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

A

ACCESS - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
ACLID - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
ALL - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
ALLOW - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
ALLOWFIRST - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
ALLSTRING - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
ATTRIBUTESYMBOL - Static variable in class edu.ucsb.nceas.metacat.QuerySpecification
 
AbstractDatabase - class edu.ucsb.nceas.dbadapter.AbstractDatabase.
Java offers uniform database access through the use of JDBC.
AbstractDatabase() - Constructor for class edu.ucsb.nceas.dbadapter.AbstractDatabase
 
AccessControlForSingleFile - class edu.ucsb.nceas.metacat.AccessControlForSingleFile.
A Class that loads eml-access.xml file containing ACL for a metadata document into relational DB.
AccessControlForSingleFile(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.AccessControlForSingleFile
Construct an instance of the AccessControlForSingleFile class.
AccessControlInterface - interface edu.ucsb.nceas.metacat.AccessControlInterface.
This interface will handle the access control for different documents: the package-orented, single eml2 document and other single file
AccessControlList - class edu.ucsb.nceas.metacat.AccessControlList.
A Class that loads eml-access.xml file containing ACL for a metadata document into relational DB.
AccessControlList(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.AccessControlList
Construct an instance of the AccessControlList class.
AccessControlList(DBConnection, String, String, String[], int) - Constructor for class edu.ucsb.nceas.metacat.AccessControlList
Construct an instance of the AccessControlList class.
AccessRule - class edu.ucsb.nceas.metacat.AccessRule.
A Class that represents an XML access rule.
AccessRule() - Constructor for class edu.ucsb.nceas.metacat.AccessRule
 
AccessSection - class edu.ucsb.nceas.metacat.AccessSection.
A Class that represents an XML access rule.
AccessSection() - Constructor for class edu.ucsb.nceas.metacat.AccessSection
 
AccessionNumber - class edu.ucsb.nceas.metacat.AccessionNumber.
(on insert of XML document) Generates a unique Accession Number or if provided check it for uniqueness and register it into the db connection (on update or delete of XML document) Check for existance of provided Accession Number
AccessionNumber() - Constructor for class edu.ucsb.nceas.metacat.AccessionNumber
Construct an AccessionNumber
AccessionNumber(String, String) - Constructor for class edu.ucsb.nceas.metacat.AccessionNumber
NEW - WHEN CLIENT ALWAYS PROVIDE ACCESSION NUMBER INCLUDING REV IN IT Construct an 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.
AddMissedSubTreeSAXHandler - class edu.ucsb.nceas.metacat.AddMissedSubTreeSAXHandler.
A database aware Class implementing callback bethods for the SAX parser to call when processing the XML stream and generating events
AddMissedSubTreeSAXHandler(Hashtable) - Constructor for class edu.ucsb.nceas.metacat.AddMissedSubTreeSAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to upadate
AssociateAccessPolicy - class edu.ucsb.nceas.metacat.AssociateAccessPolicy.
This class is in order to fix a problem.
AssociateAccessPolicy(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.AssociateAccessPolicy
construct an instance of the DBQuery class
AuthInterface - interface edu.ucsb.nceas.metacat.AuthInterface.
An interface representing the methods that should be implemented by an authentication service.
AuthLdap - class edu.ucsb.nceas.metacat.AuthLdap.
An implementation of the AuthInterface interface that allows Metacat to use the LDAP protocol for directory services.
AuthLdap() - Constructor for class edu.ucsb.nceas.metacat.AuthLdap
Construct an AuthLdap
AuthSession - class edu.ucsb.nceas.metacat.AuthSession.
A Class that implements session tracking for MetaCatServlet users.
AuthSession() - Constructor for class edu.ucsb.nceas.metacat.AuthSession
Construct an AuthSession
accNumberUsed(String) - Static method in class edu.ucsb.nceas.metacat.AccessionNumber
check for existence of Accesssion Number xml_acc_numbers table
action - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
actionPerformed(ActionEvent) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestListEditor
Implements action listeners for menu items.
addAccessRule(AccessRule) - Method in class edu.ucsb.nceas.metacat.AccessSection
Add an access rule
addChild(QueryGroup) - Method in class edu.ucsb.nceas.metacat.QueryGroup
Add a child QueryGroup to this QueryGroup
addChild(QueryTerm) - Method in class edu.ucsb.nceas.metacat.QueryGroup
Add a child QueryTerm to this QueryGroup
addChildNode(BasicNode) - Method in class edu.ucsb.nceas.metacat.BasicNode
Add a child node to this node
addPrincipal(String) - Method in class edu.ucsb.nceas.metacat.AccessRule
Set the a principle
addToServerListIfItIsNot(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
To a given server name, to check if it is in the server list.
alreadyHandle - Variable in class edu.ucsb.nceas.metacat.DBValidate
 
associateAccess() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
Associate the access policy of dataset to the docid which the data set id mapped
atFirstElement - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
attributeDecl(String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of attribute declarations
authenticate(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Determine if a user/password are valid according to the authentication service.
authenticate(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Determine if a user/password are valid according to the authentication service.
authenticate(HttpServletRequest, String, String) - Method in class edu.ucsb.nceas.metacat.AuthSession
determine if the credentials for this session are valid by authenticating them using the authService configured for this session.

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(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
BasicNode(long, String, long, int) - Constructor for class edu.ucsb.nceas.metacat.BasicNode
Construct a Basic Node
buildIndex() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Build the index records for this document.

C

CHMOD - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
CHMODSTRING - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
CatalogMessageHandler - class edu.ucsb.nceas.metacat.CatalogMessageHandler.
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the replication handler
CatalogMessageHandler() - Constructor for class edu.ucsb.nceas.metacat.CatalogMessageHandler
 
CommentNode - class edu.ucsb.nceas.metacat.CommentNode.
A Class that represents an XML Comment node and its contents,
CommentNode(long, long, String) - Constructor for class edu.ucsb.nceas.metacat.CommentNode
Construct a new CommentNode instance
ContentTypeProvider - class edu.ucsb.nceas.metacat.ContentTypeProvider.
This class will figure out which content type it is for a given data file.
ContentTypeProvider(String) - Constructor for class edu.ucsb.nceas.metacat.ContentTypeProvider
Constructor of ContentTypeProvider
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.AccessControlList
Callback method used by the SAX Parser when the text sequences of an xml stream are detected.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
Take the data out of the docid and date_updated fields
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.DocInfoHandler
put the content and the name of the tag into the hashtable.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that is called for each XML text node
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
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.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.ReplMessageHandler
Take the data out of the docid and date_updated fields
checkURLConnection(String) - Static method in class edu.ucsb.nceas.metacat.DBEntityResolver
Check URL Connection for @systemId, and return an InputStream that can be used to read from the systemId URL.
clone() - Method in class edu.ucsb.nceas.metacat.AccessRule
Copy a AccessRule to another accessrule object
close() - Method in class edu.ucsb.nceas.metacat.DBConnection
Close a DBConnection object
closeConnection() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
 
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of comments in the DTD
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that receives notification of comments in the DTD
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that receives notification of comments in the DTD
commit() - Method in class edu.ucsb.nceas.metacat.DBConnection
Method to make a commit command
compare(Object, Object) - Method in class edu.ucsb.nceas.metacat.NodeComparator
compare two objects to determine proper sort order -- delegates to the compare(NodeRecord, NodeRecord) method.
compare(NodeRecord, NodeRecord) - Method in class edu.ucsb.nceas.metacat.NodeComparator
compare two NodeRecord objects to determine proper sort order.
compare(Object, Object) - Method in class edu.ucsb.nceas.metacat.SubTree
methods from Comparator interface
compareInlineDataFiles(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
compareInlineDataFiles(String, String) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
 
connect() - Method in class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection
Make a connection to the URL
connection - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
containsAttributeReturnField() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
A method to get if the query has an attribute return field
containsExtendedSQL() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Returns true if the parsed query contains and extended xml query (i.e.
contentEquals(NodeRecord) - Method in class edu.ucsb.nceas.metacat.NodeRecord
Method compare two records
copyInlineFile(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
copyPermOrderAndAccessRules(AccessSection) - Method in class edu.ucsb.nceas.metacat.AccessSection
Method to copy a accesssection object to a new one
createMetacatConnection(String) - Static method in class edu.ucsb.nceas.metacat.client.MetacatFactory
Create a new instance of a Metacat object of raccessing a server.
createObject(String) - Static method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
Instantiate a class using the name of the class at runtime
createObject(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Instantiate a class using the name of the class at runtime
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
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
createResultDocument(String, QuerySpecification, PrintWriter, String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DBQuery
 
createSQuery(Hashtable) - Static method in class edu.ucsb.nceas.metacat.DBQuery
format a structured query as an XML document that conforms to the pathquery.dtd and is appropriate for submission to the DBQuery structured query engine
createStatement() - Method in class edu.ucsb.nceas.metacat.DBConnection
Method to create a Statement
currentDocument - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

D

DATAACCESSLEVEL - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
DBConnection - class edu.ucsb.nceas.metacat.DBConnection.
A class represent a connection object, it includes connection itself, index, status, age, createtime, connection time, usageCount, warning message
DBConnection() - Constructor for class edu.ucsb.nceas.metacat.DBConnection
Default constructor of the DBConnection class
DBConnectionPool - class edu.ucsb.nceas.metacat.DBConnectionPool.
A class represent a DBConnection pool.
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(DBConnection) - 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(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver
Construct an instance of the DBEntityResolver class
DBEntityResolver(DBConnection, DefaultHandler, Reader) - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver
Construct an instance of the DBEntityResolver class
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(String) - Constructor for class edu.ucsb.nceas.metacat.DBQuery
construct an instance of the DBQuery class
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(DBConnection, String, String, String, String, String[], String, int) - Constructor for class edu.ucsb.nceas.metacat.DBSAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to upadate
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(DBConnection, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode
Construct a new node instance for DOCUMENT nodes
DBSAXNode(DBConnection, String, String, DBSAXNode, long, String, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode
Construct a new node instance for ELEMENT nodes
DBSAXNode(DBConnection, String, String, String, DBSAXNode, long, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode
Construct a new node instance for DTD nodes This Node will write docname, publicId and systemId into db.
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() - 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() - Constructor for class edu.ucsb.nceas.metacat.DBTransform
construct a DBTransform instance.
DBUtil - class edu.ucsb.nceas.metacat.DBUtil.
A suite of utility classes for quering DB
DBUtil() - Constructor for class edu.ucsb.nceas.metacat.DBUtil
Construct an instance of the utility class
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 using an OASIS catalog file
DBValidate(String, DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBValidate
Construct a new validation object using a database entity resolver
DECLARATIONHANDLERPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
DELETE - Static variable in class edu.ucsb.nceas.metacat.ForceReplicationHandler
 
DENY - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
DENYFIRST - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
DOCNAME - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
DTD - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
DocInfoHandler - class edu.ucsb.nceas.metacat.DocInfoHandler.
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the replication handler
DocInfoHandler() - Constructor for class edu.ucsb.nceas.metacat.DocInfoHandler
 
DocumentIdentifier - class edu.ucsb.nceas.metacat.DocumentIdentifier.
A class to parse document ids The docid is of the form siteCode.uniqueId.rev
DocumentIdentifier(String) - Constructor for class edu.ucsb.nceas.metacat.DocumentIdentifier
Constructor to build a docid object and parse an incoming string.
DocumentImpl - class edu.ucsb.nceas.metacat.DocumentImpl.
A class that represents an XML document.
DocumentImpl(String, boolean) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Constructor used to create a document and read the document information from the database.
DocumentImpl(String) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Constructor, creates document from database connection, used for reading the document
DocumentImpl(DBConnection, long, String, String, String, String, String, String, String, String, int) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Construct a new document instance, writing the contents to the database.
DocumentImplWrapper - class edu.ucsb.nceas.metacat.DocumentImplWrapper.
This class a wrapper class for documentimpl for insert or update.
DocumentImplWrapper(String, boolean) - Constructor for class edu.ucsb.nceas.metacat.DocumentImplWrapper
Constructor of DocumentImpleWrapper
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.MetaCatUtil
 
debugMessage(String, int) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Utility method to print debugging messages.
delete(String, String, String[], String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Delete an XML file from the database (actually, just make it a revision in the xml_revisions table)
delete(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Delete an XML document in the repository.
delete(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Delete an XML document in the repository.
delete(String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Delete an XML document in the repository.
delete(String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Delete an XML document in the repository.
deleteInlineFiles() - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
deleteInlineFiles() - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
 
deleteRelations(String) - Method in class edu.ucsb.nceas.metacat.RelationHandler
Deletes all of the relations with a docid of 'docid'.
dequoteText(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Normalizes text prior to insertion into the HARVEST_LOG or HARVEST_DETAIL_LOG tables.
destroy() - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Close all db connections from the pool
destroy() - Method in class edu.ucsb.nceas.metacat.MetacatReplication
 
destroy() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
Stops the Harvester thread when the servlet shuts down.
destroy() - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatReplication
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
Handles GET method requests.
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
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
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatReplication
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
Handles POST method requests.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.MetUpload
Handle POST requests made to the Harvester MetUpload servlet.
docId - Variable in class edu.ucsb.nceas.metacat.SubTree
 
docType - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
docid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
docid - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
docname - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
doctype - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
dueForHarvest() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Boolean to determine whether this site is currently due for its next harvest.

E

ECOGRID - Static variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
EML200 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML210 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2KEYWORD - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
 
EML2_0_0NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2_0_1NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2_1_0NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EXTERNALSCHEMALOCATIONPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
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(TreeSet, long) - Constructor for class edu.ucsb.nceas.metacat.ElementNode
Construct a new ElementNode instance, and recursively create its children
Eml200SAXHandler - class edu.ucsb.nceas.metacat.Eml200SAXHandler.
A database aware Class implementing callback bethods for the SAX parser to call when processing the XML stream and generating events Here is the rules for user which has write permission in top level access rules(he can update metadata but can't update access module) try to update a document: 1.
Eml200SAXHandler(DBConnection, String, String, String, String, String[], String, int) - Constructor for class edu.ucsb.nceas.metacat.Eml200SAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to upadate
Eml210SAXHandler - class edu.ucsb.nceas.metacat.Eml210SAXHandler.
A database aware Class implementing callback bethods for the SAX parser to call when processing the XML stream and generating events
Eml210SAXHandler(DBConnection, String, String, String, String, String[], String, int) - Constructor for class edu.ucsb.nceas.metacat.Eml210SAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to upadate
EventLog - class edu.ucsb.nceas.metacat.EventLog.
EventLog is used to intialize and store a log of events that occur in an application.
EventLogData - class edu.ucsb.nceas.metacat.EventLogData.
A data structure holding the information to be logged about an event.
EventLogData(String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.EventLogData
Construct an EventLogData object with event log information.
edu.ucsb.nceas.dbadapter - package edu.ucsb.nceas.dbadapter
 
edu.ucsb.nceas.metacat - package edu.ucsb.nceas.metacat
 
edu.ucsb.nceas.metacat.client - package edu.ucsb.nceas.metacat.client
 
edu.ucsb.nceas.metacat.harvesterClient - package edu.ucsb.nceas.metacat.harvesterClient
 
edu.ucsb.nceas.metacat.stringclient.application - package edu.ucsb.nceas.metacat.stringclient.application
 
edu.ucsb.nceas.metacat.stringclient.impl - package edu.ucsb.nceas.metacat.stringclient.impl
 
edu.ucsb.nceas.protocols.metacat - package edu.ucsb.nceas.protocols.metacat
 
elementDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of element declarations
endCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the end of CDATA sections
endDTD() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of end of DTD
endDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of end of the document
endDocument() - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that receives notification of end of the document
endDocument() - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that receives notification of end of the document
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.AccessControlList
Callback method used by the SAX Parser when the end tag of an element is detected.
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.AddMissedSubTreeSAXHandler
SAX Handler that is called at the end of each XML element
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
This method write the indivUpdate to updates when it finds the end of
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.Eml200SAXHandler
SAX Handler that is called at the end of each XML element
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
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.
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.ReplMessageHandler
This method write the indivUpdate to updates when it finds the end of
endEntity(String) - Method in class edu.ucsb.nceas.metacat.AccessControlList
SAX Handler that receives notification of the end of entities.
endEntity(String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the end of entities
endNodeId - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
endNodeId - Variable in class edu.ucsb.nceas.metacat.SubTree
 
equals(Object) - Method in class edu.ucsb.nceas.metacat.SubTree
method from Comparator interface
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

FORCEREPLICATEDELETE - Static variable in class edu.ucsb.nceas.metacat.MetacatReplication
 
