On 28.07.2014 12:22, Peter Cock wrote:
This is standard behaviour to prevent special characters being used
to construct malicious command lines. It can be configured within
your tool definition using the sanitizer tag set:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
Peter
Thanks a lot, Peter, that solved my problem !
Unfortunately, with this one fixed I now run into an additional one:
There is one free-text text field defined in my tool, which should
accept characters outside the standard ascii code range (i.e. 127), in
particular, German Umlaute äöüÄÖÜ.
They are now no longer translated to Xs, but instead I get:
an 'ascii' codec can't decode byte 0xc3 in position 22: ordinal not in
range(128) error, while parsing the content of the field inside the
command tag.
Is there any way to make Galaxy work with things outside the ascii range
(like by using a different codec)?
Just in case, here is the complete traceback I'm seeing:
Traceback (most recent call last):
File
/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 152, in prepare_job
job_wrapper.prepare()
File /home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/jobs/__init__.py,
line 679, in prepare
self.command_line, self.extra_filenames = tool_evaluator.build()
File
/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/tools/evaluation.py, line
323, in build
self.__build_command_line( )
File
/home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/tools/evaluation.py, line
339, in __build_command_line
command_line = fill_template( command, context=param_dict )
File /home/galaxy/WMGalaxy/galaxy-dist/lib/galaxy/util/template.py,
line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
/home/galaxy/WMGalaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py,
line 1004, in __str__
return getattr(self, mainMethName)()
File
cheetah_DynamicallyCompiledCheetahTemplate_1406545596_05_93125.py,
line 163, in respond
File
/home/galaxy/WMGalaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/DummyTransaction.py,
line 47, in getvalue
(%s)''' % (nonunicode, ex))
DummyResponseFailure: Looks like you're trying to mix encoded strings
with Unicode strings
(most likely utf-8 encoded ones)
This can happen if you're using the `EncodeUnicode` filter,
or if you're manually
encoding strings as utf-8 before passing them in on the
searchList (possible offenders:
['ascii', 'ascii', ' ', 'non-ASCII characters:
\xc3\x84\xc3\x96\xc3\x9c',
'/home/galaxy/WMGalaxy/galaxy-dist/database/files/000/dataset_197.dat'])
('ascii' codec can't decode byte 0xc3 in position 22:
ordinal not in range(128))
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