galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax It is significant - and not normal behavior. Good catch! (You can disregard the 'Error: this request returned None from get_history()' message; it records the lack of a current history which is normal when you access those pages but haven't logged in yet) On Tue, Jan 29, 2013 at 12:49 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Those are both fine then.
You've got us (temporarily) stumped - even the old timers here.
Can you give some rough information on your system - what OS you're using, what your network set up would be?
Thanks again for looking into this. It's Mac OS X 10.8.2 with Chrome 24.0.1312.56, though I have the same problems with Safari 6.0.2 (8536.26.17) and Firefox 17.0. Python 2.7.2.
Also - if it's not too problematic - can you do a fresh clone of Galaxy onto your system and see if that installation has the same problem?
I did this and it seems to have pretty much the same problem but a slightly different manifestation. Now I am now getting the error message "Error: this request returned None from get_history(): http://localhost:8080/" when I try and upload a file; instead, no error messages show up in the console, but the upload still fails. I do however get that error message when I try and log in as a user after registering that user.
Another thing I notice, in the output immediately after starting run.sh:
galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax
Maybe that is significant?
Switching back to my previous distribution I get the identical behavior...
Thanks, Dan
C
On Mon, Jan 28, 2013 at 5:03 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard <carlfeberhard@gmail.com
wrote:
If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy?
SQLAlchemy-0.5.6_dev_r6498-py2.7.egg
Do you have SQLAlchemy installed already on that machine (apart from the one in Galaxy's eggs)?
I don't think so. I never knowingly installed it and in a fresh python session, 'import sqlalchemy' returns an error that there is no such module.
Thanks, Dan
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
I was incorrect in stating that the changes in the next galaxy-dist will help in this case, unfortunately. From the stack trace you posted, there is a deeper error with your instance that the client-side changes
won't
help.
Can you post the size, type, and name of the file you're trying to upload?
I can reproduce this by just typing "hello, world" into the "URL/Text:" box on the "Upload File" page. Any file of any type seems to trigger this problem.
Thanks, Dan
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum <dtenenba@fhcrc.org
wrote: > > On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard > <carlfeberhard@gmail.com> > wrote: > > Another thing you might try is to upload the file to our test > > server: > > https://test.g2.bx.psu.edu/ and see if that works. > > > > Thanks, that does work. > > Setting up an FTP server on my local installation seems pretty > complex. All I really want to do is work around this issue and fool > Galaxy into thinking that I have uploaded a file using the > uploader...since this is a local installation I can put a file > anywhere on my system, I don't have to actually upload it, just > place > it in a directory. > > If there is no such workaround, I'll wait for the fix, I guess. > Thanks > very much for working on this! > Dan > > > > > > On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard > > <carlfeberhard@gmail.com> > > wrote: > >> > >> If this is happening consistently and a refresh on the history > >> isn't > >> doing > >> anything, you might try ftp upload: > >> http://wiki.galaxyproject.org/FTPUpload > >> or if you have permissions or are an admin you can try uploading > >> to > >> a > >> data > >> library: > >> > >> > >> http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles > >> > >> > >> > >> On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum > >> <dtenenba@fhcrc.org> > >> wrote: > >>> > >>> On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard > >>> <carlfeberhard@gmail.com> > >>> wrote: > >>> > What sort of database are you using on your local instance? > >>> > > >>> > >>> The default (sqlite I guess). It's a completely vanilla > >>> instance, I > >>> have not touched the config files. > >>> Dan > >>> > >>> > >>> > > >>> > On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum > >>> > <dtenenba@fhcrc.org> > >>> > wrote: > >>> >> > >>> >> On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard > >>> >> <carlfeberhard@gmail.com> > >>> >> wrote: > >>> >> > Thanks, Dan. That helps and I'll start looking into this. > >>> >> > > >>> >> > We will be pushing out a new galaxy-dist revision sometime > >>> >> > this > >>> >> > week > >>> >> > if > >>> >> > all > >>> >> > goes well. This revision includes some code for the history > >>> >> > panel > >>> >> > that > >>> >> > may > >>> >> > help handle this situation a bit better. I'd recommend > >>> >> > updating > >>> >> > to > >>> >> > that > >>> >> > revision when it comes out. > >>> >> > > >>> >> > >>> >> Thanks! Is there a workaround to upload a file or add it to > >>> >> my > >>> >> history > >>> >> in the meantime? Command-line is ok. If there isn't one, > >>> >> that's > >>> >> ok > >>> >> too.... > >>> >> Dan > >>> >> > >>> >> > >>> >> > >>> >> > I'll let you know what I can find. > >>> >> > Carl > >>> >> > > >>> >> > > >>> >> > > >>> >> > On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum > >>> >> > <dtenenba@fhcrc.org> > >>> >> > wrote: > >>> >> >> > >>> >> >> Hi Carl, > >>> >> >> > >>> >> >> On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard > >>> >> >> <carlfeberhard@gmail.com> > >>> >> >> wrote: > >>> >> >> > Heya, Dan. > >>> >> >> > > >>> >> >> > Sorry for the trouble. > >>> >> >> > When you get that error again look