Hi Marius,

I hope you don't mind, but I went ahead and pulled your change in as
https://github.com/galaxyproject/galaxy/pull/199, since there's a bit of
backport-fixing required to get this applied correctly.

-Dannon

On Thu, Apr 30, 2015 at 2:37 PM Dannon Baker <dannon.ba...@gmail.com> wrote:

> Hi Marius,
>
> It'd be great if you wanted to submit a PR for the json issue separately
> -- I can confirm that that's a working fix.  I'll let someone else speak to
> the tool change.
>
> -Dannon
>
> On Thu, Apr 30, 2015 at 2:30 PM Marius van den Beek <
> m.vandenb...@gmail.com> wrote:
>
>> Hello all,
>>
>> Not sure if the mailing list or trello would be appropriate for this.
>> I had a problem using the gff_filter_by_attribute tool, both locally and
>> on usegalaxy.org.
>> Neither filtering for GTF or GFF were working.
>>
>> The error message was:
>>
>> Traceback (most recent call last):
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 
>> 158, in prepare_job
>>     job_wrapper.prepare()
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in 
>> prepare
>>     self.command_line, self.extra_filenames = tool_evaluator.build()
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408, 
>> in build
>>     self.__build_command_line( )
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424, 
>> in __build_command_line
>>     command_line = fill_template( command, context=param_dict )
>>   File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in 
>> fill_template
>>     return str( Template( source=template_text, searchList=[context] ) )
>>   File 
>> "/home/galaxy/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 "DynamicallyCompiledCheetahTemplate.py", line 92, in respond
>> NotFound: cannot find 'attribute_types' while searching for 
>> 'input.metadata.attribute_types'
>>
>>
>> I could fix it by importing safe_dumps from galaxy.util.json, which
>> apparently was not imported.
>> The next problem occurred because gff_filter_by_attribute expects GTF
>> attribute name-value separators (" ") but allowed GFF input, which uses
>> ("=") as separator. I added a logic to switch
>> between seperators based on the file extension. Everything works smoothly
>> now,
>> the code changes are here:
>> https://github.com/mvdbeek/galaxy
>> Should I create a pull request?
>>
>> --
>> Marius van den Beek, PhD
>>
>> Drosophila Genetics and Epigenetics
>> Institut de Biologie Paris Seine
>> <http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile>
>> 9, Quai St Bernard, BoƮte courrier 24
>> 75252 Paris Cedex 05
>> Tel +33 01 44 27 34 01
>>
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>
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