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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