Minor correction for the import, you could do:

from galaxy.util import restore_text

in a tool executed from Galaxy.

On Nov 16, 2012, at 2:50 PM, Daniel Blankenberg wrote:

> Hi Samuel,
> 
> You can import and use the restore_text function from galaxy.lib.util to 
> restore the characters.  
> 
> Alternatively, you may want to look at customizing the sanitizer you are 
> using for the tool input, e.g. only sanitize the quote character that you are 
> using around the command-line argument or even not sanitizing any characters 
> if your python script can use a file ('configfile') as the input: 
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Csanitizer.3E_tag_set
>  
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Cconfigfile.3E_tag_set
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 
> 
> On Nov 16, 2012, at 1:29 PM, Samuel Lampa wrote:
> 
>> Hi,
>> 
>> I'm creating a galaxy tool [0] for querying external SPARQL (the Semantic 
>> Web query language) endpoints to get back data in tabular formats.
>> 
>> I run into a problem though, since SPARQL queries contain curly braces, and 
>> Galaxy obviously converts these to an internal representation __oc__ and 
>> __cc__ (I found the commit for this at [1])
>> 
>> My SPARQL query for testing looks like this:
>> 
>> SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 25
>> 
>> Thus, when I send this to my (python) script as a commmand line argument, 
>> the curly braces comes in galaxy's internal representation.
>> 
>> Thus I was wondering if there is a way to get the braces in their correct 
>> format from galaxy, or if I should just go agead and convert them back in my 
>> own script? (i.e. will this behaviour be stable enough to rely on?)
>> 
>> Best
>> // Samuel
>> 
>> [0] See the sparql_import.* files in 
>> https://github.com/samuell/galaxy_semwebtools
>> [1] http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-February/001837.html
>> 
>> -- 
>> Developer at SNIC-UPPMAX www.uppmax.uu.se
>> Developer at Dept of Pharm Biosciences www.farmbio.uu.se
>> Twitter - twitter.com/samuellampa
>> Blog - saml.rilspace.org
>> G+ - gplus.to/saml
>> 
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> 
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