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
<?xml version="1.0"?>
<object_store type="hierarchical">
<backends>
<object_store type="distributed" id="primary" order="0">
<backends>
<backend id="files2" type="disk" weight="1">
<files_dir path="/data/2/galaxy_db/files"/>
<extra_dir type="temp" path="/data/2/galaxy_db/tmp"/>
<extra_dir type="job_work" path="/data/2/galaxy_db/job_working_directory"/>
</backend>
<backend id="files3" type="disk" weight="1">
<files_dir path="/data/3/galaxy_db/files"/>
<extra_dir type="temp" path="/data/3/galaxy_db/tmp"/>
<extra_dir type="job_work" path="/data/3/galaxy_db/job_working_directory"/>
</backend>
</backends>
</object_store>
<object_store type="disk" id="secondary" order="1">
<files_dir path="/data/0/galaxy_db/files"/>
<extra_dir type="temp" path="/data/0/galaxy_db/tmp"/>
<extra_dir type="job_work" path="/data/0/galaxy_db/job_working_directory"/>
</object_store>
</backends>
</object_store>
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