Index (MetaCat API)

A B C D E F G H I J K L M N O P Q R S T U V W X _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

abort(String, Exception) - Method in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker: Compose a user-friendly and informative error message, log it to 'catalina.out', and include it when throwing a RuntimeException, so it also appears in 'hostname.(date).log'
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() - Constructor for class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
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
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_LOGIN_MC - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ACTION_LOGOUT - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ACTION_ORCID_FLOW - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ACTION_PARAM - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ACTIVE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
add(IndexEvent) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
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
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
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
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
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
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.
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 metadata 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.startup.MetacatInitializer
archive(String, Identifier, String, boolean, SystemMetadataManager.SysMetaVersion) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl: Archive an object.
archive(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
archive(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
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(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
archive(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
archiveCNObject(boolean, Session, Identifier, SystemMetadata, boolean, SystemMetadataManager.SysMetaVersion) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService: Archive a object on cn and notify the replica.
ARCHIVEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
archiveObject(boolean, Session, Identifier, SystemMetadata, boolean, SystemMetadataManager.SysMetaVersion) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService: Archive an object, which 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() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Reports whether properties are fully configured, by checking the value of the property "configutil.propertiesConfigured", which is set from the Admin flow.
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
ATTR_CN_BASE_URL - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ATTR_LOGIN_METACAT_URI - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ATTR_LOGIN_ORCID_FLOW_URI - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ATTR_LOGIN_PRE_ORCID_URI - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ATTR_LOGOUT_URI - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
ATTR_USER_ID - Static variable in class edu.ucsb.nceas.metacat.util.RequestUtil
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
auth - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
AUTH_BACKUP_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate
AUTH_METADATA_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate
AuthAdmin - Class in edu.ucsb.nceas.metacat.admin: Control the display of the Authentication configuration page and the processing of the configuration values.
authBackupFilePath - Static variable in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate
authBackupProperties - Static variable in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate
authCacheSize - 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 class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Not supported for ORCID-based auth
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(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.
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.
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.
authenticateUserWithCN(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil: Authenticate the user against the CN server and/or any locally-configured certificates.
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
authMetadataFilePath - Static variable in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate
AuthOrcid - Class in edu.ucsb.nceas.metacat.authentication: Implementation of AuthInterface for ORCID auth (see orcid.org).
AuthOrcid() - Constructor for class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Constructor
AuthPropertiesDelegate - Class in edu.ucsb.nceas.metacat.properties: AuthPropertiesDelegate handles Authentication-related properties for metacat configuration.
authPropertiesMetadata - Static variable in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate
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

backup() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300: This method will backup those tables: xml_replication, xml_revisions and xml_documents
BackupAdmin - Class in edu.ucsb.nceas.metacat.admin: Control the display of the login page
backupNodesTable(DroppedTableBackupper300.NodeTableName, List<Long>) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300: Backup the records whose root node ids are in the list and in the given table
BackupPropertiesDelegate - Class in edu.ucsb.nceas.metacat.properties: BackupPropertiesDelegate handles functionality related to backing up the main properties for metacat configuration.
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
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(long, String, long, int) - Constructor for class edu.ucsb.nceas.metacat.BasicNode: Construct a Basic Node
BasicNode(String) - Constructor for class edu.ucsb.nceas.metacat.BasicNode: Construct a Basic Node
BasicNode(String, long, int) - Constructor for class edu.ucsb.nceas.metacat.BasicNode: Construct a Basic Node
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 - Variable in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
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
buildSession(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil: Construct a session object base the given user and group name
bypassAuthConfiguration() - Method in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate: (for dev use only) Bypasses the auth properties configuration utility by using the auth backup properties to overwrite the main properties.
bypassConfiguration() - Method in class edu.ucsb.nceas.metacat.properties.BackupPropertiesDelegate: (for dev use only) Bypasses the properties configuration utility by using the backup properties to overwrite the main properties.
bypassConfiguration() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: (for dev use only) Bypasses the properties configuration utility by using the backup properties to overwrite the main properties.
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 class edu.ucsb.nceas.metacat.properties.PropertyService

C

callorder - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
canBypass() - Method in class edu.ucsb.nceas.metacat.properties.BackupPropertiesDelegate: Determine if the system is able to bypass configuration.
cancel() - Method in class edu.ucsb.nceas.metacat.index.queue.FailedIndexResubmitTimerTask: Overwrite and do nothing
cancel() - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Overwrite and do nothing
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 metadata 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.MetacatResultSet
check() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.PrerequisiteChecker300: Check if the upgrade is starting from version 2.19.*
check() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.XMLNodesToFilesChecker: This method does the job - make sure all metadata object are stored in the files.
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
checkAdminPrivilege(Session, String, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Check if the given session has the admin privilege.
checkAndSetProperty(HttpServletRequest, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Deprecated.
CHECKED - Enum constant in enum class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager.SysMetaVersion
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.
checkIfConfigured(HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet: Check if the Metacat instance has been configured
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
checkSolrStatus(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Check the current solr status - such as if the solr core/solr-home directory exists, and send back actions which user can choose based on the status.
ChecksumsManager - Class in edu.ucsb.nceas.metacat.systemmetadata: The class to save, get and query checksums from db for a pid
ChecksumsManager() - Constructor for class edu.ucsb.nceas.metacat.systemmetadata.ChecksumsManager
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.
checkUrlStatus(String) - Static method in class edu.ucsb.nceas.metacat.util.NetworkUtil: Get a status code after connecting and sending an HTTP GET request to the given url
checkUrlStatus(String, int) - Static method in class edu.ucsb.nceas.metacat.util.NetworkUtil: Get a status code after connecting and sending an HTTP GET request to the given 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)
cid() - Method in record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Returns the value of the cid record component.
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
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(String, String, ClientView) - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewHelper: Creates a new instance of ClientViewHelper, using parameter values for initializing.
ClientViewHelper(HttpServletRequest) - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewHelper: Creates a new instance of ClientViewHelper, using info in an HttpServletRequest 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
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 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 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 - Class in edu.ucsb.nceas.metacat.restservice.v2: CN REST service implementation handler ****************** CNCore 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 -- 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(HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler: Constructor
CNResourceHandler(HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler: Constructor
CNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v1: Routes CN REST service requests to the appropriate handler
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.v1.CNRestServlet
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
combineDateAndGivenTime(Date, String) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager: This method will combine a given date and given time string (in short format) to a new 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
commit() - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Method to make a commit command
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.NodeComparator: compare two objects to determine proper sort order -- delegates to the compare(NodeRecord, NodeRecord) method.
compareTo(Version) - Method in class edu.ucsb.nceas.metacat.Version: Compare this Version object to another.
COMPLETE - Enum constant in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus
COMPLETE - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
CONCRETE - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
CONFIG_FILE_DIR - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService: The directory holding properties and other configuration files
CONFIG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.service.ServiceService
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 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
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
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
contextDestroyed(ServletContextEvent) - Method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer
contextInitialized(ServletContextEvent) - Method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: An implementation of ServletContextListener that is called automatically by the servlet container on startup, and used to verify that we have the essential components in place and Metacat is initialized.
contextInitialized(ServletContextEvent) - Method in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
convert() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: The method do the conversion job
convert(MCSystemMetadata) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.MCSystemMetadata: A utility method to convert an MCSystemMetadata object to a SystemMetadata object
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(int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
convertPermission(Permission) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Utility method to convert a permission object to an integer
convertStorage() - Method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Start to convert the storage if the db is configured and the storage conversion status is PENDING or FAILED
convertSystemMetadata(SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader: Transform the SystemMetadata object to an InputStream object
copy(MCSystemMetadata, SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.MCSystemMetadata: Copy all properties from a SystemMetacat object to an MCSystemMetadata object
copyFile(String, String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil: Copy a file between two locations specified as strings.
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(Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
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.CNodeService: Deprecated.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
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.MNodeService
create(Session, Identifier, InputStream, SystemMetadata, boolean) - 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 - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
CREATE_INDEX_TYPE - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
createdate - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
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.
createMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: Create a mapping between the dataone identifier and local docid in the identifier table
createMapping(String, String, DBConnection) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: Create a mapping between the dataone identifier and local docid 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
createStatement() - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Deprecated.
PreparedStatements are preferred so as to encourage parameter value binding
createSystemMetadata(String) - 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

D

D1Admin - Class in edu.ucsb.nceas.metacat.admin: Control the display of the database configuration page and the processing of the configuration values.
D1AdminCNUpdater - Class in edu.ucsb.nceas.metacat.admin
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(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 implementation of DataONE 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
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
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() - Constructor for class edu.ucsb.nceas.metacat.DBDTDHandler: Construct an instance of the DBDTDHandler class
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() - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver: Construct an instance of the DBEntityResolver class
DBEntityResolver(DefaultHandler, Reader) - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver: Construct an instance of the DBEntityResolver class
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() - Constructor for class edu.ucsb.nceas.metacat.DBSAXHandler: Construct an instance of the handler 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(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBValidate: Construct a new validation object using a database entity resolver
DBValidate(String) - Constructor for class edu.ucsb.nceas.metacat.DBValidate: Construct a new validation object using an OASIS catalog file
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
DEFAULT_TIMEOUT_MS - Static variable in class edu.ucsb.nceas.metacat.util.NetworkUtil
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
defaultProperties - Variable in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper
delete(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat: Delete an XML document in the repository.
delete(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient: Delete an XML document in the repository.
delete(String, 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(String, Identifier) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl: Delete an object totally from the db and file system.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Delete a system metadata record from the store.
delete(Identifier, DBConnection) - Method in class edu.ucsb.nceas.metacat.systemmetadata.ChecksumsManager: Delete the checksums from the table for the given pid
delete(Identifier, DBConnection) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Delete the system metadata for the given guid with the DBConnection object.
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService: Deletes an object from the Coordinating Node
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(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
DELETE - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest: HTTP Verb DELETE
DELETE - Static variable in class edu.ucsb.nceas.metacat.EventLog
DELETE - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler: HTTP Verb DELETE
DELETE_INDEX_TYPE - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
DELETE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
DELETED - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
DELETEDMESSAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
deleteFromFileSystem(Identifier) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl: Deletes a doc or data file from the filesystem using identifier.
deleteIfInvalidObject(ObjectInfo, String, String, long) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Confirms that an ObjectMetadata's content is equal to the given values.
deleteMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Deletes all metadata related for the given 'pid' from HashStore
deleteMetadata(Identifier, String) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Deletes a metadata document (ex.
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.
deleteObject(Identifier) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Deletes an object and all relevant associated files (ex.
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(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.CNodeService: Deletes the replica from the given Member Node NOTE: MN.delete() may be an "archive" operation.
deleteReplicationMetadata(Session, Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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, DBConnection) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess: Delete xml access.
DELIMITER - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
describe(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
describe(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
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(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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.MetaCatServlet: Destroy the servlet
destroy() - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
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.
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() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Determine if the system is able to bypass configuration.
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
docname - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
docname - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
docname - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
DOCNAME - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
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.
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) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl: Constructor, creates document from database connection, used for reading the document
DocumentImpl(String, boolean) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl: Constructor used to create a document and read the document information from the database.
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
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.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.restservice.D1RestServlet: 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
doMetacatLogin(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Use the ORCID auth token to log the admin user in
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.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.restservice.D1RestServlet: 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.index.queue.IndexGenerator
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: implementation of abstract method in edu.ucsb.nceas.metacat.shared.BaseService, delegated to by PropertyService, which extends BaseService
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
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
DroppedTableBackupper300 - Class in edu.ucsb.nceas.metacat.admin.upgrade: The class to back up dropped tables to the csv files during the upgrade process to 3.0.0
DroppedTableBackupper300(String) - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300: Constructor
DroppedTableBackupper300.NodeTableName - Enum Class in edu.ucsb.nceas.metacat.admin.upgrade
DTD - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl

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.solr - package edu.ucsb.nceas.metacat.admin.upgrade.solr
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.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.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.index - package edu.ucsb.nceas.metacat.index
edu.ucsb.nceas.metacat.index.queue - package edu.ucsb.nceas.metacat.index.queue
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.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.startup - package edu.ucsb.nceas.metacat.startup
edu.ucsb.nceas.metacat.storage - package edu.ucsb.nceas.metacat.storage
edu.ucsb.nceas.metacat.systemmetadata - package edu.ucsb.nceas.metacat.systemmetadata
edu.ucsb.nceas.metacat.util - package edu.ucsb.nceas.metacat.util
edu.ucsb.nceas.protocols.metacat - package edu.ucsb.nceas.protocols.metacat
elementDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler: SAX Handler that receives notification of element declarations
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
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.
EML200 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
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 - 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.
EML210 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
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.
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
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.
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
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.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.MetacatResultSet
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
endTag - Static variable in class edu.ucsb.nceas.metacat.util.DocumentUtil
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
equals(Object) - Method in record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Indicates whether some other object is "equal to" this one.
equals(AccessPolicy, AccessPolicy) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService: Compare two AccessPolicy objects
error - Static variable in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
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 initialize 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
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

FAILED - Enum constant in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus
FailedIndexResubmitTimerTask - Class in edu.ucsb.nceas.metacat.index.queue: A timer to regenerate failed index tasks or index tasks in a given time frame.
FailedIndexResubmitTimerTask() - Constructor for class edu.ucsb.nceas.metacat.index.queue.FailedIndexResubmitTimerTask: Constructor
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.
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
filter(EventLogData) - Method in class edu.ucsb.nceas.metacat.EventLogFilter: Determine if the given EventLogData object will be filtered out (not logging) or not.
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.
finalVersionAndClassMap - Static variable in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
find() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrJvmVersionFinder: Parse the solr admin information and find the jvm version
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(Reader) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService: Returns the namespace for an xml document.
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(Reader) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService: Get the attribute value of the noNamespaceSchemaLcation of the given xml
findSchemasInXML(Reader) - 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
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
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
generateFinalVersionsAndClassesMap() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Generate the final version-class ordered map which contains the versions and upgrade classes.
generateIdentifier(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
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.CNodeService
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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 metadata xml string for an object with the given system metadata.
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
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 namespace
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.
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(String, Date) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO: Get the list of the index events which have the specified event action and are younger than the specified oldest age.
get(String, Hashtable<String, String[]>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
get(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
get(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
get(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
get(Identifier) - Method in class edu.ucsb.nceas.metacat.systemmetadata.ChecksumsManager: Find all checksums for the given pid.
get(Identifier) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Get the system metadata associated with the given identifier from the store.
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(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
GET - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest: HTTP Verb GET
GET - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler: HTTP Verb GET
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.
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
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
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
getAttributes() - Method in class edu.ucsb.nceas.metacat.BasicNode: Get the attributes as a string
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthOrcid
getAttributes(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) - 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) - Method in class edu.ucsb.nceas.metacat.AuthTest: Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthOrcid
getAttributes(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface: 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, String, 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.AuthTest: Get attributes describing a user or group
getAttributes(Properties) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
getAttributesAsString(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil: Get all the attributes from the request, as a String.
getAuthBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate: Get the auth backup properties file.
getAuthBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the auth backup properties file.
getAuthMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the auth properties metadata.
getAuthPropertiesMetadata() - Method in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate: Get the auth properties metadata.
getBackupDirPath() - Method in class edu.ucsb.nceas.metacat.properties.BackupPropertiesDelegate: Get the path to the directory where the backup properties are stored, and as a side effect, update the properties file to save this path as "application.backupDir"
getBackupDirPath() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the path to the directory where the backup properties are stored, and as a side effect, update the properties file to save this path as "application.backupDir"
getBackupDirStatus(String) - Method in class edu.ucsb.nceas.metacat.admin.BackupAdmin: Find the status of the backup base directory.
getBackupPath() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300: Get the backup path
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 BeanDescriptors.
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
getCatalogVect() - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
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(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getChecksum(Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getChecksum(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService: Return the checksum of the object given the identifier
getChecksum(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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(Session, Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
getChecksums() - Method in class edu.ucsb.nceas.metacat.systemmetadata.MCSystemMetadata: Get the checksums associated with the MCSystemMetadata object
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
getCommonSkinsDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil: Get the style skins directory.
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.DocumentUtil: Get the string WITHOUT the content between the system metadata 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.
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
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
getDataByRange(LSIDRequestContext, int, int) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
getDataFileName() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Getter for property dataFileNames.
getDataFileName(int) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Indexed getter for property dataFileNames.
getDataLocations(LSID, String) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
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
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() - Static 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.
getDefaultNameSpace() - Method in class edu.ucsb.nceas.metacat.storage.Storage: Get the default namespace in the storage system
getDefaultPropertiesFilePath() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Get the path to the read-only, default properties in metacat.properties.
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.
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.
getDeniedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil: Get the denied submitters from metacat.properties
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.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.clientview.ClientView: Getter for property docId.
getDocID() - Method in class edu.ucsb.nceas.metacat.BasicNode: Get the doc id of this node
getDocID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl: Get the document identifier (docid)
getDocIdFromAccessionNumber(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil: This method will get docid from an AccessionNumber.
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
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
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
getDocumentInfoMap(String) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory: Get the document information in the format of a map.
getDocumentName() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler: Get the name of the document
getDocuments() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
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.
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
getError() - Static method in class edu.ucsb.nceas.metacat.admin.DBAdmin: Get the error message during the process
getError() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Get the error message if the conversion fails
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 EventSetDescriptors.
getException() - Method in exception edu.ucsb.nceas.metacat.McdbException: Get the tunneled Exception
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() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getFields(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
getFileFromLegacyStore(String) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory: Get a file object for the given localId from the legacyStore.
getFileName() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema: Gets the file name
getFileName(String) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.XMLNodesToFilesChecker: Get a file name concatenating the base name and current time.
getFileNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema: Gets the file namespace
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() - Method in class edu.ucsb.nceas.metacat.util.SessionData
getGroups() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Not supported for ORCID-based auth
getGroups(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface: Get all groups 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) - Method in class edu.ucsb.nceas.metacat.AuthStub: Get all groups 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.authentication.AuthFile
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Not supported for ORCID-based auth
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, 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, String) - Method in class edu.ucsb.nceas.metacat.AuthStub: Get the groups for a particular user 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
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).
getGUIDsByTimeRange(Date, Date) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: Get the list of guids whose modification dates are in the range of the given start and end times.
getHandler(String) - Method in class edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager
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.
getHeadPID(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: Get the pid of the head (current) version of objects match the specified sid.
getHexDigest(Identifier, String) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Calculates the hex digest of an object that exists in HashStore using a given persistent identifier and hash algorithm.
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
getIncludedSchemaFilePathes() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaParser: Get the included schema file paths in this schema
getInfo() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Get the information that some conversion failed
getInfo() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader: Get the info which users need to handle
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.D1AdminCNUpdater: Get the single instance
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.SolrAdmin: Get the single instance of SolrDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrSchemaAndConfigUpgrader: Get the singleton instance
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() - 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() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager: Get the singleton instance of the service
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.index.queue.IndexGenerator: Implement a Singleton pattern using "double checked locking" pattern.
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.queue.LastReindexDateManager: Get the singleton instance of the class
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() - Static method in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate: Get a shared singleton AuthPropertiesDelegate instance by calling AuthPropertiesDelegate.getInstance().
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.BackupPropertiesDelegate: Get a shared singleton BackupPropertiesDelegate instance by calling BackupPropertiesDelegate.getInstance().
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: get the current instance of the PropertiesWrapper.
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the single instance of PropertyService, only after it has been previously instantiated with a call to one of the other getInstance() methods passing either a reference to the servlet context or the config file path
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.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.
getInstance() - Static method in class edu.ucsb.nceas.metacat.storage.Storage: Get the instance of the class through the singleton pattern
getInstance() - Static method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Get the singleton SystemMetadataManager instance
getInstance(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the single instance of PropertyService for test purposes.
getInstance(ExecutorService, BookKeeperClient) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.PortalQuotaService: Get a singleton class instance
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.CNodeService: singleton accessor
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Get an instance of MNodeService.
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(HttpServletRequest, String, String) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Get an instance of MNodeService.
getInstance(ServletContext) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the single instance of PropertyService.
getInstance(ServletContext) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService: Get the single instance of ServiceService.
getInstanceForTesting(Path, Path) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the single instance of PropertyService for test purposes.
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
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
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
getLastProcessDate() - Method in class edu.ucsb.nceas.metacat.index.queue.LastReindexDateManager: Get the latest SystemMetadata modification Date of the objects that were built the solr index during the previous timed indexing process.
getLastSubdir(String) - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator: Get the last sub-directory in the path.
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
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(Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getLogRecords(Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
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(Session, Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
getLogRecords(Session, Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
getLSID() - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
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
getMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.BackupPropertiesDelegate: Get the main backup properties file.
getMainBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the main backup properties file.
getMainMetaData() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Get the main properties metadata.
getMainMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the main properties metadata.
getMainMetadataFilePath() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Get the path to the main Metadata file, which holds configuration information about main properties.
getMainMetadataFilePath() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get the path to the main Metadata file, which holds configuration information about main properties.
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() - 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.
getMessage(int) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Indexed getter for property message.
getMetacatClient() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
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.
getMetacatReleaseInfo() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil: Gets a string that holds some description about the release.
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(LSIDRequestContext, String[]) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
getMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService: Get the metadata for the given identifier
getMetaData() - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Method to get meta data
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 MethodDescriptors.
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
getNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser: Get the namespace of the document (root element).
getNamespace(String) - Method in class edu.ucsb.nceas.metacat.BasicNode: Get an uri of the namespace prefix
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.
getNeededUpgradedVersions() - Static method in class edu.ucsb.nceas.metacat.admin.DBAdmin: Get the all db versions the upgrade process should go through
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.
getNewInstance(Path, Path) - Static method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: get an instance of the PropertiesWrapper.
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.NodeRecord
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.NodeRecord: Get functions
getNodeID() - Method in class edu.ucsb.nceas.metacat.BasicNode: Get the id of this node
getNodeIndex() - Method in class edu.ucsb.nceas.metacat.BasicNode: Get nodeIndex of the node
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
getNonUpgradedSolrVersions() - Static method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Get a list of db versions in which the solr db hasn't been upgraded
getNonXMLMetadataFormatList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService: Get the list of format ids which are the non-xml metadata type
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) - 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
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.
getObjectFilePath(String, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: Get the the file path for the given object local id
getOptionList(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil: Transform a comma-delimited string of options to a vector object which contains those options
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
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
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
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 all the parameters from the request, as a Hashtable
getParametersAsString(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil: Get all the parameters from the request, as a String.
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
getParentNodeId() - Method in class edu.ucsb.nceas.metacat.NodeRecord
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.
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
getPathValue() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Getter for property pathValue.
getPermission() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule: Get permission
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.
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 class edu.ucsb.nceas.metacat.authentication.AuthOrcid
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(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.PropertiesWrapper: Get a Map of all properties that start with the groupName prefix.
getPropertiesByGroup(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get a Map of all properties that start with the groupName prefix.
getProperty(String) - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Get a property value.
getProperty(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Get a property value.
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 PropertyDescriptors.
getPropertyNames() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Get a set of all property names.
getPropertyNames() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: 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.PropertiesWrapper: Get a Set of all property names that start with the groupName prefix.
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, 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
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.
getQueryEngineDescription(String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getQueryEngineDescription(String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getQueryEngineDescription(Session, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
getQueryEngineDescription(Session, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
getQueryEngineDescritpion() - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler: Get the QueryEngineDescription
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(String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog: Retrieve the specified metadata for the specified oaiIdentifier
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
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(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
getReplica(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Essentially a get() but with different logging behavior
getReplica(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
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
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
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
getReturnfield() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Getter for property returnField.
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
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
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.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.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".
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
getServer() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil: Get the server which is made up of the server name + : + the port number.
getServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil: Get the server URL which is made up of the http or https + :// + the server name + : + the 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 class edu.ucsb.nceas.metacat.clientview.ClientView: Getter for property sessionId.
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
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
getSitePropertiesFilePath() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Get the path to the metacat-site.properties file, which holds configurable properties used to override the defaults in metacat.properties.
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.
getSolrAdminInfo() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrJvmVersionFinder: Get the solr admin information from the solr information url.
getSolrUpdateClasses() - Static method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Get the map of upgrade classes should be run in the upgrade.
getSQLDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil: Get the SQL directory.
getStatus() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Get the status of conversion.
getStatus() - Method in class edu.ucsb.nceas.metacat.database.DBConnection: get the db connetion status from the object
getStatus(String) - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Get the upgrade status for the given version
getStatus(String) - Static method in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus: Get the UpgradeStatus object from the given string
getStatus(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Get the status of the system.
getStorage() - Static method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Get the storage instance
getStoredBackupDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil: Gets the stored backup location.
getStoreProperties() - Static method in class edu.ucsb.nceas.metacat.storage.Storage: Get the store properties which initializes the hashstore instance
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.
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
getSubscriber() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage: Get the subscriber of the usage
getSubversion(int) - Method in class edu.ucsb.nceas.metacat.Version
getSystemID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl: get the system identifier
getSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.MultipartRequestWithSysmeta: Get the system meta data associate with this request
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(String) - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Get the SystemMetadata for the specified id from the distributed Map.
getSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
getSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
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(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
getSystemMetadataContent(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil: Get the content between the system metadata 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).
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.
getTableName() - Method in enum class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300.NodeTableName: Get the table name associated with the enum
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
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.
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() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier: returns the uniqueId encoded in this docid
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.
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: Get the list of the Java and Solr update class files which will run in the upgrade process
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
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".
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 class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Not supported for ORCID-based auth
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.clientview.ClientView: Getter for property userName.
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) - Method in class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Not supported for ORCID-based auth
getUsers(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface: Get all users 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) - Method in class edu.ucsb.nceas.metacat.AuthStub: Get all users 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.authentication.AuthFile
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthOrcid: Not supported for ORCID-based auth
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, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap: Get the users for a particular group 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, 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 enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus: Get the value of the enum
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
getVersionFromPropertyName(String, String) - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Get the version from the update class property name with the convention like: solr.upgradeUtility.3.0.0
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
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
GROUPDESINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
GROUPNAMEINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface

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
handle(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Handle all login-related cases: 1.
handleAction(String, Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String[], String) - Method in interface edu.ucsb.nceas.metacat.plugin.MetacatHandlerPlugin
handleClientRequest(MultipartParser) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper: Main method for handling various actions.
handleDocIdSelect() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
handleEvent(MetacatEvent) - Method in interface edu.ucsb.nceas.metacat.event.MetacatEventObserver
handleFileUpdate(MultipartParser) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
handleOrcidRedirect(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Handle the case where the User has authenticated via ORCID and the orcid site has redirected the user here.
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.
handlePackageUpload(String, HashMap, String, String, Document) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
handler - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
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
handleReindexAction(List<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Rebuild the index for one or more documents
handleReindexAllAction() - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Rebuild the index for all documents in the systemMetadata table.
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
handleWarningActions(String, HttpServletRequest, Vector<String>) - Method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Method to handle a warning message in the request, which have user's response.
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
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 record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Returns a hash code value for this object.
HashStoreConversionAdmin - Class in edu.ucsb.nceas.metacat.admin: An admin class to convert the old style file store to a HashStore
HashStoreConversionAdmin() - Constructor for class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
HashStoreUpgrader - Class in edu.ucsb.nceas.metacat.admin.upgrade
HashStoreUpgrader() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader: Constructor
hasLatestVersion(SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataValidator: Check if the given system metadata has the latest version.
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
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(Session, Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
hasReservation(Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
hasSubTreeAccessControl() - Method in class edu.ucsb.nceas.metacat.PermissionController: Return if a document has subtree access control
HEAD - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler: HTTP Verb HEAD
hexDigests() - Method in record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Returns the value of the hexDigests record component.
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
HIGH_PRIORITY - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
HIGHEST_PRIORITY - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
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
IN_PROGRESS - Enum constant in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus
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
index(Date) - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Build the index for the docs which have been modified since the specified date.
index(Date, Date) - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Build the index for the docs which have been modified between the specified dates.
index(List<String>) - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Put the ids into the index queue
indexAll() - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Build the index for all documents.
indexEphemeralAnnotation(Identifier) - Method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
IndexEventDAO - Class in edu.ucsb.nceas.metacat.index
IndexGenerator - Class in edu.ucsb.nceas.metacat.index.queue: The IndexGenerator class will publish (send) the index information to a RabbitMQ queue.
IndexGeneratorTimerTask - Class in edu.ucsb.nceas.metacat.index.queue: A timer to regenerate failed index tasks or index tasks in a given time frame.
IndexGeneratorTimerTask() - Constructor for class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Constructor
info - Static variable in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
init(FilterConfig) - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet: Initialize the servlet
init(ServletConfig) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet: Initialize the servlet.
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.restservice.D1RestServlet: Initialize servlet by setting QuotaService
initAfterMetacatConfig() - Method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Initialize the remainder of Metacat.
initCandidateList() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader: Run a query to select the list of candidate pid from the systemmetadata which will be converted.
initializeK8sInstance() - Static method in class edu.ucsb.nceas.metacat.startup.K8sAdminInitializer: Method to be called during system startup - e.g.
initializeParser(Vector<XMLSchema>, Reader, String, boolean, String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl: Set up the parser handlers for writing the document to the database
initializeSitemapTask() - Static method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Schedule a site map task
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
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
initStorage() - Static method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Initialize the storage system.
initVersionAndClassFromProperty() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Initialize the map between version and the update class name from the metacat.properties file
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.
INSERT - Enum constant in enum class edu.ucsb.nceas.metacat.MetacatHandler.Action
insertAccess(String, List<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess: Set permissions for a given document.
insertAccess(String, List<XMLAccessDAO>, DBConnection) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess: Set permissions for a given document.
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) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile: Replace existing permissions with a given block of permissions for this document.
insertPermissions(String, Long, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile: Insert a single access record into the database.
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
intValue(String) - Static method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
INVALIDCODE - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
InvalidSystemMetadata - Exception in edu.ucsb.nceas.metacat.systemmetadata: An exception class indicate the given system metadata is invalid.
InvalidSystemMetadata(String) - Constructor for exception edu.ucsb.nceas.metacat.systemmetadata.InvalidSystemMetadata: Constructor with the error message
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(Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
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.D1NodeService: Test if the user identified by the provided token has authorization for the operation on the specified object.
isAuthorized(Session, Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
isAuthorized(Session, Identifier, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
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.
isCNAdmin(Session, NodeList) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper: Compares session.subject against CN.NodeList
isConverted() - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin: Check if the hashstore was converted
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(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory: Is the record deleted?
isDeleted(String) - Method in class edu.ucsb.nceas.metacat.EventLog: A utility method to determine if the given docid was 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
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
isFreshInstall() - Static method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Check if the db is a fresh installation.
isFullyInitialized() - Static method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Get the status of full-initialization.
isGeoserverConfigured() - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil: Reports whether geoserver is configured.
isInAllowList(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService: Check if the session is in the allow list which can upload objects to this Metacat instance.
isIndexerCodeployed() - Method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin: Determine if the metacat-index context exists with metacat in the same Tomcat container.
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.
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
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 variable in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
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(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
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(Session, Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
isNodeAuthorized(Subject, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
isPublicAccess() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Getter for property publicAccess.
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.
isResourceMap(ObjectFormatIdentifier) - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: If the specified ObjectFormatIdentifier is a resroucemap namespace.
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.
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.
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.

