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/**
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* '$RCSfile$'
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* Copyright: 2000-2011 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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*
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* '$Author: $'
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* '$Date: $'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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package edu.ucsb.nceas.metacat.dataone;
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import java.util.Date;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.dataone.service.cn.CNAuthorization;
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import org.dataone.service.cn.CNCore;
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import org.dataone.service.cn.CNRead;
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import org.dataone.service.cn.CNReplication;
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import org.dataone.service.exceptions.IdentifierNotUnique;
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import org.dataone.service.exceptions.InsufficientResources;
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import org.dataone.service.exceptions.InvalidRequest;
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import org.dataone.service.exceptions.InvalidSystemMetadata;
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import org.dataone.service.exceptions.InvalidToken;
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import org.dataone.service.exceptions.NotAuthorized;
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import org.dataone.service.exceptions.NotFound;
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import org.dataone.service.exceptions.NotImplemented;
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import org.dataone.service.exceptions.ServiceFailure;
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import org.dataone.service.types.Checksum;
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import org.dataone.service.types.Identifier;
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import org.dataone.service.types.NodeList;
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import org.dataone.service.types.ObjectFormat;
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import org.dataone.service.types.ObjectFormatIdentifier;
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import org.dataone.service.types.ObjectFormatList;
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import org.dataone.service.types.ObjectList;
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import org.dataone.service.types.ObjectLocationList;
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import org.dataone.service.types.Permission;
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import org.dataone.service.types.QueryType;
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import org.dataone.service.types.Replica;
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import org.dataone.service.types.ReplicationPolicy;
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import org.dataone.service.types.ReplicationStatus;
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import org.dataone.service.types.Session;
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import org.dataone.service.types.Subject;
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import org.dataone.service.types.SystemMetadata;
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import edu.ucsb.nceas.metacat.EventLog;
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import edu.ucsb.nceas.metacat.IdentifierManager;
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import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
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import edu.ucsb.nceas.metacat.replication.ForceReplicationSystemMetadataHandler;
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/**
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* Represents Metacat's implementation of the DataONE Coordinating Node
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* service API. Methods implement the various CN* interfaces, and methods common
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* to both Member Node and Coordinating Node interfaces are found in the
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* D1NodeService super class.
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*
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*/
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public class CNodeService extends D1NodeService implements CNAuthorization,
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CNCore, CNRead, CNReplication {
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/* the instance of the CNodeService object */
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private static CNodeService instance = null;
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/* the logger instance */
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private Logger logMetacat = null;
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/**
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* singleton accessor
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*/
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public static CNodeService getInstance() {
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if (instance == null) {
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instance = new CNodeService();
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}
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return instance;
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}
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/**
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* Constructor, private for singleton access
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*/
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private CNodeService() {
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super();
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logMetacat = Logger.getLogger(CNodeService.class);
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}
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/**
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* Set the replication policy for an object given the object identifier
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - the object identifier for the given object
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* @param policy - the replication policy to be applied
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*
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* @return true or false
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*
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* @throws NotImplemented
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* @throws NotAuthorized
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* @throws ServiceFailure
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* @throws InvalidRequest
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*
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*/
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@Override
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public boolean setReplicationPolicy(Session session, Identifier pid,
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ReplicationPolicy policy)
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throws NotImplemented, NotFound, NotAuthorized, ServiceFailure, InvalidRequest, InvalidToken {
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// get the subject
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Subject subject = session.getSubject();
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// get the system metadata
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String guid = pid.getValue();
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// are we allowed to do this?
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if (!isAuthorized(session, pid, Permission.CHANGE_PERMISSION)) {
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throw new NotAuthorized("4881", Permission.CHANGE_PERMISSION + " not allowed by " + subject.getValue() + " on " + guid);
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}
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SystemMetadata systemMetadata = null;
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try {
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systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);
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} catch (McdbDocNotFoundException e) {
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throw new NotFound("4884", "No record found for: " + guid);
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}
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// set the new policy
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systemMetadata.setReplicationPolicy(policy);
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// update the metadata
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try {
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IdentifierManager.getInstance().updateSystemMetadata(systemMetadata);
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} catch (McdbDocNotFoundException e) {
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throw new ServiceFailure("4882", e.getMessage());
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}
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return true;
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}
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/**
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* Set the replication status for an object given the object identifier
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - the object identifier for the given object
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* @param status - the replication status to be applied
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*
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* @return true or false
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*
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* @throws NotImplemented
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* @throws NotAuthorized
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* @throws ServiceFailure
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* @throws InvalidRequest
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* @throws InvalidToken
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* @throws NotFound
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*
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*/
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@Override
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public boolean setReplicationStatus(Session session, Identifier pid,
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ReplicationStatus status)
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throws ServiceFailure, NotImplemented, InvalidToken, NotAuthorized,
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InvalidRequest, NotFound {
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// get the subject
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Subject subject = session.getSubject();
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// get the system metadata
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String guid = pid.getValue();
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// are we allowed to do this?
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if (!isAuthorized(session, pid, Permission.WRITE)) {
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throw new NotAuthorized("4720", Permission.WRITE + " not allowed by " + subject.getValue() + " on " + guid);
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}
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SystemMetadata systemMetadata = null;
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try {
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systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);
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} catch (McdbDocNotFoundException e) {
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throw new NotFound("4740", "No record found for: " + guid);
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}
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// set the status for each replica
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// TODO: should this method select a certain replica?
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List<Replica> replicas = systemMetadata.getReplicaList();
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for (Replica replica: replicas) {
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replica.setReplicationStatus(status);
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}
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// [re]set the list -- redundant?
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systemMetadata.setReplicaList(replicas);
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// update the metadata
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try {
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IdentifierManager.getInstance().updateSystemMetadata(systemMetadata);
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} catch (McdbDocNotFoundException e) {
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throw new ServiceFailure("4700", e.getMessage());
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}
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return true;
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}
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/**
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* Test that the specified relationship between pidOfSubject and pidOfObject exists
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param node - the node information for the given node be modified
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*
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* @return true if the relationship exists
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*
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* @throws InvalidToken
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* @throws ServiceFailure
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* @throws NotAuthorized
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* @throws NotFound
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* @throws InvalidRequest
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* @throws NotImplemented
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*/
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@Override
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public boolean assertRelation(Session session, Identifier pidOfSubject,
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String relationship, Identifier pidOfObject)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
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InvalidRequest, NotImplemented {
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// get the system metadata
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String guid1 = pidOfSubject.getValue();
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// are we allowed to do this?
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if (!isAuthorized(session, pidOfSubject, Permission.READ)) {
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throw new NotAuthorized("4881", Permission.READ + " not allowed on " + guid1);
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}
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SystemMetadata systemMetadata = null;
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try {
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systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid1);
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} catch (McdbDocNotFoundException e) {
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throw new NotFound("4884", "No record found for: " + guid1);
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}
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// check relationships
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// TODO: make this more strongly typed?
