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A

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

B

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

C

callorder - Variable in class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
 
canInsertOrUpdate(String, String[]) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Check if the specified user can insert the document
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Determine if the factory can handle the meta data with the given name space
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
It can handle all namespace
canProcess(String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
Determine if the given name space can be handled by this factory
CartManager - Class in edu.ucsb.nceas.metacat.cart
Class to query data
CartManager() - Constructor for class edu.ucsb.nceas.metacat.cart.CartManager
empty constructor to initialize query
CartManager(String) - Constructor for class edu.ucsb.nceas.metacat.cart.CartManager
 
catalogid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
CatalogMessageHandler - Class in edu.ucsb.nceas.metacat
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the replication handler
CatalogMessageHandler() - Constructor for class edu.ucsb.nceas.metacat.CatalogMessageHandler
 
changePassword(String, String) - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
Change the password on the geoserver.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Callback method used by the SAX Parser when the text sequences of an xml stream are detected.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
Take the data out of the docid and date_updated fields
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that is called for each XML text node
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that is called for each XML text node
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that is called for each XML text node
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
 
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
callback method used by the SAX Parser when the text sequences of an xml stream are detected.
characters(char[], int, int) - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
Take the data out of the docid and date_updated fields
check(NodeReference, SystemMetadata) - Static method in class edu.ucsb.nceas.metacat.dataone.NodeReplicationPolicyChecker
Check if a given object with the system meta data and from the source node can be stored as a replica
checkAndSetProperty(HttpServletRequest, String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(HttpServletRequest, String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
checkAndSetProperty(HttpServletRequest, String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(HttpServletRequest, String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(HttpServletRequest, String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Take input from the user in an HTTP request about an property to be changed and update the metacat property file with that new value if it has changed from the value that was originally set.
checkAndSetProperty(String, String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Check user input against existing value and update the metacat property file with that new value if it has changed from the value that was originally set.
CheckedFile - Class in edu.ucsb.nceas.metacat.restservice.multipart
A file object with the expected checksum
CheckedFile(String, Checksum) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.CheckedFile
Constructor
checkExpandedPermissions(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Compare all the session subjects against the expanded subjects (from listSubjects) of the object rightsholder.
checkQuota(boolean, String, String, String, double, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
Check if the quota has enough space for this request.
checkSidInModifyingSystemMetadata(SystemMetadata, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
checkURLConnection(String) - Static method in class edu.ucsb.nceas.metacat.DBEntityResolver
Check URL Connection for @systemId, and return an InputStream that can be used to read from the systemId URL.
checkV1SystemMetaPidExist(Identifier, String, String, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
A utility method for v1 api to check the specified identifier exists as a pid Uses the IdentifierManager to call the Identifier table directly - this detects Identifiers for deleted objects (where the SystemMetadata doesn't exist, but the Identifier remains)
cito - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
CITO_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
 
clear() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
clearFields() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
clearQueryResultCache() - Static method in class edu.ucsb.nceas.metacat.DBQuery
Method to clear the query result cache.
clearRequestMessages(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
Add a list of general messages to the request.
client - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
 
CLIENT_VIEW_BEAN - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
clientDeleteRequest(ClientView, ClientViewHelper) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
Handles a client's request to delete a document.
ClientFgdcHelper - Class in edu.ucsb.nceas.metacat.clientview
 
ClientFgdcHelper() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
 
ClientHtmlHelper - Class in edu.ucsb.nceas.metacat.clientview
 
ClientHtmlHelper() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientHtmlHelper
 
clientRequest(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
Main web API method for handling various actions.
ClientView - Class in edu.ucsb.nceas.metacat.clientview
Description information for the ClientView bean.
ClientView() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientView
Creates a new instance of ClientView
ClientViewBeanInfo - Class in edu.ucsb.nceas.metacat.clientview
 
ClientViewBeanInfo() - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
 
ClientViewHelper - Class in edu.ucsb.nceas.metacat.clientview
 
ClientViewHelper(HttpServletRequest) - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
Creates a new instance of ClientViewHelper, using info in an HttpServletRequest for initializing.
ClientViewHelper(String, String, ClientView) - Constructor for class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
Creates a new instance of ClientViewHelper, using parameter values for initializing.
clientViewHelperInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
This is a convenience method to reduce the amount of code in a Metacat Client.
clone() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
Copy a AccessRule to another accessrule object
close() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
Close a DBConnection object
close() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
close the repository
closeConnection() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
 
closeDBObjects(PreparedStatement, DBConnection, int, Log) - Method in class edu.ucsb.nceas.metacat.shared.BaseAccess
 
CNodeService - Class in edu.ucsb.nceas.metacat.dataone
Represents Metacat's implementation of the DataONE Coordinating Node service API.
CNodeService - Class in edu.ucsb.nceas.metacat.dataone.v1
Represents Metacat's implementation of the DataONE Coordinating Node service API.
CNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v1
CN REST service implementation handler ****************** CNCore -- DONE create() - POST /d1/cn/object/PID listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET /d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET /d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not implemented in Metacat CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET /d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules CNIdentity - not implemented at all on Metacat CNReplication setReplicationStatus() - PUT /replicaNotifications/PID updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy() - PUT /replicaPolicies/PID isNodeAuthorized() - GET /replicaAuthorizations/PID CNRegister -- not implemented at all in Metacat ******************
CNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
 
CNResourceHandler - Class in edu.ucsb.nceas.metacat.restservice.v2
CN REST service implementation handler ****************** CNCore -- DONE create() - POST /d1/cn/object/PID listFormats() - GET /d1/cn/formats getFormat() - GET /d1/cn/formats/FMTID getLogRecords - GET /d1/cn/log reserveIdentifier() - POST /d1/cn/reserve listNodes() - Not implemented registerSystemMetadata() - POST /d1/meta/PID CNRead -- DONE get() - GET /d1/cn/object/PID getSystemMetadata() - GET /d1/cn/meta/PID resolve() - GET /d1/cn/resolve/PID assertRelation() - GET /d1/cn/assertRelation/PID getChecksum() - GET /d1/cn/checksum search() - Not implemented in Metacat CNAuthorization setOwner() - PUT /d1/cn/owner/PID isAuthorized() - GET /d1/cn/isAuthorized/PID setAccessPolicy() - POST /d1/cn/accessRules CNIdentity - not implemented at all on Metacat CNReplication setReplicationStatus() - PUT /replicaNotifications/PID updateReplicationMetadata() - PUT /replicaMetadata/PID setReplicationPolicy() - PUT /replicaPolicies/PID isNodeAuthorized() - GET /replicaAuthorizations/PID CNRegister -- not implemented at all in Metacat ******************
CNResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
 
CNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v1
Routes CN REST service requests to the appropriate handler
CNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v1.CNRestServlet
 
CNRestServlet - Class in edu.ucsb.nceas.metacat.restservice.v2
Routes CN REST service requests to the appropriate handler
CNRestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.v2.CNRestServlet
 
collectMultipartFiles() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Process the MMP request that includes files for each param
collectMultipartParams() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Parse string parameters from the mime multipart entity of the request.
collectObjectFiles() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Parse the request by the streaming multiple part handler.
collectSynchronizationFailed() - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
 
collectSynchronizationFailed() - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
 
combinateCurrentDateAndGivenTime(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationHandler
This method will combine given time string(in short format) to current date.
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
SAX Handler that receives notification of comments in the DTD
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of comments in the DTD
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that receives notification of comments in the DTD
comment(char[], int, int) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that receives notification of comments in the DTD
CommentNode - Class in edu.ucsb.nceas.metacat
A Class that represents an XML Comment node and its contents,
CommentNode(long, long, String) - Constructor for class edu.ucsb.nceas.metacat.CommentNode
Construct a new CommentNode instance
commit() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
Method to make a commit command
compare(Object, Object) - Method in class edu.ucsb.nceas.metacat.NodeComparator
compare two objects to determine proper sort order -- delegates to the compare(NodeRecord, NodeRecord) method.
compare(NodeRecord, NodeRecord) - Method in class edu.ucsb.nceas.metacat.NodeComparator
compare two NodeRecord objects to determine proper sort order.
compare(Object, Object) - Method in class edu.ucsb.nceas.metacat.SubTree
methods from Comparator interface
compareInlineDataFiles(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
compareTo(Version) - Method in class edu.ucsb.nceas.metacat.Version
Compare this Version object to another.
CONCRETE - Static variable in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
 
CONFIG_FILE_DIR - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
 
CONFIG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
 
CONFIG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.service.ServiceService
 
CONFIG_FILE_PATH - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
 
ConfigurableProperties - Class in edu.ucsb.nceas.metacat.properties
A suite of utility classes for the metadata configuration utility
ConfigurableProperties() - Constructor for class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
private constructor since this is a singleton
ConfigurationUtil - Class in edu.ucsb.nceas.metacat.util
A suite of utility classes for the metadata catalog server
ConfigurationUtil() - Constructor for class edu.ucsb.nceas.metacat.util.ConfigurationUtil
 
configureAuth(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.AuthAdmin
Handle configuration of the Authentication properties
configureBackup(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
Handle configuration of the backup directory
CONFIGURED - Static variable in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
CONFIGURED - Static variable in class edu.ucsb.nceas.metacat.properties.PropertyService
 
configureDatabase(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Handle configuration of the database the first time that Metacat starts or when it is explicitly called.
configureDataONE(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.D1Admin
Handle configuration of the database the first time that Metacat starts or when it is explicitly called.
configureEZID(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.EZIDAdmin
Handle configuration of the database the first time that Metacat starts or when it is explicitly called.
configureProperties(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin
Handle configuration of the main application properties
configureQuota(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.QuotaAdmin
Handle configuration of the quota service
configureSkins(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.SkinsAdmin
Handle configuration of the application the first time that Metacat starts or when it is explicitly called in the url.
configureSolr(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.SolrAdmin
Handle configuration of the solr the first time that Metacat starts or when it is explicitly called.
connect() - Method in class edu.ucsb.nceas.protocols.metacat.MetacatURLConnection
Make a connection to the URL
connection - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
connection - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
constructDN(String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
Constructs a DN (Distinguished Name) string for the ecoinformatics.org LDAP.
constructMetacatURL(String, int, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
Constructs a URL to the metacat servlet.
CONTAINS - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
CONTAINS - Static variable in class edu.ucsb.nceas.metacat.QueryTerm
 
containsExtendedSQL() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Returns true if the parsed query contains and extended xml query (i.e.
contentEquals(NodeRecord) - Method in class edu.ucsb.nceas.metacat.NodeRecord
Method compare two records
ContentTypeProvider - Class in edu.ucsb.nceas.metacat
This class will figure out which content type it is for a given data file.
ContentTypeProvider(String) - Constructor for class edu.ucsb.nceas.metacat.ContentTypeProvider
Constructor of ContentTypeProvider
convert(Log) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter
Convert a v2 Log object to a v1 Log object
convert(LogEntry) - Method in class edu.ucsb.nceas.metacat.dataone.convert.LogV2toV1Converter.LogEntryV2toV1Converter
Convert a v2 LogEntry object to a v1 LogEntry object
convertPermission(Permission) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
 
convertPermission(int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
 
copyFile(String, String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
Copy a file between two locations specified as strings.
copyInlineFile(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
copyPermOrderAndAccessRules(AccessSection) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Method to copy a accesssection object to a new one
CREATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
create(String, Reader) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
Create an XML document into the repository, making it available for searching using the query() methods.
create(String, Reader) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
Create an XML document in the repository.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Adds a new object to the Node, where the object is a science metadata object.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Adds a new object to the Node, where the object is either a data object or a science metadata object.
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
create(Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
create(Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
create(Session, Identifier, InputStream, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
createDate - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
createdate - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
 
createDocidQuery(String[]) - Static method in class edu.ucsb.nceas.metacat.DocumentIdQuery
Create an squery using some preset values for the query parameters, only passing in the document ids to be searched.
createDocidQueryParams(String[], Hashtable) - Static method in class edu.ucsb.nceas.metacat.DocumentIdQuery
Create an squery parameters table using an already-initialized hashtable
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Subclasses should override this method to provide the appropriate handler subclass
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNRestServlet
Provide a CNResourceHandler subclass of D1ResourceHandler
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNRestServlet
Provide an MNResourceHandler subclass of D1ResourceHandler
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNRestServlet
Provide a CNResourceHandler subclass of D1ResourceHandler
createHandler(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNRestServlet
Provide an MNResourceHandler subclass of D1ResourceHandler
createHeader(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
Convert a native "item" to a "record" String.
createLDAPString(String, String, Vector<String>) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Creates an ldap credentail string from the username, organization and dn list.
createMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
create a mapping in the identifier table
createMetacatConnection(String) - Static method in class edu.ucsb.nceas.metacat.client.MetacatFactory
Create a new instance of a Metacat object of raccessing a server.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml200
Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml201
Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml210
Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml211
Perform the actual crosswalk.
createMetadata(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
Perform the actual crosswalk.
CREATEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
 
createObject(String) - Static method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
Instantiate a class using the name of the class at runtime
createObject(String) - Static method in class edu.ucsb.nceas.metacat.database.DatabaseService
Instantiate a class using the name of the class at runtime
CREATEORUPDATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
createQuery(String, String) - Static method in class edu.ucsb.nceas.metacat.DBQuery
format a simple free-text value query as an XML document that conforms to the pathquery.dtd and is appropriate for submission to the DBQuery structured query engine
createQuery(String) - Static method in class edu.ucsb.nceas.metacat.DBQuery
format a simple free-text value query as an XML document that conforms to the pathquery.dtd and is appropriate for submission to the DBQuery structured query engine
createResultDocument(String, QuerySpecification, Writer, String, String[], boolean) - Method in class edu.ucsb.nceas.metacat.DBQuery
Transforms a hashtable of documents to an xml or html result and sent the content to outputstream.
createResultDocument(String, QuerySpecification, Writer, String, String[], boolean, int, int, String, String, boolean) - Method in class edu.ucsb.nceas.metacat.DBQuery
 
createSQuery(Hashtable) - Static method in class edu.ucsb.nceas.metacat.DBQuery
format a structured query as an XML document that conforms to the pathquery.dtd and is appropriate for submission to the DBQuery structured query engine
createStatement() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
Deprecated.
PreparedStatements are preferred so as to encourage parameter value binding
createSystemMetadata(String, boolean, boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
Create a system metadata object for insertion into metacat
createSystemMetadata(boolean, String, boolean, boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
Creates a system metadata object for insertion into metacat
createUsage(Usage) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
Create a usage record for a given quota identifier in the book keeper service.
createUsage(Usage, Date) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
Create a usage record in the usages table with the given date as the reported date If the date is null, it will create a usage record without the reported date
CreateUsageTask - Class in edu.ucsb.nceas.metacat.dataone.quota
This class represents a task to report a creation of a usage to the remote bookkeeper server and set the reported date in the local usages table after the succeeded reporting
CreateUsageTask(Usage, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.CreateUsageTask
Constructor
CREATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
CREATOR - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
CREATORNAME - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
CREATORS - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
CURRENTCOREINSTANCEDIR - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
currentDocidsBeingIndexed - Variable in class edu.ucsb.nceas.metacat.IndexingQueue
 
currentDocument - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

D

D1Admin - Class in edu.ucsb.nceas.metacat.admin
Control the display of the database configuration page and the processing of the configuration values.
D1AuthHelper - Class in edu.ucsb.nceas.metacat.dataone
This is delegate class for D1NodeService and subclasses.
D1AuthHelper(HttpServletRequest, Identifier, String, String) - Constructor for class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Each instance should correspond to a single request.
D1HttpRequest - Class in edu.ucsb.nceas.metacat.restservice
 
