Package edu.ucsb.nceas.metacat.dataone

Class MNodeService

java.lang.Object

edu.ucsb.nceas.metacat.dataone.D1NodeService

edu.ucsb.nceas.metacat.dataone.MNodeService

All Implemented Interfaces:

org.dataone.service.mn.tier1.v2.MNCore, org.dataone.service.mn.tier1.v2.MNRead, org.dataone.service.mn.tier2.v2.MNAuthorization, org.dataone.service.mn.tier3.v2.MNStorage, org.dataone.service.mn.tier4.v2.MNReplication, org.dataone.service.mn.v2.MNPackage, org.dataone.service.mn.v2.MNQuery, org.dataone.service.mn.v2.MNView

public class MNodeService
extends D1NodeService
implements org.dataone.service.mn.tier2.v2.MNAuthorization, org.dataone.service.mn.tier1.v2.MNCore, org.dataone.service.mn.tier1.v2.MNRead, org.dataone.service.mn.tier4.v2.MNReplication, org.dataone.service.mn.tier3.v2.MNStorage, org.dataone.service.mn.v2.MNQuery, org.dataone.service.mn.v2.MNView, org.dataone.service.mn.v2.MNPackage

Represents Metacat's implementation of the DataONE Member Node service API. Methods implement the various MN* interfaces, and methods common to both Member Node and Coordinating Node interfaces are found in the D1NodeService base class. Implements: MNCore.ping() MNCore.getLogRecords() MNCore.getObjectStatistics() MNCore.getOperationStatistics() MNCore.getStatus() MNCore.getCapabilities() MNRead.get() MNRead.getSystemMetadata() MNRead.describe() MNRead.getChecksum() MNRead.listObjects() MNRead.synchronizationFailed() MNAuthorization.isAuthorized() MNAuthorization.setAccessPolicy() MNStorage.create() MNStorage.update() MNStorage.delete() MNStorage.updateSystemMetadata() MNReplication.replicate() MNAdmin.reindex()

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DOI_SCHEME
static final String	UUID_SCHEME

Fields inherited from class edu.ucsb.nceas.metacat.dataone.D1NodeService

DELETEDMESSAGE, handler, ipAddress, MAXIMUM_DB_RECORD_COUNT, METADATA, request, session2, userAgent