for a line like you > >>> >> >> > have > >>> >> >> > above: > >>> >> >> > Debug at: http://localhost:8080/_debug/view/1358978130 > >>> >> >> > > >>> >> >> > If you open a new tab or window in your browser and go > >>> >> >> > to > >>> >> >> > the > >>> >> >> > address > >>> >> >> > ('http://localhost:8080/_debug ...'), you should see a > >>> >> >> > more > >>> >> >> > informative > >>> >> >> > error message - complete with a list of function calls > >>> >> >> > that > >>> >> >> > led > >>> >> >> > to > >>> >> >> > the > >>> >> >> > error > >>> >> >> > (a stack trace). > >>> >> >> > > >>> >> >> > Can you post that stack trace when you see it? > >>> >> >> > > >>> >> >> > >>> >> >> Thanks for the quick response. Here it is: > >>> >> >> > >>> >> >> URL: http://localhost:8080/tool_runner/upload_async_create > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', > >>> >> >> line 364 in respond > >>> >> >> app_iter = self.application(environ, > >>> >> >> detect_start_response) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', > >>> >> >> line 98 in __call__ > >>> >> >> environ, self.app) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', > >>> >> >> line 539 in intercept_output > >>> >> >> app_iter = application(environ, > >>> >> >> replacement_start_response) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', > >>> >> >> line 80 in __call__ > >>> >> >> return self.application(environ, start_response) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', > >>> >> >> line 632 in __call__ > >>> >> >> return self.application(environ, start_response) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py', > >>> >> >> line 160 in __call__ > >>> >> >> body = method( trans, **kwargs ) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py', > >>> >> >> line 73 in decorator > >>> >> >> return simplejson.dumps( func( self, trans, *args, > >>> >> >> **kwargs > >>> >> >> ) > >>> >> >> ) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', > >>> >> >> line 317 in upload_async_create > >>> >> >> datasets.append( create_dataset( name ) ) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', > >>> >> >> line 287 in create_dataset > >>> >> >> return upload_common.new_upload( trans, cntrller, ud, > >>> >> >> library_bunch=library_bunch, > >>> >> >> > >>> >> >> state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD > >>> >> >> ) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', > >>> >> >> line 213 in new_upload > >>> >> >> return new_history_upload( trans, uploaded_dataset, > >>> >> >> state ) > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', > >>> >> >> line 118 in new_history_upload > >>> >> >> hda.state = state > >>> >> >> File > >>> >> >> > >>> >> >> > >>> >> >> '/Users/dtenenba/dev/galaxy-dist/lib/galaxy/model/__init__.py', > >>> >> >> line 1048 in set_dataset_state > >>> >> >> object_session( self ).add( self.dataset ) > >>> >> >> AttributeError: 'NoneType' object has no attribute 'add' > >>> >> >> > >>> >> >> Dan > >>> >> >> > >>> >> >> > >>> >> >> > We can take it from there and thanks, > >>> >> >> > Carl > >>> >> >> > > >>> >> >> > > >>> >> >> > On Wed, Jan 23, 2013 at 5:04 PM, Dan Tenenbaum > >>> >> >> > <dtenenba@fhcrc.org> > >>> >> >> > wrote: > >>> >> >> >> > >>> >> >> >> Hi, > >>> >> >> >> > >>> >> >> >> I installed galaxy completely from scratch: > >>> >> >> >> > >>> >> >> >> rm -rf galaxy-dist && hg clone > >>> >> >> >> https://bitbucket.org/galaxy/galaxy-dist/ > >>> >> >> >> > >>> >> >> >> I'm not a mercurial expert but I think I have changeset > >>> >> >> >> 8530:a4113cc1cb5e; at least that's the first entry in > >>> >> >> >> "hg > >>> >> >> >> log". > >>> >> >> >> > >>> >> >> >> Then started galaxy like this: > >>> >> >> >> cd galaxy-dist > >>> >> >> >> ./run.sh > >>> >> >> >> > >>> >> >> >> I went to http://localhost:8080 and tried to upload a > >>> >> >> >> file. I > >>> >> >> >> never > >>> >> >> >> saw the file in my history, and this is what printed > >>> >> >> >> out > >>> >> >> >> in > >>> >> >> >> the > >>> >> >> >> console after I clicked "Execute" on the "Upload File" > >>> >> >> >> page: > >>> >> >> >> > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 > >>> >> >> >> Error: > >>> >> >> >> this > >>> >> >> >> request > >>> >> >> >> returned None from get_history(): > >>> >> >> >> http://localhost:8080/tool_runner/upload_async_create > >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "POST > >>> >> >> >> /tool_runner/upload_async_create HTTP/1.1" 500 - > >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel > >>> >> >> >> Mac > >>> >> >> >> OS X > >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) > >>> >> >> >> Chrome/24.0.1312.56 > >>> >> >> >> Safari/537.17" > >>> >> >> >> Debug at: http://localhost:8080/_debug/view/1358978130 > >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET > >>> >> >> >> /tool_runner/upload_async_message HTTP/1.1" 200 - > >>> >> >> >> "http://localhost:8080/" "Mozilla/5.0 (Macintosh; Intel > >>> >> >> >> Mac > >>> >> >> >> OS X > >>> >> >> >> 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) > >>> >> >> >> Chrome/24.0.1312.56 > >>> >> >> >> Safari/537.17" > >>> >> >> >> 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] "GET > >>> >> >> >> /history > >>> >> >> >> HTTP/1.1" > >>> >> >> >> 200 > >>> >> >> >> - > >>> >> >> >> " http://localhost:8080/tool_runner/upload_async_message" > >>> >> >> >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) > >>> >> >> >> AppleWebKit/537.17 > >>> >> >> >> (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17" > >>> >> >> >> > >>> >> >> >> Hope someone can help. > >>> >> >> >> Thanks, > >>> >> >> >> Dan > >>> >> >> >> > >>> >> >> >> > >>> >> >> >>
> >>> >> >> >> 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/ > >>> >> >> > > >>> >> >> > > >>> >> > > >>> >> > > >>> > > >>> > > >> > >> > >