| 1 |
6179
|
cjones
|
/**
|
| 2 |
|
|
* '$RCSfile$'
|
| 3 |
|
|
* Copyright: 2000-2011 Regents of the University of California and the
|
| 4 |
|
|
* National Center for Ecological Analysis and Synthesis
|
| 5 |
|
|
*
|
| 6 |
|
|
* '$Author: $'
|
| 7 |
|
|
* '$Date: $'
|
| 8 |
|
|
*
|
| 9 |
|
|
* This program is free software; you can redistribute it and/or modify
|
| 10 |
|
|
* it under the terms of the GNU General Public License as published by
|
| 11 |
|
|
* the Free Software Foundation; either version 2 of the License, or
|
| 12 |
|
|
* (at your option) any later version.
|
| 13 |
|
|
*
|
| 14 |
|
|
* This program is distributed in the hope that it will be useful,
|
| 15 |
|
|
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
| 16 |
|
|
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
| 17 |
|
|
* GNU General Public License for more details.
|
| 18 |
|
|
*
|
| 19 |
|
|
* You should have received a copy of the GNU General Public License
|
| 20 |
|
|
* along with this program; if not, write to the Free Software
|
| 21 |
|
|
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
| 22 |
|
|
*/
|
| 23 |
|
|
|
| 24 |
|
|
package edu.ucsb.nceas.metacat.dataone;
|
| 25 |
|
|
|
| 26 |
7417
|
leinfelder
|
import java.io.ByteArrayInputStream;
|
| 27 |
7860
|
leinfelder
|
import java.io.ByteArrayOutputStream;
|
| 28 |
7850
|
leinfelder
|
import java.io.File;
|
| 29 |
8800
|
leinfelder
|
import java.io.FileInputStream;
|
| 30 |
7850
|
leinfelder
|
import java.io.FileOutputStream;
|
| 31 |
6228
|
cjones
|
import java.io.IOException;
|
| 32 |
6179
|
cjones
|
import java.io.InputStream;
|
| 33 |
8190
|
leinfelder
|
import java.io.InputStreamReader;
|
| 34 |
7860
|
leinfelder
|
import java.io.OutputStreamWriter;
|
| 35 |
9387
|
walker
|
import java.io.StringReader;
|
| 36 |
7849
|
leinfelder
|
import java.io.UnsupportedEncodingException;
|
| 37 |
7860
|
leinfelder
|
import java.io.Writer;
|
| 38 |
7021
|
leinfelder
|
import java.math.BigInteger;
|
| 39 |
7849
|
leinfelder
|
import java.net.URISyntaxException;
|
| 40 |
9352
|
walker
|
import java.nio.charset.Charset;
|
| 41 |
6228
|
cjones
|
import java.security.NoSuchAlgorithmException;
|
| 42 |
7860
|
leinfelder
|
import java.sql.SQLException;
|
| 43 |
7417
|
leinfelder
|
import java.util.ArrayList;
|
| 44 |
6525
|
leinfelder
|
import java.util.Calendar;
|
| 45 |
6179
|
cjones
|
import java.util.Date;
|
| 46 |
8437
|
walker
|
import java.util.HashMap;
|
| 47 |
7680
|
tao
|
import java.util.HashSet;
|
| 48 |
7860
|
leinfelder
|
import java.util.Hashtable;
|
| 49 |
6250
|
cjones
|
import java.util.List;
|
| 50 |
7849
|
leinfelder
|
import java.util.Map;
|
| 51 |
7417
|
leinfelder
|
import java.util.Set;
|
| 52 |
6389
|
leinfelder
|
import java.util.Timer;
|
| 53 |
7489
|
leinfelder
|
import java.util.UUID;
|
| 54 |
7418
|
leinfelder
|
import java.util.Vector;
|
| 55 |
10104
|
tao
|
import java.util.concurrent.ExecutorService;
|
| 56 |
|
|
import java.util.concurrent.Executors;
|
| 57 |
6179
|
cjones
|
|
| 58 |
6542
|
leinfelder
|
import javax.servlet.http.HttpServletRequest;
|
| 59 |
9387
|
walker
|
import javax.xml.transform.Result;
|
| 60 |
|
|
import javax.xml.transform.Source;
|
| 61 |
|
|
import javax.xml.transform.TransformerException;
|
| 62 |
|
|
import javax.xml.transform.TransformerFactory;
|
| 63 |
|
|
import javax.xml.transform.dom.DOMSource;
|
| 64 |
|
|
import javax.xml.transform.stream.StreamResult;
|
| 65 |
6542
|
leinfelder
|
|
| 66 |
6258
|
cjones
|
import org.apache.commons.io.IOUtils;
|
| 67 |
9997
|
tao
|
import org.apache.commons.lang.NotImplementedException;
|
| 68 |
6179
|
cjones
|
import org.apache.log4j.Logger;
|
| 69 |
8810
|
leinfelder
|
import org.dataone.client.v2.CNode;
|
| 70 |
|
|
import org.dataone.client.v2.itk.D1Client;
|
| 71 |
|
|
import org.dataone.client.v2.MNode;
|
| 72 |
|
|
import org.dataone.client.v2.formats.ObjectFormatCache;
|
| 73 |
6552
|
leinfelder
|
import org.dataone.client.auth.CertificateManager;
|
| 74 |
8810
|
leinfelder
|
import org.dataone.client.v2.formats.ObjectFormatInfo;
|
| 75 |
6552
|
leinfelder
|
import org.dataone.configuration.Settings;
|
| 76 |
7849
|
leinfelder
|
import org.dataone.ore.ResourceMapFactory;
|
| 77 |
6795
|
cjones
|
import org.dataone.service.exceptions.BaseException;
|
| 78 |
6179
|
cjones
|
import org.dataone.service.exceptions.IdentifierNotUnique;
|
| 79 |
|
|
import org.dataone.service.exceptions.InsufficientResources;
|
| 80 |
|
|
import org.dataone.service.exceptions.InvalidRequest;
|
| 81 |
|
|
import org.dataone.service.exceptions.InvalidSystemMetadata;
|
| 82 |
|
|
import org.dataone.service.exceptions.InvalidToken;
|
| 83 |
|
|
import org.dataone.service.exceptions.NotAuthorized;
|
| 84 |
|
|
import org.dataone.service.exceptions.NotFound;
|
| 85 |
|
|
import org.dataone.service.exceptions.NotImplemented;
|
| 86 |
|
|
import org.dataone.service.exceptions.ServiceFailure;
|
| 87 |
6185
|
leinfelder
|
import org.dataone.service.exceptions.SynchronizationFailed;
|
| 88 |
6179
|
cjones
|
import org.dataone.service.exceptions.UnsupportedType;
|
| 89 |
8810
|
leinfelder
|
import org.dataone.service.mn.tier1.v2.MNCore;
|
| 90 |
|
|
import org.dataone.service.mn.tier1.v2.MNRead;
|
| 91 |
|
|
import org.dataone.service.mn.tier2.v2.MNAuthorization;
|
| 92 |
|
|
import org.dataone.service.mn.tier3.v2.MNStorage;
|
| 93 |
|
|
import org.dataone.service.mn.tier4.v2.MNReplication;
|
| 94 |
|
|
import org.dataone.service.mn.v2.MNPackage;
|
| 95 |
|
|
import org.dataone.service.mn.v2.MNQuery;
|
| 96 |
|
|
import org.dataone.service.mn.v2.MNView;
|
| 97 |
8591
|
leinfelder
|
import org.dataone.service.types.v1.AccessRule;
|
| 98 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.Checksum;
|
| 99 |
7144
|
leinfelder
|
import org.dataone.service.types.v1.DescribeResponse;
|
| 100 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.Event;
|
| 101 |
|
|
import org.dataone.service.types.v1.Identifier;
|
| 102 |
8810
|
leinfelder
|
import org.dataone.service.types.v2.Log;
|
| 103 |
|
|
import org.dataone.service.types.v2.LogEntry;
|
| 104 |
|
|
import org.dataone.service.types.v2.OptionList;
|
| 105 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.MonitorInfo;
|
| 106 |
|
|
import org.dataone.service.types.v1.MonitorList;
|
| 107 |
8810
|
leinfelder
|
import org.dataone.service.types.v2.Node;
|
| 108 |
|
|
import org.dataone.service.types.v2.NodeList;
|
| 109 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.NodeReference;
|
| 110 |
|
|
import org.dataone.service.types.v1.NodeState;
|
| 111 |
|
|
import org.dataone.service.types.v1.NodeType;
|
| 112 |
8810
|
leinfelder
|
import org.dataone.service.types.v2.ObjectFormat;
|
| 113 |
9353
|
tao
|
import org.dataone.service.types.v1.Group;
|
| 114 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.ObjectFormatIdentifier;
|
| 115 |
|
|
import org.dataone.service.types.v1.ObjectList;
|
| 116 |
|
|
import org.dataone.service.types.v1.Permission;
|
| 117 |
|
|
import org.dataone.service.types.v1.Ping;
|
| 118 |
9340
|
tao
|
import org.dataone.service.types.v1.Replica;
|
| 119 |
6528
|
cjones
|
import org.dataone.service.types.v1.ReplicationStatus;
|
| 120 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.Schedule;
|
| 121 |
|
|
import org.dataone.service.types.v1.Service;
|
| 122 |
|
|
import org.dataone.service.types.v1.Services;
|
| 123 |
|
|
import org.dataone.service.types.v1.Session;
|
| 124 |
|
|
import org.dataone.service.types.v1.Subject;
|
| 125 |
|
|
import org.dataone.service.types.v1.Synchronization;
|
| 126 |
8810
|
leinfelder
|
import org.dataone.service.types.v2.SystemMetadata;
|
| 127 |
7417
|
leinfelder
|
import org.dataone.service.types.v1.util.AuthUtils;
|
| 128 |
6366
|
leinfelder
|
import org.dataone.service.types.v1.util.ChecksumUtil;
|
| 129 |
7417
|
leinfelder
|
import org.dataone.service.types.v1_1.QueryEngineDescription;
|
| 130 |
|
|
import org.dataone.service.types.v1_1.QueryEngineList;
|
| 131 |
7418
|
leinfelder
|
import org.dataone.service.types.v1_1.QueryField;
|
| 132 |
6476
|
jones
|
import org.dataone.service.util.Constants;
|
| 133 |
8594
|
leinfelder
|
import org.dataone.service.util.TypeMarshaller;
|
| 134 |
7849
|
leinfelder
|
import org.dspace.foresite.OREException;
|
| 135 |
|
|
import org.dspace.foresite.OREParserException;
|
| 136 |
|
|
import org.dspace.foresite.ORESerialiserException;
|
| 137 |
|
|
import org.dspace.foresite.ResourceMap;
|
| 138 |
8437
|
walker
|
import org.ecoinformatics.datamanager.parser.DataPackage;
|
| 139 |
|
|
import org.ecoinformatics.datamanager.parser.Entity;
|
| 140 |
|
|
import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
|
| 141 |
|
|
import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;
|
| 142 |
9387
|
walker
|
import org.w3c.dom.Document;
|
| 143 |
6179
|
cjones
|
|
| 144 |
7448
|
leinfelder
|
import edu.ucsb.nceas.ezid.EZIDException;
|
| 145 |
7417
|
leinfelder
|
import edu.ucsb.nceas.metacat.DBQuery;
|
| 146 |
7860
|
leinfelder
|
import edu.ucsb.nceas.metacat.DBTransform;
|
| 147 |
6234
|
cjones
|
import edu.ucsb.nceas.metacat.EventLog;
|
| 148 |
6230
|
cjones
|
import edu.ucsb.nceas.metacat.IdentifierManager;
|
| 149 |
6234
|
cjones
|
import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
|
| 150 |
7417
|
leinfelder
|
import edu.ucsb.nceas.metacat.MetaCatServlet;
|
| 151 |
6389
|
leinfelder
|
import edu.ucsb.nceas.metacat.MetacatHandler;
|
| 152 |
9478
|
tao
|
import edu.ucsb.nceas.metacat.ReadOnlyChecker;
|
| 153 |
7772
|
tao
|
import edu.ucsb.nceas.metacat.common.query.EnabledQueryEngines;
|
| 154 |
7757
|
leinfelder
|
import edu.ucsb.nceas.metacat.common.query.stream.ContentTypeByteArrayInputStream;
|
| 155 |
6648
|
leinfelder
|
import edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService;
|
| 156 |
7662
|
tao
|
import edu.ucsb.nceas.metacat.index.MetacatSolrEngineDescriptionHandler;
|
| 157 |
7620
|
tao
|
import edu.ucsb.nceas.metacat.index.MetacatSolrIndex;
|
| 158 |
6340
|
cjones
|
import edu.ucsb.nceas.metacat.properties.PropertyService;
|
| 159 |
7418
|
leinfelder
|
import edu.ucsb.nceas.metacat.shared.MetacatUtilException;
|
| 160 |
8026
|
leinfelder
|
import edu.ucsb.nceas.metacat.util.DeleteOnCloseFileInputStream;
|
| 161 |
7441
|
leinfelder
|
import edu.ucsb.nceas.metacat.util.DocumentUtil;
|
| 162 |
8810
|
leinfelder
|
import edu.ucsb.nceas.metacat.util.SkinUtil;
|
| 163 |
6542
|
leinfelder
|
import edu.ucsb.nceas.metacat.util.SystemUtil;
|
| 164 |
6340
|
cjones
|
import edu.ucsb.nceas.utilities.PropertyNotFoundException;
|
| 165 |
8190
|
leinfelder
|
import edu.ucsb.nceas.utilities.XMLUtilities;
|
| 166 |
8800
|
leinfelder
|
import edu.ucsb.nceas.utilities.export.HtmlToPdf;
|
| 167 |
7850
|
leinfelder
|
import gov.loc.repository.bagit.Bag;
|
| 168 |
|
|
import gov.loc.repository.bagit.BagFactory;
|
| 169 |
|
|
import gov.loc.repository.bagit.writer.impl.ZipWriter;
|
| 170 |
6230
|
cjones
|
|
| 171 |
6179
|
cjones
|
/**
|
| 172 |
|
|
* Represents Metacat's implementation of the DataONE Member Node
|
| 173 |
|
|
* service API. Methods implement the various MN* interfaces, and methods common
|
| 174 |
|
|
* to both Member Node and Coordinating Node interfaces are found in the
|
| 175 |
|
|
* D1NodeService base class.
|
| 176 |
6288
|
cjones
|
*
|
| 177 |
|
|
* Implements:
|
| 178 |
|
|
* MNCore.ping()
|
| 179 |
|
|
* MNCore.getLogRecords()
|
| 180 |
|
|
* MNCore.getObjectStatistics()
|
| 181 |
|
|
* MNCore.getOperationStatistics()
|
| 182 |
|
|
* MNCore.getStatus()
|
| 183 |
|
|
* MNCore.getCapabilities()
|
| 184 |
|
|
* MNRead.get()
|
| 185 |
|
|
* MNRead.getSystemMetadata()
|
| 186 |
|
|
* MNRead.describe()
|
| 187 |
|
|
* MNRead.getChecksum()
|
| 188 |
|
|
* MNRead.listObjects()
|
| 189 |
|
|
* MNRead.synchronizationFailed()
|
| 190 |
|
|
* MNAuthorization.isAuthorized()
|
| 191 |
|
|
* MNAuthorization.setAccessPolicy()
|
| 192 |
|
|
* MNStorage.create()
|
| 193 |
|
|
* MNStorage.update()
|
| 194 |
|
|
* MNStorage.delete()
|
| 195 |
9177
|
tao
|
* MNStorage.updateSystemMetadata()
|
| 196 |
6288
|
cjones
|
* MNReplication.replicate()
|
| 197 |
|
|
*
|
| 198 |
6179
|
cjones
|
*/
|
| 199 |
6599
|
cjones
|
public class MNodeService extends D1NodeService
|
| 200 |
8810
|
leinfelder
|
implements MNAuthorization, MNCore, MNRead, MNReplication, MNStorage, MNQuery, MNView, MNPackage {
|
| 201 |
6179
|
cjones
|
|
| 202 |
7772
|
tao
|
//private static final String PATHQUERY = "pathquery";
|
| 203 |
7849
|
leinfelder
|
public static final String UUID_SCHEME = "UUID";
|
| 204 |
|
|
public static final String DOI_SCHEME = "DOI";
|
| 205 |
7489
|
leinfelder
|
private static final String UUID_PREFIX = "urn:uuid:";
|
| 206 |
9387
|
walker
|
|
| 207 |
|
|
private static String XPATH_EML_ID = "/eml:eml/@packageId";
|
| 208 |
7418
|
leinfelder
|
|
| 209 |
|
|
/* the logger instance */
|
| 210 |
6475
|
jones
|
private Logger logMetacat = null;
|
| 211 |
6795
|
cjones
|
|
| 212 |
|
|
/* A reference to a remote Memeber Node */
|
| 213 |
9295
|
tao
|
//private MNode mn;
|
| 214 |
6795
|
cjones
|
|
| 215 |
|
|
/* A reference to a Coordinating Node */
|
| 216 |
|
|
private CNode cn;
|
| 217 |
10104
|
tao
|
|
| 218 |
|
|
// shared executor
|
| 219 |
|
|
private static ExecutorService executor = null;
|
| 220 |
6241
|
cjones
|
|
| 221 |
10104
|
tao
|
static {
|
| 222 |
|
|
// use a shared executor service with nThreads == one less than available processors
|
| 223 |
|
|
int availableProcessors = Runtime.getRuntime().availableProcessors();
|
| 224 |
|
|
int nThreads = availableProcessors * 1;
|
| 225 |
|
|
nThreads--;
|
| 226 |
|
|
nThreads = Math.max(1, nThreads);
|
| 227 |
|
|
executor = Executors.newFixedThreadPool(nThreads);
|
| 228 |
|
|
}
|
| 229 |
6795
|
cjones
|
|
| 230 |
10104
|
tao
|
|
| 231 |
6475
|
jones
|
/**
|
| 232 |
|
|
* Singleton accessor to get an instance of MNodeService.
|
| 233 |
|
|
*
|
| 234 |
|
|
* @return instance - the instance of MNodeService
|
| 235 |
|
|
*/
|
| 236 |
6542
|
leinfelder
|
public static MNodeService getInstance(HttpServletRequest request) {
|
| 237 |
|
|
return new MNodeService(request);
|
| 238 |
6179
|
cjones
|
}
|
| 239 |
|
|
|
| 240 |
6475
|
jones
|
/**
|
| 241 |
|
|
* Constructor, private for singleton access
|
| 242 |
|
|
*/
|
| 243 |
6542
|
leinfelder
|
private MNodeService(HttpServletRequest request) {
|
| 244 |
|
|
super(request);
|
| 245 |
6475
|
jones
|
logMetacat = Logger.getLogger(MNodeService.class);
|
| 246 |
6552
|
leinfelder
|
|
| 247 |
|
|
// set the Member Node certificate file location
|
| 248 |
|
|
CertificateManager.getInstance().setCertificateLocation(Settings.getConfiguration().getString("D1Client.certificate.file"));
|
| 249 |
6310
|
cjones
|
}
|
| 250 |
6475
|
jones
|
|
| 251 |
|
|
/**
|
| 252 |
|
|
* Deletes an object from the Member Node, where the object is either a
|
| 253 |
|
|
* data object or a science metadata object.