Fields inherited from interface org.dataone.service.mn.tier1.v2.MNCore

SERVICE_VERSION

Method Summary

Modifier and Type	Method	Description
org.dataone.service.types.v1.Identifier	archive(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid)	Archives an object, where the object is either a data object or a science metadata object.
protected void	checkAdminPrivilege(org.dataone.service.types.v1.Session session, String serviceFailureCode, String notAuthorizedCode, String error)	Check if the given session has the admin privilege.
org.dataone.service.types.v1.Identifier	create(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, InputStream object, org.dataone.service.types.v2.SystemMetadata sysmeta)
org.dataone.service.types.v1.Identifier	delete(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier id)	Deletes an object from the Member Node, where the object is either a data object or a science metadata object.
InputStream	editScienceMetadata(org.dataone.service.types.v1.Session session, InputStream object, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v1.Identifier newPid, boolean isEML, org.dataone.service.types.v2.SystemMetadata newSysmeta)	Update a science metadata document with its new Identifier
org.dataone.service.types.v1.Identifier	generateIdentifier(org.dataone.service.types.v1.Session session, String scheme, String fragment)
InputStream	get(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid)	Return the object identified by the given object identifier
org.dataone.service.types.v2.Node	getCapabilities()	Return a description of the node's capabilities and services.
org.dataone.service.types.v1.Checksum	getChecksum(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, String algorithm)	Returns a Checksum for the specified object using an accepted hashing algorithm
protected org.dataone.service.types.v1.NodeReference	getCurrentNodeId()
static MNodeService	getInstance(javax.servlet.http.HttpServletRequest request)	Get an instance of MNodeService.
static MNodeService	getInstance(javax.servlet.http.HttpServletRequest request, String ipAddress, String userAgent)	Get an instance of MNodeService.
InputStream	getPackage(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.ObjectFormatIdentifier formatId, org.dataone.service.types.v1.Identifier pid)	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
org.dataone.service.types.v1_1.QueryEngineDescription	getQueryEngineDescription(org.dataone.service.types.v1.Session session, String engine)
InputStream	getReplica(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid)	Essentially a get() but with different logging behavior
InputStream	getStatus(org.dataone.service.types.v1.Session session)	Get the status of the system.
org.dataone.service.types.v2.SystemMetadata	getSystemMetadata(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid)	Return the system metadata for a given object
protected void	handleReindexAction(List<org.dataone.service.types.v1.Identifier> pids)	Rebuild the index for one or more documents
protected void	handleReindexAllAction()	Rebuild the index for all documents in the systemMetadata table.
protected boolean	isAuthoritativeNode(org.dataone.service.types.v1.Identifier pid)	Determine if the current node is the authoritative node for the given pid.
protected boolean	isReadOnlyMode()	Check if the metacat is in the read-only mode.
org.dataone.service.types.v1.ObjectList	listObjects(org.dataone.service.types.v1.Session session, Date startTime, Date endTime, org.dataone.service.types.v1.ObjectFormatIdentifier objectFormatId, org.dataone.service.types.v1.Identifier identifier, Boolean replicaStatus, Integer start, Integer count)	Retrieve the list of objects present on the MN that match the calling parameters
org.dataone.service.types.v1_1.QueryEngineList	listQueryEngines(org.dataone.service.types.v1.Session session)
List<org.dataone.service.types.v1.Identifier>	lookupOreFor(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier guid, boolean includeObsolete)	Determines if we already have registered an ORE map for this package NOTE: uses a solr query to locate OREs for the object
InputStream	postQuery(org.dataone.service.types.v1.Session session, String engine, HashMap<String,String[]> params)	Handle the query sent by the http post method
org.dataone.service.types.v1.Identifier	publish(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier originalIdentifier)	Given an existing Science Metadata PID, this method mints a DOI and updates the original object "publishing" the update with the DOI.
void	publishIdentifier(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier identifier)	Make status of the given identifier (e.g.
InputStream	query(org.dataone.service.types.v1.Session session, String engine, String query)
Boolean	reindex(org.dataone.service.types.v1.Session session, List<org.dataone.service.types.v1.Identifier> identifiers)	The admin API call to reindex a list of documents in the instance.
Boolean	reindexAll(org.dataone.service.types.v1.Session session)	The admin API call to reindex all documents in the instance.
boolean	replicate(org.dataone.service.types.v1.Session session, org.dataone.service.types.v2.SystemMetadata sysmeta, org.dataone.service.types.v1.NodeReference sourceNode)	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.
static void	setDOIUpdater(UpdateDOI anotherDoiUpdater)	This method is for testing only - replacing the real class by a stubbed Mockito UpdateDOI class.
static void	setEnforcePublisEntirePackage(boolean enforce)	Set the value if Metacat need to make the entire package public during the publish process
static void	setMetacatSolrIndex(MetacatSolrIndex solrIndex)	This method is for testing only - replacing the real class by a stubbed Mockito MetacatSolrIndex class.
boolean	synchronizationFailed(org.dataone.service.types.v1.Session session, org.dataone.service.exceptions.SynchronizationFailed syncFailed)	A callback method used by a CN to indicate to a MN that it cannot complete synchronization of the science metadata identified by pid.
boolean	systemMetadataChanged(boolean needCheckAuthoriativeNode, org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, long serialVersion, Date dateSysMetaLastModified)	A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.
boolean	systemMetadataChanged(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, long serialVersion, Date dateSysMetaLastModified)	A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.
org.dataone.service.types.v1.Identifier	update(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, InputStream object, org.dataone.service.types.v1.Identifier newPid, org.dataone.service.types.v2.SystemMetadata sysmeta)	Updates an existing object by creating a new object identified by newPid on the Member Node which explicitly obsoletes the object identified by pid through appropriate changes to the SystemMetadata of pid and newPid
Boolean	updateAllIdMetadata(org.dataone.service.types.v1.Session session)	Update all controlled identifiers' (such as DOI) metadata on the third party service.
Boolean	updateIdMetadata(org.dataone.service.types.v1.Session session, String[] pids, String[] formatIds)	Update the given identifiers' (such as DOI) metadata on the third party service.
boolean	updateSystemMetadata(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v2.SystemMetadata sysmeta)	Update the system metadata of the specified pid.

