edu.ucsb.nceas.metacat.dataone

Class D1NodeService

java.lang.Object

edu.ucsb.nceas.metacat.dataone.D1NodeService

Direct Known Subclasses:

CNodeService, MNodeService

public abstract class D1NodeService
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DELETEDMESSAGE
protected MetacatHandler	handler
protected static int	MAXIMUM_DB_RECORD_COUNT limit paged results sets to a configured maximum
protected javax.servlet.http.HttpServletRequest	request For logging the operations
protected org.dataone.service.types.v1.Session	session2 out-of-band session object to be used when not passed in as a method parameter

Constructor Summary

Constructors

Constructor and Description
D1NodeService(javax.servlet.http.HttpServletRequest request) Constructor - used to set the metacatUrl from a subclass extending D1NodeService

Method Summary

Modifier and Type	Method and Description
protected void	archiveCNObject(boolean log, org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v2.SystemMetadata sysMeta, boolean needModifyDate) Archive a object on cn and notify the replica.
protected org.dataone.service.types.v1.Identifier	archiveObject(boolean log, org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v2.SystemMetadata sysMeta, boolean needModifyDate) Archives an object, where the object is either a data object or a science metadata object.
protected boolean	checkSidInModifyingSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta, java.lang.String invalidSystemMetadataCode, java.lang.String serviceFailureCode)
void	checkV1SystemMetaPidExist(org.dataone.service.types.v1.Identifier identifier, java.lang.String serviceFailureCode, java.lang.String serviceFailureMessage, java.lang.String noFoundCode, java.lang.String notFoundMessage) A utility method for v1 api to check the specified identifier exists as a pid Uses the IdentifierManager to call the Identifier table directly - this detects Identifiers for deleted objects (where the SystemMetadata doesn't exist, but the Identifier remains)
org.dataone.service.types.v1.Identifier	create(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, java.io.InputStream object, org.dataone.service.types.v2.SystemMetadata sysmeta) Adds a new object to the Node, where the object is either a data object or a science metadata object.
org.dataone.service.types.v1.Identifier	delete(java.lang.String username, org.dataone.service.types.v1.Identifier pid) Deletes an object from the Member Node, where the object is either a data object or a science metadata object.
org.dataone.service.types.v1.DescribeResponse	describe(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier id) This method provides a lighter weight mechanism than getSystemMetadata() for a client to determine basic properties of the referenced object.
protected java.lang.String	existsInObsoletedBy(org.dataone.service.types.v1.Identifier id)
protected java.lang.String	existsInObsoletes(org.dataone.service.types.v1.Identifier id)
protected static java.util.List<org.dataone.service.types.v1.Permission>	expandPermissions(org.dataone.service.types.v1.Permission permission) Given a Permission, returns a list of all permissions that it encompasses Permissions are hierarchical so that WRITE also allows READ.
java.io.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
protected org.dataone.service.types.v2.NodeList	getCNNodeList() A centralized point for accessing the CN Nodelist, to make it easier to cache the nodelist in the future, if it's seen as helpful performance-wise
org.dataone.service.types.v2.Log	getLogRecords(org.dataone.service.types.v1.Session session, java.util.Date fromDate, java.util.Date toDate, java.lang.String event, java.lang.String pidFilter, java.lang.Integer start, java.lang.Integer count) Return the log records associated with a given event between the start and end dates listed given a particular Subject listed in the Session
protected org.dataone.service.types.v1.Identifier	getPIDForSID(org.dataone.service.types.v1.Identifier sid, java.lang.String serviceFailureCode) Utility method to get the PID for an SID.
org.dataone.service.types.v1.Session	getSession() retrieve the out-of-band session
org.dataone.service.types.v2.SystemMetadata	getSystemMetadata(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier id) Return the system metadata for a given object
protected org.dataone.service.types.v2.SystemMetadata	getSystemMetadataForPID(org.dataone.service.types.v1.Identifier pid, java.lang.String serviceFailureCode, java.lang.String invalidRequestCode, java.lang.String notFoundCode, boolean needDeleteInfo) Get the system metadata for the given PID (not a sid).
java.lang.String	insertDataObject(java.io.InputStream object, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Checksum checksum) Insert a data document
java.lang.String	insertOrUpdateDocument(java.io.InputStream xmlStream, java.lang.String encoding, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v1.Session session, java.lang.String insertOrUpdate, java.lang.String formatId, org.dataone.service.types.v1.Checksum checksum) Insert or update an XML document into Metacat
void	insertSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta) Insert a systemMetadata document and return its localId
boolean	isAuthorized(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier id, org.dataone.service.types.v1.Permission permission) Test if the user identified by the provided token has authorization for the operation on the specified object.
static boolean	isScienceMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta) Determine if a given object should be treated as an XML science metadata object.
static boolean	isValidIdentifier(org.dataone.service.types.v1.Identifier pid) Check for whitespace in the given pid.
protected java.util.List<org.dataone.service.types.v2.Node>	listNodesBySubject(org.dataone.service.types.v1.Subject subject, org.dataone.service.types.v2.NodeList nodelist) Calls CN.listNodes() to assemble a list of nodes that have been registered with the DataONE infrastructure that match the given session subject
org.dataone.service.types.v1.ObjectList	listObjects(org.dataone.service.types.v1.Session session, java.util.Date startTime, java.util.Date endTime, org.dataone.service.types.v1.ObjectFormatIdentifier objectFormatId, org.dataone.service.types.v1.Identifier identifier, org.dataone.service.types.v1.NodeReference nodeId, java.lang.Integer start, java.lang.Integer count) Retrieve the list of objects present on the MN that match the calling parameters
org.dataone.service.types.v2.OptionList	listViews()
org.dataone.service.types.v2.OptionList	listViews(org.dataone.service.types.v1.Session arg0)
protected static void	objectExists(org.dataone.service.types.v1.Identifier id) Determine if an object with the given identifier already exists or not.
java.util.Date	ping() Low level, "are you alive" operation.
protected void	removeSolrIndex(org.dataone.service.types.v2.SystemMetadata sysMeta)
protected void	removeSystemMetaAndIdentifier(org.dataone.service.types.v1.Identifier id)
void	setSession(org.dataone.service.types.v1.Session session) Set the out-of-band session
protected boolean	updateSystemMetadata(org.dataone.service.types.v1.Session session, org.dataone.service.types.v1.Identifier pid, org.dataone.service.types.v2.SystemMetadata sysmeta, boolean needUpdateModificationDate, org.dataone.service.types.v2.SystemMetadata currentSysmeta, boolean fromCN) Update the system metadata of the specified pid.
protected void	updateSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysMeta) Update a systemMetadata document
java.io.InputStream	view(org.dataone.service.types.v1.Session session, java.lang.String format, org.dataone.service.types.v1.Identifier id)

Methods inherited from class java.lang.Object

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

Field Detail

DELETEDMESSAGE

public static final java.lang.String DELETEDMESSAGE

See Also:

Constant Field Values

request

protected javax.servlet.http.HttpServletRequest request

For logging the operations

handler

protected MetacatHandler handler

MAXIMUM_DB_RECORD_COUNT

protected static int MAXIMUM_DB_RECORD_COUNT

limit paged results sets to a configured maximum

session2

protected org.dataone.service.types.v1.Session session2

out-of-band session object to be used when not passed in as a method parameter

Constructor Detail

D1NodeService

public D1NodeService(javax.servlet.http.HttpServletRequest request)

Constructor - used to set the metacatUrl from a subclass extending D1NodeService

Parameters:

metacatUrl - - the URL of the metacat service, including the ending /d1

Method Detail

getSession

public org.dataone.service.types.v1.Session getSession()

retrieve the out-of-band session

Returns:

setSession

public void setSession(org.dataone.service.types.v1.Session session)

Set the out-of-band session

Parameters:

session -

getCNNodeList

protected org.dataone.service.types.v2.NodeList getCNNodeList()
                                                       throws org.dataone.service.exceptions.ServiceFailure,
                                                              org.dataone.service.exceptions.NotImplemented

A centralized point for accessing the CN Nodelist, to make it easier to cache the nodelist in the future, if it's seen as helpful performance-wise

Returns:

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotImplemented

describe

public org.dataone.service.types.v1.DescribeResponse describe(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

This method provides a lighter weight mechanism than getSystemMetadata() for a client to determine basic properties of the referenced object.

Parameters:

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

pid - - the identifier of the object to be described

Returns:

describeResponse - A set of values providing a basic description of the 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.InvalidRequest

delete

public org.dataone.service.types.v1.Identifier delete(java.lang.String username,
                                                      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

Deletes an object from the Member Node, where the object is either a data object or a science metadata object. No access checking.

Parameters:

username - - the name of the user who calls the method. This is only for logging.

pid - - 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

ping

public java.util.Date ping()
                    throws org.dataone.service.exceptions.NotImplemented,
                           org.dataone.service.exceptions.ServiceFailure,
                           org.dataone.service.exceptions.InsufficientResources

Low level, "are you alive" operation. A valid ping response is indicated by a HTTP status of 200.

Returns:

true if the service is alive

Throws:

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.InsufficientResources

create

public org.dataone.service.types.v1.Identifier create(org.dataone.service.types.v1.Session session,
                                                      org.dataone.service.types.v1.Identifier pid,
                                                      java.io.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

Adds a new object to the Node, where the object is either a data object or a science metadata object. This method is called by clients to create new data objects on Member Nodes or internally for Coordinating Nodes

Parameters:

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

pid - - The object identifier to be created

object - - the object bytes

sysmeta - - the system metadata that describes the object

Returns:

pid - the object identifier created

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

objectExists

protected static void objectExists(org.dataone.service.types.v1.Identifier id)
                            throws org.dataone.service.exceptions.ServiceFailure,
                                   org.dataone.service.exceptions.IdentifierNotUnique

Determine if an object with the given identifier already exists or not. (Using IdentityManager. Works for SID or PID)

Parameters:

id - - the ID to be checked.

Throws:

org.dataone.service.exceptions.ServiceFailure - if the system can't fulfill the check process

org.dataone.service.exceptions.IdentifierNotUnique - if the object with the identifier does exist

removeSystemMetaAndIdentifier

protected void removeSystemMetaAndIdentifier(org.dataone.service.types.v1.Identifier id)

removeSolrIndex

protected void removeSolrIndex(org.dataone.service.types.v2.SystemMetadata sysMeta)

getLogRecords

public org.dataone.service.types.v2.Log getLogRecords(org.dataone.service.types.v1.Session session,
                                                      java.util.Date fromDate,
                                                      java.util.Date toDate,
                                                      java.lang.String event,
                                                      java.lang.String pidFilter,
                                                      java.lang.Integer start,
                                                      java.lang.Integer count)
                                               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

Return the log records associated with a given event between the start and end dates listed given a particular Subject listed in the Session

Parameters:

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

fromDate - - the start date of the desired log records

toDate - - the end date of the desired log records

event - - restrict log records of a specific event type

start - - zero based offset from the first record in the set of matching log records. Used to assist with paging the response.

count - - maximum number of log records to return in the response. Used to assist with paging the response.

Returns:

the desired log records

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

get

public java.io.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

Parameters:

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

id - - the identifier for the given object TODO: The D1 Authorization API doesn't provide information on which authentication system the Subject belongs to, and so it's not possible to discern which Person or Group is a valid KNB LDAP DN. Fix this.

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

getSystemMetadata

public org.dataone.service.types.v2.SystemMetadata getSystemMetadata(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

Return the system metadata for a given object

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

isAuthorized

public boolean isAuthorized(org.dataone.service.types.v1.Session session,
                            org.dataone.service.types.v1.Identifier id,
                            org.dataone.service.types.v1.Permission permission)
                     throws org.dataone.service.exceptions.ServiceFailure,
                            org.dataone.service.exceptions.InvalidToken,
                            org.dataone.service.exceptions.NotFound,
                            org.dataone.service.exceptions.NotAuthorized,
                            org.dataone.service.exceptions.NotImplemented,
                            org.dataone.service.exceptions.InvalidRequest

Test if the user identified by the provided token has authorization for the operation on the specified object. Allowed subjects include: 1. CNs 2. Authoritative node 3. Owner of the object 4. Users with the specified permission in the access rules.

Parameters:

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

pid - - The identifer of the resource for which access is being checked

operation - - The type of operation which is being requested for the given pid

Returns:

true if the operation is allowed

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.InvalidToken

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.NotImplemented

org.dataone.service.exceptions.InvalidRequest

isScienceMetadata

public static boolean isScienceMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta)

Determine if a given object should be treated as an XML science metadata object.

Parameters:

sysmeta - - the SystemMetadata describing the object

Returns:

true if the object should be treated as science metadata

isValidIdentifier

public static boolean isValidIdentifier(org.dataone.service.types.v1.Identifier pid)

Check for whitespace in the given pid. null pids are also invalid by default

Parameters:

pid -

Returns:

insertOrUpdateDocument

public java.lang.String insertOrUpdateDocument(java.io.InputStream xmlStream,
                                               java.lang.String encoding,
                                               org.dataone.service.types.v1.Identifier pid,
                                               org.dataone.service.types.v1.Session session,
                                               java.lang.String insertOrUpdate,
                                               java.lang.String formatId,
                                               org.dataone.service.types.v1.Checksum checksum)
                                        throws org.dataone.service.exceptions.ServiceFailure,
                                               java.io.IOException,
                                               edu.ucsb.nceas.utilities.PropertyNotFoundException

Insert or update an XML document into Metacat

Parameters:

xml - - the XML document to insert or update

pid - - the identifier to be used for the resulting object

Returns:

localId - the resulting docid of the document created or updated

Throws:

org.dataone.service.exceptions.ServiceFailure

java.io.IOException

edu.ucsb.nceas.utilities.PropertyNotFoundException

insertDataObject

public java.lang.String insertDataObject(java.io.InputStream object,
                                         org.dataone.service.types.v1.Identifier pid,
                                         org.dataone.service.types.v1.Session session,
                                         org.dataone.service.types.v1.Checksum checksum)
                                  throws org.dataone.service.exceptions.ServiceFailure,
                                         org.dataone.service.exceptions.InvalidSystemMetadata,
                                         org.dataone.service.exceptions.NotAuthorized

Insert a data document

Parameters:

object -

pid -

sessionData -

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotAuthorized

org.dataone.service.exceptions.InvalidSystemMetadata

insertSystemMetadata

public void insertSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta)
                          throws org.dataone.service.exceptions.ServiceFailure

Insert a systemMetadata document and return its localId

Throws:

org.dataone.service.exceptions.ServiceFailure

listObjects

public org.dataone.service.types.v1.ObjectList listObjects(org.dataone.service.types.v1.Session session,
                                                           java.util.Date startTime,
                                                           java.util.Date endTime,
                                                           org.dataone.service.types.v1.ObjectFormatIdentifier objectFormatId,
                                                           org.dataone.service.types.v1.Identifier identifier,
                                                           org.dataone.service.types.v1.NodeReference nodeId,
                                                           java.lang.Integer start,
                                                           java.lang.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

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 (>=)

objectFormat - - Restrict results to the specified object format

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

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

updateSystemMetadata

protected void updateSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysMeta)
                             throws org.dataone.service.exceptions.ServiceFailure

Update a systemMetadata document

Parameters:

sysMeta - - the system metadata object in the system to update

Throws:

org.dataone.service.exceptions.ServiceFailure

updateSystemMetadata

protected boolean updateSystemMetadata(org.dataone.service.types.v1.Session session,
                                       org.dataone.service.types.v1.Identifier pid,
                                       org.dataone.service.types.v2.SystemMetadata sysmeta,
                                       boolean needUpdateModificationDate,
                                       org.dataone.service.types.v2.SystemMetadata currentSysmeta,
                                       boolean fromCN)
                                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. The caller of this method should lock the system metadata in hazelcast server.

Parameters:

session - - the identity of the client which calls the method

pid - - the identifier of the object which will be updated

sysmeta - - the new system metadata

Returns:

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

expandPermissions

protected static java.util.List<org.dataone.service.types.v1.Permission> expandPermissions(org.dataone.service.types.v1.Permission permission)

Given a Permission, returns a list of all permissions that it encompasses Permissions are hierarchical so that WRITE also allows READ.

Parameters:

permission -

Returns:

list of included Permissions for the given permission

listNodesBySubject

protected java.util.List<org.dataone.service.types.v2.Node> listNodesBySubject(org.dataone.service.types.v1.Subject subject,
                                                                               org.dataone.service.types.v2.NodeList nodelist)
                                                                        throws org.dataone.service.exceptions.ServiceFailure,
                                                                               org.dataone.service.exceptions.NotImplemented

Calls CN.listNodes() to assemble a list of nodes that have been registered with the DataONE infrastructure that match the given session subject

Parameters:

subject - - the subject serving as the filter.

Returns:

nodes - List of nodes from the registry with a matching session subject

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotImplemented

archiveObject

protected org.dataone.service.types.v1.Identifier archiveObject(boolean log,
                                                                org.dataone.service.types.v1.Session session,
                                                                org.dataone.service.types.v1.Identifier pid,
                                                                org.dataone.service.types.v2.SystemMetadata sysMeta,
                                                                boolean needModifyDate)
                                                         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. Note: it doesn't check the authorization; it doesn't lock the system metadata;it only accept pid.

