On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard <carlfeberh...@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 <dtene...@fhcrc.org> wrote: >> >> On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard <carlfeberh...@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 <dtene...@fhcrc.org> >> > wrote: >> >> >> >> Hi Carl, >> >> >> >> On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard >> >> <carlfeberh...@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 <dtene...@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/ >> >> > >> >> > >> > >> > > > ___________________________________________________________ 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/
