Metacat

Replacing MetaCatUtil.debugMessage or MetaCatUtil.logMetacat call with logMetacat (private Logger object) call

Added code to check for NaN valuse which converting string to double.

Modified 'insert xml_nodes...' so that numerical data is added into numericalnodedata also.

Add a new constructor to hanlde DTD node.

Change the prototype for debugMessage()

Every call to write into xml_nodes will return current node id.

Merge DBConnection branch to head.

hopefully fixed the connection closed error.

fixed error I introduced when I got postgres working

made a ton of changes related to keeping oracle SQL code out of the main classes. fixed a bug where the timing of the index thread was off so when it went to index a document, the document was not already in xml_documents thus breaking the FK relation between xml_documents and xml_index. I think that bug might be the reason for the blank resultset screens in morpho. made the postgres implementation much more robust.

changes to store namespace prefixes separately from the local names of nodes (elements and attributes)
in xml_nodes.nodeprefix column

added support for Namespaces.
Metacat now can store and retrieve XML documents with Namespaces.
Namespace is stored as separate record in xml_nodes table with type "NAMESPACE"
where nodename is the prefix and nodedata is the uri of the namespace.

don't need to override the old meta_file_id tags with docid without rev
since Morpho inserts docids before sending the docs to Metacat

changed all mentions of DBAdapter to the new name AbstractDatabase

commented out the use of oracle.jdbc.driver
this was harcoded use for batching the sql calls at once in order to speed up the insert of XML Index

Changed the order of generating and getting Unique ID for
xml_nodes.nodeid and for uniqueid part of the accession#
because of SQl Server capabilities:
first let the db to generate unique id on insert (by db trigger and sequence or by IDENTITY key),
then get that unique id for further use by the application....

- changed to use the DBAdapter uniform interface for all apperance of "sysdate"
and uniqueid generation from sequence
MetaCatUtil:
- reads from metacat.properties the dbadapter class implemented the interface
and creates an instance of that class (in static public variable named dbAdapter) for use....

added precise location information (class.method) to each catch statement so that errors are more easily traced.

Added license terms to source code files, and cleaned up some javadoc
documentation in a few places.

Separate thread used for writing into xml_index table.
This cut the time of the response on insert almost in half.
The tread is started afterwards
(on end of document parsing and inserting into xml_nodes) from
DBSAXHandler and uses new(separate) db connection....

writeDocID() not needed any more
throw SAXException from everywhere

changes related to decrease the time of INSERT of document.
With these changes I inserted 200KB file for 3 minutes, 50KB for 50sec.
This is mainly simplifing the DBSAXNode class and
using batching feature of Oracle JDBC driver.

store generated Access# in meta_file_id tag if there are any

added parentnodeid to xml_index

Continued code redesign for the DocumentImpl class. Now the "delete" and
"write" methods are static, so a DocumentImpl objject need not be created
in order to initiate a INSERT, UPDATE, or DELETE action (it is created
implicitly by the DBSAXHandler). When doing a "READ" action, one still...

Folded the functionality from DBSAXDocument into the DocumentImpl class.
Now DocumentImpl handles both the reads and the writes to the database.
Eventually, it will implment the full DOM Document interface. Eliminated
the DBSAXDocument.java file as it is no longer relevant....

Added "release" keyword to all metacat source files so that the release
number will be evident in software distributions.

DBSAXNode constructor simplified

Fixed bugs associated with the new UPDATE and DELETE functions of
DBWriter. There were problematic interactions between some static
variables used in DBEntityResolver and the way in which the
Servlet objects are re-used across multiple client invocations....

Merged in substantial changes to DBWriter and associated classes and to
the MetaCatServlet in order to accomodate the new UPDATE and DELETE
functions. The command line tools and the parameters for the
servlet have changed substantially.

finsihed basic functionality for structured queries based on the DBQuery and QuerySpecification classes

added code to build an index of the paths through the DOM tree to each node in the tree as the node is being inserted

for safe nodeid generation

documentation cleanup

docid is String

rewrote DBSimpleQuery and associated classes to no longer use Oracle's hierarchichal query syntax -- now this should work with any JDBC compliant backend DB

assign rootnodeid, docid for every node in xml_nodes table by given document

Renamed DBSAXElement to DBSAXNode

rearranged API for incrementing the node index within the parent node

code consolidation, cleanup, and documentation

code consolidation, cleanup, and documentation

general module cleanup

renamed BasicElement to BasicNode

Modifying storage model to use DOM TEXT nodes -- update is incomplete and query code doesn not work for this checkin

changed case 4/ to be like case 3/ when no doctype specified

document root node, doctype changes

made changes about document doctypes

Fixed package bugs in new Entity and comment handling code, updated Makefile

Included new features about writing XML documents into db
This includes writing data into db XML Catalog, document data into xml_documents,
comments into xml_nodes, added nodeindex for the order of elements by given parent element.

changed package name to edu.ucsb.nceas.metacat.*

documentation updates

documentation additions

general cleanup and documentation

created code to read XML doc from db source and emit it as an XML stream

created code to read XML doc from db source and emit it as an XML stream

consolidated table structure to eliminate xml_attributes and xml_elements in favor of a single, unified xml_nodes table

added attribute persistence to DB code

Partially functional SAS DB loader.

Added code to write element to DB using SAX parser model

Creating database loading scripts that utilize the oracle SAX parser