|
| 254 |
|
|
*
|
| 255 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 256 |
|
|
* @param pid - The object identifier to be deleted
|
| 257 |
|
|
*
|
| 258 |
|
|
* @return pid - the identifier of the object used for the deletion
|
| 259 |
|
|
*
|
| 260 |
|
|
* @throws InvalidToken
|
| 261 |
|
|
* @throws ServiceFailure
|
| 262 |
|
|
* @throws NotAuthorized
|
| 263 |
|
|
* @throws NotFound
|
| 264 |
|
|
* @throws NotImplemented
|
| 265 |
|
|
* @throws InvalidRequest
|
| 266 |
|
|
*/
|
| 267 |
|
|
@Override
|
| 268 |
|
|
public Identifier delete(Session session, Identifier pid)
|
| 269 |
6610
|
cjones
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
| 270 |
6475
|
jones
|
|
| 271 |
9478
|
tao
|
if(isReadOnlyMode()) {
|
| 272 |
9481
|
tao
|
throw new ServiceFailure("2902", ReadOnlyChecker.DATAONEERROR);
|
| 273 |
9478
|
tao
|
}
|
| 274 |
7162
|
leinfelder
|
// only admin of the MN or the CN is allowed a full delete
|
| 275 |
|
|
boolean allowed = false;
|
| 276 |
7330
|
leinfelder
|
allowed = isAdminAuthorized(session);
|
| 277 |
8360
|
tao
|
|
| 278 |
9050
|
tao
|
String serviceFailureCode = "2902";
|
| 279 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
| 280 |
|
|
if(sid != null) {
|
| 281 |
|
|
pid = sid;
|
| 282 |
|
|
}
|
| 283 |
|
|
|
| 284 |
8360
|
tao
|
//check if it is the authoritative member node
|
| 285 |
|
|
if(!allowed) {
|
| 286 |
|
|
allowed = isAuthoritativeMNodeAdmin(session, pid);
|
| 287 |
|
|
}
|
| 288 |
|
|
|
| 289 |
7162
|
leinfelder
|
if (!allowed) {
|
| 290 |
7245
|
cjones
|
throw new NotAuthorized("1320", "The provided identity does not have " + "permission to delete objects on the Node.");
|
| 291 |
7162
|
leinfelder
|
}
|
| 292 |
|
|
|
| 293 |
7077
|
leinfelder
|
// defer to superclass implementation
|
| 294 |
|
|
return super.delete(session, pid);
|
| 295 |
6250
|
cjones
|
}
|
| 296 |
|
|
|
| 297 |
6475
|
jones
|
/**
|
| 298 |
|
|
* Updates an existing object by creating a new object identified by
|
| 299 |
|
|
* newPid on the Member Node which explicitly obsoletes the object
|
| 300 |
|
|
* identified by pid through appropriate changes to the SystemMetadata
|
| 301 |
|
|
* of pid and newPid
|
| 302 |
|
|
*
|
| 303 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 304 |
|
|
* @param pid - The identifier of the object to be updated
|
| 305 |
|
|
* @param object - the new object bytes
|
| 306 |
|
|
* @param sysmeta - the new system metadata describing the object
|
| 307 |
|
|
*
|
| 308 |
|
|
* @return newPid - the identifier of the new object
|
| 309 |
|
|
*
|
| 310 |
|
|
* @throws InvalidToken
|
| 311 |
|
|
* @throws ServiceFailure
|
| 312 |
|
|
* @throws NotAuthorized
|
| 313 |
|
|
* @throws NotFound
|
| 314 |
|
|
* @throws NotImplemented
|
| 315 |
|
|
* @throws IdentifierNotUnique
|
| 316 |
|
|
* @throws UnsupportedType
|
| 317 |
|
|
* @throws InsufficientResources
|
| 318 |
|
|
* @throws InvalidSystemMetadata
|
| 319 |
|
|
* @throws InvalidRequest
|
| 320 |
|
|
*/
|
| 321 |
|
|
@Override
|
| 322 |
6575
|
cjones
|
public Identifier update(Session session, Identifier pid, InputStream object,
|
| 323 |
|
|
Identifier newPid, SystemMetadata sysmeta)
|
| 324 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
| 325 |
|
|
UnsupportedType, InsufficientResources, NotFound,
|
| 326 |
|
|
InvalidSystemMetadata, NotImplemented, InvalidRequest {
|
| 327 |
9781
|
cjones
|
|
| 328 |
10118
|
tao
|
long startTime = System.currentTimeMillis();
|
| 329 |
|
|
|
| 330 |
9781
|
cjones
|
if(isReadOnlyMode()) {
|
| 331 |
|
|
throw new ServiceFailure("1310", ReadOnlyChecker.DATAONEERROR);
|
| 332 |
|
|
}
|
| 333 |
|
|
|
| 334 |
|
|
//transform a sid to a pid if it is applicable
|
| 335 |
|
|
String serviceFailureCode = "1310";
|
| 336 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
| 337 |
|
|
if(sid != null) {
|
| 338 |
|
|
pid = sid;
|
| 339 |
|
|
}
|
| 340 |
|
|
|
| 341 |
|
|
String localId = null;
|
| 342 |
|
|
boolean allowed = false;
|
| 343 |
|
|
boolean isScienceMetadata = false;
|
| 344 |
|
|
|
| 345 |
|
|
if (session == null) {
|
| 346 |
|
|
throw new InvalidToken("1210", "No session has been provided");
|
| 347 |
|
|
}
|
| 348 |
|
|
Subject subject = session.getSubject();
|
| 349 |
|
|
|
| 350 |
|
|
// verify the pid is valid format
|
| 351 |
|
|
if (!isValidIdentifier(pid)) {
|
| 352 |
|
|
throw new InvalidRequest("1202", "The provided identifier is invalid.");
|
| 353 |
|
|
}
|
| 354 |
|
|
|
| 355 |
|
|
// verify the new pid is valid format
|
| 356 |
|
|
if (!isValidIdentifier(newPid)) {
|
| 357 |
|
|
throw new InvalidRequest("1202", "The provided identifier is invalid.");
|
| 358 |
|
|
}
|
| 359 |
|
|
|
| 360 |
|
|
// make sure that the newPid doesn't exists
|
| 361 |
|
|
boolean idExists = true;
|
| 362 |
9600
|
tao
|
try {
|
| 363 |
9781
|
cjones
|
idExists = IdentifierManager.getInstance().identifierExists(newPid.getValue());
|
| 364 |
|
|
} catch (SQLException e) {
|
| 365 |
|
|
throw new ServiceFailure("1310",
|
| 366 |
|
|
"The requested identifier " + newPid.getValue() +
|
| 367 |
|
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
| 368 |
|
|
}
|
| 369 |
|
|
if (idExists) {
|
| 370 |
|
|
throw new IdentifierNotUnique("1220",
|
| 371 |
|
|
"The requested identifier " + newPid.getValue() +
|
| 372 |
|
|
" is already used by another object and" +
|
| 373 |
|
|
"therefore can not be used for this object. Clients should choose" +
|
| 374 |
|
|
"a new identifier that is unique and retry the operation or " +
|
| 375 |
|
|
"use CN.reserveIdentifier() to reserve one.");
|
| 376 |
9044
|
tao
|
|
| 377 |
9781
|
cjones
|
}
|
| 378 |
|
|
|
| 379 |
|
|
|
| 380 |
|
|
|
| 381 |
|
|
// check for the existing identifier
|
| 382 |
|
|
try {
|
| 383 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 384 |
6575
|
cjones
|
|
| 385 |
9781
|
cjones
|
} catch (McdbDocNotFoundException e) {
|
| 386 |
|
|
throw new InvalidRequest("1202", "The object with the provided " +
|
| 387 |
|
|
"identifier was not found.");
|
| 388 |
6575
|
cjones
|
|
| 389 |
9781
|
cjones
|
} catch (SQLException ee) {
|
| 390 |
|
|
throw new ServiceFailure("1310", "The object with the provided " +
|
| 391 |
|
|
"identifier "+pid.getValue()+" can't be identified since - "+ee.getMessage());
|
| 392 |
|
|
}
|
| 393 |
|
|
|
| 394 |
10118
|
tao
|
long end =System.currentTimeMillis();
|
| 395 |
|
|
logMetacat.debug("MNodeService.update - the time spending on checking the validation of the old pid "+pid.getValue()+" and the new pid "+newPid.getValue()+" is "+(end- startTime)+ " milli seconds.");
|
| 396 |
|
|
|
| 397 |
9781
|
cjones
|
// set the originating node
|
| 398 |
|
|
NodeReference originMemberNode = this.getCapabilities().getIdentifier();
|
| 399 |
|
|
sysmeta.setOriginMemberNode(originMemberNode);
|
| 400 |
|
|
|
| 401 |
|
|
// set the submitter to match the certificate
|
| 402 |
|
|
sysmeta.setSubmitter(subject);
|
| 403 |
|
|
// set the dates
|
| 404 |
|
|
Date now = Calendar.getInstance().getTime();
|
| 405 |
|
|
sysmeta.setDateSysMetadataModified(now);
|
| 406 |
|
|
sysmeta.setDateUploaded(now);
|
| 407 |
|
|
|
| 408 |
|
|
// make sure serial version is set to something
|
| 409 |
|
|
BigInteger serialVersion = sysmeta.getSerialVersion();
|
| 410 |
|
|
if (serialVersion == null) {
|
| 411 |
|
|
sysmeta.setSerialVersion(BigInteger.ZERO);
|
| 412 |
|
|
}
|
| 413 |
10118
|
tao
|
long startTime2 = System.currentTimeMillis();
|
| 414 |
9781
|
cjones
|
// does the subject have WRITE ( == update) priveleges on the pid?
|
| 415 |
|
|
//allowed = isAuthorized(session, pid, Permission.WRITE);
|
| 416 |
|
|
//CN having the permission is allowed; user with the write permission and calling on the authoritative node is allowed.
|
| 417 |
9997
|
tao
|
try {
|
| 418 |
|
|
allowed = allowUpdating(session, pid, Permission.WRITE);
|
| 419 |
|
|
} catch (NotFound e) {
|
| 420 |
|
|
throw new NotFound("1280", "Can't determine if the client has the permission to update the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 421 |
|
|
} catch(ServiceFailure e) {
|
| 422 |
|
|
throw new ServiceFailure("1310", "Can't determine if the client has the permission to update the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 423 |
|
|
} catch(NotAuthorized e) {
|
| 424 |
|
|
throw new NotAuthorized("1200", "Can't determine if the client has the permission to update the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 425 |
|
|
} catch(NotImplemented e) {
|
| 426 |
|
|
throw new NotImplemented("1201","Can't determine if the client has the permission to update he object with id "+pid.getValue()+" since "+e.getDescription());
|
| 427 |
|
|
} catch(InvalidRequest e) {
|
| 428 |
|
|
throw new InvalidRequest("1202", "Can't determine if the client has the permission to update the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 429 |
|
|
} catch(InvalidToken e) {
|
| 430 |
|
|
throw new InvalidToken("1210", "Can't determine if the client has the permission to update the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 431 |
|
|
}
|
| 432 |
|
|
|
| 433 |
10118
|
tao
|
end =System.currentTimeMillis();
|
| 434 |
|
|
logMetacat.debug("MNodeService.update - the time spending on checking if the user has the permission to update the old pid "+pid.getValue()+" with the new pid "+newPid.getValue()+" is "+(end- startTime2)+ " milli seconds.");
|
| 435 |
|
|
|
| 436 |
9781
|
cjones
|
if (allowed) {
|
| 437 |
10118
|
tao
|
long startTime3 = System.currentTimeMillis();
|
| 438 |
9781
|
cjones
|
// check quality of SM
|
| 439 |
|
|
if (sysmeta.getObsoletedBy() != null) {
|
| 440 |
|
|
throw new InvalidSystemMetadata("1300", "Cannot include obsoletedBy when updating object");
|
| 441 |
|
|
}
|
| 442 |
|
|
if (sysmeta.getObsoletes() != null && !sysmeta.getObsoletes().getValue().equals(pid.getValue())) {
|
| 443 |
|
|
throw new InvalidSystemMetadata("1300", "The identifier provided in obsoletes does not match old Identifier");
|
| 444 |
|
|
}
|
| 445 |
|
|
|
| 446 |
|
|
// get the existing system metadata for the object
|
| 447 |
|
|
SystemMetadata existingSysMeta = getSystemMetadata(session, pid);
|
| 448 |
|
|
//System.out.println("the archive is "+existingSysMeta.getArchived());
|
| 449 |
|
|
//Base on documentation, we can't update an archived object:
|
| 450 |
|
|
//The update operation MUST fail with Exceptions.InvalidRequest on objects that have the Types.SystemMetadata.archived property set to true.
|
| 451 |
|
|
if(existingSysMeta.getArchived() != null && existingSysMeta.getArchived()) {
|
| 452 |
|
|
throw new InvalidRequest("1202","An archived object"+pid.getValue()+" can't be updated");
|
| 453 |
9200
|
tao
|
}
|
| 454 |
9781
|
cjones
|
|
| 455 |
|
|
// check for previous update
|
| 456 |
|
|
// see: https://redmine.dataone.org/issues/3336
|
| 457 |
|
|
Identifier existingObsoletedBy = existingSysMeta.getObsoletedBy();
|
| 458 |
|
|
if (existingObsoletedBy != null) {
|
| 459 |
|
|
throw new InvalidRequest("1202",
|
| 460 |
|
|
"The previous identifier has already been made obsolete by: " + existingObsoletedBy.getValue());
|
| 461 |
7400
|
leinfelder
|
}
|
| 462 |
10118
|
tao
|
end =System.currentTimeMillis();
|
| 463 |
|
|
logMetacat.debug("MNodeService.update - the time spending on checking the quality of the system metadata of the old pid "+pid.getValue()+" and the new pid "+newPid.getValue()+" is "+(end- startTime3)+ " milli seconds.");
|
| 464 |
|
|
|
| 465 |
9781
|
cjones
|
//check the sid in the system metadata. If it exists, it should be non-exist or match the old sid in the previous system metadata.
|
| 466 |
|
|
Identifier sidInSys = sysmeta.getSeriesId();
|
| 467 |
|
|
if(sidInSys != null) {
|
| 468 |
|
|
if (!isValidIdentifier(sidInSys)) {
|
| 469 |
|
|
throw new InvalidSystemMetadata("1300", "The provided series id in the system metadata is invalid.");
|
| 470 |
9046
|
tao
|
}
|
| 471 |
9781
|
cjones
|
Identifier previousSid = existingSysMeta.getSeriesId();
|
| 472 |
|
|
if(previousSid != null) {
|
| 473 |
|
|
// there is a previous sid, if the new sid doesn't match it, the new sid should be non-existing.
|
| 474 |
|
|
if(!sidInSys.getValue().equals(previousSid.getValue())) {
|
| 475 |
9044
|
tao
|
try {
|
| 476 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(sidInSys.getValue());
|
| 477 |
|
|
} catch (SQLException e) {
|
| 478 |
|
|
throw new ServiceFailure("1310",
|
| 479 |
|
|
"The requested identifier " + sidInSys.getValue() +
|
| 480 |
|
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
| 481 |
|
|
}
|
| 482 |
|
|
if(idExists) {
|
| 483 |
9781
|
cjones
|
throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata doesn't match the previous series id "
|
| 484 |
|
|
+previousSid.getValue()+", so it should NOT exist. However, it was used by another object.");
|
| 485 |
9044
|
tao
|
}
|
| 486 |
|
|
}
|
| 487 |
9781
|
cjones
|
} else {
|
| 488 |
|
|
// there is no previous sid, the new sid should be non-existing.
|
| 489 |
|
|
try {
|
| 490 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(sidInSys.getValue());
|
| 491 |
|
|
} catch (SQLException e) {
|
| 492 |
|
|
throw new ServiceFailure("1310",
|
| 493 |
|
|
"The requested identifier " + sidInSys.getValue() +
|
| 494 |
|
|
" couldn't be determined if it is unique since : "+e.getMessage());
|
| 495 |
9601
|
tao
|
}
|
| 496 |
9781
|
cjones
|
if(idExists) {
|
| 497 |
|
|
throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata should NOT exist since the previous series id is null."
|
| 498 |
|
|
+"However, it was used by another object.");
|
| 499 |
|
|
}
|
| 500 |
9601
|
tao
|
}
|
| 501 |
9781
|
cjones
|
//the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario)
|
| 502 |
|
|
if(sidInSys.getValue().equals(newPid.getValue())) {
|
| 503 |
|
|
throw new InvalidSystemMetadata("1300", "The series id "+sidInSys.getValue()+" in the system metadata shouldn't have the same value of the pid.");
|
| 504 |
|
|
}
|
| 505 |
|
|
}
|
| 506 |
10118
|
tao
|
|
| 507 |
|
|
long end2 =System.currentTimeMillis();
|
| 508 |
|
|
logMetacat.debug("MNodeService.update - the time spending on checking the sid validation of the old pid "+pid.getValue()+" and the new pid "+newPid.getValue()+" is "+(end2- end)+ " milli seconds.");
|
| 509 |
|
|
|
| 510 |
9781
|
cjones
|
|
| 511 |
|
|
isScienceMetadata = isScienceMetadata(sysmeta);
|
| 512 |
|
|
|
| 513 |
|
|
// do we have XML metadata or a data object?
|
| 514 |
|
|
if (isScienceMetadata) {
|
| 515 |
|
|
|
| 516 |
|
|
// update the science metadata XML document
|
| 517 |
|
|
// TODO: handle non-XML metadata/data documents (like netCDF)
|
| 518 |
|
|
// TODO: don't put objects into memory using stream to string
|
| 519 |
|
|
//String objectAsXML = "";
|
| 520 |
|
|
try {
|
| 521 |
|
|
//objectAsXML = IOUtils.toString(object, "UTF-8");
|
| 522 |
9783
|
leinfelder
|
String formatId = null;
|
| 523 |
|
|
if(sysmeta.getFormatId() != null) {
|
| 524 |
|
|
formatId = sysmeta.getFormatId().getValue();
|
| 525 |
|
|
}
|
| 526 |
|
|
localId = insertOrUpdateDocument(object, "UTF-8", pid, session, "update", formatId);
|
| 527 |
9781
|
cjones
|
|
| 528 |
|
|
// register the newPid and the generated localId
|
| 529 |
|
|
if (newPid != null) {
|
| 530 |
|
|
IdentifierManager.getInstance().createMapping(newPid.getValue(), localId);
|
| 531 |
9044
|
tao
|
}
|
| 532 |
9781
|
cjones
|
|
| 533 |
|
|
} catch (IOException e) {
|
| 534 |
|
|
String msg = "The Node is unable to create the object. " + "There was a problem converting the object to XML";
|
| 535 |
|
|
logMetacat.info(msg);
|
| 536 |
|
|
throw new ServiceFailure("1310", msg + ": " + e.getMessage());
|
| 537 |
|
|
|
| 538 |
9044
|
tao
|
}
|
| 539 |
9781
|
cjones
|
|
| 540 |
6475
|
jones
|
} else {
|
| 541 |
9781
|
cjones
|
|
| 542 |
|
|
// update the data object
|
| 543 |
|
|
localId = insertDataObject(object, newPid, session);
|
| 544 |
|
|
|
| 545 |
6475
|
jones
|
}
|
| 546 |
9781
|
cjones
|
|
| 547 |
10118
|
tao
|
long end3 =System.currentTimeMillis();
|
| 548 |
|
|
logMetacat.debug("MNodeService.update - the time spending on saving the object with the new pid "+newPid.getValue()+" is "+(end3- end2)+ " milli seconds.");
|
| 549 |
|
|
|
| 550 |
9781
|
cjones
|
// add the newPid to the obsoletedBy list for the existing sysmeta
|
| 551 |
|
|
existingSysMeta.setObsoletedBy(newPid);
|
| 552 |
|
|
//increase version
|
| 553 |
|
|
BigInteger current = existingSysMeta.getSerialVersion();
|
| 554 |
|
|
//System.out.println("the current version is "+current);
|
| 555 |
|
|
current = current.add(BigInteger.ONE);
|
| 556 |
|
|
//System.out.println("the new current version is "+current);
|
| 557 |
|
|
existingSysMeta.setSerialVersion(current);
|
| 558 |
|
|
// then update the existing system metadata
|
| 559 |
|
|
updateSystemMetadata(existingSysMeta);
|
| 560 |
|
|
|
| 561 |
|
|
// prep the new system metadata, add pid to the affected lists
|
| 562 |
|
|
sysmeta.setObsoletes(pid);
|
| 563 |
|
|
//sysmeta.addDerivedFrom(pid);
|
| 564 |
|
|
|
| 565 |
|
|
// and insert the new system metadata
|
| 566 |
|
|
insertSystemMetadata(sysmeta);
|
| 567 |
|
|
|
| 568 |
|
|
// log the update event
|
| 569 |
|
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), subject.getValue(), localId, Event.UPDATE.toString());
|
| 570 |
|
|
|
| 571 |
10118
|
tao
|
long end4 =System.currentTimeMillis();
|
| 572 |
|
|
logMetacat.debug("MNodeService.update - the time spending on updating/saving system metadata of the old pid "+pid.getValue()+" and the new pid "+newPid.getValue()+" and saving the log information is "+(end4- end3)+ " milli seconds.");
|
| 573 |
|
|
|
| 574 |
9781
|
cjones
|
// attempt to register the identifier - it checks if it is a doi
|
| 575 |
|
|
try {
|
| 576 |
|
|
DOIService.getInstance().registerDOI(sysmeta);
|
| 577 |
|
|
} catch (Exception e) {
|
| 578 |
|
|
throw new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
|
| 579 |
|
|
}
|
| 580 |
10118
|
tao
|
long end5 =System.currentTimeMillis();
|
| 581 |
|
|
logMetacat.debug("MNodeService.update - the time spending on registering the doi (if it is doi ) of the new pid "+newPid.getValue()+" is "+(end5- end4)+ " milli seconds.");
|
| 582 |
|
|
|
| 583 |
9781
|
cjones
|
} else {
|
| 584 |
|
|
throw new NotAuthorized("1200", "The provided identity does not have " + "permission to UPDATE the object identified by " + pid.getValue()
|
| 585 |
|
|
+ " on the Member Node.");
|
| 586 |
9600
|
tao
|
}
|
| 587 |
9781
|
cjones
|
|
| 588 |
10118
|
tao
|
long end6 =System.currentTimeMillis();
|
| 589 |
|
|
logMetacat.debug("MNodeService.update - the total time of updating the old pid " +pid.getValue() +" whth the new pid "+newPid.getValue()+" is "+(end6- startTime)+ " milli seconds.");
|
| 590 |
6475
|
jones
|
return newPid;
|
| 591 |
6250
|
cjones
|
}
|
| 592 |
6254
|
cjones
|
|
| 593 |
6475
|
jones
|
public Identifier create(Session session, Identifier pid, InputStream object, SystemMetadata sysmeta) throws InvalidToken, ServiceFailure, NotAuthorized,
|
| 594 |
|
|
IdentifierNotUnique, UnsupportedType, InsufficientResources, InvalidSystemMetadata, NotImplemented, InvalidRequest {
|
| 595 |
9781
|
cjones
|
|
| 596 |
|
|
if(isReadOnlyMode()) {
|
| 597 |
|
|
throw new ServiceFailure("1190", ReadOnlyChecker.DATAONEERROR);
|
| 598 |
|
|
}
|
| 599 |
|
|
// check for null session
|
| 600 |
|
|
if (session == null) {
|
| 601 |
|
|
throw new InvalidToken("1110", "Session is required to WRITE to the Node.");
|
| 602 |
|
|
}
|
| 603 |
|
|
// verify the pid is valid format
|
| 604 |
|
|
if (!isValidIdentifier(pid)) {
|
| 605 |
|
|
throw new InvalidRequest("1102", "The provided identifier is invalid.");
|
| 606 |
|
|
}
|
| 607 |
|
|
// set the submitter to match the certificate
|
| 608 |
|
|
sysmeta.setSubmitter(session.getSubject());
|
| 609 |
|
|
// set the originating node
|
| 610 |
|
|
NodeReference originMemberNode = this.getCapabilities().getIdentifier();
|
| 611 |
|
|
sysmeta.setOriginMemberNode(originMemberNode);
|
| 612 |
|
|
|
| 613 |
|
|
// if no authoritative MN, set it to the same
|
| 614 |
|
|
if (sysmeta.getAuthoritativeMemberNode() == null) {
|
| 615 |
|
|
sysmeta.setAuthoritativeMemberNode(originMemberNode);
|
| 616 |
|
|
}
|
| 617 |
|
|
|
| 618 |
|
|
sysmeta.setArchived(false);
|
| 619 |
|
|
|
| 620 |
|
|
// set the dates
|
| 621 |
|
|
Date now = Calendar.getInstance().getTime();
|
| 622 |
|
|
sysmeta.setDateSysMetadataModified(now);
|
| 623 |
|
|
sysmeta.setDateUploaded(now);
|
| 624 |
|
|
|
| 625 |
|
|
// set the serial version
|
| 626 |
|
|
sysmeta.setSerialVersion(BigInteger.ZERO);
|
| 627 |
|
|
|
| 628 |
|
|
// check that we are not attempting to subvert versioning
|
| 629 |
|
|
if (sysmeta.getObsoletes() != null && sysmeta.getObsoletes().getValue() != null) {
|
| 630 |
|
|
throw new InvalidSystemMetadata("1180",
|
| 631 |
|
|
"The supplied system metadata is invalid. " +
|
| 632 |
|
|
"The obsoletes field cannot have a value when creating entries.");
|
| 633 |
|
|
}
|
| 634 |
|
|
|
| 635 |
|
|
if (sysmeta.getObsoletedBy() != null && sysmeta.getObsoletedBy().getValue() != null) {
|
| 636 |
|
|
throw new InvalidSystemMetadata("1180",
|
| 637 |
|
|
"The supplied system metadata is invalid. " +
|
| 638 |
|
|
"The obsoletedBy field cannot have a value when creating entries.");
|
| 639 |
|
|
}
|
| 640 |
|
|
|
| 641 |
|
|
// verify the sid in the system metadata
|
| 642 |
|
|
Identifier sid = sysmeta.getSeriesId();
|
| 643 |
|
|
boolean idExists = false;
|
| 644 |
|
|
if(sid != null) {
|
| 645 |
|
|
if (!isValidIdentifier(sid)) {
|
| 646 |
|
|
throw new InvalidSystemMetadata("1180", "The provided series id is invalid.");
|
| 647 |
9068
|
tao
|
}
|
| 648 |
9781
|
cjones
|
try {
|
| 649 |
|
|
idExists = IdentifierManager.getInstance().identifierExists(sid.getValue());
|
| 650 |
|
|
} catch (SQLException e) {
|
| 651 |
|
|
throw new ServiceFailure("1190",
|
| 652 |
|
|
"The series identifier " + sid.getValue() +
|
| 653 |
|
|
" in the system metadata couldn't be determined if it is unique since : "+e.getMessage());
|
| 654 |
9068
|
tao
|
}
|
| 655 |
9781
|
cjones
|
if (idExists) {
|
| 656 |
|
|
throw new InvalidSystemMetadata("1180",
|
| 657 |
|
|
"The series identifier " + sid.getValue() +
|
| 658 |
|
|
" is already used by another object and" +
|
| 659 |
|
|
"therefore can not be used for this object. Clients should choose" +
|
| 660 |
|
|
"a new identifier that is unique and retry the operation or " +
|
| 661 |
|
|
"use CN.reserveIdentifier() to reserve one.");
|
| 662 |
|
|
|
| 663 |
9068
|
tao
|
}
|
| 664 |
9781
|
cjones
|
//the series id equals the pid (new pid hasn't been registered in the system, so IdentifierManager.getInstance().identifierExists method can't exclude this scenario )
|
| 665 |
|
|
if(sid.getValue().equals(pid.getValue())) {
|
| 666 |
|
|
throw new InvalidSystemMetadata("1180", "The series id "+sid.getValue()+" in the system metadata shouldn't have the same value of the pid.");
|
| 667 |
9068
|
tao
|
}
|
| 668 |
9600
|
tao
|
}
|
| 669 |
9781
|
cjones
|
|
| 670 |
|
|
// call the shared impl
|
| 671 |
|
|
Identifier resultPid = super.create(session, pid, object, sysmeta);
|
| 672 |
|
|
|
| 673 |
|
|
// attempt to register the identifier - it checks if it is a doi
|
| 674 |
|
|
try {
|
| 675 |
|
|
DOIService.getInstance().registerDOI(sysmeta);
|
| 676 |
|
|
} catch (Exception e) {
|
| 677 |
|
|
ServiceFailure sf = new ServiceFailure("1190", "Could not register DOI: " + e.getMessage());
|
| 678 |
|
|
sf.initCause(e);
|
| 679 |
|
|
throw sf;
|
| 680 |
|
|
}
|
| 681 |
|
|
|
| 682 |
7507
|
leinfelder
|
// return
|
| 683 |
|
|
return resultPid ;
|
| 684 |
6475
|
jones
|
}
|
| 685 |
6250
|
cjones
|
|
| 686 |
6475
|
jones
|
/**
|
| 687 |
|
|
* Called by a Coordinating Node to request that the Member Node create a
|
| 688 |
|
|
* copy of the specified object by retrieving it from another Member
|
| 689 |
|
|
* Node and storing it locally so that it can be made accessible to
|
| 690 |
|
|
* the DataONE system.
