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A

ACCESS_TABLE - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
AccessRuleMapper() - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.AccessRuleMapper
 
addCountry(DirContext, String) - Method in class org.dataone.cn.ldap.LDAPService
Adds the country branch of the given DN to the Context.
addDc(DirContext, String) - Method in class org.dataone.cn.ldap.LDAPService
Adds the DC branch of the given DN to the Context.
addOrg(DirContext, String) - Method in class org.dataone.cn.ldap.LDAPService
Adds the organization branch of the given DN to the Context.
addOrgUnit(DirContext, String) - Method in class org.dataone.cn.ldap.LDAPService
Adds the organization unit of the given DN to the Context.
admin - Variable in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
AuditEvent - Enum in org.dataone.cn.log
Audit Log Event enumeration.
AuditLogClient - Interface in org.dataone.cn.log
 
AuditLogClientFactory - Class in org.dataone.cn.log
Factory pattern class to hide implementation of AuditLogClient.
AuditLogClientSolrImpl - Class in org.dataone.cn.log
AuditLogClient implementation using a solr index as the backing datastore.
AuditLogClientSolrImpl() - Constructor for class org.dataone.cn.log.AuditLogClientSolrImpl
 
AuditLogClientSplunkImpl - Class in org.dataone.cn.log
 
AuditLogClientSplunkImpl() - Constructor for class org.dataone.cn.log.AuditLogClientSplunkImpl
 
AuditLogEntry - Class in org.dataone.cn.log
AuditLogEntry model class.
AuditLogEntry() - Constructor for class org.dataone.cn.log.AuditLogEntry
 
AuditLogEntry(String, String, AuditEvent, Date, String) - Constructor for class org.dataone.cn.log.AuditLogEntry
 
AuditLogEntry(String, String, AuditEvent, String) - Constructor for class org.dataone.cn.log.AuditLogEntry
 
AuditLogQueryClient - Interface in org.dataone.cn.log
 
AuditLogQueryClientNullObjectImpl - Class in org.dataone.cn.log
 
AuditLogQueryClientNullObjectImpl() - Constructor for class org.dataone.cn.log.AuditLogQueryClientNullObjectImpl
 
AuditLogWriteClient - Interface in org.dataone.cn.log
Audit log writing client interface.
AuditLogWriteClientSplunkImpl - Class in org.dataone.cn.log
 
AuditLogWriteClientSplunkImpl() - Constructor for class org.dataone.cn.log.AuditLogWriteClientSplunkImpl
 
AUTHORIZED_SUBJECTS - Static variable in class org.dataone.cn.servlet.http.ParameterKeys
 

B

BaseHazelcastMembershipListener - Class in org.dataone.cn.hazelcast.membership
 
BaseHazelcastMembershipListener(HazelcastInstance) - Constructor for class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
Used for testing only when a configuration location is not available.
BaseHazelcastMembershipListener(HazelcastInstance, String) - Constructor for class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
borrowDirContext() - Method in class org.dataone.cn.ldap.DirContextProvider
 
BufferedServletOutputStream - Class in org.dataone.cn.servlet.http
A custom servlet output stream that stores its data in a buffer, rather than sending it directly to the client.
BufferedServletOutputStream() - Constructor for class org.dataone.cn.servlet.http.BufferedServletOutputStream
 
BufferedServletResponseWrapper - Class in org.dataone.cn.servlet.http
A custom response wrapper that captures all output in a buffer.
BufferedServletResponseWrapper(HttpServletResponse) - Constructor for class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 

C

checkAttribute(DirContext, String, String, String) - Method in class org.dataone.cn.ldap.LDAPService
check the attribute for a given subject
ClientConfiguration - Class in org.dataone.cn.hazelcast
Read in a hazelcast configuration file and return settings such that a client will only connect to the localhost Default is to read the storage cluster from /etc/dataone/storage/hazelcast.xml But it can be overridden for testing purposes.
ClientConfiguration() - Constructor for class org.dataone.cn.hazelcast.ClientConfiguration
 
ClientConfiguration(String) - Constructor for class org.dataone.cn.hazelcast.ClientConfiguration
 
ClientConfiguration(Config) - Constructor for class org.dataone.cn.hazelcast.ClientConfiguration
 
closeContext() - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
clusterIsPartitioned() - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
ClusterPartitionMembershipListener - Class in org.dataone.cn.hazelcast.membership
 
ClusterPartitionMembershipListener(HazelcastInstance, String, String) - Constructor for class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
ClusterPartitionMembershipListener(HazelcastInstance, String) - Constructor for class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
ClusterPartitionMonitor - Class in org.dataone.cn.hazelcast.membership
 
