A B C D E F G I M N O P Q R S T U V W

A

AccessionNumber - class edu.ucsb.nceas.metacat.AccessionNumber.

A class that generates an Accession Number and will check a submitted accession number for uniqueness and register it into the db connection

AccessionNumber() - Constructor for class edu.ucsb.nceas.metacat.AccessionNumber

AccessionNumberException - exception edu.ucsb.nceas.metacat.AccessionNumberException.

Exception thrown when an error occurs because an AccessionNumber was invalid or used incorrectly.

AccessionNumberException(String) - Constructor for class edu.ucsb.nceas.metacat.AccessionNumberException

Create a new AccessionNumberException.

AccessionNumberGeneratedException - exception edu.ucsb.nceas.metacat.AccessionNumberGeneratedException.

Exception thrown when a new accession number is generated either because none was provided or it was not unique.

AccessionNumberGeneratedException(String) - Constructor for class edu.ucsb.nceas.metacat.AccessionNumberGeneratedException

Create a new AccessionNumberGeneratedException.

addChildNode(BasicNode) - Method in class edu.ucsb.nceas.metacat.BasicNode

Add a child node to this node

atFirstElement() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

get the document processing state

attributeDecl(String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of attribute declarations

B

BasicNode - class edu.ucsb.nceas.metacat.BasicNode.

A Class that represents an XML node and its contents

BasicNode() - Constructor for class edu.ucsb.nceas.metacat.BasicNode

Construct a Basic Node

BasicNode(long, String, long, int) - Constructor for class edu.ucsb.nceas.metacat.BasicNode

Construct a Basic Node

BasicNode(String) - Constructor for class edu.ucsb.nceas.metacat.BasicNode

Construct a Basic Node

BasicNode(String, long, int) - Constructor for class edu.ucsb.nceas.metacat.BasicNode

Construct a Basic Node

C

characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that is called for each XML text node

characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.QuerySpecification

callback method used by the SAX Parser when the text sequences of an xml stream are detected.

comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of comments in the DTD

createQuery(String) - Static method in class edu.ucsb.nceas.metacat.DBQuery

format a simple free-text value query as an XML document that conforms to the pathquery.dtd and is appropriate for submission to the DBQuery structured query engine

createQuery(String, String) - Static method in class edu.ucsb.nceas.metacat.DBQuery

format a simple free-text value query as an XML document that conforms to the pathquery.dtd and is appropriate for submission to the DBQuery structured query engine

D

DBDTDHandler - class edu.ucsb.nceas.metacat.DBDTDHandler.

A database aware Class implementing DTDHandler interface for the SAX parser to call when processing the XML stream and intercepting notations and unparsed entities

DBDTDHandler(Connection) - Constructor for class edu.ucsb.nceas.metacat.DBDTDHandler

Construct an instance of the DBDTDHandler clas

DBEntityResolver - class edu.ucsb.nceas.metacat.DBEntityResolver.

A database aware Class implementing EntityResolver interface for the SAX parser to call when processing the XML stream and intercepting any external entities (including the external DTD subset and external parameter entities, if any) before including them.

DBEntityResolver(Connection, DBSAXHandler) - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver

Construct an instance of the DBEntityResolver clas

DBQuery - class edu.ucsb.nceas.metacat.DBQuery.

A Class that searches a relational DB for elements and attributes that have free text matches a query string, or structured query matches to a path specified node in the XML hierarchy.

DBQuery(Connection, String) - Constructor for class edu.ucsb.nceas.metacat.DBQuery

construct an instance of the DBQuery class

DBReader - class edu.ucsb.nceas.metacat.DBReader.

A Class that creates an XML text document from a query to a relational DB containing a DOM representation

DBReader.DoctypeInfo - class edu.ucsb.nceas.metacat.DBReader.DoctypeInfo.

A utility class that encapsulates document type information

DBReader.DoctypeInfo(DBReader, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.DBReader.DoctypeInfo

Constructor

DBReader(Connection) - Constructor for class edu.ucsb.nceas.metacat.DBReader

construct a DBReader instance.

DBSAXDocument - class edu.ucsb.nceas.metacat.DBSAXDocument.