D1HttpRequest(ServletRequest) - Constructor for class edu.ucsb.nceas.metacat.restservice.D1HttpRequest
HttpServletRequestWrapper(HttpServletRequest request)
D1NodeService - Class in edu.ucsb.nceas.metacat.dataone
 
D1NodeService(HttpServletRequest) - Constructor for class edu.ucsb.nceas.metacat.dataone.D1NodeService
Constructor - used to set the metacatUrl from a subclass extending D1NodeService
D1NodeVersionChecker - Class in edu.ucsb.nceas.metacat.dataone
This class will contact the CN to figure out the version of the service for the given node
D1NodeVersionChecker(NodeReference) - Constructor for class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
Constructor
D1ResourceHandler - Class in edu.ucsb.nceas.metacat.restservice
Base class for handling D1 REST calls in Metacat
D1ResourceHandler(ServletContext, HttpServletRequest, HttpServletResponse) - Constructor for class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Initializes new instance by setting servlet context,request and response
D1RestServlet - Class in edu.ucsb.nceas.metacat.restservice
Metacat implemantation of Earthgrid (Ecogrid) REST API as a servlet.
D1RestServlet() - Constructor for class edu.ucsb.nceas.metacat.restservice.D1RestServlet
 
D1URLFilter - Class in edu.ucsb.nceas.metacat.restservice
 
D1URLFilter() - Constructor for class edu.ucsb.nceas.metacat.restservice.D1URLFilter
 
DATA_DISTRIBUTION - Static variable in class edu.ucsb.nceas.metacat.DistributionSection
 
DATAACCESSLEVEL - Static variable in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
DatabaseService - Class in edu.ucsb.nceas.metacat.database
 
DatabaseUtil - Class in edu.ucsb.nceas.metacat.util
 
DATACITE - Static variable in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
 
DataCiteMetadataFactory - Class in edu.ucsb.nceas.metacat.doi.datacite
A factory abstract class to generate the datacite metadata (xml format) for an DOI object.
DataCiteMetadataFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
DataONEConfigUtil - Class in edu.ucsb.nceas.metacat.util
A utility class for configuring DataONE setting
DataONEConfigUtil() - Constructor for class edu.ucsb.nceas.metacat.util.DataONEConfigUtil
 
DATAONEERROR - Static variable in class edu.ucsb.nceas.metacat.ReadOnlyChecker
 
DatapackageSummarizer - Class in edu.ucsb.nceas.metacat.annotation
 
DatapackageSummarizer() - Constructor for class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
DataQuery - Class in edu.ucsb.nceas.metacat.dataquery
Class to query data
DataQuery() - Constructor for class edu.ucsb.nceas.metacat.dataquery.DataQuery
empty constructor to initialize query
DataQuery(String) - Constructor for class edu.ucsb.nceas.metacat.dataquery.DataQuery
 
DATEREPORTED - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
DB_DOES_NOT_EXIST - Static variable in class edu.ucsb.nceas.metacat.admin.DBAdmin
 
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.util.ConfigurationUtil
 
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.util.DocumentUtil
 
dbAdapter - Static variable in class edu.ucsb.nceas.metacat.util.MetacatUtil
 
DBAdmin - Class in edu.ucsb.nceas.metacat.admin
Control the display of the database configuration page and the processing of the configuration values.
DBConnection - Class in edu.ucsb.nceas.metacat.database
A class represent a connection object, it includes connection itself, index, status, age, createtime, connection time, usageCount, warning message
DBConnection() - Constructor for class edu.ucsb.nceas.metacat.database.DBConnection
Default constructor of the DBConnection class
DBConnectionPool - Class in edu.ucsb.nceas.metacat.database
A class represent a DBConnection pool.
DBDTDHandler - Class in edu.ucsb.nceas.metacat
A database aware Class implementing DTDHandler interface for the SAX parser to call when processing the XML stream and intercepting notations and unparsed entities
DBDTDHandler(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBDTDHandler
Construct an instance of the DBDTDHandler clas
DBEntityResolver - Class in edu.ucsb.nceas.metacat
A database aware Class implementing EntityResolver interface for the SAX parser to call when processing the XML stream and intercepting any external entities (including the external DTD subset and external parameter entities, if any) before including them.
DBEntityResolver(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver
Construct an instance of the DBEntityResolver class
DBEntityResolver(DBConnection, DefaultHandler, Reader) - Constructor for class edu.ucsb.nceas.metacat.DBEntityResolver
Construct an instance of the DBEntityResolver class
DBQuery - Class in edu.ucsb.nceas.metacat
A Class that searches a relational DB for elements and attributes that have free text matches a query string, or structured query matches to a path specified node in the XML hierarchy.
DBQuery() - Constructor for class edu.ucsb.nceas.metacat.DBQuery
construct an instance of the DBQuery class
DBQuery(Vector) - Constructor for class edu.ucsb.nceas.metacat.DBQuery
Construct an instance of DBQuery Class BUT accept a docid Vector that will supersede the query.printSQL() method If a docid Vector is passed in, the docids will be used to create a simple IN query without the multiple subselects of the printSQL() method Using this constructor, we just check for a docidOverride Vector in the findResultDoclist() method
DBSAXHandler - Class in edu.ucsb.nceas.metacat
A database aware Class implementing callback bethods for the SAX parser to call when processing the XML stream and generating events.
DBSAXHandler(DBConnection, String, String, String, String, String[], String, int, Date, Date, boolean) - Constructor for class edu.ucsb.nceas.metacat.DBSAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to upadate
DBSAXNode - Class in edu.ucsb.nceas.metacat
A Class that represents an XML node and its contents and can write its own representation to a database connection
DBSAXNode(DBConnection, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode
Construct a new node instance for DOCUMENT nodes
DBSAXNode(DBConnection, String, String, DBSAXNode, long, String, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode
Construct a new node instance for ELEMENT nodes
DBSAXNode(DBConnection, String, String, String, DBSAXNode, long, String) - Constructor for class edu.ucsb.nceas.metacat.DBSAXNode
Construct a new node instance for DTD nodes This Node will write docname, publicId and systemId into db.
DBSimpleQuery - Class in edu.ucsb.nceas.metacat
A Class that searches a relational DB for elements and attributes that have free text matches to the query string.
DBSimpleQuery() - Constructor for class edu.ucsb.nceas.metacat.DBSimpleQuery
construct an instance of the DBSimpleQuery class
DBTransform - Class in edu.ucsb.nceas.metacat
A Class that transforms XML documents utitlizing XSL style sheets Building a transformer from the .xsl is expensive, so Templates are used as an intermediate construct to allow lightweight construction of Transformers.
DBTransform() - Constructor for class edu.ucsb.nceas.metacat.DBTransform
construct a DBTransform instance.
DBUtil - Class in edu.ucsb.nceas.metacat
A suite of utility classes for querying DB
DBUtil() - Constructor for class edu.ucsb.nceas.metacat.DBUtil
Construct an instance of the utility class
DBValidate - Class in edu.ucsb.nceas.metacat
Name: DBValidate.java Purpose: A Class that validates XML documents This class is designed to be parser independent i.e.
DBValidate() - Constructor for class edu.ucsb.nceas.metacat.DBValidate
Construct a new validation object
DBValidate(String) - Constructor for class edu.ucsb.nceas.metacat.DBValidate
Construct a new validation object using an OASIS catalog file
DBValidate(DBConnection) - Constructor for class edu.ucsb.nceas.metacat.DBValidate
Construct a new validation object using a database entity resolver
DBVersion - Class in edu.ucsb.nceas.metacat.database
 
DBVersion(String) - Constructor for class edu.ucsb.nceas.metacat.database.DBVersion
Create a database version.
dcterms - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
dcterms_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
DECLARATIONHANDLERPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
decode(String) - Static method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
A method to decode the given string which is a part of a uri.
DEFAULT_CN_URI - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
 
DEFAULT_ENCODING - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
 
DEFAULT_QUOTA_ID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
 
DEFAULT_REMOTE_USAGE_ID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
 
DefaultDataCiteFactory - Class in edu.ucsb.nceas.metacat.doi.datacite
Default factory to generate a simple datacite metadata xml string
DefaultDataCiteFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
 
delete(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Delete an XML document in the repository.
delete(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Delete an XML document in the repository.
DELETE - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
HTTP Verb DELETE
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Deletes an object from the Coordinating Node
delete(String, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Deletes an object from the Member Node, where the object is either a data object or a science metadata object.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
 
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Deletes an object from the Member Node, where the object is either a data object or a science metadata object.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
delete(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
delete(String, String, String[], String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Archive an object from the xml_documents table to the xml_revision table (including other changes as well).
delete(String, boolean, String, String[], String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Archive an object from the xml_documents table to the xml_revision table (including other changes as well).
DELETE - Static variable in class edu.ucsb.nceas.metacat.EventLog
 
delete(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
 
DELETE - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
HTTP Verb DELETE
delete(String, String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDataset
Deletes given docid from the spatial cache.
DELETE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
DELETE_SCHEDULED_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
 
deleteAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap
 
deleteAll(Collection<Identifier>) - Method in class edu.ucsb.nceas.metacat.index.IndexEventMapStore
 
DELETED - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
 
DELETEDMESSAGE - Static variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
deleteDocument(String) - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Given a docid, will attempt to delete it from spatial cache
deleteFromFileSystem(String, boolean) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Deletes a doc or data file from the filesystem using the accession number.
deleteInlineFiles() - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
deleteInlineFiles() - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
 
DELETEMETHOD - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
 
deleteObject(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
Delete an XML document in the repository.
deleteObject(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
Delete an XML document in the repository.
deleteRelations(String) - Method in class edu.ucsb.nceas.metacat.RelationHandler
Deletes all of the relations with a docid of 'docid'.
deleteReplica(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
Delete the replica entry with the given nodeId for the given pid
deleteReplica(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
Delete the replica entry with the given nodeId for the given pid
deleteReplicationMetadata(Session, Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Deletes the replica from the given Member Node NOTE: MN.delete() may be an "archive" operation.
deleteReplicationMetadata(Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
deleteReplicationMetadata(Session, Identifier, NodeReference, long) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
deleteSystemMetadata(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
 
deleteTempFile(File) - Static method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
Delete a temp file either immediately or on program exists according to the configuration
deleteUsage(int, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
Delete the usage with the given quota type and instance id in the remote book keeper service
deleteUsage(int, String, double) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
Delete a usage associated with the given quota id in the remote book keeper server.
DeleteUsageTask - Class in edu.ucsb.nceas.metacat.dataone.quota
This class represents a thread task to report an event to delete of an exiting usage to the remote bookkeeper server.
DeleteUsageTask(Usage, BookKeeperClient) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.DeleteUsageTask
Constructor
deleteXMLAccessForDoc(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Delete xml access.
deleteXMLAccessForDoc(String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Delete xml access.
deleteXMLQueryresulForDoc(String) - Method in class edu.ucsb.nceas.metacat.XMLQueryresultAccess
Delete xml access.
DELIMITER - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
 
dequoteText(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Normalizes text prior to insertion into the HARVEST_LOG or HARVEST_DETAIL_LOG tables.
describe(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
This method provides a lighter weight mechanism than getSystemMetadata() for a client to determine basic properties of the referenced object.
describe(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
describe(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
describe(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
describe(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
DESCRIPTIONS - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
destroy() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterServlet
When the thread is destroyed, sets the Harvester.keepRunning flag to false.
destroy() - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
 
destroy() - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Close all db connections from the pool
destroy() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
 
destroy() - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
 
destroy() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Closes the database connection.
destroy() - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
 
DetailedFileInputStream - Class in edu.ucsb.nceas.metacat.restservice.multipart
A FileInputStream class with more information, such as the object of source file itself and the expected checksum of the source file.
DetailedFileInputStream(File, Checksum) - Constructor for class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
Constructor
determine(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
Determine the quota type and instance id from the object format information in the system metadata
discoverApplicationContext(ServletContext) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the context for this application.
discoverDeployDir(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the deployment directory for this application.
discoverExternalDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the external (to the metacat installation) directory where metacat will hold backup files.
discoverServerName(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the server name.
discoverServerPort(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the server port.
discoverServerSSLPort(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Attempt to discover the server ssl port.
DistributionSection - Class in edu.ucsb.nceas.metacat
A Class that represents an XML access rule.
DistributionSection(int) - Constructor for class edu.ucsb.nceas.metacat.DistributionSection
 
doAdminAuthorization(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Does MN/CN admin authorization
doAuthoritativeMNAuthorization(Session, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Does local and AuthMN admin authorization
doBypass() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Determine if the system is configured to bypass configuration.
doBypass() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
doBypass() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Determine if the system is configured to bypass configuration.
doBypass() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
docid - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
docid - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
docid - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
 
docid - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
docId - Variable in class edu.ucsb.nceas.metacat.SubTree
 
docname - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
DOCNAME - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
docname - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
docname - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
 
doCNOnlyAuthorization(Session) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Does only localNode(CN)/CN authorization
doctype - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
doctype - Variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
doctype - Variable in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
 
docType - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
Document() - Constructor for class edu.ucsb.nceas.metacat.MetacatResultSet.Document
 
DocumentCart - Class in edu.ucsb.nceas.metacat.cart
 
DocumentCart() - Constructor for class edu.ucsb.nceas.metacat.cart.DocumentCart
 
DocumentIdentifier - Class in edu.ucsb.nceas.metacat
A class to parse document ids The docid is of the form siteCode.uniqueId.rev
DocumentIdentifier(String) - Constructor for class edu.ucsb.nceas.metacat.DocumentIdentifier
Constructor to build a docid object and parse an incoming string.
DocumentIdQuery - Class in edu.ucsb.nceas.metacat
Generate a pathquery document representing a metacat query for a list of document IDs.
DocumentIdQuery() - Constructor for class edu.ucsb.nceas.metacat.DocumentIdQuery
 
DocumentImpl - Class in edu.ucsb.nceas.metacat
A class that represents an XML document.
DocumentImpl() - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Default constructor
DocumentImpl(String, boolean) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Constructor used to create a document and read the document information from the database.
DocumentImpl(String) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Constructor, creates document from database connection, used for reading the document
DocumentImpl(DBConnection, long, String, String, String, String, String, String, String, String, int, Date, Date) - Constructor for class edu.ucsb.nceas.metacat.DocumentImpl
Construct a new document instance, writing the contents to the database.
DocumentImplWrapper - Class in edu.ucsb.nceas.metacat
This class a wrapper class for documentimpl for insert or update.
DocumentImplWrapper(String, boolean, boolean) - Constructor for class edu.ucsb.nceas.metacat.DocumentImplWrapper
Constructor of DocumentImpleWrapper
DocumentNotFoundException - Exception in edu.ucsb.nceas.metacat.client
Exception thrown when the requested docid does not exist on the server
DocumentNotFoundException(String) - Constructor for exception edu.ucsb.nceas.metacat.client.DocumentNotFoundException
Create a new InsufficientKarmaException.
DOCUMENTTABLE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
DocumentUtil - Class in edu.ucsb.nceas.metacat.util
A suite of utility classes for the metadata catalog server
DocumentUtil() - Constructor for class edu.ucsb.nceas.metacat.util.DocumentUtil
 
doDelete(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "DELETE" method requests from HTTP clients
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class edu.ucsb.nceas.metacat.restservice.D1URLFilter
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class edu.ucsb.nceas.metacat.spatial.WmsFilter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
Handles GET method requests.
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
Peform the http GET action.
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "GET" method requests from HTTP clients
doGet(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.spatial.SldFactory
Handle "GET" method requests from HTTP clients
doGetSysmetaAuthorization(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
used by getSystemMetadata, describe, and getPackage, the latter two by delegation to getSystemMetadata Very similar to doIsAuthorized, but also allows replica nodes administrative access.
doHead(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "PUT" method requests from HTTP clients
DOI - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
DOI_SCHEME - Static variable in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
doiEnabled - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
 