Methods inherited from class edu.ucsb.nceas.metacat.dataone.D1NodeService

archiveCNObject, archiveObject, checkSidInModifyingSystemMetadata, checkV1SystemMetaPidExist, create, delete, describe, equals, existsInObsoletedBy, existsInObsoletes, expandPermissions, getCNNodeList, getIpAddress, getLogRecords, getPIDForSID, getSession, getSystemMetadataForPID, getUserAgent, isAccessControlDirty, isAuthorized, isInAllowList, isScienceMetadata, isValidIdentifier, listNodesBySubject, listObjects, listViews, listViews, objectExists, ping, removeSolrIndex, removeSystemMetaAndIdentifier, setIpAddress, setSession, setUserAgent, updateSystemMetadata, updateSystemMetadata, view

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.dataone.service.mn.tier2.v2.MNAuthorization

isAuthorized

Methods inherited from interface org.dataone.service.mn.tier1.v2.MNCore

getLogRecords, ping

Methods inherited from interface org.dataone.service.mn.tier1.v2.MNRead

describe

Methods inherited from interface org.dataone.service.mn.v2.MNView

listViews, view

Field Details

UUID_SCHEME

public static final String UUID_SCHEME

See Also:

• Constant Field Values

DOI_SCHEME

public static final String DOI_SCHEME

See Also:

• Constant Field Values

Method Details

getInstance

public static MNodeService getInstance(javax.servlet.http.HttpServletRequest request)

Get an instance of MNodeService.

Returns:

instance - the instance of MNodeService

getInstance

public static MNodeService getInstance(javax.servlet.http.HttpServletRequest request,
 String ipAddress,
 String userAgent)

Get an instance of MNodeService.

Parameters:

request - the servlet request associated with the MNodeService instance

ipAddress - the ip address associated with the MNodeService instance

userAgent - the user agent associated with the MNodeService instance

Returns:

the instance of MNodeService

delete

public org.dataone.service.types.v1.Identifier delete(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier id)
                                               throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.NotImplemented

Deletes an object from the Member Node, where the object is either a data object or a science metadata object.

Specified by:

delete in interface org.dataone.service.mn.tier3.v2.MNStorage

Parameters:

session - - the Session object containing the credentials for the Subject

id - - The object identifier to be deleted

Returns:

pid - the identifier of the object used for the deletion

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.InvalidRequest

update

public org.dataone.service.types.v1.Identifier update(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid,
 InputStream object,
 org.dataone.service.types.v1.Identifier newPid,
 org.dataone.service.types.v2.SystemMetadata sysmeta)
                                               throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.IdentifierNotUnique,
org.dataone.service.exceptions.UnsupportedType,
org.dataone.service.exceptions.InsufficientResources,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.InvalidSystemMetadata,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.InvalidRequest

Updates an existing object by creating a new object identified by newPid on the Member Node which explicitly obsoletes the object identified by pid through appropriate changes to the SystemMetadata of pid and newPid

Specified by:

update in interface org.dataone.service.mn.tier3.v2.MNStorage

Parameters:

session - - the Session object containing the credentials for the Subject

pid - - The identifier of the object to be updated

object - - the new object bytes

sysmeta - - the new system metadata describing the object

Returns:

newPid - the identifier of the new object

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.IdentifierNotUnique

org.dataone.service.exceptions.UnsupportedType

org.dataone.service.exceptions.InsufficientResources

org.dataone.service.exceptions.InvalidSystemMetadata

org.dataone.service.exceptions.InvalidRequest

create

public org.dataone.service.types.v1.Identifier create(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid,
 InputStream object,
 org.dataone.service.types.v2.SystemMetadata sysmeta)
                                               throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.IdentifierNotUnique,
org.dataone.service.exceptions.UnsupportedType,
org.dataone.service.exceptions.InsufficientResources,
org.dataone.service.exceptions.InvalidSystemMetadata,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.InvalidRequest

Specified by:

create in interface org.dataone.service.mn.tier3.v2.MNStorage

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.IdentifierNotUnique

org.dataone.service.exceptions.UnsupportedType

org.dataone.service.exceptions.InsufficientResources

org.dataone.service.exceptions.InvalidSystemMetadata

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.InvalidRequest

replicate

public boolean replicate(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v2.SystemMetadata sysmeta,
 org.dataone.service.types.v1.NodeReference sourceNode)
                  throws org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.InsufficientResources,
org.dataone.service.exceptions.UnsupportedType

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.

Specified by:

replicate in interface org.dataone.service.mn.tier4.v2.MNReplication

Parameters:

session - - the Session object containing the credentials for the Subject

sysmeta - - Copy of the CN held system metadata for the object

sourceNode - - A reference to node from which the content should be retrieved. The reference should be resolved by checking the CN node registry.

Returns:

true if the replication succeeds

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.UnsupportedType

org.dataone.service.exceptions.InsufficientResources

org.dataone.service.exceptions.InvalidRequest

get

public InputStream get(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid)
                throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.NotImplemented

Return the object identified by the given object identifier

Specified by:

get in interface org.dataone.service.mn.tier1.v2.MNRead

Overrides:

get in class D1NodeService

Parameters:

session - - the Session object containing the credentials for the Subject

pid - - the object identifier for the given object

Returns:

inputStream - the input stream of the given object

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotFound

getChecksum

public org.dataone.service.types.v1.Checksum getChecksum(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid,
 String algorithm)
                                                  throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented

Returns a Checksum for the specified object using an accepted hashing algorithm

Specified by:

getChecksum in interface org.dataone.service.mn.tier1.v2.MNRead

Parameters:

session - - the Session object containing the credentials for the Subject

pid - - the object identifier for the given object

algorithm - - the name of an algorithm that will be used to compute a checksum of the bytes of the object

Returns:

checksum - the checksum of the given object

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

getSystemMetadata

public org.dataone.service.types.v2.SystemMetadata getSystemMetadata(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid)
                                                              throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.NotImplemented

Return the system metadata for a given object

Specified by:

getSystemMetadata in interface org.dataone.service.mn.tier1.v2.MNRead

Overrides:

getSystemMetadata in class D1NodeService

Parameters:

session - - the Session object containing the credentials for the Subject

pid - - the object identifier for the given object

Returns:

inputStream - the input stream of the given system metadata object

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

listObjects

public org.dataone.service.types.v1.ObjectList listObjects(org.dataone.service.types.v1.Session session,
 Date startTime,
 Date endTime,
 org.dataone.service.types.v1.ObjectFormatIdentifier objectFormatId,
 org.dataone.service.types.v1.Identifier identifier,
 Boolean replicaStatus,
 Integer start,
 Integer count)
                                                    throws org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.InvalidToken

Retrieve the list of objects present on the MN that match the calling parameters

Specified by:

listObjects in interface org.dataone.service.mn.tier1.v2.MNRead

Parameters:

session - - the Session object containing the credentials for the Subject

startTime - - Specifies the beginning of the time range from which to return object (>=)

endTime - - Specifies the beginning of the time range from which to return object (>=)

objectFormatId - - Restrict results to the specified object format

replicaStatus - - Indicates if replicated objects should be returned in the list

identifier - - identifier

start - - The zero-based index of the first value, relative to the first record of the resultset that matches the parameters.

count - - The maximum number of entries that should be returned in the response. The Member Node may return less entries than specified in this value.

Returns:

objectList - the list of objects matching the criteria

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

getCapabilities

public org.dataone.service.types.v2.Node getCapabilities()
                                                  throws org.dataone.service.exceptions.ServiceFailure

Return a description of the node's capabilities and services.

Specified by:

getCapabilities in interface org.dataone.service.mn.tier1.v2.MNCore

Returns:

node - the technical capabilities of the Member Node

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented - - not thrown by this implementation

synchronizationFailed

public boolean synchronizationFailed(org.dataone.service.types.v1.Session session,
 org.dataone.service.exceptions.SynchronizationFailed syncFailed)
                              throws org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized

A callback method used by a CN to indicate to a MN that it cannot complete synchronization of the science metadata identified by pid. Log the event in the metacat event log.

Specified by:

synchronizationFailed in interface org.dataone.service.mn.tier1.v2.MNRead

Parameters:

session -

syncFailed -

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

getReplica

public InputStream getReplica(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid)
                       throws org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.NotFound

Essentially a get() but with different logging behavior

Specified by:

getReplica in interface org.dataone.service.mn.tier1.v2.MNRead

Throws:

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.NotFound

systemMetadataChanged

public boolean systemMetadataChanged(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid,
 long serialVersion,
 Date dateSysMetaLastModified)
                              throws org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.InvalidToken

A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.

Specified by:

systemMetadataChanged in interface org.dataone.service.mn.tier1.v2.MNRead

Parameters:

session - Session information that contains the identity of the calling user as retrieved from the X.509 certificate which must be traceable to the CILogon service.

serialVersion - The serialVersion of the system metadata

dateSysMetaLastModified - The time stamp for when the system metadata was changed

Throws:

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.InvalidToken

systemMetadataChanged

public boolean systemMetadataChanged(boolean needCheckAuthoriativeNode,
 org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid,
 long serialVersion,
 Date dateSysMetaLastModified)
                              throws org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.InvalidToken

A method to notify the Member Node that the authoritative copy of system metadata on the Coordinating Nodes has changed.

Parameters:

needCheckAuthoriativeNode - this is for the dataone version 2. In the version 2, there are two scenarios: 1. If the node is the authoritative node, it only accepts serial version and replica list. 2. If the node is a replica, it accepts everything. For the v1, api, the parameter should be false.

session - Session information that contains the identity of the calling user as retrieved from the X.509 certificate which must be traceable to the CILogon service.

serialVersion - The serialVersion of the system metadata

dateSysMetaLastModified - The time stamp for when the system metadata was changed

Throws:

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.InvalidToken

generateIdentifier

public org.dataone.service.types.v1.Identifier generateIdentifier(org.dataone.service.types.v1.Session session,
 String scheme,
 String fragment)
                                                           throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.InvalidRequest

Specified by:

generateIdentifier in interface org.dataone.service.mn.tier3.v2.MNStorage

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.InvalidRequest

getQueryEngineDescription

public org.dataone.service.types.v1_1.QueryEngineDescription getQueryEngineDescription(org.dataone.service.types.v1.Session session,
 String engine)
                                                                                throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.NotFound

Specified by:

getQueryEngineDescription in interface org.dataone.service.mn.v2.MNQuery

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotFound

listQueryEngines

public org.dataone.service.types.v1_1.QueryEngineList listQueryEngines(org.dataone.service.types.v1.Session session)
                                                                throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotImplemented

Specified by:

listQueryEngines in interface org.dataone.service.mn.v2.MNQuery

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

query

public InputStream query(org.dataone.service.types.v1.Session session,
 String engine,
 String query)
                  throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.NotFound

Specified by:

query in interface org.dataone.service.mn.v2.MNQuery

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotFound

postQuery

public InputStream postQuery(org.dataone.service.types.v1.Session session,
 String engine,
 HashMap<String,String[]> params)
                      throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.NotFound

Handle the query sent by the http post method

Parameters:

session - identity information of the requester

engine - the query engine will be used. Now we only support solr

params - the query parameters with key/value pairs

Returns:

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotFound

publish

public org.dataone.service.types.v1.Identifier publish(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier originalIdentifier)
                                                throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.IdentifierNotUnique,
org.dataone.service.exceptions.UnsupportedType,
org.dataone.service.exceptions.InsufficientResources,
org.dataone.service.exceptions.InvalidSystemMetadata,
IOException

Given an existing Science Metadata PID, this method mints a DOI and updates the original object "publishing" the update with the DOI. This includes updating the ORE map that describes the Science Metadata+data.

Parameters:

session -

originalIdentifier -

Throws:

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.InvalidSystemMetadata

org.dataone.service.exceptions.InsufficientResources

org.dataone.service.exceptions.UnsupportedType

org.dataone.service.exceptions.IdentifierNotUnique

IOException

editScienceMetadata

public InputStream editScienceMetadata(org.dataone.service.types.v1.Session session,
 InputStream object,
 org.dataone.service.types.v1.Identifier pid,
 org.dataone.service.types.v1.Identifier newPid,
 boolean isEML,
 org.dataone.service.types.v2.SystemMetadata newSysmeta)
                                throws org.dataone.service.exceptions.ServiceFailure,
IOException,
UnsupportedEncodingException,
org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.NotImplemented

Update a science metadata document with its new Identifier

Parameters:

session - - the Session object containing the credentials for the Subject

object - - the InputStream for the XML object to be edited

pid - - the Identifier of the XML object to be updated

newPid - = the new Identifier to give to the modified XML doc

Returns:

newObject - The InputStream for the modified XML object

Throws:

org.dataone.service.exceptions.ServiceFailure

IOException

UnsupportedEncodingException

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.NotImplemented

lookupOreFor

public List<org.dataone.service.types.v1.Identifier> lookupOreFor(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier guid,
 boolean includeObsolete)

Determines if we already have registered an ORE map for this package NOTE: uses a solr query to locate OREs for the object

Parameters:

guid - of the EML/packaging object

Returns:

list of resource map identifiers for the given pid

getPackage

public InputStream getPackage(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.ObjectFormatIdentifier formatId,
 org.dataone.service.types.v1.Identifier pid)
                       throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.NotFound

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

Specified by:

getPackage in interface org.dataone.service.mn.v2.MNPackage

Parameters:

session - Information about the user performing the request

formatId -

pid - The pid of the resource map

Returns:

A stream of a bag

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotFound

archive

public org.dataone.service.types.v1.Identifier archive(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid)
                                                throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.NotImplemented

Archives an object, where the object is either a data object or a science metadata object.

Specified by:

archive in interface org.dataone.service.mn.tier3.v2.MNStorage

Parameters:

session - - the Session object containing the credentials for the Subject

pid - - The object identifier to be archived

Returns:

pid - the identifier of the object used for the archiving

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.InvalidRequest

updateSystemMetadata

public boolean updateSystemMetadata(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier pid,
 org.dataone.service.types.v2.SystemMetadata sysmeta)
                             throws org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.InvalidSystemMetadata,
org.dataone.service.exceptions.InvalidToken

Update the system metadata of the specified pid.

Specified by:

updateSystemMetadata in interface org.dataone.service.mn.tier3.v2.MNStorage

Throws:

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.InvalidSystemMetadata

org.dataone.service.exceptions.InvalidToken

getStatus

public InputStream getStatus(org.dataone.service.types.v1.Session session)
                      throws org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotImplemented

Get the status of the system. this is an unofficial dataone api method. Currently we only reply the size of the index queue. The method will return the input stream of a xml instance. In the future, we need to add a new dataone type to represent the result.

Parameters:

session -

Returns:

the input stream which is the xml presentation of the status report

Throws:

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotImplemented

publishIdentifier

public void publishIdentifier(org.dataone.service.types.v1.Session session,
 org.dataone.service.types.v1.Identifier identifier)
                       throws org.dataone.service.exceptions.InvalidToken,
org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.NotImplemented,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotFound,
org.dataone.service.exceptions.IdentifierNotUnique,
org.dataone.service.exceptions.UnsupportedType,
org.dataone.service.exceptions.InsufficientResources,
org.dataone.service.exceptions.InvalidSystemMetadata,
DOIException

Make status of the given identifier (e.g. a DOI) public

Parameters:

session - the subject who calls the method

identifier - the identifier whose status will be public. It can be a pid or sid.

Throws:

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.IdentifierNotUnique

org.dataone.service.exceptions.UnsupportedType

org.dataone.service.exceptions.InsufficientResources

org.dataone.service.exceptions.InvalidSystemMetadata

DOIException

reindex

public Boolean reindex(org.dataone.service.types.v1.Session session,
 List<org.dataone.service.types.v1.Identifier> identifiers)
                throws org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented

The admin API call to reindex a list of documents in the instance.

