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:



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
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))

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:

To search Galaxy mailing lists use the unified search at:

Reply via email to