FilteredSubTree - class edu.ucsb.nceas.metacat.FilteredSubTree.
A Class that represents an Filtered XML Subtree, it means a subtree which contains another subtree has different access behavor to it.
FilteredSubTree(String, String, long, long) - Constructor for class edu.ucsb.nceas.metacat.FilteredSubTree
Constructor of filteredsubtree
ForceReplicationHandler - class edu.ucsb.nceas.metacat.ForceReplicationHandler.
A class to asyncronously force the replication of each server that has an entry in the xml_replication table.
ForceReplicationHandler(String, String, boolean, String) - Constructor for class edu.ucsb.nceas.metacat.ForceReplicationHandler
Constructor of ForceReplicationHandler
ForceReplicationHandler(String, boolean, String) - Constructor for class edu.ucsb.nceas.metacat.ForceReplicationHandler
Use this constructor when the action is implied.
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
filler - Static variable in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
 
findDataSetDocIdForGivenDocument(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
To a given docid, found a dataset docid which conatains the the given doicd This will be done by searching xml_relation table If couldn't find, null will be return
findDocuments(HttpServletResponse, PrintWriter, Hashtable, String, String[], String) - Method in class edu.ucsb.nceas.metacat.DBQuery
Method put the search result set into out printerwriter
findDocuments(HttpServletResponse, PrintWriter, Hashtable, String, String[], String, boolean) - Method in class edu.ucsb.nceas.metacat.DBQuery
Method put the search result set into out printerwriter
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

geItsDataSetIdWithouAccessEntry() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
Get the docid which it's mapped dataset doesn't has access entry
generate(String, String) - Method in class edu.ucsb.nceas.metacat.AccessionNumber
Generate an Accession Number of form .. where is always 1.
generate(String, String, String) - Method in class edu.ucsb.nceas.metacat.AccessionNumber
Generate an Accession Number of form ..
getACL(String, String, String[]) - Method in class edu.ucsb.nceas.metacat.AccessControlList
Get Access Control List information for document from db connetion.
getAccessFileID(String) - Static method in class edu.ucsb.nceas.metacat.RelationHandler
Get the access file id for a package
getAccessQuery() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to append a access control query to SQL.
getAccessRules() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get all access rule
getAccessionNumberFromEcogridIdentifier(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Eocgorid identifier will look like: ecogrid://knb/tao.1.1 The AccessionNumber tao.1.1 will be returned.
getAge() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the db connetion age from the object
getAttribute(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Get an attribute value by name
getAttributeName(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
A method to get attribute name from path
getAttributes(String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get attributes describing a user or group
getAttributes(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get attributes describing a user or group
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get attributes describing a user or group
getAttributes() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the attributes as a string
getCatalogVect() - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
 
getCatalogXML() - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Returns the xml_catalog table encoded in xml
getCheckOutMethodName() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the the name of method checked out the connection from the object
getCheckOutSerialNumber() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the check out serial number
getCheckOutTime() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the when a db connetion was checked out
getChildren() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the an enumeration of the children of this node
getChildren() - Method in class edu.ucsb.nceas.metacat.QueryGroup
Retrieve an Enumeration of query terms for this QueryGroup
getCodeLevelValue(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Maps each code level to an integer value.
getConnection() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Returns a connection to the database.
getConnectionTime() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the how long db connetion used for the object
getConnections() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the connetion from the object
getContentType() - Method in class edu.ucsb.nceas.metacat.ContentTypeProvider
Method to get content type
getControlLevel() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get controllevel
getCreateDate() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the creation date
getCreateTime() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the db connetion created time from the object
getCurrentRevisionAndDocTypeForGivenDocument(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
Method to get current revision and doctype for a given docid The output will look like "rev;doctype"
getDBConnection(String) - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to get a DBConnection in connection pool 1) try to get a DBConnection from DBConnection pool 2) if 1) failed, then check the size of pool.
getDTDSystemID(String) - Static method in class edu.ucsb.nceas.metacat.DBEntityResolver
Look at db XML Catalog to get System ID (if any) for @doctype.
getDataFileLockGrant(String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Get a lock for a given document.
getDataFileLockGrant(String, int) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
The method will check if metacat can get data file lock grant If server code is 1, it get.
getDataReplication() - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Get datareplication xml or not option
getDataReplicationValue(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
To a given server name, try to get its data file replciation option If couldn't find the server in the server list, false will return
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
The function name that gets the current date and time from the database server
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracle's function name that gets the current date and time from the database server: "sysdate"
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
The PostgreSQL function name that gets the current date and time from the database server
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server's function name that gets the current date and time from the database server: "getdate()"
getDeletesVect() - Method in class edu.ucsb.nceas.metacat.ReplMessageHandler
 
getDescribedIdList() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get a described id list
getDetailLogID() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Gets the current value of the detailLogID for storage as a primary key in the DETAIL_LOG_ID field of the HARVEST_DETAIL_LOG table.
getDocHomeServer() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getDocID() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the doc id of this node
getDocID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Get the document identifier (docid)
getDocId() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get the docId
getDocId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get the docId
getDocIdFromAccessionNumber(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
This method will get docid from an AccessionNumber.
getDocIdFromString(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Utility method to get docid from a given string
getDocIdWithRevFromOnlineURL(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Get docid from online/url string
getDocIdWithoutRevFromInlineDataID(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Method to get docidwithrev from eml2 inline data id The eml inline data id would look like eml.200.2.3
getDocIdWithoutRevsion() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to get docidWithout revision
getDocInfo() - Method in class edu.ucsb.nceas.metacat.DocInfoHandler
 
getDocType() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to get docType
getDocid() - Method in class edu.ucsb.nceas.metacat.AccessionNumber
returns the docid encoded in this accession number
getDocid() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the document identifier.
getDocname() - Method in class edu.ucsb.nceas.metacat.AccessControlList
Get the document name.
getDocname() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
get the document name
getDocname() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the document name
getDoctype() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the document type (which is the PublicID)
getEndNodeId() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get end node id
getEndNodeId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get end node id
getEvent() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the event.
getException() - Method in class edu.ucsb.nceas.metacat.McdbException
Get the tunneled Exception
getExplanation(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Returns an explanation string based on the value of a harvestOperationCode string.
getFilterDocList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the filter doc types as defined in the <filterdoctype> tag in the pathquery dtd.
getFilteredSubTree() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get the filted subtree vector
getFreeDBConnectionNumber() - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to get the number of free DBConnection in DBConnection pool
getGroups(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get all groups from the authentication service
getGroups(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get the groups for a particular user from the authentication service
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all groups from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get the groups for a particular user from the authentication service
getHarvestLogID() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Gets the current value of the harvestLogID for storage as a primary key in the HARVEST_LOG_ID field of the HARVEST_LOG table.
getHarvestOperationCodeLevel(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Returns a code level string based on a harvestOperationCode string.
getHashParam(String) - Method in class edu.ucsb.nceas.metacat.MetacatURL
returns a single parameter from the hash by name
getHashParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns the parameters in a hashtable.
getHomeServerCodeForDocId(String) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Returns a home server location given a accnum
getHomeServerInfoForDocId(String) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Method to get a host server information for given docid
getHub() - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Get hub option
getHubValue(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
To a given server name, try to get its hub option If couldn't find the server in the server list, false will return
getIdentifier() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns
getIdentifier() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return the identifier of this Query
getInlineDataIdWithoutRev(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
This method will get inline data id without the revision number.
getInstance() - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Returns the single instance, creating one if it's the first time this method is called.
getInstance() - Static method in class edu.ucsb.nceas.metacat.EventLog
Return the single instance of the event log after initializing it if it wasn't previously initialized.
getIpAddress() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the internet protocol address.
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
The function name that is used to return non-NULL value
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracle's function name that is used to return non-NULL value
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
The PostgreSQL function name that is used to return non-NULL value
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server's function name that is used to return non-NULL value
getLastCheckedDate() - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Get last checked date
getLastCheckedDate(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
To a given server name, try to get its lastcheck date.
getLatestRevisionNumber(String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Get last revision number from database for a docid If couldn't find an entry, -1 will return The return value is integer because we want compare it to there new one
getLocalReplicationServerName() - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Method to get the name of local replication server
getMaxDocid(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
get the lastest Accession Number from a particular scope
getMessage() - Method in class edu.ucsb.nceas.metacat.AuthSession
Get the message associated with authenticating this session.
getMessage() - Method in class edu.ucsb.nceas.metacat.McdbException
Get the message from this exception.
getMetaData() - Method in class edu.ucsb.nceas.metacat.DBConnection
Method to get meta data
getNameSpaceAndLocationString() - Method in class edu.ucsb.nceas.metacat.SchemaLocationResolver
A method to get nameSpaceAndLocationString
getNamespace(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Get an uri of the namespace prefix
getNewestDocRevision(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
The method will return the lasted revision in metacat server for a given document id.
getNewestDocRevision(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
The method will return the lasted revision in metacat server for a given document id.
getNodeData() - Method in class edu.ucsb.nceas.metacat.CommentNode
Get the node data as a string value
getNodeData() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeData() - Method in class edu.ucsb.nceas.metacat.PINode
Get the node data as a string value
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
getNodeId() - Method in class edu.ucsb.nceas.metacat.NodeRecord
Get functions
getNodeIndex() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get nodeIndex of the node
getNodeIndex() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeName() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodePrefix() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeType() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the type of this node
getNodeType() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNotFoundDataSetId() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
Get the docid which didn't found a dataset id to map it
getOption(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Utility method to get an option value from the properties file
getOptionList(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
 