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if (relationship.equalsIgnoreCase("describes")) {
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for (Identifier pid: systemMetadata.getDescribeList()) {
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if (pid.getValue().equals(pidOfObject.getValue())) {
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return true;
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}
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}
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//return systemMetadata.getDescribeList().contains(pidOfObject);
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}
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if (relationship.equalsIgnoreCase("describedBy")) {
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for (Identifier pid: systemMetadata.getDescribedByList()) {
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if (pid.getValue().equals(pidOfObject.getValue())) {
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return true;
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}
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}
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//return systemMetadata.getDescribedByList().contains(pidOfObject);
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}
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if (relationship.equalsIgnoreCase("derivedFrom")) {
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for (Identifier pid: systemMetadata.getDerivedFromList()) {
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if (pid.getValue().equals(pidOfObject.getValue())) {
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return true;
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}
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}
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//return systemMetadata.getDerivedFromList().contains(pidOfObject);
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}
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if (relationship.equalsIgnoreCase("obsoletes")) {
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for (Identifier pid: systemMetadata.getObsoleteList()) {
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if (pid.getValue().equals(pidOfObject.getValue())) {
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return true;
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}
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}
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//return systemMetadata.getObsoleteList().contains(pidOfObject);
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}
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if (relationship.equalsIgnoreCase("obsoletedBy")) {
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for (Identifier pid: systemMetadata.getObsoletedByList()) {
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if (pid.getValue().equals(pidOfObject.getValue())) {
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return true;
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}
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}
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//return systemMetadata.getObsoletedByList().contains(pidOfObject);
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}
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return false;
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}
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/**
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* Return the checksum of the object given the identifier
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - the object identifier for the given object
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*
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* @return checksum - the checksum of the object
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*
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* @throws InvalidToken
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* @throws ServiceFailure
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* @throws NotAuthorized
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* @throws NotFound
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* @throws InvalidRequest
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* @throws NotImplemented
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*/
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@Override
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public Checksum getChecksum(Session session, Identifier pid)
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throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
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InvalidRequest, NotImplemented {
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if (!isAuthorized(session, pid, Permission.READ)) {
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throw new NotAuthorized("1400", Permission.READ + " not allowed on " + pid.getValue());
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}
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SystemMetadata systemMetadata = null;
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try {
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systemMetadata = IdentifierManager.getInstance().getSystemMetadata(pid.getValue());
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} catch (McdbDocNotFoundException e) {
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throw new NotFound("1420", "No record found for: " + pid.getValue());
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}
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Checksum checksum = systemMetadata.getChecksum();
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return checksum;
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}
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/**
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* Resolve the location of a given object
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param pid - the object identifier for the given object
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*
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* @return objectLocationList - the list of nodes known to contain the object
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*
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* @throws InvalidRequest
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* @throws InvalidToken
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* @throws ServiceFailure
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* @throws NotAuthorized
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* @throws NotFound
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* @throws NotImplemented
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*/
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@Override
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public ObjectLocationList resolve(Session session, Identifier pid)
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throws InvalidRequest, InvalidToken, ServiceFailure, NotAuthorized,
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NotFound, NotImplemented {
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throw new NotImplemented("4131", "resolve not implemented");
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}
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/**
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* Search the metadata catalog for identifiers that match the criteria
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*
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* @param session - the Session object containing the credentials for the Subject
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* @param queryType - An identifier for the type of query expression
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* provided in the query
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* @param query - The criteria for matching the characteristics of the
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* metadata objects of interest
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*
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* @return objectList - the list of objects matching the criteria
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*
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* @throws InvalidToken
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* @throws ServiceFailure
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* @throws NotAuthorized
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* @throws InvalidRequest
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* @throws NotImplemented
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*/
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@Override
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public ObjectList search(Session session, QueryType queryType, String query)
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throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,
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NotImplemented {
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374
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ObjectList objectList = null;
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try {
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objectList =
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IdentifierManager.getInstance().querySystemMetadata(
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null, //startTime,
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null, //endTime,
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null, //objectFormat,
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false, //replicaStatus,
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0, //start,
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-1 //count
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);
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386
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387
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} catch (Exception e) {
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throw new ServiceFailure("4310", "Error querying system metadata: " + e.getMessage());
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389
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}
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390
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391
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return objectList;
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392
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|
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//throw new NotImplemented("4281", "search not implemented");
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394
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|
395
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// the code block below is from an older implementation
|
396
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|
397
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/* This block commented out because of the EcoGrid circular dependency.