DOIException - Exception in edu.ucsb.nceas.metacat.doi
An exception that encapsulates errors from the DOI service.
DOIException(String) - Constructor for exception edu.ucsb.nceas.metacat.doi.DOIException
Constructor
doIsAuthorized(Session, SystemMetadata, Permission) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Performs all authorization steps used by isAuthorized.
DOIService - Class in edu.ucsb.nceas.metacat.doi
An abstract class for the DOI service
DOIService() - Constructor for class edu.ucsb.nceas.metacat.doi.DOIService
Constructor
DOIServiceFactory - Class in edu.ucsb.nceas.metacat.doi
A factory class to initialize an instance of DOIService based on the configuration in the metacat.properties file
DOIServiceFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.DOIServiceFactory
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.admin.MetacatAdminServlet
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchServlet
Executes an advanced search.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.BrowseServlet
Executes a browse-based simple search.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginServlet
Executes a metacat login action.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.advancedsearch.SearchServlet
Executes a simple search.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistration
Handles POST method requests.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvesterRegistrationLogin
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.LoginServlet
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.harvesterClient.MetUpload
Handle POST requests made to the Harvester MetUpload servlet.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.MetaCatServlet
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
Perform a POST action.
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "POST" method requests from HTTP clients
doPost(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.spatial.SldFactory
Handle "POST" method requests from HTTP clients
doPut(HttpServletRequest, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1RestServlet
Handle "PUT" method requests from HTTP clients
doRefresh() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Refresh the Hazelcast service by restarting it
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.service.SessionService
 
doRefresh() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
refresh the persistant values in this service.
doRefresh() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
 
doTransform(StreamSource, StreamResult, Transformer, Hashtable<String, String[]>, String, String) - Method in class edu.ucsb.nceas.metacat.DBTransform
Reads skin's config file if it exists, and populates Transformer paramaters with its contents.
doUpdateAuth(Session, SystemMetadata, Permission, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
The locus of updates is limited to the authoritativeMN.
download() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
 
download() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
Streams the completed bag to the caller.
DOWNLOAD_ACTION - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
DTD - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
dueForHarvest() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Boolean to determine whether this site is currently due for its next harvest.

E

ECOGRID - Static variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
ECOLOGICAL_METADATA_LANGUAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
editCart(String, String[], Map) - Method in class edu.ucsb.nceas.metacat.cart.CartManager
 
editScienceMetadata(Session, InputStream, Identifier, Identifier, boolean, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Update a science metadata document with its new Identifier
edu.ucsb.nceas.dbadapter - package edu.ucsb.nceas.dbadapter
 
edu.ucsb.nceas.metacat - package edu.ucsb.nceas.metacat
 
edu.ucsb.nceas.metacat.accesscontrol - package edu.ucsb.nceas.metacat.accesscontrol
 
edu.ucsb.nceas.metacat.admin - package edu.ucsb.nceas.metacat.admin
 
edu.ucsb.nceas.metacat.admin.upgrade - package edu.ucsb.nceas.metacat.admin.upgrade
 
edu.ucsb.nceas.metacat.admin.upgrade.dataone - package edu.ucsb.nceas.metacat.admin.upgrade.dataone
 
edu.ucsb.nceas.metacat.admin.upgrade.solr - package edu.ucsb.nceas.metacat.admin.upgrade.solr
 
edu.ucsb.nceas.metacat.advancedsearch - package edu.ucsb.nceas.metacat.advancedsearch
 
edu.ucsb.nceas.metacat.annotation - package edu.ucsb.nceas.metacat.annotation
 
edu.ucsb.nceas.metacat.authentication - package edu.ucsb.nceas.metacat.authentication
 
edu.ucsb.nceas.metacat.cart - package edu.ucsb.nceas.metacat.cart
 
edu.ucsb.nceas.metacat.client - package edu.ucsb.nceas.metacat.client
 
edu.ucsb.nceas.metacat.client.rest - package edu.ucsb.nceas.metacat.client.rest
 
edu.ucsb.nceas.metacat.clientview - package edu.ucsb.nceas.metacat.clientview
 
edu.ucsb.nceas.metacat.database - package edu.ucsb.nceas.metacat.database
 
edu.ucsb.nceas.metacat.dataone - package edu.ucsb.nceas.metacat.dataone
 
edu.ucsb.nceas.metacat.dataone.convert - package edu.ucsb.nceas.metacat.dataone.convert
 
edu.ucsb.nceas.metacat.dataone.hazelcast - package edu.ucsb.nceas.metacat.dataone.hazelcast
 
edu.ucsb.nceas.metacat.dataone.quota - package edu.ucsb.nceas.metacat.dataone.quota
 
edu.ucsb.nceas.metacat.dataone.resourcemap - package edu.ucsb.nceas.metacat.dataone.resourcemap
 
edu.ucsb.nceas.metacat.dataone.v1 - package edu.ucsb.nceas.metacat.dataone.v1
 
edu.ucsb.nceas.metacat.dataquery - package edu.ucsb.nceas.metacat.dataquery
 
edu.ucsb.nceas.metacat.doi - package edu.ucsb.nceas.metacat.doi
 
edu.ucsb.nceas.metacat.doi.datacite - package edu.ucsb.nceas.metacat.doi.datacite
 
edu.ucsb.nceas.metacat.doi.ezid - package edu.ucsb.nceas.metacat.doi.ezid
 
edu.ucsb.nceas.metacat.doi.osti - package edu.ucsb.nceas.metacat.doi.osti
 
edu.ucsb.nceas.metacat.download - package edu.ucsb.nceas.metacat.download
 
edu.ucsb.nceas.metacat.event - package edu.ucsb.nceas.metacat.event
 
edu.ucsb.nceas.metacat.harvesterClient - package edu.ucsb.nceas.metacat.harvesterClient
 
edu.ucsb.nceas.metacat.index - package edu.ucsb.nceas.metacat.index
 
edu.ucsb.nceas.metacat.lsid - package edu.ucsb.nceas.metacat.lsid
 
edu.ucsb.nceas.metacat.oaipmh.harvester - package edu.ucsb.nceas.metacat.oaipmh.harvester
 
edu.ucsb.nceas.metacat.oaipmh.provider.server - package edu.ucsb.nceas.metacat.oaipmh.provider.server
 
edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog - package edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog
 
edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk - package edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
 
edu.ucsb.nceas.metacat.object.handler - package edu.ucsb.nceas.metacat.object.handler
 
edu.ucsb.nceas.metacat.plugin - package edu.ucsb.nceas.metacat.plugin
 
edu.ucsb.nceas.metacat.properties - package edu.ucsb.nceas.metacat.properties
 
edu.ucsb.nceas.metacat.replication - package edu.ucsb.nceas.metacat.replication
 
edu.ucsb.nceas.metacat.restservice - package edu.ucsb.nceas.metacat.restservice
 
edu.ucsb.nceas.metacat.restservice.multipart - package edu.ucsb.nceas.metacat.restservice.multipart
 
edu.ucsb.nceas.metacat.restservice.v1 - package edu.ucsb.nceas.metacat.restservice.v1
 
edu.ucsb.nceas.metacat.restservice.v2 - package edu.ucsb.nceas.metacat.restservice.v2
 
edu.ucsb.nceas.metacat.service - package edu.ucsb.nceas.metacat.service
 
edu.ucsb.nceas.metacat.shared - package edu.ucsb.nceas.metacat.shared
 
edu.ucsb.nceas.metacat.spatial - package edu.ucsb.nceas.metacat.spatial
 
edu.ucsb.nceas.metacat.util - package edu.ucsb.nceas.metacat.util
 
edu.ucsb.nceas.protocols.metacat - package edu.ucsb.nceas.protocols.metacat
 
edu.ucsb.nceas.shared.xsd - package edu.ucsb.nceas.shared.xsd
 
elementDecl(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of element declarations
ElementNode - Class in edu.ucsb.nceas.metacat
A Class that represents an XML element and its contents, and can build itself from a database connection
ElementNode(TreeSet, long) - Constructor for class edu.ucsb.nceas.metacat.ElementNode
Construct a new ElementNode instance, and recursively create its children
EML200 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
Eml200 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
Provides eml-2.0.0 documents.
Eml200(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml200
The constructor assigns the schemaLocation associated with this crosswalk.
Eml200SAXHandler - Class in edu.ucsb.nceas.metacat
A database aware Class implementing callback methods for the SAX parser to call when processing the XML stream and generating events Here is the rules for user which has write permission in top level access rules(he can update metadata but can't update access module) try to update a document: 1.
Eml200SAXHandler(DBConnection, String, String, String, String, String[], String, int, Date, Date, boolean, Vector<String>) - Constructor for class edu.ucsb.nceas.metacat.Eml200SAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to upadate
Eml201 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
Provides eml-2.0.1 documents.
Eml201(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml201
The constructor assigns the schemaLocation associated with this crosswalk.
EML201DocumentCorrector - Class in edu.ucsb.nceas.metacat
Before Metacat 1.8.1 release, Metacat uses the eml201 schema with the tag RELEASE_EML_2_0_1_UPDATE_5.
EML201DocumentCorrector() - Constructor for class edu.ucsb.nceas.metacat.EML201DocumentCorrector
Default constructor
EML210 - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
Eml210 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
Provides eml-2.1.0 documents.
Eml210(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml210
The constructor assigns the schemaLocation associated with this crosswalk.
Eml210SAXHandler - Class in edu.ucsb.nceas.metacat
A database aware Class implementing callback methods for the SAX parser to call when processing the XML stream and generating events
Eml210SAXHandler(DBConnection, String, String, String, String, String[], String, int, Date, Date, boolean, Vector<String>) - Constructor for class edu.ucsb.nceas.metacat.Eml210SAXHandler
Construct an instance of the handler class In this constructor, user can specify the version need to update
Eml211 - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
Provides eml-2.1.1 documents.
Eml211(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml211
The constructor assigns the schemaLocation associated with this crosswalk.
EML2_0_0NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2_0_1NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2_1_0NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2_1_1NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2_2_0NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EML2DataCiteFactory - Class in edu.ucsb.nceas.metacat.doi.datacite
A factory to generate data cite meta data for the scientific meta data standards - eml-2.*
EML2DataCiteFactory() - Constructor for class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
 
EML2KEYWORD - Static variable in class edu.ucsb.nceas.metacat.MetaCatServlet
 
Eml2oai_dc - Class in edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk
Convert native "item" to oai_dc.
Eml2oai_dc(Properties) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.provider.server.crosswalk.Eml2oai_dc
The constructor assigns the schemaLocation associated with this crosswalk.
EMLVersionsTransformer - Class in edu.ucsb.nceas.metacat.util
A Class that transforms older eml version to newer eml version utitlizing XSL style sheets.
EMLVersionsTransformer() - Constructor for class edu.ucsb.nceas.metacat.util.EMLVersionsTransformer
Public constructor because all methods are static and do not need an instance.
EN - Static variable in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
 
enableAppendLdapGroups - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
enableSessionFromHeader - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
encoding - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
endCDATA() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
SAX Handler that receives notification of the end of CDATA sections
endCDATA() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the end of CDATA sections
endDocument() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of end of the document
endDocument() - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that receives notification of end of the document
endDocument() - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that receives notification of end of the document
endDocument() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
 
endDTD() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
SAX Handler that receives notification of end of DTD
endDTD() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of end of DTD
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Callback method used by the SAX Parser when the end tag of an element is detected.
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
This method write the indivUpdate to updates when it finds the end of
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that is called at the end of each XML element
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler that is called at the end of each XML element
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler that is called at the end of each XML element
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
 
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
callback method used by the SAX Parser when the end tag of an element is detected.
endElement(String, String, String) - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
This method write the indivUpdate to updates when it finds the end of
endEntity(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
SAX Handler that receives notification of the end of entities.
endEntity(String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of the end of entities
endNodeId - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
endNodeId - Variable in class edu.ucsb.nceas.metacat.SubTree
 
ENDS_WITH - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
endTag - Static variable in class edu.ucsb.nceas.metacat.util.ReplicationUtil
 
enforce(String, Subject, String, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.PortalQuotaService
 
enforce(String, Subject, String, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
The method will be implemented by the child classes to enforce the quota service
enforce(String, Subject, SystemMetadata, String) - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
Enforce quota service
entryAdded(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Implement the EntryListener interface for Hazelcast, reponding to entry added events in the hzSystemMetadata map.
entryEvicted(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Implement the EntryListener interface for Hazelcast, reponding to entry evicted events in the hzSystemMetadata map.
entryRemoved(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Implement the EntryListener interface for Hazelcast, reponding to entry removed events in the hzSystemMetadata map.
entryUpdated(EntryEvent<Identifier, SystemMetadata>) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Implement the EntryListener interface for Hazelcast, reponding to entry updated events in the hzSystemMetadata map.
equals(AccessPolicy, AccessPolicy) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Compare two AccessPolicy objects
EQUALS - Static variable in class edu.ucsb.nceas.metacat.QueryTerm
 
equals(Object) - Method in class edu.ucsb.nceas.metacat.SubTree
method from Comparator interface
equals(Object) - Method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
 
equals(Object) - Method in class edu.ucsb.nceas.shared.xsd.IOException
 
error(SAXParseException) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of recoverable parsing errors
ERROR_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
ErrorHandledException - Exception in edu.ucsb.nceas.metacat
Exception thrown when an error occurs in a configuration administrative class
ErrorHandledException(String) - Constructor for exception edu.ucsb.nceas.metacat.ErrorHandledException
Create a new AdminException.
ErrorSendingErrorException - Exception in edu.ucsb.nceas.metacat.util
Exception thrown when an error occurs in a utility method
ErrorSendingErrorException(String) - Constructor for exception edu.ucsb.nceas.metacat.util.ErrorSendingErrorException
Create a new AdminException.
ESCAPECHAR - Static variable in class edu.ucsb.nceas.metacat.util.AuthUtil
 
EventLog - Class in edu.ucsb.nceas.metacat
EventLog is used to intialize and store a log of events that occur in an application.
EventLogData - Class in edu.ucsb.nceas.metacat
A data structure holding the information to be logged about an event.
EventLogData(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.EventLogData
Construct an EventLogData object with event log information.
EventLogFilter - Class in edu.ucsb.nceas.metacat
This class represents a filter to prevent the events generated by some ip addresses and subjects to be logged into db
EventLogFilter() - Constructor for class edu.ucsb.nceas.metacat.EventLogFilter
Default Construct
EXACT_MATCH - Static variable in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
executeAdvancedSearch(String, Metacat, String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearch
Builds and runs an advanced search, returning HTML result string.
executeLogin(String, Metacat) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatLogin
Executes the Metacat login.
executeQuery(String) - Method in class edu.ucsb.nceas.metacat.dataquery.DataQuery
 
executeSearch(String, Metacat, String, String, String) - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearch
Builds and runs a simple search, returning HTML result string.
executor - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
 
