Re: [galaxy-dev] [galaxy-user] Data Libraries Problems
Galaxy works with Python 2.4 or higher ( but not Python 3 ). On Jul 2, 2010, at 3:15 PM, Juan Perin wrote:
No changes at all. I seem to get this with a new installation as well. Both using postgres and mysql. Is there a new python requirement perhaps? I may be running and older version.
~ juan
On Jul 2, 2010, at 14:13, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Juan,
We're not able to reproduce this error. Have you made any changes to the code in your instance?
Greg
On Jul 2, 2010, at 12:16 PM, juan perin wrote:
In my latest pull from the galaxy update server, something has caused my instance to act up. I'm getting an error when trying to upload data into libraries. This is the text based error:
URL: http://variome.chop.edu:8082/library_common/upload_library_dataset File '/home/perin/galaxy_dist2/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/perin/galaxy_dist2/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/perin/galaxy_dist2/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/perin/galaxy_dist2/lib/galaxy/web/controllers/library_common.py', line 978 in upload_library_dataset **kwd ) File '/home/perin/galaxy_dist2/lib/galaxy/web/controllers/library_common.py', line 1158 in upload_dataset message=util.sanitize_text( message ), File '/home/perin/galaxy_dist2/lib/galaxy/util/__init__.py', line 138 in sanitize_text for c in text: TypeError: 'NoneType' object is not iterable
Strangely, the data gets queued up anyway, if you go back to the library, and you can even see the first few lines of the file in the preview, but it remains queued and never fully becomes available. Not sure what's going on, so was hoping for any suggestions. I just updated to Postgresql as well, but that didn't change the problem. Thanks.
Juan _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Ok, still having the problem. I switched to a completely new clone of galaxy, and even started on a completely clean installation of Postgres for the backend. No matter what I do, i get the same error when trying to transfer data from file system paths. Managing a data library by adding data via file upload works fine, but is not useful for large files of course. I can't find any issues in the code, and have tried various file types as well. I'm at a stand still with galaxy right now, and am simply working on figuring out this problem until its resolved. Thanks for any other ideas you might have. Juan
Hi Juan, juan perin wrote, On 07/06/2010 01:37 PM:
I can't find any issues in the code, and have tried various file types as well. I'm at a stand still with galaxy right now, and am simply working on figuring out this problem until its resolved. Thanks for any other ideas you might have.
If you're sure you didn't change anything, AND it positively worked before your last pull/upgrade, AND you have some time to spare, you can try "hg bisect" to pin-point the exact changeset that broke it for you (assuming it is a changeset the causes the problem, and not some local configuration issue). Start with a fresh clone, then run: $ hg bisect --reset $ hg bisect --good XXXX (where XXXX is an old revision number which you're sure worked) $ hg bisect --bad tip (marking the current version as NOT working) and then mercurial/hg which automatically pull/update old revisions for you. Every time mercurial changes a revision, run your tests (that's the "time to spare" part...), and check whether you can upload the libraries as needed. If the tests worked, run: $ hg bisect --good if the tests failed, run: $ hg bisect --bad Mercurial will automatically change to another revision, then you test it again (and mark it again as "--good" or "--bad"), until the exact revision that introduced the problem is found. More information about "bisect" is here: http://hgbook.red-bean.com/read/finding-and-fixing-mistakes.html#x_6c6 Alternatively, you can just use "hg update -C -r XXX" and switch to older revisions by yourself, but "bisect" will probably be more efficient. -gordon
participants (3)
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Assaf Gordon -
Greg Von Kuster -
juan perin