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?


On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:

> On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard <carlfeberh...@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 <carlfeberh...@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 <dtene...@fhcrc.org>
> wrote:
> >>>
> >>> 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/
> >>> >> >> >
> >>> >> >> >
> >>> >> >
> >>> >> >
> >>> >
> >>> >
> >>
> >>
> >
>
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