EXISTINGCORE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
existsInIdentifierTable(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Determine if the given pid exists on the identifier table.
existsInObsoletedBy(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
existsInObsoletes(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
existsInXmlLRevisionTable(String, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
IF the given localId exists on the xml_revisions table
expandPermissions(Permission) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Given a Permission, returns a list of all permissions that it encompasses Permissions are hierarchical so that WRITE also allows READ.
expandRightsHolder(Subject, Subject) - Static method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
Check if the given userSession is the member of the right holder group (if the right holder is a group subject).
externalEntityDecl(String, String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler that receives notification of external entity declarations
EXTERNALNONAMESPACESCHEMALOCATIONPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EXTERNALSCHEMALOCATIONPROPERTY - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
EZIDAdmin - Class in edu.ucsb.nceas.metacat.admin
Control the display of the ezid configuration page and the processing of the configuration values.
EzidDOIService - Class in edu.ucsb.nceas.metacat.doi.ezid
Singleton for interacting with the EZID DOI library.
EzidDOIService() - Constructor for class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
Constructor

F

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

G

geItsDataSetIdWithouAccessEntry() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
Get the docid which it's mapped dataset doesn't has access entry
GENERAL_UTILITY_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
 
generateAgentResource(Subject, Model) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Generate an agent resource.
generateAnnotation(Identifier) - Method in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
Generate annotation for given metadata identifier
generateDocumentId(int) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Create a unique docid for use in inserts and updates using the default prefix from the document.accNumPrefix property.
generateDocumentId(String, int) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Create a unique docid for use in inserts and updates using the prefix that is provided.
generateDOI() - Method in class edu.ucsb.nceas.metacat.doi.DOIService
Generate a DOI using the DOI service as configured
generateDOI() - Method in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
Generate a DOI using the EZID service as configured
generateDOI() - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
Generate a DOI using the DOI service as configured
GenerateGlobalIdentifiers - Class in edu.ucsb.nceas.metacat.admin.upgrade
Optionally upgrade all of the existing identifiers in the tables to be official DOIs that are assigned by a DOI registration authority.
GenerateGlobalIdentifiers() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.GenerateGlobalIdentifiers
 
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
 
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
generateIdentifier(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
generateIdentifier(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
generateIdentifier(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
generateLocalId(String, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
 
generateLocalId(String, int, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Given a global identifier (guid), create a suitable local identifier that follows Metacat's docid semantics and format (scope.id.rev), and create a mapping between these two identifiers.
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Method to generate the datacite meta data xml string for an object with the given system meta data.
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DefaultDataCiteFactory
Method to generate the data cite xml document
generateMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
Method to generate the data cite xml document
generateNewComponent(Model, String) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Create a Resource object for the given id.
generateNewOREResource(Model, Subject, Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
This method generates a Resource object for the new ore id in the given model
GenerateORE - Class in edu.ucsb.nceas.metacat.admin.upgrade.dataone
 
GenerateORE() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
 
generateOstiMetadata(InputStream, String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
Generate the OSTI document for the given eml
generateROOTDoc() - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Generate the blank DOM document for the datacite name space
generateSitemaps() - Method in class edu.ucsb.nceas.metacat.Sitemap
Generate all of the sitemap files needed to list the URLs from this instance of Metacat, using the open sitemap format described here: http://www.sitemaps.org/protocol.html URLs are written to a one or more files and a sitemap index file is always written.
GenerateSystemMetadata - Class in edu.ucsb.nceas.metacat.admin.upgrade.dataone
 
GenerateSystemMetadata() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
 
generateSystemMetadata(List<String>, boolean, boolean) - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
Generate SystemMetadata for any object in the object store that does not already have it.
generateXMLWithSiteURL(String) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
Create a xml file with the site_url element
GeoserverUtil - Class in edu.ucsb.nceas.metacat.util
 
GET - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
HTTP Verb GET
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Return the object identified by the given object identifier
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Return the object identified by the given object identifier
get(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
get(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
get(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
get(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
 
GET - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
HTTP Verb GET
get(String, Hashtable<String, String[]>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
 
GET_SCHEDULED_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
 
getAbouts(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
Get the about elements from the item
getAccessControl(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
 
getAccessControl(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
get the access control info for a given document id.
getAccessFileIDWithRevision(String) - Static method in class edu.ucsb.nceas.metacat.RelationHandler
Get the access file id for a package
getAccessionNumberFromEcogridIdentifier(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Eocgorid identifier will look like: ecogrid://knb/tao.1.1 The AccessionNumber tao.1.1 will be returned.
getAccessPolicy(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Lookup access policy from Metacat
getAccessQuery() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to append a access control query to SQL.
getAccessRules() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get all access rule
getAccessSection() - Method in class edu.ucsb.nceas.metacat.DistributionSection
 
getAccessString() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
Get the access xml for all access on this docid
getAccessString(Vector<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
Put together an xml representation of the objects in a given access dao list
getACL(String, String[]) - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlForSingleFile
Get Access Control List information for document from db connetion.
getAction() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property action.
getAction() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
 
getAdministrators() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Get the administrators from metacat.properties
getAge() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion age from the object
getAllDocids(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
return a list of all docids that match a given scope.
getAllDocids(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
return a list of all docids that match a given scope.
getAllDocids(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
return a list of all docids that match a given scope.
getAllDocids(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
return a list of all docids that match a given scope.
getAllDocids(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
get the latest Accession Number from a particular scope
getAllDocidsByType(String, boolean) - Static method in class edu.ucsb.nceas.metacat.DBUtil
return all docids with a given doctype on all servers
getAllDocidsByType(String, boolean, int) - Static method in class edu.ucsb.nceas.metacat.DBUtil
return all docids with a given doctype for a given server
getAllIdentifiers() - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
 
getAllLocalIds() - Method in class edu.ucsb.nceas.metacat.IdentifierManager
return a listing of all local ids in the object store
getAllOREpids(String) - Static method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
Retrieves a list of all ORE objects on the given MN
getAllowedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Get the allowed submitters from metacat.properties
getAllPidsInChain(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Get all pids in the series chain
getAllSystemMetadataGUIDs() - Method in class edu.ucsb.nceas.metacat.IdentifierManager
return a listing of all guids in the object store
getAnyfield() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property anyField.
getAttribute(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Get an attribute value by name
getAttributeName(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
A method to get attribute name from path
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getAttributes(String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get attributes describing a user or group
getAttributes(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get attributes describing a user or group
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthSession
Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get attributes describing a user or group
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get attributes describing a user or group
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get attributes describing a user or group
getAttributes(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get attributes describing a user or group
getAttributes() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the attributes as a string
getAttributes(Properties) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
 
getAttributes(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
 
getAuthBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get the auth backup properties file.
getAuthBackupProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getAuthBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the auth backup properties file.
getAuthBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
getAuthMetaData() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get the auth properties metadata.
getAuthMetaData() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getAuthMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the auth properties metadata.
getAuthMetaData() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
getBackupDirStatus(String) - Method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
Find the status of the backup base directory.
getBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the main backup properties file.
getBackupProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the main backup properties file.
getBaseUrlFromSchemaURL(String) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Get a base url from the schema url.
getBeanDescriptor() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
Gets the bean's BeanDescriptors.
getBytes() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getCapabilities() - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
 
getCapabilities() - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Return a description of the node's capabilities and services.
getCapabilities() - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getCatalogId() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 
getCatalogVect() - Method in class edu.ucsb.nceas.metacat.CatalogMessageHandler
 
getCatalogXML() - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Returns the xml_catalog table encoded in xml
getCGI_URL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the CGI URL which is made up of the server URL + file separator + the CGI directory
getCheckOutMethodName() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the the name of method checked out the connection from the object
getCheckOutSerialNumber() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the check out serial number
getCheckOutTime() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the when a db connetion was checked out
getChecksum(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Return the checksum of the object given the identifier
getChecksum(Session, Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Returns a Checksum for the specified object using an accepted hashing algorithm
getChecksum(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
getChecksum(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
getChecksum(Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getChecksum(Session, Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
getChecksum() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.CheckedFile
Get the checksum of this file
getChildren() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the an enumeration of the children of this node
getCNNodeList() - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
A centralized point for accessing the CN Nodelist, to make it easier to cache the nodelist in the future, if it's seen as helpful performance-wise
getCNNodeList() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
A centralized point for accessing the CN Nodelist, to make it easier to cache the nodelist in the future, if it's seen as helpful performance-wise
getCodeLevelValue(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Maps each code level to an integer value.
getCommonSkinsDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the style skins directory.
getConnection() - Method in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
Gets a database connection from the pool
getConnection() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Returns a connection to the database.
getConnection() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
Returns a connection to the database.
getConnections() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the connetion from the object
getConnectionTime() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the how long db connetion used for the object
getContentStandard() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property contentStandard.
getContentType() - Method in class edu.ucsb.nceas.metacat.ContentTypeProvider
Method to get content type
getContentType() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
 
getContentWithoutSystemMetadata(String) - Static method in class edu.ucsb.nceas.metacat.util.ReplicationUtil
return the string WITHOUT the contents between start and end tag
getContextDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the context directory.
getContextURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the server URL with the context.
getControlLevel() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get controllevel
getCookie(HttpServletRequest, String) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
Get a cookie from a request by the cookie name
getCoreMessage() - Method in exception edu.ucsb.nceas.metacat.shared.BaseException
 
getCoreMetadataIdentifiers() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
Returns the core metadata identifiers
getCreateDate() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the creation date
getCreateTime() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion created time from the object
getCreationTime() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getCreatorOrganization() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getCreatorOrganizationQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getCreatorSurname() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getCreatorSurnameQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getCurrentNodeId() - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
getCurrentRevisionAndDocTypeForGivenDocument(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
Method to get current revision and doctype for a given docid The output will look like "rev;doctype"
getD1Report(String[], String[], String[], String, Timestamp, Timestamp, boolean, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.EventLog
 
getData(LSIDRequestContext) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
 
getDatabaseConnectionPoolInterface() - Static method in class edu.ucsb.nceas.metacat.dataquery.MetacatDatabaseConnectionPoolFactory
 
getDataByRange(LSIDRequestContext, int, int) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityData
 
getDataFileLockGrant(String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Get a lock for a given document.
getDataFileLockGrant(String, int) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
The method will check if metacat can get data file lock grant If server code is 1, it get.
getDataFileName() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get the dataFileName
getDataFileName(int) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Indexed getter for property dataFileNames.
getDataFileName() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property dataFileNames.
getDataFileName() - Method in class edu.ucsb.nceas.metacat.DistributionSection
Get the online data file name
getDataLocations(LSID, String) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
 
getDataReplication() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
Get datareplication xml or not option
getDataReplicationValue(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
To a given server name, try to get its data file replciation option If couldn't find the server in the server list, false will return
getDateField() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getDatestamp(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
get the datestamp from the item
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
The function name that gets the current date and time from the database server
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracle's function name that gets the current date and time from the database server: "sysdate"
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
The PostgreSQL function name that gets the current date and time from the database server
getDateTimeFunction() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server's function name that gets the current date and time from the database server: "getdate()"
getDBAdapter() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
gets the database adapter
getDBAdapterName() - Method in class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
Get dabase adpater name.
getDBConnection(String) - Static method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
Method to get a DBConnection in connection pool 1) try to get a DBConnection from DBConnection pool 2) if 1) failed, then check the size of pool.
getDBStatus() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Performs a status check on the database.
getDBVersion() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Get the version of the database as a string
getDefaultEventIndex() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
A bean may have a "default" event that is the event that will mostly commonly be used by human's when using the bean.
getDefaultPropertyIndex() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
A bean may have a "default" property that is the property that will mostly commonly be initially chosen for update by human's who are customizing the bean.
getDefaultQueryParams() - Static method in class edu.ucsb.nceas.metacat.DocumentIdQuery
Create a paramter list containing default parameters for a query
getDefaultReplicationPolicy() - Static method in class edu.ucsb.nceas.metacat.dataone.SystemMetadataFactory
Create a default ReplicationPolicy by reading properties from metacat's configuration and using those defaults.
getDefaultStyleURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the default style URL from metacat.properties.
getDeletesVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
 
getDeniedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Get the denied submitters from metacat.properties
getDescribedIdList() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get a described id list
getDeserializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
Get Custom Deserializer
getDeserializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.IOException
Get Custom Deserializer
getDetailLogID() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Gets the current value of the detailLogID for storage as a primary key in the DETAIL_LOG_ID field of the HARVEST_DETAIL_LOG table.
getDistributionId() - Method in class edu.ucsb.nceas.metacat.DistributionSection
Get the access type
getDistributionType() - Method in class edu.ucsb.nceas.metacat.DistributionSection
Get the access type
getDocHomeServer() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getDocid() - Method in class edu.ucsb.nceas.metacat.AccessionNumber
returns the docid encoded in this accession number
getDocID() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the doc id of this node
getDocId() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property docId.
getDocID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Get the document identifier (docid)
getDocid() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
 
getDocid() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the document identifier.
getDocId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get the docId
getDocIdFromAccessionNumber(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
This method will get docid from an AccessionNumber.
getDocIdFromInlineDataID(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Method to get docidwithrev from eml2 inline data id The eml inline data id would look like eml.200.2.3
getDocIdFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Utility method to get docid from a given string
getDocids() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
getDocIdWithoutRevsion() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to get docidWithout revision
getDocIdWithRevFromOnlineURL(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Get docid from online/url string
getDocname() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Get the document name.
getDocname() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
get the document name
getDocname() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the document name
getDoctype() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the document type (which is the PublicID)
getDoctype() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
 
getDocType(LSID) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDDataLookup
 
getDocType() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to get docType
getDocument() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
Get the OAI response as a DOM object
getDocumentCart() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getDocumentInfo(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Gets a docInfo XML snippet for the replication API
getDocumentInfoMap(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
 
getDocumentName() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 
getDocuments() - Method in class edu.ucsb.nceas.metacat.MetacatResultSet
 
getDocumentType() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 
getDOIService() - Static method in class edu.ucsb.nceas.metacat.doi.DOIServiceFactory
Get a singleton instance of DOIService
getDownloadNewSchema() - Method in class edu.ucsb.nceas.metacat.SchemaLocationResolver
Gets the downloadNewSchema's value.
getEastBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getEncoding() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Returns the character encoding used used when communicating with Metacat.
getEncoding() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
 
getEncoding() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 
getEndDate() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getEndNodeId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get end node id
getErrors() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
Get the OAI errors
getEvent() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the event.
getEventSetDescriptors() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
Gets the bean's 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
getExplanation(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Returns an explanation string based on the value of a harvestOperationCode string.
getExternalFileUri() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the external file uri
getField(String) - Method in class edu.ucsb.nceas.metacat.MetacatResultSet.Document
 