A Class that writes an XML document main data to a database connection

DBSAXDocument(Connection) - Constructor for class edu.ucsb.nceas.metacat.DBSAXDocument

Construct a new document instance, used for deleting documents

DBSAXDocument(Connection, long, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXDocument

Construct a new document instance

DBSAXHandler - class edu.ucsb.nceas.metacat.DBSAXHandler.

A database aware Class implementing callback bethods for the SAX parser to call when processing the XML stream and generating events

DBSAXHandler(Connection) - Constructor for class edu.ucsb.nceas.metacat.DBSAXHandler

Construct an instance of the handler class

DBSAXHandler(Connection, String, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXHandler

Construct an instance of the handler class

DBSAXNode - class edu.ucsb.nceas.metacat.DBSAXNode.

A Class that represents an XML node and its contents and can write its own representation to a database connection

DBSAXNode(Connection, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode

Construct a new node instance for DOCUMENT nodes

DBSAXNode(Connection, String, DBSAXNode, DBSAXNode, DBSAXDocument) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode

Construct a new node instance for ELEMENT nodes

DBSimpleQuery - class edu.ucsb.nceas.metacat.DBSimpleQuery.

A Class that searches a relational DB for elements and attributes that have free text matches to the query string.

DBSimpleQuery(Connection) - Constructor for class edu.ucsb.nceas.metacat.DBSimpleQuery

construct an instance of the DBSimpleQuery class

DBTransform - class edu.ucsb.nceas.metacat.DBTransform.

A Class that transforms XML documents utitlizing XSL style sheets

DBTransform(Connection) - Constructor for class edu.ucsb.nceas.metacat.DBTransform

construct a DBTransform instance.

DBValidate - class edu.ucsb.nceas.metacat.DBValidate.

Name: DBValidate.java Purpose: A Class that validates XML documents This class is designed to be parser independent i.e.

DBValidate(String) - Constructor for class edu.ucsb.nceas.metacat.DBValidate

Construct a new validation object

DBValidate(String, String) - Constructor for class edu.ucsb.nceas.metacat.DBValidate

Construct a new validation object

DBWriter - class edu.ucsb.nceas.metacat.DBWriter.

A Class that reads in an XML text document and write its contents to a database connection using SAX

DBWriter(Connection, String) - Constructor for class edu.ucsb.nceas.metacat.DBWriter

construct a new instance of the class to write an XML file to the database

debugMessage(int) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil

Utility method to print debugging messages

debugMessage(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil

Utility method to print debugging messages

delete(String) - Method in class edu.ucsb.nceas.metacat.DBWriter

Delete an XML file from the database (actually, just make it a revision in the xml_revisions table)

doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet

Handle "GET" method requests from HTTP clients

doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet

Handle "POST" method requests from HTTP clients

E

edu.ucsb.nceas.metacat - package edu.ucsb.nceas.metacat

elementDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of element declarations

ElementNode - class edu.ucsb.nceas.metacat.ElementNode.

A Class that represents an XML element and its contents, and can build itself from a database connection

ElementNode(Connection) - Constructor for class edu.ucsb.nceas.metacat.ElementNode

Construct a new ElementNode instance

ElementNode(Connection, long) - Constructor for class edu.ucsb.nceas.metacat.ElementNode

Construct a new ElementNode instance

ElementNode(Connection, long, long, String, String) - Constructor for class edu.ucsb.nceas.metacat.ElementNode

Construct a new ElementNode instance

endCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of the end of CDATA sections

endDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of end of the document

endDTD() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of end of DTD

endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that is called at the end of each XML element

endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification

callback method used by the SAX Parser when the end tag of an element is detected.

endEntity(String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of the end of entities

error(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of recoverable parsing errors

externalEntityDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of external entity declarations

F

fatalError(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of fatal parsing errors

fileToURL(File) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil

Utility method to convert a file handle into a URL

findDocuments(Reader) - Method in class edu.ucsb.nceas.metacat.DBQuery

routine to search the elements and attributes looking to match query

findDocuments(String) - Method in class edu.ucsb.nceas.metacat.DBSimpleQuery

routine to search the elements and attributes looking to match query

findDocuments(String, String) - Method in class edu.ucsb.nceas.metacat.DBSimpleQuery

routine to search the elements and attributes looking to match query

G

generate(String, String) - Static method in class edu.ucsb.nceas.metacat.AccessionNumber

