Metacat

upgrade to Metacat 2.1.0 on the trunk. This includes a new index_event table for storing indexing events that need to be reprocessed. https://projects.ecoinformatics.org/ecoinfo/issues/5944

additional db indexes for pathquery performance
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5696

shorten the systemmetadata* table names for Oracle's 30 character limit. move version to 2.0.5. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5717

increase amount of text the 'xml_path_index.path' column can accommodate. I was seeing errors like this during indexing:
knb 20120312-11:42:05: [ERROR]: DocumentImpl.buildIndex - SQL Exception while indexing document knb-lter-and.3147 : ERROR: value too long for type character varying(1000) [edu.ucsb.nceas.metacat.DocumentImpl]

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.

use larger ("text") db field for guid in the xml_access.accessfileid column

remove flag for independent system metadata replication -- these entries are replicated along with the data/metadata objects or via hazelcast when the actual object is not on the server.

include 'archived' system metadata element in backing DB store

refactor Metacat access handling to be on a per-revision basis so that it more closely aligns with the DataONE approach
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5560

move the DataONE 1.0.0-SNAPSHOT

add User-Agent logging to support D1 requirements

remove ORE mapping from system metadata

include obsoletes and obsoletedBy for system metadata
repurpose the "provenance" table as the ORE mapping table for system metadata

use objectFormatIdentifier for listObjects()
remove provisional system metadata indicator - Metacat will not implement reserveIdentifier()

allow for provisional SystemMetadata records (provisional=true)

add missing comma in xml_replication insert

merge changes from 1.9.5 branch for upgrade process (1.9.3->1.9.4->1.9.5)

add option for replicating system metadata (dataone)
https://redmine.dataone.org/issues/1626
also make sure the latest table changes are included in upgrade scripts

include GUID column for xml_access and related methods for storing/retrieving access rules

persist system metadata replication policy and status using db tables

remove docid and rev from systemMetadata table

add systemMetadataProvenance table for tracking those relationships

add support for temporal element query in pathquery
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=2084

fixed bugs in listObjects

adding fields for additional system metadata info

adding a system to track system metadata documents for dataone

Modified table structure to change identifiers table (previously unused) to
represent a mapping between arbitrary string identifiers and metacat docids.
More information in https://trac.dataone.org/ticket/361. Modifications to
Oracle schemas were made but not tested.

add xml_revisions docid index

Change MetaCatVersion to MetacatVersion

Add upgrade scripts for 1.9.2 (scheduler tables)

Merge 1.9 changes into Head

Add two indexes to improve deleting and update speed.

Create index to speed deleting.

Change the path data type to text

Add new index into xml_index table.

Change data type of columns to TEXT

Modifications to the table definitions to add indices that should be used
when searching the database. Added an upgrade script to create these
indices as well. Modified QueryTerm.java to use the '=' comparator rather
than 'LIKE' so that we can do index scans rather than table scans. This needs...

fixed a bug with postgres 8.1.6 where the sequence must be created before the table is created.

New SQL tables and db upgrade scripts that define a new table stucture for identifiers and delete the previously unused accession_number table. This is in anticipation of supporting LSID identifiers. Currently these tables are unused by the servlet but are in place for discussion.

Refactored the build to use a <path> element for the classpath rather
than ant properties. This makes the classpath easier to manage, but required
changes throughout the build. I think everything should still build fine --
it works for me.

Upgraded the JDBC driver for postgres to the version 8 driver....

Added code to create new tables xml_path_index and xml_nodes_revisions...

Fixed bug in previous commit

Modified postgres script so that:
1. Foreign key for rootnodeid in xml_revision points to xml_node_revision table instead of xml_nodes
2. Added a new table xml_path_index which is used to index the paths specified by user in metacat.properties
3. Addes a new table xml_nodes_revision which stores the nodes of old revisions and deleted documents...

Removing code added for creating nodedata column in xml_index table

Made changes in the sql scripts to create new tables xml_returnfield and xml_queryresult

Modified xmltables to add nodedata as part of the xml_index tables.

Modified database creation sql code so that in xml_nodes, nodedatanumerical coulmn is added.

New schema changes, including upgrade scripts. Includes renamed postgres
scripts.