|
| 691 |
|
|
*
|
| 692 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 693 |
|
|
* @param sysmeta - Copy of the CN held system metadata for the object
|
| 694 |
|
|
* @param sourceNode - A reference to node from which the content should be
|
| 695 |
|
|
* retrieved. The reference should be resolved by
|
| 696 |
|
|
* checking the CN node registry.
|
| 697 |
|
|
*
|
| 698 |
|
|
* @return true if the replication succeeds
|
| 699 |
|
|
*
|
| 700 |
|
|
* @throws ServiceFailure
|
| 701 |
|
|
* @throws NotAuthorized
|
| 702 |
|
|
* @throws NotImplemented
|
| 703 |
|
|
* @throws UnsupportedType
|
| 704 |
|
|
* @throws InsufficientResources
|
| 705 |
|
|
* @throws InvalidRequest
|
| 706 |
|
|
*/
|
| 707 |
|
|
@Override
|
| 708 |
6786
|
cjones
|
public boolean replicate(Session session, SystemMetadata sysmeta,
|
| 709 |
|
|
NodeReference sourceNode) throws NotImplemented, ServiceFailure,
|
| 710 |
|
|
NotAuthorized, InvalidRequest, InsufficientResources,
|
| 711 |
|
|
UnsupportedType {
|
| 712 |
9480
|
tao
|
/*if(isReadOnlyMode()) {
|
| 713 |
9478
|
tao
|
throw new InvalidRequest("2153", "The Metacat member node is on the read-only mode and your request can't be fulfiled. Please try again later.");
|
| 714 |
9480
|
tao
|
}*/
|
| 715 |
6786
|
cjones
|
|
| 716 |
6875
|
cjones
|
if (session != null && sysmeta != null && sourceNode != null) {
|
| 717 |
|
|
logMetacat.info("MNodeService.replicate() called with parameters: \n" +
|
| 718 |
|
|
"\tSession.Subject = " +
|
| 719 |
|
|
session.getSubject().getValue() + "\n" +
|
| 720 |
7082
|
cjones
|
"\tidentifier = " +
|
| 721 |
|
|
sysmeta.getIdentifier().getValue() +
|
| 722 |
6875
|
cjones
|
"\n" + "\tSource NodeReference =" +
|
| 723 |
|
|
sourceNode.getValue());
|
| 724 |
|
|
}
|
| 725 |
6475
|
jones
|
boolean result = false;
|
| 726 |
6786
|
cjones
|
String nodeIdStr = null;
|
| 727 |
6651
|
cjones
|
NodeReference nodeId = null;
|
| 728 |
6786
|
cjones
|
|
| 729 |
6795
|
cjones
|
// get the referenced object
|
| 730 |
|
|
Identifier pid = sysmeta.getIdentifier();
|
| 731 |
9068
|
tao
|
// verify the pid is valid format
|
| 732 |
|
|
if (!isValidIdentifier(pid)) {
|
| 733 |
|
|
throw new InvalidRequest("2153", "The provided identifier in the system metadata is invalid.");
|
| 734 |
|
|
}
|
| 735 |
6795
|
cjones
|
|
| 736 |
|
|
// get from the membernode
|
| 737 |
|
|
// TODO: switch credentials for the server retrieval?
|
| 738 |
|
|
this.cn = D1Client.getCN();
|
| 739 |
|
|
InputStream object = null;
|
| 740 |
|
|
Session thisNodeSession = null;
|
| 741 |
|
|
SystemMetadata localSystemMetadata = null;
|
| 742 |
|
|
BaseException failure = null;
|
| 743 |
6818
|
cjones
|
String localId = null;
|
| 744 |
|
|
|
| 745 |
6795
|
cjones
|
// TODO: check credentials
|
| 746 |
|
|
// cannot be called by public
|
| 747 |
7063
|
leinfelder
|
if (session == null || session.getSubject() == null) {
|
| 748 |
7082
|
cjones
|
String msg = "No session was provided to replicate identifier " +
|
| 749 |
|
|
sysmeta.getIdentifier().getValue();
|
| 750 |
8414
|
tao
|
logMetacat.error(msg);
|
| 751 |
7192
|
cjones
|
throw new NotAuthorized("2152", msg);
|
| 752 |
|
|
|
| 753 |
6795
|
cjones
|
}
|
| 754 |
|
|
|
| 755 |
|
|
|
| 756 |
6651
|
cjones
|
// get the local node id
|
| 757 |
|
|
try {
|
| 758 |
7030
|
cjones
|
nodeIdStr = PropertyService.getProperty("dataone.nodeId");
|
| 759 |
6651
|
cjones
|
nodeId = new NodeReference();
|
| 760 |
|
|
nodeId.setValue(nodeIdStr);
|
| 761 |
6786
|
cjones
|
|
| 762 |
6651
|
cjones
|
} catch (PropertyNotFoundException e1) {
|
| 763 |
7030
|
cjones
|
String msg = "Couldn't get dataone.nodeId property: " + e1.getMessage();
|
| 764 |
6795
|
cjones
|
failure = new ServiceFailure("2151", msg);
|
| 765 |
8414
|
tao
|
//setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 766 |
6795
|
cjones
|
logMetacat.error(msg);
|
| 767 |
8414
|
tao
|
//return true;
|
| 768 |
|
|
throw new ServiceFailure("2151", msg);
|
| 769 |
6786
|
cjones
|
|
| 770 |
6651
|
cjones
|
}
|
| 771 |
6795
|
cjones
|
|
| 772 |
6475
|
jones
|
try {
|
| 773 |
6786
|
cjones
|
try {
|
| 774 |
9544
|
tao
|
// do we already have a replica?
|
| 775 |
6822
|
cjones
|
try {
|
| 776 |
9544
|
tao
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 777 |
|
|
// if we have a local id, get the local object
|
| 778 |
|
|
try {
|
| 779 |
|
|
object = MetacatHandler.read(localId);
|
| 780 |
|
|
} catch (Exception e) {
|
| 781 |
|
|
// NOTE: we may already know about this ID because it could be a data file described by a metadata file
|
| 782 |
|
|
// https://redmine.dataone.org/issues/2572
|
| 783 |
|
|
// TODO: fix this so that we don't prevent ourselves from getting replicas
|
| 784 |
|
|
|
| 785 |
|
|
// let the CN know that the replication failed
|
| 786 |
|
|
logMetacat.warn("Object content not found on this node despite having localId: " + localId);
|
| 787 |
|
|
String msg = "Can't read the object bytes properly, replica is invalid.";
|
| 788 |
|
|
ServiceFailure serviceFailure = new ServiceFailure("2151", msg);
|
| 789 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, serviceFailure);
|
| 790 |
|
|
logMetacat.warn(msg);
|
| 791 |
|
|
throw serviceFailure;
|
| 792 |
|
|
|
| 793 |
|
|
}
|
| 794 |
|
|
|
| 795 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 796 |
|
|
logMetacat.info("No replica found. Continuing.");
|
| 797 |
6822
|
cjones
|
|
| 798 |
9544
|
tao
|
} catch (SQLException ee) {
|
| 799 |
|
|
throw new ServiceFailure("2151", "Couldn't identify the local id of the object with the specified identifier "
|
| 800 |
|
|
+pid.getValue()+" since - "+ee.getMessage());
|
| 801 |
6822
|
cjones
|
}
|
| 802 |
9544
|
tao
|
|
| 803 |
|
|
// no local replica, get a replica
|
| 804 |
|
|
if ( object == null ) {
|
| 805 |
|
|
/*boolean success = true;
|
| 806 |
|
|
try {
|
| 807 |
|
|
//use the v2 ping api to connect the source node
|
| 808 |
|
|
mn.ping();
|
| 809 |
|
|
} catch (Exception e) {
|
| 810 |
|
|
success = false;
|
| 811 |
|
|
}*/
|
| 812 |
|
|
D1NodeVersionChecker checker = new D1NodeVersionChecker(sourceNode);
|
| 813 |
|
|
String nodeVersion = checker.getVersion("MNRead");
|
| 814 |
|
|
if(nodeVersion != null && nodeVersion.equals(D1NodeVersionChecker.V1)) {
|
| 815 |
|
|
//The source node is a v1 node, we use the v1 api
|
| 816 |
|
|
org.dataone.client.v1.MNode mNodeV1 = org.dataone.client.v1.itk.D1Client.getMN(sourceNode);
|
| 817 |
|
|
object = mNodeV1.getReplica(thisNodeSession, pid);
|
| 818 |
|
|
} else if (nodeVersion != null && nodeVersion.equals(D1NodeVersionChecker.V2)){
|
| 819 |
|
|
// session should be null to use the default certificate
|
| 820 |
|
|
// location set in the Certificate manager
|
| 821 |
|
|
MNode mn = D1Client.getMN(sourceNode);
|
| 822 |
|
|
object = mn.getReplica(thisNodeSession, pid);
|
| 823 |
|
|
} else {
|
| 824 |
|
|
throw new ServiceFailure("2151", "The version of MNRead service is "+nodeVersion+" in the source node "+sourceNode.getValue()+" and it is supported. Please check the information in the cn");
|
| 825 |
|
|
}
|
| 826 |
|
|
|
| 827 |
|
|
logMetacat.info("MNodeService.getReplica() called for identifier "
|
| 828 |
|
|
+ pid.getValue());
|
| 829 |
6822
|
cjones
|
|
| 830 |
9544
|
tao
|
}
|
| 831 |
|
|
|
| 832 |
|
|
} catch (InvalidToken e) {
|
| 833 |
|
|
String msg = "Could not retrieve object to replicate (InvalidToken): "+ e.getMessage();
|
| 834 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 835 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 836 |
|
|
logMetacat.error(msg);
|
| 837 |
|
|
throw new ServiceFailure("2151", msg);
|
| 838 |
|
|
|
| 839 |
|
|
} catch (NotFound e) {
|
| 840 |
|
|
String msg = "Could not retrieve object to replicate (NotFound): "+ e.getMessage();
|
| 841 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 842 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 843 |
|
|
logMetacat.error(msg);
|
| 844 |
|
|
throw new ServiceFailure("2151", msg);
|
| 845 |
|
|
|
| 846 |
|
|
} catch (NotAuthorized e) {
|
| 847 |
|
|
String msg = "Could not retrieve object to replicate (NotAuthorized): "+ e.getMessage();
|
| 848 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 849 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 850 |
|
|
logMetacat.error(msg);
|
| 851 |
|
|
throw new ServiceFailure("2151", msg);
|
| 852 |
|
|
} catch (NotImplemented e) {
|
| 853 |
|
|
String msg = "Could not retrieve object to replicate (mn.getReplica NotImplemented): "+ e.getMessage();
|
| 854 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 855 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 856 |
|
|
logMetacat.error(msg);
|
| 857 |
|
|
throw new ServiceFailure("2151", msg);
|
| 858 |
|
|
} catch (ServiceFailure e) {
|
| 859 |
|
|
String msg = "Could not retrieve object to replicate (ServiceFailure): "+ e.getMessage();
|
| 860 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 861 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 862 |
|
|
logMetacat.error(msg);
|
| 863 |
|
|
throw new ServiceFailure("2151", msg);
|
| 864 |
|
|
} catch (InsufficientResources e) {
|
| 865 |
|
|
String msg = "Could not retrieve object to replicate (InsufficientResources): "+ e.getMessage();
|
| 866 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 867 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 868 |
|
|
logMetacat.error(msg);
|
| 869 |
|
|
throw new ServiceFailure("2151", msg);
|
| 870 |
6819
|
cjones
|
}
|
| 871 |
9544
|
tao
|
|
| 872 |
|
|
// verify checksum on the object, if supported
|
| 873 |
|
|
if (object.markSupported()) {
|
| 874 |
|
|
Checksum givenChecksum = sysmeta.getChecksum();
|
| 875 |
|
|
Checksum computedChecksum = null;
|
| 876 |
9288
|
tao
|
try {
|
| 877 |
9544
|
tao
|
computedChecksum = ChecksumUtil.checksum(object, givenChecksum.getAlgorithm());
|
| 878 |
|
|
object.reset();
|
| 879 |
|
|
|
| 880 |
9288
|
tao
|
} catch (Exception e) {
|
| 881 |
9544
|
tao
|
String msg = "Error computing checksum on replica: " + e.getMessage();
|
| 882 |
|
|
logMetacat.error(msg);
|
| 883 |
|
|
ServiceFailure sf = new ServiceFailure("2151", msg);
|
| 884 |
|
|
sf.initCause(e);
|
| 885 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, sf);
|
| 886 |
|
|
throw sf;
|
| 887 |
9287
|
tao
|
}
|
| 888 |
9544
|
tao
|
if (!givenChecksum.getValue().equals(computedChecksum.getValue())) {
|
| 889 |
|
|
logMetacat.error("Given checksum for " + pid.getValue() +
|
| 890 |
|
|
"is " + givenChecksum.getValue());
|
| 891 |
|
|
logMetacat.error("Computed checksum for " + pid.getValue() +
|
| 892 |
|
|
"is " + computedChecksum.getValue());
|
| 893 |
|
|
String msg = "Computed checksum does not match declared checksum";
|
| 894 |
|
|
failure = new ServiceFailure("2151", msg);
|
| 895 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 896 |
|
|
throw new ServiceFailure("2151", msg);
|
| 897 |
|
|
}
|
| 898 |
6786
|
cjones
|
}
|
| 899 |
|
|
|
| 900 |
9544
|
tao
|
// add it to local store
|
| 901 |
|
|
Identifier retPid;
|
| 902 |
6786
|
cjones
|
try {
|
| 903 |
9544
|
tao
|
// skip the MN.create -- this mutates the system metadata and we don't want it to
|
| 904 |
|
|
if ( localId == null ) {
|
| 905 |
|
|
// TODO: this will fail if we already "know" about the identifier
|
| 906 |
|
|
// FIXME: see https://redmine.dataone.org/issues/2572
|
| 907 |
|
|
retPid = super.create(session, pid, object, sysmeta);
|
| 908 |
|
|
result = (retPid.getValue().equals(pid.getValue()));
|
| 909 |
|
|
}
|
| 910 |
|
|
|
| 911 |
6786
|
cjones
|
} catch (Exception e) {
|
| 912 |
9544
|
tao
|
String msg = "Could not save object to local store (" + e.getClass().getName() + "): " + e.getMessage();
|
| 913 |
8414
|
tao
|
failure = new ServiceFailure("2151", msg);
|
| 914 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.FAILED, failure);
|
| 915 |
9544
|
tao
|
logMetacat.error(msg);
|
| 916 |
8414
|
tao
|
throw new ServiceFailure("2151", msg);
|
| 917 |
9544
|
tao
|
|
| 918 |
6786
|
cjones
|
}
|
| 919 |
9544
|
tao
|
} finally {
|
| 920 |
|
|
IOUtils.closeQuietly(object);
|
| 921 |
6693
|
leinfelder
|
}
|
| 922 |
9544
|
tao
|
|
| 923 |
6786
|
cjones
|
|
| 924 |
6795
|
cjones
|
// finish by setting the replication status
|
| 925 |
|
|
setReplicationStatus(thisNodeSession, pid, nodeId, ReplicationStatus.COMPLETED, null);
|
| 926 |
6475
|
jones
|
return result;
|
| 927 |
|
|
|
| 928 |
6250
|
cjones
|
}
|
| 929 |
9287
|
tao
|
|
| 930 |
|
|
/*
|
| 931 |
|
|
* If the given node supports v2 replication.
|
| 932 |
|
|
*/
|
| 933 |
|
|
private boolean supportV2Replication(Node node) throws InvalidRequest {
|
| 934 |
|
|
return supportVersionReplication(node, "v2");
|
| 935 |
|
|
}
|
| 936 |
|
|
|
| 937 |
|
|
/*
|
| 938 |
|
|
* If the given node support the the given version replication. Return true if it does.
|
| 939 |
|
|
*/
|
| 940 |
|
|
private boolean supportVersionReplication(Node node, String version) throws InvalidRequest{
|
| 941 |
|
|
boolean support = false;
|
| 942 |
|
|
if(node == null) {
|
| 943 |
|
|
throw new InvalidRequest("2153", "There is no capacity information about the node in the replicate.");
|
| 944 |
|
|
} else {
|
| 945 |
|
|
Services services = node.getServices();
|
| 946 |
|
|
if(services == null) {
|
| 947 |
|
|
throw new InvalidRequest("2153", "Can't get replica from a node which doesn't have the replicate service.");
|
| 948 |
|
|
} else {
|
| 949 |
|
|
List<Service> list = services.getServiceList();
|
| 950 |
|
|
if(list == null) {
|
| 951 |
|
|
throw new InvalidRequest("2153", "Can't get replica from a node which doesn't have the replicate service.");
|
| 952 |
|
|
} else {
|
| 953 |
|
|
for(Service service : list) {
|
| 954 |
|
|
if(service != null && service.getName() != null && service.getName().equals("MNReplication") &&
|
| 955 |
|
|
service.getVersion() != null && service.getVersion().equalsIgnoreCase(version) && service.getAvailable() == true ) {
|
| 956 |
|
|
support = true;
|
| 957 |
|
|
|
| 958 |
|
|
}
|
| 959 |
|
|
}
|
| 960 |
|
|
}
|
| 961 |
|
|
}
|
| 962 |
|
|
}
|
| 963 |
|
|
return support;
|
| 964 |
|
|
}
|
| 965 |
6179
|
cjones
|
|
| 966 |
6475
|
jones
|
/**
|
| 967 |
|
|
* Return the object identified by the given object identifier
|
| 968 |
|
|
*
|
| 969 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 970 |
|
|
* @param pid - the object identifier for the given object
|
| 971 |
|
|
*
|
| 972 |
|
|
* @return inputStream - the input stream of the given object
|
| 973 |
|
|
*
|
| 974 |
|
|
* @throws InvalidToken
|
| 975 |
|
|
* @throws ServiceFailure
|
| 976 |
|
|
* @throws NotAuthorized
|
| 977 |
|
|
* @throws InvalidRequest
|
| 978 |
|
|
* @throws NotImplemented
|
| 979 |
|
|
*/
|
| 980 |
|
|
@Override
|
| 981 |
6610
|
cjones
|
public InputStream get(Session session, Identifier pid)
|
| 982 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
| 983 |
6258
|
cjones
|
|
| 984 |
6475
|
jones
|
return super.get(session, pid);
|
| 985 |
6258
|
cjones
|
|
| 986 |
6259
|
cjones
|
}
|
| 987 |
6258
|
cjones
|
|
| 988 |
6475
|
jones
|
/**
|
| 989 |
|
|
* Returns a Checksum for the specified object using an accepted hashing algorithm
|
| 990 |
|
|
*
|
| 991 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 992 |
|
|
* @param pid - the object identifier for the given object
|
| 993 |
|
|
* @param algorithm - the name of an algorithm that will be used to compute
|
| 994 |
|
|
* a checksum of the bytes of the object
|
| 995 |
|
|
*
|
| 996 |
|
|
* @return checksum - the checksum of the given object
|
| 997 |
|
|
*
|
| 998 |
|
|
* @throws InvalidToken
|
| 999 |
|
|
* @throws ServiceFailure
|
| 1000 |
|
|
* @throws NotAuthorized
|
| 1001 |
|
|
* @throws NotFound
|
| 1002 |
|
|
* @throws InvalidRequest
|
| 1003 |
|
|
* @throws NotImplemented
|
| 1004 |
|
|
*/
|
| 1005 |
|
|
@Override
|
| 1006 |
6610
|
cjones
|
public Checksum getChecksum(Session session, Identifier pid, String algorithm)
|
| 1007 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 1008 |
|
|
InvalidRequest, NotImplemented {
|
| 1009 |
6258
|
cjones
|
|
| 1010 |
6475
|
jones
|
Checksum checksum = null;
|
| 1011 |
9040
|
tao
|
String serviceFailure = "1410";
|
| 1012 |
|
|
String notFound = "1420";
|
| 1013 |
|
|
//Checkum only handles the pid, not sid
|
| 1014 |
|
|
checkV1SystemMetaPidExist(pid, serviceFailure, "The checksum for the object specified by "+pid.getValue()+" couldn't be returned ", notFound,
|
| 1015 |
|
|
"The object specified by "+pid.getValue()+" does not exist at this node.");
|
| 1016 |
6475
|
jones
|
InputStream inputStream = get(session, pid);
|
| 1017 |
|
|
|
| 1018 |
6259
|
cjones
|
try {
|
| 1019 |
6475
|
jones
|
checksum = ChecksumUtil.checksum(inputStream, algorithm);
|
| 1020 |
|
|
|
| 1021 |
|
|
} catch (NoSuchAlgorithmException e) {
|
| 1022 |
|
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
|
| 1023 |
|
|
+ e.getMessage());
|
| 1024 |
6259
|
cjones
|
} catch (IOException e) {
|
| 1025 |
6475
|
jones
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned due to an internal error: "
|
| 1026 |
|
|
+ e.getMessage());
|
| 1027 |
6259
|
cjones
|
}
|
| 1028 |
6382
|
cjones
|
|
| 1029 |
6475
|
jones
|
if (checksum == null) {
|
| 1030 |
|
|
throw new ServiceFailure("1410", "The checksum for the object specified by " + pid.getValue() + "could not be returned.");
|
| 1031 |
|
|
}
|
| 1032 |
6258
|
cjones
|
|
| 1033 |
6475
|
jones
|
return checksum;
|
| 1034 |
6259
|
cjones
|
}
|
| 1035 |
6179
|
cjones
|
|
| 1036 |
6475
|
jones
|
/**
|
| 1037 |
|
|
* Return the system metadata for a given object
|
| 1038 |
|
|
*
|
| 1039 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 1040 |
|
|
* @param pid - the object identifier for the given object
|
| 1041 |
|
|
*
|
| 1042 |
|
|
* @return inputStream - the input stream of the given system metadata object
|
| 1043 |
|
|
*
|
| 1044 |
|
|
* @throws InvalidToken
|
| 1045 |
|
|
* @throws ServiceFailure
|
| 1046 |
|
|
* @throws NotAuthorized
|
| 1047 |
|
|
* @throws NotFound
|
| 1048 |
|
|
* @throws InvalidRequest
|
| 1049 |
|
|
* @throws NotImplemented
|
| 1050 |
|
|
*/
|
| 1051 |
|
|
@Override
|
| 1052 |
6610
|
cjones
|
public SystemMetadata getSystemMetadata(Session session, Identifier pid)
|
| 1053 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
| 1054 |
|
|
NotImplemented {
|
| 1055 |
6341
|
leinfelder
|
|
| 1056 |
6475
|
jones
|
return super.getSystemMetadata(session, pid);
|
| 1057 |
|
|
}
|
| 1058 |
6341
|
leinfelder
|
|
| 1059 |
6475
|
jones
|
/**
|
| 1060 |
|
|
* Retrieve the list of objects present on the MN that match the calling parameters
|
| 1061 |
|
|
*
|
| 1062 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 1063 |
|
|
* @param startTime - Specifies the beginning of the time range from which
|
| 1064 |
|
|
* to return object (>=)
|
| 1065 |
|
|
* @param endTime - Specifies the beginning of the time range from which
|
| 1066 |
|
|
* to return object (>=)
|
| 1067 |
|
|
* @param objectFormat - Restrict results to the specified object format
|
| 1068 |
|
|
* @param replicaStatus - Indicates if replicated objects should be returned in the list
|
| 1069 |
|
|
* @param start - The zero-based index of the first value, relative to the
|
| 1070 |
|
|
* first record of the resultset that matches the parameters.