ComponentActivationUtility - Class in org.dataone.cn
Class to capture common component activation logic.
configAddresses - Variable in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
constructTree(DirContext, String) - Method in class org.dataone.cn.ldap.LDAPService
Constructs the necessary LDAP tree for the given DN Assuming CILogon format: "CN=Benjamin Leinfelder A515,O=University of Chicago,C=US,DC=cilogon,DC=org" or LDAP format: "uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org"
context - Variable in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
convertPermission(Permission) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Convert string-based permission values to Metacat integer-based values
create() - Method in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 

D

D1BaseJpaRepositoryConfiguration - Class in org.dataone.cn.model.repository
These annotation need to be present where a concrete persistent model/repository is defined.
D1BaseJpaRepositoryConfiguration() - Constructor for class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
DaoFactory - Class in org.dataone.cn.dao
Factory class to provide consumers handle on data access object (dao pattern) instances.
DataAccessException - Exception in org.dataone.cn.dao.exceptions
A DataONE Data Access Exception.
DataAccessException(Throwable) - Constructor for exception org.dataone.cn.dao.exceptions.DataAccessException
Create new instance of a DataONE DataAccessException to wrap Throwable cause.
dataSource() - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
dataSource() - Method in class org.dataone.cn.model.repository.H2RepositoryConfiguration
 
dataSource() - Method in class org.dataone.cn.model.repository.PostgresRepositoryConfiguration
 
destroyObject(PooledObject<DirContext>) - Method in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
DirContextPooledObjectFactory - Class in org.dataone.cn.ldap
Wraps a DirContext as a PooledObject in order to be managed By Apache's GenericObjectPool or DirContextObjectPool.
DirContextPooledObjectFactory() - Constructor for class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
DirContextProvider - Class in org.dataone.cn.ldap
Initialize a pool to manage LDAP Contexts.
disableSynchronization() - Static method in class org.dataone.cn.ComponentActivationUtility
 
documentIdCounter - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 

E

entityManagerFactory(DataSource, JpaVendorAdapter) - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
equals(Object) - Method in class org.dataone.cn.synchronization.types.SyncObject
the taskLabel property is derived from the nodeID and pid, so can be the sole property used for equals()
ExecutionDisabledException - Exception in org.dataone.cn.batch.exceptions
A DataONE Job or Task Exception.
ExecutionDisabledException(Throwable) - Constructor for exception org.dataone.cn.batch.exceptions.ExecutionDisabledException
Create new instance of a DataONE ExecutionDisabledException to wrap Throwable cause.
ExecutionDisabledException(String) - Constructor for exception org.dataone.cn.batch.exceptions.ExecutionDisabledException
Create new instance of a DataONE ExecutionDisabledException with message
ExecutionDisabledException() - Constructor for exception org.dataone.cn.batch.exceptions.ExecutionDisabledException
Create new instance of a DataONE ExecutionDisabledException
expectedClusterSize - Variable in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
extractSystemMetadataAttrs(SystemMetadata, String) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Returns a map of attribute names and values to be used in the statement to update the given systemmetadata table

F

flushBuffer() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 

G

generate_ddl - Static variable in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
getAttempt() - Method in class org.dataone.cn.synchronization.types.SyncObject
The number of times this object has been attempted to be synchronized (after a lock has been gained)
getAttributeValues(DirContext, String, String) - Method in class org.dataone.cn.ldap.LDAPService
 
getAuditLogClient() - Static method in class org.dataone.cn.log.AuditLogClientFactory
 
getBase() - Method in class org.dataone.cn.ldap.LDAPService
 
getBuffer() - Method in class org.dataone.cn.servlet.http.BufferedServletOutputStream
 
getBuffer() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
getBufferSize() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
getClusterName() - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
getCompletedCoordinatingNodeReplicasByDate(Date, int, int) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns paged list of distinct DataONE Identifier objects with at least one coordinating node replica with a replica verified date previous to the auditDate parameter.
getCompletedCoordinatingNodeReplicasByDate(Date, int, int) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getCompletedMemberNodeReplicasByDate(Date, int, int) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns paged list of distinct DataONE Identifier objects with at least one member node replica with a replica verified date previous to the auditDate parameter.
getCompletedMemberNodeReplicasByDate(Date, int, int) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getContentType() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
getContextPath() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getCountsByNodeStatus() - Method in interface org.dataone.cn.dao.ReplicationDao
Return a map of member node status to count entries for tracking node replica status statistics.
getCountsByNodeStatus() - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
Get a map of replica counts by node-status in order to support instrumentation of system wide MN to MN replication functionality.
getD1Exception() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
getDateLogged() - Method in class org.dataone.cn.log.AuditLogEntry
 
