Metacat

In MN.getCapabilities(), the required contact subject was not being added to the node instance from the dataone properties. Add it in.

generate ORE maps only once -- and persist the flag to the main backup properties so that subsequent Metacat upgrades remember this value.

use RC-1 Dataone jars

Added DOI generation to the 2.0.0 upgrade process. To succeed, this script must be run on a fresh 2.0.0 database, or on a 1.9.5 version database, as those are the only ways to get the needed foreign keys to be marked as deferrable. The identifier conversion must be turned on by setting correct properties in metacat.properties. See the comments in GenerateGlobalIdentifiers for details. By default, conversion is set to false in the properties file. If you want to convert an instance to use DOIs, be sure to set metacat.properties up BEFORE running through the Metacat configuration and database upgrade.

Refactoring classes that throw generic Exception class to throw their more specific subclasses so that new exceptions are not hidden behind generic messages. Makes debugging easier.

try to read the local document before making the localid->guid mapping (in cases where we fail to read the data locally like if it is referenced in an EML file but does not exist on this Metacat instance)

Ensure we have the object and sysmeta params for MN.create(). We were getting a fatal SAX parsing error encapsulated in a ServiceFailure when a science metadata object param was null. Cut it off at the pass after parsing the MMP entity.

Use the Collections class from java.util.

Remove null field tests in the IdentifierManager class. Schema-level required fields are checked on serialization/deserialization using JibX during the REST resource handler classes. Other required fields are checked in MNodeService and CNodeService, higher in the stack.

For MNs that haven't set the archived flag to false on create(), set it here. Also, ensure that the CN sync code sets the authoritative and origin member node fields.