Parameters:

session - the identity of requester. It must have administrative permissions

identifiers - the list of objects' identifier which will be reindexed.

Returns:

true if the reindex request is scheduled. If something went wrong, an exception will be thrown.

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

NotImplementedException

org.dataone.service.exceptions.NotImplemented

reindexAll

public Boolean reindexAll(org.dataone.service.types.v1.Session session)
                   throws org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented

The admin API call to reindex all documents in the instance.

Parameters:

session - the identity of requester. It must have administrative permissions

Returns:

true if the reindex request is scheduled. If something went wrong, an exception will be thrown.

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

NotImplementedException

org.dataone.service.exceptions.NotImplemented

updateAllIdMetadata

public Boolean updateAllIdMetadata(org.dataone.service.types.v1.Session session)
                            throws org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented

Update all controlled identifiers' (such as DOI) metadata on the third party service.

Parameters:

session - the identity of requester. It must have administrative permissions

Returns:

true if the reindex request is scheduled. If something went wrong, an exception will be thrown.

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

updateIdMetadata

public Boolean updateIdMetadata(org.dataone.service.types.v1.Session session,
 String[] pids,
 String[] formatIds)
                         throws org.dataone.service.exceptions.ServiceFailure,
org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.NotImplemented

Update the given identifiers' (such as DOI) metadata on the third party service.

Parameters:

session - the identity of requester. It must have administrative permissions.

pids - the list of pids will be updated

formatIds - the list of format id to which the identifiers belong will be updated

Returns:

true if the reindex request is scheduled. If something went wrong, an exception will be thrown.

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.NotImplemented

checkAdminPrivilege

protected void checkAdminPrivilege(org.dataone.service.types.v1.Session session,
 String serviceFailureCode,
 String notAuthorizedCode,
 String error)
                            throws org.dataone.service.exceptions.NotAuthorized,
org.dataone.service.exceptions.ServiceFailure

Check if the given session has the admin privilege. If it does not have, a NotAuthorized exception will be thrown.

Parameters:

session - the session will be checked.

serviceFailureCode - the detail code for the ServiceFailure exception

notAuthorizedCode - the detail code for the NotAuthorized exception

error - the error message will be in the exception

Throws:

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.ServiceFailure

handleReindexAction

protected void handleReindexAction(List<org.dataone.service.types.v1.Identifier> pids)

Rebuild the index for one or more documents

Parameters:

pids - the list of identifier whose solr doc needs to be rebuilt

handleReindexAllAction

protected void handleReindexAllAction()

Rebuild the index for all documents in the systemMetadata table.

getCurrentNodeId

protected org.dataone.service.types.v1.NodeReference getCurrentNodeId()

isAuthoritativeNode

protected boolean isAuthoritativeNode(org.dataone.service.types.v1.Identifier pid)
                               throws org.dataone.service.exceptions.InvalidRequest,
org.dataone.service.exceptions.ServiceFailure

Determine if the current node is the authoritative node for the given pid. (uses HZsysmeta map)

Throws:

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.ServiceFailure

isReadOnlyMode

protected boolean isReadOnlyMode()

Check if the metacat is in the read-only mode.

Returns:

true if it is; otherwise false.

setEnforcePublisEntirePackage

public static void setEnforcePublisEntirePackage(boolean enforce)

Set the value if Metacat need to make the entire package public during the publish process

Parameters:

enforce - enforce the entire package public readable or not

setDOIUpdater

public static void setDOIUpdater(UpdateDOI anotherDoiUpdater)

This method is for testing only - replacing the real class by a stubbed Mockito UpdateDOI class.

Parameters:

anotherDoiUpdater - the stubbed Mockito UpdateDOI class which will be used to replace the real class

setMetacatSolrIndex

public static void setMetacatSolrIndex(MetacatSolrIndex solrIndex)

This method is for testing only - replacing the real class by a stubbed Mockito MetacatSolrIndex class.

Parameters:

solrIndex - the stubbed Mockito MetacatSolrIndex class which will be used to replace the real class