Add the ability for metadata to be set in an external process, this requires set_metadata_externally = True in universe_wsgi.ini.

Currently this is supported in the local runner (long running set_meta() can now be canceled the same as with jobs) and in the non-staging PBS runner.

There is a slight change to how new Metadata FileParameters are to be created in datatype.set_meta(), see the MAF datatype.

TODO:
Prevent editing of metadata on a running job when metadata is to be set externally.
Have datasets which were copied before job completion use the metadata from the original output dataset; currently .set_meta() is called locally on these.

scripts/set_metadata.py

@@ -0,0 +1,38 @@
+"""
+Execute an external process to set_meta() on a provided list of pickled datasets.
+
+This should not be called directly!  Use the set_metadata.sh script in Galaxy's
+top level directly.
+
+"""
+
+import os, sys, cPickle
+assert sys.version_info[:2] >= ( 2, 4 )
+
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+sys.path = new_path
+
+from galaxy import eggs
+import pkg_resources
+import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
+galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
+galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid
+
+def __main__():
+    file_path = sys.argv.pop( 1 )
+    tmp_dir = sys.argv.pop( 1 )
+    galaxy.model.Dataset.file_path = file_path
+    galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir
+    for pickled_filenames in sys.argv[1:]:
+        pickled_filename_in, pickled_filename_kwds, pickled_filename_out, pickled_filename_results_code = pickled_filenames.split( ',' )
+        try:
+            data = cPickle.load( open( pickled_filename_in ) )#unpickle DatasetInstance
+            kwds = cPickle.load( open( pickled_filename_kwds ) )#unpickle kwds
+            data.datatype.set_meta( data, **kwds )
+            data.metadata.to_pickled_dict( pickled_filename_out ) # write out results of set_meta
+            cPickle.dump( ( True, 'Metadata has been set successfully' ), open( pickled_filename_results_code, 'wb+' ) ) #setting metadata has suceeded
+        except Exception, e:
+            cPickle.dump( ( False, e ), open( pickled_filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
+
+__main__()