getDateLogged() - Method in class org.dataone.cn.log.MetricLogEntry
 
getDeleted() - Method in class org.dataone.cn.dao.SystemMetadataStatus
Get the deleted status of the identifier
getEnumerationValueString(NamingEnumeration) - Method in class org.dataone.cn.ldap.LDAPService
return the next value of a NamingEnumeration, or empty String if there are not any more.
getEvent() - Method in class org.dataone.cn.log.AuditLogEntry
 
getEvent() - Method in class org.dataone.cn.log.MetricLogEntry
 
getExpectedClusterSize() - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
getGroup() - Method in class org.dataone.cn.hazelcast.ClientConfiguration
 
getHazelcastClient() - Static method in class org.dataone.cn.hazelcast.HazelcastClientInstance
 
getId() - Method in class org.dataone.cn.log.AuditLogEntry
 
getInstance() - Static method in class org.dataone.cn.ldap.DirContextProvider
 
getInvalidMemberNodeReplicasByDate(Date, int, int) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns a paged list of distinct DataONE Identifier objects with at least one invalid member node replica with a replica verified date previous to the auditDate parameter.
getInvalidMemberNodeReplicasByDate(Date, int, int) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getLastSystemMetadataModificationDate() - Method in class org.dataone.cn.dao.SystemMetadataStatus
Get the last modification date of the system metadata for the identifier
getLocalhost() - Method in class org.dataone.cn.hazelcast.ClientConfiguration
 
getLockAttempt() - Method in class org.dataone.cn.synchronization.types.SyncObject
The number of times this object has been attempted to be locked for synchronization.
getLogText() - Method in class org.dataone.cn.log.AuditLogEntry
 
getMemberNode() - Method in class org.dataone.cn.dao.ReplicationPolicyEntry
Get the member node id associated with the policy entry
getMemberNodesWithQueuedReplica() - Method in interface org.dataone.cn.dao.ReplicationDao
Returns a Collection of NodeReference objects which have at least one queued replica object's targeted toward the node.
getMemberNodesWithQueuedReplica() - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getMembershipCount() - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
getMessage() - Method in class org.dataone.cn.log.MetricLogEntry
 
getMetacatDataSource() - Static method in class org.dataone.cn.dao.MetacatDataSourceFactory
Returns the data source instance for the metacat datasource.
getMethod() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getMetricLogClient() - Static method in class org.dataone.cn.log.MetricLogClientFactory
 
getNodeId() - Method in class org.dataone.cn.log.AuditLogEntry
 
getNodeId() - Method in class org.dataone.cn.log.MetricLogEntry
 
getNodeId() - Method in class org.dataone.cn.synchronization.types.SyncObject
 
getNodeMap() - Static method in class org.dataone.cn.hazelcast.HazelcastClientFactory
 
getNumDirContextActive() - Method in class org.dataone.cn.ldap.DirContextProvider
 
getNumDirContextIdle() - Method in class org.dataone.cn.ldap.DirContextProvider
 
getObjectPathMap() - Static method in class org.dataone.cn.hazelcast.HazelcastClientFactory
 
getOutputStream() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
getPackagesToScan() - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
getParameter(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getParameterMap() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getParameterNames() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getParameterValues(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getPassword() - Method in class org.dataone.cn.hazelcast.ClientConfiguration
 
getPathInfo() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getPathTranslated() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getPendingReplicasByNode() - Method in interface org.dataone.cn.dao.ReplicationDao
Return a map of member node to replica count entries where the replica status is either queued or requested
getPendingReplicasByNode() - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
Retrieve the count of pending replica requests per target node listed in the Coordinating Node's smreplicationstatus table.
getPid() - Method in class org.dataone.cn.dao.ReplicationPolicyEntry
Get the identifier associated with the replication policy entry
getPid() - Method in class org.dataone.cn.dao.SystemMetadataStatus
Get the identifier of the object
getPid() - Method in class org.dataone.cn.log.AuditLogEntry
 
getPid() - Method in class org.dataone.cn.log.MetricLogEntry
 
getPid() - Method in class org.dataone.cn.synchronization.types.SyncObject
 
getPolicy() - Method in class org.dataone.cn.dao.ReplicationPolicyEntry
Get the policy entry type (preferred or blocked) for the given entry
getPort() - Method in class org.dataone.cn.hazelcast.ClientConfiguration
 
getProcessingClient() - Static method in class org.dataone.cn.hazelcast.HazelcastClientFactory
Gets a processing client.
getProcessingConfigLocation() - Static method in class org.dataone.cn.hazelcast.HazelcastConfigLocationFactory
 