getFields(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
getFields() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
getFile() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.DetailedFileInputStream
Get the source file
getFileName() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the file name
getFileNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the file namespace
getFilterDocList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the filter doc types as defined in the <filterdoctype> tag in the pathquery dtd.
getFormAllAny() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getFormat(ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Returns the object format registered in the DataONE Object Format Vocabulary for the given format identifier
getFormat(ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.dataone.ObjectFormatService
Return the object format based on the given object format identifier
getFormat(ObjectFormatIdentifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
getFormatId() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Get the format id
getGeoserverContextURL() - Static method in class edu.ucsb.nceas.metacat.util.GeoserverUtil
Get the server URL with the Geoserver context.
getGroupNames(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Gets the user group names from the login session on the http request
getGroupNames() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getGroups(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get all groups from the authentication service
getGroups(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get the groups for a particular user from the authentication service
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all groups from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get the groups for a particular user from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthSession
Get the all groups in which the given userDN is
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get all groups from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get the groups for a particular user from the authentication service
getGroups(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get all groups from the authentication service
getGroups(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get the groups for a particular user from the authentication service
getGroups() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
 
getGUID(String, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
given a local identifer, look up the guid.
getGUIDs(String, String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Get the list of identifiers which system metadata matches the given format id and original member node id and guid or series id start with the scheme (doi for example).
getHandler(String) - Method in class edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager
 
getHarvestLogID() - Method in class edu.ucsb.nceas.metacat.harvesterClient.Harvester
Gets the current value of the harvestLogID for storage as a primary key in the HARVEST_LOG_ID field of the HARVEST_LOG table.
getHarvestOperationCodeLevel(String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Returns a code level string based on a harvestOperationCode string.
getHashParam(String) - Method in class edu.ucsb.nceas.metacat.MetacatURL
returns a single parameter from the hash by name
getHashParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns the parameters in a hashtable.
getHazelcastInstance() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
 
getHeadPID(Identifier) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Get the pid of the head (current) version of objects match the specified sid.
getHomeServerCodeForDocId(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Returns a home server location given a accnum
getHomeServerInfoForDocId(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Method to get a host server information for given docid
getHub() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
Get hub option
getHubValue(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
To a given server name, try to get its hub option If couldn't find the server in the server list, false will return
getId() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getIdentifier() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns
getIdentifier() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.GetRecord
Get the oai:identifier from the oai:header
getIdentifier() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return the identifier of this Query
getIdentifiers() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Get the identifiers set
getIncludedSchemaFilePathes() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaParser
Get the included schema file paths in this schema
getIndexEventMap() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Get the index event map
getIndexFields(Identifier, String) - Method in class edu.ucsb.nceas.metacat.EventLog
 
getIndexQueue() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Get the index queue
getInlineDataIdWithoutRev(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
This method will get inline data id without the revision number.
getInputStream() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
 
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.AuthAdmin
Get the single instance of the MetaCatConfig.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.BackupAdmin
Get the single instance of BackupAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.D1Admin
Get the single instance of D1Admin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Get the single instance of DBAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.EZIDAdmin
Get the single instance of EZIDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.LoginAdmin
Get the single instance of LoginAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.PropertiesAdmin
Get the single instance of the MetaCatConfig.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.QuotaAdmin
Get the single instance of QuotaDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.ReplicationAdmin
Get the single instance of D1Admin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.SkinsAdmin
Get the single instance of the MetaCatConfig.
getInstance() - Static method in class edu.ucsb.nceas.metacat.admin.SolrAdmin
Get the single instance of SolrDAdmin.
getInstance() - Static method in class edu.ucsb.nceas.metacat.ArchiveHandler
Get the single instance of SessionService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.database.DatabaseService
Get the single instance of DatabaseService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
Returns the single instance, creating one if it's the first time this method is called.
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.CNodeService
singleton accessor
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Get the instance of the HazelcastService that has been instantiated, or instantiate one if it has not been already.
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Get an instance of MNodeService.
getInstance(HttpServletRequest, String, String) - Static method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Get an instance of MNodeService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.ObjectFormatService
 
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.BookKeeperClient
Get the singleton instance of the BookKeeplerClient class
getInstance(ExecutorService, BookKeeperClient) - Static method in class edu.ucsb.nceas.metacat.dataone.quota.PortalQuotaService
Get a singleton class instance
getInstance() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
Get the singleton instance of the service
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
singleton accessor
getInstance(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Singleton accessor to get an instance of MNodeService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.event.MetacatEventService
 
getInstance() - Static method in class edu.ucsb.nceas.metacat.EventLog
Return the single instance of the event log after initializing it if it wasn't previously initialized.
getInstance() - Static method in class edu.ucsb.nceas.metacat.IdentifierManager
Return the single instance of the manager after initializing it if it wasn't previously initialized.
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
 
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler
Get an instance of the class.
getInstance() - Static method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
 
getInstance() - Static method in class edu.ucsb.nceas.metacat.IndexingQueue
 
getInstance() - Static method in class edu.ucsb.nceas.metacat.MetacatProfiler
get a singleton instance
getInstance() - Static method in class edu.ucsb.nceas.metacat.plugin.MetacatHandlerPluginManager
 
getInstance(ServletContext) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the single instance of PropertyService.
getInstance(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the single instance of PropertyService for test purposes.
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the single instance of PropertyService for test purposes.
getInstance() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the single instance of SkinPropertyService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Get the single instance of SessionService.
getInstance(ServletContext) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
Get the single instance of ServiceService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.service.SessionService
Get the single instance of SessionService.
getInstance() - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Get the single instance of XMLService.
getInstanceId() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
Get the instance id determined in the determine method
getInternalContextURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the internal context url.
getInternalServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the internal server URL.
getIpAddress() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Get the ip address from the service
getIpAddress() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the internet protocol address.
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
The function name that is used to return non-NULL value
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracle's function name that is used to return non-NULL value
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
The PostgreSQL function name that is used to return non-NULL value
getIsNULLFunction() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server's function name that is used to return non-NULL value
getIsRevisionDoc() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
get the the is revision doc
getKnownURIs() - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
 
getLabels() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
getLandingPage(Identifier) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
Get the landing page url string for the given identifier
getLastAccessedTime() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getLastCheckedDate() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
Get last checked date
getLastCheckedDate(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
To a given server name, try to get its lastcheck date.
getLastDocid(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Return the highest document id for a given scope.
getLastDocid(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Return the highest document id for a given scope.
getLastModifiedDate() - Method in class edu.ucsb.nceas.metacat.IdentifierManager
returns a list of system metadata-only guids since the given date
getLatestRevForLocalId(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
return the newest rev for a given localId
getLatestRevisionInDocumentTable(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
Get last revision number from database for a docid If couldn't find an entry, -1 will return The return value is integer because we want compare it to there new one
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
Syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracles's syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
PostgreSQL's syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLeftJoinQuery(String, String, String, String, String) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
MSSQL's syntax for doing a left join Add 'a.' in front of the fields for first table and 'b.' in front of the fields for the second table
getLocalFileDir() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the local file directory path
getLocalFileUri() - Method in class edu.ucsb.nceas.metacat.service.XMLSchema
Gets the local file uri
getLocalId() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
Get the local id associated with the local usage
getLocalId(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Lookup a localId given the GUID.
getLocalIdentifier(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
Extract the local identifier from the native item
getLocalIdsWithNoSystemMetadata(boolean, int) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
return all local ids in the object store that do not have associated system metadata
getLocalReplicationServerName() - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
Method to get the name of local replication server
getLocationName() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getLock(String) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
 
getloggedinuserinfo() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Get the logged in user for this session.
getloggedinuserinfo() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Method used to log in to a metacat server.
getLogRecords(Session, Date, Date, String, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Return the log records associated with a given event between the start and end dates listed given a particular Subject listed in the Session
getLogRecords(Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
getLogRecords(Session, Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
getLogRecords(Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getLogRecords(Session, Date, Date, Event, String, Integer, Integer) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
getLSID(XSLProcessorContext, ElemExtensionCall) - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
get the current LSID for the given thread, for use in XSLT so return a string
getLSID() - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
 
getMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get the main backup properties file.
getMainBackupProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getMainBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the main backup properties file.
getMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
getMainMetaData() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get the main properties metadata.
getMainMetaData() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getMainMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get the main properties metadata.
getMainMetaData() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
getMaxDateUpdated() - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
Get the most recent date that the xml_documents table was updated
getMaxDocid(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
get the latest Accession Number from a particular scope
getMaxRevFromRevisionTable(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
Method to return max rev number in xml_revision for given docid.
getMessage() - Method in class edu.ucsb.nceas.metacat.AuthSession
Get the message associated with authenticating this session.
getMessage(int) - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Indexed getter for property message.
getMessage() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property message.
getMessage() - Method in exception edu.ucsb.nceas.metacat.McdbException
Get the message from this exception.
getMetacatAuthenticatedEcogridEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
Gets the end point which Metacat implements authenticated ecogrid interface.
getMetacatClient(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.client.MetacatClient
JSP API: This is a convenience method to reduce the amount of code in a Metacat Client JSP.
getMetacatClient() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getMetacatEcogridAuthEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
 
getMetacatEcogridEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
Gets the end point which Metacat implements ecogrid interface.
getMetacatEcogridIdentifierEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
 
getMetacatEcogridPutEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
 
getMetacatReleaseInfo() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Gets a string that holds some description about the release.
getMetacatRunning() - Method in class edu.ucsb.nceas.metacat.IndexingQueue
 
getMetacatVersion() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the metacat version by getting the string representation from metacat.properties and instantiating a MetacatVersion object.
getMetaData() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
Method to get meta data
getMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
Get the metadata for the given identifier
getMetadata(LSIDRequestContext, String[]) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
 
getMetaData() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the main properties metadata.
getMetaData(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the main properties metadata.
getMetadataDoc() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getMetadataFormatsQueryString() - Method in class edu.ucsb.nceas.metacat.Sitemap
Generate a comma-separated list of metadata format IDs so generateSitemaps can filter the available objects to just metadata objects.
getMetadataLocations(LSID, String) - Method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMain
 
getMetaFileDocId() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property isMetaFileDocId.
getMetaFileName() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property metaFileName.
getMethodDescriptors() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
Gets the bean's 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
 
getNamedTimescale() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getNamedTimescaleQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getNamespace(String) - Method in class edu.ucsb.nceas.metacat.BasicNode
Get an uri of the namespace prefix
getNamespace() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
Get the namespace of the document (root element).
getNameSpaceAndLocation(String) - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Get the all schema-location pairs registered for the formatId.
getNameSpaceAndLocationStringWithoutFormatId() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Gets the name space and location string.
getNameSpaceList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Gets a list of name spaces.
getNewestDocRevision(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
The method will return the latest revision in metacat server for a given document id.
getNewestDocRevision(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
The method will return the latest revision in metacat server for a given document id.
getNext() - Method in class edu.ucsb.nceas.metacat.IndexingQueue
 
getNextObject(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
Return the highest document id for a given scope.
getNextObject(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
Return the highest document id for a given scope.
getNextRevision(String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
The method will return the latest revision in metacat server for a given document id.
getNextRevision(String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
The method will return the latest revision in metacat server for a given document id.
getNode(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getNodeData() - Method in class edu.ucsb.nceas.metacat.CommentNode
Get the node data as a string value
getNodeData() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeData() - Method in class edu.ucsb.nceas.metacat.PINode
Get the node data as a string value
getNodeData() - Method in class edu.ucsb.nceas.metacat.TextNode
Get the node data as a string value
getNodeDataDate() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeDataNumerical() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeID() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the id of this node
getNodeId() - Method in class edu.ucsb.nceas.metacat.NodeRecord
Get functions
getNodeIndex() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get nodeIndex of the node
getNodeIndex() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeList(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
Get a NodeList containing the nodes in the response DOM for the specified xpath
getNodeName() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodePrefix() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNodeText(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getNodeTextList(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getNodeTextStack(XPath, String, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getNodeType() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the type of this node
getNodeType() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getNoNamespaceSchemaLocation() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
Get the value of noNamespaceSchemaLocation of the document (root element).
getNoNamespaceSchemaLocation() - Method in class edu.ucsb.nceas.metacat.service.XMLNoNamespaceSchema
Get the no-namespace-schemal-location uri
getNonXMLMetadataFormatList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Get the list of format ids which are the non-xml metadata type
getNormalizedXMLQuery() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Gets normailized query string in xml format, which can be transformed to html
getNorthBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getNotFoundDataSetId() - Method in class edu.ucsb.nceas.metacat.AssociateAccessPolicy
Get the docid which didn't found a dataset id to map it
getOAIIdentifier(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
Construct an OAI identifier from the native item
getOAIIdentifierOld(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
Construct an OAI identifier from the native item
getObject(String, String) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
Read a public XML document , accessed by docid, and returned as a Reader.
getObject(String, String) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
Read a public XML document , accessed by docid, and returned as a Reader.
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
Implements REST version of DataONE CRUD API --> get
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
Implements REST version of DataONE CRUD API --> get
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
Implements REST version of DataONE CRUD API --> get
getObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
Implements REST version of DataONE CRUD API --> get
getObjectFilePath(String, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
Get the the file path for the given object local id
getOperator() - Method in class edu.ucsb.nceas.metacat.DBQuery
 
getOptionList(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
 
getOrganization() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
 
getOrganization() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property organization.
getOrganizations() - Static method in class edu.ucsb.nceas.metacat.util.OrganizationUtil
gets a list of organization names from metacat.properties.
getOrgDNs(String) - Static method in class edu.ucsb.nceas.metacat.util.OrganizationUtil
gets a list of organization names from metacat.properties.
getOsClass() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the OS for this system.
getOutputStream() - Method in class edu.ucsb.nceas.metacat.restservice.InputStreamDataSource
 
getOwnerList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the owner fields as defined in the <owner> tag in the pathquery dtd.
getPackage(Session, ObjectFormatIdentifier, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Exports a data package to disk using the BagIt The Bagit 0.97 format corresponds to the V1 export format The Bagit 1.0 format corresponds to the V2 export format
getPackage(Session, ObjectFormatIdentifier, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getPackage(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
Retrieve data package as Bagit zip
getPackage(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
Retrieve data package as Bagit zip
getPackageId() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
For a given site, return the packageId attribute search string for that site's EML documents.
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
for generating a query for paging
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
 
