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

## A

ABSTRACT - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
ABSTRACT - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
AbstractDatabase - Class in edu.ucsb.nceas.dbadapter
  Java offers uniform database access through the use of JDBC.
AbstractDatabase() - Constructor for class edu.ucsb.nceas.dbadapter.AbstractDatabase
AccessControlException - Exception in edu.ucsb.nceas.metacat.accesscontrol
  Exception thrown when an error occurs during access control
AccessControlException(String) - Constructor for exception edu.ucsb.nceas.metacat.accesscontrol.AccessControlException
  Create a new AccessControlException.
AccessControlException(String, BaseException) - Constructor for exception edu.ucsb.nceas.metacat.accesscontrol.AccessControlException
accessControlExists(XMLAccessDAO) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Check if access control comination for docid/principal/permission/permorder/permtype already exists.
AccessControlForSingleFile - Class in edu.ucsb.nceas.metacat.accesscontrol
  A Class that loads eml-access.xml file containing ACL for a metadata document into relational DB.
AccessControlForSingleFile(String) - Constructor for class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Construct an instance of the AccessControlForSingleFile class.
AccessControlList - Class in edu.ucsb.nceas.metacat.accesscontrol
  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.accesscontrol.AccessControlList
  Construct an instance of the AccessControlList class.
AccessControlList(DBConnection, String, int, String, String[], int) - Constructor for class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
  Construct an instance of the AccessControlList class.
AccessException - Exception in edu.ucsb.nceas.metacat.shared
  Exception thrown when an error occurs in a configuration administrative class
AccessException(String) - Constructor for exception edu.ucsb.nceas.metacat.shared.AccessException
  Create a new AccessException.
AccessException(String, BaseException) - Constructor for exception edu.ucsb.nceas.metacat.shared.AccessException
AccessionNumber - Class in edu.ucsb.nceas.metacat
  (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(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 in edu.ucsb.nceas.metacat
  Exception thrown when an error occurs because an AccessionNumber was invalid or used incorrectly.
AccessionNumberException(String) - Constructor for exception edu.ucsb.nceas.metacat.AccessionNumberException
  Create a new AccessionNumberException.
AccessRule - Class in edu.ucsb.nceas.metacat.accesscontrol
  A Class that represents an XML access rule.
AccessRule() - Constructor for class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
AccessSection - Class in edu.ucsb.nceas.metacat.accesscontrol
  A Class that represents an XML access rule.
AccessSection() - Constructor for class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
accNumberUsed(String) - Static method in class edu.ucsb.nceas.metacat.AccessionNumber
  check for existence of Accesssion Number xml_acc_numbers table
ACTION - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
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.
ACTIVE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
add(IndexEvent) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
add(String, String) - Method in class edu.ucsb.nceas.metacat.IndexingQueue
add(IndexingQueueObject) - Method in class edu.ucsb.nceas.metacat.IndexingQueue
add(String, SimpleFeature) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
  Adds a new feature (from a SpatialDocument) This is faster than insertOrUpdate but relying on this method might cause duplication of docids in the spatial cache.
addAccessRule(AccessRule) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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
addDataFile(SystemMetadata, InputStream) - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Adds a data file's stream to the bag
addDocument(String, Map) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
addField(String, String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
addFields(Map) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
addFormat(Session, ObjectFormatIdentifier, ObjectFormat) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
addGroup(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
  Add a group into the file
addHandler(MetacatHandlerPlugin) - Method in class edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager
addIdentifier(Document, String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Add the identifier element to the root document.
addLanguage(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Append a subject to the document.
addLSID(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Adds identifierId (Metacat Server does not support it!)
addLSID(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Adds identifierId
addMetacatEventObserver(MetacatEventObserver) - Method in class edu.ucsb.nceas.metacat.event.MetacatEventService
addPrincipal(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
  Set the a principle
addProperty(String, String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Utility method to add a property value both in memory and to the properties file
addProperty(String, String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
addProperty(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Utility method to add a property value both in memory and to the properties file
addProperty(String, String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Utility method to add a property value both in memory and to the properties file
addPublicationYear(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Add the publication year node
addPublisher(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Add the publisher node
addQueryGroup(AdvancedSearchQueryGroup) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryGroup
  Adds a AdvancedSearchQueryGroup to this AdvancedSearchQueryGroup's list of querygroups.
addQueryTerm(AdvancedSearchQueryTerm) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryGroup
  Adds a AdvancedSearchQueryTerm to this AdvancedSearchQueryGroup's list of queryterms.
addResourceMap() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Adds the resource map to the bag.
addResourceType(Document, String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Add the resource type to the document
addReturnField(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchPathQuery
  Adds a returnfield to the pathquery xml.
addScienceMetadata(SystemMetadata, InputStream) - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Adds a system metadata document and its InputStream to the class record
addScienceMetadatas() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
addScienceSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Sets the science metadata
addSciPdf(InputStream, SystemMetadata, Identifier) - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
  Creates a pdf out of the science metadata and adds it to the bag.
addSystemMetadata(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Adds a system metadata object to the bag
addToDeleteQue(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Delete a given document from spatial cache.
addToServerListIfItIsNot(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  To a given server name, to check if it is in the server list.
addToUpdateQue(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Currently just a wrapper around the harvestDocument method.
addUser(String, String[], String, String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
  Add a user to the file
addUserToGroup(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
  Add a user to a group
addVersion(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Add the version element to the document
addXMLAccess(String, String, Long, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Add permissions for a given principal on a given document.
AdminException - Exception in edu.ucsb.nceas.metacat.admin
  Exception thrown when an error occurs in a configuration administrative class
AdminException(String) - Constructor for exception edu.ucsb.nceas.metacat.admin.AdminException
  Create a new AdminException.
AdvancedSearch - Class in edu.ucsb.nceas.metacat.advancedsearch
AdvancedSearch(AdvancedSearchBean) - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearch
  Constructor.
AdvancedSearchBean - Class in edu.ucsb.nceas.metacat.advancedsearch
AdvancedSearchBean() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
AdvancedSearchPathQuery - Class in edu.ucsb.nceas.metacat.advancedsearch
AdvancedSearchPathQuery(String, AdvancedSearchQueryGroup, String) - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchPathQuery
  Constructor.
AdvancedSearchQueryGroup - Class in edu.ucsb.nceas.metacat.advancedsearch
AdvancedSearchQueryGroup(String, String) - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryGroup
  Constructor.
AdvancedSearchQueryTerm - Class in edu.ucsb.nceas.metacat.advancedsearch
AdvancedSearchQueryTerm(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryTerm
  Constructor.
AdvancedSearchServlet - Class in edu.ucsb.nceas.metacat.advancedsearch
AdvancedSearchServlet() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchServlet
AGENT_URI - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
AGGREGATION - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
allowedVersionLevels - Static variable in class edu.ucsb.nceas.metacat.Version
alreadyHandle - Variable in class edu.ucsb.nceas.metacat.DBValidate
appendCreator(String, Document, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Append a creator element to the root element.
appendDescription(String, Document, String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Append a description to the document.
appendFormat(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Add the format (MIME type) of the meta data object to the document
appendRev(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  If the given docid only have one seperter, we need append rev for it.
appendSubject(String, Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Append a subject to the document
appendTitle(String, Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Append a title to the title list element
APPLICATION_NAME - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
archive(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Archives an object from the Coordinating Node
archive(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Archives an object, where the object is either a data object or a science metadata object.
archive(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
archive(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
archive(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
archive(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
archiveCNObject(boolean, Session, Identifier, SystemMetadata, boolean) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Archive a object on cn and notify the replica.
ArchiveHandler - Class in edu.ucsb.nceas.metacat
ARCHIVEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
archiveObject(boolean, Session, Identifier, SystemMetadata, boolean) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Archives an object, where the object is either a data object or a science metadata object.
areAllSchemasRegistered(Vector<XMLSchema>) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Checks to see that all schemas are registered.
areOrganizationsConfigured() - Static method in class edu.ucsb.nceas.metacat.util.OrganizationUtil
  Reports whether LDAP is fully configured.
arePropertiesConfigured() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Reports whether properties are fully configured.
arePropertiesConfigured() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
arePropertiesConfigured() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Reports whether properties are fully configured.
arePropertiesConfigured() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
areSkinsConfigured() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Reports whether properties are fully configured.
areSkinsConfigured() - Static method in class edu.ucsb.nceas.metacat.util.SkinUtil
  Reports whether skins are fully configured.
associateAccess() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
  Associate the access policy of dataset to the docid which the data set id mapped
AssociateAccessPolicy - Class in edu.ucsb.nceas.metacat
  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
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
attributesMap - Variable in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
ATTRIBUTESYMBOL - Static variable in class edu.ucsb.nceas.metacat.QuerySpecification
auth - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
AuthAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the Authentication configuration page and the processing of the configuration values.
authCacheSzie - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
authenticate(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
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.
authenticate(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Determine if a user/password are valid according to the authentication service.
authenticate(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Determine if a user/password are valid according to the authentication service.
authenticatedGetObject(String, String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Read XML document from server session, accessed by docid, and returned as a Reader.
authenticatedGetObject(String, String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Read XML document from server session, accessed by docid, and returned as a Reader.
authenticatedQuery(Reader) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
authenticatedQuery(Reader) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Query (as an authenticated user) the metacat document store with the given Ecogrid-compatible query document and return the Ecogrid result set as a Reader.
authenticateUser(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin
  Handle configuration of the Authentication properties
AuthenticationException - Exception in edu.ucsb.nceas.metacat.authentication
  Exception class will be used in the authentication process
AuthenticationException(String) - Constructor for exception edu.ucsb.nceas.metacat.authentication.AuthenticationException
  Constructor
AuthFile - Class in edu.ucsb.nceas.metacat.authentication
  This an authentication class base on a username/password file.
AuthFile() - Constructor for class edu.ucsb.nceas.metacat.authentication.AuthFile
  Constructor
AuthFile(String) - Constructor for class edu.ucsb.nceas.metacat.authentication.AuthFile
AuthFileBCryptHash - Class in edu.ucsb.nceas.metacat.authentication
  A class to use the BCryptHash algorithm to generate the hash.
AuthFileBCryptHash() - Constructor for class edu.ucsb.nceas.metacat.authentication.AuthFileBCryptHash
  Default Constructor
AuthFileHashInterface - Interface in edu.ucsb.nceas.metacat.authentication
  This an interface for different hash algorithms using to protect users' password in the username/password file
AuthInterface - Interface in edu.ucsb.nceas.metacat
  An interface representing the methods that should be implemented by an authentication service.
AuthLdap - Class in edu.ucsb.nceas.metacat
  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 in edu.ucsb.nceas.metacat
  A Class that implements session tracking for MetaCatServlet users.
AuthSession() - Constructor for class edu.ucsb.nceas.metacat.AuthSession
  Construct an AuthSession
AuthSession(int) - Constructor for class edu.ucsb.nceas.metacat.AuthSession
  Constructor with cached group information for users.
AuthStub - Class in edu.ucsb.nceas.metacat
  An implementation of the AuthInterface interface that allows Metacat to use the LDAP protocol for directory services.
AuthStub() - Constructor for class edu.ucsb.nceas.metacat.AuthStub
  Construct an AuthTest
AuthTest - Class in edu.ucsb.nceas.metacat
  An implementation of the AuthInterface interface that allows Metacat to use the LDAP protocol for directory services.
AuthTest() - Constructor for class edu.ucsb.nceas.metacat.AuthTest
  Construct an AuthTest
AuthTLSException - Exception in edu.ucsb.nceas.metacat
  Exception thrown when an error occurs in a configuration administrative class
AuthTLSException(String) - Constructor for exception edu.ucsb.nceas.metacat.AuthTLSException
  Create a new AuthTLSException.
AuthUtil - Class in edu.ucsb.nceas.metacat.util
autoPublishDOI - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService

## B

BackupAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the login page
BASE_EXISTS_ONLY - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
BaseAccess - Class in edu.ucsb.nceas.metacat.shared
BaseAccess() - Constructor for class edu.ucsb.nceas.metacat.shared.BaseAccess
BaseException - Exception in edu.ucsb.nceas.metacat.shared
  Exception thrown when an error occurs in a configuration administrative class
BaseException(String) - Constructor for exception edu.ucsb.nceas.metacat.shared.BaseException
  Create a new AccessException.
BaseException(String, BaseException) - Constructor for exception edu.ucsb.nceas.metacat.shared.BaseException
  Create a new BaseException.
BaseService - Class in edu.ucsb.nceas.metacat.shared
  A suite of utility classes for querying DB
BaseService() - Constructor for class edu.ucsb.nceas.metacat.shared.BaseService
baseURI - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
baseURL - Variable in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
BasicNode - Class in edu.ucsb.nceas.metacat
  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
BIN - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
BioPortalService - Class in edu.ucsb.nceas.metacat.annotation
BioPortalService() - Constructor for class edu.ucsb.nceas.metacat.annotation.BioPortalService
BookKeeperClient - Class in edu.ucsb.nceas.metacat.dataone.quota
  A client class to access the BookKeeper service
BookKeeperClient() - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
  A private constructor
bookkeeperClient - Variable in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
BrowseServlet - Class in edu.ucsb.nceas.metacat.advancedsearch
BrowseServlet() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.BrowseServlet
buildIndex() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  Build the index records for this document.
bypassConfiguration() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Reports whether the metacat configuration utility should be run.
bypassConfiguration() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
bypassConfiguration() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Reports whether the metacat configuration utility should be run.
bypassConfiguration() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
bypassConfiguration() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Reports whether the metacat configuration utility should be run.
bypassConfiguration() - Static method in class edu.ucsb.nceas.metacat.util.ConfigurationUtil
  Reports whether the metacat configuration utility should be run.
BYPASSED - Static variable in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
BYPASSED - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService

## C

callorder - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
canInsertOrUpdate(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Check if the specified user can insert the document
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Determine if the factory can handle the meta data with the given name space
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
  It can handle all namespace
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
  Determine if the given name space can be handled by this factory
CartManager - Class in edu.ucsb.nceas.metacat.cart
  Class to query data
CartManager() - Constructor for class edu.ucsb.nceas.metacat.cart.CartManager
  empty constructor to initialize query
CartManager(String) - Constructor for class edu.ucsb.nceas.metacat.cart.CartManager
catalogid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
CatalogMessageHandler - Class in edu.ucsb.nceas.metacat
  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
changePassword(String, String) - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
  Change the password on the geoserver.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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.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.MetacatResultSet
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.replication.ReplMessageHandler
  Take the data out of the docid and date_updated fields
check(NodeReference, SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.dataone.NodeReplicationPolicyChecker
  Check if a given object with the system meta data and from the source node can be stored as a replica
checkAndSetProperty(HttpServletRequest, String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(HttpServletRequest, String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
checkAndSetProperty(HttpServletRequest, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(HttpServletRequest, String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(HttpServletRequest, String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(String, String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Check user input against existing value and update the metacat property file with that new value if it has changed from the value that was originally set.
CheckedFile - Class in edu.ucsb.nceas.metacat.restservice.multipart
  A file object with the expected checksum
CheckedFile(String, Checksum) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.CheckedFile
  Constructor
checkExpandedPermissions(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Compare all the session subjects against the expanded subjects (from listSubjects) of the object rightsholder.
checkQuota(boolean, String, String, String, double, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
  Check if the quota has enough space for this request.
checkSidInModifyingSystemMetadata(SystemMetadata, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
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.
checkV1SystemMetaPidExist(Identifier, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  A utility method for v1 api to check the specified identifier exists as a pid Uses the IdentifierManager to call the Identifier table directly - this detects Identifiers for deleted objects (where the SystemMetadata doesn't exist, but the Identifier remains)
cito - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
CITO_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
clear() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
clearFields() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
clearQueryResultCache() - Static method in class edu.ucsb.nceas.metacat.DBQuery
  Method to clear the query result cache.
clearRequestMessages(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Add a list of general messages to the request.
client - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
CLIENT_VIEW_BEAN - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
clientDeleteRequest(ClientView, ClientViewHelper) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
  Handles a client's request to delete a document.
ClientFgdcHelper - Class in edu.ucsb.nceas.metacat.clientview
ClientFgdcHelper() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
ClientHtmlHelper - Class in edu.ucsb.nceas.metacat.clientview
ClientHtmlHelper() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientHtmlHelper
clientRequest(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Main web API method for handling various actions.
ClientView - Class in edu.ucsb.nceas.metacat.clientview
  Description information for the ClientView bean.
ClientView() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientView
  Creates a new instance of ClientView
ClientViewBeanInfo - Class in edu.ucsb.nceas.metacat.clientview
ClientViewBeanInfo() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
ClientViewHelper - Class in edu.ucsb.nceas.metacat.clientview
ClientViewHelper(HttpServletRequest) - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Creates a new instance of ClientViewHelper, using info in an HttpServletRequest for initializing.
ClientViewHelper(String, String, ClientView) - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Creates a new instance of ClientViewHelper, using parameter values for initializing.
clientViewHelperInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  This is a convenience method to reduce the amount of code in a Metacat Client.
clone() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
  Copy a AccessRule to another accessrule object
close() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Close a DBConnection object
close() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  close the repository
closeConnection() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
closeDBObjects(PreparedStatement, DBConnection, int, Log) - Method in class edu.ucsb.nceas.metacat.shared.BaseAccess
CNodeService - Class in edu.ucsb.nceas.metacat.dataone
  Represents Metacat's implementation of the DataONE Coordinating Node service API.
CNodeService - Class in edu.ucsb.nceas.metacat.dataone.v1
  Represents Metacat's implementation of the DataONE Coordinating Node service API.
CNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v1
  CN REST service implementation handler ****************** CNCore -- DONE create() - POST /d1/cn/object/PID listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET /d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET /d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not implemented in Metacat CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET /d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules CNIdentity - not implemented at all on Metacat CNReplication setReplicationStatus() - PUT /replicaNotifications/PID updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy() - PUT /replicaPolicies/PID isNodeAuthorized() - GET /replicaAuthorizations/PID CNRegister -- not implemented at all in Metacat ******************
CNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
CNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v2
  CN REST service implementation handler ****************** CNCore -- DONE create() - POST /d1/cn/object/PID listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET /d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET /d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not implemented in Metacat CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET /d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules CNIdentity - not implemented at all on Metacat CNReplication setReplicationStatus() - PUT /replicaNotifications/PID updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy() - PUT /replicaPolicies/PID isNodeAuthorized() - GET /replicaAuthorizations/PID CNRegister -- not implemented at all in Metacat ******************
CNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
CNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v1
  Routes CN REST service requests to the appropriate handler
CNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.CNRestServlet
CNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v2
  Routes CN REST service requests to the appropriate handler
CNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.CNRestServlet
collectMultipartFiles() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Process the MMP request that includes files for each param
collectMultipartParams() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Parse string parameters from the mime multipart entity of the request.
collectObjectFiles() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Parse the request by the streaming multiple part handler.
collectSynchronizationFailed() - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
collectSynchronizationFailed() - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
combinateCurrentDateAndGivenTime(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationHandler
  This method will combine given time string(in short format) to current date.
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
  SAX Handler that receives notification of comments in the DTD
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
CommentNode - Class in edu.ucsb.nceas.metacat
  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
commit() - Method in class edu.ucsb.nceas.metacat.database.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
compareTo(Version) - Method in class edu.ucsb.nceas.metacat.Version
  Compare this Version object to another.
CONCRETE - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
CONFIG_FILE_DIR - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
CONFIG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
CONFIG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.service.ServiceService
CONFIG_FILE_PATH - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
ConfigurableProperties - Class in edu.ucsb.nceas.metacat.properties
  A suite of utility classes for the metadata configuration utility
ConfigurableProperties() - Constructor for class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  private constructor since this is a singleton
ConfigurationUtil - Class in edu.ucsb.nceas.metacat.util
  A suite of utility classes for the metadata catalog server
ConfigurationUtil() - Constructor for class edu.ucsb.nceas.metacat.util.ConfigurationUtil
configureAuth(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.AuthAdmin
  Handle configuration of the Authentication properties
configureBackup(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
  Handle configuration of the backup directory
CONFIGURED - Static variable in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
CONFIGURED - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
configureDatabase(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Handle configuration of the database the first time that Metacat starts or when it is explicitly called.
configureDataONE(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.D1Admin
  Handle configuration of the database the first time that Metacat starts or when it is explicitly called.
configureEZID(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.EZIDAdmin
  Handle configuration of the database the first time that Metacat starts or when it is explicitly called.
configureProperties(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin
  Handle configuration of the main application properties
configureQuota(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.QuotaAdmin
  Handle configuration of the quota service
configureSkins(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.SkinsAdmin
  Handle configuration of the application the first time that Metacat starts or when it is explicitly called in the url.
configureSolr(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.SolrAdmin
  Handle configuration of the solr the first time that Metacat starts or when it is explicitly called.
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
connection - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
constructDN(String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
  Constructs a DN (Distinguished Name) string for the ecoinformatics.org LDAP.
constructMetacatURL(String, int, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
  Constructs a URL to the metacat servlet.
CONTAINS - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
CONTAINS - Static variable in class edu.ucsb.nceas.metacat.QueryTerm
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
ContentTypeProvider - Class in edu.ucsb.nceas.metacat
  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
convert(Log) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter
  Convert a v2 Log object to a v1 Log object
convert(LogEntry) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.LogEntryV2toV1Converter
  Convert a v2 LogEntry object to a v1 LogEntry object
convertPermission(Permission) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
convertPermission(int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
copyFile(String, String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  Copy a file between two locations specified as strings.
copyInlineFile(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
copyPermOrderAndAccessRules(AccessSection) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Method to copy a accesssection object to a new one
CREATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
create(String, Reader) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Create an XML document into the repository, making it available for searching using the query() methods.
create(String, Reader) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Create an XML document in the repository.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Adds a new object to the Node, where the object is a science metadata object.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Adds a new object to the Node, where the object is either a data object or a science metadata object.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
create(Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
create(Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
createDate - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
createdate - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
createDocidQuery(String[]) - Static method in class edu.ucsb.nceas.metacat.DocumentIdQuery
  Create an squery using some preset values for the query parameters, only passing in the document ids to be searched.
createDocidQueryParams(String[], Hashtable) - Static method in class edu.ucsb.nceas.metacat.DocumentIdQuery
  Create an squery parameters table using an already-initialized hashtable
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Subclasses should override this method to provide the appropriate handler subclass
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNRestServlet
  Provide a CNResourceHandler subclass of D1ResourceHandler
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNRestServlet
  Provide an MNResourceHandler subclass of D1ResourceHandler
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNRestServlet
  Provide a CNResourceHandler subclass of D1ResourceHandler
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNRestServlet
  Provide an MNResourceHandler subclass of D1ResourceHandler
createHeader(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Convert a native "item" to a "record" String.
createLDAPString(String, String, Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Creates an ldap credentail string from the username, organization and dn list.
createMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  create a mapping in the identifier table
createMetacatConnection(String) - Static method in class edu.ucsb.nceas.metacat.client.MetacatFactory
  Create a new instance of a Metacat object of raccessing a server.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml200
  Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml201
  Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml210
  Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml211
  Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
  Perform the actual crosswalk.
CREATEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
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.database.DatabaseService
  Instantiate a class using the name of the class at runtime
CREATEORUPDATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
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, Writer, String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DBQuery
  Transforms a hashtable of documents to an xml or html result and sent the content to outputstream.
createResultDocument(String, QuerySpecification, Writer, String, String[], boolean, int, int, 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.database.DBConnection
  Deprecated.
  PreparedStatements are preferred so as to encourage parameter value binding
createSystemMetadata(String, boolean, boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
  Create a system metadata object for insertion into metacat
createSystemMetadata(boolean, String, boolean, boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
  Creates a system metadata object for insertion into metacat
createUsage(Usage) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
  Create a usage record for a given quota identifier in the book keeper service.
createUsage(Usage, Date) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
  Create a usage record in the usages table with the given date as the reported date If the date is null, it will create a usage record without the reported date
CreateUsageTask - Class in edu.ucsb.nceas.metacat.dataone.quota
  This class represents a task to report a creation of a usage to the remote bookkeeper server and set the reported date in the local usages table after the succeeded reporting
CreateUsageTask(Usage, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.CreateUsageTask
  Constructor
CREATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
CREATOR - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
CREATORNAME - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
CREATORS - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
CURRENTCOREINSTANCEDIR - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
currentDocidsBeingIndexed - Variable in class edu.ucsb.nceas.metacat.IndexingQueue
currentDocument - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler

## D

D1Admin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the database configuration page and the processing of the configuration values.
D1AuthHelper - Class in edu.ucsb.nceas.metacat.dataone
  This is delegate class for D1NodeService and subclasses.
D1AuthHelper(HttpServletRequest, Identifier, String, String) - Constructor for class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Each instance should correspond to a single request.
D1HttpRequest - Class in edu.ucsb.nceas.metacat.restservice
D1HttpRequest(ServletRequest) - Constructor for class edu.ucsb.nceas.metacat.restservice.D1HttpRequest
  HttpServletRequestWrapper(HttpServletRequest request)
D1NodeService - Class in edu.ucsb.nceas.metacat.dataone
D1NodeService(HttpServletRequest) - Constructor for class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Constructor - used to set the metacatUrl from a subclass extending D1NodeService
D1NodeVersionChecker - Class in edu.ucsb.nceas.metacat.dataone
  This class will contact the CN to figure out the version of the service for the given node
D1NodeVersionChecker(NodeReference) - Constructor for class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
  Constructor
D1ResourceHandler - Class in edu.ucsb.nceas.metacat.restservice
  Base class for handling D1 REST calls in Metacat
D1ResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Initializes new instance by setting servlet context,request and response
D1RestServlet - Class in edu.ucsb.nceas.metacat.restservice
  Metacat implemantation of Earthgrid (Ecogrid) REST API as a servlet.
D1RestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.D1RestServlet
D1URLFilter - Class in edu.ucsb.nceas.metacat.restservice
D1URLFilter() - Constructor for class edu.ucsb.nceas.metacat.restservice.D1URLFilter
DATA_DISTRIBUTION - Static variable in class edu.ucsb.nceas.metacat.DistributionSection
DATAACCESSLEVEL - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
DatabaseService - Class in edu.ucsb.nceas.metacat.database
DatabaseUtil - Class in edu.ucsb.nceas.metacat.util
DATACITE - Static variable in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
DataCiteMetadataFactory - Class in edu.ucsb.nceas.metacat.doi.datacite
  A factory abstract class to generate the datacite metadata (xml format) for an DOI object.
DataCiteMetadataFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
DataONEConfigUtil - Class in edu.ucsb.nceas.metacat.util
  A utility class for configuring DataONE setting
DataONEConfigUtil() - Constructor for class edu.ucsb.nceas.metacat.util.DataONEConfigUtil
DATAONEERROR - Static variable in class edu.ucsb.nceas.metacat.ReadOnlyChecker
DatapackageSummarizer - Class in edu.ucsb.nceas.metacat.annotation
DatapackageSummarizer() - Constructor for class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
DataQuery - Class in edu.ucsb.nceas.metacat.dataquery
  Class to query data
DataQuery() - Constructor for class edu.ucsb.nceas.metacat.dataquery.DataQuery
  empty constructor to initialize query
DataQuery(String) - Constructor for class edu.ucsb.nceas.metacat.dataquery.DataQuery
DATEREPORTED - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
DB_DOES_NOT_EXIST - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.util.ConfigurationUtil
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.util.DocumentUtil
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.util.MetacatUtil
DBAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the database configuration page and the processing of the configuration values.
DBConnection - Class in edu.ucsb.nceas.metacat.database
  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.database.DBConnection
  Default constructor of the DBConnection class
DBConnectionPool - Class in edu.ucsb.nceas.metacat.database
  A class represent a DBConnection pool.
DBDTDHandler - Class in edu.ucsb.nceas.metacat
  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 in edu.ucsb.nceas.metacat
  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 in edu.ucsb.nceas.metacat
  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() - Constructor for class edu.ucsb.nceas.metacat.DBQuery
  construct an instance of the DBQuery class
DBQuery(Vector) - Constructor for class edu.ucsb.nceas.metacat.DBQuery
  Construct an instance of DBQuery Class BUT accept a docid Vector that will supersede the query.printSQL() method If a docid Vector is passed in, the docids will be used to create a simple IN query without the multiple subselects of the printSQL() method Using this constructor, we just check for a docidOverride Vector in the findResultDoclist() method
DBSAXHandler - Class in edu.ucsb.nceas.metacat
  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, Date, Date, boolean) - 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 in edu.ucsb.nceas.metacat
  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 in edu.ucsb.nceas.metacat
  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 in edu.ucsb.nceas.metacat
  A Class that transforms XML documents utitlizing XSL style sheets Building a transformer from the .xsl is expensive, so Templates are used as an intermediate construct to allow lightweight construction of Transformers.
DBTransform() - Constructor for class edu.ucsb.nceas.metacat.DBTransform
  construct a DBTransform instance.
DBUtil - Class in edu.ucsb.nceas.metacat
  A suite of utility classes for querying DB
DBUtil() - Constructor for class edu.ucsb.nceas.metacat.DBUtil
  Construct an instance of the utility class
DBValidate - Class in edu.ucsb.nceas.metacat
  Name: DBValidate.java Purpose: A Class that validates XML documents This class is designed to be parser independent i.e.
DBValidate() - Constructor for class edu.ucsb.nceas.metacat.DBValidate
  Construct a new validation object
DBValidate(String) - Constructor for class edu.ucsb.nceas.metacat.DBValidate
  Construct a new validation object using an OASIS catalog file
DBValidate(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBValidate
  Construct a new validation object using a database entity resolver
DBVersion - Class in edu.ucsb.nceas.metacat.database
DBVersion(String) - Constructor for class edu.ucsb.nceas.metacat.database.DBVersion
  Create a database version.
dcterms - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
dcterms_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
DECLARATIONHANDLERPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
decode(String) - Static method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  A method to decode the given string which is a part of a uri.
DEFAULT_CN_URI - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
DEFAULT_ENCODING - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
DEFAULT_QUOTA_ID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
DEFAULT_REMOTE_USAGE_ID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
DefaultDataCiteFactory - Class in edu.ucsb.nceas.metacat.doi.datacite
  Default factory to generate a simple datacite metadata xml string
DefaultDataCiteFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
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 - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  HTTP Verb DELETE
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Deletes an object from the Coordinating Node
delete(String, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Deletes an object from the Member Node, where the object is either a data object or a science metadata object.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Deletes an object from the Member Node, where the object is either a data object or a science metadata object.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
delete(String, String, String[], String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Archive an object from the xml_documents table to the xml_revision table (including other changes as well).
delete(String, boolean, String, String[], String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Archive an object from the xml_documents table to the xml_revision table (including other changes as well).
DELETE - Static variable in class edu.ucsb.nceas.metacat.EventLog
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
DELETE - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  HTTP Verb DELETE
delete(String, String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
  Deletes given docid from the spatial cache.
DELETE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
DELETE_SCHEDULED_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
deleteAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
deleteAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
DELETED - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
DELETEDMESSAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
deleteDocument(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Given a docid, will attempt to delete it from spatial cache
deleteFromFileSystem(String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Deletes a doc or data file from the filesystem using the accession number.
deleteInlineFiles() - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
deleteInlineFiles() - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
DELETEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
deleteObject(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Delete an XML document in the repository.
deleteObject(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Delete an XML document in the repository.
deleteRelations(String) - Method in class edu.ucsb.nceas.metacat.RelationHandler
  Deletes all of the relations with a docid of 'docid'.
deleteReplica(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Delete the replica entry with the given nodeId for the given pid
deleteReplica(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Delete the replica entry with the given nodeId for the given pid
deleteReplicationMetadata(Session, Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Deletes the replica from the given Member Node NOTE: MN.delete() may be an "archive" operation.
deleteReplicationMetadata(Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
deleteReplicationMetadata(Session, Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
deleteSystemMetadata(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
deleteTempFile(File) - Static method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
  Delete a temp file either immediately or on program exists according to the configuration
deleteUsage(int, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
  Delete the usage with the given quota type and instance id in the remote book keeper service
deleteUsage(int, String, double) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
  Delete a usage associated with the given quota id in the remote book keeper server.
DeleteUsageTask - Class in edu.ucsb.nceas.metacat.dataone.quota
  This class represents a thread task to report an event to delete of an exiting usage to the remote bookkeeper server.
DeleteUsageTask(Usage, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.DeleteUsageTask
  Constructor
deleteXMLAccessForDoc(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Delete xml access.
deleteXMLAccessForDoc(String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Delete xml access.
deleteXMLQueryresulForDoc(String) - Method in class edu.ucsb.nceas.metacat.XMLQueryresultAccess
  Delete xml access.
DELIMITER - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
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.
describe(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  This method provides a lighter weight mechanism than getSystemMetadata() for a client to determine basic properties of the referenced object.
describe(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
describe(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
describe(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
describe(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
DESCRIPTIONS - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
destroy() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
  When the thread is destroyed, sets the Harvester.keepRunning flag to false.
destroy() - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
destroy() - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
  Close all db connections from the pool
destroy() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
destroy() - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
destroy() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Closes the database connection.
destroy() - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
DetailedFileInputStream - Class in edu.ucsb.nceas.metacat.restservice.multipart
  A FileInputStream class with more information, such as the object of source file itself and the expected checksum of the source file.
DetailedFileInputStream(File, Checksum) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
  Constructor
determine(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
  Determine the quota type and instance id from the object format information in the system metadata
discoverApplicationContext(ServletContext) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Attempt to discover the context for this application.
discoverDeployDir(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Attempt to discover the deployment directory for this application.
discoverExternalDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Attempt to discover the external (to the metacat installation) directory where metacat will hold backup files.
discoverServerName(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Attempt to discover the server name.
discoverServerPort(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Attempt to discover the server port.
discoverServerSSLPort(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Attempt to discover the server ssl port.
DistributionSection - Class in edu.ucsb.nceas.metacat
  A Class that represents an XML access rule.
DistributionSection(int) - Constructor for class edu.ucsb.nceas.metacat.DistributionSection
doAdminAuthorization(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Does MN/CN admin authorization
doAuthoritativeMNAuthorization(Session, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Does local and AuthMN admin authorization
doBypass() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Determine if the system is configured to bypass configuration.
doBypass() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
doBypass() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Determine if the system is configured to bypass configuration.
doBypass() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
docid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
docid - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
docid - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
docid - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
docId - Variable in class edu.ucsb.nceas.metacat.SubTree
docname - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
DOCNAME - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
docname - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
docname - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
doCNOnlyAuthorization(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Does only localNode(CN)/CN authorization
doctype - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
doctype - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
doctype - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
docType - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
Document() - Constructor for class edu.ucsb.nceas.metacat.MetacatResultSet.Document
DocumentCart - Class in edu.ucsb.nceas.metacat.cart
DocumentCart() - Constructor for class edu.ucsb.nceas.metacat.cart.DocumentCart
DocumentIdentifier - Class in edu.ucsb.nceas.metacat
  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.
DocumentIdQuery - Class in edu.ucsb.nceas.metacat
  Generate a pathquery document representing a metacat query for a list of document IDs.
DocumentIdQuery() - Constructor for class edu.ucsb.nceas.metacat.DocumentIdQuery
DocumentImpl - Class in edu.ucsb.nceas.metacat
  A class that represents an XML document.
DocumentImpl() - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
  Default constructor
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, Date, Date) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
  Construct a new document instance, writing the contents to the database.
DocumentImplWrapper - Class in edu.ucsb.nceas.metacat
  This class a wrapper class for documentimpl for insert or update.
DocumentImplWrapper(String, boolean, boolean) - Constructor for class edu.ucsb.nceas.metacat.DocumentImplWrapper
  Constructor of DocumentImpleWrapper
DocumentNotFoundException - Exception in edu.ucsb.nceas.metacat.client
  Exception thrown when the requested docid does not exist on the server
DocumentNotFoundException(String) - Constructor for exception edu.ucsb.nceas.metacat.client.DocumentNotFoundException
  Create a new InsufficientKarmaException.
DOCUMENTTABLE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
DocumentUtil - Class in edu.ucsb.nceas.metacat.util
  A suite of utility classes for the metadata catalog server
DocumentUtil() - Constructor for class edu.ucsb.nceas.metacat.util.DocumentUtil
doDelete(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Handle "DELETE" method requests from HTTP clients
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
  Handle "GET" method requests from HTTP clients
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
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.oaipmh.provider.server.OAIHandler
  Peform the http GET action.
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.spatial.SldFactory
  Handle "GET" method requests from HTTP clients
doGetSysmetaAuthorization(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  used by getSystemMetadata, describe, and getPackage, the latter two by delegation to getSystemMetadata Very similar to doIsAuthorized, but also allows replica nodes administrative access.
doHead(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Handle "PUT" method requests from HTTP clients
DOI - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
DOI_SCHEME - Static variable in class edu.ucsb.nceas.metacat.dataone.MNodeService
doiEnabled - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
DOIException - Exception in edu.ucsb.nceas.metacat.doi
  An exception that encapsulates errors from the DOI service.
DOIException(String) - Constructor for exception edu.ucsb.nceas.metacat.doi.DOIException
  Constructor
doIsAuthorized(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Performs all authorization steps used by isAuthorized.
DOIService - Class in edu.ucsb.nceas.metacat.doi
  An abstract class for the DOI service
DOIService() - Constructor for class edu.ucsb.nceas.metacat.doi.DOIService
  Constructor
DOIServiceFactory - Class in edu.ucsb.nceas.metacat.doi
  A factory class to initialize an instance of DOIService based on the configuration in the metacat.properties file
DOIServiceFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.DOIServiceFactory
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
  Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchServlet
  Executes an advanced search.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.BrowseServlet
  Executes a browse-based simple search.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginServlet
  Executes a metacat login action.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.SearchServlet
  Executes a simple search.
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.
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.oaipmh.provider.server.OAIHandler
  Perform a POST action.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.spatial.SldFactory
  Handle "POST" method requests from HTTP clients
doPut(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Handle "PUT" method requests from HTTP clients
doRefresh() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
doRefresh() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Refresh the Hazelcast service by restarting it
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
doRefresh() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
doRefresh() - Method in class edu.ucsb.nceas.metacat.service.SessionService
doRefresh() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  refresh the persistant values in this service.
doRefresh() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
doTransform(StreamSource, StreamResult, Transformer, Hashtable<String, String[]>, String, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
  Reads skin's config file if it exists, and populates Transformer paramaters with its contents.
doUpdateAuth(Session, SystemMetadata, Permission, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  The locus of updates is limited to the authoritativeMN.
download() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
download() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Streams the completed bag to the caller.
DOWNLOAD_ACTION - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
DTD - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
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
ECOLOGICAL_METADATA_LANGUAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
editCart(String, String[], Map) - Method in class edu.ucsb.nceas.metacat.cart.CartManager
editScienceMetadata(Session, InputStream, Identifier, Identifier, boolean, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Update a science metadata document with its new Identifier
edu.ucsb.nceas.dbadapter - package edu.ucsb.nceas.dbadapter
edu.ucsb.nceas.metacat - package edu.ucsb.nceas.metacat
edu.ucsb.nceas.metacat.accesscontrol - package edu.ucsb.nceas.metacat.accesscontrol
edu.ucsb.nceas.metacat.admin - package edu.ucsb.nceas.metacat.admin
edu.ucsb.nceas.metacat.admin.upgrade - package edu.ucsb.nceas.metacat.admin.upgrade
edu.ucsb.nceas.metacat.admin.upgrade.dataone - package edu.ucsb.nceas.metacat.admin.upgrade.dataone
edu.ucsb.nceas.metacat.admin.upgrade.solr - package edu.ucsb.nceas.metacat.admin.upgrade.solr
edu.ucsb.nceas.metacat.advancedsearch - package edu.ucsb.nceas.metacat.advancedsearch
edu.ucsb.nceas.metacat.annotation - package edu.ucsb.nceas.metacat.annotation
edu.ucsb.nceas.metacat.authentication - package edu.ucsb.nceas.metacat.authentication
edu.ucsb.nceas.metacat.cart - package edu.ucsb.nceas.metacat.cart
edu.ucsb.nceas.metacat.client - package edu.ucsb.nceas.metacat.client
edu.ucsb.nceas.metacat.client.rest - package edu.ucsb.nceas.metacat.client.rest
edu.ucsb.nceas.metacat.clientview - package edu.ucsb.nceas.metacat.clientview
edu.ucsb.nceas.metacat.database - package edu.ucsb.nceas.metacat.database
edu.ucsb.nceas.metacat.dataone - package edu.ucsb.nceas.metacat.dataone
edu.ucsb.nceas.metacat.dataone.convert - package edu.ucsb.nceas.metacat.dataone.convert
edu.ucsb.nceas.metacat.dataone.hazelcast - package edu.ucsb.nceas.metacat.dataone.hazelcast
edu.ucsb.nceas.metacat.dataone.quota - package edu.ucsb.nceas.metacat.dataone.quota
edu.ucsb.nceas.metacat.dataone.resourcemap - package edu.ucsb.nceas.metacat.dataone.resourcemap
edu.ucsb.nceas.metacat.dataone.v1 - package edu.ucsb.nceas.metacat.dataone.v1
edu.ucsb.nceas.metacat.dataquery - package edu.ucsb.nceas.metacat.dataquery
edu.ucsb.nceas.metacat.doi - package edu.ucsb.nceas.metacat.doi
edu.ucsb.nceas.metacat.doi.datacite - package edu.ucsb.nceas.metacat.doi.datacite
edu.ucsb.nceas.metacat.doi.ezid - package edu.ucsb.nceas.metacat.doi.ezid
edu.ucsb.nceas.metacat.doi.osti - package edu.ucsb.nceas.metacat.doi.osti
edu.ucsb.nceas.metacat.download - package edu.ucsb.nceas.metacat.download
edu.ucsb.nceas.metacat.event - package edu.ucsb.nceas.metacat.event
edu.ucsb.nceas.metacat.harvesterClient - package edu.ucsb.nceas.metacat.harvesterClient
edu.ucsb.nceas.metacat.index - package edu.ucsb.nceas.metacat.index
edu.ucsb.nceas.metacat.lsid - package edu.ucsb.nceas.metacat.lsid
edu.ucsb.nceas.metacat.oaipmh.harvester - package edu.ucsb.nceas.metacat.oaipmh.harvester
edu.ucsb.nceas.metacat.oaipmh.provider.server - package edu.ucsb.nceas.metacat.oaipmh.provider.server
edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog - package edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog
edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk - package edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
edu.ucsb.nceas.metacat.object.handler - package edu.ucsb.nceas.metacat.object.handler
edu.ucsb.nceas.metacat.plugin - package edu.ucsb.nceas.metacat.plugin
edu.ucsb.nceas.metacat.properties - package edu.ucsb.nceas.metacat.properties
edu.ucsb.nceas.metacat.replication - package edu.ucsb.nceas.metacat.replication
edu.ucsb.nceas.metacat.restservice - package edu.ucsb.nceas.metacat.restservice
edu.ucsb.nceas.metacat.restservice.multipart - package edu.ucsb.nceas.metacat.restservice.multipart
edu.ucsb.nceas.metacat.restservice.v1 - package edu.ucsb.nceas.metacat.restservice.v1
edu.ucsb.nceas.metacat.restservice.v2 - package edu.ucsb.nceas.metacat.restservice.v2
edu.ucsb.nceas.metacat.service - package edu.ucsb.nceas.metacat.service
edu.ucsb.nceas.metacat.shared - package edu.ucsb.nceas.metacat.shared
edu.ucsb.nceas.metacat.spatial - package edu.ucsb.nceas.metacat.spatial
edu.ucsb.nceas.metacat.util - package edu.ucsb.nceas.metacat.util
edu.ucsb.nceas.protocols.metacat - package edu.ucsb.nceas.protocols.metacat
edu.ucsb.nceas.shared.xsd - package edu.ucsb.nceas.shared.xsd
elementDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of element declarations
ElementNode - Class in edu.ucsb.nceas.metacat
  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
EML200 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
Eml200 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
  Provides eml-2.0.0 documents.
Eml200(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml200
  The constructor assigns the schemaLocation associated with this crosswalk.
Eml200SAXHandler - Class in edu.ucsb.nceas.metacat
  A database aware Class implementing callback methods 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, Date, Date, boolean, Vector<String>) - 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
Eml201 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
  Provides eml-2.0.1 documents.
Eml201(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml201
  The constructor assigns the schemaLocation associated with this crosswalk.
EML201DocumentCorrector - Class in edu.ucsb.nceas.metacat
  Before Metacat 1.8.1 release, Metacat uses the eml201 schema with the tag RELEASE_EML_2_0_1_UPDATE_5.
EML201DocumentCorrector() - Constructor for class edu.ucsb.nceas.metacat.EML201DocumentCorrector
  Default constructor
EML210 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
Eml210 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
  Provides eml-2.1.0 documents.
Eml210(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml210
  The constructor assigns the schemaLocation associated with this crosswalk.
Eml210SAXHandler - Class in edu.ucsb.nceas.metacat
  A database aware Class implementing callback methods for the SAX parser to call when processing the XML stream and generating events
Eml210SAXHandler(DBConnection, String, String, String, String, String[], String, int, Date, Date, boolean, Vector<String>) - 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 update
Eml211 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
  Provides eml-2.1.1 documents.
Eml211(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml211
  The constructor assigns the schemaLocation associated with this crosswalk.
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
EML2_1_1NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
EML2_2_0NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
EML2DataCiteFactory - Class in edu.ucsb.nceas.metacat.doi.datacite
  A factory to generate data cite meta data for the scientific meta data standards - eml-2.*
EML2DataCiteFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
EML2KEYWORD - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
Eml2oai_dc - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
  Convert native "item" to oai_dc.
Eml2oai_dc(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
  The constructor assigns the schemaLocation associated with this crosswalk.
EMLVersionsTransformer - Class in edu.ucsb.nceas.metacat.util
  A Class that transforms older eml version to newer eml version utitlizing XSL style sheets.
EMLVersionsTransformer() - Constructor for class edu.ucsb.nceas.metacat.util.EMLVersionsTransformer
  Public constructor because all methods are static and do not need an instance.
EN - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
enableAppendLdapGroups - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
enableSessionFromHeader - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
encoding - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
endCDATA() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
  SAX Handler that receives notification of the end of CDATA sections
endCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of the end of CDATA sections
endDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of end of the document
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
endDocument() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
endDTD() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
  SAX Handler that receives notification of end of DTD
endDTD() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of end of DTD
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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.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.MetacatResultSet
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.replication.ReplMessageHandler
  This method write the indivUpdate to updates when it finds the end of
endEntity(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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
ENDS_WITH - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
endTag - Static variable in class edu.ucsb.nceas.metacat.util.ReplicationUtil
enforce(String, Subject, String, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.PortalQuotaService
enforce(String, Subject, String, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
  The method will be implemented by the child classes to enforce the quota service
enforce(String, Subject, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
  Enforce quota service
entryAdded(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Implement the EntryListener interface for Hazelcast, reponding to entry added events in the hzSystemMetadata map.
entryEvicted(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Implement the EntryListener interface for Hazelcast, reponding to entry evicted events in the hzSystemMetadata map.
entryRemoved(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Implement the EntryListener interface for Hazelcast, reponding to entry removed events in the hzSystemMetadata map.
entryUpdated(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Implement the EntryListener interface for Hazelcast, reponding to entry updated events in the hzSystemMetadata map.
equals(AccessPolicy, AccessPolicy) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Compare two AccessPolicy objects
EQUALS - Static variable in class edu.ucsb.nceas.metacat.QueryTerm
equals(Object) - Method in class edu.ucsb.nceas.metacat.SubTree
  method from Comparator interface
equals(Object) - Method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
equals(Object) - Method in class edu.ucsb.nceas.shared.xsd.IOException
error(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of recoverable parsing errors
ERROR_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
ErrorHandledException - Exception in edu.ucsb.nceas.metacat
  Exception thrown when an error occurs in a configuration administrative class
ErrorHandledException(String) - Constructor for exception edu.ucsb.nceas.metacat.ErrorHandledException
  Create a new AdminException.
ErrorSendingErrorException - Exception in edu.ucsb.nceas.metacat.util
  Exception thrown when an error occurs in a utility method
ErrorSendingErrorException(String) - Constructor for exception edu.ucsb.nceas.metacat.util.ErrorSendingErrorException
  Create a new AdminException.
ESCAPECHAR - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
EventLog - Class in edu.ucsb.nceas.metacat
  EventLog is used to intialize and store a log of events that occur in an application.
EventLogData - Class in edu.ucsb.nceas.metacat
  A data structure holding the information to be logged about an event.
EventLogData(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.EventLogData
  Construct an EventLogData object with event log information.
EventLogFilter - Class in edu.ucsb.nceas.metacat
  This class represents a filter to prevent the events generated by some ip addresses and subjects to be logged into db
EventLogFilter() - Constructor for class edu.ucsb.nceas.metacat.EventLogFilter
  Default Construct
EXACT_MATCH - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
executeAdvancedSearch(String, Metacat, String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearch
  Builds and runs an advanced search, returning HTML result string.
executeLogin(String, Metacat) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatLogin
  Executes the Metacat login.
executeQuery(String) - Method in class edu.ucsb.nceas.metacat.dataquery.DataQuery
executeSearch(String, Metacat, String, String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearch
  Builds and runs a simple search, returning HTML result string.
executor - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
EXISTINGCORE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
existsInIdentifierTable(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Determine if the given pid exists on the identifier table.
existsInObsoletedBy(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
existsInObsoletes(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
existsInXmlLRevisionTable(String, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  IF the given localId exists on the xml_revisions table
expandPermissions(Permission) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Given a Permission, returns a list of all permissions that it encompasses Permissions are hierarchical so that WRITE also allows READ.
expandRightsHolder(Subject, Subject) - Static method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Check if the given userSession is the member of the right holder group (if the right holder is a group subject).
externalEntityDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of external entity declarations
EXTERNALNONAMESPACESCHEMALOCATIONPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
EXTERNALSCHEMALOCATIONPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
EZIDAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the ezid configuration page and the processing of the configuration values.
EzidDOIService - Class in edu.ucsb.nceas.metacat.doi.ezid
  Singleton for interacting with the EZID DOI library.
EzidDOIService() - Constructor for class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
  Constructor

