Metacat

Pass the doc xml as a string to docImpl.write and writeRepication. This is so a reader can be create for the parsing and for the write to disk. Also created a db access class for xml query result deletion.

Add comments

make constants final

Fix the bug of http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4645. handleGetRevisionAndDocTypeAction will search both xml_documents and xml_revisions table.
It also changed some constrain in AccessionNumber when user update a document, of which all previous versions are in xml_revisions table.

Add a sleep statement between getting the dtd from source and checking for it via url. Add method names to log output.

Log doc and rev query counts and times. Fix mis-spellings.

Log doc and rev query counts and times. Fix mis-spellings.

remove call to print busy db connections

Add debug to show sql

Fix for Bug #4637 - Metacat Harvester fails to catch some insert and update failures. As per comments in the bug entry, the Metacat Harvester logic has been modified to examine the Metacat client return string to confirm that it contains the substring "<success>" following an insert or update operation. It no longer considers just the absence of an exception as indicative of a successful operation.