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.
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.
> 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
>> File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in
>> 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
>> return str( Template( source=template_text, searchList=[context] ) )
>> line 1004, in __str__
>> return getattr(self, mainMethName)()
>> File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond
>> NotFound: cannot find 'attribute_types' while searching for
>> 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
>> the code changes are here:
>> Should I create a pull request?
>> Marius van den Beek, PhD
>> Drosophila Genetics and Epigenetics
>> Institut de Biologie Paris Seine
>> 9, Quai St Bernard, Boîte courrier 24
>> 75252 Paris Cedex 05
>> Tel +33 01 44 27 34 01
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