|
| 1071 |
|
|
* @param count - The maximum number of entries that should be returned in
|
| 1072 |
|
|
* the response. The Member Node may return less entries
|
| 1073 |
|
|
* than specified in this value.
|
| 1074 |
|
|
*
|
| 1075 |
|
|
* @return objectList - the list of objects matching the criteria
|
| 1076 |
|
|
*
|
| 1077 |
|
|
* @throws InvalidToken
|
| 1078 |
|
|
* @throws ServiceFailure
|
| 1079 |
|
|
* @throws NotAuthorized
|
| 1080 |
|
|
* @throws InvalidRequest
|
| 1081 |
|
|
* @throws NotImplemented
|
| 1082 |
|
|
*/
|
| 1083 |
|
|
@Override
|
| 1084 |
8810
|
leinfelder
|
public ObjectList listObjects(Session session, Date startTime, Date endTime, ObjectFormatIdentifier objectFormatId, Identifier identifier, Boolean replicaStatus, Integer start,
|
| 1085 |
6475
|
jones
|
Integer count) throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken {
|
| 1086 |
9249
|
tao
|
NodeReference nodeId = null;
|
| 1087 |
|
|
if(!replicaStatus) {
|
| 1088 |
|
|
//not include those objects whose authoritative node is not this mn
|
| 1089 |
|
|
nodeId = new NodeReference();
|
| 1090 |
|
|
try {
|
| 1091 |
|
|
String currentNodeId = PropertyService.getInstance().getProperty("dataone.nodeId"); // return only pids for which this mn
|
| 1092 |
|
|
nodeId.setValue(currentNodeId);
|
| 1093 |
|
|
} catch(Exception e) {
|
| 1094 |
|
|
throw new ServiceFailure("1580", e.getMessage());
|
| 1095 |
|
|
}
|
| 1096 |
|
|
}
|
| 1097 |
|
|
return super.listObjects(session, startTime, endTime, objectFormatId, identifier, nodeId, start, count);
|
| 1098 |
6229
|
cjones
|
}
|
| 1099 |
6179
|
cjones
|
|
| 1100 |
6475
|
jones
|
/**
|
| 1101 |
6476
|
jones
|
* Return a description of the node's capabilities and services.
|
| 1102 |
6475
|
jones
|
*
|
| 1103 |
|
|
* @return node - the technical capabilities of the Member Node
|
| 1104 |
|
|
*
|
| 1105 |
|
|
* @throws ServiceFailure
|
| 1106 |
|
|
* @throws NotAuthorized
|
| 1107 |
|
|
* @throws InvalidRequest
|
| 1108 |
|
|
* @throws NotImplemented
|
| 1109 |
|
|
*/
|
| 1110 |
|
|
@Override
|
| 1111 |
6610
|
cjones
|
public Node getCapabilities()
|
| 1112 |
|
|
throws NotImplemented, ServiceFailure {
|
| 1113 |
6179
|
cjones
|
|
| 1114 |
6475
|
jones
|
String nodeName = null;
|
| 1115 |
|
|
String nodeId = null;
|
| 1116 |
6492
|
jones
|
String subject = null;
|
| 1117 |
6938
|
cjones
|
String contactSubject = null;
|
| 1118 |
6475
|
jones
|
String nodeDesc = null;
|
| 1119 |
6476
|
jones
|
String nodeTypeString = null;
|
| 1120 |
|
|
NodeType nodeType = null;
|
| 1121 |
9253
|
tao
|
List<String> mnCoreServiceVersions = null;
|
| 1122 |
|
|
List<String> mnReadServiceVersions = null;
|
| 1123 |
|
|
List<String> mnAuthorizationServiceVersions = null;
|
| 1124 |
|
|
List<String> mnStorageServiceVersions = null;
|
| 1125 |
|
|
List<String> mnReplicationServiceVersions = null;
|
| 1126 |
6179
|
cjones
|
|
| 1127 |
6475
|
jones
|
boolean nodeSynchronize = false;
|
| 1128 |
|
|
boolean nodeReplicate = false;
|
| 1129 |
9253
|
tao
|
List<String> mnCoreServiceAvailables = null;
|
| 1130 |
|
|
List<String> mnReadServiceAvailables = null;
|
| 1131 |
|
|
List<String> mnAuthorizationServiceAvailables = null;
|
| 1132 |
|
|
List<String> mnStorageServiceAvailables = null;
|
| 1133 |
|
|
List<String> mnReplicationServiceAvailables = null;
|
| 1134 |
6179
|
cjones
|
|
| 1135 |
6475
|
jones
|
try {
|
| 1136 |
|
|
// get the properties of the node based on configuration information
|
| 1137 |
9253
|
tao
|
nodeName = Settings.getConfiguration().getString("dataone.nodeName");
|
| 1138 |
|
|
nodeId = Settings.getConfiguration().getString("dataone.nodeId");
|
| 1139 |
|
|
subject = Settings.getConfiguration().getString("dataone.subject");
|
| 1140 |
|
|
contactSubject = Settings.getConfiguration().getString("dataone.contactSubject");
|
| 1141 |
|
|
nodeDesc = Settings.getConfiguration().getString("dataone.nodeDescription");
|
| 1142 |
|
|
nodeTypeString = Settings.getConfiguration().getString("dataone.nodeType");
|
| 1143 |
6476
|
jones
|
nodeType = NodeType.convert(nodeTypeString);
|
| 1144 |
9253
|
tao
|
nodeSynchronize = new Boolean(Settings.getConfiguration().getString("dataone.nodeSynchronize")).booleanValue();
|
| 1145 |
|
|
nodeReplicate = new Boolean(Settings.getConfiguration().getString("dataone.nodeReplicate")).booleanValue();
|
| 1146 |
6475
|
jones
|
|
| 1147 |
6476
|
jones
|
// Set the properties of the node based on configuration information and
|
| 1148 |
|
|
// calls to current status methods
|
| 1149 |
9809
|
tao
|
String serviceName = SystemUtil.getContextURL() + "/" + PropertyService.getProperty("dataone.serviceName");
|
| 1150 |
6476
|
jones
|
Node node = new Node();
|
| 1151 |
6542
|
leinfelder
|
node.setBaseURL(serviceName + "/" + nodeTypeString);
|
| 1152 |
6476
|
jones
|
node.setDescription(nodeDesc);
|
| 1153 |
6475
|
jones
|
|
| 1154 |
6476
|
jones
|
// set the node's health information
|
| 1155 |
|
|
node.setState(NodeState.UP);
|
| 1156 |
|
|
|
| 1157 |
|
|
// set the ping response to the current value
|
| 1158 |
|
|
Ping canPing = new Ping();
|
| 1159 |
|
|
canPing.setSuccess(false);
|
| 1160 |
|
|
try {
|
| 1161 |
6803
|
leinfelder
|
Date pingDate = ping();
|
| 1162 |
|
|
canPing.setSuccess(pingDate != null);
|
| 1163 |
|
|
} catch (BaseException e) {
|
| 1164 |
6476
|
jones
|
e.printStackTrace();
|
| 1165 |
6803
|
leinfelder
|
// guess it can't be pinged
|
| 1166 |
6476
|
jones
|
}
|
| 1167 |
6610
|
cjones
|
|
| 1168 |
6476
|
jones
|
node.setPing(canPing);
|
| 1169 |
6475
|
jones
|
|
| 1170 |
6476
|
jones
|
NodeReference identifier = new NodeReference();
|
| 1171 |
|
|
identifier.setValue(nodeId);
|
| 1172 |
|
|
node.setIdentifier(identifier);
|
| 1173 |
6492
|
jones
|
Subject s = new Subject();
|
| 1174 |
|
|
s.setValue(subject);
|
| 1175 |
|
|
node.addSubject(s);
|
| 1176 |
6938
|
cjones
|
Subject contact = new Subject();
|
| 1177 |
|
|
contact.setValue(contactSubject);
|
| 1178 |
|
|
node.addContactSubject(contact);
|
| 1179 |
6476
|
jones
|
node.setName(nodeName);
|
| 1180 |
|
|
node.setReplicate(nodeReplicate);
|
| 1181 |
|
|
node.setSynchronize(nodeSynchronize);
|
| 1182 |
6475
|
jones
|
|
| 1183 |
6476
|
jones
|
// services: MNAuthorization, MNCore, MNRead, MNReplication, MNStorage
|
| 1184 |
|
|
Services services = new Services();
|
| 1185 |
6475
|
jones
|
|
| 1186 |
9253
|
tao
|
mnCoreServiceVersions = Settings.getConfiguration().getList("dataone.mnCore.serviceVersion");
|
| 1187 |
|
|
mnCoreServiceAvailables = Settings.getConfiguration().getList("dataone.mnCore.serviceAvailable");
|
| 1188 |
|
|
if(mnCoreServiceVersions != null && mnCoreServiceAvailables != null && mnCoreServiceVersions.size() == mnCoreServiceAvailables.size()) {
|
| 1189 |
|
|
for(int i=0; i<mnCoreServiceVersions.size(); i++) {
|
| 1190 |
|
|
String version = mnCoreServiceVersions.get(i);
|
| 1191 |
|
|
boolean available = new Boolean(mnCoreServiceAvailables.get(i)).booleanValue();
|
| 1192 |
|
|
Service sMNCore = new Service();
|
| 1193 |
|
|
sMNCore.setName("MNCore");
|
| 1194 |
|
|
sMNCore.setVersion(version);
|
| 1195 |
|
|
sMNCore.setAvailable(available);
|
| 1196 |
|
|
services.addService(sMNCore);
|
| 1197 |
|
|
}
|
| 1198 |
|
|
}
|
| 1199 |
|
|
|
| 1200 |
|
|
mnReadServiceVersions = Settings.getConfiguration().getList("dataone.mnRead.serviceVersion");
|
| 1201 |
|
|
mnReadServiceAvailables = Settings.getConfiguration().getList("dataone.mnRead.serviceAvailable");
|
| 1202 |
|
|
if(mnReadServiceVersions != null && mnReadServiceAvailables != null && mnReadServiceVersions.size()==mnReadServiceAvailables.size()) {
|
| 1203 |
|
|
for(int i=0; i<mnReadServiceVersions.size(); i++) {
|
| 1204 |
|
|
String version = mnReadServiceVersions.get(i);
|
| 1205 |
|
|
boolean available = new Boolean(mnReadServiceAvailables.get(i)).booleanValue();
|
| 1206 |
|
|
Service sMNRead = new Service();
|
| 1207 |
|
|
sMNRead.setName("MNRead");
|
| 1208 |
|
|
sMNRead.setVersion(version);
|
| 1209 |
|
|
sMNRead.setAvailable(available);
|
| 1210 |
|
|
services.addService(sMNRead);
|
| 1211 |
|
|
}
|
| 1212 |
|
|
}
|
| 1213 |
|
|
|
| 1214 |
|
|
mnAuthorizationServiceVersions = Settings.getConfiguration().getList("dataone.mnAuthorization.serviceVersion");
|
| 1215 |
|
|
mnAuthorizationServiceAvailables = Settings.getConfiguration().getList("dataone.mnAuthorization.serviceAvailable");
|
| 1216 |
|
|
if(mnAuthorizationServiceVersions != null && mnAuthorizationServiceAvailables != null && mnAuthorizationServiceVersions.size()==mnAuthorizationServiceAvailables.size()) {
|
| 1217 |
|
|
for(int i=0; i<mnAuthorizationServiceVersions.size(); i++) {
|
| 1218 |
|
|
String version = mnAuthorizationServiceVersions.get(i);
|
| 1219 |
|
|
boolean available = new Boolean(mnAuthorizationServiceAvailables.get(i)).booleanValue();
|
| 1220 |
|
|
Service sMNAuthorization = new Service();
|
| 1221 |
|
|
sMNAuthorization.setName("MNAuthorization");
|
| 1222 |
|
|
sMNAuthorization.setVersion(version);
|
| 1223 |
|
|
sMNAuthorization.setAvailable(available);
|
| 1224 |
|
|
services.addService(sMNAuthorization);
|
| 1225 |
|
|
}
|
| 1226 |
|
|
}
|
| 1227 |
|
|
|
| 1228 |
|
|
mnStorageServiceVersions = Settings.getConfiguration().getList("dataone.mnStorage.serviceVersion");
|
| 1229 |
|
|
mnStorageServiceAvailables = Settings.getConfiguration().getList("dataone.mnStorage.serviceAvailable");
|
| 1230 |
|
|
if(mnStorageServiceVersions != null && mnStorageServiceAvailables != null && mnStorageServiceVersions.size() == mnStorageServiceAvailables.size()) {
|
| 1231 |
|
|
for(int i=0; i<mnStorageServiceVersions.size(); i++) {
|
| 1232 |
|
|
String version = mnStorageServiceVersions.get(i);
|
| 1233 |
|
|
boolean available = new Boolean(mnStorageServiceAvailables.get(i)).booleanValue();
|
| 1234 |
|
|
Service sMNStorage = new Service();
|
| 1235 |
|
|
sMNStorage.setName("MNStorage");
|
| 1236 |
|
|
sMNStorage.setVersion(version);
|
| 1237 |
|
|
sMNStorage.setAvailable(available);
|
| 1238 |
|
|
services.addService(sMNStorage);
|
| 1239 |
|
|
}
|
| 1240 |
|
|
}
|
| 1241 |
|
|
|
| 1242 |
|
|
mnReplicationServiceVersions = Settings.getConfiguration().getList("dataone.mnReplication.serviceVersion");
|
| 1243 |
|
|
mnReplicationServiceAvailables = Settings.getConfiguration().getList("dataone.mnReplication.serviceAvailable");
|
| 1244 |
|
|
if(mnReplicationServiceVersions != null && mnReplicationServiceAvailables != null && mnReplicationServiceVersions.size() == mnReplicationServiceAvailables.size()) {
|
| 1245 |
|
|
for (int i=0; i<mnReplicationServiceVersions.size(); i++) {
|
| 1246 |
|
|
String version = mnReplicationServiceVersions.get(i);
|
| 1247 |
|
|
boolean available = new Boolean(mnReplicationServiceAvailables.get(i)).booleanValue();
|
| 1248 |
|
|
Service sMNReplication = new Service();
|
| 1249 |
|
|
sMNReplication.setName("MNReplication");
|
| 1250 |
|
|
sMNReplication.setVersion(version);
|
| 1251 |
|
|
sMNReplication.setAvailable(available);
|
| 1252 |
|
|
services.addService(sMNReplication);
|
| 1253 |
|
|
}
|
| 1254 |
|
|
}
|
| 1255 |
|
|
|
| 1256 |
6476
|
jones
|
node.setServices(services);
|
| 1257 |
6475
|
jones
|
|
| 1258 |
6476
|
jones
|
// Set the schedule for synchronization
|
| 1259 |
|
|
Synchronization synchronization = new Synchronization();
|
| 1260 |
|
|
Schedule schedule = new Schedule();
|
| 1261 |
|
|
Date now = new Date();
|
| 1262 |
6689
|
leinfelder
|
schedule.setYear(PropertyService.getProperty("dataone.nodeSynchronization.schedule.year"));
|
| 1263 |
|
|
schedule.setMon(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mon"));
|
| 1264 |
|
|
schedule.setMday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.mday"));
|
| 1265 |
|
|
schedule.setWday(PropertyService.getProperty("dataone.nodeSynchronization.schedule.wday"));
|
| 1266 |
|
|
schedule.setHour(PropertyService.getProperty("dataone.nodeSynchronization.schedule.hour"));
|
| 1267 |
|
|
schedule.setMin(PropertyService.getProperty("dataone.nodeSynchronization.schedule.min"));
|
| 1268 |
|
|
schedule.setSec(PropertyService.getProperty("dataone.nodeSynchronization.schedule.sec"));
|
| 1269 |
6476
|
jones
|
synchronization.setSchedule(schedule);
|
| 1270 |
|
|
synchronization.setLastHarvested(now);
|
| 1271 |
|
|
synchronization.setLastCompleteHarvest(now);
|
| 1272 |
|
|
node.setSynchronization(synchronization);
|
| 1273 |
6475
|
jones
|
|
| 1274 |
6476
|
jones
|
node.setType(nodeType);
|
| 1275 |
|
|
return node;
|
| 1276 |
6475
|
jones
|
|
| 1277 |
6476
|
jones
|
} catch (PropertyNotFoundException pnfe) {
|
| 1278 |
|
|
String msg = "MNodeService.getCapabilities(): " + "property not found: " + pnfe.getMessage();
|
| 1279 |
|
|
logMetacat.error(msg);
|
| 1280 |
|
|
throw new ServiceFailure("2162", msg);
|
| 1281 |
|
|
}
|
| 1282 |
6228
|
cjones
|
}
|
| 1283 |
6179
|
cjones
|
|
| 1284 |
8810
|
leinfelder
|
|
| 1285 |
6179
|
cjones
|
|
| 1286 |
6475
|
jones
|
/**
|
| 1287 |
|
|
* A callback method used by a CN to indicate to a MN that it cannot
|
| 1288 |
|
|
* complete synchronization of the science metadata identified by pid. Log
|
| 1289 |
|
|
* the event in the metacat event log.
|
| 1290 |
|
|
*
|
| 1291 |
|
|
* @param session
|
| 1292 |
|
|
* @param syncFailed
|
| 1293 |
|
|
*
|
| 1294 |
|
|
* @throws ServiceFailure
|
| 1295 |
|
|
* @throws NotAuthorized
|
| 1296 |
|
|
* @throws NotImplemented
|
| 1297 |
|
|
*/
|
| 1298 |
|
|
@Override
|
| 1299 |
6991
|
leinfelder
|
public boolean synchronizationFailed(Session session, SynchronizationFailed syncFailed)
|
| 1300 |
6610
|
cjones
|
throws NotImplemented, ServiceFailure, NotAuthorized {
|
| 1301 |
6179
|
cjones
|
|
| 1302 |
6475
|
jones
|
String localId;
|
| 1303 |
7075
|
cjones
|
Identifier pid;
|
| 1304 |
|
|
if ( syncFailed.getPid() != null ) {
|
| 1305 |
|
|
pid = new Identifier();
|
| 1306 |
|
|
pid.setValue(syncFailed.getPid());
|
| 1307 |
|
|
boolean allowed;
|
| 1308 |
|
|
|
| 1309 |
|
|
//are we allowed? only CNs
|
| 1310 |
|
|
try {
|
| 1311 |
7142
|
leinfelder
|
allowed = isAdminAuthorized(session);
|
| 1312 |
7075
|
cjones
|
if ( !allowed ){
|
| 1313 |
|
|
throw new NotAuthorized("2162",
|
| 1314 |
|
|
"Not allowed to call synchronizationFailed() on this node.");
|
| 1315 |
|
|
}
|
| 1316 |
|
|
} catch (InvalidToken e) {
|
| 1317 |
|
|
throw new NotAuthorized("2162",
|
| 1318 |
|
|
"Not allowed to call synchronizationFailed() on this node.");
|
| 1319 |
6331
|
leinfelder
|
|
| 1320 |
7075
|
cjones
|
}
|
| 1321 |
|
|
|
| 1322 |
|
|
} else {
|
| 1323 |
|
|
throw new ServiceFailure("2161", "The identifier cannot be null.");
|
| 1324 |
|
|
|
| 1325 |
|
|
}
|
| 1326 |
|
|
|
| 1327 |
6475
|
jones
|
try {
|
| 1328 |
7075
|
cjones
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 1329 |
6475
|
jones
|
} catch (McdbDocNotFoundException e) {
|
| 1330 |
7075
|
cjones
|
throw new ServiceFailure("2161", "The identifier specified by " +
|
| 1331 |
|
|
syncFailed.getPid() + " was not found on this node.");
|
| 1332 |
6179
|
cjones
|
|
| 1333 |
9024
|
tao
|
} catch (SQLException e) {
|
| 1334 |
|
|
throw new ServiceFailure("2161", "Couldn't identify the local id of the identifier specified by " +
|
| 1335 |
|
|
syncFailed.getPid() + " since "+e.getMessage());
|
| 1336 |
6475
|
jones
|
}
|
| 1337 |
|
|
// TODO: update the CN URL below when the CNRead.SynchronizationFailed
|
| 1338 |
|
|
// method is changed to include the URL as a parameter
|
| 1339 |
9380
|
rnahf
|
logMetacat.warn("Synchronization for the object identified by " +
|
| 1340 |
7075
|
cjones
|
pid.getValue() + " failed from " + syncFailed.getNodeId() +
|
| 1341 |
9380
|
rnahf
|
" with message: " + syncFailed.getDescription() +
|
| 1342 |
|
|
". Logging the event to the Metacat EventLog as a 'syncFailed' event.");
|
| 1343 |
6475
|
jones
|
// TODO: use the event type enum when the SYNCHRONIZATION_FAILED event is added
|
| 1344 |
6532
|
leinfelder
|
String principal = Constants.SUBJECT_PUBLIC;
|
| 1345 |
6506
|
leinfelder
|
if (session != null && session.getSubject() != null) {
|
| 1346 |
6575
|
cjones
|
principal = session.getSubject().getValue();
|
| 1347 |
6506
|
leinfelder
|
}
|
| 1348 |
|
|
try {
|
| 1349 |
6575
|
cjones
|
EventLog.getInstance().log(request.getRemoteAddr(), request.getHeader("User-Agent"), principal, localId, "synchronization_failed");
|
| 1350 |
6506
|
leinfelder
|
} catch (Exception e) {
|
| 1351 |
7075
|
cjones
|
throw new ServiceFailure("2161", "Could not log the error for: " + pid.getValue());
|
| 1352 |
6991
|
leinfelder
|
}
|
| 1353 |
6475
|
jones
|
//EventLog.getInstance().log("CN URL WILL GO HERE",
|
| 1354 |
|
|
// session.getSubject().getValue(), localId, Event.SYNCHRONIZATION_FAILED);
|
| 1355 |
6991
|
leinfelder
|
return true;
|
| 1356 |
6179
|
cjones
|
|
| 1357 |
6260
|
cjones
|
}
|
| 1358 |
|
|
|
| 1359 |
6475
|
jones
|
/**
|
| 1360 |
|
|
* Essentially a get() but with different logging behavior
|
| 1361 |
|
|
*/
|
| 1362 |
|
|
@Override
|
| 1363 |
6540
|
cjones
|
public InputStream getReplica(Session session, Identifier pid)
|
| 1364 |
9314
|
tao
|
throws NotAuthorized, NotImplemented, ServiceFailure, InvalidToken, NotFound {
|
| 1365 |
6179
|
cjones
|
|
| 1366 |
6540
|
cjones
|
logMetacat.info("MNodeService.getReplica() called.");
|
| 1367 |
|
|
|
| 1368 |
6653
|
leinfelder
|
// cannot be called by public
|
| 1369 |
|
|
if (session == null) {
|
| 1370 |
|
|
throw new InvalidToken("2183", "No session was provided.");
|
| 1371 |
|
|
}
|
| 1372 |
|
|
|
| 1373 |
6631
|
cjones
|
logMetacat.info("MNodeService.getReplica() called with parameters: \n" +
|
| 1374 |
|
|
"\tSession.Subject = " + session.getSubject().getValue() + "\n" +
|
| 1375 |
|
|
"\tIdentifier = " + pid.getValue());
|
| 1376 |
|
|
|
| 1377 |
6475
|
jones
|
InputStream inputStream = null; // bytes to be returned
|
| 1378 |
|
|
handler = new MetacatHandler(new Timer());
|
| 1379 |
|
|
boolean allowed = false;
|
| 1380 |
|
|
String localId; // the metacat docid for the pid
|
| 1381 |
6179
|
cjones
|
|
| 1382 |
6475
|
jones
|
// get the local docid from Metacat
|
| 1383 |
|
|
try {
|
| 1384 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 1385 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 1386 |
9314
|
tao
|
throw new NotFound("2185", "The object specified by " +
|
| 1387 |
6610
|
cjones
|
pid.getValue() + " does not exist at this node.");
|
| 1388 |
|
|
|
| 1389 |
9024
|
tao
|
} catch (SQLException e) {
|
| 1390 |
|
|
throw new ServiceFailure("2181", "The local id of the object specified by " +
|
| 1391 |
|
|
pid.getValue() + " couldn't be identified since "+e.getMessage());
|
| 1392 |
6475
|
jones
|
}
|
| 1393 |
6234
|
cjones
|
|
| 1394 |
6552
|
leinfelder
|
Subject targetNodeSubject = session.getSubject();
|
| 1395 |
6185
|
leinfelder
|
|
| 1396 |
6552
|
leinfelder
|
// check for authorization to replicate, null session to act as this source MN
|
| 1397 |
6610
|
cjones
|
try {
|
| 1398 |
6777
|
leinfelder
|
allowed = D1Client.getCN().isNodeAuthorized(null, targetNodeSubject, pid);
|
| 1399 |
6610
|
cjones
|
} catch (InvalidToken e1) {
|
| 1400 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
| 1401 |
|
|
+ e1.getMessage());
|
| 1402 |
|
|
|
| 1403 |
|
|
} catch (NotFound e1) {
|
| 1404 |
9314
|
tao
|
throw new NotFound("2185", "Could not find the object "+pid.getValue()+" in this node - "
|
| 1405 |
6610
|
cjones
|
+ e1.getMessage());
|
| 1406 |
6384
|
cjones
|
|
| 1407 |
6610
|
cjones
|
} catch (InvalidRequest e1) {
|
| 1408 |
|
|
throw new ServiceFailure("2181", "Could not determine if node is authorized: "
|
| 1409 |
|
|
+ e1.getMessage());
|
| 1410 |
|
|
|
| 1411 |
|
|
}
|
| 1412 |
|
|
|
| 1413 |
6540
|
cjones
|
logMetacat.info("Called D1Client.isNodeAuthorized(). Allowed = " + allowed +
|
| 1414 |
|
|
" for identifier " + pid.getValue());
|
| 1415 |
|
|
|
| 1416 |
6475
|
jones
|
// if the person is authorized, perform the read
|
| 1417 |
|
|
if (allowed) {
|
| 1418 |
|
|
try {
|
| 1419 |
6986
|
jones
|
inputStream = MetacatHandler.read(localId);
|
| 1420 |
6475
|
jones
|
} catch (Exception e) {
|
| 1421 |
9314
|
tao
|
throw new ServiceFailure("2181", "The object specified by " +
|
| 1422 |
6610
|
cjones
|
pid.getValue() + "could not be returned due to error: " + e.getMessage());
|
| 1423 |
6475
|
jones
|
}
|
| 1424 |
9314
|
tao
|
} else {
|
| 1425 |
|
|
throw new NotAuthorized("2182", "The pid "+pid.getValue()+" is not authorized to be read by the client.");
|
| 1426 |
6475
|
jones
|
}
|
| 1427 |
6384
|
cjones
|
|
| 1428 |
6475
|
jones
|
// if we fail to set the input stream
|
| 1429 |
|
|
if (inputStream == null) {
|
| 1430 |
6610
|
cjones
|
throw new ServiceFailure("2181", "The object specified by " +
|
| 1431 |
9314
|
tao
|
pid.getValue() + " can't be returned from the node.");
|
| 1432 |
6475
|
jones
|
}
|
| 1433 |
|
|
|
| 1434 |
|
|
// log the replica event
|
| 1435 |
|
|
String principal = null;
|
| 1436 |
|
|
if (session.getSubject() != null) {
|
| 1437 |
|
|
principal = session.getSubject().getValue();
|
| 1438 |
|
|
}
|
| 1439 |
6576
|
cjones
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
| 1440 |
|
|
request.getHeader("User-Agent"), principal, localId, "replicate");
|
| 1441 |
6475
|
jones
|
|
| 1442 |
|
|
return inputStream;
|
| 1443 |
|
|
}
|
| 1444 |
9340
|
tao
|
|
| 1445 |
6573
|
cjones
|
/**
|
| 1446 |
6600
|
cjones
|
* A method to notify the Member Node that the authoritative copy of
|
| 1447 |
6599
|
cjones
|
* system metadata on the Coordinating Nodes has changed.