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
 
getPagedQuery(String, Integer, Integer) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
 
getParam(int) - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns a single parameter and value as a 1D string array.
getParameters(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
Get a cookie from a request by the cookie name
getParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns the parameters as a 2D string array.
getParentID() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the parent id of this node
getParentNode() - Method in class edu.ucsb.nceas.metacat.DBSAXNode
get the parent of this node
getParentNodeId() - Method in class edu.ucsb.nceas.metacat.NodeRecord
 
getPassword() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
 
getPassword() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property password.
getPassword() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getPathContent(File, String) - Static method in class edu.ucsb.nceas.metacat.DBTransform
gets the content of a tag in a given xml file with the given path
getPathExpr() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property pathExpr.
getPathExpression() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the path expression parameter
getPathInfo() - Method in class edu.ucsb.nceas.metacat.restservice.D1HttpRequest
override getPathInfo to handle special characters
getPaths() - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
getPathsForIndexing() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get a list of xml paths that need to be indexed
getPathValue() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property pathValue.
getPercentageSymbolCount() - Method in class edu.ucsb.nceas.metacat.QueryGroup
 
getPercentageSymbolCount() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the percentage count for one query term
getPermission() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
Get permission
getPermissionOrder() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get permissionOrder
getPermissionType() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
 
getPIDForSID(Identifier, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Utility method to get the PID for an SID.
getPointFeature() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDocument
Returns a geotools (multi)point feature with geometry plus attributes ready to be inserted into our spatial dataset cache
getPointFeatureType() - Static method in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
Creates the featuretype schema for point centroids
getPolygonFeature() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialDocument
Returns a geotools (multi)polygon feature with geometry plus attributes ready to be inserted into our spatial dataset cache
getPolygonFeatureType() - Static method in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
Creates the featuretype schema for polygon bounds
getPrincipal() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessRule
Get the principle vector
getPrincipal() - Method in class edu.ucsb.nceas.metacat.EventLogData
Get the current value of the principal.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getPrincipals(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get all groups and users from authentication service.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all groups and users from authentication scheme.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthSession
Get all groups and users from authentication scheme.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get all groups and users from authentication scheme.
getPrincipals(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get all groups and users from authentication scheme.
getProfiles() - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
return a hashtable of the profiles
getProperties() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the main backup properties file.
getProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get the main backup properties file.
getPropertiesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get a Map of all properties that start with the groupName prefix.
getPropertiesByGroup(String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getPropertiesByGroup(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get a Map of all properties that start with the groupName prefix.
getPropertiesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
Get a Map of all properties that start with the groupName prefix.
getProperty(String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Utility method to get a property value from the properties file
getProperty(String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getProperty(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Utility method to get a property value from the properties file
getProperty(String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
Utility method to get a property value from the properties file
getProperty(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Utility method to get a property value from the properties file for a specific skin.
getPropertyDescriptors() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewBeanInfo
Gets the bean's PropertyDescriptors.
getPropertyNames() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get a set of all property names.
getPropertyNames() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getPropertyNames() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get a set of all property names.
getPropertyNames() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
Get a set of all property names.
getPropertyNames(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get a set of all property names for a given skin.
getPropertyNamesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Get a Set of all property names that start with the groupName prefix.
getPropertyNamesByGroup(String) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
getPropertyNamesByGroup(String) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Get a Set of all property names that start with the groupName prefix.
getPropertyNamesByGroup(String) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
Get a Set of all property names that start with the groupName prefix.
getPropertyNamesByGroup(String, String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Get a Set of all property names that start with the groupName prefix.
getProtocol() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Returns the type of the url.
getProtocolVersion() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.Identify
Get the oai:protocolVersion value from the Identify response
getPublicaccess() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getPublicSession() - Method in class edu.ucsb.nceas.metacat.service.SessionService
Get the public session from the session hash table.
getQformat() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property qformat.
getQformat() - Method in class edu.ucsb.nceas.metacat.DBQuery
 
getQueryEngineDescription(Session, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
 
getQueryEngineDescription(Session, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
getQueryEngineDescription(String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
getQueryEngineDescription(String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getQueryEngineDescritpion() - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler
Get the QueryEngineDescription
getQueryGroup() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
get the QueryGroup used to express query constraints
getQueryTitle() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return the title of this Query
getQuotaType() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
Get the quota type of the usage
getQuotaType() - Method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
Get the quota type determined in the determine method
getRealApplicationContext() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
Get the servlet context name
getRealConfigDir() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
Convert the relative config directory to a full path
getRealSkinDir() - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
Convert the relative skins directory to a full path
getRecommendedExternalDir() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Returns the recommended external base directory.
GetRecord - Class in edu.ucsb.nceas.metacat.oaipmh.harvester
This class represents an GetRecord response on either the server or on the client
GetRecord() - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.GetRecord
Mock object constructor (for unit testing purposes)
GetRecord(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.oaipmh.harvester.GetRecord
Client-side GetRecord verb constructor
getRecord(String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
Retrieve the specified metadata for the specified oaiIdentifier
getReferences() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get the references
getRegisteredNoNamespaceSchemaList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Gets the registered schema list without the name space.
getRegisteredSchemaList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Gets the registered schema list.
getRegisteredSession(String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
Get a registered session from the session hash table.
getReplica(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Essentially a get() but with different logging behavior
getReplica(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getReplica(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
getReplication() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
Get replication xml or not option
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
This method will return the sql command to get document list in xml_document in replication.
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
Return a hard code string to get xml_document list in timed replcation
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
Return a hard code string to get xml_document list in timed replcation
getReplicationDocumentListSQL() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
Return a hard code string to get xml_document list in timed replcation
getReplicationValue(String) - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServerList
To a given server name, try to get its xml replciation option If couldn't find the server in the server list, false will return
getReport(String[], String[], String[], String[], Timestamp, Timestamp, boolean) - Method in class edu.ucsb.nceas.metacat.EventLog
Get a report of the log events that match a set of filters.
getRequestor() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
Get the requestor associated with the usage
getRequestURL() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
Get the OAI request URL for this response
getResource(Model, String) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Get the Resource object which has the given identifier
getResult(HashMap, HttpServletRequest, HttpServletResponse, Transformer, HashMap) - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
 
getResultsetXSL(HttpServletRequest) - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
Gets the path to the resultset XSL file.
getResultsJSP() - Method in class edu.ucsb.nceas.metacat.advancedsearch.MetacatHelper
Gets the relative path to the advancedsearchresults.jsp file.
getResumptionToken() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.ListIdentifiers
Get the oai:resumptionToken from the response
getResumptionToken() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.ListRecords
Get the oai:resumptionToken from the response
getResumptionToken() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.ListSets
Get the oai:resumptionToken from the response
getReturnDocList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the return document types as defined in the <returndoctype> tag in the pathquery dtd.
getReturnfield() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property returnField.
getReturnFieldList() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Accessor method to return a vector of the extended return fields as defined in the <returnfield> tag in the pathquery dtd.
getRev() - Method in class edu.ucsb.nceas.metacat.AccessionNumber
returns the revision number encoded in this accession number
getRev() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the revision number encoded in this docid
getRev() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getRevision() - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to get revsion
getRevisionFromAccessionNumber(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
This method will get revision from an AccessionNumber.
getRevisionStringFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Utility method to get version string from a given string
getRevisionsVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
 
getRevListFromRevisionTable(String) - Static method in class edu.ucsb.nceas.metacat.DBUtil
Method to return a rev list in xml_revision for given docid.
getRootNodeID() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the root node id of this node
getRootNodeId() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
 
getRootNodeID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the root node identifier
getSchemaFileNameFromUri(String) - Static method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Get a schema file name from the schema uri.
getSchemaLocation() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Accessor method for the schemaLocation field.
getSchemaLocation() - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
Get the xsi:schemaLocation for the OAI response
getSchemaLocations(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatCatalog
Retrieve a list of schemaLocation values associated with the specified oaiIdentifier.
getScienceMetadataIdentifiers() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
Gets all of the science metadata documents in the downloader
getScienceMetadataIds() - Method in class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
 
getScriptSuffixes() - Static method in class edu.ucsb.nceas.metacat.util.DatabaseUtil
Gets the available upgrade versions for metacat by getting a list of upgrade script from properties in metacat.properties that start with "database.upgradeVersion".
getSearchMode() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the searchmode parameter
getSecureContextURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the secure server URL with the context.
getSecureServer() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the secure server which is made up of the server name + : + the https port number.
getSecureServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the secure server URL which is made up of the server name + : + the https port number.
getSelectQueryMap() - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
Queries Metacat for document listings, and returns the results in a TreeMap, where the key is the Doc Id, and the value is the Create Date.
getSeparator() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the separator used in the accession number
getSerializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
Get Custom Serializer
getSerializer(String, Class, QName) - Static method in class edu.ucsb.nceas.shared.xsd.IOException
Get Custom Serializer
getServerCode(String) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Given a server name, return its servercode in xml_replication table.
getServerCodeForServerName(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Returns a server code given a server name
getServerCodes() - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Returns a Map of serverCode=serverName
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateORE
 
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.dataone.GenerateSystemMetadata
 
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
 
getServerLocation() - Method in class edu.ucsb.nceas.metacat.admin.upgrade.UpdateDOI
 
getServerlocation() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getServerName() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationServer
Get server name
getServerName() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
Gets the server name
getServerNameForServerCode(int) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Returns the name of a server given a serverCode
getServerURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the server URL which is made up of the server name + : + the http port number.
getServletURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the servlet URL.
getSession() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
retrieve the out-of-band session
getSessionData(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
Get the session data from a request.
getSessionDataFromToken(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
Get SessionData from the DataONE auth token
getSessionFromHeader() - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Get the session from the header of the request.
getSessionId() - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Get the session identifier for this session.
getSessionId() - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Get the session identifier for this session.
getSessionId() - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
Get the session identifier for this session.
getSessionId() - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
 
getSessionid() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property sessionId.
getSessionId() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatAuthenticatedEcogridEndPoint
 
getSessions() - Method in class edu.ucsb.nceas.metacat.AuthSession
Get the new session
getSetSpecs(Object) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
get the setspec from the item
getSingleString(String) - Method in class edu.ucsb.nceas.metacat.oaipmh.harvester.HarvesterVerb
Get the String value for the given XPath location in the response DOM
getSiteCode() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the siteCode encoded in this docid
getSiteDocument() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Retrieve the document from the site using its value.
getSiteKeyword() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
Get the keyword string for this site.
getSiteValue() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getSizeOfDBConnectionPool() - Method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
Method to get the size of DBConnectionPool
getSkinNames() - Static method in class edu.ucsb.nceas.metacat.util.SkinUtil
Gets a list of available skin names by parsing a csv property from metacat.properties.
getSmartDocId(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
This method will call both getDocIdFromString and getDocIdFromAccessionNumber.
getSolrUpdateClasses() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Get the list of classes that should be run to update the solr server.
getSortedReturnFieldString() - Method in class edu.ucsb.nceas.metacat.QuerySpecification
Method to return a String generated after sorting the returnFieldList Vector
getSouthBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getSQLDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the SQL directory.
getSRBEcogridEndPoint() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
Gets the end point which SRB implements ecogrid interface.
getSRBMachineName() - Method in class edu.ucsb.nceas.metacat.dataquery.MetacatEcogridEndPoint
Gets the machine name which srb protocol will be used.
getStartDate() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getStartedDescribesNodeId() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get the start described id
getStartElementName() - Method in class edu.ucsb.nceas.metacat.SubTree
Get startElementName
getStartNodeId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get start node id
getStatus() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion status from the object
getStatus(Session) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Get the status of the system.
getStoredBackupDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Gets the stored backup location.
getStoredTmpNodeStack() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessSection
Get storedTempNodeStack
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
The character that the specific database implementation uses to indicate string literals in SQL.
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracles's string delimiter character: single quote (')
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
PostgreSQL's string delimiter character: single quote (')
getStringDelimiter() - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server's string delimiter character: single quote (')
getStringFromInputStream(InputStream) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getStringFromInputStream(InputStream) - Static method in class edu.ucsb.nceas.metacat.lsid.LSIDAuthorityMetaData
 
getStyleCommonURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the style common URL.
getStyleSkinsDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the style skins directory.
getStyleSkinsURL() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the style skins URL.
getSubjectAllAny() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getSubjectField() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getSubjectQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getSubjectsOfDocumentedBy(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Get all subjects of the triple - * is documentedBy metadataId on the resource map
getSubjectsOfDocumentedBy(Identifier, Model) - Static method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Get all subjects of the triple - * is documentedBy metadataId in the given model
getSubjectValue() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getSubscriber() - Method in class edu.ucsb.nceas.metacat.dataone.quota.LocalUsage
Get the subscriber of the usage
getSubTreeId() - Method in class edu.ucsb.nceas.metacat.SubTree
Get the subTreeId
getSubTreeNodeStack() - Method in class edu.ucsb.nceas.metacat.SubTree
Get subtree node stack
getSubversion(int) - Method in class edu.ucsb.nceas.metacat.Version
 
getSystem() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LTERSite
For a given site, return system attribute search string for that site's EML documents.
getSystemID() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the system identifier
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Return the system metadata for a given object
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Return the system metadata for a given object
getSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
getSystemMetadata(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
getSystemMetadata(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
getSystemMetadata(String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
return a hash of all of the info that is in the systemmetadata table
getSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.MultipartRequestWithSysmeta
Get the system meta data associate with this request
getSystemMetadataContent(String) - Static method in class edu.ucsb.nceas.metacat.util.ReplicationUtil
return the contents between start and end tag
getSystemMetadataForPID(Identifier, String, String, String, boolean) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Get the system metadata for the given PID (not a sid).
getSystemMetadataMap() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Get the system metadata map
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
Implements REST version of DataONE CRUD API --> getSystemMetadata
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
Retrieve System Metadata
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
Implements REST version of DataONE CRUD API --> getSystemMetadata
getSystemMetadataObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
Retrieve System Metadata
getSystemMetadataPart() - Method in class edu.ucsb.nceas.metacat.restservice.multipart.StreamingMultipartRequestResolver
Get the system metadata object which was extracted from the sysmeta part.
getSystemMetadataVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
 
getTag() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion tag from the object
getTagName() - Method in class edu.ucsb.nceas.metacat.BasicNode
Get the name of this node
getTaxon() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getTaxonQueryType() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getTempDirectory() - Static method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
return the directory where temp files are stored
getTextContent(XPath, Node) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
getTransformer(String) - Static method in class edu.ucsb.nceas.metacat.DBTransform
The method that manages the Templates Map instances that will be used to build transformers from.
getType() - Static method in class edu.ucsb.nceas.metacat.service.XMLNoNamespaceSchema
Return the type of schema.
getType() - Static method in class edu.ucsb.nceas.metacat.service.XMLSchema
Return the type of the schema.
getTypeDesc() - Static method in class edu.ucsb.nceas.shared.xsd.FileNotFoundException
Return type metadata object
getTypeDesc() - Static method in class edu.ucsb.nceas.shared.xsd.IOException
Return type metadata object
getUnfoundDocId() - Method in exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
Method to get the docid which couldn't be found
getUnfoundRevision() - Method in exception edu.ucsb.nceas.metacat.McdbDocNotFoundException
Method to get the docid's revsion which couldn't be found
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.AbstractDatabase
Unique ID generator
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.OracleAdapter
The Oracle unique ID generator through use of sequences The name of the sequence used to generate the unique id is made from the name of the table that uses the id by appending "_id_seq" to it.
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
The PostgreSQL unique ID /sequence generator The name of the sequence used to generate the unique id is made from the name of the table that uses the id by appending "_id_seq" to it.
getUniqueID(Connection, String) - Method in class edu.ucsb.nceas.dbadapter.SqlserverAdapter
The SQL Server unique ID generator through use of IDENTITY key The IDENTITY key is a column in the table.
getUniqueId() - Method in class edu.ucsb.nceas.metacat.DocumentIdentifier
returns the uniqueId encoded in this docid
getUnReadableInlineDataIdList(String, String, String[]) - Static method in class edu.ucsb.nceas.metacat.PermissionController
A static method to get Hashtable which cointains a inlinedata object list that user can't read it.
getUnRegisteredDBVersion() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Finds the version of the database for a database that does not have a dbVersion table yet.
getUnReportedUsages() - Static method in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
Get the result set from the table which haven't been reported to the bookkeeper server.
getUnWritableInlineDataIdList(String, String, String[], boolean) - Static method in class edu.ucsb.nceas.metacat.PermissionController
A static method to get Hashtable which cointains a inline data object list that user can't overwrite it.
getUpdateClasses() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
 