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398
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* For now, query will not be supported until the circularity can be
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399
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* resolved, probably by moving the ecogrid query syntax transformers
|
400
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* directly into the Metacat codebase. MBJ 2010-02-03
|
401
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402
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try {
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403
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EcogridQueryParser parser = new EcogridQueryParser(request
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.getReader());
|
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parser.parseXML();
|
406
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QueryType queryType = parser.getEcogridQuery();
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407
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EcogridJavaToMetacatJavaQueryTransformer queryTransformer =
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408
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new EcogridJavaToMetacatJavaQueryTransformer();
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409
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QuerySpecification metacatQuery = queryTransformer
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410
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.transform(queryType);
|
411
|
|
412
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DBQuery metacat = new DBQuery();
|
413
|
|
414
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boolean useXMLIndex = (new Boolean(PropertyService
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415
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.getProperty("database.usexmlindex"))).booleanValue();
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String xmlquery = "query"; // we don't care the query in resultset,
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// the query can be anything
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PrintWriter out = null; // we don't want metacat result, so set out null
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419
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420
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// parameter: queryspecification, user, group, usingIndexOrNot
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StringBuffer result = metacat.createResultDocument(xmlquery,
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metacatQuery, out, username, groupNames, useXMLIndex);
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423
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424
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// create result set transfer
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425
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String saxparser = PropertyService.getProperty("xml.saxparser");
|
426
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MetacatResultsetParser metacatResultsetParser = new MetacatResultsetParser(
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427
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new StringReader(result.toString()), saxparser, queryType
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428
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.getNamespace().get_value());
|
429
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ResultsetType records = metacatResultsetParser.getEcogridResult();
|
430
|
|
431
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System.out
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432
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.println(EcogridResultsetTransformer.toXMLString(records));
|
433
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response.setContentType("text/xml");
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434
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out = response.getWriter();
|
435
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out.print(EcogridResultsetTransformer.toXMLString(records));
|
436
|
|
437
|
} catch (Exception e) {
|
438
|
e.printStackTrace();
|
439
|
}*/
|
440
|
|
441
|
|
442
|
}
|
443
|
|
444
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/**
|
445
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* Returns the object format registered in the DataONE Object Format
|
446
|
* Vocabulary for the given format identifier
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447
|
*
|
448
|
* @param fmtid - the identifier of the format requested
|
449
|
*
|
450
|
* @return objectFormat - the object format requested
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451
|
*
|
452
|
* @throws InvalidRequest
|
453
|
* @throws ServiceFailure
|
454
|
* @throws NotFound
|
455
|
* @throws InsufficientResources
|
456
|
* @throws NotImplemented
|
457
|
*/
|
458
|
@Override
|
459
|
public ObjectFormat getFormat(ObjectFormatIdentifier fmtid)
|
460
|
throws InvalidRequest, ServiceFailure, NotFound, InsufficientResources,
|
461
|
NotImplemented {
|
462
|
|
463
|
return ObjectFormatService.getInstance().getFormat(fmtid);
|
464
|
|
465
|
}
|
466
|
|
467
|
/**
|
468
|
* Returns a list of all object formats registered in the DataONE Object
|
469
|
* Format Vocabulary
|
470
|
*
|
471
|
* @return objectFormatList - The list of object formats registered in
|
472
|
* the DataONE Object Format Vocabulary
|
473
|
*
|
474
|
* @throws InvalidRequest
|
475
|
* @throws ServiceFailure
|
476
|
* @throws NotImplemented
|
477
|
* @throws NotFound
|
478
|
* @throws InsufficientResources
|
479
|
*/
|
480
|
@Override
|
481
|
public ObjectFormatList listFormats()
|
482
|
throws InvalidRequest, ServiceFailure, NotFound, InsufficientResources,
|
483
|
NotImplemented {
|
484
|
|
485
|
return ObjectFormatService.getInstance().listFormats();
|
486
|
}
|
487
|
|
488
|
/**
|
489
|
* Returns a list of nodes that have been registered with the DataONE infrastructure
|
490
|
*
|
491
|
* @return nodeList - List of nodes from the registry
|
492
|
*
|
493
|
* @throws ServiceFailure
|
494
|
* @throws NotImplemented
|
495
|
*/
|
496
|
@Override
|
497
|
public NodeList listNodes()
|
498
|
throws NotImplemented, ServiceFailure {
|
499
|
|
500
|
throw new NotImplemented("4800", "listNodes not implemented");
|
501
|
}
|
502
|
|
503
|
/**
|
504
|
* Provides a mechanism for adding system metadata independently of its
|
505
|
* associated object, such as when adding system metadata for data objects.