getOwnerList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the owner fields as defined in the <owner> tag in the pathquery dtd.
getParam(int) - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns a single parameter and value as a 1D string array.
getParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns the parameters as a 2D string array.
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
getParentNodeId() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getPathContent(File, String) - Static method in class edu.ucsb.nceas.metacat.DBTransform
gets the content of a tag in a given xml file with the given path
getPathExpression() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the path expression parameter
getPercentageSymbolCount() - Method in class edu.ucsb.nceas.metacat.QueryGroup
 
getPercentageSymbolCount() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the percentage count for one query term
getPermission() - Method in class edu.ucsb.nceas.metacat.AccessRule
Get permission
getPermissionOrder() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get permissionOrder
getPermissionType() - Method in class edu.ucsb.nceas.metacat.AccessRule
 
getPrincipal() - Method in class edu.ucsb.nceas.metacat.AccessRule
Get the principle vector
getPrincipal() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the principal.
getPrincipals(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get all groups and users from authentication service.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all groups and users from authentication scheme.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthSession
Get all groups and users from authentication scheme.
getProtocol() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns the type of the url.
getPublicaccess() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getQueryGroup() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
get the QueryGroup used to express query constraints
getQueryTitle() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return the title of this Query
getReferences() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get the references
getReplication() - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Get replication xml or not option
getReplicationValue(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
To a given server name, try to get its xml replciation option If couldn't find the server in the server list, false will return
getReport(String[], String[], String[], String[], Timestamp, Timestamp) - Method in class edu.ucsb.nceas.metacat.EventLog
Get a report of the log events that match a set of filters.
getReturnDocList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the return document types as defined in the <returndoctype> tag in the pathquery dtd.
getReturnFieldList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the extended return fields as defined in the <returnfield> tag in the pathquery dtd.
getRev() - Method in class edu.ucsb.nceas.metacat.AccessionNumber
returns the revision number encoded in this accession number
getRev() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the revision number encoded in this docid
getRev() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getRevision() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to get revsion
getRevisionFromAccessionNumber(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
This method will get revision from an AccessionNumber.
getRevisionStringFromString(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Utility method to get version string from a given string
getRootNodeID() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the root node id of this node
getRootNodeID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the root node identifier
getSchemaLocation() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Accessor method for the schemaLocation field.
getSearchMode() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the searchmode parameter
getSeparator() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the separator used in the accession number
getServerCodeForServerName(String) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Returns a server code given a server name
getServerName() - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Get server name
getServerNameForServerCode(int) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Returns the name of a server given a serverCode
getServerlocation() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getSessionId() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Get the session identifier for this session.
getSessionId() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Get the session identifier for this session.
getSessions() - Method in class edu.ucsb.nceas.metacat.AuthSession
Get the new session
getSiteCode() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the siteCode encoded in this docid
getSiteDocument() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Retrieve the document from the site using its value.
getSiteList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the site fields as defined in the <site> tag in the pathquery dtd.
getSizeOfDBConnectionPool() - Method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to get the size of DBConnectionPool
getSmartDocId(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
This method will call both getDocIdFromString and getDocIdFromAccessionNumber.
getSortedReturnFieldString() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to return a String generated after sorting the returnFieldList Vector
getStartElementName() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get startElementName
getStartElementName() - Method in class edu.ucsb.nceas.metacat.SubTree
Get startElementName
getStartNodeId() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get start node id
getStartNodeId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get start node id
getStartedDescribesNodeId() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get the start described id
getStatus() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the db connetion status from the object
getStoredTmpNodeStack() - Method in class edu.ucsb.nceas.metacat.AccessSection
Get storedTempNodeStack
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
The character that the specific database implementation uses to indicate string literals in SQL.
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracles's string delimiter character: single quote (')
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
PostgreSQL's string delimiter character: single quote (')
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server's string delimiter character: single quote (')
getStyleSystemId(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
Lookup a stylesheet reference from the db catalog
getSubTreeId() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get the subTreeId
getSubTreeId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get the subTreeId
getSubTreeNodeStack() - Method in class edu.ucsb.nceas.metacat.SubTree
Get subtree node stack
getSystemID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the system identifier
getTag() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the db connetion tag from the object
getTagName() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the name of this node
getURLContent(URL) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
This method returns the content of a url
getUnReadableInlineDataIdList(String, String, String[], boolean) - Static method in class edu.ucsb.nceas.metacat.PermissionController
A static method to get Hashtable which cointains a inlinedata object list that user can't read it.
getUnWritableInlineDataIdList(String, String, String[], boolean) - Static method in class edu.ucsb.nceas.metacat.PermissionController
A static method to get Hashtable which cointains a inline data object list that user can't overwrite it.
getUnfilteredSubTreeNodeList() - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Get unfiltered subtree node list
getUnfoundDocId() - Method in class edu.ucsb.nceas.metacat.McdbDocNotFoundException
Method to get the docid which couldn't be found
getUnfoundRevision() - Method in class edu.ucsb.nceas.metacat.McdbDocNotFoundException
Method to get the docid's revsion which couldn't be found
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
Unique ID generator
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracle unique ID generator through use of sequences The name of the sequence used to generate the unique id is made from the name of the table that uses the id by appending "_id_seq" to it.
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
The PostgreSQL unique ID /sequence generator The name of the sequence used to generate the unique id is made from the name of the table that uses the id by appending "_id_seq" to it.
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server unique ID generator through use of IDENTITY key The IDENTITY key is a column in the table.
getUniqueId() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the uniqueId encoded in this docid
getUpdateDate() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the update date
getUpdatesVect() - Method in class edu.ucsb.nceas.metacat.ReplMessageHandler
 
getUsageCount() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the db connetion usage times from the object
getUserowner() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getUsers(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get all users from the authentication service
getUsers(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get the users for a particular group from the authentication service
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all users from the authentication service
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get the users for a particular group from the authentication service
getUserupdated() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getValidateType() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getValue() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the Value parameter
getVersion() - Static method in class edu.ucsb.nceas.metacat.Version
Get the current version string for this metacat instance.
getVersionAsXml() - Static method in class edu.ucsb.nceas.metacat.Version
Get the version number in an XML document.
getVersionFromString(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Utility method to get version number from a given string
getWarningMessage() - Method in class edu.ucsb.nceas.metacat.DBConnection
get the db connetion waring message from the object
getZippedPackage(String, ServletOutputStream, String, String[], String) - Method in class edu.ucsb.nceas.metacat.DBQuery
put a data packadge into a zip output stream
groups - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

H

Handler - class edu.ucsb.nceas.protocols.metacat.Handler.
Class handling metacat scheme URLs by delegating connection requests to the MetacatURLConnection class
Handler() - Constructor for class edu.ucsb.nceas.protocols.metacat.Handler
 
HarvestDetailLog - class edu.ucsb.nceas.metacat.harvesterClient.HarvestDetailLog.
HarvestDetailLog manages data and operations corresponding to the HARVEST_DETAIL_LOG table.
HarvestDetailLog(Harvester, Connection, int, int, HarvestDocument, String) - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvestDetailLog
Creates a new instance of HarvestDetailLog and inserts the data into the HARVEST_DETAIL_LOG table.
HarvestDocument - class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument.
HarvestDocument manages operations and data for a single document to be harvested.
HarvestDocument(Harvester, HarvestSiteSchedule, String, int, int, String, String) - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Creates a new instance of HarvestDocument.
HarvestListEditor - class edu.ucsb.nceas.metacat.harvesterClient.HarvestListEditor.
The Harvest List Editor reads a Harvest List XML file and displays it as a JTable.
HarvestListEditor() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvestListEditor
Constructor for HarvestListEditor class.
HarvestLog - class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog.
Manages log entries to be inserted to the HARVEST_LOG table.
HarvestLog(Harvester, Connection, int, Date, int, String, String, int) - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Creates a new instance of HarvestLog.
HarvestLog(Harvester, Connection, int, int, Date, int, String, String, int, HarvestDocument, String) - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Creates a new instance of HarvestLog and inserts this entry to the HARVEST_LOG table.
HarvestSiteSchedule - class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule.
HarvestSiteSchedule manages a single entry in the HARVEST_SITE_SCHEDULE table, determining when and how to harvest the documents for a given site.
HarvestSiteSchedule(Harvester, int, String, String, String, String, String, int, String, String) - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Creates a new instance of HarvestSiteSchedule.
Harvester - class edu.ucsb.nceas.metacat.harvesterClient.Harvester.
Harvester is the main class for the Harvester application.
Harvester() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Constructor.
HarvesterRegistration - class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration.
HarvesterRegistration is a servlet that implements harvester registration.
HarvesterRegistration() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
 
HarvesterRegistrationLogin - class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin.
HarvesterRegistrationLogin implements a servlet to login to the Harvester Registration servlet.
HarvesterRegistrationLogin() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin
 
HarvesterServlet - class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet.
HarvesterServlet class allows Harvester to be run as a background process.
HarvesterServlet() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
 
handleQuery(PrintWriter, Hashtable, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Create the xml query, execute it and display the results.
handleReturnField(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to transfer string to return field
handleSQuery(PrintWriter, Hashtable, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Retreive the squery xml, execute it and display it
harvestDocument() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Harvest the document from the site.
harvestDocumentList() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Harvests each document in the site document list.
hasPermission(String, String[], String) - Method in class edu.ucsb.nceas.metacat.PermissionController
Check from db connection if at least one of the list of @principals
hasPermissionForSubTreeNode(String, String[], String, long) - Method in class edu.ucsb.nceas.metacat.PermissionController
The method to determine of a node can be access by a user just by subtree access control
hasReadPermission(String, String[], String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Check for "READ" permission base on docid, user and group
hasSubTreeAccessControl() - Method in class edu.ucsb.nceas.metacat.PermissionController
Return if a document has subtree access control
hasUnaccessableSubTree(String, String[], String) - Method in class edu.ucsb.nceas.metacat.PermissionController
This method will return a hasTable of subtree which user doesn't has the permssion to access
hitTextNode - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

I

INDEXDELAY - Static variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
INLINE - Static variable in class edu.ucsb.nceas.metacat.AddMissedSubTreeSAXHandler
 
INLINE - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
INLINE - Static variable in class edu.ucsb.nceas.metacat.Eml210SAXHandler
 
InsufficientKarmaException - exception edu.ucsb.nceas.metacat.client.InsufficientKarmaException.
Exception thrown when an error occurs because a Metacat server operation requires higher access rights than the currently logged in user has.
InsufficientKarmaException(String) - Constructor for class edu.ucsb.nceas.metacat.client.InsufficientKarmaException
Create a new InsufficientKarmaException.
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
ignorableWhitespace(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that is called for each XML text node that is Ignorable white space
ignorableWhitespace(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
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
increaseCheckOutSerialNumber(int) - Method in class edu.ucsb.nceas.metacat.DBConnection
Increase a usage number to this object
increaseUsageCount(int) - Method in class edu.ucsb.nceas.metacat.DBConnection
Increase a usage number to this object
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Initialize the servlet by creating appropriate database connections
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.MetacatReplication
Initialize the servlet by creating appropriate database connections
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
Initializes the servlet.
init() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
Initializes the servlet by starting a separate thread in which to run the Harvester main program.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.harvesterClient.MetUpload
Initializes the servlet.
initLogIDs() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Initializes the detailLogID and harvestLogID values to their current maximums + 1.
initParser(DefaultHandler) - Static method in class edu.ucsb.nceas.metacat.ReplicationHandler
Method to initialize the message parser
insert(String, Reader, Reader) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Insert an XML document into the repository.
insert(String, Reader, Reader) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Insert an XML document into the repository.
insert(String, String, String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Insert an XML document into the repository.
insert(String, String, String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Insert an XML document into the repository.
insertPermissions() - Method in class edu.ucsb.nceas.metacat.AccessControlForSingleFile
Method to insert records into xml_access table
intValue(String) - Static method in class edu.ucsb.nceas.metacat.AccessControlList
 
internalEntityDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of internal entity declarations
isCaseSensitive() - Method in class edu.ucsb.nceas.metacat.QueryTerm
determine if the QueryTerm is case sensitive
isEmpty() - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
Method to determine the server list is empty or not
isGivenServerInList(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
Method to determine if a given server in the replication server list
isPercentageSearch() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to indicate this query is a percentage search

L

LEXICALPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
LoginServlet - class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet.
LoginServlet implements a Harvester servlet to login to Metacat
LoginServlet() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
 
loadOptions(boolean) - Static method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Loads Harvester options from a configuration file.
log(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.EventLog
Log an event of interest to the application.
login(String, String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Method used to log in to a metacat server.
login(String, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Method used to log in to a metacat server.
login(String, String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Method used to log in to a metacat server.
login(String, String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Method used to log in to a metacat server.
logout() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Method used to log out a metacat server.
logout() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Method used to log out a metacat server.
logout() - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Method used to log out a metacat server.
logout() - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Method used to log out a metacat server.

M

MAXDATACHARS - Static variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
McdbDocNotFoundException - exception edu.ucsb.nceas.metacat.McdbDocNotFoundException.
Exception thrown when an error occurs because a document with a given ID could not be found in the metacat database.
McdbDocNotFoundException() - Constructor for class edu.ucsb.nceas.metacat.McdbDocNotFoundException
Create a new McdbDocNotFoundException.
McdbDocNotFoundException(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.McdbDocNotFoundException
Create a new McdbDocNotFoundException.
McdbDocNotFoundException(Exception) - Constructor for class edu.ucsb.nceas.metacat.McdbDocNotFoundException
Create a new McdbDocNotFoundException.
McdbDocNotFoundException(String, Exception) - Constructor for class edu.ucsb.nceas.metacat.McdbDocNotFoundException
Create a new McdbDocNotFoundException.
McdbException - exception edu.ucsb.nceas.metacat.McdbException.
Exception thrown when an error occurs because a problem occurred in the metacat database.
McdbException() - Constructor for class edu.ucsb.nceas.metacat.McdbException
Create a new McdbException.
McdbException(String) - Constructor for class edu.ucsb.nceas.metacat.McdbException
Create a new McdbException.
McdbException(Exception) - Constructor for class edu.ucsb.nceas.metacat.McdbException
Create a new McdbException.
McdbException(String, Exception) - Constructor for class edu.ucsb.nceas.metacat.McdbException
Create a new McdbException.
MetUpload - class edu.ucsb.nceas.metacat.harvesterClient.MetUpload.
MetUpload implements a Harvester servlet to insert, update, or delete a single file to Metacat.
MetUpload() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.MetUpload
 
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
 
Metacat - interface edu.ucsb.nceas.metacat.client.Metacat.
This interface provides methods for initializing and logging in to a Metacat server, and then querying, reading, transforming, inserting, updating and deleting documents from that server.
MetacatAuthException - exception edu.ucsb.nceas.metacat.client.MetacatAuthException.
Exception thrown when a Metacat server denies a login authentication request.
MetacatAuthException(String) - Constructor for class edu.ucsb.nceas.metacat.client.MetacatAuthException
Create a new MetacatAuthException.
MetacatClient - class edu.ucsb.nceas.metacat.client.MetacatClient.
This interface provides methods for initializing and logging in to a Metacat server, and then querying, reading, transforming, inserting, updating and deleting documents from that server.
MetacatClient() - Constructor for class edu.ucsb.nceas.metacat.client.MetacatClient
Constructor to create a new instance.
MetacatException - exception edu.ucsb.nceas.metacat.client.MetacatException.
Exception thrown when an error occurs during a metacat operation.
MetacatException(String) - Constructor for class edu.ucsb.nceas.metacat.client.MetacatException
Create a new MetacatException.
MetacatFactory - class edu.ucsb.nceas.metacat.client.MetacatFactory.
This class is a factory which allows the caller to create an instance of a Metacat object for accessing a metacat server.
MetacatFactory() - Constructor for class edu.ucsb.nceas.metacat.client.MetacatFactory
 
MetacatInaccessibleException - exception edu.ucsb.nceas.metacat.client.MetacatInaccessibleException.
Exception thrown when a Metacat server is not accessible for the operation requested.
MetacatInaccessibleException(String) - Constructor for class edu.ucsb.nceas.metacat.client.MetacatInaccessibleException
Create a new MetacatInaccessibleException.
MetacatReplication - class edu.ucsb.nceas.metacat.MetacatReplication.
 
MetacatReplication() - Constructor for class edu.ucsb.nceas.metacat.MetacatReplication
 
MetacatString - interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString.
This interface provides methods for initializing and logging in to a Metacat server, and then querying, reading, transforming, inserting, updating and deleting documents from that server.
MetacatStringImpl - class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl.
This interface provides methods for initializing and logging in to a Metacat server, and then querying, reading, transforming, inserting, updating and deleting documents from that server.
MetacatStringImpl() - Constructor for class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
 
MetacatStringServiceApplication - class edu.ucsb.nceas.metacat.stringclient.application.MetacatStringServiceApplication.
 
