edu.ucsb.nceas.metacat

Class IdentifierManager

java.lang.Object

edu.ucsb.nceas.metacat.IdentifierManager

public class IdentifierManager
extends java.lang.Object

Manage the relationship between Metacat local identifiers (LocalIDs) that are codified as the (docid, rev) pair with globally unique string identifiers (GUIDs) that are opaque strings. This class provides methods to manage these identifiers, and to search for and look up LocalIDs based on their GUID and vice versa. IdentifierManager is a singleton.

Author:

Matthew Jones

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	TYPE_IDENTIFIER
static java.lang.String	TYPE_SYSTEM_METADATA

Method Summary

Modifier and Type	Method and Description
java.util.List<org.dataone.service.types.v1.Permission>	convertPermission(int permission)
int	convertPermission(org.dataone.service.types.v1.Permission permission)
void	createMapping(java.lang.String guid, java.lang.String localId) create a mapping in the identifier table
boolean	deleteSystemMetadata(java.lang.String guid)
boolean	existsInIdentifierTable(org.dataone.service.types.v1.Identifier pid) Determine if the given pid exists on the identifier table.
boolean	existsInXmlLRevisionTable(java.lang.String docid, int rev) IF the given localId exists on the xml_revisions table
java.lang.String	generateLocalId(java.lang.String guid, int rev)
java.lang.String	generateLocalId(java.lang.String guid, int rev, boolean isSystemMetadata) Given a global identifier (guid), create a suitable local identifier that follows Metacat's docid semantics and format (scope.id.rev), and create a mapping between these two identifiers.
org.dataone.service.types.v1.AccessPolicy	getAccessPolicy(java.lang.String guid) Lookup access policy from Metacat
java.util.List<java.lang.String>	getAllLocalIds() return a listing of all local ids in the object store
java.util.List<java.lang.String>	getAllSystemMetadataGUIDs() return a listing of all guids in the object store
java.lang.String	getGUID(java.lang.String docid, int rev) given a local identifer, look up the guid.
java.util.List<java.lang.String>	getGUIDs(java.lang.String formatId, java.lang.String nodeId, java.lang.String scheme) Get the list of identifiers which system metadata matches the given format id and original member node id and guid or series id start with the scheme (doi for example).
org.dataone.service.types.v1.Identifier	getHeadPID(org.dataone.service.types.v1.Identifier sid) Get the pid of the head (current) version of objects match the specified sid.
static IdentifierManager	getInstance() Return the single instance of the manager after initializing it if it wasn't previously initialized.
java.util.Date	getLastModifiedDate() returns a list of system metadata-only guids since the given date
int	getLatestRevForLocalId(java.lang.String localId) return the newest rev for a given localId
java.lang.String	getLocalId(java.lang.String guid) Lookup a localId given the GUID.
java.util.List<java.lang.String>	getLocalIdsWithNoSystemMetadata(boolean includeRevisions, int serverLocation) return all local ids in the object store that do not have associated system metadata
java.lang.String	getObjectFilePath(java.lang.String localId, boolean isScienceMetadata) Get the the file path for the given object local id
org.dataone.service.types.v2.SystemMetadata	getSystemMetadata(java.lang.String guid) return a hash of all of the info that is in the systemmetadata table
java.util.List<java.lang.String>	getUpdatedSystemMetadataIds(java.util.Date since) returns a list of system metadata-only guids since the given date
boolean	identifierExists(java.lang.String guid) Determine if an identifier exists already, returning true if so.
void	insertOrUpdateSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta) creates a system metadata mapping and adds additional fields from sysmeta to the table for quick searching.
boolean	mappingExists(java.lang.String guid) Determine if an identifier mapping exists already, returning true if so.
boolean	objectFileExists(java.lang.String localId, boolean isScienceMetadata) Determine if the object file exist for the given localId.
org.dataone.service.types.v1.ObjectList	querySystemMetadata(java.util.Date startTime, java.util.Date endTime, org.dataone.service.types.v1.ObjectFormatIdentifier objectFormatId, org.dataone.service.types.v1.NodeReference nodeId, int start, int count, org.dataone.service.types.v1.Identifier identifier, boolean isSID) query the systemmetadata table based on the given parameters
void	removeMapping(java.lang.String guid, java.lang.String localId) remove a mapping in the identifier table
boolean	systemMetadataPIDExists(org.dataone.service.types.v1.Identifier pid) Determine if the specified identifier object exists or not.
boolean	systemMetadataPIDExists(java.lang.String guid)
boolean	systemMetadataSIDExists(org.dataone.service.types.v1.Identifier sid) Check if the specified sid object exists on the serial id field on the system metadata table
boolean	systemMetadataSIDExists(java.lang.String sid) Check if the specified sid exists on the serial id field on the system metadata table
void	updateAuthoritativeMemberNodeId(java.lang.String existingMemberNodeId, java.lang.String newMemberNodeId)
void	updateMapping(java.lang.String guid, java.lang.String localId) update a mapping
void	updateSystemMetadata(org.dataone.service.types.v2.SystemMetadata sm, DBConnection dbConn) Insert the system metadata fields into the db

Methods inherited from class java.lang.Object

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

Field Detail

TYPE_SYSTEM_METADATA

public static final java.lang.String TYPE_SYSTEM_METADATA

See Also:

Constant Field Values

TYPE_IDENTIFIER

public static final java.lang.String TYPE_IDENTIFIER

See Also:

Constant Field Values

Method Detail

getInstance

public static IdentifierManager getInstance()

Return the single instance of the manager after initializing it if it wasn't previously initialized.

Returns:

the single IdentifierManager instance

getSystemMetadata

public org.dataone.service.types.v2.SystemMetadata getSystemMetadata(java.lang.String guid)
                                                              throws McdbDocNotFoundException

return a hash of all of the info that is in the systemmetadata table

Parameters:

guid -

Returns:

Throws:

McdbDocNotFoundException

getLatestRevForLocalId

public int getLatestRevForLocalId(java.lang.String localId)
                           throws McdbDocNotFoundException

return the newest rev for a given localId

Parameters:

localId -

Returns:

Throws:

McdbDocNotFoundException

getLocalIdsWithNoSystemMetadata

public java.util.List<java.lang.String> getLocalIdsWithNoSystemMetadata(boolean includeRevisions,
                                                                        int serverLocation)

return all local ids in the object store that do not have associated system metadata

getAllLocalIds

public java.util.List<java.lang.String> getAllLocalIds()

return a listing of all local ids in the object store

Returns:

a list of all local ids in metacat

getAllSystemMetadataGUIDs

public java.util.List<java.lang.String> getAllSystemMetadataGUIDs()

return a listing of all guids in the object store

Returns:

a list of all GUIDs in metacat

getUpdatedSystemMetadataIds

public java.util.List<java.lang.String> getUpdatedSystemMetadataIds(java.util.Date since)
                                                             throws java.lang.Exception

returns a list of system metadata-only guids since the given date

Returns:

a list of system ids in metacat that do not correspond to objects TODO: need to check which server they are on

Throws:

java.lang.Exception

getLastModifiedDate

public java.util.Date getLastModifiedDate()
                                   throws java.lang.Exception

returns a list of system metadata-only guids since the given date

Returns:

a list of system ids in metacat that do not correspond to objects TODO: need to check which server they are on

Throws:

java.lang.Exception

identifierExists

public boolean identifierExists(java.lang.String guid)
                         throws java.sql.SQLException

Determine if an identifier exists already, returning true if so. NOTE: looks in the identifier and system metadata table for a match (in that order) Can return true for both PIDs and SIDs.

Parameters:

guid - the global identifier to look up

Returns:

boolean true if the identifier exists

Throws:

java.sql.SQLException

mappingExists

public boolean mappingExists(java.lang.String guid)
                      throws java.sql.SQLException

Determine if an identifier mapping exists already, returning true if so.

Parameters:

guid - the global identifier to look up

Returns:

boolean true if the identifier exists

Throws:

java.sql.SQLException

generateLocalId

public java.lang.String generateLocalId(java.lang.String guid,
                                        int rev)

Parameters:

guid -

rev -

Returns:

generateLocalId

public java.lang.String generateLocalId(java.lang.String guid,
                                        int rev,
                                        boolean isSystemMetadata)

Given a global identifier (guid), create a suitable local identifier that follows Metacat's docid semantics and format (scope.id.rev), and create a mapping between these two identifiers. This effectively reserves both the global and the local identifier, as they will now be present in the identifier mapping table. REMOVED feature: If the incoming guid has the syntax of a Metacat docid (scope.id.rev), then simply use it. WHY: because "test.1.001" becomes "test.1.1" which is not correct for DataONE identifier use (those revision numbers are just chartacters and should not be interpreted)

Parameters:

guid - the global string identifier

rev - the revision number to be used in the localId

Returns:

String containing the localId to be used for Metacat operations

getGUID

public java.lang.String getGUID(java.lang.String docid,
                                int rev)
                         throws McdbDocNotFoundException

given a local identifer, look up the guid. Throw McdbDocNotFoundException if the docid, rev is not found in the identifiers or systemmetadata tables

Parameters:

docid - the docid to look up

rev - the revision of the docid to look up

Returns:

String containing the mapped guid

Throws:

McdbDocNotFoundException - if the docid, rev is not found

getGUIDs

public java.util.List<java.lang.String> getGUIDs(java.lang.String formatId,
                                                 java.lang.String nodeId,
                                                 java.lang.String scheme)

Get the list of identifiers which system metadata matches the given format id and original member node id and guid or series id start with the scheme (doi for example).

Parameters:

formatId - the format id of the identifier must match the given formatId.

nodeId - the original member node of the identifier must match the given nodeId.

scheme - the guid or series id must start with the given scheme (doi for exampe)

Returns:

the list of identifier string. An empty list will be returned if nothing was found.

getHeadPID

public org.dataone.service.types.v1.Identifier getHeadPID(org.dataone.service.types.v1.Identifier sid)
                                                   throws java.sql.SQLException

Get the pid of the head (current) version of objects match the specified sid. 1. locate all candidate chain-ends for S1: determined by: seriesId == S1 AND (obsoletedBy == null OR obsoletedBy.seriesId != S1) // these are the type1 and type2 ends If obsoletedBy is missing, we generally consider it a type 2 end except: there is another object in the chain (has the same series id) that obsoletes the missing object. 2. if only 1 candidate chain-end, return it as the HEAD 3. otherwise return the one in the chain with the latest dateUploaded value. However, we find that dateUpload doesn't refect the obsoletes information (espically on the cn), so we will check osoletes information as well. https://redmine.dataone.org/issues/7624

Parameters:

sid - specified sid which should match.

Returns:

the pid of the head version. The null will be returned if there is no pid found.

Throws:

java.sql.SQLException

systemMetadataSIDExists

public boolean systemMetadataSIDExists(org.dataone.service.types.v1.Identifier sid)
                                throws java.sql.SQLException

Check if the specified sid object exists on the serial id field on the system metadata table

Parameters:

sid -

Returns:

true if it exists; false otherwise.

Throws:

java.sql.SQLException

systemMetadataSIDExists

public boolean systemMetadataSIDExists(java.lang.String sid)
                                throws java.sql.SQLException

Check if the specified sid exists on the serial id field on the system metadata table

Parameters:

id -

Returns:

true if it exists; false otherwise.

Throws:

java.sql.SQLException

systemMetadataPIDExists

public boolean systemMetadataPIDExists(org.dataone.service.types.v1.Identifier pid)
                                throws java.sql.SQLException

Determine if the specified identifier object exists or not.

Parameters:

pid - - the specified identifier

Returns:

true if it is exists.

Throws:

java.sql.SQLException

java.lang.NullPointerException

systemMetadataPIDExists

public boolean systemMetadataPIDExists(java.lang.String guid)
                                throws java.sql.SQLException

Throws:

java.sql.SQLException

insertOrUpdateSystemMetadata

public void insertOrUpdateSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta)
                                  throws McdbDocNotFoundException,
                                         java.sql.SQLException,
                                         org.dataone.service.exceptions.InvalidSystemMetadata

creates a system metadata mapping and adds additional fields from sysmeta to the table for quick searching.