getProcessingInstance() - Static method in class org.dataone.cn.hazelcast.HazelcastInstanceFactory
Returns the existing instance of the dataone processing member.
getProcessingPartition() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
getQueryString() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getQueuedReplicaCountByNode(String) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns the count of replicas in the 'queued' status that are targeted toward nodeId node.
getQueuedReplicaCountByNode(String) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getQueuedReplicasByNode(String) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns a Collection of ReplicaDto objects that represent a replica object in 'queued' status and targeted at mnId node.
getQueuedReplicasByNode(String) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getRecentCompletedReplicas() - Method in interface org.dataone.cn.dao.ReplicationDao
Return a map of member node to replica count entries where the replica status is completed and the date_verified is within a given timeframe
getRecentCompletedReplicas() - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
Retrieve the count of recently completed replica requests per target node listed in the Coordinating Node's systemetadatareplicationstatus table.
getRecentFailedReplicas() - Method in interface org.dataone.cn.dao.ReplicationDao
Return a map of member node to replica count entries where the replica status is failed and the date_verified is within a given timeframe
getRecentFailedReplicas() - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
Retrieve the count of recently failed replica requests per target node listed in the Coordinating Node's systemetadatareplicationstatus table.
getReplicationDao() - Static method in class org.dataone.cn.dao.DaoFactory
Returns a concrete instance of the ReplicationDao interface.
getRequestedReplicasByDate(Date) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns a List of ReplicaDto objects, which represent replica objects that are in 'Requested' status and have a verified date before cuttoffDate.
getRequestedReplicasByDate(Date) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getRequestedReplicationCount(NodeReference) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns the count of replica objects in 'requested' status and targeted to nodeReference node.
getRequestedReplicationCount(NodeReference) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
getRequestURI() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getSerialVersion() - Method in class org.dataone.cn.dao.SystemMetadataStatus
Get the serial version of the object
getServletPath() - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
getSessionClient() - Static method in class org.dataone.cn.hazelcast.HazelcastClientFactory
Gets a session client using the configuration.
getSessionConfigLocation() - Static method in class org.dataone.cn.hazelcast.HazelcastConfigLocationFactory
 
getSessionPartition() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
getSleepUntil() - Method in class org.dataone.cn.synchronization.types.SyncObject
 
getStatus() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
getStorageClient() - Static method in class org.dataone.cn.hazelcast.HazelcastClientFactory
 
getStorageConfigLocation() - Static method in class org.dataone.cn.hazelcast.HazelcastConfigLocationFactory
 
getStoragePartion() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
getSysMetaAttrTypes() - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Returns the attribute types for the systemmetadata table as an int array
getSysMetaAttrValues(Map<String, Object>) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Returns the values from the given map as an Object array
getSysMetaUpdateStatement(String) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Builds a SQL update statement for use against the systemmetadata table
getSystemMetadata(Identifier) - Method in interface org.dataone.cn.dao.SystemMetadataDao
Get a systemMetadata object for a given Identifier, using the given JdbcTemplate and map of system metadata table names.
getSystemMetadata(Identifier) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
getSystemMetadata(Identifier, Map<String, String>) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
getSystemMetadataCount() - Method in interface org.dataone.cn.dao.SystemMetadataDao
Get the total count of the system metadata records in the database
getSystemMetadataCount() - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
getSystemMetadataCount(Map<String, String>) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
getSystemMetadataDao() - Static method in class org.dataone.cn.dao.DaoFactory
Returns a concrete instance of the SystemMetadataDao interface.
getSystemMetadataMap() - Static method in class org.dataone.cn.hazelcast.HazelcastClientFactory
 
getTimeToCompleteEventMS() - Method in class org.dataone.cn.log.MetricLogEntry
 
getWriter() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 

H

H2RepositoryConfiguration - Class in org.dataone.cn.model.repository
 
H2RepositoryConfiguration() - Constructor for class org.dataone.cn.model.repository.H2RepositoryConfiguration
 
handleMemberAddedEvent(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
handleMemberAddedEvent(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
handleMemberRemovedEvent(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
handleMemberRemovedEvent(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
hashCode() - Method in class org.dataone.cn.synchronization.types.SyncObject
the taskLabel property is derived from the nodeID and pid, so can be the sole property used for generating the hashCode()
HazelcastClientFactory - Class in org.dataone.cn.hazelcast
Encapsulation layer for the various hazelcast cluster configurations and associated client instances.
HazelcastClientInstance - Class in org.dataone.cn.hazelcast
Create a Settings property to point the hazelcast client instance to a configuration file.
HazelcastClientInstance() - Constructor for class org.dataone.cn.hazelcast.HazelcastClientInstance
 