|
| 1448 |
9340
|
tao
|
*
|
| 1449 |
6599
|
cjones
|
* @param session Session information that contains the identity of the
|
| 1450 |
|
|
* calling user as retrieved from the X.509 certificate
|
| 1451 |
|
|
* which must be traceable to the CILogon service.
|
| 1452 |
|
|
* @param serialVersion The serialVersion of the system metadata
|
| 1453 |
|
|
* @param dateSysMetaLastModified The time stamp for when the system metadata was changed
|
| 1454 |
|
|
* @throws NotImplemented
|
| 1455 |
|
|
* @throws ServiceFailure
|
| 1456 |
|
|
* @throws NotAuthorized
|
| 1457 |
|
|
* @throws InvalidRequest
|
| 1458 |
|
|
* @throws InvalidToken
|
| 1459 |
|
|
*/
|
| 1460 |
6991
|
leinfelder
|
public boolean systemMetadataChanged(Session session, Identifier pid,
|
| 1461 |
6599
|
cjones
|
long serialVersion, Date dateSysMetaLastModified)
|
| 1462 |
|
|
throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest,
|
| 1463 |
|
|
InvalidToken {
|
| 1464 |
9340
|
tao
|
boolean needCheckAuthoriativeNode = true;
|
| 1465 |
|
|
return systemMetadataChanged(needCheckAuthoriativeNode, session, pid,serialVersion, dateSysMetaLastModified);
|
| 1466 |
|
|
}
|
| 1467 |
|
|
|
| 1468 |
|
|
/**
|
| 1469 |
|
|
* A method to notify the Member Node that the authoritative copy of
|
| 1470 |
|
|
* system metadata on the Coordinating Nodes has changed.
|
| 1471 |
|
|
* @param needCheckAuthoriativeNode this is for the dataone version 2. In the
|
| 1472 |
|
|
* version 2, there are two scenarios:
|
| 1473 |
|
|
* 1. If the node is the authoritative node, it only accepts serial version and replica list.
|
| 1474 |
|
|
* 2. If the node is a replica, it accepts everything.
|
| 1475 |
|
|
* For the v1, api, the parameter should be false.
|
| 1476 |
|
|
* @param session Session information that contains the identity of the
|
| 1477 |
|
|
* calling user as retrieved from the X.509 certificate
|
| 1478 |
|
|
* which must be traceable to the CILogon service.
|
| 1479 |
|
|
* @param serialVersion The serialVersion of the system metadata
|
| 1480 |
|
|
* @param dateSysMetaLastModified The time stamp for when the system metadata was changed
|
| 1481 |
|
|
* @throws NotImplemented
|
| 1482 |
|
|
* @throws ServiceFailure
|
| 1483 |
|
|
* @throws NotAuthorized
|
| 1484 |
|
|
* @throws InvalidRequest
|
| 1485 |
|
|
* @throws InvalidToken
|
| 1486 |
|
|
*/
|
| 1487 |
|
|
public boolean systemMetadataChanged(boolean needCheckAuthoriativeNode, Session session, Identifier pid,
|
| 1488 |
|
|
long serialVersion, Date dateSysMetaLastModified)
|
| 1489 |
|
|
throws NotImplemented, ServiceFailure, NotAuthorized, InvalidRequest,
|
| 1490 |
|
|
InvalidToken {
|
| 1491 |
6599
|
cjones
|
|
| 1492 |
9479
|
tao
|
/*if(isReadOnlyMode()) {
|
| 1493 |
9478
|
tao
|
throw new InvalidRequest("1334", "The Metacat member node is on the read-only mode and your request can't be fulfiled. Please try again later.");
|
| 1494 |
9479
|
tao
|
}*/
|
| 1495 |
7600
|
cjones
|
// cannot be called by public
|
| 1496 |
|
|
if (session == null) {
|
| 1497 |
9051
|
tao
|
throw new InvalidToken("1332", "No session was provided.");
|
| 1498 |
7600
|
cjones
|
}
|
| 1499 |
|
|
|
| 1500 |
9051
|
tao
|
String serviceFailureCode = "1333";
|
| 1501 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
| 1502 |
|
|
if(sid != null) {
|
| 1503 |
|
|
pid = sid;
|
| 1504 |
|
|
}
|
| 1505 |
|
|
|
| 1506 |
6600
|
cjones
|
SystemMetadata currentLocalSysMeta = null;
|
| 1507 |
|
|
SystemMetadata newSysMeta = null;
|
| 1508 |
|
|
CNode cn = D1Client.getCN();
|
| 1509 |
|
|
NodeList nodeList = null;
|
| 1510 |
|
|
Subject callingSubject = null;
|
| 1511 |
|
|
boolean allowed = false;
|
| 1512 |
|
|
|
| 1513 |
|
|
// are we allowed to call this?
|
| 1514 |
|
|
callingSubject = session.getSubject();
|
| 1515 |
|
|
nodeList = cn.listNodes();
|
| 1516 |
|
|
|
| 1517 |
|
|
for(Node node : nodeList.getNodeList()) {
|
| 1518 |
|
|
// must be a CN
|
| 1519 |
|
|
if ( node.getType().equals(NodeType.CN)) {
|
| 1520 |
|
|
List<Subject> subjectList = node.getSubjectList();
|
| 1521 |
|
|
// the calling subject must be in the subject list
|
| 1522 |
|
|
if ( subjectList.contains(callingSubject)) {
|
| 1523 |
|
|
allowed = true;
|
| 1524 |
|
|
|
| 1525 |
|
|
}
|
| 1526 |
|
|
|
| 1527 |
|
|
}
|
| 1528 |
|
|
}
|
| 1529 |
|
|
|
| 1530 |
|
|
if (!allowed ) {
|
| 1531 |
|
|
String msg = "The subject identified by " + callingSubject.getValue() +
|
| 1532 |
|
|
" is not authorized to call this service.";
|
| 1533 |
|
|
throw new NotAuthorized("1331", msg);
|
| 1534 |
|
|
|
| 1535 |
|
|
}
|
| 1536 |
|
|
try {
|
| 1537 |
9340
|
tao
|
HazelcastService.getInstance().getSystemMetadataMap().lock(pid);
|
| 1538 |
6600
|
cjones
|
|
| 1539 |
9340
|
tao
|
// compare what we have locally to what is sent in the change notification
|
| 1540 |
6600
|
cjones
|
try {
|
| 1541 |
9340
|
tao
|
currentLocalSysMeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
| 1542 |
|
|
|
| 1543 |
|
|
} catch (RuntimeException e) {
|
| 1544 |
|
|
String msg = "SystemMetadata for pid " + pid.getValue() +
|
| 1545 |
|
|
" couldn't be updated because it couldn't be found locally: " +
|
| 1546 |
|
|
e.getMessage();
|
| 1547 |
6692
|
leinfelder
|
logMetacat.error(msg);
|
| 1548 |
9340
|
tao
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
| 1549 |
6692
|
leinfelder
|
sf.initCause(e);
|
| 1550 |
9340
|
tao
|
throw sf;
|
| 1551 |
6600
|
cjones
|
}
|
| 1552 |
6692
|
leinfelder
|
|
| 1553 |
9340
|
tao
|
if(currentLocalSysMeta == null) {
|
| 1554 |
|
|
throw new InvalidRequest("1334", "We can't find the system metadata in the node for the id "+pid.getValue());
|
| 1555 |
|
|
}
|
| 1556 |
9382
|
tao
|
if (currentLocalSysMeta.getSerialVersion().longValue() <= serialVersion ) {
|
| 1557 |
9340
|
tao
|
try {
|
| 1558 |
|
|
newSysMeta = cn.getSystemMetadata(null, pid);
|
| 1559 |
|
|
} catch (NotFound e) {
|
| 1560 |
|
|
// huh? you just said you had it
|
| 1561 |
|
|
String msg = "On updating the local copy of system metadata " +
|
| 1562 |
|
|
"for pid " + pid.getValue() +", the CN reports it is not found." +
|
| 1563 |
|
|
" The error message was: " + e.getMessage();
|
| 1564 |
|
|
logMetacat.error(msg);
|
| 1565 |
|
|
//ServiceFailure sf = new ServiceFailure("1333", msg);
|
| 1566 |
|
|
InvalidRequest sf = new InvalidRequest("1334", msg);
|
| 1567 |
|
|
sf.initCause(e);
|
| 1568 |
|
|
throw sf;
|
| 1569 |
9056
|
tao
|
}
|
| 1570 |
9340
|
tao
|
|
| 1571 |
|
|
//check about the sid in the system metadata
|
| 1572 |
|
|
Identifier newSID = newSysMeta.getSeriesId();
|
| 1573 |
|
|
if(newSID != null) {
|
| 1574 |
|
|
if (!isValidIdentifier(newSID)) {
|
| 1575 |
|
|
throw new InvalidRequest("1334", "The series identifier in the new system metadata is invalid.");
|
| 1576 |
|
|
}
|
| 1577 |
|
|
Identifier currentSID = currentLocalSysMeta.getSeriesId();
|
| 1578 |
|
|
if( currentSID != null && currentSID.getValue() != null) {
|
| 1579 |
|
|
if(!newSID.getValue().equals(currentSID.getValue())) {
|
| 1580 |
|
|
//newSID doesn't match the currentSID. The newSID shouldn't be used.
|
| 1581 |
|
|
try {
|
| 1582 |
|
|
if(IdentifierManager.getInstance().identifierExists(newSID.getValue())) {
|
| 1583 |
|
|
throw new InvalidRequest("1334", "The series identifier "+newSID.getValue()+" in the new system metadata has been used by another object.");
|
| 1584 |
|
|
}
|
| 1585 |
|
|
} catch (SQLException sql) {
|
| 1586 |
|
|
throw new ServiceFailure("1333", "Couldn't determine if the SID "+newSID.getValue()+" in the system metadata exists in the node since "+sql.getMessage());
|
| 1587 |
|
|
}
|
| 1588 |
|
|
|
| 1589 |
|
|
}
|
| 1590 |
|
|
} else {
|
| 1591 |
|
|
//newSID shouldn't be used
|
| 1592 |
9056
|
tao
|
try {
|
| 1593 |
|
|
if(IdentifierManager.getInstance().identifierExists(newSID.getValue())) {
|
| 1594 |
|
|
throw new InvalidRequest("1334", "The series identifier "+newSID.getValue()+" in the new system metadata has been used by another object.");
|
| 1595 |
|
|
}
|
| 1596 |
|
|
} catch (SQLException sql) {
|
| 1597 |
|
|
throw new ServiceFailure("1333", "Couldn't determine if the SID "+newSID.getValue()+" in the system metadata exists in the node since "+sql.getMessage());
|
| 1598 |
|
|
}
|
| 1599 |
|
|
}
|
| 1600 |
9340
|
tao
|
}
|
| 1601 |
|
|
// update the local copy of system metadata for the pid
|
| 1602 |
|
|
try {
|
| 1603 |
|
|
if(needCheckAuthoriativeNode) {
|
| 1604 |
|
|
//this is for the v2 api.
|
| 1605 |
|
|
if(isAuthoritativeNode(pid)) {
|
| 1606 |
|
|
//this is the authoritative node, so we only accept replica and serial version
|
| 1607 |
9375
|
tao
|
logMetacat.debug("MNodeService.systemMetadataChanged - this is the authoritative node for the pid "+pid.getValue());
|
| 1608 |
9340
|
tao
|
List<Replica> replicas = newSysMeta.getReplicaList();
|
| 1609 |
|
|
newSysMeta = currentLocalSysMeta;
|
| 1610 |
|
|
newSysMeta.setSerialVersion(new BigInteger((new Long(serialVersion)).toString()));
|
| 1611 |
|
|
newSysMeta.setReplicaList(replicas);
|
| 1612 |
9375
|
tao
|
} else {
|
| 1613 |
|
|
//we need to archive the object in the replica node
|
| 1614 |
|
|
logMetacat.debug("MNodeService.systemMetadataChanged - this is NOT the authoritative node for the pid "+pid.getValue());
|
| 1615 |
|
|
logMetacat.debug("MNodeService.systemMetadataChanged - the new value of archive is "+newSysMeta.getArchived()+" for the pid "+pid.getValue());
|
| 1616 |
|
|
logMetacat.debug("MNodeService.systemMetadataChanged - the local value of archive is "+currentLocalSysMeta.getArchived()+" for the pid "+pid.getValue());
|
| 1617 |
|
|
if (newSysMeta.getArchived() != null && newSysMeta.getArchived() == true &&
|
| 1618 |
|
|
((currentLocalSysMeta.getArchived() != null && currentLocalSysMeta.getArchived() == false ) || currentLocalSysMeta.getArchived() == null)){
|
| 1619 |
|
|
logMetacat.debug("MNodeService.systemMetadataChanged - start to archive object "+pid.getValue());
|
| 1620 |
|
|
boolean logArchive = false;
|
| 1621 |
|
|
boolean needUpdateModificationDate = false;
|
| 1622 |
|
|
try {
|
| 1623 |
|
|
archiveObject(logArchive, session, pid, newSysMeta, needUpdateModificationDate);
|
| 1624 |
|
|
} catch (NotFound e) {
|
| 1625 |
|
|
throw new InvalidRequest("1334", "Can't find the pid "+pid.getValue()+" for archive.");
|
| 1626 |
|
|
}
|
| 1627 |
|
|
|
| 1628 |
9384
|
tao
|
} else if((newSysMeta.getArchived() == null || newSysMeta.getArchived() == false) && (currentLocalSysMeta.getArchived() != null && currentLocalSysMeta.getArchived() == true )) {
|
| 1629 |
|
|
throw new InvalidRequest("1334", "The pid "+pid.getValue()+" has been archived and it can't be reset to false.");
|
| 1630 |
9375
|
tao
|
}
|
| 1631 |
9056
|
tao
|
}
|
| 1632 |
|
|
}
|
| 1633 |
9340
|
tao
|
HazelcastService.getInstance().getSystemMetadataMap().put(newSysMeta.getIdentifier(), newSysMeta);
|
| 1634 |
|
|
logMetacat.info("Updated local copy of system metadata for pid " +
|
| 1635 |
|
|
pid.getValue() + " after change notification from the CN.");
|
| 1636 |
|
|
|
| 1637 |
|
|
// TODO: consider inspecting the change for archive
|
| 1638 |
|
|
// see: https://projects.ecoinformatics.org/ecoinfo/issues/6417
|
| 1639 |
|
|
// if (newSysMeta.getArchived() != null && newSysMeta.getArchived().booleanValue()) {
|
| 1640 |
|
|
// try {
|
| 1641 |
|
|
// this.archive(session, newSysMeta.getIdentifier());
|
| 1642 |
|
|
// } catch (NotFound e) {
|
| 1643 |
|
|
// // do we care? nothing to do about it now
|
| 1644 |
|
|
// logMetacat.error(e.getMessage(), e);
|
| 1645 |
|
|
// }
|
| 1646 |
|
|
// }
|
| 1647 |
|
|
|
| 1648 |
|
|
} catch (RuntimeException e) {
|
| 1649 |
|
|
String msg = "SystemMetadata for pid " + pid.getValue() +
|
| 1650 |
|
|
" couldn't be updated: " +
|
| 1651 |
|
|
e.getMessage();
|
| 1652 |
|
|
logMetacat.error(msg);
|
| 1653 |
|
|
ServiceFailure sf = new ServiceFailure("1333", msg);
|
| 1654 |
|
|
sf.initCause(e);
|
| 1655 |
|
|
throw sf;
|
| 1656 |
9056
|
tao
|
}
|
| 1657 |
6600
|
cjones
|
|
| 1658 |
9375
|
tao
|
try {
|
| 1659 |
|
|
String localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 1660 |
|
|
EventLog.getInstance().log(request.getRemoteAddr(),
|
| 1661 |
|
|
request.getHeader("User-Agent"), session.getSubject().getValue(),
|
| 1662 |
|
|
localId, "updateSystemMetadata");
|
| 1663 |
|
|
} catch (Exception e) {
|
| 1664 |
|
|
// do nothing, no localId to log with
|
| 1665 |
|
|
logMetacat.warn("MNodeService.systemMetadataChanged - Could not log 'updateSystemMetadata' event because no localId was found for pid: " + pid.getValue());
|
| 1666 |
|
|
}
|
| 1667 |
|
|
|
| 1668 |
9340
|
tao
|
|
| 1669 |
6600
|
cjones
|
}
|
| 1670 |
9340
|
tao
|
} finally {
|
| 1671 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().unlock(pid);
|
| 1672 |
|
|
}
|
| 1673 |
|
|
|
| 1674 |
9382
|
tao
|
if (currentLocalSysMeta.getSerialVersion().longValue() <= serialVersion ) {
|
| 1675 |
9248
|
leinfelder
|
// attempt to re-register the identifier (it checks if it is a doi)
|
| 1676 |
|
|
try {
|
| 1677 |
9340
|
tao
|
DOIService.getInstance().registerDOI(newSysMeta);
|
| 1678 |
|
|
} catch (Exception e) {
|
| 1679 |
|
|
logMetacat.warn("Could not [re]register DOI: " + e.getMessage(), e);
|
| 1680 |
|
|
}
|
| 1681 |
9248
|
leinfelder
|
|
| 1682 |
8464
|
leinfelder
|
// submit for indexing
|
| 1683 |
|
|
try {
|
| 1684 |
9340
|
tao
|
MetacatSolrIndex.getInstance().submit(newSysMeta.getIdentifier(), newSysMeta, null, true);
|
| 1685 |
|
|
} catch (Exception e) {
|
| 1686 |
8464
|
leinfelder
|
logMetacat.error("Could not submit changed systemMetadata for indexing, pid: " + newSysMeta.getIdentifier().getValue(), e);
|
| 1687 |
9340
|
tao
|
}
|
| 1688 |
6600
|
cjones
|
}
|
| 1689 |
|
|
|
| 1690 |
6991
|
leinfelder
|
return true;
|
| 1691 |
|
|
|
| 1692 |
6599
|
cjones
|
}
|
| 1693 |
|
|
|
| 1694 |
6795
|
cjones
|
/*
|
| 1695 |
|
|
* Set the replication status for the object on the Coordinating Node
|
| 1696 |
|
|
*
|
| 1697 |
|
|
* @param session - the session for the this target node
|
| 1698 |
|
|
* @param pid - the identifier of the object being updated
|
| 1699 |
|
|
* @param nodeId - the identifier of this target node
|
| 1700 |
|
|
* @param status - the replication status to set
|
| 1701 |
|
|
* @param failure - the exception to include, if any
|
| 1702 |
|
|
*/
|
| 1703 |
|
|
private void setReplicationStatus(Session session, Identifier pid,
|
| 1704 |
|
|
NodeReference nodeId, ReplicationStatus status, BaseException failure)
|
| 1705 |
|
|
throws ServiceFailure, NotImplemented, NotAuthorized,
|
| 1706 |
|
|
InvalidRequest {
|
| 1707 |
|
|
|
| 1708 |
|
|
// call the CN as the MN to set the replication status
|
| 1709 |
|
|
try {
|
| 1710 |
|
|
this.cn = D1Client.getCN();
|
| 1711 |
|
|
this.cn.setReplicationStatus(session, pid, nodeId,
|
| 1712 |
|
|
status, failure);
|
| 1713 |
|
|
|
| 1714 |
|
|
} catch (InvalidToken e) {
|
| 1715 |
7091
|
leinfelder
|
String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (InvalidToken): " + e.getMessage();
|
| 1716 |
|
|
logMetacat.error(msg);
|
| 1717 |
|
|
throw new ServiceFailure("2151",
|
| 1718 |
|
|
msg);
|
| 1719 |
6795
|
cjones
|
|
| 1720 |
|
|
} catch (NotFound e) {
|
| 1721 |
7091
|
leinfelder
|
String msg = "Could not set the replication status for " + pid.getValue() + " on the CN (NotFound): " + e.getMessage();
|
| 1722 |
|
|
logMetacat.error(msg);
|
| 1723 |
|
|
throw new ServiceFailure("2151",
|
| 1724 |
|
|
msg);
|
| 1725 |
6795
|
cjones
|
|
| 1726 |
|
|
}
|
| 1727 |
|
|
}
|
| 1728 |
8591
|
leinfelder
|
|
| 1729 |
|
|
private SystemMetadata makePublicIfNot(SystemMetadata sysmeta, Identifier pid) throws ServiceFailure, InvalidToken, NotFound, NotImplemented, InvalidRequest {
|
| 1730 |
|
|
// check if it is publicly readable
|
| 1731 |
|
|
boolean isPublic = false;
|
| 1732 |
|
|
Subject publicSubject = new Subject();
|
| 1733 |
|
|
publicSubject.setValue(Constants.SUBJECT_PUBLIC);
|
| 1734 |
|
|
Session publicSession = new Session();
|
| 1735 |
|
|
publicSession.setSubject(publicSubject);
|
| 1736 |
|
|
AccessRule publicRule = new AccessRule();
|
| 1737 |
|
|
publicRule.addPermission(Permission.READ);
|
| 1738 |
|
|
publicRule.addSubject(publicSubject);
|
| 1739 |
|
|
|
| 1740 |
|
|
// see if we need to add the rule
|
| 1741 |
|
|
try {
|
| 1742 |
|
|
isPublic = this.isAuthorized(publicSession, pid, Permission.READ);
|
| 1743 |
|
|
} catch (NotAuthorized na) {
|
| 1744 |
|
|
// well, certainly not authorized for public read!