Get an accession number from the user, check it for uniqueness and register it into new db connection.

getAttribute(String) - Method in class edu.ucsb.nceas.metacat.BasicNode

Get an attribute value by name

getAttributes() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the attributes as a string

getChildren() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the an enumeration of the children of this node

getDocID() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the doc id of this node

getDocID() - Method in class edu.ucsb.nceas.metacat.DBSAXDocument

Get doc id

getDocname() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

get the document name

getDocname() - Method in class edu.ucsb.nceas.metacat.DBReader.DoctypeInfo

get the document name

getDoctype() - Method in class edu.ucsb.nceas.metacat.DBReader.DoctypeInfo

get the document type

getDoctype() - Method in class edu.ucsb.nceas.metacat.DBSAXDocument

Get doctype

getDoctypeInfo(String) - Method in class edu.ucsb.nceas.metacat.DBReader

Look up the document type information from the database

getNodeData() - Method in class edu.ucsb.nceas.metacat.TextNode

Get the node data as a string value

getNodeID() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the id of this node

getNodeIndex() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get nodeIndex of the node

getNodeType() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the type of this node

getOption(String) - Method in class edu.ucsb.nceas.metacat.MetaCatUtil

Utility method to get an option value from the properties file

getParentID() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the parent id of this node

getParentNode() - Method in class edu.ucsb.nceas.metacat.DBSAXNode

get the parent of this node

getRootNode(String) - Method in class edu.ucsb.nceas.metacat.DBReader

Get the root node id for an XML document given a document id

getRootNodeID() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the root node id of this node

getSystemID() - Method in class edu.ucsb.nceas.metacat.DBReader.DoctypeInfo

get the system identifier

getSystemId(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBTransform

Lookup a stylesheet reference from the db catalog

getTagName() - Method in class edu.ucsb.nceas.metacat.BasicNode

Get the name of this node

getTitle() - Method in class edu.ucsb.nceas.metacat.DBSAXDocument

Get the document title

I

ignorableWhitespace(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that is called for each XML text node that is Ignorable white space

incChildNum() - Method in class edu.ucsb.nceas.metacat.BasicNode

increase childNum when new child for the node is created

init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet

Initialize the servlet by creating appropriate database connections

internalEntityDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of internal entity declarations

M

main(String[]) - Static method in class edu.ucsb.nceas.metacat.DBTransform

the main routine used to test the transform utility.

main(String[]) - Static method in class edu.ucsb.nceas.metacat.DBQuery

the main routine used to test the DBQuery utility.

main(String[]) - Static method in class edu.ucsb.nceas.metacat.DBValidate

main method for testing

main(String[]) - Static method in class edu.ucsb.nceas.metacat.DBWriter

the main routine used to test the DBWriter utility.

main(String[]) - Static method in class edu.ucsb.nceas.metacat.DBReader

main routine used for testing.

main(String[]) - Static method in class edu.ucsb.nceas.metacat.DBSimpleQuery

the main routine used to test the DBSimpleQuery utility.

main(String[]) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification

Main routine for testing

MetaCatServlet - class edu.ucsb.nceas.metacat.MetaCatServlet.

A metadata catalog server implemented as a Java Servlet

MetaCatServlet() - Constructor for class edu.ucsb.nceas.metacat.MetaCatServlet

MetaCatUtil - class edu.ucsb.nceas.metacat.MetaCatUtil.

A suite of utility classes for the metadata catalog server

MetaCatUtil() - Constructor for class edu.ucsb.nceas.metacat.MetaCatUtil

Construct an instance of the utility class

N

notationDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler

Notation declarations are not signaled

O

openDBConnection() - Method in class edu.ucsb.nceas.metacat.MetaCatUtil

Utility method to establish a JDBC database connection using connection info from the properties file

openDBConnection(String, String, String, String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil

Utility method to establish a JDBC database connection

P

printSQL() - Method in class edu.ucsb.nceas.metacat.QuerySpecification

create a SQL serialization of the query that this instance represents

processingInstruction(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler called once for each processing instruction found: node that PI may occur before or after the root element.

