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. 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: