Index

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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
 
add(String, SimpleFeature) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
Adds a new feature (from a SpatialDocument) This is faster than insertOrUpdate but relying on this method might cause duplication of docids in the spatial cache.
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
addToDeleteQue(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Delete a given document from spatial cache.
addToUpdateQue(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Currently just a wrapper around the harvestDocument method.
addUser(String, String[], String, String, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
Add a user to the file
addUserToGroup(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
Add a user to a group
addVersion(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Add the version element to the document
addXMLAccess(String, String, Long, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Add permissions for a given principal on a given document.
AdminException - Exception in edu.ucsb.nceas.metacat.admin
Exception thrown when an error occurs in a configuration administrative class
AdminException(String) - Constructor for exception edu.ucsb.nceas.metacat.admin.AdminException
Create a new AdminException.
AGENT_URI - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
 
AGGREGATION - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
 
allowedVersionLevels - Static variable in class edu.ucsb.nceas.metacat.Version
 
alreadyHandle - Variable in class edu.ucsb.nceas.metacat.DBValidate
 
appendCreator(String, Document, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Append a creator element to the root element.
appendDescription(String, Document, String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Append a description to the document.
appendFormat(Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Add the format (MIME type) of the meta data object to the document
appendRev(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
If the given docid only have one seperter, we need append rev for it.
appendSubject(String, Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Append a subject to the document
appendTitle(String, Document, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Append a title to the title list element
APPLICATION_NAME - Static variable in class edu.ucsb.nceas.metacat.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
 
authCacheSzie - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
authenticate(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
authenticate(String, String) - Method in 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
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 meta data with the given name space
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
It can handle all namespace
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
Determine if the given name space can be handled by this factory
CartManager - Class in edu.ucsb.nceas.metacat.cart
Class to query data
CartManager() - Constructor for class edu.ucsb.nceas.metacat.cart.CartManager
empty constructor to initialize query
CartManager(String) - Constructor for class edu.ucsb.nceas.metacat.cart.CartManager
 
catalogid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
CatalogMessageHandler - Class in edu.ucsb.nceas.metacat
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the replication handler
CatalogMessageHandler() - Constructor for class edu.ucsb.nceas.metacat.CatalogMessageHandler
 
changePassword(String, String) - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
Change the password on the geoserver.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Callback method used by the SAX Parser when the text sequences of an xml stream are detected.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
Take the data out of the docid and date_updated fields
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that is called for each XML text node
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.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
 
CheckedFile - Class in edu.ucsb.nceas.metacat.restservice.multipart
A file object with the expected checksum
CheckedFile(String, Checksum) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.CheckedFile
Constructor
checkExpandedPermissions(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Compare all the session subjects against the expanded subjects (from listSubjects) of the object rightsHolder.
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.
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)
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 -- DONE create() - POST /d1/cn/object/PID listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET /d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET /d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not implemented in Metacat CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET /d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules CNIdentity - not implemented at all on Metacat CNReplication setReplicationStatus() - PUT /replicaNotifications/PID updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy() - PUT /replicaPolicies/PID isNodeAuthorized() - GET /replicaAuthorizations/PID CNRegister -- not implemented at all in Metacat ******************
CNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v2
CN REST service implementation handler ****************** CNCore -- DONE create() - POST /d1/cn/object/PID listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET /d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET /d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not implemented in Metacat CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET /d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules CNIdentity - not implemented at all on Metacat CNReplication setReplicationStatus() - PUT /replicaNotifications/PID updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy() - PUT /replicaPolicies/PID isNodeAuthorized() - GET /replicaAuthorizations/PID CNRegister -- not implemented at all in Metacat ******************
CNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
 
CNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
 
CNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v1
Routes CN REST service requests to the appropriate handler
CNRestServlet - 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.
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(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
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(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Initializes new instance by setting servlet context,request and response
D1RestServlet - Class in edu.ucsb.nceas.metacat.restservice
Metacat 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, String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
Deletes given docid from the spatial cache.
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.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
 
deleteDocument(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Given a docid, will attempt to delete it from spatial cache
deleteFromFileSystem(String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Deletes a doc or data file from the filesystem using the accession number.
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.
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
 
destroy() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Closes the database connection.
destroy() - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
 
DetailedFileInputStream - Class in edu.ucsb.nceas.metacat.restservice.multipart
A FileInputStream class with more information, such as the object of source file itself and the expected checksum of the source file.
DetailedFileInputStream(File, Checksum) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
Constructor
determine(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
Determine the quota type and instance id from the object format information in the system metadata
discoverApplicationContext(ServletContext) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the context for this application.
discoverDeployDir(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the deployment directory for this application.
discoverExternalDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the external (to the metacat installation) directory where metacat will hold backup files.
discoverServerName(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the server name.
discoverServerPort(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the server port.
discoverServerSSLPort(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the server ssl port.
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
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.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
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.spatial.SldFactory
Handle "GET" method requests from HTTP clients
doGetSysmetaAuthorization(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
used by getSystemMetadata, describe, and getPackage, the latter two by delegation to getSystemMetadata Very similar to doIsAuthorized, but also allows replica nodes administrative access.
doHead(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "PUT" method requests from HTTP clients
DOI - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
DOI_SCHEME - Static variable in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
doiEnabled - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
 
DOIException - Exception in edu.ucsb.nceas.metacat.doi
An exception that encapsulates errors from the DOI service.
DOIException(String) - Constructor for exception edu.ucsb.nceas.metacat.doi.DOIException
Constructor
doIsAuthorized(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Performs all authorization steps used by isAuthorized.
DOIService - Class in edu.ucsb.nceas.metacat.doi
An abstract class for the DOI service
DOIService() - Constructor for class edu.ucsb.nceas.metacat.doi.DOIService
Constructor
DOIServiceFactory - Class in edu.ucsb.nceas.metacat.doi
A factory class to initialize an instance of DOIService based on the configuration in the metacat.properties file
DOIServiceFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.DOIServiceFactory
 
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
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.spatial.SldFactory
Handle "POST" method requests from HTTP clients
doPut(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "PUT" method requests from HTTP clients
doRefresh() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.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.spatial - package edu.ucsb.nceas.metacat.spatial
 
edu.ucsb.nceas.metacat.startup - package edu.ucsb.nceas.metacat.startup
 
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(AccessPolicy, AccessPolicy) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Compare two AccessPolicy objects
error(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of recoverable parsing errors
ERROR_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
ErrorHandledException - Exception in edu.ucsb.nceas.metacat
Exception thrown when an error occurs in a configuration administrative class
ErrorHandledException(String) - Constructor for exception edu.ucsb.nceas.metacat.ErrorHandledException
Create a new AdminException.
ErrorSendingErrorException - Exception in edu.ucsb.nceas.metacat.util
Exception thrown when an error occurs in a utility method
ErrorSendingErrorException(String) - Constructor for exception edu.ucsb.nceas.metacat.util.ErrorSendingErrorException
Create a new AdminException.
ESCAPECHAR - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
 
EventLog - Class in edu.ucsb.nceas.metacat
EventLog is used to intialize and store a log of events that occur in an application.
EventLogData - Class in edu.ucsb.nceas.metacat
A data structure holding the information to be logged about an event.
EventLogData(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.EventLogData
Construct an EventLogData object with event log information.
EventLogFilter - Class in edu.ucsb.nceas.metacat
This class represents a filter to prevent the events generated by some ip addresses and subjects to be logged into db
EventLogFilter() - Constructor for class edu.ucsb.nceas.metacat.EventLogFilter
Default Construct
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

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.
filterByBbox(float, float, float, float) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialQuery
Querys all features in the spatial cache and filters based on bouding coordinates.
filterRequest(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
Override to do any pre-qualification; return false if the response should be returned immediately, without further action.
find() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.solr.SolrJvmVersionFinder
Parse the solr admin information and find the jvm version
findBoundaryString(InputStream) - Static method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
locate the boundary marker for an MMP
findDataSetDocIdForGivenDocument(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
To a given docid, found a dataset docid which contains the the given docid This will be done by searching xml_relation table If couldn't find, null will be return
findDocumentNamespace(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
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 meta data xml string for an object with the given system meta data.
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
Method to generate the data cite xml document
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
Method to generate the data cite xml document
generateNewComponent(Model, String) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Create a Resource object for the given id.
generateNewOREResource(Model, Subject, Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
This method generates a Resource object for the new ore id in the given model
generateOstiMetadata(InputStream, String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
Generate the OSTI document for the given eml
generateROOTDoc() - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Generate the blank DOM document for the datacite name space
generateSitemaps() - Method in class edu.ucsb.nceas.metacat.Sitemap
Generate all of the sitemap files needed to list the URLs from this instance of Metacat, using the open sitemap format described here: http://www.sitemaps.org/protocol.html URLs are written to a one or more files and a sitemap index file is always written.
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.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() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.CheckedFile
Get the checksum of this file
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.
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
 
getDataDir() - Method in class edu.ucsb.nceas.metacat.MetacatHandler
Get the data object directory
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.
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
 
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
getExpectedChecksum() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
Get the expected checksum of the source file
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
 
getFile() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
Get the source file
getFileName() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the file name
getFileNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the file namespace
getFilePath(Identifier) - Static method in class edu.ucsb.nceas.metacat.index.queue.IndexGenerator
Get the relative file path for the identifier.
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.
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
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.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
getMetadataDir() - Method in class edu.ucsb.nceas.metacat.MetacatHandler
Get the metadata object directory
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.
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.
getPointFeature() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDocument
Returns a geotools (multi)point feature with geometry plus attributes ready to be inserted into our spatial dataset cache
getPointFeatureType() - Static method in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
Creates the featuretype schema for point centroids
getPolygonFeature() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDocument
Returns a geotools (multi)polygon feature with geometry plus attributes ready to be inserted into our spatial dataset cache
getPolygonFeatureType() - Static method in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
Creates the featuretype schema for polygon bounds
getPrincipal() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
Get the principle vector
getPrincipal() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the principal.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getPrincipals(String, String) - Method in 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() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion status from the object
getStatus(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Get the status of the system.
getStoredBackupDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Gets the stored backup location.
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
 
getVersion(String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
Get the version of the service name for the node.
getVERSION() - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
Get the VERSION number
getVersionAsXml() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
Get the version number in an XML document.
getVersionFromDB() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
Get the version number from DB
getVersionFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Utility method to get version number from a given string
getVersionID() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
Get the current version string for this metacat instance.
getVersionString() - Method in class edu.ucsb.nceas.metacat.Version
 
getWarningMessage() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion waring message from the object
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.
harvestDocument(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Given a new or updated docid, will update the spatial cache accordingly.
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
hasAllPermission(String, String[], String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Check for "ALL" or "CHMOD" permission on @docid for @user and/or @groups from DB connection
hash(String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFileBCryptHash
 
hash(String) - Method in interface edu.ucsb.nceas.metacat.authentication.AuthFileHashInterface
Generate the hash value for a specified plaint password
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
hasWritePermission(String, String[], String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Check for "WRITE" permission on @docid for @user and/or @groups from DB connection
HEAD - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
HTTP Verb HEAD
HIDDEN_EXISTS_POPULATED - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
 
HIDDEN_EXISTS_UNPOPULATED - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
 
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 - 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
init(FilterConfig) - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
 
init(FilterConfig) - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
 
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.
initializeDir(String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
Create a directory based on the given path if it is necessary.
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
 
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.
insertOrUpdate(String, SimpleFeature, String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
Either inserts or updates the spatial cache with the new spatial document depending on if it currently exists.
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
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
 
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
 
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.D1ResourceHandler
 
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.
main(String[]) - Static method in class edu.ucsb.nceas.metacat.spatial.XSLTransform
the main routine used to test the transform utility.
makeRedirectUrl() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
mappingExists(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Determine if an identifier mapping exists already, returning true if so.
mapToHtmlSelect(Map, String, String, int) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientHtmlHelper
JSP API: A static helper method which takes a map (key, value pairs) and returns an XHTML SELECT String.
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.
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 -- DONE ping() - GET /d1/mn/monitor/ping log() - GET /d1/mn/log **getObjectStatistics() - GET /d1/mn/monitor/object getOperationsStatistics - GET /d1/mn/monitor/event **getStatus - GET /d1/mn/monitor/status getCapabilities() - GET /d1/mn/ and /d1/mn/node MNRead -- DONE get() - GET /d1/mn/object/PID getSystemMetadata() - GET /d1/mn/meta/PID describe() - HEAD /d1/mn/object/PID getChecksum() - GET /d1/mn/checksum/PID listObjects() - GET /d1/mn/object synchronizationFailed() - POST /d1/mn/error MNAuthorization -- DONE isAuthorized() - GET /d1/mn/isAuthorized/PID setAccessPolicy() - PUT /d1/mn/accessRules/PID MNStorage - DONE create() - POST /d1/mn/object/PID update() - PUT /d1/mn/object/PID delete() - DELETE /d1/mn/object/PID archive() - PUT /d1/mn/archive/PID systemMetadataChanged() - POST /dirtySystemMetadata/PID MNReplication replicate() - POST /d1/mn/replicate getReplica() - GET /d1/mn/replica ******************
MNResourceHandler - 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(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
Initializes new instance by setting servlet context,request and response
MNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
Initializes new instance by setting servlet context,request and response
MNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v1
Routes MN REST service requests to the appropriate handler
MNRestServlet - 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.
notationDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBDTDHandler
Notation declarations are not signaled
notify(String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiErrorEmailAgent
Send the email with error messages to recipients
notifyMetacatEventObservers(MetacatEvent) - Method in class edu.ucsb.nceas.metacat.event.MetacatEventService
 
notifyReplicaNodes(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Notify replica Member Nodes of system metadata changes for a given pid

O

oa - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
oa_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
OAIHandler - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server
OAIHandler is the primary Servlet for OAICat.
OAIHandler() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
 
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.
objectFileExists(String, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Determine if the object file exist for the given localId.
ObjectFormatService - Class in edu.ucsb.nceas.metacat.dataone
Implements a subset of the DataONE CNCore services in Metacat.
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.
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.
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
 
pointShpUri - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
 
polygonShpUri - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
 
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
 
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(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
 
queryAllDocids() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Returns a Vector of all the current versions of public docids
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.
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.
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.
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
regenerate() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Completely regenerates the spatial cache.
REGISTER - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
REGISTERANDUPDATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
REGISTERANDUPDATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
registerDocument(String, String, 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
 
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 sheme 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
 
removeSolrIndex(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
removeSystemMetaAndIdentifier(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
removeUserFromGroup(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
Remove a user from a group.
removeXMLAccessForPrincipal(String, String, Long) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Remove xml access.
REPLACE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
replaceAccess(String, List<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Set permissions for a given document.
replaceObsoletedId(Identifier, Identifier, OutputStream, Subject) - Method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Create new resource map by replacing obsoleted ids by new ids.
replaceWhiteSpaceForURL(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
A method to replace whitespace in url
replicate(Session, SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.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 - 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
 
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
runSQLFile(String) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Runs the commands in a sql script.
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() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
Saves the SpatialDataset object to the spatial cache.
save(SystemMetadata, boolean, MetacatHandler.Action, String, InputStream, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
Save the object into disk
saveBytes(InputStream, String, Checksum, String, Identifier) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
Save the bytes from a input stream 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
 
servletContext - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
session - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
session2 - Variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
out-of-band session object to be used when not passed in as a method parameter
SessionData - Class in edu.ucsb.nceas.metacat.util
 
SessionData(String, String, String[], String, String) - Constructor for class edu.ucsb.nceas.metacat.util.SessionData
 
SessionService - Class in edu.ucsb.nceas.metacat.service
 
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
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
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
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
 
SldFactory - Class in edu.ucsb.nceas.metacat.spatial
Class to generate Styled Layer Descriptors allowing geoserver to filter the feature rendering based on various contraints such as permissions, non-spatial queries and skin configuration.
SldFactory() - Constructor for class edu.ucsb.nceas.metacat.spatial.SldFactory
 
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"
SpatialDataset - Class in edu.ucsb.nceas.metacat.spatial
Class providing direct read/write access to the persistent spatial cache.
SpatialDataset() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialDataset
empty constructor for SpatialDataset
SpatialDocument - Class in edu.ucsb.nceas.metacat.spatial
Class representing the spatial portions of an xml document as a geotools Feature.
SpatialDocument(String, DBConnection) - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialDocument
Constructor that queries the db
SpatialFeatureSchema - Class in edu.ucsb.nceas.metacat.spatial
Class representing the geotools feature schemas and file paths for the spatial data cache.
SpatialFeatureSchema() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
empty constructor
SpatialHarvester - Class in edu.ucsb.nceas.metacat.spatial
Harvests spatial data from metacat database and saves to persistent cache
SpatialHarvester() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
constructor to initialize db connection
SpatialQuery - Class in edu.ucsb.nceas.metacat.spatial
Class to query the persistent spatial cache and returns docids matching spatial constraints
SpatialQuery() - Constructor for class edu.ucsb.nceas.metacat.spatial.SpatialQuery
empty constructor to initialize spatial query
speedBag - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
 
speedBag - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
 
split(String, String, String) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Convert a delimited string to a Vector by splitting on a particular character
SqlserverAdapter - Class in edu.ucsb.nceas.dbadapter
The MS SQL Server db adapter implementation.
SqlserverAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.SqlserverAdapter
 
srid - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
 
start - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
 
startCDATA() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
SAX Handler that receives notification of the start of CDATA sections
startCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the start of CDATA sections
startDailyCheck() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
Start a timer to check failed usage reporting and report them again in daily base.
startDocument() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Callback method used by the SAX Parser when beginning of the document
startDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of beginning of the document
startDocument() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
 
startDTD(String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
SAX Handler that receives notification of DOCTYPE.
startDTD(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of DOCTYPE.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Callback method used by the SAX Parser when the start tag of an element is detected.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
This method starts a new vector for each updatedDocument tag.
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that is called at the start of each XML element
startElement(String, String, String, Attributes) - Method in class edu.ucsb.nceas.metacat.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 - 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 The modification time will be changed and system metadata version will be checked during the process
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
storeExternalDirLocation(String) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Store the location of the backup file location into a file at //backup-location
StreamingMultipartRequestResolver - Class in edu.ucsb.nceas.metacat.restservice.multipart
This class will stream the file parts of the multipart request into a temporary file.
StreamingMultipartRequestResolver(String, int) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
Constructor
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
 
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.
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
 
transform(Reader, String, PrintWriter, Hashtable) - Static method in class edu.ucsb.nceas.metacat.spatial.XSLTransform
Transform an XML document using an XSLT stylesheet to another format, probably HTML or another XML document format.
transform(String, String, PrintWriter, Hashtable) - Static method in class edu.ucsb.nceas.metacat.spatial.XSLTransform
Transform an XML document using an XSLT stylesheet to another format, probably HTML or another XML document format.
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 - Static variable in class edu.ucsb.nceas.metacat.admin.BackupAdmin
 
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
UNKNOWN - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
 
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.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
 
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.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(byte[], 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(byte[], 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.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.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_ACTIVE - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
 
VERSION_INACTIVE - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
 
versionString - Variable in class edu.ucsb.nceas.metacat.Version
 
view(Session, String, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
view(Session, String, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 

W

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
 
WmsFilter - Class in edu.ucsb.nceas.metacat.spatial
 
WmsFilter() - Constructor for class edu.ucsb.nceas.metacat.spatial.WmsFilter
 
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
 
writeStreamToCheckedFile(File, InputStream, String, String) - Static method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
Write the input stream into the given fileName and directory while calculate the checksum.
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.

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.
XSLTransform - Class in edu.ucsb.nceas.metacat.spatial
A Class that transforms XML documents utitlizing XSL style sheets.
XSLTransform() - Constructor for class edu.ucsb.nceas.metacat.spatial.XSLTransform
Private constructor because all methids are static and do not need an instance.

_

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