10:03 a.m.
Dear all,
I noticed that with params of type "text" Galaxy seems to replace
certain characters before passing them to the shell. As examples, it
changes "@" to "__at__", "}" to "__cc__" and
"\" to "X".
Is this the standard behavior or am I doing something wrong ? And if
it's standard, are there workarounds ?
Best,
Wolfgang
10:22 a.m.
On Mon, Jul 28, 2014 at 11:03 AM, Wolfgang Maier
<wolfgang.maier(a)biologie.uni-freiburg.de> wrote:
Dear all,
I noticed that with params of type "text" Galaxy seems to replace certain
characters before passing them to the shell. As examples, it changes "@" to
"__at__", "}" to "__cc__" and "\" to
"X".
Is this the standard behavior or am I doing something wrong ? And if it's
standard, are there workarounds ?
Best,
Wolfgang
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...
Peter
11:23 a.m.
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...
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))
11:32 a.m.
On Mon, Jul 28, 2014 at 12:23 PM, Wolfgang Maier
<wolfgang.maier(a)biologie.uni-freiburg.de> wrote:
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...
>
> 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.
Hmm. This may be very complicated since a lot will depend on the
local server/cluster's locale settings. Not everything will be UTF-8.
Peter
11:39 a.m.
On 28.07.2014 13:32, Peter Cock wrote:
On Mon, Jul 28, 2014 at 12:23 PM, Wolfgang Maier
<wolfgang.maier(a)biologie.uni-freiburg.de> wrote:
> 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...
>>
>> 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.
Hmm. This may be very complicated since a lot will depend on the
local server/cluster's locale settings. Not everything will be UTF-8.
Peter
Hmm, I just thought that maybe Galaxy has some clever way of
interpreting environmental variables. It's not terribly important to get
this right. I guess I'll just add a remark to the parameter help then.
Wolfgang
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