I can confirm this is error. Switching the tool to use
$outfile.files_path instead of $outfile.extra_files_path improves the
situation in my testing.

I thought for sure .extra_files_path had been deprecated in terms of
files_path - but the only Trello card I could find indicates the
opposite may be true - https://trello.com/c/ar9zF40y? I think that for
some more exotic features such as parameter rewriting by setting
outputs_to_working_directory (required for running such tools are real
users I suspect) and the LWR, usage of files_path in tool wrappers
will be reworked for the job and extra_files_path will not be.

Hopefully someone with a longer history on the project will comment on
usage of .files_path versus .extra_files_path.

-John



On Fri, Jun 13, 2014 at 7:43 AM, bjoern.gruen...@googlemail.com
<bjoern.gruen...@gmail.com> wrote:
> Hi Nate,
>
> we encountered an addition bug related to the object-store:
>
> Traceback (most recent call last):
>   File "/usr/local/galaxy/galaxy-
> dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job
>     job_wrapper.prepare()
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 712, in prepare
>     self.command_line, self.extra_filenames = tool_evaluator.build()
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line
> 348, in build
>     self.__build_command_line( )
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line
> 364, in __build_command_line
>     command_line = fill_template( command, context=param_dict )
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9,
> in fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/usr/local/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py",
> line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1402663002_65_42228.py",
> line 94, in respond
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/wrappers.py", line
> 203, in __getattr__
>     return getattr( self.dataset, key )
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line
> 1493, in extra_files_path
>     return self.dataset.extra_files_path
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line
> 1349, in extra_files_path
>     return self.object_store.get_filename( self, dir_only=True,
> extra_dir=self._extra_files_path or "dataset_%d_files" % self.id )
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
> line 416, in get_filename
>     return self.__call_method('get_filename', obj, ObjectNotFound, True,
> **kwargs)
>   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
> line 436, in __call_method
>     % ( method, str( obj ), str( kwargs ) ) )
> ObjectNotFound: objectstore, __call_method failed: get_filename on
> <galaxy.model.Dataset object at 0x7f7ee103fb90>, kwargs: {'dir_only': True,
> 'extra_dir': 'dataset_118453_files'}
>
> It should be reproducible with the latest Galaxy stable release and the
> latest NCBI Blast+ wrappers if you are trying to generate a Blast+ database.
>
> Thanks,
> Bjoern
>
>
>
> 2014-06-12 16:50 GMT+02:00 Björn Grüning <bjoern.gruen...@gmail.com>:
>
>> Hi Nate,
>>
>> yes that is fixing it for me!
>>
>> Thanks!
>> Bjoern
>>
>> Am 12.06.2014 16:26, schrieb Nate Coraor:
>>
>>> writeable (e.g. what you have new_files_path set to), that'd confirm it.
>
>
>
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