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

K8sAdminInitializer - Class in edu.ucsb.nceas.metacat.startup: Collection of administrative initialization tasks that need to be performed automatically on startup, when running in Kubernetes.
KEEP - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin

L

LastReindexDateManager - Class in edu.ucsb.nceas.metacat.index.queue: A class to save/retrieve the last re-index date.
LDAPCLASS - Static variable in class edu.ucsb.nceas.metacat.admin.AuthAdmin
length(InputStream) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
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(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog: Retrieve the next set of Identifiers associated with the resumptionToken
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 - 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) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers: Client-side ListIdentifiers verb constructor (resumptionToken version)
ListIdentifiers(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers: Client-side ListIdentifiers verb constructor
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(Date, Date, ObjectFormatIdentifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
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.CNodeService: Deprecated.
listObjects(Session, Date, Date, ObjectFormatIdentifier, Boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService: Deprecated.
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(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, NodeReference, Identifier, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
listQueryEngines() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
listQueryEngines() - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
listQueryEngines(Session) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
listQueryEngines(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
listQuotas(String, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient: List the quotas associated with the given subject
listRecords(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog: Retrieve the next set of records associated with the resumptionToken
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 - 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) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords: Client-side ListRecords verb constructor (resumptionToken version)
ListRecords(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords: Client-side ListRecords 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
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
listViews() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
listViews(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
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.
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
lock(Identifier) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Lock a PID so only one thread can modify the system metadata in database/file system.
log - Static variable in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeEmptyReplicatedDataFile
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
logMetacat - Static 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.
logOutAdminUser(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Put user in a logged-out state by removing userId from session, and invalidating session.
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
LOW_PRIORITY - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
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

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.admin.upgrade.UpgradeEmptyReplicatedDataFile
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.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.EML201DocumentCorrector: Runs the job to correct eml201 documents - deleting extral nodes in
main(String[]) - Static method in class edu.ucsb.nceas.metacat.MetacatURL: Test method for this class.
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.
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.
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
maxAgeOfFailedIndexTask - Static variable in class edu.ucsb.nceas.metacat.index.queue.FailedIndexResubmitTimerTask
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
MAXWAITNUMBER - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask
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(Exception) - 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(String, Exception) - 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.
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(Exception) - 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(String, Exception) - Constructor for exception edu.ucsb.nceas.metacat.McdbException: Create a new McdbException.
MCSystemMetadata - Class in edu.ucsb.nceas.metacat.systemmetadata: A class of SystemMetadata which can hold multiple checksums
MCSystemMetadata() - Constructor for class edu.ucsb.nceas.metacat.systemmetadata.MCSystemMetadata: Default constructor
MEDIUM_PRIORITY - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
MEDIUM_RESOURCEMAP_PRIORITY - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
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.
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
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.
MetacatDocumentEvent - Class in edu.ucsb.nceas.metacat.event
MetacatDocumentEvent() - Constructor for class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
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() - Constructor for class edu.ucsb.nceas.metacat.MetacatHandler: Default constructor.
MetacatHandler.Action - Enum Class in edu.ucsb.nceas.metacat
MetacatHandlerPlugin - Interface in edu.ucsb.nceas.metacat.plugin
MetacatHandlerPluginManager - Class in edu.ucsb.nceas.metacat.plugin
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.
MetacatInitializer - Class in edu.ucsb.nceas.metacat.startup: A class to initialize Metacat
MetacatInitializer() - Constructor for class edu.ucsb.nceas.metacat.startup.MetacatInitializer
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 All actions are disabled since Metacat 3.0.0
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
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 -- 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 -- 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 -- isAuthorized() - GET /d1/mn/isAuthorized/PID setAccessPolicy() - PUT /d1/mn/accessRules/PID MNStorage - 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 - Class in edu.ucsb.nceas.metacat.restservice.v2: MN REST service implementation handler ****************** MNCore 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 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 isAuthorized() - GET /d1/mn/isAuthorized/PID setAccessPolicy() - PUT /d1/mn/accessRules/PID MNStorage 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 MNAdmin reindex() - PUT /d1/mn/index updateIdMetadata() - PUT /d1/mn/identifiers ******************
MNResourceHandler(HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler: Initializes new instance by setting servlet context,request and response
MNResourceHandler(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 - 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.v1.MNRestServlet
MNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.MNRestServlet
mockSolrTestUrl - Variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
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

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
needsLoginAdminHandling(HttpServletRequest, String) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Utility method to determine if an incoming request action requires intervention by this class
NetworkUtil - Class in edu.ucsb.nceas.metacat.util: A collection of static utility methods for networking
newNonXMLMetadataHandler(ObjectFormatIdentifier) - Static method in class edu.ucsb.nceas.metacat.object.handler.NonXMLMetadataHandlers: Create a NonXMLMetadataHandler instance to handle the given formatId.
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
NODE_ID - Static variable in class edu.ucsb.nceas.metacat.DBSAXHandler
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.QuotaService
nodeId - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
NODEID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
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
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 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.
NOT_REQUIRED - Enum constant in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus
NOT_REQUIRED - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
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
nThreads - Static variable in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader

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
OBJECT - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
OBJECT_FORMAT_PID_PREFIX - 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.
ObjectFormatService - Class in edu.ucsb.nceas.metacat.dataone: Implements a subset of the DataONE CNCore services in Metacat.
ObjectInfo - Record Class in edu.ucsb.nceas.metacat.storage: This is the Metacat version of the ObjectMetadata of Hashstore ObjectMetadata is a class that models a unique identifier for an object in the HashStore.
ObjectInfo(String, String, long, Map<String, String>) - Constructor for record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Creates an instance of a ObjectInfo record class.
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
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
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
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
PATH_ADMIN_HOMEPAGE - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
PATH_D1_PORTAL_LOGOUT - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
PATH_D1_PORTAL_OAUTH - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
PATH_D1_PORTAL_TOKEN - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
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, long, String, float, Timestamp) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry: Construct a new PathIndexEntry for the xml_path_index table.
PathIndexEntry(long, String, String, String, long) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry: Construct a new PathIndexEntry for the xml_index table.
PENDING - Enum constant in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus
PENDING - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
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
persistAuthBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.AuthPropertiesDelegate: Writes out configurable properties to a backup file outside the metacat install directory, so they are not lost if metacat installation is overwritten during an upgrade.
persistAuthBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Writes out configurable properties to a backup file outside the metacat install directory, so they are not lost if metacat installation is overwritten during an upgrade.
persistMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.BackupPropertiesDelegate: Writes out configurable properties to a backup file outside the metacat install directory, so they are not lost if metacat installation is overwritten during an upgrade.
persistMainBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Writes out configurable properties to a backup file outside the metacat install directory, so they are not lost if metacat installation is overwritten during an upgrade.
persistProperties() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Save the properties to the metacat-site.properties file.
persistProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: Save the properties to a properties file on disk.
pid() - Method in record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Returns the value of the pid record component.
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
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
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(HttpClient, String, HashMap<String, String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil: Post a request and return the response body
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
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
prepareAndThrowNotAuthorized(Session, Identifier, Permission, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper: Format a 'NotAuthorized' exception
prepareStatement(String) - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Method to create a PreparedStatement by sending a sql statement
PrerequisiteChecker300 - Class in edu.ucsb.nceas.metacat.admin.upgrade: This class will ensure the upgrade process to 3.0.0 is from version 2.19.*.
PrerequisiteChecker300() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.PrerequisiteChecker300
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
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
printParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL: Prints the parameters neatly to system.out
printSortedCSV(File, String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler: print a sorted CSV file.
processingDTD - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
processingDTD() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList: Get the document processing state.
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.
processResponse(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Process the user's choices to the solr server
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.
PropertiesWrapper - Class in edu.ucsb.nceas.metacat.properties: A Class that provides a wrapper around standard java.util.Properties to provide backwards compatibility with metacat's original properties implementation
PROPERTYNAMEOFPORTALNAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
propertyPrefix - Static variable in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
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
PUBLICID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
publish(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
publish(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
publish(Identifier, String, int) - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator: Publish the given information to the index queue
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
publishIdentifier(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler: Make the status of the identifier public
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
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) - 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.v1.MNResourceHandler: Inserts or updates the object
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) - 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) - 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(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, 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(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, 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(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(Checksum) - Method in class edu.ucsb.nceas.metacat.systemmetadata.ChecksumsManager: Find the list of pid which has the checksum matching the given value.
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
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
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, String) - Static method in class edu.ucsb.nceas.metacat.MetacatHandler: Read a document from metacat and return the InputStream.
read(Identifier) - Static method in class edu.ucsb.nceas.metacat.MetacatHandler: Read the object input stream for a given pid
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
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.
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.
readInputStreamFromLegacyStore(Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory: This method is used for the HashStoreUpgrader class to read the object from the Metacat legacy store since the Hashtore hasn't been successfully converted.
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
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.index.queue.IndexGenerator: This service is not refreshable
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
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
refreshInstance() - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator: This method sets the instance to null and forces the getInstance method to create a new instance.
refreshInstance() - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Reset the manager instance to null.
refreshLogProperties() - Method in class edu.ucsb.nceas.metacat.EventLog: Refresh the class fields controlled by properties
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
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, DBConnection, String, String) - 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(SessionData) - Method in class edu.ucsb.nceas.metacat.service.SessionService: Register a session in the session hash table.
registerSession(String, String, String[], String, String) - Method in class edu.ucsb.nceas.metacat.service.SessionService: Register a session in the session hash table.
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
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(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.
registerToDB(Identifier, MetacatHandler.Action, DBConnection, String, String, Identifier) - Method in class edu.ucsb.nceas.metacat.MetacatHandler: Register the dataone identifier into database (the xml_documents/revisions, identifier tables).
REGISTERWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
reindex(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler: Handle the reindex request
reindex(Session, List<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: The admin API call to reindex a list of documents in the instance.
reindexAll(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: The admin API call to reindex all documents in the instance.
release() - Static method in class edu.ucsb.nceas.metacat.database.DBConnectionPool: Method to shut down all connections
remove(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
removeCompleteFuture(Set<Future>) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader: This method removes the Future objects from a set which have the done status.
removeDocument(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
removeField(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
removeIdSchemePrefix(String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory: Remove the scheme prefix for a given id.
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
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.v1.MNodeService: Deprecated.
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
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
reserveIdentifier(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
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(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
resetCNList() - Static method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper: Reset the cn list to a empty list.
resolve(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
resolve(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService: Resolve the location of a given object
resolve(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
resolve(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader: Get the object path for the given pid.
RESOLVE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
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_IDENTIFIERS - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
RESOURCE_INDEX - Static variable in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
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
retrieveMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.storage.Storage
retrieveMetadata(Identifier, String) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Returns an InputStream to the metadata content of a given pid and metadata namespace from HashStore.
retrieveObject(Identifier) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Returns an InputStream to an object from HashStore using a given persistent identifier.
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
REVISIONTABLE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
rollback() - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Method to roll back
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.index.queue.FailedIndexResubmitTimerTask
run() - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask
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.
RUNNING_IN_CONTAINER - Variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
runQuery(String) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300: Get the ResultSet object after running the given query
runtimeProperties - Variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
runVerb() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb: Preforms the OAI request for this OAI-PMH verb

S

save(Identifier, Map<String, String>, DBConnection) - Method in class edu.ucsb.nceas.metacat.systemmetadata.ChecksumsManager: Save the checksums into database.
save(SystemMetadata, boolean, MetacatHandler.Action, String, InputStream, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler: Save the object into disk
scheduleSitemapGeneration() - Static method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: 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.DBSAXHandler
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(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
search(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService: Metacat does not implement this method at the CN level
search(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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
sendNotSupportMessage(HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetacatHandler: Send back the not-support message
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.
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
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
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
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
setAccess(String, String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
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) - Method in interface edu.ucsb.nceas.metacat.client.Metacat: set the access on an XML document in the repository.
setAccess(String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient: set the access on an XML document in the repository.
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.CNodeService: Set access for a given object using the object identifier and a Subject under a given Session.
setAccessPolicy(Session, Identifier, AccessPolicy, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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
setAutoCommit(boolean) - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Method to set commit mode
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
setChecksums(Map<String, String>) - Method in class edu.ucsb.nceas.metacat.systemmetadata.MCSystemMetadata: Set the checksums for the MCSystemMetadata 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
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
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
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.
setDirPath(String) - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
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.clientview.ClientView: Setter for property docId.
setDocID(String) - Method in class edu.ucsb.nceas.metacat.BasicNode: Set the doc id of this node
setDoctype(String) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
setDocumentCart(DocumentCart) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setDOIUpdater(UpdateDOI) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService: This method is for testing only - replacing the real class by a stubbed Mockito UpdateDOI class.
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
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(String) - Method in class edu.ucsb.nceas.metacat.EventLogData: Set the current value of the event.
setEvent(Event) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.V2LogEntryWrapper
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
setForceRebuild(boolean) - Static method in class edu.ucsb.nceas.metacat.DBTransform: Set the field of forceRebuild
setFormatId(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchema: Set the format id.
setGroupNames(String[]) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setGroups(String[]) - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
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
setLastAccessedTime() - Method in class edu.ucsb.nceas.metacat.util.SessionData
setLastProcessDate(Date) - Method in class edu.ucsb.nceas.metacat.index.queue.LastReindexDateManager: Set the SystemMetadata modification Date of the objects that were built the solr index during the previous timed indexing process.
setLocalId(int) - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage: Set the local id
setLoggedIn(boolean) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
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.
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.
setMetacatSolrIndex(MetacatSolrIndex) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService: This method is for testing only - replacing the real class by a stubbed Mockito MetacatSolrIndex class.
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(InputStream) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setMetadataDoc(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
setMetadataDoc(Document) - 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.
setMNBaseURL(Collection<String>) - Method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin: Set the property of dataone.mn.baseURL automatically
setName(String) - Method in class edu.ucsb.nceas.metacat.util.SessionData
setNamespace(String, String) - Method in class edu.ucsb.nceas.metacat.BasicNode: Add a namespace to this node
setNodeData(String) - Method in class edu.ucsb.nceas.metacat.NodeRecord: A method used to set the node data of the current node
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.NodeRecord: A method used to set the node id of the current node
setNodeID(long) - Method in class edu.ucsb.nceas.metacat.BasicNode: Set the id of this node
setNodeIndex(int) - Method in class edu.ucsb.nceas.metacat.BasicNode: Set the node index of this node
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
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
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.CNodeService: Set the obsoletedBy attribute in System Metadata
setObsoletedBy(Session, Identifier, Identifier, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
setOrganization(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Setter for property organization.
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.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.
setPermissionType(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule: Set the permssionType
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.PropertiesWrapper: Utility method to set a property value both in memory and to the properties file
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
setPropertyNoPersist(String, String) - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: Utility method to set a property value in memory.
setPropertyNoPersist(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: 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.
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.
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
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.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(Session, Identifier, ReplicationPolicy, long) - 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
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.CNodeService: Set the replication status for an object given the object identifier
setReplicationStatus(Session, Identifier, NodeReference, ReplicationStatus, BaseException) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
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.
setReturnfield(String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView: Setter for property returnfield.
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.CNodeService: Changes ownership (RightsHolder) of the specified object to the subject specified by userId
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
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 class edu.ucsb.nceas.metacat.clientview.ClientView: Setter for property sessionid.
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
setSkinName(Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.SkinUtil: Set the names of skin.
setSolrConfigUpgrader(SolrConfigUpgrader) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrSchemaAndConfigUpgrader: Set the SolrConfigUpgrader instance.
setSolrSchemaUpgrader(SolrSchemaUpgrader) - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrSchemaAndConfigUpgrader: Set the SolrSchemaUpgrader instance.
setStatus(int) - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Set a connection status to this object
setStatus(String, UpgradeStatus) - Static method in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
setSubscriber(String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage: Set the subscriber associated with the usage
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
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.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.util.SessionData
setWarningMessage(SQLWarning) - Method in class edu.ucsb.nceas.metacat.database.DBConnection: Set a warning message to this object
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
SITE_PROPERTIES_DIR_PATH_KEY - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
SITE_PROPERTIES_FILENAME - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
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.
size() - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator: Get the number of messages in the index queue
size() - Method in record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Returns the value of the size record component.
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
SkinUtil - Class in edu.ucsb.nceas.metacat.util
SLASH - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
SOLR_BASE_URL_PROP_KEY - Static variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
SOLR_CONFIGURED_PROP_KEY - Static variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
SOLR_CORE_NAME_PROP_KEY - Static variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
SOLR_SCHEMA_LOCATOR_PROP_KEY - Static variable in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
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
SolrJvmVersionFinder - Class in edu.ucsb.nceas.metacat.admin.upgrade.solr: A class to find the version of a JVM against which the solr is running
SolrJvmVersionFinder(String) - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrJvmVersionFinder: Constructor
SolrSchemaAndConfigUpgrader - Class in edu.ucsb.nceas.metacat.admin.upgrade.solr: A class to upgrade solr configuration files in the upgrade process to Metacat 3.0.0
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"
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
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.MetacatResultSet
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
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
startIndexReGenerator() - Static method in class edu.ucsb.nceas.metacat.startup.MetacatInitializer: Start to re-generate indexes for those haven't been indexed in another thread.
startLoginFlow(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Begin the login flow
startPrefixMapping(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler: SAX Handler that is called at the start of Namespace
startTag - Static variable in class edu.ucsb.nceas.metacat.util.DocumentUtil
startTime(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler: start the timing on a profile
StartupRequirementsChecker - Class in edu.ucsb.nceas.metacat.startup: An implementation of ServletContextListener that is called automatically by the servlet container on startup, and used to verify that we have the essential components in place for Metacat to run successfully.
StartupRequirementsChecker() - Constructor for class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker
STATUS - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
stop - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
stop() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
stop() - Method in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator: Stop the service
stop() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
stop() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
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
stopTime(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler: stop the timing on a profile
Storage - Class in edu.ucsb.nceas.metacat.storage: The HashStore implementation of the Storage interface.
STORAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
store(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Store a system metadata record into the store Note: This method is not thread safe.
store(SystemMetadata, boolean, DBConnection, SystemMetadataManager.SysMetaVersion) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Store a system metadata record into the store.
store(SystemMetadata, boolean, SystemMetadataManager.SysMetaVersion) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Store a system metadata record into the store Note: This method is not thread safe.
storeData(Storage, InputStream, SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Store the input stream into hash store
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
storeMetadata(InputStream, Identifier) - Method in class edu.ucsb.nceas.metacat.storage.Storage
storeMetadata(InputStream, Identifier, String) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Adds/updates metadata (ex.
storeObject(InputStream) - Method in class edu.ucsb.nceas.metacat.storage.Storage
storeObject(InputStream, Identifier, String, String, String, long) - Method in class edu.ucsb.nceas.metacat.storage.Storage: The `storeObject` method is responsible for the atomic storage of objects to disk using a given InputStream.
storeRollBack(Identifier, Exception, DBConnection, SystemMetadata...) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: RollBack the change in database and hashtore when the store methods failed
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
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, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex: Submit the index task to the index queue
submit(Identifier, SystemMetadata, boolean, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex: Submit a index task into the index queue
submit(Identifier, SystemMetadata, boolean, boolean, int) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex: Submit a index task into the index queue
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).
submitIndex(String) - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask: Submit the index task to the queue for the given id
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(SynchronizationFailed) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
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(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() - Method in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: The properties on the dataONE Setting class aren't synchronized with changes to the Metacat properties files.
syncToSettings() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService: The properties on the dataONE Setting class isn't synchronized with changes to the Metacat properties files.
SYSMETA - Static variable in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
SYSMETA_CHANGE_TYPE - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
systemid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
SYSTEMID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
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.MNodeService: A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.
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
SystemMetadataManager - Class in edu.ucsb.nceas.metacat.systemmetadata
SystemMetadataManager.SysMetaVersion - Enum Class in edu.ucsb.nceas.metacat.systemmetadata
systemMetadataPIDExists(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
systemMetadataPIDExists(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: Determine if the specified identifier object exists or not.
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
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
SystemMetadataValidator - Class in edu.ucsb.nceas.metacat.systemmetadata: A class to validate the given system metadata object
SystemMetadataValidator() - Constructor for class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataValidator
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
tagObject(Identifier, String) - Method in class edu.ucsb.nceas.metacat.storage.Storage: Creates references that allow objects stored in HashStore to be discoverable.
TERM_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
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
textBuffer - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
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.
toString() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier: returns the whole docid as a string
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.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.properties.PropertiesWrapper: Provides a string representation of all the properties seen by the application at runtime, in the format: key1=property1 key2=property2 key3=property3 ...etc.
toString() - Method in record class edu.ucsb.nceas.metacat.storage.ObjectInfo: Returns a string representation of this record class.
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.
toZipFileName(String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
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
TYPE_IDENTIFIER - Static variable in class edu.ucsb.nceas.metacat.IdentifierManager
TYPE_SYSTEM_METADATA - Static variable in class edu.ucsb.nceas.metacat.IdentifierManager

