Hi Carl, On Mon, Feb 4, 2013 at 10:22 AM, Carl Eberhard <carlfeberhard@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 <dtenenba@fhcrc.org> wrote:
Hi Carl,
On Thu, Jan 31, 2013 at 1:37 PM, Dan Tenenbaum <dtenenba@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 <carlfeberhard@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