MetacatStringServiceApplication() - Constructor for class edu.ucsb.nceas.metacat.stringclient.application.MetacatStringServiceApplication
 
MetacatURL - class edu.ucsb.nceas.metacat.MetacatURL.
 
MetacatURL(String) - Constructor for class edu.ucsb.nceas.metacat.MetacatURL
This constructor takes a string url and parses it according to the following rules.
MetacatURLConnection - class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection.
Handle requests for metacat scheme URLs
MetacatURLConnection(URL) - Constructor for class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection
Construct a new metacat scheme URL connection
main(String[]) - Static method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
the main routine used to test the dbadapter utility.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
the main routine used to associate access policy
main(String[]) - Static method in class edu.ucsb.nceas.metacat.AuthLdap
Test method for the class
main(String[]) - Static method in class edu.ucsb.nceas.metacat.ContentTypeProvider
 
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.DBSimpleQuery
the main routine used to test the DBSimpleQuery utility.
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.DBUtil
main routine used for testing.
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.DocumentIdentifier
Test driver.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
the main routine used to test the DBWriter utility.
main(String) - Static method in class edu.ucsb.nceas.metacat.FilteredSubTree
 
main(String[]) - Static method in class edu.ucsb.nceas.metacat.MetacatURL
Test method for this class.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.SchemaLocationResolver
 
main(String[]) - Static method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestListEditor
The main program.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Harvester main method.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.stringclient.application.MetacatStringServiceApplication
 
marker - Static variable in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
 
metacatHighestRevision() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Determines the highest revision that Metacat has for this document.
metacatLogin() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Login to Metacat using the ldapDN and ldapPwd

N

NAMESPACEFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
NAMESPACEPREFIXESFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
NONAMESPACELOCATION - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
 
NodeComparator - class edu.ucsb.nceas.metacat.NodeComparator.
A utility class that sorts two node records.
NodeComparator() - Constructor for class edu.ucsb.nceas.metacat.NodeComparator
Constructor
NodeRecord - class edu.ucsb.nceas.metacat.NodeRecord.
A utility class that encapsulates a node and its data
NodeRecord(long, long, long, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.NodeRecord
Constructor
namespaces - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
newPathExpressionWithOutAttribute(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
A method to get rid of attribute part in path expression
nodeId - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
nodeIndex - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
nodeStack - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
nodedata - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
nodeid - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
nodeindex - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
nodename - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
nodeprefix - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
nodetype - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
normalize(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Normalizes the given string.
notationDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler
Notation declarations are not signaled

O

OracleAdapter - class edu.ucsb.nceas.dbadapter.OracleAdapter.
The Oracle db adapter implementation.
OracleAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.OracleAdapter
 
openConnection() - Static method in class edu.ucsb.nceas.metacat.DBConnection
Method to establish DBConnection
openConnection(URL) - Method in class edu.ucsb.nceas.protocols.metacat.Handler
Open a new connection to the URL by delegating to the MetacatURLConnection
options - Static variable in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
 

P

PERMISSION - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
PINode - class edu.ucsb.nceas.metacat.PINode.
A Class that represents an XML PI node and its contents,
PINode(long, long, String, String) - Constructor for class edu.ucsb.nceas.metacat.PINode
Construct a new PINode instance
PRINCIPAL - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
PUBLIC - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
PUBLICID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
PathIndexEntry - class edu.ucsb.nceas.metacat.PathIndexEntry.
PathIndexEntry contains all of the data fields needed to insert an path into the xml_index table.
PathIndexEntry(long, String, String, String, long) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry
Construct a new PathIndexEntry.
PermissionController - class edu.ucsb.nceas.metacat.PermissionController.
 
PermissionController(String) - Constructor for class edu.ucsb.nceas.metacat.PermissionController
Constructor for PermissionController
PermissionController(String, boolean) - Constructor for class edu.ucsb.nceas.metacat.PermissionController
Constructor for PermssionController
PostgresqlAdapter - class edu.ucsb.nceas.dbadapter.PostgresqlAdapter.
The PostgreSQL db adapter implementation.
PostgresqlAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
 
parentId - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
parentnodeid - Variable in class edu.ucsb.nceas.metacat.NodeRecord
 
parseHarvestList() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Parses the site harvest list XML file to find out which documents to harvest.
parseQuery(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Utility method to parse the query part of a URL into parameters.
path - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
prepareStatement(String) - Method in class edu.ucsb.nceas.metacat.DBConnection
Method to create a PreparedStatement by sending a sql statement
prettyPrint(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Print the document URL following by its scope.identifier.revision.
printAccessControlSQLForReturnField(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
This sql command will selecet startnodeid and endnodeid that user can NOT access
printAttributeQuery(String, boolean) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
This method prints sql that finds the values of attributes in the xml documents based upon the whether the returnfield tag in the pathquery document has an attribute symbol (@).
printAttributeQuery(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
This method prints sql that finds the values of attributes in the xml documents based upon the whether the returnfield tag in the pathquery document has an attribute symbol (@).
printExtendedSQL(String, Hashtable, boolean) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
This method prints sql based upon the <returnfield> tag in the pathquery document.
printExtendedSQL(String, Hashtable) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
This method prints sql based upon the <returnfield> tag in the pathquery document.
printGetDocByDoctypeSQL(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
 
printHashParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
 
printMethodNameHavingBusyDBConnection() - Method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to print out the method name which have busy DBconnection
printOutput(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDetailLog
Prints the contents of this HarvestLog object.
printOutput(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Print the data fields and values in this HarvestDocument object.
printOutput(PrintStream, String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Prints the contents of this HarvestLog object.
printOutput(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Prints the data that is stored in this HarvestSiteSchedule object.
printParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Prints the parameters neatly to system.out
printRelationSQL(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
 
printSQL(boolean) - Method in class edu.ucsb.nceas.metacat.QueryGroup
create a SQL serialization of the query that this instance represents
printSQL(boolean) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
create a SQL serialization of the query that this instance represents
printSQL(boolean) - Method in class edu.ucsb.nceas.metacat.QueryTerm
create a SQL serialization of the query that this instance represents
processingDTD() - Method in class edu.ucsb.nceas.metacat.AccessControlList
Get the document processing state.
processingDTD - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
processingDTD() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
get the document processing state
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.
processingInstruction(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler called once for each processing instruction found: node that PI may occur before or after the root element.
processingInstruction(String, String) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler called once for each processing instruction found: node that PI may occur before or after the root element.
pub - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

Q

QueryGroup - class edu.ucsb.nceas.metacat.QueryGroup.
a utility class that represents a group of terms in a query
QueryGroup(String) - Constructor for class edu.ucsb.nceas.metacat.QueryGroup
construct a new QueryGroup
QuerySpecification - class edu.ucsb.nceas.metacat.QuerySpecification.
A Class that represents a structured query, and can be constructed from an XML serialization conforming to
QuerySpecification(Reader, String, String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification
construct an instance of the QuerySpecification class
QuerySpecification(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification
construct an instance of the QuerySpecification class
QuerySpecification(String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification
construct an instance of the QuerySpecification class which don't need to parser a xml document
QueryTerm - class edu.ucsb.nceas.metacat.QueryTerm.
a utility class that represents a single term in a query
QueryTerm(boolean, String, String) - Constructor for class edu.ucsb.nceas.metacat.QueryTerm
Construct a new instance of a query term for a free text search (using the value only)
QueryTerm(boolean, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.QueryTerm
Construct a new instance of a query term for a structured search (matching the value only for those nodes in the pathexpr)
query(Reader) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Query the metacat document store with the given metacat-compatible query document, and return the result set as a Reader.
query(Reader) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Query the metacat document store with the given metacat-compatible query document, and return the result set as a Reader.
query(String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Query the metacat document store with the given metacat-compatible query document, and return the result set as a String
query(String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Query the metacat document store with the given metacat-compatible query document, and return the result set as a Reader.

R

READ - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
READSTRING - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
RelationHandler - class edu.ucsb.nceas.metacat.RelationHandler.
 