U

UNCHECKED - Enum constant in enum class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager.SysMetaVersion
UNCONFIGURED - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
UNKNOWN - Enum constant in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.admin.MetacatAdmin
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
unLock(Identifier) - Static method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Unlock a pid so allow another thread to modify the system metadata in database/file system Note: put this method in the final block while put the lock and store method in the try block
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.
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(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(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(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 - Enum constant in enum class edu.ucsb.nceas.metacat.MetacatHandler.Action
UPDATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
UPDATE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
updateAllIdMetadata(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Update all controlled identifiers' (such as DOI) metadata on the third party service.
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
updateIdMetadata(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler: Handle the request to update identifiers' (such as DOI) metadata on the third party service
updateIdMetadata(Session, String[], String[]) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService: Update the given identifiers' (such as DOI) metadata on the third party service.
updateMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager: update a mapping
updateMetacatPropertiesPath(String, String) - Method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin
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
updateNodeText(Node, XPath, String, String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
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
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.CNodeService: Full replacement of replication metadata in the system metadata for the specified object, changes date system metadata modified
updateReplicationMetadata(Session, Identifier, Replica, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService: Deprecated.
updateSolrStatus(String, boolean) - Static method in class edu.ucsb.nceas.metacat.admin.SolrAdmin: Update the solr_upgraded status for the given metacat version
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
updateSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService: 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(Session, Identifier, SystemMetadata, boolean, SystemMetadata, boolean, SystemMetadataManager.SysMetaVersion) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService: Update the system metadata of the specified pid.
updateSystemMetadata(SystemMetadata, boolean, SystemMetadataManager.SysMetaVersion) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService: Update system metadata.
updateSystemMetadata(SystemMetadata, DBConnection) - Method in class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager: Insert the system metadata fields into the db
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, 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.
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
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
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader
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.SolrSchemaAndConfigUpgrader
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.Upgrade3_0_0: This method will run the class - XMLNodesToFilesChecker, which basically makes sure that every metadata document has been imported from xml_nodes or xml_nodes_revision tables to the file system.
upgrade() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpgradeEmptyReplicatedDataFile
upgrade() - Method in interface edu.ucsb.nceas.metacat.admin.upgrade.UpgradeUtilityInterface
Upgrade3_0_0 - Class in edu.ucsb.nceas.metacat.admin.upgrade: Run this class when the users upgrade their Metacat instances to 3.0.0.
Upgrade3_0_0() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.Upgrade3_0_0
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
UpgradeStatus - Enum Class in edu.ucsb.nceas.metacat.admin
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, File) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient: 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, 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
upRegD1MemberNode() - Method in class edu.ucsb.nceas.metacat.admin.D1Admin: upReg: Either update ("up") or register ("reg") DataONE Member Node (MN) config, depending upon whether this Metacat instance is already registered as a DataONE MN.
uriTemplate - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
usage - Variable in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
USAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
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.
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(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
validate(String) - Method in class edu.ucsb.nceas.metacat.DBValidate: validate an xml document against its DTD
validateDBConnectivity(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin: Validate connectivity to the database.
validateDefaultProperties(ServletContextEvent) - Method in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker: Check that the default properties file is readable and writeable, without throwing any exceptions.
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.AuthAdmin: Validate that a user has supplied an ORCID identifier by parsing the http request's 'auth.administrators' parameter.
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.HashStoreConversionAdmin
validateOptions(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.admin.LoginAdmin: Required override from superclass.
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.SolrAdmin: Validate the most important configuration options submitted by the user.
validateSciMeta(Identifier, ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.MetacatHandler: Validate a scientific metadata object.
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.client.MetacatClient: Method used to log in to a metacat server.
validateSession(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService: Check if a session is registered in the session hash table.
validateSiteProperties(Properties) - Method in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker: Check if we can load properties from, and write properties to, 'metacat-site.properties', or can create a new one if it doesn't already exist (protected to allow test access)
validateSolrAvailable() - Method in class edu.ucsb.nceas.metacat.startup.StartupRequirementsChecker: Ensure we get an HTTP 200 OK response and can retrieve the schema doc from the solr service that is configured in the properties file.
validateString(String) - Method in class edu.ucsb.nceas.metacat.DBValidate: validate an xml document against its DTD
validateXmlSciMeta(Identifier, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler: Validate an XML object.
VALIDATIONFEATURE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
valueOf(String) - Static method in enum class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300.NodeTableName: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class edu.ucsb.nceas.metacat.MetacatHandler.Action: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager.SysMetaVersion: Returns the enum constant of this class with the specified name.
values() - Static method in enum class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300.NodeTableName: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class edu.ucsb.nceas.metacat.admin.UpgradeStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class edu.ucsb.nceas.metacat.MetacatHandler.Action: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class edu.ucsb.nceas.metacat.systemmetadata.SystemMetadataManager.SysMetaVersion: Returns an array containing the constants of this enum class, in the order they are declared.
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_000 - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
VERSION_ACTIVE - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
VERSION_INACTIVE - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
versionAndClassMapInProperty - Static variable in class edu.ucsb.nceas.metacat.admin.HashStoreConversionAdmin
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

WAITTIME - Static variable in class edu.ucsb.nceas.metacat.index.queue.IndexGeneratorTimerTask
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
WRITEABLE_DEFAULTS - Static variable in class edu.ucsb.nceas.metacat.properties.PropertiesWrapper: TODO: Eliminate the need for this list! It is here for legacy reasons; See GitHub Issue #1638: https://github.com/NCEAS/metacat/issues/1638 Whenever setPropertyNoPersist() is called, the code checks to see if the passed propertyName parameter is listed in 'writeableDefaults'.
writeConfig() - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
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.
writeStoredBackupFile(String) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
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.
writeToFile(String, BufferedWriter) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader
writeToFile(String, Exception, BufferedWriter) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.HashStoreUpgrader

X

XML_LANG - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
XML_NODES - Enum constant in enum class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300.NodeTableName
XML_NODES_REVISIONS - Enum constant in enum class edu.ucsb.nceas.metacat.admin.upgrade.DroppedTableBackupper300.NodeTableName
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
XMLNodesToFilesChecker - Class in edu.ucsb.nceas.metacat.admin.upgrade: Historically, early versions of Metacat only store the metadata documents in the xml_nodes and xml_nodes_revsions tables rather than the files.
XMLNodesToFilesChecker() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.XMLNodesToFilesChecker: Default 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
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.

_

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

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