getUpdateDate() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
get the update date
getUpdatedSystemMetadataIds(Date) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
returns a list of system metadata-only guids since the given date
getUpdateScripts() - Method in class edu.ucsb.nceas.metacat.admin.DBAdmin
Creates a list of database update script names by looking at the database version and the metacat version and then getting any script that is inbetween the two (inclusive of metacat version).
getUpdateScripts() - Method in class edu.ucsb.nceas.metacat.database.DBVersion
Get the update script list for this version
getUpdatesVect() - Method in class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
 
getUpgradeVersions() - Static method in class edu.ucsb.nceas.metacat.util.DatabaseUtil
Gets the available upgrade versions for metacat by getting a list of upgrade script from properties in metacat.properties that start with "database.upgradeVersion".
getURLBytes(URL) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
This method returns a byte array after opening a url
getURLContent(URL) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
This method returns the content of a url
getURLStream(URL) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
This method returns the InputStream after opening a url
getUsageCount() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion usage times from the object
getUser() - Method in class edu.ucsb.nceas.metacat.event.MetacatDocumentEvent
 
getUserAgent() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Get the user agent from the service
getUserAgent() - Method in class edu.ucsb.nceas.metacat.EventLogData
 
getUserHomeDir() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the current user's home directory
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getUserInfo(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get information for a user - name, organization and email address.
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all users from the authentication service
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get all users from the authentication service
getUserInfo(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get all users from the authentication service
getUserManagementUrl() - Static method in class edu.ucsb.nceas.metacat.util.SystemUtil
Get the url pointing to the user management page.
getUsername() - Method in class edu.ucsb.nceas.metacat.advancedsearch.LoginBean
 
getUsername() - Method in class edu.ucsb.nceas.metacat.clientview.ClientView
Getter for property userName.
getUserName(HttpServletRequest) - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Gets the user name from the login session on the http request
getUserName() - Method in class edu.ucsb.nceas.metacat.util.SessionData
 
getUserowner() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
 
getUsers(String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get all users from the authentication service
getUsers(String, String, String) - Method in interface edu.ucsb.nceas.metacat.AuthInterface
Get the users for a particular group from the authentication service
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get all users from the authentication service
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthLdap
Get the users for a particular group from the authentication service
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get all users from the authentication service
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthStub
Get the users for a particular group from the authentication service
getUsers(String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get all users from the authentication service
getUsers(String, String, String) - Method in class edu.ucsb.nceas.metacat.AuthTest
Get the users for a particular group from the authentication service
getUserupdated() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getValidateType() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
 
getValue() - Method in class edu.ucsb.nceas.metacat.QueryTerm
get the Value parameter
getVersion(String) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeVersionChecker
Get the version of the service name for the node.
getVERSION() - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
Get the VERSION number
getVersionAsXml() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
Get the version number in an XML document.
getVersionFromDB() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
Get the version number from DB
getVersionFromString(String) - Static method in class edu.ucsb.nceas.metacat.util.DocumentUtil
Utility method to get version number from a given string
getVersionID() - Static method in class edu.ucsb.nceas.metacat.MetacatVersion
Get the current version string for this metacat instance.
getVersionString() - Method in class edu.ucsb.nceas.metacat.Version
 
getWarningMessage() - Method in class edu.ucsb.nceas.metacat.database.DBConnection
get the db connetion waring message from the object
getWestBound() - Method in class edu.ucsb.nceas.metacat.advancedsearch.AdvancedSearchBean
 
getWriter(HttpServletRequest, HttpServletResponse) - Static method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.OAIHandler
Get a response Writer depending on acceptable encodings
getXMLAccessForDoc(String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Get all xml access for a document
getXMLAccessForPrincipal(String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Get all xml access for a principal for a certain document
getXMLAccessForPrincipal(String, String, String, String) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Get all xml access for a principal/permType/permOrder for a certain document
getZippedPackage(String, ServletOutputStream, String, String[], String) - Method in class edu.ucsb.nceas.metacat.DBQuery
put a data packadge into a zip output stream
GROUPDESINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
 
GROUPNAMEINDEX - Static variable in interface edu.ucsb.nceas.metacat.AuthInterface
 
groups - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 

H

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

I

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

J

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

K

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

L

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

M

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

N

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

O

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

P

PackageDownloaderV1 - Class in edu.ucsb.nceas.metacat.download
 
PackageDownloaderV1(Identifier) - Constructor for class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
Creates a PackageDownloaderV1 object.
PackageDownloaderV2 - Class in edu.ucsb.nceas.metacat.download
A class that handles downloading data packages under the V2 format.
PackageDownloaderV2(Identifier, ResourceMap, SystemMetadata) - Constructor for class edu.ucsb.nceas.metacat.download.PackageDownloaderV2
Creates a PackageDownloader object
packagePids - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
 
params - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
parentId - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
parse() - Method in class edu.ucsb.nceas.metacat.service.XMLNamespaceParser
Parse the xml file
parse() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaParser
Parse the schema file
parseFileInfo(String) - Static method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
parseHarvestList() - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Parses the site harvest list XML file to find out which documents to harvest.
parseQuery(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
Utility method to parse the query part of a URL into parameters.
parseTrailing(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
parseXml(String, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
password - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
 
path - Variable in class edu.ucsb.nceas.metacat.PathIndexEntry
 
PATH4ANCESTOR - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientFgdcHelper
 
PathIndexEntry - Class in edu.ucsb.nceas.metacat
PathIndexEntry contains all of the data fields needed to insert an path into the xml_index table or the xml_path_index table, depending on which constructor is used.
PathIndexEntry(long, String, String, String, long) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry
Construct a new PathIndexEntry for the xml_index table.
PathIndexEntry(long, String, String, long, String, float, Timestamp) - Constructor for class edu.ucsb.nceas.metacat.PathIndexEntry
Construct a new PathIndexEntry for the xml_path_index table.
performPathquery(String, String, String[]) - Method in class edu.ucsb.nceas.metacat.DBQuery
 
PERMISSION_TYPE_ALLOW - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
PERMISSION_TYPE_DISALLOW - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
 
PermissionController - Class in edu.ucsb.nceas.metacat
 
PermissionController(String) - Constructor for class edu.ucsb.nceas.metacat.PermissionController
Constructor for PermissionController
PermOrderException - Exception in edu.ucsb.nceas.metacat.accesscontrol
Exception thrown when an error occurs with a permission order
PermOrderException(String) - Constructor for exception edu.ucsb.nceas.metacat.accesscontrol.PermOrderException
Create a new PermOrderException.
PermOrderException(String, BaseException) - Constructor for exception edu.ucsb.nceas.metacat.accesscontrol.PermOrderException
 
persistAllProperties() - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Save the properties to a properties file.
persistAuthBackupProperties(ServletContext) - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Writes out backup configurable properties to a file.
persistAuthBackupProperties(ServletContext) - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
persistAuthBackupProperties(ServletContext) - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Writes out backup configurable properties to a file.
persistAuthBackupProperties(ServletContext) - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
persistBackupProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Writes out backup configurable properties to a file.
persistMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Writes out backup configurable properties to a file.
persistMainBackupProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
persistMainBackupProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Writes out backup configurable properties to a file.
persistMainBackupProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
persistProperties() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
Save the properties to a properties file.
persistProperties() - Method in interface edu.ucsb.nceas.metacat.properties.PropertiesInterface
 
persistProperties() - Static method in class edu.ucsb.nceas.metacat.properties.PropertyService
Save the properties to a properties file.
persistProperties() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
Save the properties to a properties file.
persistProperties(String) - Static method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
Save the properties to a properties file.
pidMapping - Variable in class edu.ucsb.nceas.metacat.download.PackageDownloaderV1
 
ping() - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
Low level, "are you alive" operation.
ping() - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
ping() - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
PINode - Class in edu.ucsb.nceas.metacat
A Class that represents an XML PI node and its contents,
PINode(long, long, String, String) - Constructor for class edu.ucsb.nceas.metacat.PINode
Construct a new PINode instance
pointShpUri - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
 
polygonShpUri - Static variable in class edu.ucsb.nceas.metacat.spatial.SpatialFeatureSchema
 
populate() - Method in class edu.ucsb.nceas.metacat.util.MetacatPopulator
populate from the source
populateAllowedSubmitters() - Static method in class edu.ucsb.nceas.metacat.util.AuthUtil
Get the vector of allowed submitter credentials from metacat.properties and put into global allowedSubmitters list
populateDAO(ResultSet) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Populate a job data object with the current row in a resultset
populateDAO(ResultSet) - Method in class edu.ucsb.nceas.metacat.shared.BaseAccess
 
populateDAO(ResultSet) - Method in class edu.ucsb.nceas.metacat.XMLQueryresultAccess
Populate a job data object with the current row in a resultset
populateRegisteredSchemaList() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
Populate the list of registered schemas.
PORTAL - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
 
PortalQuotaService - Class in edu.ucsb.nceas.metacat.dataone.quota
A class enforce the portal quota service, which controls how many portals users can create
POST - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
HTTP Verb POST
POST - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
HTTP Verb POST
post(HttpClient, String, HashMap<String, String>) - Static method in class edu.ucsb.nceas.metacat.util.RequestUtil
Post a request and return the response body
PostgresDatabaseConnectionPool - Class in edu.ucsb.nceas.metacat.dataquery
This class implements DataConnetionPoolInterface to provide a connection for testing.
PostgresDatabaseConnectionPool() - Constructor for class edu.ucsb.nceas.metacat.dataquery.PostgresDatabaseConnectionPool
Constructor.
PostgresqlAdapter - Class in edu.ucsb.nceas.dbadapter
The PostgreSQL db adapter implementation.
PostgresqlAdapter() - Constructor for class edu.ucsb.nceas.dbadapter.PostgresqlAdapter
 
postQuery(Session, String, HashMap<String, String[]>) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Handle the query sent by the http post method
predicate2SQL(String, List<Object>) - Static method in class edu.ucsb.nceas.metacat.QueryTerm
 
PREDICATE_END - Static variable in class edu.ucsb.nceas.metacat.QuerySpecification
 
PREDICATE_START - Static variable in class edu.ucsb.nceas.metacat.QuerySpecification
 
prepareAndThrowNotAuthorized(Session, Identifier, Permission, String) - Method in class edu.ucsb.nceas.metacat.dataone.D1AuthHelper
 
prepareStatement(String) - Method in class edu.ucsb.nceas.metacat.database.DBConnection
Method to create a PreparedStatement by sending a sql statement
prettyPrint(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Print the document URL following by its scope.identifier.revision.
PRIMARY_SHOULDER_INDEX - Static variable in class edu.ucsb.nceas.metacat.doi.DOIService
 
printCSV(File) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
print the CSV file with no sorting
printError(String, HttpServletResponse) - Method in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
Prints xml response
printExtendedSQL(String, boolean, List<Object>, List<Object>) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
This method prints sql based upon the <returnfield> tag in the pathquery document.
printGetDocByDoctypeSQL(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
 
printHashParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
 
printLogMsg(String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
print a message to the log in real-time
printOutput(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDetailLog
Prints the contents of this HarvestLog object.
printOutput(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestDocument
Print the data fields and values in this HarvestDocument object.
printOutput(PrintStream, String) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestLog
Prints the contents of this HarvestLog object.
printOutput(PrintStream) - Method in class edu.ucsb.nceas.metacat.harvesterClient.HarvestSiteSchedule
Prints the data that is stored in this HarvestSiteSchedule object.
printParams() - Method in class edu.ucsb.nceas.metacat.MetacatURL
Prints the parameters neatly to system.out
printRelationSQL(String) - Static method in class edu.ucsb.nceas.metacat.QuerySpecification
 
printSearchExprSQL(List<Object>) - Method in class edu.ucsb.nceas.metacat.QueryTerm
 
printSortedCSV(File, String) - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
print a sorted CSV file.
printSQL(boolean, List<Object>) - Method in class edu.ucsb.nceas.metacat.QueryGroup
create a SQL serialization of the query that this instance represents
printSQL(boolean, List<Object>) - Method in class edu.ucsb.nceas.metacat.QuerySpecification
create a SQL serialization of the query that this instance represents
printSQL(boolean, List<Object>) - Method in class edu.ucsb.nceas.metacat.QueryTerm
create a SQL serialization of the query that this instance represents
processingDTD() - Method in class edu.ucsb.nceas.metacat.accesscontrol.AccessControlList
Get the document processing state.
processingDTD - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
processingDTD() - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
get the document processing state
processingInstruction(String, String) - Method in class edu.ucsb.nceas.metacat.DBSAXHandler
SAX Handler called once for each processing instruction found: node that PI may occur before or after the root element.
processingInstruction(String, String) - Method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
SAX Handler called once for each processing instruction found: node that PI may occur before or after the root element.
processingInstruction(String, String) - Method in class edu.ucsb.nceas.metacat.Eml210SAXHandler
SAX Handler called once for each processing instruction found: node that PI may occur before or after the root element.
Profile() - Constructor for class edu.ucsb.nceas.metacat.MetacatProfiler.Profile
 
PropertiesAdmin - Class in edu.ucsb.nceas.metacat.admin
Control the display of the main properties configuration page and the processing of the configuration values.
PropertiesInterface - Interface in edu.ucsb.nceas.metacat.properties
This interface will handle properties access
PROPERTY_NOT_FOUND - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
 
PROPERTYNAMEOFPORTALNAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
 
PropertyService - Class in edu.ucsb.nceas.metacat.properties
A suite of utility classes for the metadata configuration utility
prov - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
prov_source - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
proxyKey - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
pub - Variable in class edu.ucsb.nceas.metacat.DBSAXHandler
 
PUBLICID - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
publish(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Given an existing Science Metadata PID, this method mints a DOI and updates the original object "publishing" the update with the DOI.
publish(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
publish(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
 
publish(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
 
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Make status of the given identifier (e.g.
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
Make the status of the identifier to be public
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.doi.ezid.EzidDOIService
Make the status of the identifier to be public
publishIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.doi.osti.OstiDOIService
Make the status of the identifier to be public
publishIdentifier(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
Make the status of the identifier public
PUT - Static variable in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
HTTP Verb PUT
PUT - Static variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
HTTP Verb PUT
putObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
putObject(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.v1.MNResourceHandler
Inserts or updates the object
putObject(String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
Earthgrid API > Put Service >Put Function : calls MetacatHandler > handleInsertOrUpdateAction
putObject(String, String) - Method in class edu.ucsb.nceas.metacat.restservice.v2.MNResourceHandler
Inserts or updates the object

