What sort of database are you using on your local instance?


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
>> >> ___________________________________________________________
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>> >
>> >
>
>