Parameters:

guid - the id to insert

localId - the systemMetadata object to get the local id for

Throws:

McdbDocNotFoundException

java.sql.SQLException

org.dataone.service.exceptions.InvalidSystemMetadata

updateMapping

public void updateMapping(java.lang.String guid,
                          java.lang.String localId)

update a mapping

Parameters:

guid -

localId -

updateSystemMetadata

public void updateSystemMetadata(org.dataone.service.types.v2.SystemMetadata sm,
                                 DBConnection dbConn)
                          throws McdbDocNotFoundException,
                                 java.sql.SQLException,
                                 org.dataone.service.exceptions.InvalidSystemMetadata,
                                 AccessException

Insert the system metadata fields into the db

Parameters:

sm -

Throws:

McdbDocNotFoundException

java.sql.SQLException

org.dataone.service.exceptions.InvalidSystemMetadata

AccessException

getAccessPolicy

public org.dataone.service.types.v1.AccessPolicy getAccessPolicy(java.lang.String guid)
                                                          throws McdbDocNotFoundException,
                                                                 AccessException

Lookup access policy from Metacat

Parameters:

guid -

Returns:

Throws:

McdbDocNotFoundException

AccessException

convertPermission

public int convertPermission(org.dataone.service.types.v1.Permission permission)

convertPermission

public java.util.List<org.dataone.service.types.v1.Permission> convertPermission(int permission)

getLocalId

public java.lang.String getLocalId(java.lang.String guid)
                            throws McdbDocNotFoundException,
                                   java.sql.SQLException

Lookup a localId given the GUID. If the identifier is not found, throw an exception.

Parameters:

guid - the global identifier to look up

Returns:

String containing the corresponding LocalId

Throws:

McdbDocNotFoundException - if the identifier is not found

java.sql.SQLException

querySystemMetadata

public org.dataone.service.types.v1.ObjectList querySystemMetadata(java.util.Date startTime,
                                                                   java.util.Date endTime,
                                                                   org.dataone.service.types.v1.ObjectFormatIdentifier objectFormatId,
                                                                   org.dataone.service.types.v1.NodeReference nodeId,
                                                                   int start,
                                                                   int count,
                                                                   org.dataone.service.types.v1.Identifier identifier,
                                                                   boolean isSID)
                                                            throws java.sql.SQLException,
                                                                   edu.ucsb.nceas.utilities.PropertyNotFoundException,
                                                                   ServiceException

query the systemmetadata table based on the given parameters

Parameters:

startTime -

endTime -

objectFormat -

nodeId -

start -

count -

Returns:

ObjectList

Throws:

java.sql.SQLException

ServiceException

edu.ucsb.nceas.utilities.PropertyNotFoundException

createMapping

public void createMapping(java.lang.String guid,
                          java.lang.String localId)

create a mapping in the identifier table

Parameters:

guid -

localId -

removeMapping

public void removeMapping(java.lang.String guid,
                          java.lang.String localId)

remove a mapping in the identifier table

Parameters:

guid -

localId -

deleteSystemMetadata

public boolean deleteSystemMetadata(java.lang.String guid)

updateAuthoritativeMemberNodeId

public void updateAuthoritativeMemberNodeId(java.lang.String existingMemberNodeId,
                                            java.lang.String newMemberNodeId)

objectFileExists

public boolean objectFileExists(java.lang.String localId,
                                boolean isScienceMetadata)
                         throws edu.ucsb.nceas.utilities.PropertyNotFoundException

Determine if the object file exist for the given localId.

Parameters:

localId -

isScienceMetadata -

Returns:

Throws:

edu.ucsb.nceas.utilities.PropertyNotFoundException

getObjectFilePath

public java.lang.String getObjectFilePath(java.lang.String localId,
                                          boolean isScienceMetadata)
                                   throws edu.ucsb.nceas.utilities.PropertyNotFoundException

Get the the file path for the given object local id

Parameters:

localId -

isScienceMetadata -

Returns:

Throws:

edu.ucsb.nceas.utilities.PropertyNotFoundException

existsInXmlLRevisionTable

public boolean existsInXmlLRevisionTable(java.lang.String docid,
                                         int rev)
                                  throws java.sql.SQLException

IF the given localId exists on the xml_revisions table

Parameters:

localId -

Returns:

Throws:

java.sql.SQLException

existsInIdentifierTable

public boolean existsInIdentifierTable(org.dataone.service.types.v1.Identifier pid)
                                throws java.sql.SQLException

Determine if the given pid exists on the identifier table.

Parameters:

pid - must be a PID

Returns:

true if it exists; false otherwise.

Throws:

java.sql.SQLException