HazelcastConfigLocationFactory - Class in org.dataone.cn.hazelcast
 
HazelcastConfigLocationFactory() - Constructor for class org.dataone.cn.hazelcast.HazelcastConfigLocationFactory
 
HazelcastInstanceFactory - Class in org.dataone.cn.hazelcast
Encapsulation of retrieving existing hazelcast instance objects.
hzInstance - Variable in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 

I

identifier - Variable in class org.dataone.cn.dao.ReplicationDao.ReplicaDto
 
IDENTIFIER_TABLE - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
initContext() - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
IS_CN_ADMINISTRATOR - Static variable in class org.dataone.cn.servlet.http.ParameterKeys
 
IS_MN_ADMINISTRATOR - Static variable in class org.dataone.cn.servlet.http.ParameterKeys
 
isException() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 

J

jpaVendorAdapter() - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
jpaVendorAdapter() - Method in class org.dataone.cn.model.repository.H2RepositoryConfiguration
 
jpaVendorAdapter() - Method in class org.dataone.cn.model.repository.PostgresRepositoryConfiguration
 

L

LDAPService - Class in org.dataone.cn.ldap
Base LDAP class for shared LDAP operations.
LDAPService() - Constructor for class org.dataone.cn.ldap.LDAPService
 
listening - Variable in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
listSystemMetadataStatus(int, int) - Method in interface org.dataone.cn.dao.SystemMetadataDao
List object status information with SystemMetadata in the database
listSystemMetadataStatus(int, int) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
listSystemMetadataStatus(int, int, Map<String, String>) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
log - Static variable in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
log - Static variable in class org.dataone.cn.ldap.DirContextProvider
 
log - Static variable in class org.dataone.cn.ldap.LDAPService
 
logAuditEvent(AuditLogEntry) - Method in class org.dataone.cn.log.AuditLogClientSolrImpl
 
logAuditEvent(AuditLogEntry) - Method in class org.dataone.cn.log.AuditLogClientSplunkImpl
 
logAuditEvent(AuditLogEntry) - Method in interface org.dataone.cn.log.AuditLogWriteClient
Add a new log entry to the audit log.
logAuditEvent(AuditLogEntry) - Method in class org.dataone.cn.log.AuditLogWriteClientSplunkImpl
 
logEvent(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
logger - Static variable in class org.dataone.cn.hazelcast.HazelcastClientFactory
 
logger - Static variable in class org.dataone.cn.hazelcast.HazelcastClientInstance
 
logger - Static variable in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
logMetricEvent(MetricLogEntry) - Method in interface org.dataone.cn.log.MetricLogClient
 
logMetricEvent(MetricLogEntry) - Method in class org.dataone.cn.log.MetricLogClientLog4JImpl
 

M

main(String[]) - Static method in class org.dataone.cn.log.AuditLogClientSolrImpl
 
mapRow(ResultSet, int) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.AccessRuleMapper
 
mapRow(ResultSet, int) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.ReplicaEntryMapper
Map each row into a ReplicaEntry object
mapRow(ResultSet, int) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.ReplicationPolicyEntryMapper
Map each row into a ReplicationPolicyEntry object
mapRow(ResultSet, int) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.SystemMetadataMapper
Map each row into a SystemMetadata object
mapRow(ResultSet, int) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.SystemMetadataStatusMapper
Map each row into a SystemMetadataStatus object
memberAdded(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
memberRemoved(MembershipEvent) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
MetacatDataSourceFactory - Class in org.dataone.cn.dao
Factory class to provide consumers obtaining a handle on a metacat db schema BasicDataSource instances.
MetricEvent - Enum in org.dataone.cn.log
Metric Event enumeration.
MetricLogClient - Interface in org.dataone.cn.log
Provides a uniform manner to report MetricEvents through a MetricLogEntry
MetricLogClientFactory - Class in org.dataone.cn.log
Factory pattern class to hide implementation of MetricLogClient.
MetricLogClientLog4JImpl - Class in org.dataone.cn.log
 
MetricLogClientLog4JImpl() - Constructor for class org.dataone.cn.log.MetricLogClientLog4JImpl
 
MetricLogEntry - Class in org.dataone.cn.log
Represents an metric log entry message.
MetricLogEntry(MetricEvent) - Constructor for class org.dataone.cn.log.MetricLogEntry
 
MetricLogEntry(MetricEvent, NodeReference) - Constructor for class org.dataone.cn.log.MetricLogEntry
 
MetricLogEntry(MetricEvent, NodeReference, Identifier) - Constructor for class org.dataone.cn.log.MetricLogEntry
 
MetricLogEntry(MetricEvent, NodeReference, Identifier, String) - Constructor for class org.dataone.cn.log.MetricLogEntry
 