## F

FailedReportingAttemptChecker - Class in edu.ucsb.nceas.metacat.dataone.quota
  This class periodically gets reporting usages which were failed to be reported to the remote book keeper service (e.g.
FailedReportingAttemptChecker(ExecutorService, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.FailedReportingAttemptChecker
  Constructor
FAILURE - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
fatalError(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of fatal parsing errors
FEDERAL_GEOGRAPHIC_DATA_COMMITTEE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
FGDC_DATA_FILE_DOCID_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
  Data Document ID location within an FGDC document.
FGDC_DATA_FILE_NAME_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
FGDC_DATA_FILE_NODES_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
  FGDC Data Document ID location within an FGDC document, relative to the "distinfo" parent node.
FGDC_DATA_FILE_QUERY_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
FGDC_DOCID_ROOT_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
FGDC_DOCID_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
  Metadata Document ID location within an FGDC document.
FGDC_FILE_NAME_XPATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
FGDC_SYSTEM_ID - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
  Identifies the FGDC DTD.
FGDCDOCTYPE - Static variable in class edu.ucsb.nceas.metacat.MetacatHandler
FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
FILECLASS - Static variable in class edu.ucsb.nceas.metacat.admin.AuthAdmin
fileNames - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
FileNotFoundException - Class in edu.ucsb.nceas.shared.xsd
FileNotFoundException() - Constructor for class edu.ucsb.nceas.shared.xsd.FileNotFoundException
FileNotFoundException(Object) - Constructor for class edu.ucsb.nceas.shared.xsd.FileNotFoundException
filler - Static variable in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
filter(EventLogData) - Method in class edu.ucsb.nceas.metacat.EventLogFilter
  Determine if the given EventLogData object will be filtered out (not logging) or not.
filterByBbox(float, float, float, float) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialQuery
  Querys all features in the spatial cache and filters based on bouding coordinates.
filterRequest(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
  Override to do any pre-qualification; return false if the response should be returned immediately, without further action.
findBoundaryString(InputStream) - Static method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  locate the boundary marker for an MMP
findDataSetDocIdForGivenDocument(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  To a given docid, found a dataset docid which contains the the given docid This will be done by searching xml_relation table If couldn't find, null will be return
findDocumentNamespace(StringReader) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Returns the namespace for an xml document.
findDocuments(HttpServletResponse, Writer, Hashtable, String, String[], String) - 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
findNamespaceAndSchemaLocalLocation(String, String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get the namespace-schemaLocation pairs string based on given formatId and namespace.
findNoNamespaceSchemaLocalLocation(String, String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get the local (official) location for a no-namespace schema based on the given format id or no-name-space schema location uri.
findNoNamespaceSchemaLocationAttr(StringReader) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get the attribute value of the noNamespaceSchemaLcation of the given xml
findSchemasInXML(StringReader) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  See if schemas have been specified in the xml:schemalocation attribute.
foaf - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
foaf_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
FORCEREPLICATEDELETE - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
FORCEREPLICATEDELETEALL - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
ForceReplicationHandler - Class in edu.ucsb.nceas.metacat.replication
  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.replication.ForceReplicationHandler
  Constructor of ForceReplicationHandler
ForceReplicationHandler(String, boolean, String) - Constructor for class edu.ucsb.nceas.metacat.replication.ForceReplicationHandler
  Use this constructor when the action is implied.
FORMAT_TYPE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
FORMATS - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
forwardRequest(HttpServletRequest, HttpServletResponse, String, Hashtable<String, String[]>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Forward a request that was received by this servlet on to another JSP page or servlet to continue handling the request.
forwardRequest(HttpServletRequest, HttpServletResponse, Hashtable<String, String[]>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Forward a request that was received by this servlet on to another JSP page or servlet to continue handling the request.
fromOAIIdentifier(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Utility method to parse the 'local identifier' from the OAI identifier
FULLSCHEMAVALIDATIONFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
FUNCTION_KEYWORD - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function keyword
FUNCTION_NAME_GETALLDOCS - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for getalldocids function
FUNCTION_NAME_GETNEXTOBJ - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for getnextobject function
FUNCTION_NAME_GETNEXTREV - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for getnextrevision function
FUNCTION_NAME_INSERT - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for insert function
FUNCTION_NAME_INSERT - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
FUNCTION_NAME_ISREGISTERED - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for isregistered function
FUNCTION_NAME_LOGIN - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for login function
FUNCTION_NAME_LOGOUT - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for logout function
FUNCTION_NAME_UPDATE - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Function name for update function
FUNCTION_NAME_UPDATE - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler

## G

geItsDataSetIdWithouAccessEntry() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
  Get the docid which it's mapped dataset doesn't has access entry
GENERAL_UTILITY_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
generateAgentResource(Subject, Model) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Generate an agent resource.
generateAnnotation(Identifier) - Method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
  Generate annotation for given metadata identifier
generateDocumentId(int) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Create a unique docid for use in inserts and updates using the default prefix from the document.accNumPrefix property.
generateDocumentId(String, int) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Create a unique docid for use in inserts and updates using the prefix that is provided.
generateDOI() - Method in class edu.ucsb.nceas.metacat.doi.DOIService
  Generate a DOI using the DOI service as configured
generateDOI() - Method in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
  Generate a DOI using the EZID service as configured
generateDOI() - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Generate a DOI using the DOI service as configured
GenerateGlobalIdentifiers - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Optionally upgrade all of the existing identifiers in the tables to be official DOIs that are assigned by a DOI registration authority.
GenerateGlobalIdentifiers() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.GenerateGlobalIdentifiers
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
generateIdentifier(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
generateIdentifier(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
generateLocalId(String, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
generateLocalId(String, int, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Given a global identifier (guid), create a suitable local identifier that follows Metacat's docid semantics and format (scope.id.rev), and create a mapping between these two identifiers.
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Method to generate the datacite meta data xml string for an object with the given system meta data.
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
  Method to generate the data cite xml document
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
  Method to generate the data cite xml document
generateNewComponent(Model, String) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Create a Resource object for the given id.
generateNewOREResource(Model, Subject, Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  This method generates a Resource object for the new ore id in the given model
GenerateORE - Class in edu.ucsb.nceas.metacat.admin.upgrade.dataone
GenerateORE() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
generateOstiMetadata(InputStream, String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Generate the OSTI document for the given eml
generateROOTDoc() - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Generate the blank DOM document for the datacite name space
generateSitemaps() - Method in class edu.ucsb.nceas.metacat.Sitemap
  Generate all of the sitemap files needed to list the URLs from this instance of Metacat, using the open sitemap format described here: http://www.sitemaps.org/protocol.html URLs are written to a one or more files and a sitemap index file is always written.
GenerateSystemMetadata - Class in edu.ucsb.nceas.metacat.admin.upgrade.dataone
GenerateSystemMetadata() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
generateSystemMetadata(List<String>, boolean, boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
  Generate SystemMetadata for any object in the object store that does not already have it.
generateXMLWithSiteURL(String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Create a xml file with the site_url element
GeoserverUtil - Class in edu.ucsb.nceas.metacat.util
GET - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  HTTP Verb GET
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Return the object identified by the given object identifier
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Return the object identified by the given object identifier
get(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
get(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
get(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
GET - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  HTTP Verb GET
get(String, Hashtable<String, String[]>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
GET_SCHEDULED_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
getAbouts(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Get the about elements from the item
getAccessControl(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
getAccessControl(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  get the access control info for a given document id.
getAccessFileIDWithRevision(String) - Static method in class edu.ucsb.nceas.metacat.RelationHandler
  Get the access file id for a package
getAccessionNumberFromEcogridIdentifier(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Eocgorid identifier will look like: ecogrid://knb/tao.1.1 The AccessionNumber tao.1.1 will be returned.
getAccessPolicy(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Lookup access policy from Metacat
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.accesscontrol.AccessSection
  Get all access rule
getAccessSection() - Method in class edu.ucsb.nceas.metacat.DistributionSection
getAccessString() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Get the access xml for all access on this docid
getAccessString(Vector<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Put together an xml representation of the objects in a given access dao list
getACL(String, String[]) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Get Access Control List information for document from db connetion.
getAction() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property action.
getAction() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
getAdministrators() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Get the administrators from metacat.properties
getAge() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the db connetion age from the object
getAllDocids(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  return a list of all docids that match a given scope.
getAllDocids(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  return a list of all docids that match a given scope.
getAllDocids(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  return a list of all docids that match a given scope.
getAllDocids(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  return a list of all docids that match a given scope.
getAllDocids(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  get the latest Accession Number from a particular scope
getAllDocidsByType(String, boolean) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  return all docids with a given doctype on all servers
getAllDocidsByType(String, boolean, int) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  return all docids with a given doctype for a given server
getAllIdentifiers() - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
getAllLocalIds() - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  return a listing of all local ids in the object store
getAllOREpids(String) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
  Retrieves a list of all ORE objects on the given MN
getAllowedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Get the allowed submitters from metacat.properties
getAllPidsInChain(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Get all pids in the series chain
getAllSystemMetadataGUIDs() - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  return a listing of all guids in the object store
getAnyfield() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property anyField.
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 class edu.ucsb.nceas.metacat.authentication.AuthFile
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
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(String) - Method in class edu.ucsb.nceas.metacat.AuthSession
  Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get attributes describing a user or group
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get attributes describing a user or group
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get attributes describing a user or group
getAttributes() - Method in class edu.ucsb.nceas.metacat.BasicNode
  Get the attributes as a string
getAttributes(Properties) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
getAuthBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get the auth backup properties file.
getAuthBackupProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getAuthBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the auth backup properties file.
getAuthBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
getAuthMetaData() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get the auth properties metadata.
getAuthMetaData() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getAuthMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the auth properties metadata.
getAuthMetaData() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
getBackupDirStatus(String) - Method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
  Find the status of the backup base directory.
getBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the main backup properties file.
getBackupProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the main backup properties file.
getBaseUrlFromSchemaURL(String) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get a base url from the schema url.
getBeanDescriptor() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
  Gets the bean's `BeanDescriptor`s.
getBytes() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
getCapabilities() - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
getCapabilities() - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Return a description of the node's capabilities and services.
getCapabilities() - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getCatalogId() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
getCatalogVect() - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
getCatalogXML() - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Returns the xml_catalog table encoded in xml
getCGI_URL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the CGI URL which is made up of the server URL + file separator + the CGI directory
getCheckOutMethodName() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the the name of method checked out the connection from the object
getCheckOutSerialNumber() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the check out serial number
getCheckOutTime() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the when a db connetion was checked out
getChecksum(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Return the checksum of the object given the identifier
getChecksum(Session, Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Returns a Checksum for the specified object using an accepted hashing algorithm
getChecksum(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getChecksum(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
getChecksum(Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getChecksum(Session, Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
getChecksum() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.CheckedFile
  Get the checksum of this file
getChildren() - Method in class edu.ucsb.nceas.metacat.BasicNode
  Get the an enumeration of the children of this node
getCNNodeList() - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  A centralized point for accessing the CN Nodelist, to make it easier to cache the nodelist in the future, if it's seen as helpful performance-wise
getCNNodeList() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  A centralized point for accessing the CN Nodelist, to make it easier to cache the nodelist in the future, if it's seen as helpful performance-wise
getCodeLevelValue(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
  Maps each code level to an integer value.
getCommonSkinsDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the style skins directory.
getConnection() - Method in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
  Gets a database connection from the pool
getConnection() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
  Returns a connection to the database.
getConnection() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Returns a connection to the database.
getConnections() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the connetion from the object
getConnectionTime() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the how long db connetion used for the object
getContentStandard() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property contentStandard.
getContentType() - Method in class edu.ucsb.nceas.metacat.ContentTypeProvider
  Method to get content type
getContentType() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
getContentWithoutSystemMetadata(String) - Static method in class edu.ucsb.nceas.metacat.util.ReplicationUtil
  return the string WITHOUT the contents between start and end tag
getContextDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the context directory.
getContextURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the server URL with the context.
getControlLevel() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Get controllevel
getCookie(HttpServletRequest, String) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Get a cookie from a request by the cookie name
getCoreMessage() - Method in exception edu.ucsb.nceas.metacat.shared.BaseException
getCoreMetadataIdentifiers() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Returns the core metadata identifiers
getCreateDate() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  get the creation date
getCreateTime() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the db connetion created time from the object
getCreationTime() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getCreatorOrganization() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getCreatorOrganizationQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getCreatorSurname() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getCreatorSurnameQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getCurrentNodeId() - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
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"
getD1Report(String[], String[], String[], String, Timestamp, Timestamp, boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.EventLog
getData(LSIDRequestContext) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
getDatabaseConnectionPoolInterface() - Static method in class edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory
getDataByRange(LSIDRequestContext, int, int) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
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.
getDataFileName() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Get the dataFileName
getDataFileName(int) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Indexed getter for property dataFileNames.
getDataFileName() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property dataFileNames.
getDataFileName() - Method in class edu.ucsb.nceas.metacat.DistributionSection
  Get the online data file name
getDataLocations(LSID, String) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
getDataReplication() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Get datareplication xml or not option
getDataReplicationValue(String) - Method in class edu.ucsb.nceas.metacat.replication.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
getDateField() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getDatestamp(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  get the datestamp from the item
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()"
getDBAdapter() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
  gets the database adapter
getDBAdapterName() - Method in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
  Get dabase adpater name.
getDBConnection(String) - Static method in class edu.ucsb.nceas.metacat.database.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.
getDBStatus() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Performs a status check on the database.
getDBVersion() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Get the version of the database as a string
getDefaultEventIndex() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
  A bean may have a "default" event that is the event that will mostly commonly be used by human's when using the bean.
getDefaultPropertyIndex() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
  A bean may have a "default" property that is the property that will mostly commonly be initially chosen for update by human's who are customizing the bean.
getDefaultQueryParams() - Static method in class edu.ucsb.nceas.metacat.DocumentIdQuery
  Create a paramter list containing default parameters for a query
getDefaultReplicationPolicy() - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
  Create a default ReplicationPolicy by reading properties from metacat's configuration and using those defaults.
getDefaultStyleURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the default style URL from metacat.properties.
getDeletesVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
getDeniedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Get the denied submitters from metacat.properties
getDescribedIdList() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Get a described id list
getDeserializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
  Get Custom Deserializer
getDeserializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.IOException
  Get Custom Deserializer
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.
getDistributionId() - Method in class edu.ucsb.nceas.metacat.DistributionSection
  Get the access type
getDistributionType() - Method in class edu.ucsb.nceas.metacat.DistributionSection
  Get the access type
getDocHomeServer() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
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.BasicNode
  Get the doc id of this node
getDocId() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property docId.
getDocID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  Get the document identifier (docid)
getDocid() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
getDocid() - Method in class edu.ucsb.nceas.metacat.EventLogData
  Get the current value of the document identifier.
getDocId() - Method in class edu.ucsb.nceas.metacat.SubTree
  Get the docId
getDocIdFromAccessionNumber(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  This method will get docid from an AccessionNumber.
getDocIdFromInlineDataID(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Method to get docidwithrev from eml2 inline data id The eml inline data id would look like eml.200.2.3
getDocIdFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Utility method to get docid from a given string
getDocids() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getDocIdWithoutRevsion() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
  Method to get docidWithout revision
getDocIdWithRevFromOnlineURL(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Get docid from online/url string
getDocname() - Method in class edu.ucsb.nceas.metacat.accesscontrol.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)
getDoctype() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
getDocType(LSID) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
getDocType() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
  Method to get docType
getDocument() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Get the OAI response as a DOM object
getDocumentCart() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getDocumentInfo(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Gets a docInfo XML snippet for the replication API
getDocumentInfoMap(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
getDocumentName() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
getDocuments() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
getDocumentType() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
getDOIService() - Static method in class edu.ucsb.nceas.metacat.doi.DOIServiceFactory
  Get a singleton instance of DOIService
getDownloadNewSchema() - Method in class edu.ucsb.nceas.metacat.SchemaLocationResolver
  Gets the downloadNewSchema's value.
getEastBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getEncoding() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Returns the character encoding used used when communicating with Metacat.
getEncoding() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
getEncoding() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
getEndDate() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getEndNodeId() - Method in class edu.ucsb.nceas.metacat.SubTree
  Get end node id
getErrors() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Get the OAI errors
getEvent() - Method in class edu.ucsb.nceas.metacat.EventLogData
  Get the current value of the event.
getEventSetDescriptors() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
  Gets the bean's `EventSetDescriptor`s.
getException() - Method in exception edu.ucsb.nceas.metacat.McdbException
  Get the tunneled Exception
getExpectedChecksum() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
  Get the expected checksum of the source file
getExplanation(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
  Returns an explanation string based on the value of a harvestOperationCode string.
getExternalFileUri() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Gets the external file uri
getField(String) - Method in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
getFields(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getFields() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getFile() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
  Get the source file
getFileName() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Gets the file name
getFileNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Gets the file namespace
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.
getFormAllAny() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getFormat(ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Returns the object format registered in the DataONE Object Format Vocabulary for the given format identifier
getFormat(ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.dataone.ObjectFormatService
  Return the object format based on the given object format identifier
getFormat(ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getFormatId() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Get the format id
getGeoserverContextURL() - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
  Get the server URL with the Geoserver context.
getGroupNames(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Gets the user group names from the login session on the http request
getGroupNames() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
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
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthSession
  Get the all groups in which the given userDN is
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get all groups from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get the groups for a particular user from the authentication service
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get all groups from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get the groups for a particular user from the authentication service
getGroups() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
getGUID(String, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  given a local identifer, look up the guid.
getGUIDs(String, String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Get the list of identifiers which system metadata matches the given format id and original member node id and guid or series id start with the scheme (doi for example).
getHandler(String) - Method in class edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager
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.
getHazelcastInstance() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
getHeadPID(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Get the pid of the head (current) version of objects match the specified sid.
getHomeServerCodeForDocId(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Returns a home server location given a accnum
getHomeServerInfoForDocId(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Method to get a host server information for given docid
getHub() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Get hub option
getHubValue(String) - Method in class edu.ucsb.nceas.metacat.replication.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
getId() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getIdentifier() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
  returns
getIdentifier() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.GetRecord
  Get the oai:identifier from the oai:header
getIdentifier() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Accessor method to return the identifier of this Query
getIdentifiers() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Get the identifiers set
getIncludedSchemaFilePathes() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaParser
  Get the included schema file paths in this schema
getIndexEventMap() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Get the index event map
getIndexFields(Identifier, String) - Method in class edu.ucsb.nceas.metacat.EventLog
getIndexQueue() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Get the index queue
getInlineDataIdWithoutRev(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  This method will get inline data id without the revision number.
getInputStream() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.AuthAdmin
  Get the single instance of the MetaCatConfig.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
  Get the single instance of BackupAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.D1Admin
  Get the single instance of D1Admin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Get the single instance of DBAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.EZIDAdmin
  Get the single instance of EZIDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.LoginAdmin
  Get the single instance of LoginAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin
  Get the single instance of the MetaCatConfig.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.QuotaAdmin
  Get the single instance of QuotaDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.ReplicationAdmin
  Get the single instance of D1Admin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.SkinsAdmin
  Get the single instance of the MetaCatConfig.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.SolrAdmin
  Get the single instance of SolrDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.ArchiveHandler
  Get the single instance of SessionService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.database.DatabaseService
  Get the single instance of DatabaseService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
  Returns the single instance, creating one if it's the first time this method is called.
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  singleton accessor
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Get the instance of the HazelcastService that has been instantiated, or instantiate one if it has not been already.
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Get an instance of MNodeService.
getInstance(HttpServletRequest, String, String) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Get an instance of MNodeService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.ObjectFormatService
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
  Get the singleton instance of the BookKeeplerClient class
getInstance(ExecutorService, BookKeeperClient) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.PortalQuotaService
  Get a singleton class instance
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
  Get the singleton instance of the service
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  singleton accessor
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Singleton accessor to get an instance of MNodeService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.event.MetacatEventService
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.
getInstance() - Static method in class edu.ucsb.nceas.metacat.IdentifierManager
  Return the single instance of the manager after initializing it if it wasn't previously initialized.
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler
  Get an instance of the class.
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
getInstance() - Static method in class edu.ucsb.nceas.metacat.IndexingQueue
getInstance() - Static method in class edu.ucsb.nceas.metacat.MetacatProfiler
  get a singleton instance
getInstance() - Static method in class edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager
getInstance(ServletContext) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the single instance of PropertyService.
getInstance(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the single instance of PropertyService for test purposes.
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the single instance of PropertyService for test purposes.
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the single instance of SkinPropertyService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Get the single instance of SessionService.
getInstance(ServletContext) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
  Get the single instance of ServiceService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.service.SessionService
  Get the single instance of SessionService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get the single instance of XMLService.
getInstanceId() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
  Get the instance id determined in the determine method
getInternalContextURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the internal context url.
getInternalServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the internal server URL.
getIpAddress() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Get the ip address from the service
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
getIsRevisionDoc() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  get the the is revision doc
getKnownURIs() - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
getLabels() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getLandingPage(Identifier) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
  Get the landing page url string for the given identifier
getLastAccessedTime() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getLastCheckedDate() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Get last checked date
getLastCheckedDate(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  To a given server name, try to get its lastcheck date.
getLastDocid(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Return the highest document id for a given scope.
getLastDocid(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Return the highest document id for a given scope.
getLastModifiedDate() - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  returns a list of system metadata-only guids since the given date
getLatestRevForLocalId(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  return the newest rev for a given localId
getLatestRevisionInDocumentTable(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  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
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
  Syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
  The Oracles's syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
  PostgreSQL's syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
  MSSQL's syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLocalFileDir() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Gets the local file directory path
getLocalFileUri() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Gets the local file uri
getLocalId() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Get the local id associated with the local usage
getLocalId(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Lookup a localId given the GUID.
getLocalIdentifier(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Extract the local identifier from the native item
getLocalIdsWithNoSystemMetadata(boolean, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  return all local ids in the object store that do not have associated system metadata
getLocalReplicationServerName() - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  Method to get the name of local replication server
getLocationName() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getLock(String) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
getloggedinuserinfo() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Get the logged in user for this session.
getloggedinuserinfo() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Method used to log in to a metacat server.
getLogRecords(Session, Date, Date, String, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Return the log records associated with a given event between the start and end dates listed given a particular Subject listed in the Session
getLogRecords(Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getLogRecords(Session, Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
getLogRecords(Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getLogRecords(Session, Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
getLSID(XSLProcessorContext, ElemExtensionCall) - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
  get the current LSID for the given thread, for use in XSLT so return a string
getLSID() - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
getMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get the main backup properties file.
getMainBackupProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getMainBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the main backup properties file.
getMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
getMainMetaData() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get the main properties metadata.
getMainMetaData() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getMainMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get the main properties metadata.
getMainMetaData() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
getMaxDateUpdated() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Get the most recent date that the xml_documents table was updated
getMaxDocid(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
  get the latest Accession Number from a particular scope
getMaxRevFromRevisionTable(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  Method to return max rev number in xml_revision for given docid.
getMessage() - Method in class edu.ucsb.nceas.metacat.AuthSession
  Get the message associated with authenticating this session.
getMessage(int) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Indexed getter for property message.
getMessage() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property message.
getMessage() - Method in exception edu.ucsb.nceas.metacat.McdbException
  Get the message from this exception.
getMetacatAuthenticatedEcogridEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
  Gets the end point which Metacat implements authenticated ecogrid interface.
getMetacatClient(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.client.MetacatClient
  JSP API: This is a convenience method to reduce the amount of code in a Metacat Client JSP.
getMetacatClient() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getMetacatEcogridAuthEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
getMetacatEcogridEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
  Gets the end point which Metacat implements ecogrid interface.
getMetacatEcogridIdentifierEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
getMetacatEcogridPutEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
getMetacatReleaseInfo() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Gets a string that holds some description about the release.
getMetacatRunning() - Method in class edu.ucsb.nceas.metacat.IndexingQueue
getMetacatVersion() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the metacat version by getting the string representation from metacat.properties and instantiating a MetacatVersion object.
getMetaData() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Method to get meta data
getMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Get the metadata for the given identifier
getMetadata(LSIDRequestContext, String[]) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
getMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the main properties metadata.
getMetaData(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the main properties metadata.
getMetadataDoc() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getMetadataFormatsQueryString() - Method in class edu.ucsb.nceas.metacat.Sitemap
  Generate a comma-separated list of metadata format IDs so generateSitemaps can filter the available objects to just metadata objects.
getMetadataLocations(LSID, String) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
getMetaFileDocId() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property isMetaFileDocId.
getMetaFileName() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property metaFileName.
getMethodDescriptors() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
  Gets the bean's `MethodDescriptor`s.
getModerators() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Get the moderators from metacat.properties
getName() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
getName() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getNamedTimescale() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getNamedTimescaleQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getNamespace(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
  Get an uri of the namespace prefix
getNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
  Get the namespace of the document (root element).
getNameSpaceAndLocation(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get the all schema-location pairs registered for the formatId.
getNameSpaceAndLocationStringWithoutFormatId() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Gets the name space and location string.
getNameSpaceList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Gets a list of name spaces.
getNewestDocRevision(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  The method will return the latest 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 latest revision in metacat server for a given document id.
getNext() - Method in class edu.ucsb.nceas.metacat.IndexingQueue
getNextObject(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Return the highest document id for a given scope.
getNextObject(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Return the highest document id for a given scope.
getNextRevision(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  The method will return the latest revision in metacat server for a given document id.
getNextRevision(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  The method will return the latest revision in metacat server for a given document id.
getNode(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
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
getNodeDataDate() - Method in class edu.ucsb.nceas.metacat.NodeRecord
getNodeDataNumerical() - Method in class edu.ucsb.nceas.metacat.NodeRecord
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
getNodeList(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Get a NodeList containing the nodes in the response DOM for the specified xpath
getNodeName() - Method in class edu.ucsb.nceas.metacat.NodeRecord
getNodePrefix() - Method in class edu.ucsb.nceas.metacat.NodeRecord
getNodeText(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getNodeTextList(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getNodeTextStack(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getNodeType() - Method in class edu.ucsb.nceas.metacat.BasicNode
  Get the type of this node
getNodeType() - Method in class edu.ucsb.nceas.metacat.NodeRecord
getNoNamespaceSchemaLocation() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
  Get the value of noNamespaceSchemaLocation of the document (root element).
getNoNamespaceSchemaLocation() - Method in class edu.ucsb.nceas.metacat.service.XMLNoNamespaceSchema
  Get the no-namespace-schemal-location uri
getNonXMLMetadataFormatList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get the list of format ids which are the non-xml metadata type
getNormalizedXMLQuery() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Gets normailized query string in xml format, which can be transformed to html
getNorthBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getNotFoundDataSetId() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
  Get the docid which didn't found a dataset id to map it
getOAIIdentifier(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Construct an OAI identifier from the native item
getOAIIdentifierOld(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Construct an OAI identifier from the native item
getObject(String, String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Read a public XML document , accessed by docid, and returned as a Reader.
getObject(String, String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Read a public XML document , accessed by docid, and returned as a Reader.
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Implements REST version of DataONE CRUD API --> get
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
  Implements REST version of DataONE CRUD API --> get
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Implements REST version of DataONE CRUD API --> get
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Implements REST version of DataONE CRUD API --> get
getObjectFilePath(String, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Get the the file path for the given object local id
getOperator() - Method in class edu.ucsb.nceas.metacat.DBQuery
getOptionList(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
getOrganization() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
getOrganization() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property organization.
getOrganizations() - Static method in class edu.ucsb.nceas.metacat.util.OrganizationUtil
  gets a list of organization names from metacat.properties.
getOrgDNs(String) - Static method in class edu.ucsb.nceas.metacat.util.OrganizationUtil
  gets a list of organization names from metacat.properties.
getOsClass() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the OS for this system.
getOutputStream() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
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.
getPackage(Session, ObjectFormatIdentifier, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Exports a data package to disk using the BagIt The Bagit 0.97 format corresponds to the V1 export format The Bagit 1.0 format corresponds to the V2 export format
getPackage(Session, ObjectFormatIdentifier, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getPackage(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
  Retrieve data package as Bagit zip
getPackage(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Retrieve data package as Bagit zip
getPackageId() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
  For a given site, return the packageId attribute search string for that site's EML documents.
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
  for generating a query for paging
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
getParam(int) - Method in class edu.ucsb.nceas.metacat.MetacatURL
  Returns a single parameter and value as a 1D string array.
getParameters(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Get a cookie from a request by the cookie name
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
getPassword() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
getPassword() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property password.
getPassword() - Method in class edu.ucsb.nceas.metacat.util.SessionData
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
getPathExpr() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property pathExpr.
getPathExpression() - Method in class edu.ucsb.nceas.metacat.QueryTerm
  get the path expression parameter
getPathInfo() - Method in class edu.ucsb.nceas.metacat.restservice.D1HttpRequest
  override getPathInfo to handle special characters
getPaths() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getPathsForIndexing() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get a list of xml paths that need to be indexed
getPathValue() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property pathValue.
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.accesscontrol.AccessRule
  Get permission
getPermissionOrder() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Get permissionOrder
getPermissionType() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
getPIDForSID(Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Utility method to get the PID for an SID.
getPointFeature() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDocument
  Returns a geotools (multi)point feature with geometry plus attributes ready to be inserted into our spatial dataset cache
getPointFeatureType() - Static method in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
  Creates the featuretype schema for point centroids
getPolygonFeature() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDocument
  Returns a geotools (multi)polygon feature with geometry plus attributes ready to be inserted into our spatial dataset cache
getPolygonFeatureType() - Static method in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
  Creates the featuretype schema for polygon bounds
getPrincipal() - Method in class edu.ucsb.nceas.metacat.accesscontrol.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 class edu.ucsb.nceas.metacat.authentication.AuthFile
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.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get all groups and users from authentication scheme.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get all groups and users from authentication scheme.
getProfiles() - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  return a hashtable of the profiles
getProperties() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the main backup properties file.
getProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get the main backup properties file.
getPropertiesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get a Map of all properties that start with the groupName prefix.
getPropertiesByGroup(String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getPropertiesByGroup(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get a Map of all properties that start with the groupName prefix.
getPropertiesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Get a Map of all properties that start with the groupName prefix.
getProperty(String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Utility method to get a property value from the properties file
getProperty(String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getProperty(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Utility method to get a property value from the properties file
getProperty(String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Utility method to get a property value from the properties file
getProperty(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Utility method to get a property value from the properties file for a specific skin.
getPropertyDescriptors() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
  Gets the bean's `PropertyDescriptor`s.
getPropertyNames() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get a set of all property names.
getPropertyNames() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getPropertyNames() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get a set of all property names.
getPropertyNames() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Get a set of all property names.
getPropertyNames(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get a set of all property names for a given skin.
getPropertyNamesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Get a Set of all property names that start with the groupName prefix.
getPropertyNamesByGroup(String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
getPropertyNamesByGroup(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Get a Set of all property names that start with the groupName prefix.
getPropertyNamesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Get a Set of all property names that start with the groupName prefix.
getPropertyNamesByGroup(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Get a Set of all property names that start with the groupName prefix.
getProtocol() - Method in class edu.ucsb.nceas.metacat.MetacatURL
  Returns the type of the url.
getProtocolVersion() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.Identify
  Get the oai:protocolVersion value from the Identify response
getPublicaccess() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
getPublicSession() - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Get the public session from the session hash table.
getQformat() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property qformat.
getQformat() - Method in class edu.ucsb.nceas.metacat.DBQuery
getQueryEngineDescription(Session, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
getQueryEngineDescription(Session, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
getQueryEngineDescription(String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getQueryEngineDescription(String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getQueryEngineDescritpion() - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler
  Get the QueryEngineDescription
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
getQuotaType() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Get the quota type of the usage
getQuotaType() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
  Get the quota type determined in the determine method
getRealApplicationContext() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
  Get the servlet context name
getRealConfigDir() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
  Convert the relative config directory to a full path
getRealSkinDir() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
  Convert the relative skins directory to a full path
getRecommendedExternalDir() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Returns the recommended external base directory.
GetRecord - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  This class represents an GetRecord response on either the server or on the client
GetRecord() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.GetRecord
  Mock object constructor (for unit testing purposes)
GetRecord(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.GetRecord
  Client-side GetRecord verb constructor
getRecord(String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Retrieve the specified metadata for the specified oaiIdentifier
getReferences() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Get the references
getRegisteredNoNamespaceSchemaList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Gets the registered schema list without the name space.
getRegisteredSchemaList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Gets the registered schema list.
getRegisteredSession(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Get a registered session from the session hash table.
getReplica(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Essentially a get() but with different logging behavior
getReplica(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getReplica(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
getReplication() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Get replication xml or not option
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
  This method will return the sql command to get document list in xml_document in replication.
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
  Return a hard code string to get xml_document list in timed replcation
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
  Return a hard code string to get xml_document list in timed replcation
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
  Return a hard code string to get xml_document list in timed replcation
getReplicationValue(String) - Method in class edu.ucsb.nceas.metacat.replication.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, boolean) - Method in class edu.ucsb.nceas.metacat.EventLog
  Get a report of the log events that match a set of filters.
getRequestor() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Get the requestor associated with the usage
getRequestURL() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Get the OAI request URL for this response
getResource(Model, String) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Get the Resource object which has the given identifier
getResult(HashMap, HttpServletRequest, HttpServletResponse, Transformer, HashMap) - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
getResultsetXSL(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
  Gets the path to the resultset XSL file.
getResultsJSP() - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
  Gets the relative path to the advancedsearchresults.jsp file.
getResumptionToken() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers
  Get the oai:resumptionToken from the response
getResumptionToken() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords
  Get the oai:resumptionToken from the response
getResumptionToken() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.ListSets
  Get the oai:resumptionToken from the response
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.
getReturnfield() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property returnField.
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.util.DocumentUtil
  This method will get revision from an AccessionNumber.
getRevisionStringFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Utility method to get version string from a given string
getRevisionsVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
getRevListFromRevisionTable(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
  Method to return a rev list in xml_revision for given docid.
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.DBSAXHandler
getRootNodeID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  get the root node identifier
getSchemaFileNameFromUri(String) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Get a schema file name from the schema uri.
getSchemaLocation() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
  Accessor method for the schemaLocation field.
getSchemaLocation() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Get the xsi:schemaLocation for the OAI response
getSchemaLocations(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Retrieve a list of schemaLocation values associated with the specified oaiIdentifier.
getScienceMetadataIdentifiers() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Gets all of the science metadata documents in the downloader
getScienceMetadataIds() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
getScriptSuffixes() - Static method in class edu.ucsb.nceas.metacat.util.DatabaseUtil
  Gets the available upgrade versions for metacat by getting a list of upgrade script from properties in metacat.properties that start with "database.upgradeVersion".
getSearchMode() - Method in class edu.ucsb.nceas.metacat.QueryTerm
  get the searchmode parameter
getSecureContextURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the secure server URL with the context.
getSecureServer() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the secure server which is made up of the server name + : + the https port number.
getSecureServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the secure server URL which is made up of the server name + : + the https port number.
getSelectQueryMap() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Queries Metacat for document listings, and returns the results in a TreeMap, where the key is the Doc Id, and the value is the Create Date.
getSeparator() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
  returns the separator used in the accession number
getSerializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
  Get Custom Serializer
getSerializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.IOException
  Get Custom Serializer
getServerCode(String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Given a server name, return its servercode in xml_replication table.
getServerCodeForServerName(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Returns a server code given a server name
getServerCodes() - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Returns a Map of serverCode=serverName
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
getServerlocation() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
getServerName() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Get server name
getServerName() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
  Gets the server name
getServerNameForServerCode(int) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Returns the name of a server given a serverCode
getServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the server URL which is made up of the server name + : + the http port number.
getServletURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the servlet URL.
getSession() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  retrieve the out-of-band session
getSessionData(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Get the session data from a request.
getSessionDataFromToken(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Get SessionData from the DataONE auth token
getSessionFromHeader() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Get the session from the header of the request.
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.
getSessionId() - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Get the session identifier for this session.
getSessionId() - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
getSessionid() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property sessionId.
getSessionId() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
getSessions() - Method in class edu.ucsb.nceas.metacat.AuthSession
  Get the new session
getSetSpecs(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  get the setspec from the item
getSingleString(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Get the String value for the given XPath location in the response DOM
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.
getSiteKeyword() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
  Get the keyword string for this site.
getSiteValue() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getSizeOfDBConnectionPool() - Method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
  Method to get the size of DBConnectionPool
getSkinNames() - Static method in class edu.ucsb.nceas.metacat.util.SkinUtil
  Gets a list of available skin names by parsing a csv property from metacat.properties.
getSmartDocId(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  This method will call both getDocIdFromString and getDocIdFromAccessionNumber.
getSolrUpdateClasses() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Get the list of classes that should be run to update the solr server.
getSortedReturnFieldString() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Method to return a String generated after sorting the returnFieldList Vector
getSouthBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getSQLDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the SQL directory.
getSRBEcogridEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
  Gets the end point which SRB implements ecogrid interface.
getSRBMachineName() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
  Gets the machine name which srb protocol will be used.
getStartDate() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getStartedDescribesNodeId() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Get the start described id
getStartElementName() - Method in class edu.ucsb.nceas.metacat.SubTree
  Get startElementName
getStartNodeId() - Method in class edu.ucsb.nceas.metacat.SubTree
  Get start node id
getStatus() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the db connetion status from the object
getStatus(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Get the status of the system.
getStoredBackupDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Gets the stored backup location.
getStoredTmpNodeStack() - Method in class edu.ucsb.nceas.metacat.accesscontrol.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 (')
getStringFromInputStream(InputStream) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getStringFromInputStream(InputStream) - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
getStyleCommonURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the style common URL.
getStyleSkinsDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the style skins directory.
getStyleSkinsURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the style skins URL.
getSubjectAllAny() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getSubjectField() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getSubjectQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getSubjectsOfDocumentedBy(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Get all subjects of the triple - * is documentedBy metadataId on the resource map
getSubjectsOfDocumentedBy(Identifier, Model) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Get all subjects of the triple - * is documentedBy metadataId in the given model
getSubjectValue() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getSubscriber() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Get the subscriber of the usage
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
getSubversion(int) - Method in class edu.ucsb.nceas.metacat.Version
getSystem() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
  For a given site, return system attribute search string for that site's EML documents.
getSystemID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  get the system identifier
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Return the system metadata for a given object
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Return the system metadata for a given object
getSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
getSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
getSystemMetadata(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  return a hash of all of the info that is in the systemmetadata table
getSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.MultipartRequestWithSysmeta
  Get the system meta data associate with this request
getSystemMetadataContent(String) - Static method in class edu.ucsb.nceas.metacat.util.ReplicationUtil
  return the contents between start and end tag
getSystemMetadataForPID(Identifier, String, String, String, boolean) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Get the system metadata for the given PID (not a sid).
getSystemMetadataMap() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Get the system metadata map
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Implements REST version of DataONE CRUD API --> getSystemMetadata
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
  Retrieve System Metadata
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Implements REST version of DataONE CRUD API --> getSystemMetadata
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Retrieve System Metadata
getSystemMetadataPart() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
  Get the system metadata object which was extracted from the sysmeta part.
getSystemMetadataVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
getTag() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the db connetion tag from the object
getTagName() - Method in class edu.ucsb.nceas.metacat.BasicNode
  Get the name of this node
getTaxon() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getTaxonQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getTempDirectory() - Static method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  return the directory where temp files are stored
getTextContent(XPath, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
getTransformer(String) - Static method in class edu.ucsb.nceas.metacat.DBTransform
  The method that manages the Templates Map instances that will be used to build transformers from.
getType() - Static method in class edu.ucsb.nceas.metacat.service.XMLNoNamespaceSchema
  Return the type of schema.
getType() - Static method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Return the type of the schema.
getTypeDesc() - Static method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
  Return type metadata object
getTypeDesc() - Static method in class edu.ucsb.nceas.shared.xsd.IOException
  Return type metadata object
getUnfoundDocId() - Method in exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
  Method to get the docid which couldn't be found
getUnfoundRevision() - Method in exception 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
getUnReadableInlineDataIdList(String, String, String[]) - 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.
getUnRegisteredDBVersion() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Finds the version of the database for a database that does not have a dbVersion table yet.
getUnReportedUsages() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
  Get the result set from the table which haven't been reported to the bookkeeper server.
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.
getUpdateClasses() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
getUpdateDate() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  get the update date
getUpdatedSystemMetadataIds(Date) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  returns a list of system metadata-only guids since the given date
getUpdateScripts() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Creates a list of database update script names by looking at the database version and the metacat version and then getting any script that is inbetween the two (inclusive of metacat version).
getUpdateScripts() - Method in class edu.ucsb.nceas.metacat.database.DBVersion
  Get the update script list for this version
getUpdatesVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
getUpgradeVersions() - Static method in class edu.ucsb.nceas.metacat.util.DatabaseUtil
  Gets the available upgrade versions for metacat by getting a list of upgrade script from properties in metacat.properties that start with "database.upgradeVersion".
getURLBytes(URL) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  This method returns a byte array after opening a url
getURLContent(URL) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  This method returns the content of a url
getURLStream(URL) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  This method returns the InputStream after opening a url
getUsageCount() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the db connetion usage times from the object
getUser() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
getUserAgent() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Get the user agent from the service
getUserAgent() - Method in class edu.ucsb.nceas.metacat.EventLogData
getUserHomeDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the current user's home directory
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
getUserInfo(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
  Get information for a user - name, organization and email address.
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
  Get all users from the authentication service
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get all users from the authentication service
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get all users from the authentication service
getUserManagementUrl() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Get the url pointing to the user management page.
getUsername() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
getUsername() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property userName.
getUserName(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Gets the user name from the login session on the http request
getUserName() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getUserowner() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
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
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get all users from the authentication service
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
  Get the users for a particular group from the authentication service
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  Get all users from the authentication service
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
  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(String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
  Get the version of the service name for the node.
getVERSION() - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
  Get the VERSION number
getVersionAsXml() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
  Get the version number in an XML document.
getVersionFromDB() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
  Get the version number from DB
getVersionFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Utility method to get version number from a given string
getVersionID() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
  Get the current version string for this metacat instance.
getVersionString() - Method in class edu.ucsb.nceas.metacat.Version
getWarningMessage() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  get the db connetion waring message from the object
getWestBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
getWriter(HttpServletRequest, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
  Get a response Writer depending on acceptable encodings
getXMLAccessForDoc(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Get all xml access for a document
getXMLAccessForPrincipal(String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Get all xml access for a principal for a certain document
getXMLAccessForPrincipal(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Get all xml access for a principal/permType/permOrder for a certain document
getZippedPackage(String, ServletOutputStream, String, String[], String) - Method in class edu.ucsb.nceas.metacat.DBQuery
  put a data packadge into a zip output stream
GROUPDESINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
GROUPNAMEINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
groups - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler

## H

handle(byte) - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  This function is called from REST API servlet and handles each request
handle(byte) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  This function is called from REST API servlet and handles each request to the servlet
handle(byte) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
  This function is called from REST API servlet and handles each request to the servlet
handle(byte) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  This function is called from REST API servlet and handles each request to the servlet
handle(byte) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  This function is called from REST API servlet and handles each request to the servlet
handleAction(String, Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[], String) - Method in interface edu.ucsb.nceas.metacat.plugin.MetacatHandlerPlugin
handleBuildIndexAction(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Rebuild the index for one or more documents.
handleClientRequest(MultipartParser) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Main method for handling various actions.
handleDataquery(Hashtable<String, String[]>, HttpServletResponse, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
handleDeleteAction(PrintWriter, Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the database delete request and delete an XML document from the database connection
handleDocIdSelect() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
handleEditCart(Hashtable<String, String[]>, HttpServletResponse, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
handleEvent(MetacatEvent) - Method in interface edu.ucsb.nceas.metacat.event.MetacatEventObserver
handleExportAction(Hashtable<String, String[]>, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the "export" request of data package from Metacat in zip format
handleFileUpdate(MultipartParser) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
handleForceReplicateDataFileRequest(Hashtable<String, String[]>, HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  when a forcereplication data file request comes in, local host sends a readdata request to the requesting server (remote server) for the specified docid.
handleForceReplicateDeleteRequest(Hashtable<String, String[]>, HttpServletResponse, HttpServletRequest, boolean) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
handleForceReplicateRequest(Hashtable<String, String[]>, HttpServletResponse, HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  when a forcereplication request comes in, local host sends a read request to the requesting server (remote server) for the specified docid.
handleForceReplicateSystemMetadataRequest(Hashtable<String, String[]>, HttpServletResponse, HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  when a forcereplication request comes in, local host sends a read request to the requesting server (remote server) for the specified docid.
handleGetAccessControlAction(PrintWriter, Hashtable<String, String[]>, HttpServletResponse, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle "getaccesscontrol" action.
handleGetAllDocidsAction(PrintWriter, Hashtable<String, String[]>, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the "getalldocids" action.
handleGetCatalogRequest(Hashtable<String, String[]>, HttpServletResponse, boolean) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends the contents of the xml_catalog table encoded in xml The xml format is: All of the sub elements of row are #PCDATA If printFlag == false then do not print to out.
handleGetDataFileRequest(OutputStream, Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends a datafile to a remote host
handleGetDocid(Hashtable<String, String[]>, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Look up the pid (guid)-to-docid mapping.
handleGetDoctypesAction(PrintWriter, Hashtable<String, String[]>, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle "getdoctypes" action.
handleGetDocumentInfoRequest(Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends all of the xml_documents information encoded in xml to a requestor the format is: all of the subelements of document info are #PCDATA
handleGetDocumentRequest(Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends a document to a remote host
handleGetDTDSchemaAction(PrintWriter, Hashtable<String, String[]>, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the "getdtdschema" action.
handleGetLockRequest(Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Grants or denies a lock to a requesting host.
handleGetLogAction(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Print a report from the event log based on filter parameters passed in from the web.
handleGetMaxDocidAction(PrintWriter, Hashtable<String, String[]>, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the "getlastdocid" action.
handleGetPrincipalsAction(Writer, String, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the "getprincipals" action.
handleGetRevisionAndDocTypeAction(PrintWriter, Hashtable<String, String[]>) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle "getrevsionanddoctype" action Given a docid, return it's current revision and doctype from data base The output is String look like "rev;doctype"
handleGetSystemMetadataRequest(Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends System Metadata as XML
handleGetTimeRequest(Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends the current system date to the remote server.
handleIdIsRegisteredAction(PrintWriter, Hashtable<String, String[]>, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Check if the document is registered in either the xml_documents or xml_revisions table
handleInsertOrUpdateAction(String, String, HttpServletResponse, PrintWriter, Hashtable<String, String[]>, String, String[], boolean, boolean, byte[], String, Checksum, File) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the database putdocument request and write an XML document to the database connection
handleLoginAction(Writer, Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the login request.
handleLogoutAction(Writer, Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the logout request.
handleMultipartForm(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle documents passed to metacat that are encoded using the "multipart/form-data" mime type.
handlePackageUpload(String, HashMap, String, String, Document) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
handlePackageUpload(ClientView, MultipartParser) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Handles metadata file and data file uploads for inserting new Metacat data packages.
handleQuery(Writer, Hashtable<String, String[]>, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Create the xml query, execute it and display the results.
handler - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
handler - Variable in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handler - Class in edu.ucsb.nceas.protocols.metacat
  Class handling metacat scheme URLs by delegating connection requests to the MetacatURLConnection class
Handler() - Constructor for class edu.ucsb.nceas.protocols.metacat.Handler
handleReadAction(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the "read" request of metadata/data files from Metacat or any files from Internet; transformed metadata XML document into HTML presentation if requested; zip files when more than one were requested.
handleReadInlineDataAction(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  In eml2 document, the xml can have inline data and data was stripped off and store in file system.
handleReindexAction(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Rebuild the index for one or more documents.
handleReindexAllAction(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[]) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Rebuild the index for all documents in the systemMetadata table.
handleRequest(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.ReplicationAdmin
  Handle configuration of replication -- pass through to the other handler
handleReturnField(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Method to handle return field.
HandlerException - Exception in edu.ucsb.nceas.metacat.shared
  Exception thrown when an error occurs in a configuration administrative class
HandlerException(String) - Constructor for exception edu.ucsb.nceas.metacat.shared.HandlerException
  Create a new AdminException.
handlesAction(String) - Method in interface edu.ucsb.nceas.metacat.plugin.MetacatHandlerPlugin
handleServerControlRequest(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  This method can add, delete and list the servers currently included in xml_replication.
handleSetAccessAction(PrintWriter, Hashtable<String, String[]>, String, HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
handleSpatialQuery(Writer, Hashtable<String, String[]>, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  handles all spatial queries -- these queries may include any of the queries supported by the WFS / WMS standards handleSQuery(out, params, response, username, groupnames, sess_id);
handleSQuery(Writer, Hashtable<String, String[]>, HttpServletResponse, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Retrieve the squery xml, execute it and display it
handleUpdateRequest(Hashtable<String, String[]>, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Sends a list of all of the documents on this sever along with their revision numbers.
handleValidateAction(PrintWriter, Hashtable<String, String[]>) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Handle the validation request and return the results to the requestor
HarvestDetailLog - Class in edu.ucsb.nceas.metacat.harvesterClient
  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 in edu.ucsb.nceas.metacat.harvesterClient
  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.
harvestDocument() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
  Harvest the document from the site.
harvestDocument(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Given a new or updated docid, will update the spatial cache accordingly.
harvestDocumentList() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
  Harvests each document in the site document list.
Harvester - Class in edu.ucsb.nceas.metacat.harvesterClient
  Harvester is the main class for the Harvester application.
Harvester() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.Harvester
  Constructor.
HarvesterRegistration - Class in edu.ucsb.nceas.metacat.harvesterClient
  HarvesterRegistration is a servlet that implements harvester registration.
HarvesterRegistration() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
HarvesterRegistrationLogin - Class in edu.ucsb.nceas.metacat.harvesterClient
  HarvesterRegistrationLogin implements a servlet to login to the Harvester Registration servlet.
HarvesterRegistrationLogin() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin
HarvesterServlet - Class in edu.ucsb.nceas.metacat.harvesterClient
  HarvesterServlet class allows Harvester to be run as a background process.
HarvesterServlet() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
HarvesterVerb - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  HarvesterVerb is the parent class for each of the OAI verbs.
HarvesterVerb() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Mock object creator (for unit testing purposes)
HarvesterVerb(String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Performs the OAI request
HarvestListEditor - Class in edu.ucsb.nceas.metacat.harvesterClient
  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 in edu.ucsb.nceas.metacat.harvesterClient
  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 in edu.ucsb.nceas.metacat.harvesterClient
  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.
hasAllPermission(String, String[], String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Check for "ALL" or "CHMOD" permission on @docid for @user and/or @groups from DB connection
hash(String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFileBCryptHash
hash(String) - Method in interface edu.ucsb.nceas.metacat.authentication.AuthFileHashInterface
  Generate the hash value for a specified plaint password
hashCode() - Method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
hashCode() - Method in class edu.ucsb.nceas.shared.xsd.IOException
hasMetacatInfo(String, Document) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
hasPermission(String, String) - Method in class edu.ucsb.nceas.metacat.PermissionController
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 Administrators are allowed all permission
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
hasReservation(Session, Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Checks whether the pid is reserved by the subject in the session param If the reservation is held on the pid by the subject, we return true.
hasReservation(Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
hasReservation(Session, Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
hasSameSearchValue(QueryTerm) - Method in class edu.ucsb.nceas.metacat.QueryTerm
  Compare two query terms to see if they have same search value.
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
hasWritePermission(String, String[], String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Check for "WRITE" permission on @docid for @user and/or @groups from DB connection
HazelcastService - Class in edu.ucsb.nceas.metacat.dataone.hazelcast
  The Hazelcast service enables Metacat as a Hazelcast cluster member
HEAD - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  HTTP Verb HEAD
HIDDEN_EXISTS_POPULATED - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
HIDDEN_EXISTS_UNPOPULATED - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
HIGHESTVERSION - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
hitTextNode - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
homeDir - Variable in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog

## I

identifierExists(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Determine if an identifier exists already, returning true if so.
IdentifierManager - Class in edu.ucsb.nceas.metacat
  Manage the relationship between Metacat local identifiers (LocalIDs) that are codified as the (docid, rev) pair with globally unique string identifiers (GUIDs) that are opaque strings.
Identify - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  This class represents an Identify response on either the server or on the client
Identify() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.Identify
  Mock object constructor (for unit testing purposes)
Identify(String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.Identify
  Client-side Identify verb constructor
idExists(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
  return true if the given docid is registered in either the xml_documents or xml_revisions table
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
ignoreDenyFirst - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
IN_PROGRESS - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
INACTIVE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
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.database.DBConnection
  Increase a usage number to this object
increaseUsageCount(int) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Increase a usage number to this object
indexEphemeralAnnotation(Identifier) - Method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
IndexEventDAO - Class in edu.ucsb.nceas.metacat.index
IndexEventMapStore - Class in edu.ucsb.nceas.metacat.index
IndexEventMapStore() - Constructor for class edu.ucsb.nceas.metacat.index.IndexEventMapStore
IndexingQueue - Class in edu.ucsb.nceas.metacat
IndexingTimerTask - Class in edu.ucsb.nceas.metacat
IndexingTimerTask() - Constructor for class edu.ucsb.nceas.metacat.IndexingTimerTask
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
  Initialize the servlet
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchServlet
  Initializes the servlet.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.advancedsearch.BrowseServlet
  Initializes the servlet.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginServlet
  Initializes the servlet.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.advancedsearch.SearchServlet
  Initializes the servlet.
init() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Initializes the Hazelcast service
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
  Initializes the servlet.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
  Initializes the servlet.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.harvesterClient.MetUpload
  Initializes the servlet.
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.oaipmh.provider.server.OAIHandler
  init is called one time when the Servlet is loaded.
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
  Initialize the servlet by creating appropriate database connections
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
  Initalize servlet by setting logger
init(FilterConfig) - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
init(FilterConfig) - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
initializeSitemapTask(MetacatHandler) - Static method in class edu.ucsb.nceas.metacat.MetaCatServlet
initLogIDs() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
  Initializes the detailLogID and harvestLogID values to their current maximums + 1.
initMultipartParams() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Collect the multipart params from the request
initParams() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  copies request parameters to a hashtable which is given as argument to native metacathandler functions
initParser(DefaultHandler) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationHandler
  Method to initialize the message parser
initSecondHalf(ServletContext) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
  Initialize the remainder of the servlet.
initService(LSIDServiceConfig) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
initService(LSIDServiceConfig) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
initService(LSIDServiceConfig) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
INLINE - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
INLINE - Static variable in class edu.ucsb.nceas.metacat.Eml210SAXHandler
INLINE_DATA_DISTRIBUTION - Static variable in class edu.ucsb.nceas.metacat.DistributionSection
InputStreamDataSource - Class in edu.ucsb.nceas.metacat.restservice
  Encapsulate an InputStream within a DataSource interface so that it is accessible to MIME processors.
InputStreamDataSource(String, InputStream) - Constructor for class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
insert(String, Reader, Reader) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Insert an XML document into the repository, making it available for searching using the query() methods.
insert(String, Reader, Reader) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Insert an XML document into the repository.
insertAccess(String, List<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Set permissions for a given document.
insertDataObject(InputStream, Identifier, Session, Checksum) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Insert a data object into Metacat
insertDataObject(InputStream, Identifier, Session, Checksum, EventLogData) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Insert a data object into Metacat
insertObject(InputStream, String, Identifier, String, Session, Checksum, EventLogData) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Insert an object into the given directory
insertOrUpdate(String, SimpleFeature, String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
  Either inserts or updates the spatial cache with the new spatial document depending on if it currently exists.
insertOrUpdateDocument(InputStream, String, Identifier, Session, String, String, Checksum) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Insert or update an XML document into Metacat
insertOrUpdateSystemMetadata(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  creates a system metadata mapping and adds additional fields from sysmeta to the table for quick searching.
insertPermissions(XMLAccessDAO) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Insert a single access record into the database based on access DAO object
insertPermissions(String, Long, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Insert a single access record into the database.
insertPermissions(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
  Replace existing permissions with a given block of permissions for this document.
insertSystemMetadata(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Insert a systemMetadata document and return its localId
INSTANCEID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
InsufficientKarmaException - Exception in edu.ucsb.nceas.metacat.client
  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 exception edu.ucsb.nceas.metacat.client.InsufficientKarmaException
  Create a new InsufficientKarmaException.
internalEntityDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of internal entity declarations
INTERSECT - Static variable in class edu.ucsb.nceas.metacat.QueryGroup
intValue(String) - Static method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
INVALIDCODE - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
IOException - Class in edu.ucsb.nceas.shared.xsd
IOException() - Constructor for class edu.ucsb.nceas.shared.xsd.IOException
IOException(Object) - Constructor for class edu.ucsb.nceas.shared.xsd.IOException
ipAddress - Variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
isAccessControlDirty(SystemMetadata, SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Check if the access control was modified between two system metadata objects.
isAdministrator(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Check if the specified user is part of the administrators list
isAllowedSubmitter(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Check if the specified user is part of the moderators list
isAuthConfigured() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Reports whether LDAP is fully configured.
isAuthoritativeMNodeAdmin(Session, NodeReference, NodeList) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Compare the session.subject to the authoritativeMN Node.nodeSubjects list of Subjects.
isAuthoritativeNode(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Determine if the current node is the authoritative node for the given pid.
isAuthorized(String, String, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Method used to log in to a metacat server.
isAuthorized(Session, Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Test if the user identified by the provided token has authorization for the operation on the specified object.
isAuthorized(Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
isAuthorized(Session, Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
isAuthorized(Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
isAuthorized(Session, Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
isAuthorized(PrintWriter, Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
isAuthorizedBySysMetaSubjects(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Returns the authorization status of the Session vs.
isAvailableFor(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml200
  Can this nativeItem be represented in 'eml-2.0.0' format?
isAvailableFor(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml201
  Can this nativeItem be represented in 'eml-2.0.1' format?
isAvailableFor(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml210
  Can this nativeItem be represented in 'eml-2.1.0' format?
isAvailableFor(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml211
  Can this nativeItem be represented in 'eml-2.1.1' format?
isAvailableFor(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
  Can this nativeItem be represented in DC format?
isBackupDirConfigured() - Static method in class edu.ucsb.nceas.metacat.util.ConfigurationUtil
  Check if the application.backupDir property is populated in metacat.properties and that it points to a writable directory.
isBoundaryContained() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
isCaseSensitive() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
isCaseSensitive() - Method in class edu.ucsb.nceas.metacat.QueryTerm
  determine if the QueryTerm is case sensitive
isCNAdmin(Session, NodeList) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  compares session.subject against CN.NodeList
isD1Enabled() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  subclasses should provide a more useful implementation
isD1Enabled() - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
isD1Enabled() - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
isDatabaseConfigured() - Static method in class edu.ucsb.nceas.metacat.util.DatabaseUtil
  Reports whether database is fully configured.
isDataOneConfigured() - Static method in class edu.ucsb.nceas.metacat.util.DataONEConfigUtil
  Reports whether dataONE is configured.
isDeleted(String) - Method in class edu.ucsb.nceas.metacat.EventLog
  A utility method to determine if the given docid was deleted.
isDeleted(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Is the record deleted?
isDeniedSubmitter(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Check if the specified user is part of the moderators list
isElementContentWhitespace(Text) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
isEmpty(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
  Boolean to determine whether a string is empty.
isEmpty() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  Method to determine the server list is empty or not
isEnabled() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
  Check if the quota service is enabled.
isEqual(AccessPolicy, AccessPolicy) - Method in class edu.ucsb.nceas.metacat.dataone.SyncAccessPolicy
  Compare two d1 system metadata access policies for equivalence.
isEZIDConfigured() - Static method in class edu.ucsb.nceas.metacat.util.ConfigurationUtil
isFGDC(Document) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
isFullyInitialized() - Static method in class edu.ucsb.nceas.metacat.MetaCatServlet
  Reports whether the MetaCatServlet has been fully initialized
isGeoserverConfigured() - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
  Reports whether geoserver is configured.
isGivenServerInList(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  Method to determine if a given server in the replication server list
isIntegratedWithMetacat() - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
  Boolean to determine whether the Data Provider code is executing in a Metacat application.
isInternalURLReplacedByExternal() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Check if the internal url has been replaced by external url.
isInUnionGroup() - Method in class edu.ucsb.nceas.metacat.QueryTerm
  If this query group in Union group
isLastUnarchivedInChain(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
  Checking if the given pid is last one in this series chain hasn't been archived
isLastUndeletedInChain(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
  Checking if the given pid is last one in this series chain hasn't been deleted
isLimitedByBoundaries() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
isLimitedByDate() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
isLocalCNAdmin(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Test if the user identified by the provided token has administrative authorization on this node because they are calling themselves (the implementation uses property Settings to build a Node instance)
isLocalMNAdmin(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Test if the user identified by the provided token has administrative authorization on this node because they are calling themselves (the implementation uses property Settings to build a Node instance)
isLocalNodeAdmin(Session, NodeType) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  Checks Metacat properties representing the local Node document for matching Node.subjects.
isLoggedIn() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  A convenience method to be used by client code that requires the user to be logged in.
isLoggedLocally - Variable in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
isMetacatConfigured() - Static method in class edu.ucsb.nceas.metacat.util.ConfigurationUtil
  Reports whether metacat is fully configured.
isMetadataFile(File) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Override this method if some files exist in the filesystem that aren't metadata records.
isModerator(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Check if the specified user is part of the moderators list
isNamespaceRegistered(String) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Test if the given namespace registered in Metacat
isNodeAuthorized(Session, Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Verify that a replication task is authorized by comparing the target node's Subject (from the X.509 certificate-derived Session) with the list of subjects in the known, pending replication tasks map.
isNodeAuthorized(Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
isNodeAuthorized(Session, Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
isNodeAuthorized(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Pass the request to get node replication authorization to CNodeService
isNodeAuthorized(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Pass the request to get node replication authorization to CNodeService
isNotEqualTerm() - Method in class edu.ucsb.nceas.metacat.QueryTerm
isPercentageSearch() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Method to indicate this query is a percentage search
isPublicAccess() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Getter for property publicAccess.
isReadOnly(HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.MetaCatServlet
isReadOnly() - Method in class edu.ucsb.nceas.metacat.ReadOnlyChecker
  Check if the mode is the read-only.
isReadOnlyMode() - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Check if the metacat is in the read-only mode.
isRegistered(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  return true of the given docid is registered, false if not
isRegistered(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  return true of the given docid is registered, false if not
isRegistered(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  return true of the given docid is registered, false if not
isRegistered(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  return true of the given docid is registered, false if not
isReplicaMNodeAdmin(Session, SystemMetadata, NodeList) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
  determines if the session represents a replicaMN of the given systemMetadata.
isSchemaRegistered(XMLSchema) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Returns true if the schema is registered.
isScienceMetadata(SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Determine if a given object should be treated as an XML science metadata object.
isServiceUnavailable(Properties) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
  Should the server report itself down for maintenance? Override this method if you want to do this check another way.
isSessionRegistered(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Check if a session is registered in the session hash table.
isSuccessXML(String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
isUserLoggedIn(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Checks to see if the user is logged in by grabbing the session from the request and seeing if it exists in the global session list.
isUserLoggedInAsAdmin(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Checks to see if the user is logged in as admin by first checking if the user is logged in and then seeing if the user's account is on the administrators list in metacat.properties.
isValidIdentifier(Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Check for whitespace in the given pid.
isValidSite() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
  Boolean to determine whether a given string is a valid LTER site.
isVersion_3_4(String) - Method in class edu.ucsb.nceas.metacat.admin.SolrVersionChecker
  Check if given the solr home is for Lucene version 3.4.
itemAdded(ItemEvent<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Respond to itemAdded events on the hzMissingIdentifiers Set.
itemRemoved(ItemEvent<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Respond to itemRemoved events on the hzMissingIdentifiers Set

## J

JSON_LD - Static variable in class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandlers
JsonLDHandler - Class in edu.ucsb.nceas.metacat.object.handler
  The handler of JSON-LD objects to save bytes to disk
JsonLDHandler() - Constructor for class edu.ucsb.nceas.metacat.object.handler.JsonLDHandler
  Default constructor

## K

KEEP - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin

## L

LDAPCLASS - Static variable in class edu.ucsb.nceas.metacat.admin.AuthAdmin
LEXICALPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
LINUX_OS - Static variable in class edu.ucsb.nceas.metacat.util.SystemUtil
listChecksumAlgorithms() - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Returns a list of checksum algorithms that are supported by DataONE.
listChecksumAlgorithms() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
listFormats() - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Returns a list of all object formats registered in the DataONE Object Format Vocabulary
listFormats() - Method in class edu.ucsb.nceas.metacat.dataone.ObjectFormatService
  Return the list of object formats registered from the Coordinating Node.
listFormats() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
ListIdentifiers - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  This class represents an ListIdentifiers response on either the server or on the client.
ListIdentifiers() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers
  Mock object constructor (for unit testing purposes)
ListIdentifiers(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers
  Client-side ListIdentifiers verb constructor
ListIdentifiers(String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers
  Client-side ListIdentifiers verb constructor (resumptionToken version)
listIdentifiers(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Retrieve a list of Identifiers that satisfy the criteria parameters
listIdentifiers(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Retrieve the next set of Identifiers associated with the resumptionToken
ListMetadataFormats - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  This class represents an ListMetadataFormats response on either the server or on the client
ListMetadataFormats() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListMetadataFormats
  Mock object constructor (for unit testing purposes)
ListMetadataFormats(String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListMetadataFormats
  Client-side ListMetadataFormats verb constructor
ListMetadataFormats(String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListMetadataFormats
  Client-side ListMetadataFormats verb constructor (identifier version)
listNodes() - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Returns a list of nodes that have been registered with the DataONE infrastructure
listNodes() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
listNodesBySubject(Subject, NodeList) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Calls CN.listNodes() to assemble a list of nodes that have been registered with the DataONE infrastructure that match the given session subject
listObjects(Session, Date, Date, ObjectFormatIdentifier, NodeReference, Identifier, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
listObjects(Session, Date, Date, ObjectFormatIdentifier, Identifier, NodeReference, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Retrieve the list of objects present on the MN that match the calling parameters
listObjects(Session, Date, Date, ObjectFormatIdentifier, Identifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Retrieve the list of objects present on the MN that match the calling parameters
listObjects(Date, Date, ObjectFormatIdentifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
listObjects(Session, Date, Date, ObjectFormatIdentifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
listObjects(Date, Date, ObjectFormatIdentifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
listObjects(Session, Date, Date, ObjectFormatIdentifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
listQueryEngines(Session) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
listQueryEngines(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
listQueryEngines() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
listQueryEngines() - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
listQuotas(String, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
  List the quotas associated with the given subject
ListRecords - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  This class represents an ListRecords response on either the server or on the client
ListRecords() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords
  Mock object constructor (for unit testing purposes)
ListRecords(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords
  Client-side ListRecords verb constructor
ListRecords(String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords
  Client-side ListRecords verb constructor (resumptionToken version)
listRecords(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Retrieve a list of records that satisfy the specified criteria
listRecords(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Retrieve the next set of records associated with the resumptionToken
ListSets - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  This class represents an ListSets response on either the server or on the client
ListSets() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListSets
  Mock object constructor (for unit testing purposes)
ListSets(String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListSets
  Client-side ListSets verb constructor
listSets() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
listSets(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
listViews(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
listViews() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
load(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.ObjectPathMap
  Implementation of hazelcast MapLoader interface method.
load(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
load(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
  The map store/loader methods
loadAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.ObjectPathMap
  Implementation of hazelcast MapLoader interface method.
loadAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
loadAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
loadAllKeys() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.ObjectPathMap
  Return the full set of guids in the local metacat repository as dataone Identifiers.
loadAllKeys() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
  Returning null so that no entries are loaded on map initialization
loadAllKeys() - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
loadCatalog() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
  Run a query of the Metacat database to load the catalog of EML documents.
loadProperties(String) - Static method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
  Loads Harvester options from a configuration file.
loadSQLFromFile(String) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Very basic utility to read sql from a file and return a vector of the individual sql statements.
LocalUsage - Class in edu.ucsb.nceas.metacat.dataone.quota
  A child class of the Usage class of BookKeeper.
LocalUsage() - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
log - Static variable in class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
log - Static variable in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeEmptyReplicatedDataFile
log - Static variable in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime
log - Static variable in class edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory
log - Static variable in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
log(String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.EventLog
  Log an event of interest to the application.
LogEntryV2toV1Converter() - Constructor for class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.LogEntryV2toV1Converter
  Default constructor
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.client.rest.MetacatRest
  Method used to log in to a metacat server through REST API
login(String, String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Method used to log in to a metacat server through REST API.
LOGIN_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
LoginAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the login page
LoginBean - Class in edu.ucsb.nceas.metacat.advancedsearch
LoginBean() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
LoginServlet - Class in edu.ucsb.nceas.metacat.advancedsearch
LoginServlet() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.LoginServlet
LoginServlet - Class in edu.ucsb.nceas.metacat.harvesterClient
  LoginServlet implements a Harvester servlet to login to Metacat
LoginServlet() - Constructor for class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
logMetacat - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
logMetacat - Variable in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
logMetacat - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
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.client.rest.MetacatRest
  Method used to log out a metacat server.
logout() - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Method used to log out a metacat server.
logUserIn(HttpServletRequest, String, String) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  log the user in against ldap.
LogV2toV1Converter - Class in edu.ucsb.nceas.metacat.dataone.convert
  This class represents a converter to convert an DataONE v2 Log object to a v1 Log object.
LogV2toV1Converter() - Constructor for class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter
  Default constructor
LogV2toV1Converter.LogEntryV2toV1Converter - Class in edu.ucsb.nceas.metacat.dataone.convert
  A class to convert a v2 LogEntry object to a v1 LogEntry object
LogV2toV1Converter.V1LogEntryWrapper - Class in edu.ucsb.nceas.metacat.dataone.convert
  A wrapper class to gap the difference in the signature of setEvent between the v2 and v1 LogEntry objects.
LogV2toV1Converter.V2LogEntryWrapper - Class in edu.ucsb.nceas.metacat.dataone.convert
  A wrapper class to gap the difference in the signature of setEvent between the v2 and v1 LogEntry objects.
lookupAnnotationClass(OntClass, String, String) - Static method in class edu.ucsb.nceas.metacat.annotation.BioPortalService
  Look up possible concept from BioPortal annotation service.
lookupCreators(boolean) - Static method in class edu.ucsb.nceas.metacat.annotation.OrcidService
  Look up indexed creators
lookupFormat(SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Figure out the format (mime type) of the data object
lookupOrcid(String, String, List<String>, List<String>) - Static method in class edu.ucsb.nceas.metacat.annotation.OrcidService
  Look up possible ORCID from orcid service.
lookupOreFor(Session, Identifier, boolean) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Determines if we already have registered an ORE map for this package NOTE: uses a solr query to locate OREs for the object
lookupRemoteUsageId(int, String) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
  Find the remote usage id in the local database for the given quota id and instance id
LSIDAuthorityData - Class in edu.ucsb.nceas.metacat.lsid
LSIDAuthorityData() - Constructor for class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
LSIDAuthorityMain - Class in edu.ucsb.nceas.metacat.lsid
LSIDAuthorityMain() - Constructor for class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
LSIDAuthorityMetaData - Class in edu.ucsb.nceas.metacat.lsid
LSIDAuthorityMetaData() - Constructor for class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
lsidData(LSID) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
LSIDDataLookup - Class in edu.ucsb.nceas.metacat.lsid
LSIDDataLookup() - Constructor for class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
lsidType(LSID) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
LTERSite - Class in edu.ucsb.nceas.metacat.advancedsearch
LTERSite(String) - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.LTERSite

