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>
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
wrote: 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/