MetricLogEntry(MetricEvent, NodeReference, Identifier, String, Long) - Constructor for class org.dataone.cn.log.MetricLogEntry
 
MetricLogEntry(MetricEvent, String, NodeReference, Identifier, Long, Date) - Constructor for class org.dataone.cn.log.MetricLogEntry
 

O

org.dataone.cn - package org.dataone.cn
 
org.dataone.cn.batch.exceptions - package org.dataone.cn.batch.exceptions
 
org.dataone.cn.dao - package org.dataone.cn.dao
 
org.dataone.cn.dao.exceptions - package org.dataone.cn.dao.exceptions
 
org.dataone.cn.hazelcast - package org.dataone.cn.hazelcast
 
org.dataone.cn.hazelcast.membership - package org.dataone.cn.hazelcast.membership
 
org.dataone.cn.ldap - package org.dataone.cn.ldap
 
org.dataone.cn.log - package org.dataone.cn.log
 
org.dataone.cn.model.repository - package org.dataone.cn.model.repository
 
org.dataone.cn.servlet.http - package org.dataone.cn.servlet.http
 
org.dataone.cn.synchronization.types - package org.dataone.cn.synchronization.types
 

P

ParameterKeys - Class in org.dataone.cn.servlet.http
This is Constants class Two parameter keys that will be used by the solr extension classes for authorization
ParameterKeys() - Constructor for class org.dataone.cn.servlet.http.ParameterKeys
 
parseAttribute(String, String) - Method in class org.dataone.cn.ldap.LDAPService
 
password - Variable in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
PostgresRepositoryConfiguration - Class in org.dataone.cn.model.repository
 
PostgresRepositoryConfiguration() - Constructor for class org.dataone.cn.model.repository.PostgresRepositoryConfiguration
 
PROCESSING - Static variable in class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
proxyParameterMap - Variable in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
ProxyServletRequestWrapper - Class in org.dataone.cn.servlet.http
 
ProxyServletRequestWrapper(HttpServletRequest) - Constructor for class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 

Q

queryLog(String, Integer, Integer) - Method in class org.dataone.cn.log.AuditLogClientSolrImpl
 
queryLog(AuditLogEntry, Integer, Integer) - Method in class org.dataone.cn.log.AuditLogClientSolrImpl
 
queryLog(String, Integer, Integer) - Method in class org.dataone.cn.log.AuditLogClientSplunkImpl
 
queryLog(AuditLogEntry, Integer, Integer) - Method in class org.dataone.cn.log.AuditLogClientSplunkImpl
 
queryLog(String, Integer, Integer) - Method in interface org.dataone.cn.log.AuditLogQueryClient
Query the audit log datastore by query string.
queryLog(AuditLogEntry, Integer, Integer) - Method in interface org.dataone.cn.log.AuditLogQueryClient
Query the audit log datastore by AuditLogEntry instance.
queryLog(String, Integer, Integer) - Method in class org.dataone.cn.log.AuditLogQueryClientNullObjectImpl
 
queryLog(AuditLogEntry, Integer, Integer) - Method in class org.dataone.cn.log.AuditLogQueryClientNullObjectImpl
 
queuedReplicaExists(String, String) - Method in interface org.dataone.cn.dao.ReplicationDao
Returns true if there is a replica object with 'queued' status for identifier targeted at nodeId.
queuedReplicaExists(String, String) - Method in class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 

R

removeEntry(DirContext, String) - Method in class org.dataone.cn.ldap.LDAPService
 
removeReplicaAuditEvent(AuditLogEntry) - Method in class org.dataone.cn.log.AuditLogClientSolrImpl
 
removeReplicaAuditEvent(AuditLogEntry) - Method in class org.dataone.cn.log.AuditLogClientSplunkImpl
 
removeReplicaAuditEvent(AuditLogEntry) - Method in interface org.dataone.cn.log.AuditLogWriteClient
Removes audit log entries based on the pid, nodeId, event type contained in AuditLogEntry parameter logEntry.
removeReplicaAuditEvent(AuditLogEntry) - Method in class org.dataone.cn.log.AuditLogWriteClientSplunkImpl
 
replica - Variable in class org.dataone.cn.dao.ReplicationDao.ReplicaDto
 
ReplicaDto() - Constructor for class org.dataone.cn.dao.ReplicationDao.ReplicaDto
 
ReplicaEntryMapper() - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.ReplicaEntryMapper
 
replicationCNAuditorIsActive() - Static method in class org.dataone.cn.ComponentActivationUtility
 