Q

QuerySpecification - class edu.ucsb.nceas.metacat.QuerySpecification.

A Class that represents a structured query, and can be constructed from an XML serialization conforming to @see pathquery.dtd.

QuerySpecification(Reader, String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification

construct an instance of the QuerySpecification class

QuerySpecification(String, String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification

construct an instance of the QuerySpecification class

R

readXMLDocument(String) - Method in class edu.ucsb.nceas.metacat.DBReader

Create an XML document from the database starting with the element having element_id nodeid

resolveEntity(String, String) - Method in class edu.ucsb.nceas.metacat.DBEntityResolver

The Parser call this method before opening any external entity except the top-level document entity (including the external DTD subset, external entities referenced within the DTD, and external entities referenced within the document element)

returnErrors() - Method in class edu.ucsb.nceas.metacat.DBValidate

provide a list of errors fromthe validation process

S

saveDocument(String) - Method in class edu.ucsb.nceas.metacat.DBSAXDocument

Save a document entry in the xml_revisions table

setAttribute(String, String) - Method in class edu.ucsb.nceas.metacat.BasicNode

Add a new attribute to this node, or set its value

setAttribute(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode

Add a new attribute to this node, or set its value

setDocID(String) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the doc id of this node

setNodeData(String) - Method in class edu.ucsb.nceas.metacat.TextNode

Set the node data to the given string

setNodeID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the id of this node

setNodeIndex(int) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the node index of this node

setNodeType(String) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the type of this node

setParentID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the parent id of this node

setRootNodeID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the root node id of this node

setTagName(String) - Method in class edu.ucsb.nceas.metacat.BasicNode

Set the name of this node

setTitle(String) - Method in class edu.ucsb.nceas.metacat.DBSAXDocument

Set the document title

setTitleFromChildElement() - Method in class edu.ucsb.nceas.metacat.DBSAXDocument

Look up the title of the first child element named "title" and record it as the document title

startCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of the start of CDATA sections

startDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of beginning of the document

startDTD(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of DOCTYPE.

startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that is called at the start of each XML element

startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.QuerySpecification

callback method used by the SAX Parser when the start tag of an element is detected.

startEntity(String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of the start of entities

T

TextNode - class edu.ucsb.nceas.metacat.TextNode.

A Class that represents an XML Text node and its contents,

TextNode(long, long, String, String) - Constructor for class edu.ucsb.nceas.metacat.TextNode

Construct a new TextNode instance

toString() - Method in class edu.ucsb.nceas.metacat.TextNode

String representation of this text node

toString() - Method in class edu.ucsb.nceas.metacat.ElementNode

String representation for display purposes (recursively descends through children to create an XML subtree)

toString() - Method in class edu.ucsb.nceas.metacat.QuerySpecification

create a String description of the query that this instance represents.

transformXMLDocument(String, String, String, PrintWriter) - Method in class edu.ucsb.nceas.metacat.DBTransform

Transform an XML document using the stylesheet reference from the db

U

unparsedEntityDecl(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler

All are reported after startDocument and before first startElement event

V

validate(String) - Method in class edu.ucsb.nceas.metacat.DBValidate

validate an xml document against its DTD

validateString(String) - Method in class edu.ucsb.nceas.metacat.DBValidate

validate an xml document against its DTD

W

warning(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

SAX Handler that receives notification of warnings

write(Reader, String, String) - Method in class edu.ucsb.nceas.metacat.DBWriter

Insert XML stream to the database

write(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBWriter

Insert an XML file to the database

writeChildNodeToDB(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode

creates SQL code and inserts new node into DB connection

writeDocID(String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode

creates SQL code to put doc ID for the document node and for comment/PI nodes under document node into DB connection

writeNodename(String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode

creates SQL code to put nodename for the document node into DB connection

writeRootNodeID(long) - Method in class edu.ucsb.nceas.metacat.DBSAXNode

creates SQL code to put root node id for the document node into DB connection

A B C D E F G I M N O P Q R S T U V W