Metacat

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)

add note to enable ssl mod

-include instructions about enabling AJP connector in Tomcat config
-use postgres 8.4
-include hint to disable default Apache site (otherwise the knb config never gets used!)

include instructions for installing Sun's Java6 JDK since it is no longer in apt-get repos

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.

An example python script that uses the python client to loop through a list of
files, read them from disk, and insert them into metacat.

make it clear that the Apache config files are samples and may need to be modified for different servers
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5516

update system requirements to be more reasonable