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

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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