It's difficult to pinpoint what exactly went wrong with your update without a full log of your hg commands and outputs, but I'd wager that now that it appears you're actually running stable you'll be ok in the future.
For what it's worth, I would recommend for the future that you go ahead and commit any outstanding intentional changes you've made that you do want to keep around. This should make it easier to deal with future updates and potential merges, while preserving a concrete history of local changes.
Glad you're up and running again, in any event!
Dannon
On Tue, Apr 30, 2013 at 1:26 PM, Olivia Doppelt olivia.doppelt@pasteur.frwrote:
The updates we made are not committed as some are not tested yet.
We compared the __init__.py from lib/galaxy/web/framework and the one from the mercurial repository and they were completely different whereas none of our local changes concern this file.
So to test, we just copied the last version on our directory, and the api now works fine.
We wonder though why the merge didn't work on the __init__.py. Any idea ?
Thank you very much for your help.
-- Olivia
Le 30/04/13 18:04, Dannon Baker a écrit :
Are the updates you made committed? If so, to what branch? What's the output of 'hg status'?
The problem here is definitely that your __init__.py file is not the correct version that exists on the stable branch.
On Tue, Apr 30, 2013 at 12:02 PM, Olivia Doppelt < olivia.doppelt@pasteur.fr> wrote:
The command:
# galaxypa@bic-web00 ~/galaxy-dist > cat lib/galaxy/web/framework/__init__.py | sed '509!d'
generates this result:
"use_remote_user is set but no HTTP_REMOTE_USER variable"We have made a few changes but not in this file.
The update was easy as it didn't generate any conflict.
We had one problem though concerning the class JobRunnerMapper which now takes only 2 arguments now:
# PREVIOUS self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination, self.app.job_config ) self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination )
I don't know if this information is usefull for you. Thank you for your help.
Le 30/04/13 17:27, Dannon Baker a écrit :
Ok, just to make sure I'm not crazy, can you execute:
`cat lib/galaxy/web/framework/__init__.py | sed '509!d'`
That line *should* be: log.warning( "User '%s' is marked deleted, invalidating session" % galaxy_session.user.email )
If it's not, somehow, your working directory state is wonky and we'll have to dig a little deeper. Have you made any local changes (committed, or not)?
Did the update to the stable branch work cleanly, without any outstanding changes requiring a merge? (Perhaps the symlink bit that you may have seen on the list?)
On Tue, Apr 30, 2013 at 11:23 AM, Olivia Doppelt < olivia.doppelt@pasteur.fr> wrote:
hg tip:
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.
hg branch:
stable
Le 30/04/13 17:19, Dannon Baker a écrit :
Can you send me the output of 'hg tip' and 'hg branch'?
On Tue, Apr 30, 2013 at 11:15 AM, Olivia Doppelt < olivia.doppelt@pasteur.fr> wrote:
Yes many times.
Le 30/04/13 16:53, Dannon Baker a écrit :
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/ 3.13.6.0 zlib/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