You did restart your galaxy server after updating to the stable branch, correct? Line 509 in lib/galaxy/web/frameowrk/__init__ should be a log statement, not an assertion. That assertion should be on line 482 in an up-to-date galaxy-dist on the stable branch. On Tue, Apr 30, 2013 at 10:49 AM, Olivia Doppelt <olivia.doppelt@pasteur.fr>wrote:
Dear Dannon,
We were on the default branch and we updated our galaxy-dist directory. We are now on the stable branch.
However, the problem persists and i have more information for you:
Here in the lines from the log file:
127.0.0.1 - - [30/Apr/2013:16:30:35 +0200] "GET /api/users HTTP/1.1" 500 - "-" "curl/7.19.7 (x86_64-redhat-linux-gnu) libcurl/7.19.7 NSS/3.13.6.0zlib/1.2.3 libidn/1.18 libssh2/1.4.2"
Error - <type 'exceptions.AssertionError'>: use_remote_user is set but no HTTP_REMOTE_USER variable
I also attach a html file which contains more details on the following python error:
</div> <br> <script type="text/javascript"> show_button('text_version', 'text version') </script> <div id="text_version" class="hidden-data"> <textarea style="width: 100%" rows=10 cols=60>URL: http://localhost:18084/api/users?key=c23d8cb98671911813305051710d4ae1 File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 96 in __call__ return self.app( environ, start_response ) File '/pasteur/projets/common/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__ return self.handle_request( environ, start_response ) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 157 in handle_request trans = self.transaction_factory( environ ) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 244 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 275 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 348 in __init__ self._ensure_valid_session( session_cookie ) File '/pasteur/projets/common/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 509 in _ensure_valid_session
"use_remote_user is set but no HTTP_REMOTE_USER variable" AssertionError: use_remote_user is set but no HTTP_REMOTE_USER variable</textarea> </div>
This problem is quite annoying as we are maintening a Galaxy for a lot of persons. For example the api enables us to deal automatocally with the users libraries.
Since last monday, we are forced to deal with that user by user.
Thanks in advance for your help, -- Olivia Doppelt-Azeroual Pasteur Institute, Paris.
Le 29/04/13 17:12, Dannon Baker a écrit :
You can verify this with 'hg branch', but it looks like you're tracking the default branch of -dist, where you want to be on stable. 'hg update stable' should fix this, and the issue you're seeing.
You should only have to do this once, next time you update (with just hg pull -u) you'll stay on stable.
On Mon, Apr 29, 2013 at 9:24 AM, Olivia Doppelt <olivia.doppelt@pasteur.fr
wrote:
Dear Dannon,
Here is the 'hg tip' result:
changeset: 9312:788cd3d06541 tag: tip parent: 9310:19f6e62bd372 parent: 9311:d7f37a2fe690 user: Nate Coraor <nate@bx.psu.edu> <nate@bx.psu.edu> date: Mon Apr 08 12:30:08 2013 -0400 summary: Merged stable.
-- Olivia
Le 29/04/13 15:05, Dannon Baker a écrit :
Olivia,
There's a fix for this available in galaxy-central, but I'm surprised you're seeing it in -dist as I thought the problem was introduced after the dist freeze. Can you provide the output of 'hg tip'?
-Dannon
On Mon, Apr 29, 2013 at 6:53 AM, Olivia Doppelt < olivia.doppelt@pasteur.fr> wrote:
Hello to All,
I would like to reiterate this problem because it is causing major problems in tha managment of our Galaxy instance
Are there some clues on how to solve this issue ?
Best regards,
-- Olivia Doppelt-Azeroual, PhD Pasteur Institute, Paris
Le 23/04/13 22:38, Fabien Mareuil a écrit :
Hi all,
We encountoured an error with the galaxy api since the last galaxy-dist revision.
here is an example of a command line that doesn't work (xxx stand for the admin key) :
./display.py xxxxxxxxxxxxxxxxxxxxxxxxxx http://localhost:18084/api/users
we obtain the following error:
HTTP Error 500: Internal Server Error
As you can see, the request is done locally, without going through a proxy or apache.
The galaxy log is the following:
127.0.0.1 - - [23/Apr/2013:19:55:26 +0200] "GET /api/users?key= xxxxxxxxxxxxxxxxxxxxx HTTP/1.1" 500 - "-" "Python-urllib/2.6" Error - <type 'exceptions.AssertionError'>: use_remote_user is set but no HTTP_REMOTE_USER variable
Do you have an idea to solve this problem? Thank in advance for your answer. Best regards
-- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur
-- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur