Hello
Like Matthias
(http://gmod.827538.n3.nabble.com/Fatal-Error-while-uploading-a-File-with-special-Characters-td4051157.html)
I can't upload a file with special characters.
My test file is : Frédéric.txt
The database itself seems to be ok, I can see that the insertion is ok in
"history_dataset_association" :
id history_id dataset_id create_time
update_time copied_from_history_dataset_association_id hid
name info
328 1 330 2017-03-01 08:13:56 2017-03-01
08:14:05 NULL 293 Frédéric.txt uploaded txt
file 1 line
But until I change Frédéric.txt to Frederic.txt within the name column, my
history is broken.
Errors are the same as described by Matthias.
galaxy.web.framework.decorators ERROR 2017-03-01 09:14:18,321 Uncaught
exception in exposed API method:
Traceback (most recent call last):
File "/softs/bioinfo/galaxy-prod/lib/galaxy/web/framework/decorators.py",
line 284, in decorator
rval = _format_return_as_json( rval, jsonp_callback, pretty=trans.debug )
File "/softs/bioinfo/galaxy-prod/lib/galaxy/web/framework/decorators.py",
line 317, in _format_return_as_json
json = safe_dumps( rval, **dumps_kwargs )
File "/softs/bioinfo/galaxy-prod/lib/galaxy/util/json.py", line 67, in
safe_dumps
dumped = json.dumps( obj, allow_nan=False, **kwargs )
File "/usr/local/lib/python2.7/json/__init__.py", line 251, in dumps
sort_keys=sort_keys, **kw).encode(obj)
File "/usr/local/lib/python2.7/json/encoder.py", line 209, in encode
chunks = list(chunks)
File "/usr/local/lib/python2.7/json/encoder.py", line 431, in _iterencode
for chunk in _iterencode_list(o, _current_indent_level):
File "/usr/local/lib/python2.7/json/encoder.py", line 332, in _iterencode_list
for chunk in chunks:
File "/usr/local/lib/python2.7/json/encoder.py", line 390, in _iterencode_dict
yield _encoder(value)
UnicodeDecodeError: 'utf8' codec can't decode byte 0xe9 in position 2: invalid
continuation byte
I have read a lot of threads about this kind of error (mostly from
stackoverflow)
It is related to Galaxy or it's related to my python installation ?
For a production server, it means that I will have to update manually the
database each time a user try to upload such a file (find his id, find the
broken history and the file name to correct !)
I'm running Galaxy 17.01 with a mysql (5.7.11-4, UTF-8) database.
I've modified lib/galaxy/datatypes/binary.py (for XLS datatypes) and
lib/galaxy/jobs/runners/__init__.py (truncate the job name for PBS-PRO)
# On branch release_17.01
# Your branch is ahead of 'origin/release_17.01' by 3 commits.
#
# Changed but not updated:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: lib/galaxy/datatypes/binary.py
# modified: lib/galaxy/jobs/runners/__init__.py
Thanks in advance!
Fred
---
Frederic Sapet
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Centre de Recherche de Chappes
CS 90126
63720 CHAPPES
FRANCE
Tel : +33 (0)4 73 67 88 54
Fax : +33 (0)4 73 67 88 99
E-mail : [email protected]<mailto:[email protected]>
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