## M

MAC_OS - Static variable in class edu.ucsb.nceas.metacat.util.SystemUtil
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.accesscontrol.AccessControlList
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.GenerateGlobalIdentifiers
  Main method, solely for testing.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade1_5_0
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_0_0
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeEmptyReplicatedDataFile
main(String[]) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime
main(String[]) - Static method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearch
  Main program to run a test query from the command line.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
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.authentication.AuthFile
  A method is used to help administrator to manage users and groups
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.client.MetacatClient
main(String[]) - Static method in class edu.ucsb.nceas.metacat.ContentTypeProvider
main(String[]) - Static method in class edu.ucsb.nceas.metacat.dataone.SyncAccessPolicy
  Run pid synch script on the given pids Each argument is an individual pid because pids cannot contain whitespace.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory
main(String[]) - Static method in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
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.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.DocumentIdQuery
  Main method used for testing the class output
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.EML201DocumentCorrector
  Runs the job to correct eml201 documents - deleting extral nodes in
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.harvesterClient.HarvestListEditor
  The main program.
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.oaipmh.harvester.OaipmhHarvester
  The main() method.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.spatial.XSLTransform
  the main routine used to test the transform utility.
makeRedirectUrl() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
mappingExists(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Determine if an identifier mapping exists already, returning true if so.
mapToHtmlSelect(Map, String, String, int) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientHtmlHelper
  JSP API: A static helper method which takes a map (key, value pairs) and returns an XHTML SELECT String.
marker - Static variable in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
match(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFileBCryptHash
match(String, String) - Method in interface edu.ucsb.nceas.metacat.authentication.AuthFileHashInterface
  Check if the plain password matches the hashed password.
MATCH_ALL - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
MATCH_ANY - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
MAX_UPLOAD_SIZE - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Maximum size of uploads, defaults to 1GB if not set in property file
MAXDATACHARS - Static variable in class edu.ucsb.nceas.metacat.DBSAXHandler
MAXIMUM_DB_RECORD_COUNT - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  limit paged results sets to a configured maximum
McdbDocNotFoundException - Exception in edu.ucsb.nceas.metacat
  Exception thrown when an error occurs because a document with a given ID could not be found in the metacat database.
McdbDocNotFoundException() - Constructor for exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
  Create a new McdbDocNotFoundException.
McdbDocNotFoundException(String, String, String) - Constructor for exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
  Create a new McdbDocNotFoundException.
McdbDocNotFoundException(String) - Constructor for exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
  Create a new exception but only set the message.
McdbDocNotFoundException(Exception) - Constructor for exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
  Create a new McdbDocNotFoundException.
McdbDocNotFoundException(String, Exception) - Constructor for exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
  Create a new McdbDocNotFoundException.
McdbException - Exception in edu.ucsb.nceas.metacat
  Exception thrown when an error occurs because a problem occurred in the metacat database.
McdbException() - Constructor for exception edu.ucsb.nceas.metacat.McdbException
  Create a new McdbException.
McdbException(String) - Constructor for exception edu.ucsb.nceas.metacat.McdbException
  Create a new McdbException.
McdbException(Exception) - Constructor for exception edu.ucsb.nceas.metacat.McdbException
  Create a new McdbException.
McdbException(String, Exception) - Constructor for exception edu.ucsb.nceas.metacat.McdbException
  Create a new McdbException.
memberAdded(MembershipEvent) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  When there is missing SystemMetadata on the local member, we retrieve it from the shared map and add it to the local backing store for safe keeping.
memberRemoved(MembershipEvent) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Metacat - Interface in edu.ucsb.nceas.metacat.client
  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.
METACAT_REPL_ERROR_MSG - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
METACAT_UTILITY_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
MetacatAdmin - Class in edu.ucsb.nceas.metacat.admin
  A suite of utility classes for querying DB
MetacatAdmin() - Constructor for class edu.ucsb.nceas.metacat.admin.MetacatAdmin
MetacatAdminServlet - Class in edu.ucsb.nceas.metacat.admin
  Entry servlet for the metadata configuration utility
MetacatAdminServlet() - Constructor for class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
MetacatAuthenticatedEcogridEndPoint - Class in edu.ucsb.nceas.metacat.dataquery
  This class implements AuthenticatedEcogridEndPointInterface and is configurable using the properties file.
MetacatAuthenticatedEcogridEndPoint() - Constructor for class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
MetacatAuthenticatedEcogridEndPoint(String) - Constructor for class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
MetacatAuthException - Exception in edu.ucsb.nceas.metacat.client
  Exception thrown when a Metacat server denies a login authentication request.
MetacatAuthException(String) - Constructor for exception edu.ucsb.nceas.metacat.client.MetacatAuthException
  Create a new MetacatAuthException.
MetacatCatalog - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog
  MetacatCatalog is an implementation of AbstractCatalog interface.
MetacatCatalog(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
MetacatClient - Class in edu.ucsb.nceas.metacat.client
  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.
MetacatDatabaseConnectionPoolFactory - Class in edu.ucsb.nceas.metacat.dataquery
  This class provides an implementation of DataConnetionPoolInterface Implementation and database information for this class will be read from property file.
MetacatDatabaseConnectionPoolFactory() - Constructor for class edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory
  Constructor.
MetacatDocumentEvent - Class in edu.ucsb.nceas.metacat.event
MetacatDocumentEvent() - Constructor for class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
MetacatEcogridEndPoint - Class in edu.ucsb.nceas.metacat.dataquery
  This class implements EcogridEndPointInterface and is configurable using a properties file.
MetacatEcogridEndPoint() - Constructor for class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
MetacatEvent - Interface in edu.ucsb.nceas.metacat.event
MetacatEventObserver - Interface in edu.ucsb.nceas.metacat.event
MetacatEventService - Class in edu.ucsb.nceas.metacat.event
MetacatException - Exception in edu.ucsb.nceas.metacat.client
  Exception thrown when an error occurs during a metacat operation.
MetacatException(String) - Constructor for exception edu.ucsb.nceas.metacat.client.MetacatException
  Create a new MetacatException.
MetacatFactory - Class in edu.ucsb.nceas.metacat.client
  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
MetacatHandler - Class in edu.ucsb.nceas.metacat
  General entry point for the Metacat server which is called from various mechanisms such as the standard MetacatServlet class and the various web service servlets such as RestServlet class.
MetacatHandler(Timer) - Constructor for class edu.ucsb.nceas.metacat.MetacatHandler
  Constructor with a timer object.
MetacatHandler() - Constructor for class edu.ucsb.nceas.metacat.MetacatHandler
  Default constructor.
MetacatHandlerPlugin - Interface in edu.ucsb.nceas.metacat.plugin
MetacatHandlerPluginManager - Class in edu.ucsb.nceas.metacat.plugin
MetacatHelper - Class in edu.ucsb.nceas.metacat.advancedsearch
MetacatHelper() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
metacatHighestRevision() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
  Determines the highest revision that Metacat has for this document.
MetacatInaccessibleException - Exception in edu.ucsb.nceas.metacat.client
  Exception thrown when a Metacat server is not accessible for the operation requested.
MetacatInaccessibleException(String) - Constructor for exception edu.ucsb.nceas.metacat.client.MetacatInaccessibleException
  Create a new MetacatInaccessibleException.
MetacatLogin - Class in edu.ucsb.nceas.metacat.advancedsearch
MetacatLogin(LoginBean) - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.MetacatLogin
  Constructor.
metacatLogin() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
  Login to Metacat using the ldapDN and ldapPwd
MetacatPopulator - Class in edu.ucsb.nceas.metacat.util
MetacatPopulator(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.util.MetacatPopulator
  create a new MetacatPopulator with given source and destination urls.
MetacatProfiler - Class in edu.ucsb.nceas.metacat
MetacatProfiler.Profile - Class in edu.ucsb.nceas.metacat
  container class for profile information
MetacatRecordFactory - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog
  MetacatRecordFactory converts native Metacat documents to OAI-PMH records.
MetacatRecordFactory(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Construct a MetacatRecordFactory capable of producing the Crosswalk(s) specified in the properties file.
MetacatRest - Interface in edu.ucsb.nceas.metacat.client.rest
  This interface provides methods for initializing and logging in to a Metacat REST API, and then querying, reading, transforming, inserting, updating and deleting documents from that server.
MetacatRestClient - Class in edu.ucsb.nceas.metacat.client.rest
MetacatRestClient(String) - Constructor for class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Constructor to create a new instance.
MetacatResultSet - Class in edu.ucsb.nceas.metacat
MetacatResultSet(String) - Constructor for class edu.ucsb.nceas.metacat.MetacatResultSet
MetacatResultSet.Document - Class in edu.ucsb.nceas.metacat
MetaCatServlet - Class in edu.ucsb.nceas.metacat
  A metadata catalog server implemented as a Java Servlet Valid actions are: action=login username password qformat action=logout qformat action=query -- query the values of all elements and attributes and return a result set of nodes meta_file_id -- returndoctype -- filterdoctype -- returnfield -- owner -- site -- operator -- casesensitive -- searchmode -- anyfield -- action=spatial_query -- run a spatial query.
MetaCatServlet() - Constructor for class edu.ucsb.nceas.metacat.MetaCatServlet
MetacatSolrEngineDescriptionHandler - Class in edu.ucsb.nceas.metacat.index
  This class handles the request for getting the solr engine description.
MetacatSolrIndex - Class in edu.ucsb.nceas.metacat.index
  This class will query the solr server and return the result.
MetacatURL - Class in edu.ucsb.nceas.metacat
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 in edu.ucsb.nceas.protocols.metacat
  Handle requests for metacat scheme URLs
MetacatURLConnection(URL) - Constructor for class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection
  Construct a new metacat scheme URL connection
MetacatUtil - Class in edu.ucsb.nceas.metacat.util
  A suite of utility classes for the metadata catalog server
MetacatUtil() - Constructor for class edu.ucsb.nceas.metacat.util.MetacatUtil
MetacatUtilException - Exception in edu.ucsb.nceas.metacat.shared
  Exception thrown when an error occurs in a utility method
MetacatUtilException(String) - Constructor for exception edu.ucsb.nceas.metacat.shared.MetacatUtilException
  Create a new AdminException.
MetacatVersion - Class in edu.ucsb.nceas.metacat
MetacatVersion(String) - Constructor for class edu.ucsb.nceas.metacat.MetacatVersion
METADATA - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
methodcalls - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
MetUpload - Class in edu.ucsb.nceas.metacat.harvesterClient
  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
MNodeService - Class in edu.ucsb.nceas.metacat.dataone
  Represents Metacat's implementation of the DataONE Member Node service API.
MNodeService - Class in edu.ucsb.nceas.metacat.dataone.v1
  Represents Metacat's implementation of the DataONE Member Node service API, v1.
MNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v1
  MN REST service implementation handler ****************** MNCore -- DONE ping() - GET /d1/mn/monitor/ping log() - GET /d1/mn/log **getObjectStatistics() - GET /d1/mn/monitor/object getOperationsStatistics - GET /d1/mn/monitor/event **getStatus - GET /d1/mn/monitor/status getCapabilities() - GET /d1/mn/ and /d1/mn/node MNRead -- DONE get() - GET /d1/mn/object/PID getSystemMetadata() - GET /d1/mn/meta/PID describe() - HEAD /d1/mn/object/PID getChecksum() - GET /d1/mn/checksum/PID listObjects() - GET /d1/mn/object synchronizationFailed() - POST /d1/mn/error MNAuthorization -- DONE isAuthorized() - GET /d1/mn/isAuthorized/PID setAccessPolicy() - PUT /d1/mn/accessRules/PID MNStorage - DONE create() - POST /d1/mn/object/PID update() - PUT /d1/mn/object/PID delete() - DELETE /d1/mn/object/PID archive() - PUT /d1/mn/archive/PID systemMetadataChanged() - POST /dirtySystemMetadata/PID MNReplication replicate() - POST /d1/mn/replicate getReplica() - GET /d1/mn/replica ******************
MNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
  Initializes new instance by setting servlet context,request and response
MNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v2
  MN REST service implementation handler ****************** MNCore -- DONE ping() - GET /d1/mn/monitor/ping log() - GET /d1/mn/log **getObjectStatistics() - GET /d1/mn/monitor/object getOperationsStatistics - GET /d1/mn/monitor/event **getStatus - GET /d1/mn/monitor/status getCapabilities() - GET /d1/mn/ and /d1/mn/node MNRead -- DONE get() - GET /d1/mn/object/PID getSystemMetadata() - GET /d1/mn/meta/PID describe() - HEAD /d1/mn/object/PID getChecksum() - GET /d1/mn/checksum/PID listObjects() - GET /d1/mn/object synchronizationFailed() - POST /d1/mn/error MNAuthorization -- DONE isAuthorized() - GET /d1/mn/isAuthorized/PID setAccessPolicy() - PUT /d1/mn/accessRules/PID MNStorage - DONE create() - POST /d1/mn/object/PID update() - PUT /d1/mn/object/PID delete() - DELETE /d1/mn/object/PID archive() - PUT /d1/mn/archive/PID updateSystemMetadata() - PUT /d1/mn/meta systemMetadataChanged() - POST /dirtySystemMetadata/PID MNReplication replicate() - POST /d1/mn/replicate getReplica() - GET /d1/mn/replica ******************
MNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Initializes new instance by setting servlet context,request and response
MNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v1
  Routes MN REST service requests to the appropriate handler
MNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.MNRestServlet
MNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v2
  Routes MN REST service requests to the appropriate handler
MNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.MNRestServlet
modifyPassWithHash(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
  Change the password of the user to the new one which is hashed
modifyPassWithPlain(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
  Change the password of the user to the new one which is plain.
multipartparams - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
MultipartRequestWithSysmeta - Class in edu.ucsb.nceas.metacat.restservice.multipart
  A class extends from the MultipartRequest class with the extra information of system meta data
MultipartRequestWithSysmeta(HttpServletRequest, Map<String, File>, Map<String, List<String>>) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.MultipartRequestWithSysmeta
  Constructor
multiThreadUpgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
  Use multiple threads to process parts of the complete ID list concurrently

## N

name - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
NAMESPACEFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
NAMESPACEKEYWORD - Static variable in class edu.ucsb.nceas.metacat.service.XMLSchemaService
NAMESPACEPREFIXESFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
namespaces - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
newNonXMLMetadataHandler(ObjectFormatIdentifier) - Static method in class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandlers
  Create a NonXMLMetadataHandler instance to handle the given formatId.
newPathExpressionWithOutAttribute(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
  A method to get rid of attribute part in path expression
NEWSOLCORENAME - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
NEWSOLRCORE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
NEWSOLRCOREORNOT - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
nextVersion(String, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
NO_READ_PERMISSION - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
NodeComparator - Class in edu.ucsb.nceas.metacat
  A utility class that sorts two node records.
NodeComparator() - Constructor for class edu.ucsb.nceas.metacat.NodeComparator
  Constructor
nodeData - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
nodeDataDate - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
nodeDataNumerical - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
NODEID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
nodeId - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
nodeId - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
nodeIndex - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
NodeRecord - Class in edu.ucsb.nceas.metacat
  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
NodeRecord(long, long, long, String, String, String, String, float, Timestamp) - Constructor for class edu.ucsb.nceas.metacat.NodeRecord
NodeReplicationPolicyChecker - Class in edu.ucsb.nceas.metacat.dataone
  This class enforces the node replication policies such as the allowed node list, maximum size and allowed format list
NodeReplicationPolicyChecker() - Constructor for class edu.ucsb.nceas.metacat.dataone.NodeReplicationPolicyChecker
nodeStack - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
NONAMESPACELOCATION - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
NONAMESPACESCHEMA - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
NONEEXIST - Static variable in class edu.ucsb.nceas.metacat.DBUtil
NONXML - Static variable in class edu.ucsb.nceas.metacat.service.XMLSchemaService
NonXMLMetadataHandler - Class in edu.ucsb.nceas.metacat.object.handler
  The abstract class to save and validate non-xml meta data objects
NonXMLMetadataHandler() - Constructor for class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandler
NonXMLMetadataHandlers - Class in edu.ucsb.nceas.metacat.object.handler
  The factory and utility methods for the NonXMLMetadataHandlers
NonXMLMetadataHandlers() - Constructor for class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandlers
normalize(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  Normalizes a string read from DB.
notationDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler
  Notation declarations are not signaled
notify(String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiErrorEmailAgent
  Send the email with error messages to recipients
notifyMetacatEventObservers(MetacatEvent) - Method in class edu.ucsb.nceas.metacat.event.MetacatEventService
notifyReplicaNodes(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Notify replica Member Nodes of system metadata changes for a given pid

## O

oa - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
oa_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
OAIHandler - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server
  OAIHandler is the primary Servlet for OAICat.
OAIHandler() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
OaipmhHarvester - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
  Main class for running the OAI-PMH Harvester program
OaipmhHarvester() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.OaipmhHarvester
OBJECT - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
OBJECT_FORMAT_DOCID - Static variable in class edu.ucsb.nceas.metacat.dataone.ObjectFormatService
objectExists(Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Determine if an object with the given identifier already exists or not.
objectFileExists(String, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Determine if the object file exist for the given localId.
ObjectFormatService - Class in edu.ucsb.nceas.metacat.dataone
  Implements a subset of the DataONE CNCore services in Metacat.
ObjectPathMap - Class in edu.ucsb.nceas.metacat.dataone.hazelcast
  MapLoader implementation for a hazelcast hzObjectPath.
ObjectPathMap() - Constructor for class edu.ucsb.nceas.metacat.dataone.hazelcast.ObjectPathMap
  creates an ObjectPathMap
oboe - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
OBOE - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
oboe_characteristics - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
oboe_core - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
oboe_sbc - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
OFFLINE_DATA_DISTRIBUTION - Static variable in class edu.ucsb.nceas.metacat.DistributionSection
ONLINE_DATA_DISTRIBUTION - Static variable in class edu.ucsb.nceas.metacat.DistributionSection
openConnection() - Static method in class edu.ucsb.nceas.metacat.database.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
OracleAdapter - Class in edu.ucsb.nceas.dbadapter
  The Oracle db adapter implementation.
OracleAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.OracleAdapter
OrcidService - Class in edu.ucsb.nceas.metacat.annotation
OrcidService() - Constructor for class edu.ucsb.nceas.metacat.annotation.OrcidService
ORE_TER_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
oreExistsFor(Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
  Checks for potential ORE object existence
OrganizationUtil - Class in edu.ucsb.nceas.metacat.util
OstiDOIService - Class in edu.ucsb.nceas.metacat.doi.osti
  The implementation class for the OSTI (DOE Office of Scientific and Technical Information) DOI service Details of OSTI eink: https://www.osti.gov/elink/241-6api.jsp
OstiDOIService() - Constructor for class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Constructor
OstiErrorEmailAgent - Class in edu.ucsb.nceas.metacat.doi.osti
  A class sends emails to clients when errors happened during the interaction process between Metacat and the OSTI Elink service.
OstiErrorEmailAgent() - Constructor for class edu.ucsb.nceas.metacat.doi.osti.OstiErrorEmailAgent
  Constructor - set the email settings
OTHER_OS - Static variable in class edu.ucsb.nceas.metacat.util.SystemUtil
owl - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer

## P

PackageDownloaderV1 - Class in edu.ucsb.nceas.metacat.download
PackageDownloaderV1(Identifier) - Constructor for class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
  Creates a PackageDownloaderV1 object.
PackageDownloaderV2 - Class in edu.ucsb.nceas.metacat.download
  A class that handles downloading data packages under the V2 format.
PackageDownloaderV2(Identifier, ResourceMap, SystemMetadata) - Constructor for class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
  Creates a PackageDownloader object
packagePids - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
params - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
parentId - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
parse() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
  Parse the xml file
parse() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaParser
  Parse the schema file
parseFileInfo(String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
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.util.MetacatUtil
  Utility method to parse the query part of a URL into parameters.
parseTrailing(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
parseXml(String, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
password - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
path - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
PATH4ANCESTOR - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
PathIndexEntry - Class in edu.ucsb.nceas.metacat
  PathIndexEntry contains all of the data fields needed to insert an path into the xml_index table or the xml_path_index table, depending on which constructor is used.
PathIndexEntry(long, String, String, String, long) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry
  Construct a new PathIndexEntry for the xml_index table.
PathIndexEntry(long, String, String, long, String, float, Timestamp) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry
  Construct a new PathIndexEntry for the xml_path_index table.
performPathquery(String, String, String[]) - Method in class edu.ucsb.nceas.metacat.DBQuery
PERMISSION_TYPE_ALLOW - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
PERMISSION_TYPE_DISALLOW - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
PermissionController - Class in edu.ucsb.nceas.metacat
PermissionController(String) - Constructor for class edu.ucsb.nceas.metacat.PermissionController
  Constructor for PermissionController
PermOrderException - Exception in edu.ucsb.nceas.metacat.accesscontrol
  Exception thrown when an error occurs with a permission order
PermOrderException(String) - Constructor for exception edu.ucsb.nceas.metacat.accesscontrol.PermOrderException
  Create a new PermOrderException.
PermOrderException(String, BaseException) - Constructor for exception edu.ucsb.nceas.metacat.accesscontrol.PermOrderException
persistAllProperties() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Save the properties to a properties file.
persistAuthBackupProperties(ServletContext) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Writes out backup configurable properties to a file.
persistAuthBackupProperties(ServletContext) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
persistAuthBackupProperties(ServletContext) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Writes out backup configurable properties to a file.
persistAuthBackupProperties(ServletContext) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
persistBackupProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Writes out backup configurable properties to a file.
persistMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Writes out backup configurable properties to a file.
persistMainBackupProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
persistMainBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Writes out backup configurable properties to a file.
persistMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
persistProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Save the properties to a properties file.
persistProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
persistProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Save the properties to a properties file.
persistProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Save the properties to a properties file.
persistProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Save the properties to a properties file.
pidMapping - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
ping() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Low level, "are you alive" operation.
ping() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
ping() - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
PINode - Class in edu.ucsb.nceas.metacat
  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
pointShpUri - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
polygonShpUri - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
populate() - Method in class edu.ucsb.nceas.metacat.util.MetacatPopulator
  populate from the source
populateAllowedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Get the vector of allowed submitter credentials from metacat.properties and put into global allowedSubmitters list
populateDAO(ResultSet) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Populate a job data object with the current row in a resultset
populateDAO(ResultSet) - Method in class edu.ucsb.nceas.metacat.shared.BaseAccess
populateDAO(ResultSet) - Method in class edu.ucsb.nceas.metacat.XMLQueryresultAccess
  Populate a job data object with the current row in a resultset
populateRegisteredSchemaList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Populate the list of registered schemas.
PORTAL - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
PortalQuotaService - Class in edu.ucsb.nceas.metacat.dataone.quota
  A class enforce the portal quota service, which controls how many portals users can create
POST - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  HTTP Verb POST
POST - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  HTTP Verb POST
post(HttpClient, String, HashMap<String, String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Post a request and return the response body
PostgresDatabaseConnectionPool - Class in edu.ucsb.nceas.metacat.dataquery
  This class implements DataConnetionPoolInterface to provide a connection for testing.
PostgresDatabaseConnectionPool() - Constructor for class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
  Constructor.
PostgresqlAdapter - Class in edu.ucsb.nceas.dbadapter
  The PostgreSQL db adapter implementation.
PostgresqlAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
postQuery(Session, String, HashMap<String, String[]>) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Handle the query sent by the http post method
predicate2SQL(String, List<Object>) - Static method in class edu.ucsb.nceas.metacat.QueryTerm
PREDICATE_END - Static variable in class edu.ucsb.nceas.metacat.QuerySpecification
PREDICATE_START - Static variable in class edu.ucsb.nceas.metacat.QuerySpecification
prepareAndThrowNotAuthorized(Session, Identifier, Permission, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
prepareStatement(String) - Method in class edu.ucsb.nceas.metacat.database.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.
PRIMARY_SHOULDER_INDEX - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
printCSV(File) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  print the CSV file with no sorting
printError(String, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  Prints xml response
printExtendedSQL(String, boolean, List<Object>, List<Object>) - 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
printLogMsg(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  print a message to the log in real-time
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
printSearchExprSQL(List<Object>) - Method in class edu.ucsb.nceas.metacat.QueryTerm
printSortedCSV(File, String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  print a sorted CSV file.
printSQL(boolean, List<Object>) - Method in class edu.ucsb.nceas.metacat.QueryGroup
  create a SQL serialization of the query that this instance represents
printSQL(boolean, List<Object>) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  create a SQL serialization of the query that this instance represents
printSQL(boolean, List<Object>) - 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.accesscontrol.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.
Profile() - Constructor for class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
PropertiesAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the main properties configuration page and the processing of the configuration values.
PropertiesInterface - Interface in edu.ucsb.nceas.metacat.properties
  This interface will handle properties access
PROPERTY_NOT_FOUND - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
PROPERTYNAMEOFPORTALNAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
PropertyService - Class in edu.ucsb.nceas.metacat.properties
  A suite of utility classes for the metadata configuration utility
prov - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
prov_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
proxyKey - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
pub - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
PUBLICID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
publish(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Given an existing Science Metadata PID, this method mints a DOI and updates the original object "publishing" the update with the DOI.
publish(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
publish(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
publish(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Make status of the given identifier (e.g.
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
  Make the status of the identifier to be public
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
  Make the status of the identifier to be public
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Make the status of the identifier to be public
publishIdentifier(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Make the status of the identifier public
PUT - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  HTTP Verb PUT
PUT - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  HTTP Verb PUT
putObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
putObject(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
  Inserts or updates the object
putObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
putObject(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Inserts or updates the object

## Q

QUANTITY - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
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, String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Query the metacat document store with the given metacat-compatible query document and qformat, 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 default qformat xml, and return the result set as a Reader.
query(Reader, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Query the metacat document store with the given metacat-compatible query document and qformat, and return the result set as a Reader.
query(Reader) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  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.rest.MetacatRestClient
  Query the metacat document store with the given Ecogrid-compatible query document and return the Ecogrid result set as a Reader.
query(String, String, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  Query metacat for documents that 'CONTAINS' the value at the specified XPath expression.
query(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
query(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
query(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
query(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
query(String, Set<Subject>, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
  Query the solr server
query(SolrParams, Set<Subject>, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
  Use the default GET method to handle the query when the query is on the key/value format
query(SolrParams, Set<Subject>, boolean, SolrRequest.METHOD) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
  Handle the query when the query is on the key/value format
query(String, Hashtable<String, String[]>, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
queryAllDocids() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Returns a Vector of all the current versions of public docids
QueryGroup - Class in edu.ucsb.nceas.metacat
  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
QueryResultTableBuilder - Class in edu.ucsb.nceas.metacat
  QueryResutlTableBuilder is class to build xml_queryresult table during metacat initialization.
QuerySpecification - Class in edu.ucsb.nceas.metacat
  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
querySystemMetadata(Date, Date, ObjectFormatIdentifier, NodeReference, int, int, Identifier, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  query the systemmetadata table based on the given parameters
QueryTerm - Class in edu.ucsb.nceas.metacat
  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)
quickCreate(Object, String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
  Allows classes that implement RecordFactory to override the default create() method.
QuotaAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the quota -service configuration page and the processing of the configuration values.
QuotaDBManager - Class in edu.ucsb.nceas.metacat.dataone.quota
  Represents a class to manipulate the usages table for the quota service in the postgresql database
QuotaDBManager() - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
QUOTAID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
QuotaService - Class in edu.ucsb.nceas.metacat.dataone.quota
  A class represents an abstract quota service.
QuotaService() - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
QuotaServiceManager - Class in edu.ucsb.nceas.metacat.dataone.quota
  A class manages the quota service for users
QUOTASUBJECT - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
QUOTASUBJECTHEADER - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
QUOTATYPE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
QuotaTypeDeterminer - Class in edu.ucsb.nceas.metacat.dataone.quota
  A class to decide the quota type (storage, portal and etc) based on the given name space
QuotaTypeDeterminer(List<String>) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
  Constructor

