Nate, John,
that bug bites me with so many tools. Next one is MACS2
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_1403081606_9_13081.py", line
253, 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 0x7eff89510310>, kwargs: {'dir_only':
True, 'extra_dir': 'dataset_118783_files'}
Is there anything I can do? It is affecting our productive server right
now. Any quick fix would be very much appreciated. The object store is
not a beta feature or? I'm wondering who is using it at the moment?
Cheers,
Bjoern
Am 16.06.2014 16:04, schrieb John Chilton:
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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___________________________________________________________
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