error uploading file with fresh installation: this request returned None from get_history()
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
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?
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
"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:
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
"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:
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
"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:
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
"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:
What sort of database are you using on your local instance?
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
"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:
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
"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:
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/
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.
On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard carlfeberhard@gmail.comwrote:
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/ > >
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/ > > > >
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?
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/ >> > >> > > >
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/ > >> > > >> > > > > >
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/ >> >> > >> >> > >> > >> > > >
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard carlfeberhard@gmail.com wrote:
If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy?
SQLAlchemy-0.5.6_dev_r6498-py2.7.egg
Do you have SQLAlchemy installed already on that machine (apart from the one in Galaxy's eggs)?
I don't think so. I never knowingly installed it and in a fresh python session, 'import sqlalchemy' returns an error that there is no such module.
Thanks, Dan
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/ > >> >> > > >> >> > > >> > > >> > > > > >
galaxy-dev@lists.galaxyproject.org
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Carl Eberhard -
Dan Tenenbaum