Q

QUANTITY - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
query(Reader) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Query the metacat document store with the given metacat-compatible query document, and return the result set as a Reader.
query(Reader, String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Query the metacat document store with the given metacat-compatible query document and qformat, and return the result set as a Reader.
query(Reader) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Query the metacat document store with the given metacat-compatible query document and default qformat xml, and return the result set as a Reader.
query(Reader, String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Query the metacat document store with the given metacat-compatible query document and qformat, and return the result set as a Reader.
query(Reader) - Method in interface edu.ucsb.nceas.metacat.client.rest.MetacatRest
Query the metacat document store with the given metacat-compatible query document, and return the result set as a Reader.
query(Reader) - Method in class edu.ucsb.nceas.metacat.client.rest.MetacatRestClient
Query the metacat document store with the given Ecogrid-compatible query document and return the Ecogrid result set as a Reader.
query(String, String, String) - Method in class edu.ucsb.nceas.metacat.clientview.ClientViewHelper
Query metacat for documents that 'CONTAINS' the value at the specified XPath expression.
query(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
 
query(Session, String, String) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
 
query(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
query(String, String) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
query(String, Set<Subject>, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
Query the solr server
query(SolrParams, Set<Subject>, boolean) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
Use the default GET method to handle the query when the query is on the key/value format
query(SolrParams, Set<Subject>, boolean, SolrRequest.METHOD) - Method in class edu.ucsb.nceas.metacat.index.MetacatSolrIndex
Handle the query when the query is on the key/value format
query(String, Hashtable<String, String[]>, String, String[], String) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
 
queryAllDocids() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Returns a Vector of all the current versions of public docids
QueryGroup - Class in edu.ucsb.nceas.metacat
a utility class that represents a group of terms in a query
QueryGroup(String) - Constructor for class edu.ucsb.nceas.metacat.QueryGroup
construct a new QueryGroup
QueryResultTableBuilder - Class in edu.ucsb.nceas.metacat
QueryResutlTableBuilder is class to build xml_queryresult table during metacat initialization.
QuerySpecification - Class in edu.ucsb.nceas.metacat
A Class that represents a structured query, and can be constructed from an XML serialization conforming to
QuerySpecification(Reader, String, String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification
construct an instance of the QuerySpecification class
QuerySpecification(String, String, String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification
construct an instance of the QuerySpecification class
QuerySpecification(String) - Constructor for class edu.ucsb.nceas.metacat.QuerySpecification
construct an instance of the QuerySpecification class which don't need to parser a xml document
querySystemMetadata(Date, Date, ObjectFormatIdentifier, NodeReference, int, int, Identifier, boolean) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
query the systemmetadata table based on the given parameters
QueryTerm - Class in edu.ucsb.nceas.metacat
a utility class that represents a single term in a query
QueryTerm(boolean, String, String) - Constructor for class edu.ucsb.nceas.metacat.QueryTerm
Construct a new instance of a query term for a free text search (using the value only)
QueryTerm(boolean, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.QueryTerm
Construct a new instance of a query term for a structured search (matching the value only for those nodes in the pathexpr)
quickCreate(Object, String, String) - Method in class edu.ucsb.nceas.metacat.oaipmh.provider.server.catalog.MetacatRecordFactory
Allows classes that implement RecordFactory to override the default create() method.
QuotaAdmin - Class in edu.ucsb.nceas.metacat.admin
Control the display of the quota -service configuration page and the processing of the configuration values.
QuotaDBManager - Class in edu.ucsb.nceas.metacat.dataone.quota
Represents a class to manipulate the usages table for the quota service in the postgresql database
QuotaDBManager() - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
QUOTAID - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
QuotaService - Class in edu.ucsb.nceas.metacat.dataone.quota
A class represents an abstract quota service.
QuotaService() - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.QuotaService
 
QuotaServiceManager - Class in edu.ucsb.nceas.metacat.dataone.quota
A class manages the quota service for users
QUOTASUBJECT - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
QUOTASUBJECTHEADER - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaServiceManager
 
QUOTATYPE - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
QuotaTypeDeterminer - Class in edu.ucsb.nceas.metacat.dataone.quota
A class to decide the quota type (storage, portal and etc) based on the given name space
QuotaTypeDeterminer(List<String>) - Constructor for class edu.ucsb.nceas.metacat.dataone.quota.QuotaTypeDeterminer
Constructor

R

rdf - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
RDF_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
 
RDF_SYNTAX_NAMESPACE - Static variable in class edu.ucsb.nceas.metacat.DocumentImpl
 
rdfs - Static variable in class edu.ucsb.nceas.metacat.annotation.DatapackageSummarizer
 
read(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Read an XML document from the metacat server session, accessed by docid, and returned as a Reader.
read(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Read an XML document from the metacat server session, accessed by docid, and returned as a Reader.
read(String) - Static method in class edu.ucsb.nceas.metacat.MetacatHandler
Read a document from metacat and return the InputStream.
read(String, String) - Static method in class edu.ucsb.nceas.metacat.MetacatHandler
Read a document from metacat and return the InputStream.
readArchiveEntry(Hashtable<String, String[]>, HttpServletRequest, HttpServletResponse, String, String, String[]) - Method in class edu.ucsb.nceas.metacat.ArchiveHandler
 
readDoctypes() - Method in class edu.ucsb.nceas.metacat.DBUtil
read all doctypes from db connection in XML format select all Public Id from xml_catalog table
readDocumentFromRemoteServer(ServletOutputStream) - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to read both xml and data file from remote server and put the output into the given output stream
readDocumentFromRemoteServerByZip(ZipOutputStream) - Method in class edu.ucsb.nceas.metacat.RemoteDocument
Method to read both xml and data file from remote server by zip output and put the output into the given output stream
readDTDSchema(String) - Method in class edu.ucsb.nceas.metacat.DBUtil
read DTD or Schema file from Metacat's XML catalog system
readFromFileSystem(OutputStream, String, String[], String) - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Read the XML document from the file system and write to a Writer.
readFromMetacat(String, String, HttpServletResponse, OutputStream, String, String, String, String[], boolean, Hashtable<String, String[]>) - Method in class edu.ucsb.nceas.metacat.MetacatHandler
read metadata or data from Metacat
readInlineData(String) - Method in interface edu.ucsb.nceas.metacat.client.Metacat
Read inline data from the metacat server session, accessed by inlinedataid, and returned as a Reader.
readInlineData(String) - Method in class edu.ucsb.nceas.metacat.client.MetacatClient
Read inline data from the metacat server session, accessed by inlinedataid and returned as a Reader.
readInlineDataFromFileSystem(String, String) - Static method in class edu.ucsb.nceas.metacat.Eml200SAXHandler
 
ReadOnlyChecker - Class in edu.ucsb.nceas.metacat
A checker to determine if the Metacat is in the read-only mode by checking the property of database.readOnly.
ReadOnlyChecker() - Constructor for class edu.ucsb.nceas.metacat.ReadOnlyChecker
Default constructor
readUsingSlowAlgorithm() - Method in class edu.ucsb.nceas.metacat.DocumentImpl
Get a text representation of the XML document as a string This older algorithm uses a recursive tree of Objects to represent the nodes of the tree.
redirectResponse(HttpServletRequest, HttpServletResponse, String) - Static method in class edu.ucsb.nceas.metacat.util.ResponseUtil
Redirect a response.
refresh() - Static method in class edu.ucsb.nceas.metacat.dataone.NodeReplicationPolicyChecker
Refresh those properties from the metacat.peroperties file
refresh() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.database.DatabaseService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
Indicate whether or not this service is refreshable.
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.ConfigurableProperties
 
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.PropertyService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.SimpleProperties
 
refreshable() - Method in class edu.ucsb.nceas.metacat.properties.SkinPropertyService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.replication.ReplicationService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.service.SessionService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.service.XMLSchemaService
 
refreshable() - Method in class edu.ucsb.nceas.metacat.shared.BaseService
 
refreshService(String) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
Refresh a service.
refreshStatus() - Method in class edu.ucsb.nceas.metacat.doi.DOIService
Refresh the status (enable or disable) of the DOI service from property file
refreshSystemMetadataEntry(String) - Method in class edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService
When Metacat changes the underlying store, we need to refresh the in-memory representation of it.
regenerate() - Method in class edu.ucsb.nceas.metacat.spatial.SpatialHarvester
Completely regenerates the spatial cache.
REGISTER - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
REGISTERANDUPDATE - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
REGISTERANDUPDATEWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
registerDocument(String, String, String, String, String[]) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
This method will be call in handleUploadRequest in MetacatServlet class
registerDocument(String, String, String, String, String[], int) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Register a document that resides on the filesystem with the database.
registerDocumentInReplication(String, String, String, String, int, String, Date, Date) - Static method in class edu.ucsb.nceas.metacat.DocumentImpl
Register a document that resides on the filesystem with the database.
registerDOI(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.doi.DOIService
Submits DOI metadata information about the object to DOI services
registerService(String, BaseService) - Static method in class edu.ucsb.nceas.metacat.service.ServiceService
Register a service with the system.
registerSession(String, String, String[], String, String) - Method in class edu.ucsb.nceas.metacat.service.SessionService
Register a session in the session hash table.
registerSession(SessionData) - Method in class edu.ucsb.nceas.metacat.service.SessionService
Register a session in the session hash table.
registerSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Provides a mechanism for adding system metadata independently of its associated object, such as when adding system metadata for data objects.
registerSystemMetadata(Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
registerSystemMetadata(Session, Identifier, SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
registerSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.v1.CNResourceHandler
Register System Metadata without data or metadata object
registerSystemMetadata() - Method in class edu.ucsb.nceas.metacat.restservice.v2.CNResourceHandler
Register System Metadata without data or metadata object
REGISTERWITHWARN - Static variable in class edu.ucsb.nceas.metacat.admin.SolrAdmin
 
RelationHandler - Class in edu.ucsb.nceas.metacat
 
RelationHandler(String, String, DBConnection, TripleCollection) - Constructor for class edu.ucsb.nceas.metacat.RelationHandler
Constructor for this class.
release() - Static method in class edu.ucsb.nceas.metacat.database.DBConnectionPool
Method to shut down all connections
RemoteDocument - Class in edu.ucsb.nceas.metacat
A class represents a document in remote metacat server.
RemoteDocument(String, String, String, String, String) - Constructor for class edu.ucsb.nceas.metacat.RemoteDocument
Constructor of RemoteDcoument
remove(Identifier) - Method in class edu.ucsb.nceas.metacat.index.IndexEventDAO
 
remove(String, String) - Method in class edu.ucsb.nceas.metacat.IndexingQueue
Removes the Indexing Task object from the queue for the given docid.
removeDocument(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
removeField(String) - Method in class edu.ucsb.nceas.metacat.cart.DocumentCart
 
removeIdFromIdentifierTable(Identifier) - Static method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
removeIdSchemePrefix(String, String) - Method in class edu.ucsb.nceas.metacat.doi.datacite.DataCiteMetadataFactory
Remove the sheme prefix for a given id.
RemoveInvalidReplicas - Class in edu.ucsb.nceas.metacat.admin.upgrade
Used for forcibly removing invalid replicas from a target node.
RemoveInvalidReplicas() - Constructor for class edu.ucsb.nceas.metacat.admin.upgrade.RemoveInvalidReplicas
 
removeMapping(String, String) - Method in class edu.ucsb.nceas.metacat.IdentifierManager
remove a mapping in the identifier table
removeMetacatEventObserver(MetacatEventObserver) - Method in class edu.ucsb.nceas.metacat.event.MetacatEventService
 
removeSolrIndex(SystemMetadata) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
removeSystemMetaAndIdentifier(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.D1NodeService
 
removeUserFromGroup(String, String) - Method in class edu.ucsb.nceas.metacat.authentication.AuthFile
Remove a user from a group.
removeXMLAccessForPrincipal(String, String, Long) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Remove xml access.
REPLACE_MESSAGE - Static variable in class edu.ucsb.nceas.metacat.clientview.ClientView
 
replaceAccess(String, List<XMLAccessDAO>) - Method in class edu.ucsb.nceas.metacat.accesscontrol.XMLAccessAccess
Set permissions for a given document.
replaceObsoletedId(Identifier, Identifier, OutputStream, Subject) - Method in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
Create new resource map by replacing obsoleted ids by new ids.
replaceWhiteSpaceForURL(String) - Static method in class edu.ucsb.nceas.metacat.util.MetacatUtil
A method to replace whitespace in url
replicate(Session, SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.MNodeService
Called by a Coordinating Node to request that the Member Node create a copy of the specified object by retrieving it from another Member Node and storing it locally so that it can be made accessible to the DataONE system.
replicate(SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
 
replicate(Session, SystemMetadata, NodeReference) - Method in class edu.ucsb.nceas.metacat.dataone.v1.MNodeService
Deprecated.
REPLICATION_LOG_FILE_NAME - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
 
ReplicationAdmin - Class in edu.ucsb.nceas.metacat.admin
Control the display of the database configuration page and the processing of the configuration values.
ReplicationHandler - Class in edu.ucsb.nceas.metacat.replication
This class handles deltaT replication checking.
ReplicationHandler() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationHandler
 
ReplicationHandler(int) - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationHandler
 
ReplicationServer - Class in edu.ucsb.nceas.metacat.replication
A class express a entry in xml_replication.
ReplicationServer() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationServer
Constructor of ReplicationServer
ReplicationServerList - Class in edu.ucsb.nceas.metacat.replication
A class represent a replication server list in xml_replcation table
ReplicationServerList() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationServerList
constructor of ReplicationServerList It will build server list.
ReplicationService - Class in edu.ucsb.nceas.metacat.replication
 
ReplicationServlet - Class in edu.ucsb.nceas.metacat.replication
 
ReplicationServlet() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplicationServlet
 
REPLICATIONUSER - Static variable in class edu.ucsb.nceas.metacat.replication.ReplicationService
 
ReplicationUtil - Class in edu.ucsb.nceas.metacat.util
A suite of utility classes for the system metadata replication functions
ReplicationUtil() - Constructor for class edu.ucsb.nceas.metacat.util.ReplicationUtil
 
ReplMessageHandler - Class in edu.ucsb.nceas.metacat.replication
A Class implementing callback bethods for the SAX parser to call when processing the XML messages from the replication handler
ReplMessageHandler() - Constructor for class edu.ucsb.nceas.metacat.replication.ReplMessageHandler
 
replToServer(String) - Static method in class edu.ucsb.nceas.metacat.replication.ReplicationService
Returns true if the replicate field for server in xml_replication is 1.
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.CreateUsageTask
 
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.DeleteUsageTask
 
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.UpdateUsageTask
 
reportToBookKeeper() - Method in class edu.ucsb.nceas.metacat.dataone.quota.UsageTask
The child class needs to implement this method to detail how to report the usage to the remote book keeper server.
request - Variable in class edu.ucsb.nceas.metacat.dataone.D1NodeService
For logging the operations
request - Variable in class edu.ucsb.nceas.metacat.restservice.D1ResourceHandler
 
REQUESTOR - Static variable in class edu.ucsb.nceas.metacat.dataone.quota.QuotaDBManager
 
RequestUtil - Class in edu.ucsb.nceas.metacat.util
 
RESCHEDULE_WORKFLOW_ERROR - Static variable in class edu.ucsb.nceas.metacat.util.ResponseUtil
 
reserveIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Given an optional scope and format, reserves and returns an identifier within that scope and format that is unique and will not be used by any other sessions.
reserveIdentifier(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
reserveIdentifier(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
reset() - Method in class edu.ucsb.nceas.metacat.MetacatProfiler
reset all times in the singleton
resolve(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.CNodeService
Resolve the location of a given object
RESOLVE - Static variable in class edu.ucsb.nceas.metacat.dataone.resourcemap.ResourceMapModifier
 
resolve(Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
 
resolve(Session, Identifier) - Method in class edu.ucsb.nceas.metacat.dataone.v1.CNodeService
Deprecated.
resolveEntity(String, String) - Method in class edu.ucsb.nceas.metacat.DBEntityResolver
The Parser call this method before opening any external entity except the top-level document entity (including the external DTD subset, external entities referenced within the DTD, and external entities referenced within the document element)