|
| 1745 |
|
|
}
|
| 1746 |
|
|
if (!isPublic) {
|
| 1747 |
|
|
sysmeta.getAccessPolicy().addAllow(publicRule);
|
| 1748 |
|
|
}
|
| 1749 |
|
|
|
| 1750 |
|
|
return sysmeta;
|
| 1751 |
|
|
}
|
| 1752 |
7099
|
leinfelder
|
|
| 1753 |
|
|
@Override
|
| 1754 |
7441
|
leinfelder
|
public Identifier generateIdentifier(Session session, String scheme, String fragment)
|
| 1755 |
7099
|
leinfelder
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
|
| 1756 |
|
|
InvalidRequest {
|
| 1757 |
7448
|
leinfelder
|
|
| 1758 |
8210
|
leinfelder
|
// check for null session
|
| 1759 |
|
|
if (session == null) {
|
| 1760 |
|
|
throw new InvalidToken("2190", "Session is required to generate an Identifier at this Node.");
|
| 1761 |
|
|
}
|
| 1762 |
|
|
|
| 1763 |
7441
|
leinfelder
|
Identifier identifier = new Identifier();
|
| 1764 |
7448
|
leinfelder
|
|
| 1765 |
7489
|
leinfelder
|
// handle different schemes
|
| 1766 |
|
|
if (scheme.equalsIgnoreCase(UUID_SCHEME)) {
|
| 1767 |
|
|
// UUID
|
| 1768 |
|
|
UUID uuid = UUID.randomUUID();
|
| 1769 |
|
|
identifier.setValue(UUID_PREFIX + uuid.toString());
|
| 1770 |
|
|
} else if (scheme.equalsIgnoreCase(DOI_SCHEME)) {
|
| 1771 |
7512
|
leinfelder
|
// generate a DOI
|
| 1772 |
7448
|
leinfelder
|
try {
|
| 1773 |
7512
|
leinfelder
|
identifier = DOIService.getInstance().generateDOI();
|
| 1774 |
7448
|
leinfelder
|
} catch (EZIDException e) {
|
| 1775 |
7512
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("2191", "Could not generate DOI: " + e.getMessage());
|
| 1776 |
|
|
sf.initCause(e);
|
| 1777 |
|
|
throw sf;
|
| 1778 |
7448
|
leinfelder
|
}
|
| 1779 |
7489
|
leinfelder
|
} else {
|
| 1780 |
|
|
// default if we don't know the scheme
|
| 1781 |
|
|
if (fragment != null) {
|
| 1782 |
|
|
// for now, just autogen with fragment
|
| 1783 |
|
|
String autogenId = DocumentUtil.generateDocumentId(fragment, 0);
|
| 1784 |
|
|
identifier.setValue(autogenId);
|
| 1785 |
|
|
} else {
|
| 1786 |
|
|
// autogen with no fragment
|
| 1787 |
|
|
String autogenId = DocumentUtil.generateDocumentId(0);
|
| 1788 |
|
|
identifier.setValue(autogenId);
|
| 1789 |
|
|
}
|
| 1790 |
7448
|
leinfelder
|
}
|
| 1791 |
|
|
|
| 1792 |
7441
|
leinfelder
|
// TODO: reserve the identifier with the CN. We can only do this when
|
| 1793 |
|
|
// 1) the MN is part of a CN cluster
|
| 1794 |
|
|
// 2) the request is from an authenticated user
|
| 1795 |
|
|
|
| 1796 |
|
|
return identifier;
|
| 1797 |
7099
|
leinfelder
|
}
|
| 1798 |
7144
|
leinfelder
|
|
| 1799 |
8810
|
leinfelder
|
|
| 1800 |
7144
|
leinfelder
|
|
| 1801 |
|
|
@Override
|
| 1802 |
8810
|
leinfelder
|
public QueryEngineDescription getQueryEngineDescription(Session session, String engine)
|
| 1803 |
7144
|
leinfelder
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotImplemented,
|
| 1804 |
|
|
NotFound {
|
| 1805 |
7772
|
tao
|
if(engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1806 |
8162
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1807 |
|
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1808 |
|
|
}
|
| 1809 |
7634
|
tao
|
QueryEngineDescription qed = new QueryEngineDescription();
|
| 1810 |
7772
|
tao
|
qed.setName(EnabledQueryEngines.PATHQUERYENGINE);
|
| 1811 |
7634
|
tao
|
qed.setQueryEngineVersion("1.0");
|
| 1812 |
|
|
qed.addAdditionalInfo("This is the traditional structured query for Metacat");
|
| 1813 |
|
|
Vector<String> pathsForIndexing = null;
|
| 1814 |
|
|
try {
|
| 1815 |
|
|
pathsForIndexing = SystemUtil.getPathsForIndexing();
|
| 1816 |
|
|
} catch (MetacatUtilException e) {
|
| 1817 |
|
|
logMetacat.warn("Could not get index paths", e);
|
| 1818 |
|
|
}
|
| 1819 |
|
|
for (String fieldName: pathsForIndexing) {
|
| 1820 |
|
|
QueryField field = new QueryField();
|
| 1821 |
|
|
field.addDescription("Indexed field for path '" + fieldName + "'");
|
| 1822 |
|
|
field.setName(fieldName);
|
| 1823 |
|
|
field.setReturnable(true);
|
| 1824 |
|
|
field.setSearchable(true);
|
| 1825 |
|
|
field.setSortable(false);
|
| 1826 |
|
|
// TODO: determine type and multivaluedness
|
| 1827 |
|
|
field.setType(String.class.getName());
|
| 1828 |
|
|
//field.setMultivalued(true);
|
| 1829 |
|
|
qed.addQueryField(field);
|
| 1830 |
|
|
}
|
| 1831 |
|
|
return qed;
|
| 1832 |
7772
|
tao
|
} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
|
| 1833 |
7781
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
|
| 1834 |
7772
|
tao
|
throw new NotImplemented("0000", "MNodeService.getQueryEngineDescription - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1835 |
7781
|
tao
|
}
|
| 1836 |
7634
|
tao
|
try {
|
| 1837 |
7662
|
tao
|
QueryEngineDescription qed = MetacatSolrEngineDescriptionHandler.getInstance().getQueryEngineDescritpion();
|
| 1838 |
7634
|
tao
|
return qed;
|
| 1839 |
|
|
} catch (Exception e) {
|
| 1840 |
|
|
e.printStackTrace();
|
| 1841 |
|
|
throw new ServiceFailure("Solr server error", e.getMessage());
|
| 1842 |
|
|
}
|
| 1843 |
|
|
} else {
|
| 1844 |
|
|
throw new NotFound("404", "The Metacat member node can't find the query engine - "+engine);
|
| 1845 |
|
|
}
|
| 1846 |
|
|
|
| 1847 |
7417
|
leinfelder
|
}
|
| 1848 |
|
|
|
| 1849 |
|
|
@Override
|
| 1850 |
8810
|
leinfelder
|
public QueryEngineList listQueryEngines(Session session) throws InvalidToken,
|
| 1851 |
7417
|
leinfelder
|
ServiceFailure, NotAuthorized, NotImplemented {
|
| 1852 |
|
|
QueryEngineList qel = new QueryEngineList();
|
| 1853 |
7781
|
tao
|
//qel.addQueryEngine(EnabledQueryEngines.PATHQUERYENGINE);
|
| 1854 |
|
|
//qel.addQueryEngine(EnabledQueryEngines.SOLRENGINE);
|
| 1855 |
|
|
List<String> enables = EnabledQueryEngines.getInstance().getEnabled();
|
| 1856 |
7772
|
tao
|
for(String name : enables) {
|
| 1857 |
|
|
qel.addQueryEngine(name);
|
| 1858 |
7781
|
tao
|
}
|
| 1859 |
7417
|
leinfelder
|
return qel;
|
| 1860 |
|
|
}
|
| 1861 |
|
|
|
| 1862 |
|
|
@Override
|
| 1863 |
8810
|
leinfelder
|
public InputStream query(Session session, String engine, String query) throws InvalidToken,
|
| 1864 |
7417
|
leinfelder
|
ServiceFailure, NotAuthorized, InvalidRequest, NotImplemented,
|
| 1865 |
|
|
NotFound {
|
| 1866 |
7648
|
tao
|
String user = Constants.SUBJECT_PUBLIC;
|
| 1867 |
|
|
String[] groups= null;
|
| 1868 |
7680
|
tao
|
Set<Subject> subjects = null;
|
| 1869 |
7648
|
tao
|
if (session != null) {
|
| 1870 |
|
|
user = session.getSubject().getValue();
|
| 1871 |
7680
|
tao
|
subjects = AuthUtils.authorizedClientSubjects(session);
|
| 1872 |
7648
|
tao
|
if (subjects != null) {
|
| 1873 |
|
|
List<String> groupList = new ArrayList<String>();
|
| 1874 |
|
|
for (Subject subject: subjects) {
|
| 1875 |
|
|
groupList.add(subject.getValue());
|
| 1876 |
|
|
}
|
| 1877 |
|
|
groups = groupList.toArray(new String[0]);
|
| 1878 |
|
|
}
|
| 1879 |
7680
|
tao
|
} else {
|
| 1880 |
|
|
//add the public user subject to the set
|
| 1881 |
|
|
Subject subject = new Subject();
|
| 1882 |
|
|
subject.setValue(Constants.SUBJECT_PUBLIC);
|
| 1883 |
7757
|
leinfelder
|
subjects = new HashSet<Subject>();
|
| 1884 |
7680
|
tao
|
subjects.add(subject);
|
| 1885 |
7648
|
tao
|
}
|
| 1886 |
7680
|
tao
|
//System.out.println("====== user is "+user);
|
| 1887 |
|
|
//System.out.println("====== groups are "+groups);
|
| 1888 |
7772
|
tao
|
if (engine != null && engine.equals(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1889 |
8162
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.PATHQUERYENGINE)) {
|
| 1890 |
|
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1891 |
|
|
}
|
| 1892 |
7417
|
leinfelder
|
try {
|
| 1893 |
|
|
DBQuery queryobj = new DBQuery();
|
| 1894 |
7648
|
tao
|
|
| 1895 |
7417
|
leinfelder
|
String results = queryobj.performPathquery(query, user, groups);
|
| 1896 |
7757
|
leinfelder
|
ContentTypeByteArrayInputStream ctbais = new ContentTypeByteArrayInputStream(results.getBytes(MetaCatServlet.DEFAULT_ENCODING));
|
| 1897 |
|
|
ctbais.setContentType("text/xml");
|
| 1898 |
|
|
return ctbais;
|
| 1899 |
7417
|
leinfelder
|
|
| 1900 |
|
|
} catch (Exception e) {
|
| 1901 |
7757
|
leinfelder
|
throw new ServiceFailure("Pathquery error", e.getMessage());
|
| 1902 |
7417
|
leinfelder
|
}
|
| 1903 |
|
|
|
| 1904 |
7772
|
tao
|
} else if (engine != null && engine.equals(EnabledQueryEngines.SOLRENGINE)) {
|
| 1905 |
7781
|
tao
|
if(!EnabledQueryEngines.getInstance().isEnabled(EnabledQueryEngines.SOLRENGINE)) {
|
| 1906 |
7772
|
tao
|
throw new NotImplemented("0000", "MNodeService.query - the query engine "+engine +" hasn't been implemented or has been disabled.");
|
| 1907 |
7781
|
tao
|
}
|
| 1908 |
7634
|
tao
|
logMetacat.info("The query is ==================================== \n"+query);
|
| 1909 |
7620
|
tao
|
try {
|
| 1910 |
7634
|
tao
|
|
| 1911 |
7680
|
tao
|
return MetacatSolrIndex.getInstance().query(query, subjects);
|
| 1912 |
7620
|
tao
|
} catch (Exception e) {
|
| 1913 |
|
|
// TODO Auto-generated catch block
|
| 1914 |
|
|
throw new ServiceFailure("Solr server error", e.getMessage());
|
| 1915 |
|
|
}
|
| 1916 |
7417
|
leinfelder
|
}
|
| 1917 |
|
|
return null;
|
| 1918 |
|
|
}
|
| 1919 |
7849
|
leinfelder
|
|
| 1920 |
|
|
/**
|
| 1921 |
|
|
* Given an existing Science Metadata PID, this method mints a DOI
|
| 1922 |
|
|
* and updates the original object "publishing" the update with the DOI.
|
| 1923 |
|
|
* This includes updating the ORE map that describes the Science Metadata+data.
|
| 1924 |
|
|
* TODO: ensure all referenced objects allow public read
|
| 1925 |
|
|
*
|
| 1926 |
|
|
* @see https://projects.ecoinformatics.org/ecoinfo/issues/6014
|
| 1927 |
|
|
*
|
| 1928 |
|
|
* @param originalIdentifier
|
| 1929 |
|
|
* @param request
|
| 1930 |
7864
|
leinfelder
|
* @throws InvalidRequest
|
| 1931 |
|
|
* @throws NotImplemented
|
| 1932 |
|
|
* @throws NotAuthorized
|
| 1933 |
|
|
* @throws ServiceFailure
|
| 1934 |
|
|
* @throws InvalidToken
|
| 1935 |
7849
|
leinfelder
|
* @throws NotFound
|
| 1936 |
7864
|
leinfelder
|
* @throws InvalidSystemMetadata
|
| 1937 |
|
|
* @throws InsufficientResources
|
| 1938 |
|
|
* @throws UnsupportedType
|
| 1939 |
|
|
* @throws IdentifierNotUnique
|
| 1940 |
7849
|
leinfelder
|
*/
|
| 1941 |
9387
|
walker
|
public Identifier publish(Session session, Identifier originalIdentifier) throws InvalidToken,
|
| 1942 |
|
|
ServiceFailure, NotAuthorized, NotImplemented, InvalidRequest, NotFound, IdentifierNotUnique,
|
| 1943 |
|
|
UnsupportedType, InsufficientResources, InvalidSystemMetadata, IOException {
|
| 1944 |
7849
|
leinfelder
|
|
| 1945 |
9092
|
tao
|
String serviceFailureCode = "1030";
|
| 1946 |
|
|
Identifier sid = getPIDForSID(originalIdentifier, serviceFailureCode);
|
| 1947 |
|
|
if(sid != null) {
|
| 1948 |
|
|
originalIdentifier = sid;
|
| 1949 |
|
|
}
|
| 1950 |
8141
|
leinfelder
|
// get the original SM
|
| 1951 |
|
|
SystemMetadata originalSystemMetadata = this.getSystemMetadata(session, originalIdentifier);
|
| 1952 |
|
|
|
| 1953 |
8594
|
leinfelder
|
// make copy of it using the marshaller to ensure DEEP copy
|
| 1954 |
|
|
SystemMetadata sysmeta = null;
|
| 1955 |
8141
|
leinfelder
|
try {
|
| 1956 |
8594
|
leinfelder
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 1957 |
|
|
TypeMarshaller.marshalTypeToOutputStream(originalSystemMetadata, baos);
|
| 1958 |
|
|
sysmeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
|
| 1959 |
8141
|
leinfelder
|
} catch (Exception e) {
|
| 1960 |
|
|
// report as service failure
|
| 1961 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 1962 |
|
|
sf.initCause(e);
|
| 1963 |
|
|
throw sf;
|
| 1964 |
|
|
}
|
| 1965 |
|
|
|
| 1966 |
7849
|
leinfelder
|
// mint a DOI for the new revision
|
| 1967 |
|
|
Identifier newIdentifier = this.generateIdentifier(session, MNodeService.DOI_SCHEME, null);
|
| 1968 |
8141
|
leinfelder
|
|
| 1969 |
|
|
// set new metadata values
|
| 1970 |
7849
|
leinfelder
|
sysmeta.setIdentifier(newIdentifier);
|
| 1971 |
|
|
sysmeta.setObsoletes(originalIdentifier);
|
| 1972 |
|
|
sysmeta.setObsoletedBy(null);
|
| 1973 |
|
|
|
| 1974 |
8591
|
leinfelder
|
// ensure it is publicly readable
|
| 1975 |
|
|
sysmeta = makePublicIfNot(sysmeta, originalIdentifier);
|
| 1976 |
|
|
|
| 1977 |
9387
|
walker
|
//Get the bytes
|
| 1978 |
|
|
InputStream inputStream = null;
|
| 1979 |
|
|
boolean isScienceMetadata = isScienceMetadata(sysmeta);
|
| 1980 |
|
|
//If it's a science metadata doc, we want to update the packageId first
|
| 1981 |
|
|
if(isScienceMetadata){
|
| 1982 |
|
|
InputStream originalObject = this.get(session, originalIdentifier);
|
| 1983 |
|
|
|
| 1984 |
|
|
//Edit the science metadata with the new package Id (EML)
|
| 1985 |
|
|
inputStream = editScienceMetadata(session, originalObject, originalIdentifier, newIdentifier);
|
| 1986 |
|
|
}
|
| 1987 |
|
|
else{
|
| 1988 |
|
|
inputStream = this.get(session, originalIdentifier);
|
| 1989 |
|
|
}
|
| 1990 |
7849
|
leinfelder
|
|
| 1991 |
|
|
// update the object
|
| 1992 |
7864
|
leinfelder
|
this.update(session, originalIdentifier, inputStream, newIdentifier, sysmeta);
|
| 1993 |
7849
|
leinfelder
|
|
| 1994 |
7864
|
leinfelder
|
// update ORE that references the scimeta
|
| 1995 |
8190
|
leinfelder
|
// first try the naive method, then check the SOLR index
|
| 1996 |
7849
|
leinfelder
|
try {
|
| 1997 |
7864
|
leinfelder
|
String localId = IdentifierManager.getInstance().getLocalId(originalIdentifier.getValue());
|
| 1998 |
7849
|
leinfelder
|
|
| 1999 |
7864
|
leinfelder
|
Identifier potentialOreIdentifier = new Identifier();
|
| 2000 |
|
|
potentialOreIdentifier.setValue(SystemMetadataFactory.RESOURCE_MAP_PREFIX + localId);
|
| 2001 |
7849
|
leinfelder
|
|
| 2002 |
7864
|
leinfelder
|
InputStream oreInputStream = null;
|
| 2003 |
|
|
try {
|
| 2004 |
|
|
oreInputStream = this.get(session, potentialOreIdentifier);
|
| 2005 |
|
|
} catch (NotFound nf) {
|
| 2006 |
|
|
// this is probably okay for many sci meta data docs
|
| 2007 |
|
|
logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
|
| 2008 |
8190
|
leinfelder
|
// try the SOLR index
|
| 2009 |
8200
|
leinfelder
|
List<Identifier> potentialOreIdentifiers = this.lookupOreFor(originalIdentifier, false);
|
| 2010 |
8190
|
leinfelder
|
if (potentialOreIdentifiers != null) {
|
| 2011 |
|
|
potentialOreIdentifier = potentialOreIdentifiers.get(0);
|
| 2012 |
|
|
try {
|
| 2013 |
|
|
oreInputStream = this.get(session, potentialOreIdentifier);
|
| 2014 |
|
|
} catch (NotFound nf2) {
|
| 2015 |
|
|
// this is probably okay for many sci meta data docs
|
| 2016 |
|
|
logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
|
| 2017 |
|
|
}
|
| 2018 |
|
|
}
|
| 2019 |
7864
|
leinfelder
|
}
|
| 2020 |
|
|
if (oreInputStream != null) {
|
| 2021 |
|
|
Identifier newOreIdentifier = MNodeService.getInstance(request).generateIdentifier(session, MNodeService.UUID_SCHEME, null);
|
| 2022 |
|
|
|
| 2023 |
|
|
Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
|
| 2024 |
|
|
Map<Identifier, List<Identifier>> sciMetaMap = resourceMapStructure.get(potentialOreIdentifier);
|
| 2025 |
|
|
List<Identifier> dataIdentifiers = sciMetaMap.get(originalIdentifier);
|
| 2026 |
8591
|
leinfelder
|
|
| 2027 |
7864
|
leinfelder
|
// reconstruct the ORE with the new identifiers
|
| 2028 |
|
|
sciMetaMap.remove(originalIdentifier);
|
| 2029 |
|
|
sciMetaMap.put(newIdentifier, dataIdentifiers);
|
| 2030 |
|
|
|
| 2031 |
|
|
ResourceMap resourceMap = ResourceMapFactory.getInstance().createResourceMap(newOreIdentifier, sciMetaMap);
|
| 2032 |
|
|
String resourceMapString = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);
|
| 2033 |
|
|
|
| 2034 |
|
|
// get the original ORE SM and update the values
|
| 2035 |
8141
|
leinfelder
|
SystemMetadata originalOreSysMeta = this.getSystemMetadata(session, potentialOreIdentifier);
|
| 2036 |
|
|
SystemMetadata oreSysMeta = new SystemMetadata();
|
| 2037 |
|
|
try {
|
| 2038 |
8594
|
leinfelder
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 2039 |
|
|
TypeMarshaller.marshalTypeToOutputStream(originalOreSysMeta, baos);
|
| 2040 |
|
|
oreSysMeta = TypeMarshaller.unmarshalTypeFromStream(SystemMetadata.class, new ByteArrayInputStream(baos.toByteArray()));
|
| 2041 |
8141
|
leinfelder
|
} catch (Exception e) {
|
| 2042 |
|
|
// report as service failure
|
| 2043 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2044 |
|
|
sf.initCause(e);
|
| 2045 |
|
|
throw sf;
|
| 2046 |
|
|
}
|
| 2047 |
|
|
|
| 2048 |
7864
|
leinfelder
|
oreSysMeta.setIdentifier(newOreIdentifier);
|
| 2049 |
|
|
oreSysMeta.setObsoletes(potentialOreIdentifier);
|
| 2050 |
|
|
oreSysMeta.setObsoletedBy(null);
|
| 2051 |
|
|
oreSysMeta.setSize(BigInteger.valueOf(resourceMapString.getBytes("UTF-8").length));
|
| 2052 |
|
|
oreSysMeta.setChecksum(ChecksumUtil.checksum(resourceMapString.getBytes("UTF-8"), oreSysMeta.getChecksum().getAlgorithm()));
|
| 2053 |
|
|
|
| 2054 |
8591
|
leinfelder
|
// ensure ORE is publicly readable
|
| 2055 |
8594
|
leinfelder
|
oreSysMeta = makePublicIfNot(oreSysMeta, potentialOreIdentifier);
|
| 2056 |
8591
|
leinfelder
|
|
| 2057 |
|
|
// ensure all data objects allow public read
|
| 2058 |
|
|
List<String> pidsToSync = new ArrayList<String>();
|
| 2059 |
|
|
for (Identifier dataId: dataIdentifiers) {
|
| 2060 |
|
|
SystemMetadata dataSysMeta = this.getSystemMetadata(session, dataId);
|
| 2061 |
|
|
dataSysMeta = makePublicIfNot(dataSysMeta, dataId);
|
| 2062 |
|
|
this.updateSystemMetadata(dataSysMeta);
|
| 2063 |
|
|
pidsToSync.add(dataId.getValue());
|
| 2064 |
|
|
}
|
| 2065 |
|
|
SyncAccessPolicy sap = new SyncAccessPolicy();
|
| 2066 |
|
|
try {
|
| 2067 |
|
|
sap.sync(pidsToSync);
|
| 2068 |
|
|
} catch (Exception e) {
|
| 2069 |
|
|
// ignore
|
| 2070 |
|
|
logMetacat.warn("Error attempting to sync access for data objects when publishing package");
|
| 2071 |
|
|
}
|
| 2072 |
|
|
|
| 2073 |
7864
|
leinfelder
|
// save the updated ORE
|
| 2074 |
|
|
this.update(
|
| 2075 |
|
|
session,
|
| 2076 |
|
|
potentialOreIdentifier,
|
| 2077 |
|
|
new ByteArrayInputStream(resourceMapString.getBytes("UTF-8")),
|
| 2078 |
|
|
newOreIdentifier,
|
| 2079 |
|
|
oreSysMeta);
|
| 2080 |
|
|
|
| 2081 |
8362
|
leinfelder
|
} else {
|
| 2082 |
|
|
// create a new ORE for them
|
| 2083 |
|
|
// https://projects.ecoinformatics.org/ecoinfo/issues/6194
|
| 2084 |
|
|
try {
|
| 2085 |
|
|
// find the local id for the NEW package.
