?
>
the folder where you keep the datasets, eg:
<your local path>/galaxy_dist/database/
and it particular
<your local path>/galaxy_dist/database/files/000/dataset_*.dat
if you have an empty PostgreSQL database, then there should also be no
datasets.
Hans
>>
>> - 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<greg(a)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=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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> Greg Von Kuster
>>>>> Galaxy Development Team
>>>>> greg(a)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/
>
>