If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy?

Do you have SQLAlchemy installed already on that machine (apart from the one in Galaxy's eggs)?



On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
> 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?
>

I can reproduce this by just typing "hello, world" into the
"URL/Text:" box on the "Upload File" page. Any file of any type seems
to trigger this problem.

Thanks,
Dan


>
> On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
>>
>> On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard <carlfeberhard@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 <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/
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >
>> >>> >> >
>> >>> >
>> >>> >
>> >>
>> >>
>> >
>
>