|
| 2086 |
|
|
String newLocalId = IdentifierManager.getInstance().getLocalId(newIdentifier.getValue());
|
| 2087 |
|
|
|
| 2088 |
|
|
@SuppressWarnings("unused")
|
| 2089 |
|
|
SystemMetadata extraSysMeta = SystemMetadataFactory.createSystemMetadata(newLocalId, true, false);
|
| 2090 |
8591
|
leinfelder
|
// should be done generating the ORE here, and the same permissions were used from the metadata object
|
| 2091 |
8362
|
leinfelder
|
|
| 2092 |
|
|
} catch (Exception e) {
|
| 2093 |
|
|
// oops, guess there was a problem - no package for you
|
| 2094 |
|
|
logMetacat.error("Could not generate new ORE for published object: " + newIdentifier.getValue(), e);
|
| 2095 |
|
|
}
|
| 2096 |
7864
|
leinfelder
|
}
|
| 2097 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 2098 |
|
|
// report as service failure
|
| 2099 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2100 |
|
|
sf.initCause(e);
|
| 2101 |
|
|
throw sf;
|
| 2102 |
|
|
} catch (UnsupportedEncodingException e) {
|
| 2103 |
|
|
// report as service failure
|
| 2104 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2105 |
|
|
sf.initCause(e);
|
| 2106 |
|
|
throw sf;
|
| 2107 |
|
|
} catch (OREException e) {
|
| 2108 |
|
|
// report as service failure
|
| 2109 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2110 |
|
|
sf.initCause(e);
|
| 2111 |
|
|
throw sf;
|
| 2112 |
|
|
} catch (URISyntaxException e) {
|
| 2113 |
|
|
// report as service failure
|
| 2114 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2115 |
|
|
sf.initCause(e);
|
| 2116 |
|
|
throw sf;
|
| 2117 |
|
|
} catch (OREParserException e) {
|
| 2118 |
|
|
// report as service failure
|
| 2119 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2120 |
|
|
sf.initCause(e);
|
| 2121 |
|
|
throw sf;
|
| 2122 |
|
|
} catch (ORESerialiserException e) {
|
| 2123 |
|
|
// report as service failure
|
| 2124 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2125 |
|
|
sf.initCause(e);
|
| 2126 |
|
|
throw sf;
|
| 2127 |
|
|
} catch (NoSuchAlgorithmException e) {
|
| 2128 |
|
|
// report as service failure
|
| 2129 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2130 |
|
|
sf.initCause(e);
|
| 2131 |
|
|
throw sf;
|
| 2132 |
9024
|
tao
|
} catch (SQLException e) {
|
| 2133 |
|
|
// report as service failure
|
| 2134 |
|
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2135 |
|
|
sf.initCause(e);
|
| 2136 |
|
|
throw sf;
|
| 2137 |
|
|
}
|
| 2138 |
7849
|
leinfelder
|
|
| 2139 |
|
|
return newIdentifier;
|
| 2140 |
|
|
}
|
| 2141 |
7850
|
leinfelder
|
|
| 2142 |
|
|
/**
|
| 2143 |
9387
|
walker
|
* Update a science metadata document with its new Identifier
|
| 2144 |
|
|
*
|
| 2145 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 2146 |
|
|
* @param object - the InputStream for the XML object to be edited
|
| 2147 |
|
|
* @param pid - the Identifier of the XML object to be updated
|
| 2148 |
|
|
* @param newPid = the new Identifier to give to the modified XML doc
|
| 2149 |
|
|
*
|
| 2150 |
|
|
* @return newObject - The InputStream for the modified XML object
|
| 2151 |
|
|
*
|
| 2152 |
|
|
* @throws ServiceFailure
|
| 2153 |
|
|
* @throws IOException
|
| 2154 |
|
|
* @throws UnsupportedEncodingException
|
| 2155 |
|
|
* @throws InvalidToken
|
| 2156 |
|
|
* @throws NotAuthorized
|
| 2157 |
|
|
* @throws NotFound
|
| 2158 |
|
|
* @throws NotImplemented
|
| 2159 |
|
|
*/
|
| 2160 |
|
|
public InputStream editScienceMetadata(Session session, InputStream object, Identifier pid, Identifier newPid)
|
| 2161 |
|
|
throws ServiceFailure, IOException, UnsupportedEncodingException, InvalidToken, NotAuthorized, NotFound, NotImplemented {
|
| 2162 |
|
|
|
| 2163 |
|
|
logMetacat.debug("D1NodeService.editScienceMetadata() called.");
|
| 2164 |
|
|
|
| 2165 |
|
|
InputStream newObject = null;
|
| 2166 |
|
|
|
| 2167 |
|
|
try{
|
| 2168 |
|
|
//Get the root node of the XML document
|
| 2169 |
|
|
byte[] xmlBytes = IOUtils.toByteArray(object);
|
| 2170 |
|
|
String xmlStr = new String(xmlBytes, "UTF-8");
|
| 2171 |
|
|
|
| 2172 |
|
|
Document doc = XMLUtilities.getXMLReaderAsDOMDocument(new StringReader(xmlStr));
|
| 2173 |
|
|
org.w3c.dom.Node docNode = doc.getDocumentElement();
|
| 2174 |
|
|
|
| 2175 |
|
|
//Get the system metadata for this object
|
| 2176 |
|
|
SystemMetadata sysMeta = null;
|
| 2177 |
|
|
try{
|
| 2178 |
|
|
sysMeta = getSystemMetadata(session, pid);
|
| 2179 |
|
|
} catch(NotAuthorized e){
|
| 2180 |
|
|
throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
|
| 2181 |
|
|
"This session is not authorized to access the system metadata for " +
|
| 2182 |
|
|
pid.getValue() + " : " + e.getMessage());
|
| 2183 |
|
|
} catch(NotFound e){
|
| 2184 |
|
|
throw new ServiceFailure("1030", "D1NodeService.editScienceMetadata(): " +
|
| 2185 |
|
|
"Could not find the system metadata for " +
|
| 2186 |
|
|
pid.getValue() + " : " + e.getMessage());
|
| 2187 |
|
|
}
|
| 2188 |
|
|
|
| 2189 |
|
|
//Get the formatId
|
| 2190 |
|
|
ObjectFormatIdentifier objFormatId = sysMeta.getFormatId();
|
| 2191 |
|
|
String formatId = objFormatId.getValue();
|
| 2192 |
|
|
|
| 2193 |
|
|
//For all EML formats
|
| 2194 |
|
|
if(formatId.indexOf("eml") == 0){
|
| 2195 |
|
|
//Update or add the id attribute
|
| 2196 |
|
|
XMLUtilities.addAttributeNodeToDOMTree(docNode, XPATH_EML_ID, newPid.getValue());
|
| 2197 |
|
|
}
|
| 2198 |
|
|
|
| 2199 |
|
|
//The modified object InputStream
|
| 2200 |
|
|
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
|
| 2201 |
|
|
Source xmlSource = new DOMSource(docNode);
|
| 2202 |
|
|
Result outputTarget = new StreamResult(outputStream);
|
| 2203 |
|
|
TransformerFactory.newInstance().newTransformer().transform(xmlSource, outputTarget);
|
| 2204 |
|
|
newObject = new ByteArrayInputStream(outputStream.toByteArray());
|
| 2205 |
|
|
|
| 2206 |
|
|
} catch(TransformerException e) {
|
| 2207 |
|
|
throw new ServiceFailure("1030", "MNNodeService.editScienceMetadata(): " +
|
| 2208 |
|
|
"Could not update the ID in the XML document for " +
|
| 2209 |
|
|
"pid " + pid.getValue() +" : " + e.getMessage());
|
| 2210 |
|
|
} catch(IOException e){
|
| 2211 |
|
|
throw new ServiceFailure("1030", "MNNodeService.editScienceMetadata(): " +
|
| 2212 |
|
|
"Could not update the ID in the XML document for " +
|
| 2213 |
|
|
"pid " + pid.getValue() +" : " + e.getMessage());
|
| 2214 |
|
|
}
|
| 2215 |
|
|
|
| 2216 |
|
|
return newObject;
|
| 2217 |
|
|
}
|
| 2218 |
|
|
|
| 2219 |
|
|
/**
|
| 2220 |
8190
|
leinfelder
|
* Determines if we already have registered an ORE map for this package
|
| 2221 |
|
|
* NOTE: uses a solr query to locate OREs for the object
|
| 2222 |
|
|
* @param guid of the EML/packaging object
|
| 2223 |
|
|
* @return list of resource map identifiers for the given pid
|
| 2224 |
|
|
*/
|
| 2225 |
8200
|
leinfelder
|
public List<Identifier> lookupOreFor(Identifier guid, boolean includeObsolete) {
|
| 2226 |
8190
|
leinfelder
|
// Search for the ORE if we can find it
|
| 2227 |
|
|
String pid = guid.getValue();
|
| 2228 |
|
|
List<Identifier> retList = null;
|
| 2229 |
|
|
try {
|
| 2230 |
8745
|
leinfelder
|
String query = "fl=id,resourceMap&wt=xml&q=-obsoletedBy:[* TO *]+resourceMap:[* TO *]+id:\"" + pid + "\"";
|
| 2231 |
8200
|
leinfelder
|
if (includeObsolete) {
|
| 2232 |
8745
|
leinfelder
|
query = "fl=id,resourceMap&wt=xml&q=resourceMap:[* TO *]+id:\"" + pid + "\"";
|
| 2233 |
8200
|
leinfelder
|
}
|
| 2234 |
|
|
|
| 2235 |
8810
|
leinfelder
|
InputStream results = this.query(null, "solr", query);
|
| 2236 |
8190
|
leinfelder
|
org.w3c.dom.Node rootNode = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new InputStreamReader(results, "UTF-8"));
|
| 2237 |
|
|
//String resultString = XMLUtilities.getDOMTreeAsString(rootNode);
|
| 2238 |
|
|
org.w3c.dom.NodeList nodeList = XMLUtilities.getNodeListWithXPath(rootNode, "//arr[@name=\"resourceMap\"]/str");
|
| 2239 |
|
|
if (nodeList != null && nodeList.getLength() > 0) {
|
| 2240 |
|
|
retList = new ArrayList<Identifier>();
|
| 2241 |
|
|
for (int i = 0; i < nodeList.getLength(); i++) {
|
| 2242 |
|
|
String found = nodeList.item(i).getFirstChild().getNodeValue();
|
| 2243 |
|
|
Identifier oreId = new Identifier();
|
| 2244 |
|
|
oreId.setValue(found);
|
| 2245 |
|
|
retList.add(oreId);
|
| 2246 |
|
|
}
|
| 2247 |
|
|
}
|
| 2248 |
|
|
} catch (Exception e) {
|
| 2249 |
|
|
logMetacat.error("Error checking for resourceMap[s] on pid " + pid + ". " + e.getMessage(), e);
|
| 2250 |
|
|
}
|
| 2251 |
|
|
|
| 2252 |
|
|
return retList;
|
| 2253 |
|
|
}
|
| 2254 |
|
|
|
| 2255 |
8810
|
leinfelder
|
|
| 2256 |
|
|
@Override
|
| 2257 |
|
|
public InputStream getPackage(Session session, ObjectFormatIdentifier formatId,
|
| 2258 |
|
|
Identifier pid) throws InvalidToken, ServiceFailure,
|
| 2259 |
|
|
NotAuthorized, InvalidRequest, NotImplemented, NotFound {
|
| 2260 |
9290
|
tao
|
if(formatId == null) {
|
| 2261 |
|
|
throw new InvalidRequest("2873", "The format type can't be null in the getpackage method.");
|
| 2262 |
9305
|
tao
|
} else if(!formatId.getValue().equals("application/bagit-097")) {
|
| 2263 |
9290
|
tao
|
throw new NotImplemented("", "The format "+formatId.getValue()+" is not supported in the getpackage method");
|
| 2264 |
|
|
}
|
| 2265 |
9092
|
tao
|
String serviceFailureCode = "2871";
|
| 2266 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
| 2267 |
|
|
if(sid != null) {
|
| 2268 |
|
|
pid = sid;
|
| 2269 |
|
|
}
|
| 2270 |
7850
|
leinfelder
|
InputStream bagInputStream = null;
|
| 2271 |
|
|
BagFactory bagFactory = new BagFactory();
|
| 2272 |
|
|
Bag bag = bagFactory.createBag();
|
| 2273 |
|
|
|
| 2274 |
|
|
// track the temp files we use so we can delete them when finished
|
| 2275 |
|
|
List<File> tempFiles = new ArrayList<File>();
|
| 2276 |
|
|
|
| 2277 |
|
|
// the pids to include in the package
|
| 2278 |
|
|
List<Identifier> packagePids = new ArrayList<Identifier>();
|
| 2279 |
|
|
|
| 2280 |
7855
|
leinfelder
|
// catch non-D1 service errors and throw as ServiceFailures
|
| 2281 |
|
|
try {
|
| 2282 |
8437
|
walker
|
//Create a map of dataone ids and file names
|
| 2283 |
|
|
Map<Identifier, String> fileNames = new HashMap<Identifier, String>();
|
| 2284 |
7855
|
leinfelder
|
|
| 2285 |
8800
|
leinfelder
|
// track the pid-to-file mapping
|
| 2286 |
|
|
StringBuffer pidMapping = new StringBuffer();
|
| 2287 |
|
|
|
| 2288 |
7855
|
leinfelder
|
// find the package contents
|
| 2289 |
|
|
SystemMetadata sysMeta = this.getSystemMetadata(session, pid);
|
| 2290 |
8025
|
leinfelder
|
if (ObjectFormatCache.getInstance().getFormat(sysMeta.getFormatId()).getFormatType().equals("RESOURCE")) {
|
| 2291 |
8437
|
walker
|
//Get the resource map as a map of Identifiers
|
| 2292 |
7855
|
leinfelder
|
InputStream oreInputStream = this.get(session, pid);
|
| 2293 |
|
|
Map<Identifier, Map<Identifier, List<Identifier>>> resourceMapStructure = ResourceMapFactory.getInstance().parseResourceMap(oreInputStream);
|
| 2294 |
|
|
packagePids.addAll(resourceMapStructure.keySet());
|
| 2295 |
8437
|
walker
|
//Loop through each object in this resource map
|
| 2296 |
7855
|
leinfelder
|
for (Map<Identifier, List<Identifier>> entries: resourceMapStructure.values()) {
|
| 2297 |
8437
|
walker
|
//Loop through each metadata object in this entry
|
| 2298 |
|
|
Set<Identifier> metadataIdentifiers = entries.keySet();
|
| 2299 |
|
|
for(Identifier metadataID: metadataIdentifiers){
|
| 2300 |
|
|
try{
|
| 2301 |
|
|
//Get the system metadata for this metadata object
|
| 2302 |
|
|
SystemMetadata metadataSysMeta = this.getSystemMetadata(session, metadataID);
|
| 2303 |
|
|
|
| 2304 |
8800
|
leinfelder
|
// include user-friendly metadata
|
| 2305 |
|
|
if (ObjectFormatCache.getInstance().getFormat(metadataSysMeta.getFormatId()).getFormatType().equals("METADATA")) {
|
| 2306 |
|
|
InputStream metadataStream = this.get(session, metadataID);
|
| 2307 |
|
|
|
| 2308 |
|
|
try {
|
| 2309 |
|
|
// transform
|
| 2310 |
|
|
String format = "default";
|
| 2311 |
|
|
|
| 2312 |
|
|
DBTransform transformer = new DBTransform();
|
| 2313 |
|
|
String documentContent = IOUtils.toString(metadataStream, "UTF-8");
|
| 2314 |
|
|
String sourceType = metadataSysMeta.getFormatId().getValue();
|
| 2315 |
|
|
String targetType = "-//W3C//HTML//EN";
|
| 2316 |
|
|
ByteArrayOutputStream baos = new ByteArrayOutputStream();
|
| 2317 |
|
|
Writer writer = new OutputStreamWriter(baos , "UTF-8");
|
| 2318 |
|
|
// TODO: include more params?
