Hi Björn,

I believe the problem is most likely this bug:

    https://trello.com/c/OHlQoCrx

If you symlink /usr/local/galaxy/galaxy-dist/database/tmp to somewhere
writeable (e.g. what you have new_files_path set to), that'd confirm it.

I'm going to take a look at fixing this today.

--nate


On Thu, Jun 12, 2014 at 8:43 AM, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:

> Hi,
>
> I have configured to use the hierarchical object store but as soon as I
> try to reset the filetpye of a dataset Galaxy is crashing with:
>
> galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend
> 'files3' for creation of MetadataFile 5963
> 132.230.153.57 - - [12/Jun/2014:14:39:20 +0200] "POST
> /datasets/966f24627ef70c12/edit HTTP/1.1" 500 - "
> http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit";
> "Mozilla/5.0 (X11; Linux x86_64; rv:29.0) Gecko/20100101 Fire
> fox/29.0"
> Error - <type 'exceptions.OSError'>: [Errno 2] No such file or directory:
> 'database/tmp/metadata_temp_file_1xnGcE'
> URL: http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit
> File
> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File
> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> line 84 in __call__
>   return self.application(environ, start_response)
> File
> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> line 633 in __call__
>   return self.application(environ, start_response)
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 190 in handle_request
>   body = method( trans, **kwargs )
> File
> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py',
> line 295 in edit
>
> trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
> trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming =
> { 'input1':data }, overwrite = False ) #overwrite is False as per existi
> ng behavior
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py',
> line 18 in execute
>   overwrite, history, job_params )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py',
> line 79 in execute_via_app
>   kwds = { 'overwrite' : overwrite } )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py',
> line 717 in setup_external_metadata
>   shutil.copy( dataset.metadata.get( meta_key, None ).file_name,
> metadata_temp.file_name )
> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py',
> line 575 in file_name
>   self._filename = abspath( tempfile.NamedTemporaryFile( dir =
> self.tmp_dir, prefix = "metadata_temp_file_" ).name )
> File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 454 in
> NamedTemporaryFile
>   (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags)
> File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 235 in
> _mkstemp_inner
>   fd = _os.open(file, flags, 0600)
> OSError: [Errno 2] No such file or directory:
> 'database/tmp/metadata_temp_file_1xnGcE'
>
>
> I have attached my object_store_conf.xml file.
> Thanks,
> Bjoern
>
>
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