Metacat

Update the D1Admin class to set the dataone.contactSubject property. I've added the property to the http request to be added to the JSP form, but for now am setting the property using the dataone.subject field value. Not sure if we want to expose the contact subject in the form yet or not.

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

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.

Use the Collections class from java.util.

-generate system meta for all docids, even those not originating on the server (replicas from the past)
-generate ORE docs and download remote data only for those documents that originated on this server being upgraded.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

refactor generate system meta loop to the factory class -- to be reused in sysmeta and ORE generation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

do NOT generate ORE maps or download data when we do the initial System Metadata generation -- this is deferred until D1 registration.

make more generic so that a custom list of IDs can be passed in.

insert OR update system metadata -- no need to do an update right after initial insert...