|
506
|
*
|
507
|
* @param session - the Session object containing the credentials for the Subject
|
508
|
* @param pid - The identifier of the object to register the system metadata against
|
509
|
* @param sysmeta - The system metadata to be registered
|
510
|
*
|
511
|
* @return true if the registration succeeds
|
512
|
*
|
513
|
* @throws NotImplemented
|
514
|
* @throws NotAuthorized
|
515
|
* @throws ServiceFailure
|
516
|
* @throws InvalidRequest
|
517
|
* @throws InvalidSystemMetadata
|
518
|
*/
|
519
|
@Override
|
520
|
public boolean registerSystemMetadata(Session session, Identifier guid,
|
521
|
SystemMetadata sysmeta)
|
522
|
throws NotImplemented, NotAuthorized, ServiceFailure, InvalidRequest,
|
523
|
InvalidSystemMetadata {
|
524
|
|
525
|
// TODO: control who can call this?
|
526
|
if (session == null) {
|
527
|
//TODO: many of the thrown exceptions do not use the correct error codes
|
528
|
//check these against the docs and correct them
|
529
|
throw new NotAuthorized("4861", "No Session - could not authorize for registration." +
|
530
|
" If you are not logged in, please do so and retry the request.");
|
531
|
}
|
532
|
|
533
|
// verify that guid == SystemMetadata.getIdentifier()
|
534
|
logMetacat.debug("Comparing guid|sysmeta_guid: " + guid.getValue() + "|" + sysmeta.getIdentifier().getValue());
|
535
|
if (!guid.getValue().equals(sysmeta.getIdentifier().getValue())) {
|
536
|
throw new InvalidRequest("4863",
|
537
|
"GUID in method call (" + guid.getValue() + ") does not match GUID in system metadata (" +
|
538
|
sysmeta.getIdentifier().getValue() + ").");
|
539
|
}
|
540
|
|
541
|
logMetacat.debug("Checking if identifier exists...");
|
542
|
// Check that the identifier does not already exist
|
543
|
if (IdentifierManager.getInstance().identifierExists(guid.getValue())) {
|
544
|
throw new InvalidRequest("4863",
|
545
|
"GUID is already in use by an existing object.");
|
546
|
|
547
|
}
|
548
|
|
549
|
// insert the system metadata into the object store
|
550
|
logMetacat.debug("Starting to insert SystemMetadata...");
|
551
|
sysmeta.setDateSysMetadataModified(new Date());
|
552
|
try {
|
553
|
IdentifierManager.getInstance().createSystemMetadata(sysmeta);
|
554
|
// force replication of this record
|
555
|
ForceReplicationSystemMetadataHandler forceReplication =
|
556
|
new ForceReplicationSystemMetadataHandler(guid.getValue(), null);
|
557
|
} catch (Exception e) {
|
558
|
throw new ServiceFailure("4862", "Error inserting system metadata: " + e.getClass() + ": " + e.getMessage());
|
559
|
}
|
560
|
|
561
|
logMetacat.debug("Returning from registerSystemMetadata");
|
562
|
EventLog.getInstance().log(null, session.getSubject().getValue(), guid.getValue(), "registerSystemMetadata");
|
563
|
return true;
|
564
|
}
|
565
|
|
566
|
/**
|
567
|
* Given an optional scope and format, reserves and returns an identifier
|
568
|
* within that scope and format that is unique and will not be
|
569
|
* used by any other sessions.
|
570
|
*
|
571
|
* @param session - the Session object containing the credentials for the Subject
|
572
|
* @param pid - The identifier of the object to register the system metadata against
|
573
|
* @param scope - An optional string to be used to qualify the scope of
|
574
|
* the identifier namespace, which is applied differently
|
575
|
* depending on the format requested. If scope is not
|
576
|
* supplied, a default scope will be used.
|
577
|
* @param format - The optional name of the identifier format to be used,
|
578
|
* drawn from a DataONE-specific vocabulary of identifier
|
579
|
* format names, including several common syntaxes such
|
580
|
* as DOI, LSID, UUID, and LSRN, among others. If the
|
581
|
* format is not supplied by the caller, the CN service
|
582
|
* will use a default identifier format, which may change
|
583
|
* over time.