## R

rdf - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
RDF_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
RDF_SYNTAX_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
rdfs - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
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) - Static method in class edu.ucsb.nceas.metacat.MetacatHandler
  Read a document from metacat and return the InputStream.
read(String, String) - Static method in class edu.ucsb.nceas.metacat.MetacatHandler
  Read a document from metacat and return the InputStream.
readArchiveEntry(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String, String[]) - Method in class edu.ucsb.nceas.metacat.ArchiveHandler
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
readDTDSchema(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
  read DTD or Schema file from Metacat's XML catalog system
readFromFileSystem(OutputStream, String, String[], String) - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  Read the XML document from the file system and write to a Writer.
readFromMetacat(String, String, HttpServletResponse, OutputStream, String, String, String, String[], boolean, Hashtable<String, String[]>) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  read metadata or data from Metacat
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, String) - Static method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
ReadOnlyChecker - Class in edu.ucsb.nceas.metacat
  A checker to determine if the Metacat is in the read-only mode by checking the property of database.readOnly.
ReadOnlyChecker() - Constructor for class edu.ucsb.nceas.metacat.ReadOnlyChecker
  Default constructor
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.
redirectResponse(HttpServletRequest, HttpServletResponse, String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
  Redirect a response.
refresh() - Static method in class edu.ucsb.nceas.metacat.dataone.NodeReplicationPolicyChecker
  Refresh those properties from the metacat.peroperties file
refresh() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
refreshable() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
refreshable() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Indicate whether or not this service is refreshable.
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
refreshable() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
refreshable() - Method in class edu.ucsb.nceas.metacat.service.SessionService
refreshable() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
refreshable() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
refreshService(String) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
  Refresh a service.
refreshStatus() - Method in class edu.ucsb.nceas.metacat.doi.DOIService
  Refresh the status (enable or disable) of the DOI service from property file
refreshSystemMetadataEntry(String) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  When Metacat changes the underlying store, we need to refresh the in-memory representation of it.
regenerate() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  Completely regenerates the spatial cache.
REGISTER - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
REGISTERANDUPDATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
REGISTERANDUPDATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
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, String, Date, Date) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Register a document that resides on the filesystem with the database.
registerDOI(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
  Submits DOI metadata information about the object to DOI services
registerService(String, BaseService) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
  Register a service with the system.
registerSession(String, String, String[], String, String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Register a session in the session hash table.
registerSession(SessionData) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Register a session in the session hash table.
registerSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Provides a mechanism for adding system metadata independently of its associated object, such as when adding system metadata for data objects.
registerSystemMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
registerSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
registerSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Register System Metadata without data or metadata object
registerSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Register System Metadata without data or metadata object
REGISTERWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
RelationHandler - Class in edu.ucsb.nceas.metacat
RelationHandler(String, String, DBConnection, TripleCollection) - Constructor for class edu.ucsb.nceas.metacat.RelationHandler
  Constructor for this class.
release() - Static method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
  Method to shut down all connections
RemoteDocument - Class in edu.ucsb.nceas.metacat
  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
remove(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
remove(String, String) - Method in class edu.ucsb.nceas.metacat.IndexingQueue
  Removes the Indexing Task object from the queue for the given docid.
removeDocument(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
removeField(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
removeIdFromIdentifierTable(Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
removeIdSchemePrefix(String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Remove the sheme prefix for a given id.
RemoveInvalidReplicas - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Used for forcibly removing invalid replicas from a target node.
RemoveInvalidReplicas() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
removeMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  remove a mapping in the identifier table
removeMetacatEventObserver(MetacatEventObserver) - Method in class edu.ucsb.nceas.metacat.event.MetacatEventService
removeSolrIndex(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
removeSystemMetaAndIdentifier(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
removeUserFromGroup(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
  Remove a user from a group.
removeXMLAccessForPrincipal(String, String, Long) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Remove xml access.
REPLACE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
replaceAccess(String, List<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
  Set permissions for a given document.
replaceObsoletedId(Identifier, Identifier, OutputStream, Subject) - Method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Create new resource map by replacing obsoleted ids by new ids.
replaceWhiteSpaceForURL(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  A method to replace whitespace in url
replicate(Session, SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Called by a Coordinating Node to request that the Member Node create a copy of the specified object by retrieving it from another Member Node and storing it locally so that it can be made accessible to the DataONE system.
replicate(SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
replicate(Session, SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
REPLICATION_LOG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
ReplicationAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the database configuration page and the processing of the configuration values.
ReplicationHandler - Class in edu.ucsb.nceas.metacat.replication
  This class handles deltaT replication checking.
ReplicationHandler() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationHandler
ReplicationHandler(int) - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationHandler
ReplicationServer - Class in edu.ucsb.nceas.metacat.replication
  A class express a entry in xml_replication.
ReplicationServer() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Constructor of ReplicationServer
ReplicationServerList - Class in edu.ucsb.nceas.metacat.replication
  A class represent a replication server list in xml_replcation table
ReplicationServerList() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  constructor of ReplicationServerList It will build server list.
ReplicationService - Class in edu.ucsb.nceas.metacat.replication
ReplicationServlet - Class in edu.ucsb.nceas.metacat.replication
ReplicationServlet() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationServlet
REPLICATIONUSER - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
ReplicationUtil - Class in edu.ucsb.nceas.metacat.util
  A suite of utility classes for the system metadata replication functions
ReplicationUtil() - Constructor for class edu.ucsb.nceas.metacat.util.ReplicationUtil
ReplMessageHandler - Class in edu.ucsb.nceas.metacat.replication
  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.replication.ReplMessageHandler
replToServer(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  Returns true if the replicate field for server in xml_replication is 1.
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.CreateUsageTask
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.DeleteUsageTask
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.UpdateUsageTask
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
  The child class needs to implement this method to detail how to report the usage to the remote book keeper server.
request - Variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  For logging the operations
request - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
REQUESTOR - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
RequestUtil - Class in edu.ucsb.nceas.metacat.util
RESCHEDULE_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
reserveIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Given an optional scope and format, reserves and returns an identifier within that scope and format that is unique and will not be used by any other sessions.
reserveIdentifier(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
reserveIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
reset() - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  reset all times in the singleton
resolve(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Resolve the location of a given object
RESOLVE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
resolve(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
resolve(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
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)
resolveMultipart(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
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
RESOURCE - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
RESOURCE_ACCESS_RULES - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_BASE_URL - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_ERROR - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_ERROR - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_FORMATS - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_FORMATS - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_GENERATE_ID - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_GENERATE_ID - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_IDENTIFIER - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  API IDENTIFIER Resource which controls object unique identifier operations
RESOURCE_IS_AUTHORIZED - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_LOG - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_MAP_PREFIX - Static variable in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
RESOURCE_META - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_META_CHANGED - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_META_CHANGED - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_MONITOR - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_MONITOR - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_NODE - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_NODE - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_OBJECTS - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  API OBJECTS Resource which handles with document operations
RESOURCE_OBJECTS - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_OWNER - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_OWNER - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_PACKAGE - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_PACKAGE - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_PUBLISH - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_PUBLISH - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_PUBLISH_IDENTIFIER - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_QUERY - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_REPLICAS - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_REPLICAS - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_REPLICATE - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_REPLICATE - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_REPLICATION_AUTHORIZED - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_REPLICATION_AUTHORIZED - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_REPLICATION_META - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_REPLICATION_META - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_REPLICATION_NOTIFY - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_REPLICATION_NOTIFY - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_REPLICATION_POLICY - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_REPLICATION_POLICY - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_RESERVE - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  CN-specific operations
RESOURCE_RESERVE - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  CN-specific operations
RESOURCE_RESOLVE - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
RESOURCE_RESOLVE - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
RESOURCE_SESSION - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  API SESSION Resource which handles with user session operations
RESOURCE_TOKEN - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_TOKEN - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_VIEWS - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
RESOURCE_VIEWS - Static variable in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
RESOURCE_WHOAMI - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
ResourceMapModifier - Class in edu.ucsb.nceas.metacat.dataone.resourcemap
  This class will create a new resource map by modifying a given resourceMap input stream.
ResourceMapModifier(Identifier, InputStream, Identifier) - Constructor for class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
  Constructor
response - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
ResponseUtil - Class in edu.ucsb.nceas.metacat.util
resultsetToHTML(String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.Stylizer
  Applies the resultset.xsl stylesheet to the pathquery result string returned by Metacat.
resynchInThread() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
returnConnection(Connection) - Method in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
  Returns checked out dabase connection to the pool
returnDBConnection(DBConnection, int) - Static method in class edu.ucsb.nceas.metacat.database.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<NodeRecord>) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
  Revise stack change a stack to opposite order
revision - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
REVISIONTABLE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
rollback() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Method to roll back
rootNode - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
rootnodeid - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
run() - Method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
  periodically to recycle the connection
run() - Method in class edu.ucsb.nceas.metacat.dataone.quota.FailedReportingAttemptChecker
  It will get the list of unreported usages and re-submit them to the book keeper server again.
run() - Method in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
run() - Method in class edu.ucsb.nceas.metacat.EML201DocumentCorrector
  It will remove the records - attribute system="document" of element "refrence" in both xml_nodes and xml_index table.
run() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
  Runs the Harvester main program in a separate thread.
run() - Method in class edu.ucsb.nceas.metacat.IndexingTimerTask
run(String, String, String, String, String, String, String) - Static method in class edu.ucsb.nceas.metacat.oaipmh.harvester.OaipmhHarvester
  Runs a OAI-PMH harvest.
run() - Method in class edu.ucsb.nceas.metacat.QueryResultTableBuilder
  Builds the result table base on the given docid list and returnfields
run() - Method in class edu.ucsb.nceas.metacat.replication.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.replication.ReplicationHandler
  Method that implements TimerTask.run().
run() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
  this method handles the timeout for a file lock.
run() - Method in class edu.ucsb.nceas.metacat.Sitemap
  Execute the timed task when called, in this case by generating the sitemap files needed for this Metacat instance.
runOnce() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
runSQLFile(String) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Runs the commands in a sql script.
runVerb() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Preforms the OAI request for this OAI-PMH verb

## S

save(InputStream, SystemMetadata, Session, EventLogData) - Method in class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandler
  Save the bytes to the disk
save() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
  Saves the SpatialDataset object to the spatial cache.
saveReplication(InputStream, String, SystemMetadata, String, int, String, EventLogData) - Method in class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandler
  Save the bytes to the disk from a replication process
SCHEDULE_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
scheduleSitemapGeneration() - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  Schedule the sitemap generator to run periodically and update all of the sitemap files for search indexing engines
SCHEMA - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
SCHEMA_DIR - Static variable in class edu.ucsb.nceas.metacat.service.XMLSchemaService
SCHEMA_LOCATION_V2_0 - Static variable in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
schemaList - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
SCHEMALOCATION - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
SCHEMALOCATIONKEYWORD - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
SchemaLocationResolver - Class in edu.ucsb.nceas.metacat
  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
SchemaLocationResolver(String, String) - Constructor for class edu.ucsb.nceas.metacat.SchemaLocationResolver
  Construct an instance of the SchemaLocationResolver class
SCHEMAVALIDATIONFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
search(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Metacat does not implement this method at the CN level
search(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
search(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
SearchServlet - Class in edu.ucsb.nceas.metacat.advancedsearch
SearchServlet() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.SearchServlet
searchUser(String, String[][]) - Static method in class edu.ucsb.nceas.metacat.AuthLdap
  Method for getting index of user DN in User info array
SECONDHIGHESTVERSION - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
SELECT_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
send(HttpServletResponse, String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
sendErrorXML(HttpServletResponse, Long, BaseException) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
sendErrorXML(HttpServletResponse, Long, String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
sendParameters(Properties) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Send a request to Metacat.
sendParametersInverted(Properties) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Send a request to Metacat.
sendSuccessXML(HttpServletResponse, String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
serializeDoc(Document) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
  Serialize the given doc object to a string
serializeException(BaseException, OutputStream) - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
  serialize a D1 exception using jibx
serverAt(int) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  Method to get a server object given a index number
serverCode - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
serviceBaseUrl - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
ServiceException - Exception in edu.ucsb.nceas.metacat.shared
  Exception thrown when an error occurs in a configuration administrative class
ServiceException(String) - Constructor for exception edu.ucsb.nceas.metacat.shared.ServiceException
  Create a new AdminException.
ServiceException(String, BaseException) - Constructor for exception edu.ucsb.nceas.metacat.shared.ServiceException
ServiceService - Class in edu.ucsb.nceas.metacat.service
servletContext - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
session - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
session2 - Variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  out-of-band session object to be used when not passed in as a method parameter
SessionData - Class in edu.ucsb.nceas.metacat.util
SessionData(String, String, String[], String, String) - Constructor for class edu.ucsb.nceas.metacat.util.SessionData
SessionService - Class in edu.ucsb.nceas.metacat.service
set_sitemapScheduled(boolean) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
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) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
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.
setAccess(String, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Set access for a given doc id.
setAccess(String, String, String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
  set the access permissions on the document specified
setAccess(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  set the access perms on a document
setAccess(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  set the access perms on a document
setAccessPolicy(Session, Identifier, AccessPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Set access for a given object using the object identifier and a Subject under a given Session.
setAccessPolicy(Identifier, AccessPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
setAccessPolicy(Session, Identifier, AccessPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
setAccessSection(AccessSection) - Method in class edu.ucsb.nceas.metacat.DistributionSection
setAction(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property action.
setAction(String) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
setAge(long) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a connection age to this object
setAnyfield(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property anyfield.
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.database.DBConnection
  Method to set commit mode
setBoundaryContained(boolean) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setCaseSensitive(boolean) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setCheckOutMethodName(String) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a method name to the checkOutMethodName
setCheckOutSerialNumber(int) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set check out serial number to this object
setCheckOutTime(long) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set check out time to this object
setConnections(Connection) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a connection to this object
setConnectionTime(long) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a connection time to this object It is accumulated
setContainsExtenedSQL(boolean) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  set if this query sepcification has extendQuery(has return doc type or not)
setContentStandard(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property contentStandard.
setContextRootUrl(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  When the MetacatFactory creates an instance it needs to set the MetacatUrl to which connections should be made.
setContextRootUrl(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
setControlLevel(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set a controllevel
setCoreMessage(String) - Method in exception edu.ucsb.nceas.metacat.shared.BaseException
setCreateTime(long) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a usage number to this object
setCreatorOrganization(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setCreatorOrganizationQueryType(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setCreatorSurname(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setCreatorSurnameQueryType(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setDataFileName(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set the dataFileName
setDataFileName(int, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Indexed setter for property dataFileName.
setDataFileName(String[]) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property dataFileName.
setDataFileName(String) - Method in class edu.ucsb.nceas.metacat.DistributionSection
  Set the online data file name
setDataReplication(boolean) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Set data replication option
setDateField(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setDescribedIdList(Vector<String>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set a described id list (in data access part)
setDirPath(String) - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
setDistributionId(int) - Method in class edu.ucsb.nceas.metacat.DistributionSection
  Set the distribution id
setDistributionType(int) - Method in class edu.ucsb.nceas.metacat.DistributionSection
  Set the distribution type
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.clientview.ClientView
  Setter for property docId.
setDocid(String) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
setDocid(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
  Set the document identifier.
setDocId(String) - Method in class edu.ucsb.nceas.metacat.SubTree
  Set the a docId
setDoctype(String) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
setDocumentCart(DocumentCart) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setEastBound(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setEncoding(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Returns the character encoding used used when communicating with Metacat.
setEncoding(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
setEncoding(String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
setEndDate(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setEndNodeId(long) - Method in class edu.ucsb.nceas.metacat.SubTree
  Set a end node id
setEnforcePublisEntirePackage(boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Set the value if Metacat need to make the entire package public during the publish process
setEvent(String) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.V1LogEntryWrapper
setEvent(Event) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.V2LogEntryWrapper
setEvent(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
  Set the current value of the event.
setExternalFileUri(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Sets the external file uri.
setField(String, String) - Method in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
setFileName(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Set the file name.
setFileNamespace(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Sets the file namespace
setFilterDocList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  method to set the list of filter docs of this query
setForceRebuild(boolean) - Static method in class edu.ucsb.nceas.metacat.DBTransform
  Set the field of forceRebuild
setFormAllAny(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setFormatId(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
  Set the format id.
setGroup(String[]) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Method to set user group
setGroupNames(String[]) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setGroups(String[]) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
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.replication.ReplicationServer
  Set hub option
setIdentifier(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  method to set the identifier of this query
setIncludeOuterQueryGroup(boolean) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryGroup
  Sets the boolean value of includeOuterQueryGroup.
setInUnionGroup(boolean) - Method in class edu.ucsb.nceas.metacat.QueryTerm
  Set the query term in a union group
setIpAddress(String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Set the ip address for the service
setIpAddress(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
  Set the current value of the internet protocol address.
setIsLoggedLocally(boolean) - Method in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
  Set the property if the usage has been logged locally or not
setIsRevisionDoc(boolean) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  Set the the handler is for revisionDoc
setLastAccessedTime() - Method in class edu.ucsb.nceas.metacat.util.SessionData
setLastCheckedDate(Date) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Set a string as last checked date
setLocalId(int) - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Set the local id
setLocationName(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setLoggedIn(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
  After calling "login(ldapUserName, pwd)", call this with the username and servers response message.
setLoggedIn(boolean) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setMessage(int, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Indexed setter for property message.
setMessage(String[]) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property message.
setMetacatRunning(boolean) - Method in class edu.ucsb.nceas.metacat.IndexingQueue
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.
setMetadataDoc(Document) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setMetadataDoc(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setMetadataDoc(InputStream) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setMetaFileDocId(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property isMetaFileDocId.
setMetaFileName(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property metaFileName.
setName(String) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setNamedTimescale(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setNamedTimescaleQueryType(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
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.NodeRecord
  A method used to set the node data of the current node
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
setNodeDataDate(Timestamp) - Method in class edu.ucsb.nceas.metacat.NodeRecord
setNodeDataNumerical(float) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the numerical node data of the current node
setNodeID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode
  Set the id of this node
setNodeId(long) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the node id of the current node
setNodeIndex(int) - Method in class edu.ucsb.nceas.metacat.BasicNode
  Set the node index of this node
setNodeIndex(long) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the node index of the current node
setNodeName(String) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the node name of the current node
setNodePrefix(String) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the node prefix of the current node
setNodeType(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
  Set the type of this node
setNodeType(String) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the node type of the current node
setNoNamespaceSchemaLocation(String) - Method in class edu.ucsb.nceas.metacat.service.XMLNoNamespaceSchema
  Set the no-namespace-schemal-location uri
setNorthBound(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setObsoletedBy(Session, Identifier, Identifier, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Set the obsoletedBy attribute in System Metadata
setObsoletedBy(Identifier, Identifier, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
setObsoletedBy(Session, Identifier, Identifier, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
setObsoletedBy(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Update the system metadata for a given pid, setting it to be obsoleted by the obsoletedByPid
setObsoletedBy(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Update the system metadata for a given pid, setting it to be obsoleted by the obsoletedByPid
setOperator(String) - Method in class edu.ucsb.nceas.metacat.DBQuery
  Specifies if and how docid overrides should be included in the general query
setOrganization(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
setOrganization(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property organization.
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
setParentNodeId(long) - Method in class edu.ucsb.nceas.metacat.NodeRecord
  A method used to set the node parent id of the current node
setPassword(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
setPassword(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property password.
setPassword(String) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setPathExpr(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property pathExpr.
setPathValue(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property pathValue.
setPermission(int) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
  Set a permission.
setPermissionOrder(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set a permissionOrder
setPermissionType(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
  Set the permssionType
setPreparedStatementValues(List<Object>, PreparedStatement) - Static method in class edu.ucsb.nceas.metacat.DBQuery
  Set the parameter values in the prepared statement using instrospection of the given value objects
setPrincipal(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
  Set the current value of the principal.
setProperty(String, String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Utility method to set a property value both in memory and to the properties file
setProperty(String, String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
setProperty(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Utility method to set a property value both in memory and to the properties file
setProperty(String, String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Utility method to set a property value both in memory and to the properties file
setProperty(String, String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Utility method to set a property value both in memory and to the properties file
setPropertyNoPersist(String, String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
  Utility method to set a property value in memory.
setPropertyNoPersist(String, String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
setPropertyNoPersist(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Utility method to set a property value in memory.
setPropertyNoPersist(String, String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
  Utility method to set a property value in memory.
setPropertyNoPersist(String, String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
  Utility method to set a property value in memory.
setPublicAccess(boolean) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property publicAccess.
setQformat(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property qformat.
setQformat(String) - Method in class edu.ucsb.nceas.metacat.DBQuery
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
setQuotaType(String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Set the given quota type to the usage
setRecommendedExternalDir(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  Sets the recommended external directory.
setReferences(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set a references
setReplication(boolean) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Set replication option
setReplicationPolicy(Session, Identifier, ReplicationPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Set the replication policy for an object given the object identifier It only is applied to objects whose authoritative mn is a v1 node.
setReplicationPolicy(Identifier, ReplicationPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
setReplicationPolicy(Session, Identifier, ReplicationPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
setReplicationPolicy(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Pass the request to set the replication policy to CNodeService
setReplicationPolicy(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Pass the request to set the replication policy to CNodeService
setReplicationStatus(Session, Identifier, NodeReference, ReplicationStatus, BaseException) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Set the replication status for an object given the object identifier
setReplicationStatus(Identifier, NodeReference, ReplicationStatus, BaseException) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
setReplicationStatus(Session, Identifier, NodeReference, ReplicationStatus, BaseException) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
setReplicationStatus(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Pass the request to set the replication status to CNodeService
setReplicationStatus(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Pass the request to set the replication status to CNodeService
setReportedDateAndRemoteId(int, Date, int) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
  Set the reported date and remote id for a given usage local id
setRequestErrors(HttpServletRequest, Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Add a list of errors to the request.
setRequestFormErrors(HttpServletRequest, Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Add a list of form errors to the request.
setRequestHeader(String, String) - Method in class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection
  Set the request header for the URL
setRequestMessage(HttpServletRequest, Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Add a list of general messages to the request.
setRequestor(String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Set requestor for this usage
setRequestSuccess(HttpServletRequest, Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Add a list of success messages to the request.
setReturnDocList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  method to set the list of return docs of this query
setReturnfield(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property returnfield.
setReturnFieldList(Vector) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  method to set the list of fields to be returned by this query
setRightsHolder(Session, Identifier, Subject, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Changes ownership (RightsHolder) of the specified object to the subject specified by userId
setRightsHolder(Identifier, Subject, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
setRightsHolder(Session, Identifier, Subject, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
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.
setServerLocation(int) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
setServerLocation(int) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
setServerLocation(int) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
setServerLocation(int) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
setServerName(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
  Set a sting as server name
setSession(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Set the out-of-band session
setSession(Session) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
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.
setSessionId(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Set the session identifier for this session.
setSessionId(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
setSessionid(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property sessionid.
setSessionId(String) - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
setSiteValue(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setSkinName(Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.SkinUtil
  Set the names of skin.
setSouthBound(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setStartDate(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setStartedDescribesNodeId(long) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set the start "describes" node id
setStartElementName(String) - Method in class edu.ucsb.nceas.metacat.SubTree
  Set a startElementName
setStartNodeId(long) - Method in class edu.ucsb.nceas.metacat.SubTree
  Set a start node id
setStatus(int) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a connection status to this object
setStoredTmpNodeStack(Stack<NodeRecord>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
  Set a storedTempNodeStack
setSubjectAllAny(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
  Sets the subjectAllAny value.
setSubjectField(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setSubjectQueryType(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setSubjectValue(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setSubscriber(String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
  Set the subscriber associated with the usage
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
setSystemMetadata(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.restservice.multipart.MultipartRequestWithSysmeta
  Set the system meta data for this request
setTag(String) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a connection status to this object
setTagName(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
  Set the name of this node
setTaxon(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setTaxonQueryType(int) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
setTextContent(XPath, Node, String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setUsageCount(int) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a usage number to this object
setUser(String) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
setUserAgent(String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Set the user agent for the service
setUserAgent(String) - Method in class edu.ucsb.nceas.metacat.EventLogData
setUserId(HttpServletRequest, String) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
  Add the user's login id to the session on this request
setUsername(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
setUsername(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
  Setter for property username.
setUserName(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setUserName(String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
  Method to set user name
setUserName(String) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setWarningMessage(SQLWarning) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
  Set a warning message to this object
setWestBound(String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
shoulderMap - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
shrinkConnectionPoolSize() - Static method in class edu.ucsb.nceas.metacat.database.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 initial value
shrinkDBConnectionPoolSize() - Static method in class edu.ucsb.nceas.metacat.database.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
SimpleProperties - Class in edu.ucsb.nceas.metacat.properties
  A suite of utility classes for the metadata configuration utility
SimpleProperties() - Constructor for class edu.ucsb.nceas.metacat.properties.SimpleProperties
  private constructor since this is a singleton
site - Variable in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
siteKeywords - Variable in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
Sitemap - Class in edu.ucsb.nceas.metacat
  A Sitemap represents a document that lists all of the content of the Metacat server for use by harvesting spiders that wish to index the contents of the Metacat site.
Sitemap(File, String, String, String, List<String>) - Constructor for class edu.ucsb.nceas.metacat.Sitemap
  Construct a new instance of the Sitemap class.
siteNames - Variable in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
sites - Variable in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
size() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
  Method to get the size of serverList
sizeOfStream(InputStream) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
  Find the size (in bytes) of a stream.
SkinPropertyService - Class in edu.ucsb.nceas.metacat.properties
  A suite of utility classes for the skin configuration utility
SkinsAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the skins configuration page and the processing of the configuration values.
SkinUtil - Class in edu.ucsb.nceas.metacat.util
SLASH - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
SldFactory - Class in edu.ucsb.nceas.metacat.spatial
  Class to generate Styled Layer Descriptors allowing geoserver to filter the feature rendering based on various contraints such as permissions, non-spatial queries and skin configuration.
SldFactory() - Constructor for class edu.ucsb.nceas.metacat.spatial.SldFactory
SolrAdmin - Class in edu.ucsb.nceas.metacat.admin
  Control the display of the Solr configuration page and the processing of the configuration values.
SolrConfigUpgrader - Class in edu.ucsb.nceas.metacat.admin.upgrade.solr
  This class represents an object to upgrade the solrconfig.xml on the Metacat upgrade process.
SolrConfigUpgrader() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrConfigUpgrader
  Constructor
SOLRCORENAME - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
SolrSchemaModificationException - Exception in edu.ucsb.nceas.metacat.admin.upgrade.solr
  An exception happens when an administrator modified a the schema.xml in the solr home.
SolrSchemaModificationException(String) - Constructor for exception edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrSchemaModificationException
  Constructor
SolrSchemaUpgrader - Class in edu.ucsb.nceas.metacat.admin.upgrade.solr
  This class will overwrite the existing schema under the /solr-home/conf/schema.xml Here is the algorithm: 1.
SolrSchemaUpgrader() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrSchemaUpgrader
  Constructor
SolrVersionChecker - Class in edu.ucsb.nceas.metacat.admin
  This class will check if the given solr home directory is for an embedded solr server which is used in the earlier Metacat versions.
SolrVersionChecker() - Constructor for class edu.ucsb.nceas.metacat.admin.SolrVersionChecker
  Default constructor to initialize the parser factory.
sortProfiles(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  sort the profiles by "callorder", "callcount" or "total"
SpatialDataset - Class in edu.ucsb.nceas.metacat.spatial
  Class providing direct read/write access to the persistent spatial cache.
SpatialDataset() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialDataset
  empty constructor for SpatialDataset
SpatialDocument - Class in edu.ucsb.nceas.metacat.spatial
  Class representing the spatial portions of an xml document as a geotools Feature.
SpatialDocument(String, DBConnection) - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialDocument
  Constructor that queries the db
SpatialFeatureSchema - Class in edu.ucsb.nceas.metacat.spatial
  Class representing the geotools feature schemas and file paths for the spatial data cache.
SpatialFeatureSchema() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
  empty constructor
SpatialHarvester - Class in edu.ucsb.nceas.metacat.spatial
  Harvests spatial data from metacat database and saves to persistent cache
SpatialHarvester() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
  constructor to initialize db connection
SpatialQuery - Class in edu.ucsb.nceas.metacat.spatial
  Class to query the persistent spatial cache and returns docids matching spatial constraints
SpatialQuery() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialQuery
  empty constructor to initialize spatial query
speedBag - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
speedBag - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
split(String, String, String) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
  Convert a delimited string to a Vector by splitting on a particular character
SqlserverAdapter - Class in edu.ucsb.nceas.dbadapter
  The MS SQL Server db adapter implementation.
SqlserverAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.SqlserverAdapter
srid - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
start - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
startCDATA() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
  SAX Handler that receives notification of the start of CDATA sections
startCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of the start of CDATA sections
startDailyCheck() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
  Start a timer to check failed usage reporting and report them again in daily base.
startDocument() - Method in class edu.ucsb.nceas.metacat.accesscontrol.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
startDocument() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
startDTD(String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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.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.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.MetacatResultSet
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.replication.ReplMessageHandler
  This method starts a new vector for each updatedDocument tag.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
  SAX Handler that is called at the start of each XML element
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaParser
  SAX Handler that is called at the start of each XML element
startElementName - Variable in class edu.ucsb.nceas.metacat.SubTree
startEntity(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.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
startReplication(Hashtable<String, String[]>) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
STARTS_WITH - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
startTag - Static variable in class edu.ucsb.nceas.metacat.util.ReplicationUtil
startTime(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  start the timing on a profile
stateChanged(LifecycleEvent) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  In cases where this cluster is paused, we want to check that the local store accurately reflects the shared SystemMetadata map
STATUS - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
stop() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
stop() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
  Stop the HazelcastService.
stop - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
stop() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
stop() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
stop() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
stop() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
stop() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
stop() - Method in class edu.ucsb.nceas.metacat.service.SessionService
stop() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
stop() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
stopAllServices() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
stopReplication() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
stopTime(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
  stop the timing on a profile
STORAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
store(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
store(Identifier, IndexEvent) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
storeAll(Map<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
storeAll(Map<Identifier, IndexEvent>) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
storeExternalDirLocation(String) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
  Store the location of the backup file location into a file at //backup-location
StreamingMultipartRequestResolver - Class in edu.ucsb.nceas.metacat.restservice.multipart
  This class will stream the file parts of the multipart request into a temporary file.
StreamingMultipartRequestResolver(String, int) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
  Constructor
Stylizer - Class in edu.ucsb.nceas.metacat.advancedsearch
Stylizer() - Constructor for class edu.ucsb.nceas.metacat.advancedsearch.Stylizer
SUB_DOCS_PATH - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
SUBJECTS - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
submit(Identifier, SystemMetadata, Map<String, List<Object>>, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
  Submit the index task to the index queue
submit(Identifier, SystemMetadata, boolean, Map<String, List<Object>>, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
submitDeleteTask(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
  Submit a deleting-index task
submitDOIMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
  Submit the doi metadata for the given id.
submitDOIMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
  Submit the metadata to the EZID service for a specific identifier(DOI).
submitDOIMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
  Submit the metadata in the osti service for a specific identifier(DOI).
SubTree - Class in edu.ucsb.nceas.metacat
  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
subTreeId - Variable in class edu.ucsb.nceas.metacat.SubTree
subversions - Variable in class edu.ucsb.nceas.metacat.Version
SUCCESS - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
sync(List<String>) - Method in class edu.ucsb.nceas.metacat.dataone.SyncAccessPolicy
  Convenience function that accepts a list of guids to sync
SyncAccessPolicy - Class in edu.ucsb.nceas.metacat.dataone
SyncAccessPolicy() - Constructor for class edu.ucsb.nceas.metacat.dataone.SyncAccessPolicy
syncAll() - Method in class edu.ucsb.nceas.metacat.dataone.SyncAccessPolicy
  For all guids for which current MN is authoritative, check that access policy is synced with CN.
synchronizationFailed(Session, SynchronizationFailed) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  A callback method used by a CN to indicate to a MN that it cannot complete synchronization of the science metadata identified by pid.
synchronizationFailed(SynchronizationFailed) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
synchronizationFailed(Session, SynchronizationFailed) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
synchronize(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
syncToSettings() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
  The properties on the Setting class isn't synchronized with the change the Metacat properties file.
SYSMETA - Static variable in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
systemid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
SYSTEMID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
systemMetadataChanged(Session, Identifier, long, Date) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.
systemMetadataChanged(boolean, Session, Identifier, long, Date) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.
systemMetadataChanged(Identifier, long, Date) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
systemMetadataChanged(Session, Identifier, long, Date) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
SystemMetadataFactory - Class in edu.ucsb.nceas.metacat.dataone
SystemMetadataFactory() - Constructor for class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
SystemMetadataMap - Class in edu.ucsb.nceas.metacat.dataone.hazelcast
  Storage implementation for Hazelcast System Metadata
SystemMetadataMap() - Constructor for class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
systemMetadataPIDExists(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Determine if the specified identifier object exists or not.
systemMetadataPIDExists(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
systemMetadataSIDExists(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Check if the specified sid object exists on the serial id field on the system metadata table
systemMetadataSIDExists(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Check if the specified sid exists on the serial id field on the system metadata table
SystemUtil - Class in edu.ucsb.nceas.metacat.util

