Metacat

marked the properties that are only editable manually in metacat.properties
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

Add the dataone.contactSubject property to be used when getCapabilities() returns the MN node instance.

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

format xml/eml table -- added missing row delimiter
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

some minimal editing on replication configuration -- bulk of it had been done in the Word doc before rst conversion
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

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)