Metacat

The incoming source node param is just a string, not XML, so don't attempt to deserialize it. Rather, just make a new NodeReference object and set it's value to the value of the incoming param.

add User-Agent logging to support D1 requirements

remove old RestServlet handler -- not used now

Add debugging output to MNodeService.

use default fmtid if we can't find the user-supplied data mime type in our list

including newer d1 libclient that uses Foresite (and Jena) to construct/parse ORE resource maps for DataONE

delete the xml access rules by either docid or guid to make sure we have the most up to date information

Fix a data-typing issue when pulling replicationAllowed from postgres. Use getBoolean(), not getString().

cleaned up to use for populating a DataONE MN using the D1 api. Retrieves packages from a Metacat and generates system metadata for them before calling MN.create() for both data and metadata.
NOTE: you need a client certificate that the target server accepts (either DataONE-generated for testing or a CILogon one for more official use). I was only able to get the former certificate type to work with our existing MN servers

IdentifierManager.getSystemMetadata() was missing the number_replicas and replication_allowed fields when building a ReplicationPolicy section of a SystemMetadata document being returned. Add in these two attributes.