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.


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