Metacat

Fixed bug in DBWriter using the new SAX2 interface. Turned out it was a bug in xerces-1_1_1, which was fixed by Andy Clark after I reported it.

1) Simplified database connection creation by adding new utility routine in MetaCatUtil that reads configuration information from the properties file.
2) Created MetaCatUtil.getOption() to retrieve options from properties file.
3) Unified SAX Parser creation by specifying parser driver in the properties file and dynamically loading it using the XMLReaderFactory interface....

cleaned up code for getting options from the properties file, made the database connection inthe MetaCatUtil class use the properties file for the conneciton info

updated javadoc documentation

integrated new structured query facility (DBQuery) into the servlet demo (MetaCatServlet)

removed debugging code

fixed QuerySpecification to produce SQL that does UNION or INTERSECT set operations for query group combinations

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

completed work on creating structured query prototype in DBQuery and QuerySpecification classes

added missed conn.close()

continued work on structured query. Now QuerySpecification generates SQL for a given xml input, and DBQuery uses that SQL to send the query to the db

fixed string broken over two lines

documentation cleanup

minor modifications to fix problems introduced with AccessionNumber module

minor modifications to fix problems introduced with AccessionNumber module

docid is String

docid is String
docid is generated from AccessionNumber.generate() call

gen acc # in new connection
changing to static methods
include action parameter

continued work on structured query -- now it reads the queryspec xml docuemnt and can digest its contents

continued work on developing structured query functionality using the QuerySpecification class -- incomplete still

minor changes to TextNode

added incomplete classes for structured query

added result-set filter to DBSimpleQuery to only return specified document type

changed getDocID() only to:
return docid;

put checkURLConnection(systemId) before
its register in db or using from the parser

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

to use single transaction

no message

new class for registering of Accession numbers into metacat db

renamed DBSAXWriter to DBWriter

reincorporated Title registration code for documents

updated documentation

Renamed DBSAXElement to DBSAXNode

rearranged API for incrementing the node index within the parent node

rearranged API for incrementing the node index within the parent node

code consolidation, cleanup, and documentation

code consolidation, cleanup, and documentation

improved error handling when docid not found

general module cleanup

renamed ReaderElement to ElementNode

renamed BasicElement to BasicNode

continuing work on changing to DOM Text node model

continued changing to DOM TEXT node model

continued changing to DOM TEXT node model

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

minor formatting and display update

updated servlet UI and added new intgrated document validity feature to servlet. Working on transformation feature.

debugging form submission

fixing transform bugs

fixed transformation bug, added test method

improved query result handling

fixed entity parsing bug

fixed transformation problems

made changes about document doctypes

Update to handle retreival of datafile from server

updated handler to deal better with Public IDs

xsl stylesheet fix for resultset format

created XSL transformation module based on the internal database catalog

added XSL formatting to document display for metacat servlet

creating automatic transformation for XML docs retreived from catalog

changed location of catalog file to config parameter

created options file for MetaCatServlet

added catalog loading code

fixed DBSimpleQuery after doctype additions done by Jivka

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

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.

XMLValidate added to same package as MetaCatServlet

GenericXMLValidate added to same package as MetaCatServlet

MetaCatServlet Modifications for XML Validation;

added GenericXMLValidate

updated javadoc documentation for changes

further work on XML docuemnt loading facility in the MetaCatServlet

added xml doc loading to servlet actions

documentation changes

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

changed database connection code, added utility class MetaCatUtil.java

added document display function to servlet

continued work on interface to servlet

improvements to MetaCatServlet engine, added html access pages for catalog query

started servlet to do XML query and return result set

documentation updates

documentation additions

general cleanup and documentation

general cleanup and documentation

Finished modifications to DBSimpleQuery.java to allow simple, free text searching on element and attribute content

added DBSimpleQuery.java to illustrate a simple query strategy over the XML set in the database

completed basic DBReader functionality. Can now read XML from DB using DBReader

adding recursive build for ReaderElement

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.

Split XML SAX handler class into seperate file DBSAXHandler.java