## T

TABLE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
TABLES_DO_NOT_EXIST - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
TABLES_EXIST - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
TERM_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
TEST_CONFIG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
testConnection(String, String, String, String) - Static method in class edu.ucsb.nceas.metacat.database.DBConnection
  Method to test a JDBC database connection
testGenerate() - Static method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
testSummary() - Static method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
textBuffer - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
TextNode - Class in edu.ucsb.nceas.metacat
  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
TITLES - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
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.
TOPLEVEL - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
toString() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchPathQuery
  Creates the pathquery xml string.
toString() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryGroup
  Creates the XML string that represents this AdvancedSearchQueryGroup, including the querygroups and queryterms that are descendants of this querygroup.
toString() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchQueryTerm
  Produce a xml string fragment that represents this queryterm.
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 NOTE: this detects the character encoding, or uses the XML default
toString() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  Print a string representation of the XML document NOTE: this detects the character encoding, or uses the XML default
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.MetacatProfiler.Profile
toString() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
toString() - Method in class edu.ucsb.nceas.metacat.MetacatURL
  returns a string representation of this metacatURL
toString() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
  Transform the document content to a string and return it.
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
  Deprecated.
  This should not be used for performing the query because the parameter values are not bound in the raw SQL
toString() - Method in class edu.ucsb.nceas.metacat.TextNode
  String representation of this text node
total - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
touchSession(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Keep a session active by updating its last accessed time.
toXml(OutputStream, String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  Print a text representation of the XML document to a Writer
toXml(Writer) - Method in exception edu.ucsb.nceas.metacat.McdbException
  Print the message from this exception in XML format.
toXmlFromDb(OutputStream, String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DocumentImpl
  Print a text representation of the XML document to a Writer
toZipFileName(String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
transform(String, String, PrintWriter, Hashtable) - Static method in class edu.ucsb.nceas.metacat.spatial.XSLTransform
  Transform an XML document using an XSLT stylesheet to another format, probably HTML or another XML document format.
transform(Reader, String, PrintWriter, Hashtable) - Static method in class edu.ucsb.nceas.metacat.spatial.XSLTransform
  Transform an XML document using an XSLT stylesheet to another format, probably HTML or another XML document format.
transformXMLDocument(String, String, String, String, Writer, Hashtable<String, String[]>, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
  Transform an XML document using the stylesheet reference from the db
txtValue(int) - Static method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
TYPE_IDENTIFIER - Static variable in class edu.ucsb.nceas.metacat.IdentifierManager
TYPE_SYSTEM_METADATA - Static variable in class edu.ucsb.nceas.metacat.IdentifierManager

## U

UNCONFIGURED - Static variable in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
UNCONFIGURED - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
UNION - Static variable in class edu.ucsb.nceas.metacat.QueryGroup
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
UNKNOWN_DISTRIBUTION - Static variable in class edu.ucsb.nceas.metacat.DistributionSection
unparsedEntityDecl(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler
  All are reported after startDocument and before first startElement event
unRegisterAllSessions() - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Unregister all sessions from the session hash table except the public session.
unRegisterSession(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Unregister a session from the session hash table.
UNSCHEDULE_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
UPDATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
update(String, Reader, Reader) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Update an XML document in the repository by providing a new version of the XML document.
update(String, Reader, Reader) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Update an XML document in the repository.
update(String, Reader) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
  Update an XML document into the repository, making it available for searching using the query() methods.
update(String, Reader) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
  Update an XML document in the repository, replacing an existing document.
update(Session, Identifier, InputStream, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Updates an existing object by creating a new object identified by newPid on the Member Node which explicitly obsoletes the object identified by pid through appropriate changes to the SystemMetadata of pid and newPid
update(Identifier, InputStream, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
update(Session, Identifier, InputStream, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
  Deprecated.
UPDATE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
updateAuthoritativeMemberNodeId(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
updateDate - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
updatedate - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
UpdateDOI - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Updates existing DOI registrations for EML versions
UpdateDOI() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
  Public constructor
updateFileNameAndType(Node, String, String[]) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
updateMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  update a mapping
updateMetadataFileName(Node, String, String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
UPDATEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
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
updateNodeText(Node, XPath, String, String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
updateOREdateFormat(String) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
  Need to update the existing ORE maps to have correct dateTime serializations see: https://redmine.dataone.org/issues/3046
updateOREs(List<Identifier>, String, String) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
  Updates the given OREs by regenerating and reserializing the RDF using the updated foresite library Only non-obsolete, non-archived ORE objects are updated and their SystemMetadata is based on the original version.
updateReplicationMetadata(Session, Identifier, Replica, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Full replacement of replication metadata in the system metadata for the specified object, changes date system metadata modified
updateReplicationMetadata(Identifier, Replica, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
updateReplicationMetadata(Session, Identifier, Replica, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
  Deprecated.
updateReplicationMetadata(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
  Pass the request to update the replication metadata to CNodeService
updateReplicationMetadata(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Pass the request to update the replication metadata to CNodeService
updateRootNodeID(long) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
  update rootnodeid=nodeid for 'DOCUMENT' type of nodes only
updateSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
  Update the system metadata of the specified pid.
updateSystemMetadata(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Update a systemMetadata document
updateSystemMetadata(Session, Identifier, SystemMetadata, boolean, SystemMetadata, boolean) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
  Update the system metadata of the specified pid.
updateSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
  Update the system metadata of the specified pid.
updateSystemMetadata(SystemMetadata, DBConnection) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
  Insert the system metadata fields into the db
updateSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
  Update the system metadata for a specified pid
updateSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
  Update the system metadata for a specified identifier
updateUpgradeStatus(String, String, boolean) - Static method in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
  Update the status of an sub upgrade process (e.g.
updateUsage(int, String, Usage) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
  Update an existing usage with the given quota id and instance id
updateUsage(int, String, double) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
  Update a usage with the archived status associated with the given quota id in the remote book keeper server.
UpdateUsageTask - Class in edu.ucsb.nceas.metacat.dataone.quota
  This class represents a thread task to report a updating of an exiting usage to the remote bookkeeper server.
UpdateUsageTask(Usage, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.UpdateUsageTask
  Constructor
updateUserOwner(DBConnection, String, String, String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.GenerateGlobalIdentifiers
  The main upgrade() procedure, which first upgrades identifiers in the database, then registers these with EZID.
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrConfigUpgrader
  Upgrade the solrconfig.xml on the solr home.
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrSchemaUpgrader
  Upgrade the schema in the solr home
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
  Update the DOI registration of all ids in this server with EML formatIds
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade1_5_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_0_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_10_0
  Upgrade the solr schema.xml and solrconfig.xml file
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_10_1
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_10_3
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_11_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_12_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_3_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_4_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_4_2
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_5_1
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_7_0
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_8_1
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeEmptyReplicatedDataFile
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime
upgrade() - Method in interface edu.ucsb.nceas.metacat.admin.upgrade.UpgradeUtilityInterface
upgrade() - Method in class edu.ucsb.nceas.metacat.util.EMLVersionsTransformer
  Method to upgrade old versions of eml to new version
Upgrade1_5_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
Upgrade1_5_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade1_5_0
Upgrade2_0_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
Upgrade2_0_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_0_0
Upgrade2_10_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.7.0
Upgrade2_10_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_10_0
Upgrade2_10_1 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.10.1
Upgrade2_10_1() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_10_1
Upgrade2_10_3 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.10.3
Upgrade2_10_3() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_10_3
Upgrade2_11_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.11.0 (mainly copy the new Solr schema to the Solr home)
Upgrade2_11_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_11_0
Upgrade2_12_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.12.0 (mainly copy the new Solr schema to the Solr home)
Upgrade2_12_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_12_0
Upgrade2_3_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.3.0.
Upgrade2_3_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_3_0
Upgrade2_4_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.4.0.
Upgrade2_4_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_4_0
Upgrade2_4_2 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.4.2.
Upgrade2_4_2() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_4_2
Upgrade2_5_1 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.5.1
Upgrade2_5_1() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_5_1
Upgrade2_7_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.7.0
Upgrade2_7_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_7_0
Upgrade2_8_1 - Class in edu.ucsb.nceas.metacat.admin.upgrade
  Upgrade the application to version 2.7.0
Upgrade2_8_1() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_8_1
upgradeByFormatId(List<String>) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
  Update the registration of all DOIs in this server with the specified formatId
upgradeById(List<String>) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
  Update the registration of all DOIs with the specified guids in this server
upgradeDatabase() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Iterates through the list of scripts that need to be run to upgrade the database and calls runSQLFile on each.
UpgradeEmptyReplicatedDataFile - Class in edu.ucsb.nceas.metacat.admin.upgrade
UpgradeEmptyReplicatedDataFile() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeEmptyReplicatedDataFile
UpgradeNodeDataDatetime - Class in edu.ucsb.nceas.metacat.admin.upgrade
UpgradeNodeDataDatetime() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime
UpgradeUtilityInterface - Interface in edu.ucsb.nceas.metacat.admin.upgrade
upload(String, File) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Upload a data document into the repository.
upload(String, String, InputStream, int) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
  Upload a data 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.
UPLOAD_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
uriTemplate - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
USAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
usage - Variable in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
USAGELOCALID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
USAGEREMOTEID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
UsageTask - Class in edu.ucsb.nceas.metacat.dataone.quota
  The parent class reporting usages to the remote book keeper server and logging the quota usages events into the local database.
UsageTask(Usage, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
  Constructor
useFullSchemaValidation() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
  Report whether xml parsing is set to use full schema parsing.
useNestedStatements(String, List<Object>) - Static method in class edu.ucsb.nceas.metacat.QueryTerm
user - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
userAgent - Variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
USERCNINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
USERDNINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
USEREMAILINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
USERINFOCNINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
USERINFOEMAILINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
USERINFOORGANIDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
username - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
USERORGINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
USERORGUNITINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
UUID_SCHEME - Static variable in class edu.ucsb.nceas.metacat.dataone.MNodeService

## V

V1 - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
V1LogEntryWrapper() - Constructor for class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.V1LogEntryWrapper
V2 - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
V2LogEntryWrapper() - Constructor for class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.V2LogEntryWrapper
V2V1MISSMATCH - Static variable in class edu.ucsb.nceas.metacat.dataone.CNodeService
validate(String) - Method in class edu.ucsb.nceas.metacat.DBValidate
  validate an xml document against its DTD
validate(InputStream) - Method in class edu.ucsb.nceas.metacat.object.handler.JsonLDHandler
validate(InputStream) - Method in class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandler
  The abstract method to validate the non-xml object
validateDBConnectivity(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Validate connectivity to the database.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.AuthAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.D1Admin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.EZIDAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
  Require subclasses to implement a properties validator.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.QuotaAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.ReplicationAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.SkinsAdmin
validateOptions(HttpServletRequest, String) - Method in class edu.ucsb.nceas.metacat.admin.SkinsAdmin
  Validate the most important configuration options submitted by the user.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.SolrAdmin
  Validate the most important configuration options submitted by the user.
validateSession(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
  Method used to log in to a metacat server.
validateSession(Writer, HttpServletResponse, String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Check if a session is registered in the session hash table.
validateSession(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
  Check if a session is registered in the session hash table.
validateString(String) - Method in class edu.ucsb.nceas.metacat.DBValidate
  validate an xml document against its DTD
VALIDATIONFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
Version - Class in edu.ucsb.nceas.metacat
Version(String) - Constructor for class edu.ucsb.nceas.metacat.Version
  Create a Version object, setting sub version levels based on the given version id.
VERSION_ACTIVE - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
VERSION_INACTIVE - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
versionString - Variable in class edu.ucsb.nceas.metacat.Version
view(Session, String, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
view(Session, String, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService

## W

warning(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
  SAX Handler that receives notification of warnings
WIN_OS - Static variable in class edu.ucsb.nceas.metacat.util.SystemUtil
WmsFilter - Class in edu.ucsb.nceas.metacat.spatial
WmsFilter() - Constructor for class edu.ucsb.nceas.metacat.spatial.WmsFilter
write(DBConnection, String, String, Reader, String, String, String, String[], String, boolean, boolean, byte[], String, Checksum, File) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Write an XML file to the database, given a filename
write(DBConnection, String, String, Reader, String, String, String, String[], int, boolean, String, boolean, boolean, byte[], String, Checksum, File) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Write an XML file to the database, given a Reader
write(DBConnection, String, String, Reader, String, String, String, String[], byte[], String, Checksum, File) - Method in class edu.ucsb.nceas.metacat.DocumentImplWrapper
writeAccessRules - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
writeChildNodeToDB(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
  creates SQL code and inserts new node into DB connection
writeChildNodeToDBDataLimited(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
  creates SQL code and inserts new node into DB connection
writeConfig() - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
writeDataFileInReplication(InputStream, String, String, String, String, String, String, String, String, boolean, Date, Date) - 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..
writeDebugToDelimiteredFile(String, boolean) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  Writes debug information into a file in delimitered format
writeDebugToFile(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  Writes debug information into a file.
writeDTDNodeToDB(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXNode
  creates SQL code and inserts new node into DB connection
writeFileToOutput(HttpServletResponse, String, String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
writeFileToOutput(HttpServletResponse, String, String, int) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
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, String, byte[], String, Reader, String, String, String, String[], String, String, String, boolean, String, boolean, Date, Date, String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
  Write an XML file to the database during replication
writeReplication(DBConnection, String, byte[], String, Reader, String, String, String, String[], String, String, Date, Date) - Method in class edu.ucsb.nceas.metacat.DocumentImplWrapper
writeReplication(DBConnection, String, byte[], String, Reader, String, String, String, String[], String, String, String, boolean, Date, Date) - Method in class edu.ucsb.nceas.metacat.DocumentImplWrapper
  Constructor with tableName - this doc is in xml_documents or xml_revsions If in xml_revisions, it need a special handler.
writeStoredBackupFile(String) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
writeStreamToCheckedFile(File, InputStream, String, String) - Static method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
  Write the input stream into the given fileName and directory while calculate the checksum.
writeStreamToFile(File, String, InputStream, Checksum, Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
writeTempUploadFile(FileItem, String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
  Write the uploaded file to disk for temporary storage before moving it to its final Metacat location.
writeTextForDBSAXNode(long, StringBuffer, DBSAXNode) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler

## X

XML_LANG - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
XMLAccessAccess - Class in edu.ucsb.nceas.metacat.accesscontrol
XMLAccessAccess() - Constructor for class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
XMLFORMAT - Static variable in class edu.ucsb.nceas.metacat.util.MetacatUtil
XMLNamespaceParser - Class in edu.ucsb.nceas.metacat.service
  This class will parse the root element to figure out the namespace of the root element(we also call it the namespace of the element).
XMLNamespaceParser(Reader) - Constructor for class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
  Constructor
XMLNoNamespaceSchema - Class in edu.ucsb.nceas.metacat.service
  This class represents the information for a schema without a namespace
XMLNoNamespaceSchema(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.service.XMLNoNamespaceSchema
  Constructor of the object
XMLQueryresultAccess - Class in edu.ucsb.nceas.metacat
XMLQueryresultAccess() - Constructor for class edu.ucsb.nceas.metacat.XMLQueryresultAccess
XMLSchema - Class in edu.ucsb.nceas.metacat.service
XMLSchema(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.service.XMLSchema
  Constructor - the schema file name will be extracted from the external file uri.
XMLSchemaParser - Class in edu.ucsb.nceas.metacat.service
  A class will parse an schema file to get information - such as included xsd files in this schema
XMLSchemaParser(InputStream) - Constructor for class edu.ucsb.nceas.metacat.service.XMLSchemaParser
  Constructor
XMLSchemaService - Class in edu.ucsb.nceas.metacat.service
xpath - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
XPATH_QUERY_TEMPLATE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
  Metadata Document ID query template within an FGDC document.
XPATHQUERYOFFINFO - Static variable in class edu.ucsb.nceas.metacat.DBQuery
XSLTransform - Class in edu.ucsb.nceas.metacat.spatial
  A Class that transforms XML documents utitlizing XSL style sheets.
XSLTransform() - Constructor for class edu.ucsb.nceas.metacat.spatial.XSLTransform
  Private constructor because all methids are static and do not need an instance.

## _

_serviceName - Variable in class edu.ucsb.nceas.metacat.shared.BaseService

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

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