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/ > >> >> > > >> >> > > >> > > >> > > > > >