On 04/18/2011 11:28 AM, Louise-Amélie Schmitt wrote:
Hello again

I tried deleting the compiled templates like Sarah Diehl did for her
user registration issue:

first thank you for your help. I tried reloading everything, cleared
the cache of my browser and tried it on a different computer whose
browser never before was on the Galaxy website. All of this did not
work. What worked in the end was deleting the compiled_templates
directory.

But it didn't work either. I'm back to square one, with no option in
sight. I keep getting the same error message when trying to add
datasets.

Any idea?

well, do it the hard way and start from "square one":

- is galaxy working out of the box (fresh checkout, using SQLite)

- is galaxy working out of the box (using a non-root user called
  galaxy, using a fresh checkout downloaded and installed into the
  galaxy user home directory and use PostgreSQL)

   + is it still working when you change to "require_login = True"

   + is it still working when you change to "use_remote_user = True"


at which point does it stop working?



Hans



Cheers,
L-A


Le vendredi 15 avril 2011 à 16:52 +0200, Louise-Amélie Schmitt a écrit :
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<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




___________________________________________________________
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/




___________________________________________________________
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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