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Fix setting metadata in galaxy.json for working directory isolation change.

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This has been broken since 16.04 I guess? Maybe retry internally means it hasn't been an issue?
This commit is contained in:
John Chilton
2016-08-04 13:36:38 -04:00
parent 65f0a836e0
commit dfccd902b0
1 changed files with 3 additions and 2 deletions
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lib/galaxy_ext/metadata/set_metadata.py
+3 -2
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@@ -141,10 +141,11 @@ def set_metadata():
json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) # setting metadata has failed somehow
for i, ( filename, file_dict ) in enumerate( new_job_metadata_dict.iteritems(), start=1 ):
new_dataset = galaxy.model.Dataset( id=-i, external_filename=os.path.join( tool_job_working_directory, file_dict[ 'filename' ] ) )
new_dataset_filename = os.path.join( tool_job_working_directory, "working", file_dict[ 'filename' ] )
new_dataset = galaxy.model.Dataset( id=-i, external_filename=new_dataset_filename )
extra_files = file_dict.get( 'extra_files', None )
if extra_files is not None:
new_dataset._extra_files_path = os.path.join( tool_job_working_directory, extra_files )
new_dataset._extra_files_path = os.path.join( tool_job_working_directory, "working", extra_files )
new_dataset.state = new_dataset.states.OK
new_dataset_instance = galaxy.model.HistoryDatasetAssociation( id=-i, dataset=new_dataset, extension=file_dict.get( 'ext', 'data' ) )
set_meta_with_tool_provided( new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry )