opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.

Browse Source
This commit is contained in:
Daniel Blankenberg
2009-11-30 14:55:30 -05:00
parent ed381c7333
commit 77bd226f2b
5 changed files with 87 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/set_metadata.py
+21 -2
View File
@@ -50,17 +50,36 @@ def __main__():
except:
continue
for filenames in sys.argv[1:]:
filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' )
fields = filenames.split( ',' )
filename_in = fields.pop( 0 )
filename_kwds = fields.pop( 0 )
filename_out = fields.pop( 0 )
filename_results_code = fields.pop( 0 )
dataset_filename_override = fields.pop( 0 )
#Need to be careful with the way that these parameters are populated from the filename splitting,
#because if a job is running when the server is updated, any existing external metadata command-lines
#will not have info about the newly added override_metadata file
if fields:
override_metadata = fields.pop( 0 )
else:
override_metadata = None
try:
dataset = cPickle.load( open( filename_in ) ) #load DatasetInstance
if dataset_filename_override:
dataset.dataset.external_filename = dataset_filename_override
if ext_override.get( dataset.dataset.id, None ):
dataset.extension = ext_override[ dataset.dataset.id ]
#Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
if override_metadata:
override_metadata = simplejson.load( open( override_metadata ) )
for metadata_name, metadata_file_override in override_metadata:
if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
setattr( dataset.metadata, metadata_name, metadata_file_override )
kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )#load kwds; need to ensure our keywords are not unicode
dataset.datatype.set_meta( dataset, **kwds )
dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta
simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded
simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has succeeded
except Exception, e:
simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
clear_mappers()