RelationHandler(String, String, DBConnection, TripleCollection) - Constructor for class edu.ucsb.nceas.metacat.RelationHandler
Constructor for this class.
RemoteDocument - class edu.ucsb.nceas.metacat.RemoteDocument.
A class represents a document in remote metacat server.
RemoteDocument(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.RemoteDocument
Constructor of RemoteDcoument
ReplMessageHandler - class edu.ucsb.nceas.metacat.ReplMessageHandler.
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the replication handler
ReplMessageHandler() - Constructor for class edu.ucsb.nceas.metacat.ReplMessageHandler
 
ReplicationHandler - class edu.ucsb.nceas.metacat.ReplicationHandler.
This class handles deltaT replication checking.
ReplicationHandler(PrintWriter) - Constructor for class edu.ucsb.nceas.metacat.ReplicationHandler
 
ReplicationHandler(PrintWriter, int) - Constructor for class edu.ucsb.nceas.metacat.ReplicationHandler
 
ReplicationServer - class edu.ucsb.nceas.metacat.ReplicationServer.
A class express a entry in xml_replication.
ReplicationServer() - Constructor for class edu.ucsb.nceas.metacat.ReplicationServer
Consturctor of ReplicationServer
ReplicationServerList - class edu.ucsb.nceas.metacat.ReplicationServerList.
A class represent a replication server list in xml_replcation table
ReplicationServerList() - Constructor for class edu.ucsb.nceas.metacat.ReplicationServerList
constructor of ReplicationServerList It will build server list.
read(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Read an XML document from the metacat server session, accessed by docid, and returned as a Reader.
read(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Read an XML document from the metacat server session, accessed by docid, and returned as a Reader.
read(String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Read an XML document from the metacat server session, accessed by docid, and returned as a String.
read(String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Read an XML document from the metacat server session, accessed by docid, and returned as a String.
readDTDSchema(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
read DTD or Schema file from Metacat's XML catalog system
readDoctypes() - Method in class edu.ucsb.nceas.metacat.DBUtil
read all doctypes from db connection in XML format select all Public Id from xml_catalog table
readDocumentFromRemoteServer(ServletOutputStream) - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to read both xml and data file from remote server and put the output into the given output stream
readDocumentFromRemoteServerByZip(ZipOutputStream) - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to read both xml and data file from remote server by zip output and put the output into the given output stream
readInlineData(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Read inline data from the metacat server session, accessed by inlinedataid, and returned as a Reader.
readInlineData(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Read inline data from the metacat server session, accessed by inlinedataid and returned as a Reader.
readInlineDataFromFileSystem(String) - Static method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
readInlineDataFromFileSystem(String) - Static method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
 
readUsingSlowAlgorithm() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Get a text representation of the XML document as a string This older algorithm uses a recursive tree of Objects to represent the nodes of the tree.
registerDocument(String, String, String, String, String[]) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
This method will be call in handleUploadRequest in MetacatServlet class
registerDocument(String, String, String, String, String[], int) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Register a document that resides on the filesystem with the database.
registerDocumentInReplication(String, String, String, String, int) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Register a document that resides on the filesystem with the database.
release() - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to shut down all connections
replErrorLog(String) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Method for writing replication messages to a log file specified in metacat.properties
replLog(String) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Method for writing replication messages to a log file specified in metacat.properties
replToServer(String) - Static method in class edu.ucsb.nceas.metacat.MetacatReplication
Returns true if the replicate field for server in xml_replication is 1.
replaceWhiteSpaceForURL(String) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
A method to replace whitespace in url
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)
resolveNameSpace() - Method in class edu.ucsb.nceas.metacat.SchemaLocationResolver
When got a name space, check if it is in the database, if it is do nothing else upload it to metacat to store it and register it in catalog table
returnDBConnection(DBConnection, int) - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to return a connection to DBConnection pool.
returnErrors() - Method in class edu.ucsb.nceas.metacat.DBValidate
provide a list of errors from the validation process
reviseStack(Stack) - Static method in class edu.ucsb.nceas.metacat.MetaCatUtil
Revise stack change a stack to opposite order
revision - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
rollback() - Method in class edu.ucsb.nceas.metacat.DBConnection
Method to roll back
rootNode - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
run() - Method in class edu.ucsb.nceas.metacat.AuthLdap
This method will be called by start a thread.
run() - Method in class edu.ucsb.nceas.metacat.DBConnectionPool
periodically to recycle the connection
run() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 
run() - Method in class edu.ucsb.nceas.metacat.ForceReplicationHandler
Method to send force replication command to other server to get a new or updated docid
run() - Method in class edu.ucsb.nceas.metacat.MetacatReplication
this method handles the timeout for a file lock.
run() - Method in class edu.ucsb.nceas.metacat.ReplicationHandler
Method that implements TimerTask.run().
run() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
Runs the Harvester main program in a separate thread.

S

SCHEMA - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
SCHEMALOCATIONKEYWORD - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
 
SCHEMAVALIDATIONFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
SYSTEMID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
SchemaLocationResolver - class edu.ucsb.nceas.metacat.SchemaLocationResolver.
A database aware Class to handle schema location.
SchemaLocationResolver() - Constructor for class edu.ucsb.nceas.metacat.SchemaLocationResolver
 
SchemaLocationResolver(String) - Constructor for class edu.ucsb.nceas.metacat.SchemaLocationResolver
Construct an instance of the SchemaLocationResolver class
SqlserverAdapter - class edu.ucsb.nceas.dbadapter.SqlserverAdapter.
The MS SQL Server db adapter implementation.
SqlserverAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.SqlserverAdapter
 
SubTree - class edu.ucsb.nceas.metacat.SubTree.
A Class that represents an XML Subtree
SubTree() - Constructor for class edu.ucsb.nceas.metacat.SubTree
Defualt constructor
SubTree(String, String, long, long) - Constructor for class edu.ucsb.nceas.metacat.SubTree
Constructor of subtree
seStartedDescribesNodeId(long) - Method in class edu.ucsb.nceas.metacat.AccessSection
Set a the start "describes" node id
serverAt(int) - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
Method to get a server object given a index number
serverCode - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
setAccess(String, String, String, String, String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
set the access on an XML document in the repository.
setAccess(String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
set the access on an XML document in the repository.
setAge(long) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a connection age to this object
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, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
Add a new attribute to this node, or set its value
setAutoCommit(boolean) - Method in class edu.ucsb.nceas.metacat.DBConnection
Method to set commit mode
setCheckOutMethodName(String) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a method name to the checkOutMethodName
setCheckOutSerialNumber(int) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set check out serial number to this object
setCheckOutTime(long) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set check out time to this object
setConnectionTime(long) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a connection time to this object It is accumulated
setConnections(Connection) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a connection to this object
setContainsExtenedSQL(boolean) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
set if this query sepcification has extendQuery(has return doc type or not)
setControlLevel(String) - Method in class edu.ucsb.nceas.metacat.AccessSection
Set a controllevel
setCreateTime(long) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a usage number to this object
setDataReplication(boolean) - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Set data replication option
setDescribedIdList(Vector) - Method in class edu.ucsb.nceas.metacat.AccessSection
Set a described id list (in data access part)
setDocID(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Set the doc id of this node
setDocId(String) - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Set the a docId
setDocId(String) - Method in class edu.ucsb.nceas.metacat.SubTree
Set the a docId
setDocid(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
Set the document identifier.
setEndNodeId(long) - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Set a end node id
setEndNodeId(long) - Method in class edu.ucsb.nceas.metacat.SubTree
Set a end node id
setEvent(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
Set the current value of the event.
setFilterDocList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the list of filter docs of this query
setFilteredSubTree(Hashtable) - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Set a filtered subtree(subtree should be merger equivlent
setGroup(String[]) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to set user group
setHarvestStartTime(Date) - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Sets the harvest start time for this harvest run.
setHub(boolean) - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Set hub option
setIdentifier(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the identifier of this query
setIpAddress(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
Set the current value of the internet protocol address.
setLastCheckedDate(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Set a string as last checked date
setMetacatUrl(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
When the MetacatFactory creates an instance it needs to set the MetacatUrl to which connections should be made.
setMetacatUrl(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
When the MetacatFactory creates an instance it needs to set the MetacatUrl to which connections should be made.
setMetacatUrl(String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
When the MetacatFactory creates an instance it needs to set the MetacatUrl to which connections should be made.
setMetacatUrl(String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
When the MetacatFactory creates an instance it needs to set the MetacatUrl to which connections should be made.
setNamespace(String, String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Add a namespace to this node
setNamespace(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
Add a namespace to this node
setNodeData(String) - Method in class edu.ucsb.nceas.metacat.CommentNode
Set the node data to the given string
setNodeData(String) - Method in class edu.ucsb.nceas.metacat.PINode
Set the node data to the given string
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
setOwnerList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the list of owners used to constrain this query
setParentID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode
Set the parent id of this node
setPermission(int) - Method in class edu.ucsb.nceas.metacat.AccessRule
Set a permission.
setPermissionOrder(String) - Method in class edu.ucsb.nceas.metacat.AccessSection
Set a permissionOrder
setPermissionType(String) - Method in class edu.ucsb.nceas.metacat.AccessRule
Set the permssionType
setPrincipal(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
Set the current value of the principal.
setQueryGroup(QueryGroup) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
set the querygroup
setQueryTitle(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the title of this query
setReferences(String) - Method in class edu.ucsb.nceas.metacat.AccessSection
Set a references
setReplication(boolean) - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Set replication option
setRequestHeader(String, String) - Method in class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection
Set the request header for the URL
setReturnDocList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the list of return docs of this query
setReturnFieldList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the list of fields to be returned by this query
setRootNodeID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode
Set the root node id of this node
setSchemaLocation(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Accessor method for setting the value of the schemaLocation field.
setServerName(String) - Method in class edu.ucsb.nceas.metacat.ReplicationServer
Set a sting as server name
setSessionId(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Set the session identifier for this session.
setSessionId(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Set the session identifier for this session.
setSiteList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
method to set the list of sites used to constrain this query
setStartElementName(String) - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Set a startElementName
setStartElementName(String) - Method in class edu.ucsb.nceas.metacat.SubTree
Set a startElementName
setStartNodeId(long) - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Set a start node id
setStartNodeId(long) - Method in class edu.ucsb.nceas.metacat.SubTree
Set a start node id
setStatus(int) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a connection status to this object
setStoredTmpNodeStack(Stack) - Method in class edu.ucsb.nceas.metacat.AccessSection
Set a storedTempNodeStack
setSubTreeId(String) - Method in class edu.ucsb.nceas.metacat.FilteredSubTree
Set the a subtreeId
setSubTreeId(String) - Method in class edu.ucsb.nceas.metacat.SubTree
Set the a subtreeId
setSubTreeNodeStack(Stack) - Method in class edu.ucsb.nceas.metacat.SubTree
Set subtree node stack
setTag(String) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a connection status to this object
setTagName(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Set the name of this node
setUsageCount(int) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a usage number to this object
setUserName(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to set user name
setWarningMessage(SQLWarning) - Method in class edu.ucsb.nceas.metacat.DBConnection
Set a warning message to this object
shrinkConnectionPoolSize() - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to decrease dbconnection pool size when all dbconnections are idle If all connections are free and connection pool size greater than initial value, shrink connection pool size to intital value
shrinkDBConnectionPoolSize() - Static method in class edu.ucsb.nceas.metacat.DBConnectionPool
Method to decrease dbconnection pool size when all dbconnections are idle If all connections are free and connection pool size greater than initial value, shrink connection pool size to intital value
size() - Method in class edu.ucsb.nceas.metacat.ReplicationServerList
Method to get the size of serverList
startCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the start of CDATA sections
startDTD(String, String, String) - Method in class edu.ucsb.nceas.metacat.AccessControlList
SAX Handler that receives notification of DOCTYPE.
startDTD(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of DOCTYPE.
startDocument() - Method in class edu.ucsb.nceas.metacat.AccessControlList
Callback method used by the SAX Parser when beginning of the document
startDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of beginning of the document
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.AccessControlList
Callback method used by the SAX Parser when the start tag of an element is detected.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.AddMissedSubTreeSAXHandler
SAX Handler that is called at the start of each XML element
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
This method starts a new vector for each updatedDocument tag.
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.DocInfoHandler
capture the name of the tag.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that is called at the start of each XML element
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
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.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.ReplMessageHandler
This method starts a new vector for each updatedDocument tag.
startElementName - Variable in class edu.ucsb.nceas.metacat.SubTree
 