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

archiveCNObject

protected void archiveCNObject(boolean log,
                               org.dataone.service.types.v1.Session session,
                               org.dataone.service.types.v1.Identifier pid,
                               org.dataone.service.types.v2.SystemMetadata sysMeta,
                               boolean needModifyDate)
                        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

Archive a object on cn and notify the replica. This method doesn't lock the system metadata map. The caller should lock it. This method doesn't check the authorization; this method only accept a pid. It wouldn't notify the replca that the system metadata has been changed.

Parameters:

session -

pid -

sysMeta -

notifyReplica -

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

checkV1SystemMetaPidExist

public void checkV1SystemMetaPidExist(org.dataone.service.types.v1.Identifier identifier,
                                      java.lang.String serviceFailureCode,
                                      java.lang.String serviceFailureMessage,
                                      java.lang.String noFoundCode,
                                      java.lang.String notFoundMessage)
                               throws org.dataone.service.exceptions.ServiceFailure,
                                      org.dataone.service.exceptions.NotFound

A utility method for v1 api to check the specified identifier exists as a pid Uses the IdentifierManager to call the Identifier table directly - this detects Identifiers for deleted objects (where the SystemMetadata doesn't exist, but the Identifier remains)

Parameters:

identifier - the specified identifier

serviceFailureCode - the detail error code for the service failure exception

noFoundCode - the detail error code for the not found exception

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotFound

getPIDForSID

protected org.dataone.service.types.v1.Identifier getPIDForSID(org.dataone.service.types.v1.Identifier sid,
                                                               java.lang.String serviceFailureCode)
                                                        throws org.dataone.service.exceptions.ServiceFailure

Utility method to get the PID for an SID. If the specified identifier is not an SID , null will be returned.

Parameters:

sid - the specified sid

serviceFailureCode - the detail error code for the service failure exception

Returns:

the pid for the sid. If the specified identifier is not an SID, null will be returned.

Throws:

org.dataone.service.exceptions.ServiceFailure

See Also:

as well for situations where you need the SystemMetadata. The advantage of this method is that it doesn't unmarshall systemmetadata, and doesn't throw NotFound exceptions.

getSystemMetadataForPID

protected org.dataone.service.types.v2.SystemMetadata getSystemMetadataForPID(org.dataone.service.types.v1.Identifier pid,
                                                                              java.lang.String serviceFailureCode,
                                                                              java.lang.String invalidRequestCode,
                                                                              java.lang.String notFoundCode,
                                                                              boolean needDeleteInfo)
                                                                       throws org.dataone.service.exceptions.ServiceFailure,
                                                                              org.dataone.service.exceptions.InvalidRequest,
                                                                              org.dataone.service.exceptions.NotFound

Get the system metadata for the given PID (not a sid).

Parameters:

pid -

serviceFailureCode -

invalidRequestCode -

Returns:

the system metadata associated with the pid

Throws:

org.dataone.service.exceptions.ServiceFailure

org.dataone.service.exceptions.NotFound

org.dataone.service.exceptions.InvalidRequest

checkSidInModifyingSystemMetadata

protected boolean checkSidInModifyingSystemMetadata(org.dataone.service.types.v2.SystemMetadata sysmeta,
                                                    java.lang.String invalidSystemMetadataCode,
                                                    java.lang.String serviceFailureCode)
                                             throws org.dataone.service.exceptions.InvalidSystemMetadata,
                                                    org.dataone.service.exceptions.ServiceFailure

Throws:

org.dataone.service.exceptions.InvalidSystemMetadata

org.dataone.service.exceptions.ServiceFailure

listViews

public org.dataone.service.types.v2.OptionList listViews(org.dataone.service.types.v1.Session arg0)
                                                  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

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

listViews

public org.dataone.service.types.v2.OptionList listViews()
                                                  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

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

view

public java.io.InputStream view(org.dataone.service.types.v1.Session session,
                                java.lang.String format,
                                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.InvalidRequest,
                                org.dataone.service.exceptions.NotImplemented,
                                org.dataone.service.exceptions.NotFound

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

existsInObsoletes

protected java.lang.String existsInObsoletes(org.dataone.service.types.v1.Identifier id)
                                      throws org.dataone.service.exceptions.InvalidRequest,
                                             org.dataone.service.exceptions.ServiceFailure

Throws:

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.ServiceFailure

existsInObsoletedBy

protected java.lang.String existsInObsoletedBy(org.dataone.service.types.v1.Identifier id)
                                        throws org.dataone.service.exceptions.InvalidRequest,
                                               org.dataone.service.exceptions.ServiceFailure

Throws:

org.dataone.service.exceptions.InvalidRequest

org.dataone.service.exceptions.ServiceFailure