ReplicationDao - Interface in org.dataone.cn.dao
Abstract definition of a replication data access object used to identify replicas that need to be audited and replicas that are pending/queued.
ReplicationDao.ReplicaDto - Class in org.dataone.cn.dao
Data transfer object for replica queries.
ReplicationDaoMetacatImpl - Class in org.dataone.cn.dao
ReplicationDao implementation based on the metacat products database schema.
ReplicationDaoMetacatImpl() - Constructor for class org.dataone.cn.dao.ReplicationDaoMetacatImpl
 
replicationIsActive() - Static method in class org.dataone.cn.ComponentActivationUtility
 
replicationMNAuditorIsActive() - Static method in class org.dataone.cn.ComponentActivationUtility
 
ReplicationPolicyEntry - Class in org.dataone.cn.dao
A data transfer object the represents a replication policy record, used to transfer the preferred and blocked lists found in a policy in the database.
ReplicationPolicyEntry() - Constructor for class org.dataone.cn.dao.ReplicationPolicyEntry
Constructor.
ReplicationPolicyEntryMapper() - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.ReplicationPolicyEntryMapper
 
reset() - Method in class org.dataone.cn.servlet.http.BufferedServletOutputStream
 
reset() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
resetBuffer() - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
returnDirContext(DirContext) - Method in class org.dataone.cn.ldap.DirContextProvider
 

S

saveSystemMetadata(SystemMetadata, Map<String, String>) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Saves the given system metadata to the tables indicated in the tableMap
server - Variable in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
SESSION - Static variable in class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
setAttempt(Integer) - Method in class org.dataone.cn.synchronization.types.SyncObject
 
setBase(String) - Method in class org.dataone.cn.ldap.LDAPService
 
setBufferSize(int) - Method in class org.dataone.cn.servlet.http.BufferedServletOutputStream
 
setBufferSize(int) - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
setContentType(String) - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
setContextPath(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setD1Exception(BaseException) - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
setDateLogged(Date) - Method in class org.dataone.cn.log.AuditLogEntry
 
setDateLogged(Date) - Method in class org.dataone.cn.log.MetricLogEntry
 
setDeleted(Boolean) - Method in class org.dataone.cn.dao.SystemMetadataStatus
Set the deleted status of the identifier
setEvent(AuditEvent) - Method in class org.dataone.cn.log.AuditLogEntry
 
setEvent(MetricEvent) - Method in class org.dataone.cn.log.MetricLogEntry
 
setExpectedClusterSize(int) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
setExpectedIPList(String) - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
setId(String) - Method in class org.dataone.cn.log.AuditLogEntry
 
setLastSystemMetadataModificationDate(Date) - Method in class org.dataone.cn.dao.SystemMetadataStatus
Set the last modification date of the system metadata for the identifier
setLockAttempt(Integer) - Method in class org.dataone.cn.synchronization.types.SyncObject
 
setLogText(String) - Method in class org.dataone.cn.log.AuditLogEntry
 
setMemberNode(NodeReference) - Method in class org.dataone.cn.dao.ReplicationPolicyEntry
Set the member node id associated with the policy entry
setMessage(String) - Method in class org.dataone.cn.log.MetricLogEntry
 
setMethod(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setNodeId(String) - Method in class org.dataone.cn.log.AuditLogEntry
 
setNodeId(NodeReference) - Method in class org.dataone.cn.log.MetricLogEntry
 
setParameterValues(String, String[]) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setPathInfo(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setPathTranslated(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setPid(Identifier) - Method in class org.dataone.cn.dao.ReplicationPolicyEntry
Set the identifier associated with the replication policy entry
setPid(Identifier) - Method in class org.dataone.cn.dao.SystemMetadataStatus
Set the identifier of the object
setPid(String) - Method in class org.dataone.cn.log.AuditLogEntry
 
setPid(Identifier) - Method in class org.dataone.cn.log.MetricLogEntry
 
setPolicy(String) - Method in class org.dataone.cn.dao.ReplicationPolicyEntry
Set the policy entry type (preferred or blocked) for the given entry
setProcessingPartition(boolean) - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
setQueryString(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setRequestURI(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setSerialVersion(BigInteger) - Method in class org.dataone.cn.dao.SystemMetadataStatus
Set the serial version of the identifier
setServletPath(String) - Method in class org.dataone.cn.servlet.http.ProxyServletRequestWrapper
 
setSessionPartition(boolean) - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
setSleepUntil(long) - Method in class org.dataone.cn.synchronization.types.SyncObject
 
setStatus(int) - Method in class org.dataone.cn.servlet.http.BufferedServletResponseWrapper
 
setStorageConfigurationLocation(String) - Method in class org.dataone.cn.hazelcast.ClientConfiguration
 
setStoragePartition(boolean) - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
setTimeToCompleteEventMS(Long) - Method in class org.dataone.cn.log.MetricLogEntry
 
show_sql - Static variable in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 
SM_POLICY_TABLE - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
SM_STATUS_TABLE - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
startListener() - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
startProcessingMonitor() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
startSessionMonitor() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
startStorageMonitor() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
stopListener() - Method in class org.dataone.cn.hazelcast.membership.BaseHazelcastMembershipListener
 
stopMonitors() - Static method in class org.dataone.cn.hazelcast.membership.ClusterPartitionMonitor
 
