Hi Shaun,
Yes, this was definitely a bug - thanks for finding it and supplying the fix. It will be available to the distribution with the next update.
On Aug 2, 2010, at 10:38 AM, SHAUN WEBB wrote:
I've only just got around to looking at this problem and thanks to Gordons suggestion I have found a solution:
The error is thrown in library_common.py, the upload proceeds through this line at 1134: if response_code == 200:
Then it is redirected to the get_path_paste_uploaded_datasets method at 1142: uploaded_datasets, response_code, message = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, response_code, message )
If everything goes ok here then a response code 'None' is returned at 1264: return uploaded_datasets, None, None
Which means the upload now fails at 1147 and goes in to error handling: if response_code != 200:
I have replaced line 1264 with: return uploaded_datasets, 200, None
This seems to have solved the problem. Hopefully it is this simple, I'd appreciate if some one from the Galaxy team could check if this is a bug and let me know.
Thanks Shaun Webb
Quoting Assaf Gordon gordon@cshl.edu:
Hello Shaun,
I'm not from the galaxy team, but I've looked at a similar exception for Juan Perin: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/002948.html
It looks like you get the exact same exception as he does, indicating that the upload has failed but galaxy throws and exception while trying to show you the error.
If you feel comfortable with tweaking the python code you can try to further pin-point the problem.
-gordon
SHAUN WEBB wrote, On 07/15/2010 04:39 PM:
Hi,
after updating to the latest galaxy changeset I am getting an error when trying to upload files from system path, the traceback is below.
The new files then appear in the library as queued jobs.
Thanks in advance for your help
Shaun Webb
URL: http://bifx3.bio.ed.ac.uk:8080/library_common/upload_library_dataset File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/opt/galaxy_dist/lib/galaxy/web/controllers/library_common.py', line 978 in upload_library_dataset **kwd ) File '/opt/galaxy_dist/lib/galaxy/web/controllers/library_common.py', line 1158 in upload_dataset message=util.sanitize_text( message ), File '/opt/galaxy_dist/lib/galaxy/util/__init__.py', line 138 in sanitize_text for c in text: TypeError: 'NoneType' object is not iterable
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