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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