startEntity(String) - Method in class edu.ucsb.nceas.metacat.AccessControlList
SAX Handler that receives notification of the start of entities.
startEntity(String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the start of entities
startNodeId - Variable in class edu.ucsb.nceas.metacat.SubTree
 
startPrefixMapping(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that is called at the start of Namespace
startPrefixMapping(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that is called at the start of Namespace
startPrefixMapping(String, String) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that is called at the start of Namespace
subTreeId - Variable in class edu.ucsb.nceas.metacat.SubTree
 
systemid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

T

TOPLEVEL - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
TextNode - class edu.ucsb.nceas.metacat.TextNode.
A Class that represents an XML Text node and its contents,
TextNode(long, long, String) - Constructor for class edu.ucsb.nceas.metacat.TextNode
Construct a new TextNode instance
textBuffer - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
textBufferStack - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
toDate(String, String) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
MSSQL didn't support to_date function which to transfer a text string to date type.
toDate(String, String) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
MSSQL doesn't support the to_date function, so we transfer text directly.
toString() - Method in class edu.ucsb.nceas.metacat.CommentNode
String representation of this text node
toString() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the whole docid as a string
toString(String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Print a string representation of the XML document
toString() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Print a string representation of the XML document
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.MetacatURL
returns a string representation of this metacatURL
toString() - Method in class edu.ucsb.nceas.metacat.PINode
String representation of this text node
toString() - Method in class edu.ucsb.nceas.metacat.QueryGroup
create a String description of the query that this instance represents.
toString() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
create a String description of the query that this instance represents.
toString() - Method in class edu.ucsb.nceas.metacat.QueryTerm
create a String description of the query that this instance represents.
toString() - Method in class edu.ucsb.nceas.metacat.TextNode
String representation of this text node
toXml(Writer, String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Print a text representation of the XML document to a Writer
toXml(PrintWriter) - Method in class edu.ucsb.nceas.metacat.McdbException
Print the message from this exception in XML format.
transformXMLDocument(String, String, String, String, PrintWriter, Hashtable) - Method in class edu.ucsb.nceas.metacat.DBTransform
 
transformXMLDocument(String, String, String, String, StringWriter) - Method in class edu.ucsb.nceas.metacat.DBTransform
 
transformXMLDocument(String, String, String, String, PrintWriter, Hashtable, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
Transform an XML document using the stylesheet reference from the db
transformXMLDocument(String, String, String, String, StringWriter, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
Transform an XML document to StringWriter using the stylesheet reference from the db
transformXMLDocument(StringReader, String, String, String, PrintWriter, Hashtable, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
Method to do transform for a string reader

U

unparsedEntityDecl(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler
All are reported after startDocument and before first startElement event
update(String, Reader, Reader) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Update an XML document in the repository.
update(String, Reader, Reader) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Update an XML document in the repository.
update(String, String, String) - Method in interface edu.ucsb.nceas.metacat.stringclient.impl.MetacatString
Update an XML document in the repository.
update(String, String, String) - Method in class edu.ucsb.nceas.metacat.stringclient.impl.MetacatStringImpl
Update an XML document in the repository.
updateNodeIndex(DBConnection, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
USED FROM SEPARATE THREAD RUNNED from DBSAXHandler on endDocument() Update the node index (xml_index) for this node by generating test strings that represent all of the relative and absolute paths through the XML tree from document root to this node
updateRootNodeID(long) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
update rootnodeid=nodeid for 'DOCUMENT' type of nodes only
upload(String, File) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Upload an XML document into the repository.
upload(String, String, InputStream, int) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Upload an XML document into the repository.
upload(String, File) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Upload a data document into the repository.
upload(String, String, InputStream, int) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Upload a data document into the repository.
useNestedStatements(String) - Static method in class edu.ucsb.nceas.metacat.QueryTerm
 
user - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

V

VALIDATIONFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
Version - class edu.ucsb.nceas.metacat.Version.
 
Version() - Constructor for class edu.ucsb.nceas.metacat.Version
 
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

WRITE - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
WRITESTRING - Static variable in interface edu.ucsb.nceas.metacat.AccessControlInterface
 
warning(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of warnings
write(DBConnection, Reader, String, Reader, String, String, String, String[], String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Write an XML file to the database, given a filename
write(DBConnection, Reader, String, Reader, String, String, String, String[], int, boolean, String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Write an XML file to the database, given a Reader
write(DBConnection, Reader, String, Reader, String, String, String, String[]) - Method in class edu.ucsb.nceas.metacat.DocumentImplWrapper
 
writeChildNodeToDB(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
creates SQL code and inserts new node into DB connection
writeDTDNodeToDB(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
creates SQL code and inserts new node into DB connection
writeDataFileInReplication(InputStream, String, String, String, String, String, String, String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
This method will register a data file entry in xml_documents and save a data file input Stream into file system..
writeNodename(String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
creates SQL code to put nodename for the document node into DB connection
writeReplication(DBConnection, Reader, String, Reader, String, String, String, String[], String, String, String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Write an XML file to the database during replication
writeReplication(DBConnection, Reader, String, Reader, String, String, String, String[], String, String) - Method in class edu.ucsb.nceas.metacat.DocumentImplWrapper
 
writeTextForDBSAXNode(long, StringBuffer, DBSAXNode) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 

X

XMLFORMAT - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
 
xmlIndex - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

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