STORAGE - Static variable in class org.dataone.cn.hazelcast.membership.ClusterPartitionMembershipListener
 
synchronizationIsActive() - Static method in class org.dataone.cn.ComponentActivationUtility
 
SyncObject - Class in org.dataone.cn.synchronization.types
A localization of a DataONE object using the Identifier and NodeId
SyncObject(NodeReference, Identifier) - Constructor for class org.dataone.cn.synchronization.types.SyncObject
 
SyncObject(String, String) - Constructor for class org.dataone.cn.synchronization.types.SyncObject
 
SYSMETA_TABLE - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
SystemMetadataDao - Interface in org.dataone.cn.dao
A specification for accessing and manipulating system metadata attributes in a database
SystemMetadataDaoMetacatImpl - Class in org.dataone.cn.dao
A concrete implementation of the systemMetadataDao inteface against the Metacat database tables (systemmetadata, smreplicationpolicy, smreplicationstatus, xml_access).
SystemMetadataDaoMetacatImpl() - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Constructor.
SystemMetadataDaoMetacatImpl(DataSource) - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Constructor.
SystemMetadataDaoMetacatImpl.AccessRuleMapper - Class in org.dataone.cn.dao
A class to map access control entry results into AccessRule objects to populate the AccessPolicy section of SystemMetadata objects
SystemMetadataDaoMetacatImpl.ReplicaEntryMapper - Class in org.dataone.cn.dao
A class to map replica entry list results into ReplicayEntry data transfer objects
SystemMetadataDaoMetacatImpl.ReplicationPolicyEntryMapper - Class in org.dataone.cn.dao
A class to map replication policy list results into ReplicationPolicyEntry data transfer objects
SystemMetadataDaoMetacatImpl.SystemMetadataMapper - Class in org.dataone.cn.dao
A class used to map system metadata status results into SystemMetadata data transfer objects
SystemMetadataDaoMetacatImpl.SystemMetadataStatusMapper - Class in org.dataone.cn.dao
A class used to map system metadata status results into SystemMetadataStatus data transfer objects
SystemMetadataMapper(Map<String, String>) - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.SystemMetadataMapper
 
SystemMetadataStatus - Class in org.dataone.cn.dao
* A data transfer object that represents minimal information about an object, including its Identifier, serial version, last system metadata modification date, and deleted status of an object
SystemMetadataStatus() - Constructor for class org.dataone.cn.dao.SystemMetadataStatus
Constructor.
SystemMetadataStatusMapper() - Constructor for class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl.SystemMetadataStatusMapper
 

T

tableMap - Static variable in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
 
taskLabel() - Method in class org.dataone.cn.synchronization.types.SyncObject
 
toString() - Method in enum org.dataone.cn.log.AuditEvent
 
toString() - Method in class org.dataone.cn.log.AuditLogEntry
 
toString() - Method in enum org.dataone.cn.log.MetricEvent
 
toString() - Method in class org.dataone.cn.log.MetricLogEntry
Transform the object into JSON
transactionManager() - Method in class org.dataone.cn.model.repository.D1BaseJpaRepositoryConfiguration
 

U

updateSystemMetadata(SystemMetadata, Map<String, String>) - Method in class org.dataone.cn.dao.SystemMetadataDaoMetacatImpl
Update the given system metadata using the provided table map.
useTLS - Variable in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 

V

validateObject(PooledObject<DirContext>) - Method in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
valueOf(String) - Static method in enum org.dataone.cn.log.AuditEvent
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.dataone.cn.log.MetricEvent
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.dataone.cn.log.AuditEvent
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.dataone.cn.log.MetricEvent
Returns an array containing the constants of this enum type, in the order they are declared.

W

wrap(DirContext) - Method in class org.dataone.cn.ldap.DirContextPooledObjectFactory
 
write(int) - Method in class org.dataone.cn.servlet.http.BufferedServletOutputStream
This method must be defined for custom servlet output streams.
write(byte[]) - Method in class org.dataone.cn.servlet.http.BufferedServletOutputStream
This method must be defined for custom servlet output streams.
write(byte[], int, int) - Method in class org.dataone.cn.servlet.http.BufferedServletOutputStream
This method must be defined for custom servlet output streams.
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