Metacat

Minor formatting for querySystemMetadata().

exapnd permissions on the exisiting access rule not on the permission being checked. (hierarchical permissions)

upgrade routine to purge empty replicated data files so that they can be re-replicated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5536

Make sure the local id isn't null when we try to get the object from the local instance.

Simplify the error handling, and throw the exception once the CN is updated with the new status.

Set the replica status to failed (not invalidated) when we get exceptions trying to read the object bytes. Not much of a difference, but only the CN, in theory, is supposed to be able to set the invalidated status.

Set the replication status to invalidated when we have a localId, but getting the object bytes fails for any reason.

Only call super.create() if there's no localId found on the MN (ie a replica is there from an out of band process).

Get the object inputstream from the local metacat instance using MetacatHandler.get() rather than MN.getReplica() so we don't throw an InvalidToken exception when passing in a null Session. The D1Client object is never used for this local call.

interpret permissions as hierarchical
https://redmine.dataone.org/issues/2150