|
584
|
*
|
585
|
* @return true if the registration succeeds
|
586
|
*
|
587
|
* @throws InvalidToken
|
588
|
* @throws ServiceFailure
|
589
|
* @throws NotAuthorized
|
590
|
* @throws IdentifierNotUnique
|
591
|
* @throws NotImplemented
|
592
|
*/
|
593
|
@Override
|
594
|
public Identifier reserveIdentifier(Session session, Identifier pid,
|
595
|
String scope, String format)
|
596
|
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
597
|
NotImplemented, InvalidRequest {
|
598
|
|
599
|
throw new NotImplemented("4191", "reserveIdentifier not implemented on this node");
|
600
|
}
|
601
|
|
602
|
/**
|
603
|
* Checks whether the pid is reserved by the subject in the session param
|
604
|
* If the reservation is held on the pid by the subject, we return true.
|
605
|
*
|
606
|
* @param session - the Session object containing the Subject
|
607
|
* @param pid - The identifier to check
|
608
|
*
|
609
|
* @return true if the reservation exists for the subject/pid
|
610
|
*
|
611
|
* @throws InvalidToken
|
612
|
* @throws ServiceFailure
|
613
|
* @throws NotFound - when the pid is not found (in use or in reservation)
|
614
|
* @throws NotAuthorized - when the subject does not hold a reservation on the pid
|
615
|
* @throws IdentifierNotUnique - when the pid is in use
|
616
|
* @throws NotImplemented
|
617
|
*/
|
618
|
|
619
|
@Override
|
620
|
public boolean hasReservation(Session session, Identifier pid)
|
621
|
throws InvalidToken, ServiceFailure, NotFound, NotAuthorized, IdentifierNotUnique,
|
622
|
NotImplemented, InvalidRequest {
|
623
|
|
624
|
throw new NotImplemented("4191", "hasReservation not implemented on this node");
|
625
|
}
|
626
|
|
627
|
/**
|
628
|
* Changes ownership (RightsHolder) of the specified object to the
|
629
|
* subject specified by userId
|
630
|
*
|
631
|
* @param session - the Session object containing the credentials for the Subject
|
632
|
* @param pid - Identifier of the object to be modified
|
633
|
* @param userId - The subject that will be taking ownership of the specified object.
|
634
|
*
|
635
|
* @return pid - the identifier of the modified object
|
636
|
*
|
637
|
* @throws ServiceFailure
|
638
|
* @throws InvalidToken
|
639
|
* @throws NotFound
|
640
|
* @throws NotAuthorized
|
641
|
* @throws NotImplemented
|
642
|
* @throws InvalidRequest
|
643
|
*/
|
644
|
@Override
|
645
|
public Identifier setOwner(Session session, Identifier pid, Subject userId)
|
646
|
throws InvalidToken, ServiceFailure, NotFound, NotAuthorized,
|
647
|
NotImplemented, InvalidRequest {
|
648
|
|
649
|
// get the subject
|
650
|
Subject subject = session.getSubject();
|
651
|
// get the system metadata
|
652
|
String guid = pid.getValue();
|
653
|
|
654
|
// are we allowed to do this?
|
655
|
if (!isAuthorized(session, pid, Permission.CHANGE_PERMISSION)) {
|
656
|
throw new NotAuthorized("4440", "not allowed by " + subject.getValue() + " on " + guid);
|
657
|
}
|
658
|
|
659
|
SystemMetadata systemMetadata = null;
|
660
|
try {
|
661
|
systemMetadata = IdentifierManager.getInstance().getSystemMetadata(guid);
|
662
|
} catch (McdbDocNotFoundException e) {
|
663
|
throw new NotFound("4460", "No record found for: " + guid);
|
664
|
}
|
665
|
|
666
|
// set the new rights holder
|
667
|
systemMetadata.setRightsHolder(userId);
|
668
|
|
669
|
// update the metadata
|
670
|
try {
|
671
|
IdentifierManager.getInstance().updateSystemMetadata(systemMetadata);
|
672
|
} catch (McdbDocNotFoundException e) {
|
673
|
throw new ServiceFailure("4490", e.getMessage());
|
674
|
}
|
675
|
|
676
|
return pid;
|
677
|
}
|
678
|
|
679
|
}
|