Sorry about the miscommunication: when I mentioned 'make sure you're using
a fresh history' I meant that you may want to go to the history options
menu (the gear in the upper right of the history panel and click 'Create
new'). It may be that previous datasets are causing some of the problems
we're seeing (and you wouldn't see deleted datasets - even though they are
still there - unless you checked the 'Include deleted datasets' from that
same history options menu).

Re: login: I believe there's a redirect in place that moves you past the
older 'Return to the homepage' message automatically - I think you're good
there (and logged in). Are you seeing the 'Logged in as <your email>' in
the 'User' menu at the top?

Re: the error: so it looks like this is back to square one (the original
error). If this still happens after you've ensured you're using a new
history - I'll keep digging.
C


On Mon, Feb 4, 2013 at 1:30 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:

> Hi Carl,
>
> On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard <carlfeberh...@gmail.com>
> wrote:
> > Hello, Dan.
> > I'm glad you updated.
> >
> > I noticed another error in your log:
> > 127.0.0.1 - - [04/Feb/2013:09:50:43 -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/24.0.1312.57 Safari/537.17"
> > Debug at: http://localhost:8080/_debug/view/1360000104
> >
> > Two things -
> >
> > 1. Can you restart your daemon and make sure you're using a fresh history
> > before the upload?
>
> Not sure what you mean by this. I have no items in my history...
>
> > 2. If you're upload fails this time, would you search your paster.log for
> > something close to "Debug at: http://localhost:8080/_debug/view/";... and
> > navigate there with your browser? It should show that error in more depth
> > and allow you to post that here.
> >
>
> 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'
>
> I did try and log in. The green panel that says I have logged in
> flashed past for a split second.
>
> I'm attaching the latest paster.log again as well.
>
>
> Thanks,
> Dan
>
>
> > Thanks for the help,
> > C
> >
> >
> >
> >
> > On Mon, Feb 4, 2013 at 12:55 PM, Dan Tenenbaum <dtene...@fhcrc.org>
> wrote:
> >>
> >> Hi Carl,
> >>
> >> On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtene...@fhcrc.org>
> wrote:
> >> > Here you go. I notice a couple of stack traces.
> >> > Thanks!
> >> > Dan
> >> >
> >> >
> >>
> >> I noticed that another user on the list seemed to have a similar
> >> problem and I saw that that problem was possibly addressed in a new
> >> commit. I updated to 8531:3299529e0fe8 and I still have the same
> >> problem, but perhaps different output.
> >>
> >> I tried logging in and the UI does not seem to recognize that I have
> >> logged in. Then I tried to upload a file and it failed, with a
> >> traceback in the console:
> >>
> >> 127.0.0.1 - - [04/Feb/2013:09:45:13 -0700] "GET /history HTTP/1.1" 200
> >> - "http://localhost:8080/tool_runner/index"; "Mozilla/5.0 (Macintosh;
> >> Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko)
> >> Chrome/24.0.1312.57 Safari/537.17"
> >> 127.0.0.1 - - [04/Feb/2013:09:45:12 -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/24.0.1312.57 Safari/537.17"
> >> ----------------------------------------
> >> Exception happened during processing of request from ('127.0.0.1',
> 49617)
> >> Traceback (most recent call last):
> >>   File
> >>
> "/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> >> line 1053, in process_request_in_thread
> >>     self.finish_request(request, client_address)
> >>   File
> >>
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
> >> line 323, in finish_request
> >>     self.RequestHandlerClass(request, client_address, self)
> >>   File
> >>
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
> >> line 641, in __init__
> >>     self.finish()
> >>   File
> >>
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py",
> >> line 694, in finish
> >>     self.wfile.flush()
> >>   File
> >>
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py",
> >> line 303, in flush
> >>     self._sock.sendall(view[write_offset:write_offset+buffer_size])
> >> error: [Errno 32] Broken pipe
> >> ----------------------------------------
> >>
> >> Then I started a daemon session in order to be able to send you the
> >> full output, but, although the upload still fails, I don't get this
> >> same traceback in the paster.log. I attach it anyway.
> >>
> >> Thanks,
> >> Dan
> >>
> >>
> >>
> >> > On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard
> >> > <carlfeberh...@gmail.com> wrote:
> >> >> Ok - interesting!
> >> >> Can you send me the paster.log from a daemon session where you try an
> >> >> upload?
> >> >>
> >> >> Steps for that are:
> >> >> 1. from the directory of your galaxy installation: sh run.sh --daemon
> >> >> (you
> >> >> should see 'Entering daemon mode')
> >> >> 2. Wait a minute, then load localhost:8080 in your browser, login,
> and
> >> >> try
> >> >> an upload
> >> >> 3. When that fails, you can shut down: (from the galaxy installation
> >> >> again)
> >> >> sh run.sh --stop-daemon
> >> >>
> >> >> The file 'paster.log' should be in that same directory.
> >> >>
> >> >> Let me know if there are any problems,
> >> >> C
> >> >>
> >> >>
> >
> >
>
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