|
| 2319 |
|
|
Hashtable<String, String[]> params = new Hashtable<String, String[]>();
|
| 2320 |
|
|
String localId = null;
|
| 2321 |
|
|
try {
|
| 2322 |
|
|
localId = IdentifierManager.getInstance().getLocalId(pid.getValue());
|
| 2323 |
|
|
} catch (McdbDocNotFoundException e) {
|
| 2324 |
|
|
throw new NotFound("1020", e.getMessage());
|
| 2325 |
|
|
}
|
| 2326 |
|
|
params.put("qformat", new String[] {format});
|
| 2327 |
|
|
params.put("docid", new String[] {localId});
|
| 2328 |
|
|
params.put("pid", new String[] {pid.getValue()});
|
| 2329 |
|
|
params.put("displaymodule", new String[] {"printall"});
|
| 2330 |
|
|
|
| 2331 |
|
|
transformer.transformXMLDocument(
|
| 2332 |
|
|
documentContent ,
|
| 2333 |
|
|
sourceType,
|
| 2334 |
|
|
targetType ,
|
| 2335 |
|
|
format,
|
| 2336 |
|
|
writer,
|
| 2337 |
|
|
params,
|
| 2338 |
|
|
null //sessionid
|
| 2339 |
|
|
);
|
| 2340 |
|
|
|
| 2341 |
|
|
// finally, get the HTML back
|
| 2342 |
|
|
ContentTypeByteArrayInputStream resultInputStream = new ContentTypeByteArrayInputStream(baos.toByteArray());
|
| 2343 |
|
|
|
| 2344 |
|
|
// write to temp file with correct css path
|
| 2345 |
|
|
File tmpDir = File.createTempFile("package_", "_dir");
|
| 2346 |
|
|
tmpDir.delete();
|
| 2347 |
|
|
tmpDir.mkdir();
|
| 2348 |
|
|
File htmlFile = File.createTempFile("metadata", ".html", tmpDir);
|
| 2349 |
|
|
File cssDir = new File(tmpDir, format);
|
| 2350 |
|
|
cssDir.mkdir();
|
| 2351 |
|
|
File cssFile = new File(tmpDir, format + "/" + format + ".css");
|
| 2352 |
|
|
String pdfFileName = metadataID.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-METADATA.pdf";
|
| 2353 |
|
|
File pdfFile = new File(tmpDir, pdfFileName);
|
| 2354 |
|
|
//File pdfFile = File.createTempFile("metadata", ".pdf", tmpDir);
|
| 2355 |
|
|
|
| 2356 |
|
|
// put the CSS file in place for the html to find it
|
| 2357 |
|
|
String originalCssPath = SystemUtil.getContextDir() + "/style/skins/" + format + "/" + format + ".css";
|
| 2358 |
|
|
IOUtils.copy(new FileInputStream(originalCssPath), new FileOutputStream(cssFile));
|
| 2359 |
|
|
|
| 2360 |
|
|
// write the HTML file
|
| 2361 |
|
|
IOUtils.copy(resultInputStream, new FileOutputStream(htmlFile));
|
| 2362 |
|
|
|
| 2363 |
|
|
// convert to PDF
|
| 2364 |
|
|
HtmlToPdf.export(htmlFile.getAbsolutePath(), pdfFile.getAbsolutePath());
|
| 2365 |
|
|
|
| 2366 |
|
|
//add to the package
|
| 2367 |
|
|
bag.addFileToPayload(pdfFile);
|
| 2368 |
|
|
pidMapping.append(metadataID.getValue() + " (pdf)" + "\t" + "data/" + pdfFile.getName() + "\n");
|
| 2369 |
|
|
|
| 2370 |
|
|
// mark for clean up after we are done
|
| 2371 |
|
|
htmlFile.delete();
|
| 2372 |
|
|
cssFile.delete();
|
| 2373 |
|
|
cssDir.delete();
|
| 2374 |
|
|
tempFiles.add(tmpDir);
|
| 2375 |
|
|
tempFiles.add(pdfFile); // delete this first later on
|
| 2376 |
|
|
|
| 2377 |
|
|
} catch (Exception e) {
|
| 2378 |
|
|
logMetacat.warn("Could not transform metadata", e);
|
| 2379 |
|
|
}
|
| 2380 |
|
|
}
|
| 2381 |
|
|
|
| 2382 |
|
|
|
| 2383 |
8437
|
walker
|
//If this is in eml format, extract the filename and GUID from each entity in its package
|
| 2384 |
|
|
if (metadataSysMeta.getFormatId().getValue().startsWith("eml://")) {
|
| 2385 |
|
|
//Get the package
|
| 2386 |
|
|
DataPackageParserInterface parser = new Eml200DataPackageParser();
|
| 2387 |
|
|
InputStream emlStream = this.get(session, metadataID);
|
| 2388 |
|
|
parser.parse(emlStream);
|
| 2389 |
|
|
DataPackage dataPackage = parser.getDataPackage();
|
| 2390 |
|
|
|
| 2391 |
|
|
//Get all the entities in this package and loop through each to extract its ID and file name
|
| 2392 |
|
|
Entity[] entities = dataPackage.getEntityList();
|
| 2393 |
|
|
for(Entity entity: entities){
|
| 2394 |
|
|
try{
|
| 2395 |
|
|
//Get the file name from the metadata
|
| 2396 |
|
|
String fileNameFromMetadata = entity.getName();
|
| 2397 |
|
|
|
| 2398 |
|
|
//Get the ecogrid URL from the metadata
|
| 2399 |
|
|
String ecogridIdentifier = entity.getEntityIdentifier();
|
| 2400 |
|
|
//Parse the ecogrid URL to get the local id
|
| 2401 |
|
|
String idFromMetadata = DocumentUtil.getAccessionNumberFromEcogridIdentifier(ecogridIdentifier);
|
| 2402 |
|
|
|
| 2403 |
|
|
//Get the docid and rev pair
|
| 2404 |
|
|
String docid = DocumentUtil.getDocIdFromString(idFromMetadata);
|
| 2405 |
|
|
String rev = DocumentUtil.getRevisionStringFromString(idFromMetadata);
|
| 2406 |
|
|
|
| 2407 |
|
|
//Get the GUID
|
| 2408 |
|
|
String guid = IdentifierManager.getInstance().getGUID(docid, Integer.valueOf(rev));
|
| 2409 |
|
|
Identifier dataIdentifier = new Identifier();
|
| 2410 |
|
|
dataIdentifier.setValue(guid);
|
| 2411 |
|
|
|
| 2412 |
|
|
//Add the GUID to our GUID & file name map
|
| 2413 |
|
|
fileNames.put(dataIdentifier, fileNameFromMetadata);
|
| 2414 |
|
|
}
|
| 2415 |
|
|
catch(Exception e){
|
| 2416 |
|
|
//Prevent just one entity error
|
| 2417 |
|
|
e.printStackTrace();
|
| 2418 |
|
|
logMetacat.debug(e.getMessage(), e);
|
| 2419 |
|
|
}
|
| 2420 |
|
|
}
|
| 2421 |
|
|
}
|
| 2422 |
|
|
}
|
| 2423 |
|
|
catch(Exception e){
|
| 2424 |
|
|
//Catch errors that would prevent package download
|
| 2425 |
|
|
logMetacat.debug(e.toString());
|
| 2426 |
|
|
}
|
| 2427 |
|
|
}
|
| 2428 |
7855
|
leinfelder
|
packagePids.addAll(entries.keySet());
|
| 2429 |
|
|
for (List<Identifier> dataPids: entries.values()) {
|
| 2430 |
|
|
packagePids.addAll(dataPids);
|
| 2431 |
|
|
}
|
| 2432 |
7850
|
leinfelder
|
}
|
| 2433 |
7855
|
leinfelder
|
} else {
|
| 2434 |
|
|
// just the lone pid in this package
|
| 2435 |
9493
|
tao
|
//packagePids.add(pid);
|
| 2436 |
|
|
//throw an invalid request exception
|
| 2437 |
9494
|
tao
|
throw new InvalidRequest("2873", "The given pid "+pid.getValue()+" is not a package id (resource map id). Please use a package id instead.");
|
| 2438 |
7850
|
leinfelder
|
}
|
| 2439 |
8436
|
walker
|
|
| 2440 |
8437
|
walker
|
//Create a temp file, then delete it and make a directory with that name
|
| 2441 |
|
|
File tempDir = File.createTempFile("temp", Long.toString(System.nanoTime()));
|
| 2442 |
|
|
tempDir.delete();
|
| 2443 |
|
|
tempDir = new File(tempDir.getPath() + "_dir");
|
| 2444 |
|
|
tempDir.mkdir();
|
| 2445 |
8436
|
walker
|
tempFiles.add(tempDir);
|
| 2446 |
8800
|
leinfelder
|
File pidMappingFile = new File(tempDir, "pid-mapping.txt");
|
| 2447 |
8436
|
walker
|
|
| 2448 |
7855
|
leinfelder
|
// loop through the package contents
|
| 2449 |
|
|
for (Identifier entryPid: packagePids) {
|
| 2450 |
8436
|
walker
|
//Get the system metadata for each item
|
| 2451 |
8437
|
walker
|
SystemMetadata entrySysMeta = this.getSystemMetadata(session, entryPid);
|
| 2452 |
8436
|
walker
|
|
| 2453 |
|
|
String objectFormatType = ObjectFormatCache.getInstance().getFormat(entrySysMeta.getFormatId()).getFormatType();
|
| 2454 |
8437
|
walker
|
String fileName = null;
|
| 2455 |
8436
|
walker
|
|
| 2456 |
8437
|
walker
|
//TODO: Be more specific of what characters to replace. Make sure periods arent replaced for the filename from metadata
|
| 2457 |
|
|
//Our default file name is just the ID + format type (e.g. walker.1.1-DATA)
|
| 2458 |
|
|
fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + objectFormatType;
|
| 2459 |
|
|
|
| 2460 |
9542
|
leinfelder
|
if (fileNames.containsKey(entryPid)){
|
| 2461 |
8437
|
walker
|
//Let's use the file name and extension from the metadata is we have it
|
| 2462 |
|
|
fileName = entryPid.getValue().replaceAll("[^a-zA-Z0-9\\-\\.]", "_") + "-" + fileNames.get(entryPid).replaceAll("[^a-zA-Z0-9\\-\\.]", "_");
|
| 2463 |
|
|
}
|
| 2464 |
|
|
|
| 2465 |
9541
|
leinfelder
|
// ensure there is a file extension for the object
|
| 2466 |
|
|
String extension = ObjectFormatInfo.instance().getExtension(entrySysMeta.getFormatId().getValue());
|
| 2467 |
|
|
fileName += extension;
|
| 2468 |
|
|
|
| 2469 |
9542
|
leinfelder
|
// if SM has the file name, ignore everything else and use that
|
| 2470 |
|
|
if (entrySysMeta.getFileName() != null) {
|
| 2471 |
|
|
fileName = entrySysMeta.getFileName().replaceAll("[^a-zA-Z0-9\\-\\.]", "_");
|
| 2472 |
|
|
}
|
| 2473 |
|
|
|
| 2474 |
8436
|
walker
|
//Create a new file for this item and add to the list
|
| 2475 |
8437
|
walker
|
File tempFile = new File(tempDir, fileName);
|
| 2476 |
7855
|
leinfelder
|
tempFiles.add(tempFile);
|
| 2477 |
8436
|
walker
|
|
| 2478 |
|
|
InputStream entryInputStream = this.get(session, entryPid);
|
| 2479 |
7855
|
leinfelder
|
IOUtils.copy(entryInputStream, new FileOutputStream(tempFile));
|
| 2480 |
|
|
bag.addFileToPayload(tempFile);
|
| 2481 |
|
|
pidMapping.append(entryPid.getValue() + "\t" + "data/" + tempFile.getName() + "\n");
|
| 2482 |
|
|
}
|
| 2483 |
|
|
|
| 2484 |
|
|
//add the the pid to data file map
|
| 2485 |
|
|
IOUtils.write(pidMapping.toString(), new FileOutputStream(pidMappingFile));
|
| 2486 |
|
|
bag.addFileAsTag(pidMappingFile);
|
| 2487 |
8026
|
leinfelder
|
tempFiles.add(pidMappingFile);
|
| 2488 |
|
|
|
| 2489 |
7855
|
leinfelder
|
bag = bag.makeComplete();
|
| 2490 |
8026
|
leinfelder
|
|
| 2491 |
8436
|
walker
|
///Now create the zip file
|
| 2492 |
8437
|
walker
|
//Use the pid as the file name prefix, replacing all non-word characters
|
| 2493 |
|
|
String zipName = pid.getValue().replaceAll("\\W", "_");
|
| 2494 |
8160
|
leinfelder
|
|
| 2495 |
8436
|
walker
|
File bagFile = new File(tempDir, zipName+".zip");
|
| 2496 |
|
|
|
| 2497 |
7855
|
leinfelder
|
bag.setFile(bagFile);
|
| 2498 |
7860
|
leinfelder
|
ZipWriter zipWriter = new ZipWriter(bagFactory);
|
| 2499 |
7855
|
leinfelder
|
bag.write(zipWriter, bagFile);
|
| 2500 |
|
|
bagFile = bag.getFile();
|
| 2501 |
8026
|
leinfelder
|
// use custom FIS that will delete the file when closed
|
| 2502 |
|
|
bagInputStream = new DeleteOnCloseFileInputStream(bagFile);
|
| 2503 |
|
|
// also mark for deletion on shutdown in case the stream is never closed
|
| 2504 |
|
|
bagFile.deleteOnExit();
|
| 2505 |
8436
|
walker
|
tempFiles.add(bagFile);
|
| 2506 |
7855
|
leinfelder
|
|
| 2507 |
8026
|
leinfelder
|
// clean up other temp files
|
| 2508 |
8800
|
leinfelder
|
for (int i=tempFiles.size()-1; i>=0; i--){
|
| 2509 |
|
|
tempFiles.get(i).delete();
|
| 2510 |
7855
|
leinfelder
|
}
|
| 2511 |
8436
|
walker
|
|
| 2512 |
7855
|
leinfelder
|
} catch (IOException e) {
|
| 2513 |
|
|
// report as service failure
|
| 2514 |
9538
|
tao
|
e.printStackTrace();
|
| 2515 |
7855
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2516 |
|
|
sf.initCause(e);
|
| 2517 |
|
|
throw sf;
|
| 2518 |
|
|
} catch (OREException e) {
|
| 2519 |
|
|
// report as service failure
|
| 2520 |
9538
|
tao
|
e.printStackTrace();
|
| 2521 |
7855
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2522 |
|
|
sf.initCause(e);
|
| 2523 |
|
|
throw sf;
|
| 2524 |
|
|
} catch (URISyntaxException e) {
|
| 2525 |
|
|
// report as service failure
|
| 2526 |
9538
|
tao
|
e.printStackTrace();
|
| 2527 |
7855
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2528 |
|
|
sf.initCause(e);
|
| 2529 |
|
|
throw sf;
|
| 2530 |
|
|
} catch (OREParserException e) {
|
| 2531 |
|
|
// report as service failure
|
| 2532 |
9538
|
tao
|
e.printStackTrace();
|
| 2533 |
7855
|
leinfelder
|
ServiceFailure sf = new ServiceFailure("1030", e.getMessage());
|
| 2534 |
|
|
sf.initCause(e);
|
| 2535 |
|
|
throw sf;
|
| 2536 |
7850
|
leinfelder
|
}
|
| 2537 |
|
|
|
| 2538 |
|
|
return bagInputStream;
|
| 2539 |
8810
|
leinfelder
|
}
|
| 2540 |
9353
|
tao
|
|
| 2541 |
|
|
/**
|
| 2542 |
|
|
* Archives an object, where the object is either a
|
| 2543 |
|
|
* data object or a science metadata object.
|
| 2544 |
|
|
*
|
| 2545 |
|
|
* @param session - the Session object containing the credentials for the Subject
|
| 2546 |
|
|
* @param pid - The object identifier to be archived
|
| 2547 |
|
|
*
|
| 2548 |
|
|
* @return pid - the identifier of the object used for the archiving
|
| 2549 |
|
|
*
|
| 2550 |
|
|
* @throws InvalidToken
|
| 2551 |
|
|
* @throws ServiceFailure
|
| 2552 |
|
|
* @throws NotAuthorized
|
| 2553 |
|
|
* @throws NotFound
|
| 2554 |
|
|
* @throws NotImplemented
|
| 2555 |
|
|
* @throws InvalidRequest
|
| 2556 |
|
|
*/
|
| 2557 |
|
|
public Identifier archive(Session session, Identifier pid)
|
| 2558 |
|
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound, NotImplemented {
|
| 2559 |
9478
|
tao
|
if(isReadOnlyMode()) {
|
| 2560 |
9481
|
tao
|
throw new ServiceFailure("2912", ReadOnlyChecker.DATAONEERROR);
|
| 2561 |
9478
|
tao
|
}
|
| 2562 |
9353
|
tao
|
boolean allowed = false;
|
| 2563 |
|
|
// do we have a valid pid?
|
| 2564 |
|
|
if (pid == null || pid.getValue().trim().equals("")) {
|
| 2565 |
|
|
throw new ServiceFailure("1350", "The provided identifier was invalid.");
|
| 2566 |
|
|
}
|
| 2567 |
|
|
|
| 2568 |
|
|
String serviceFailureCode = "1350";
|
| 2569 |
|
|
Identifier sid = getPIDForSID(pid, serviceFailureCode);
|
| 2570 |
|
|
if(sid != null) {
|
| 2571 |
|
|
pid = sid;
|
| 2572 |
|
|
}
|
| 2573 |
|
|
// does the subject have archive (a D1 CHANGE_PERMISSION level) privileges on the pid?
|
| 2574 |
|
|
try {
|
| 2575 |
|
|
allowed = isAuthorized(session, pid, Permission.CHANGE_PERMISSION);
|
| 2576 |
|
|
} catch (InvalidRequest e) {
|
| 2577 |
|
|
throw new ServiceFailure("1350", e.getDescription());
|
| 2578 |
|
|
}
|
| 2579 |
|
|
|
| 2580 |
|
|
if (allowed) {
|
| 2581 |
|
|
try {
|
| 2582 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().lock(pid);
|
| 2583 |
|
|
logMetacat.debug("MNodeService.archive - lock the identifier "+pid.getValue()+" in the system metadata map.");
|
| 2584 |
|
|
SystemMetadata sysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
| 2585 |
9354
|
tao
|
boolean needModifyDate = true;
|
| 2586 |
9373
|
tao
|
boolean logArchive = true;
|
| 2587 |
|
|
super.archiveObject(logArchive, session, pid, sysmeta, needModifyDate);
|
| 2588 |
9353
|
tao
|
} finally {
|
| 2589 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().unlock(pid);
|
| 2590 |
|
|
logMetacat.debug("MNodeService.archive - unlock the identifier "+pid.getValue()+" in the system metadata map.");
|
| 2591 |
|
|
}
|
| 2592 |
|
|
|
| 2593 |
|
|
|
| 2594 |
|
|
} else {
|
| 2595 |
|
|
throw new NotAuthorized("1320", "The provided identity does not have " + "permission to archive the object on the Node.");
|
| 2596 |
|
|
}
|
| 2597 |
|
|
|
| 2598 |
|
|
return pid;
|
| 2599 |
|
|
}
|
| 2600 |
9190
|
tao
|
|
| 2601 |
|
|
/**
|
| 2602 |
|
|
* Update the system metadata of the specified pid.
|
| 2603 |
|
|
*/
|
| 2604 |
9177
|
tao
|
@Override
|
| 2605 |
|
|
public boolean updateSystemMetadata(Session session, Identifier pid,
|
| 2606 |
|
|
SystemMetadata sysmeta) throws NotImplemented, NotAuthorized,
|
| 2607 |
|
|
ServiceFailure, InvalidRequest, InvalidSystemMetadata, InvalidToken {
|
| 2608 |
9478
|
tao
|
|
| 2609 |
|
|
if(isReadOnlyMode()) {
|
| 2610 |
9481
|
tao
|
throw new ServiceFailure("4868", ReadOnlyChecker.DATAONEERROR);
|
| 2611 |
9478
|
tao
|
}
|
| 2612 |
9177
|
tao
|
if(sysmeta == null) {
|
| 2613 |
9478
|
tao
|
throw new InvalidRequest("4869", "The system metadata object should NOT be null in the updateSystemMetadata request.");
|
| 2614 |
9177
|
tao
|
}
|
| 2615 |
9190
|
tao
|
if(pid == null || pid.getValue() == null) {
|
| 2616 |
9478
|
tao
|
throw new InvalidRequest("4869", "Please specify the id in the updateSystemMetadata request ") ;
|
| 2617 |
9190
|
tao
|
}
|
| 2618 |
|
|
|
| 2619 |
|
|
if (session == null) {
|
| 2620 |
|
|
//TODO: many of the thrown exceptions do not use the correct error codes
|
| 2621 |
|
|
//check these against the docs and correct them
|
| 2622 |
|
|
throw new NotAuthorized("4861", "No Session - could not authorize for updating system metadata." +
|
| 2623 |
|
|
" If you are not logged in, please do so and retry the request.");
|
| 2624 |
|
|
} else {
|
| 2625 |
|
|
try {
|
| 2626 |
|
|
//Following session can do the change:
|
| 2627 |
9263
|
tao
|
//- Authoritative Member Node (we can use isNodeAdmin since we checked isAuthoritativeNode )
|
| 2628 |
9190
|
tao
|
//- Owner of object (coved by the userHasPermission method)
|
| 2629 |
|
|
//- user subjects with the change permission
|
| 2630 |
|
|
//Note: Coordinating Node can not because MN is authoritative
|
| 2631 |
9263
|
tao
|
/*if(!isAuthoritativeNode(pid)) {
|
| 2632 |
|
|
throw new InvalidRequest("4863", "Client can only call updateSystemMetadata request on the authoritative memember node.");
|
| 2633 |
|
|
}
|
| 2634 |
9190
|
tao
|
if(!isNodeAdmin(session) && !userHasPermission(session, pid, Permission.CHANGE_PERMISSION)) {
|
| 2635 |
|
|
throw new NotAuthorized("4861", "The client -"+ session.getSubject().getValue()+ "is not authorized for updating the system metadata of the object "+pid.getValue());
|
| 2636 |
9263
|
tao
|
}*/
|
| 2637 |
|
|
if(!allowUpdating(session, pid, Permission.CHANGE_PERMISSION)) {
|
| 2638 |
|
|
throw new NotAuthorized("4861", "The client -"+ session.getSubject().getValue()+ "is not authorized for updating the system metadata of the object "+pid.getValue());
|
| 2639 |
9190
|
tao
|
}
|
| 2640 |
|
|
} catch (NotFound e) {
|
| 2641 |
9478
|
tao
|
throw new InvalidRequest("4869", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 2642 |
9997
|
tao
|
} catch(ServiceFailure e) {
|
| 2643 |
|
|
throw new ServiceFailure("4868", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 2644 |
|
|
} catch(NotAuthorized e) {
|
| 2645 |
|
|
throw new NotAuthorized("4861", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 2646 |
|
|
} catch(NotImplemented e) {
|
| 2647 |
|
|
throw new NotImplemented("4866","Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 2648 |
|
|
} catch(InvalidRequest e) {
|
| 2649 |
|
|
throw new InvalidRequest("4869", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 2650 |
|
|
} catch(InvalidToken e) {
|
| 2651 |
|
|
throw new InvalidToken("4957", "Can't determine if the client has the permission to update the system metacat of the object with id "+pid.getValue()+" since "+e.getDescription());
|
| 2652 |
9190
|
tao
|
}
|
| 2653 |
|
|
|
| 2654 |
|
|
}
|
| 2655 |
9335
|
tao
|
//update the system metadata locally
|
| 2656 |
|
|
boolean success = false;
|
| 2657 |
|
|
try {
|
| 2658 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().lock(pid);
|
| 2659 |
|
|
SystemMetadata currentSysmeta = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
| 2660 |
|
|
if(currentSysmeta == null) {
|
| 2661 |
9478
|
tao
|
throw new InvalidRequest("4869", "We can't find the current system metadata on the member node for the id "+pid.getValue());
|
| 2662 |
9335
|
tao
|
}
|
| 2663 |
|
|
Date currentModiDate = currentSysmeta.getDateSysMetadataModified();
|
| 2664 |
|
|
Date commingModiDate = sysmeta.getDateSysMetadataModified();
|
| 2665 |
|
|
if(commingModiDate == null) {
|
| 2666 |
9478
|
tao
|
throw new InvalidRequest("4869", "The system metadata modification date can't be null.");
|
| 2667 |
9335
|
tao
|
}
|
| 2668 |
|
|
if(currentModiDate != null && commingModiDate.getTime() != currentModiDate.getTime()) {
|
| 2669 |
9478
|
tao
|
throw new InvalidRequest("4869", "Your system metadata modification date is "+commingModiDate.toString()+
|
| 2670 |
9335
|
tao
|
". It doesn't match our current system metadata modification date in the member node - "+currentModiDate.toString()+
|
| 2671 |
|
|
". Please check if you have got the newest version of the system metadata before the modification.");
|
| 2672 |
|
|
}
|
| 2673 |
|
|
boolean needUpdateModificationDate = true;
|
| 2674 |
9354
|
tao
|
boolean fromCN = false;
|
| 2675 |
|
|
success = updateSystemMetadata(session, pid, sysmeta, needUpdateModificationDate, currentSysmeta, fromCN);
|
| 2676 |
9335
|
tao
|
} finally {
|
| 2677 |
|
|
HazelcastService.getInstance().getSystemMetadataMap().unlock(pid);
|
| 2678 |
|
|
}
|
| 2679 |
9177
|
tao
|
|
| 2680 |
|
|
if(success) {
|
| 2681 |
10102
|
tao
|
this.cn = D1Client.getCN();
|
| 2682 |
9190
|
tao
|
//TODO
|
| 2683 |
9177
|
tao
|
//notify the cns the synchornize the new system metadata.
|
| 2684 |
10102
|
tao
|
// run it in a thread to avoid connection timeout
|
| 2685 |
|
|
Runnable runner = new Runnable() {
|
| 2686 |
|
|
private CNode cNode = null;
|
| 2687 |
|
|
private SystemMetadata sys = null;
|
| 2688 |
|
|
private Identifier id = null;
|
| 2689 |
|
|
@Override
|
| 2690 |
|
|
public void run() {
|
| 2691 |
|
|
try {
|
| 2692 |
|
|
if(this.cNode == null) {
|
| 2693 |
|
|
logMetacat.warn("MNodeService.updateSystemMetadata - can't get the instance of the CN. So can't call cn.synchronize to update the system metadata in CN.");
|
| 2694 |
|
|
} else if(id != null) {
|
| 2695 |
|
|
logMetacat.info("MNodeService.updateSystemMetadata - calling cn.synchornized in another thread for pid "+id.getValue());
|
| 2696 |
|
|
this.cNode.synchronize(null, id);
|
| 2697 |
|
|
} else {
|
| 2698 |
10104
|
tao
|
logMetacat.warn("MNodeService.updateSystemMetadata - the pid is null. So can't call cn.synchronize to update the system metadata in CN.");
|
| 2699 |
10102
|
tao
|
}
|
| 2700 |
|
|
} catch (BaseException e) {
|
| 2701 |
|
|
e.printStackTrace();
|
| 2702 |
|
|
logMetacat.error("It is a DataONEBaseException and its detail code is "+e.getDetail_code() +" and its code is "+e.getCode());
|
| 2703 |
|
|
logMetacat.error("Can't update the systemmetadata of pid "+id.getValue()+" in CNs through cn.synchronize method since "+e.getMessage(), e);
|
| 2704 |
|
|
} catch (Exception e) {
|
| 2705 |
|
|
e.printStackTrace();
|
| 2706 |
|
|
logMetacat.error("Can't update the systemmetadata of pid "+id.getValue()+" in CNs through cn.synchronize method since "+e.getMessage(), e);
|
| 2707 |
|
|
}
|
| 2708 |
|
|
|
| 2709 |
|
|
// attempt to re-register the identifier (it checks if it is a doi)
|
| 2710 |
|
|
try {
|
| 2711 |
|
|
logMetacat.info("MNodeSerice.updateSystemMetadata - register doi if the pid "+sys.getIdentifier().getValue()+" is a doi");
|
| 2712 |
|
|
DOIService.getInstance().registerDOI(sys);
|
| 2713 |
|
|
} catch (Exception e) {
|
| 2714 |
|
|
logMetacat.warn("Could not [re]register DOI: " + e.getMessage(), e);
|
| 2715 |
|
|
}
|
| 2716 |
9256
|
tao
|
}
|
| 2717 |
10102
|
tao
|
private Runnable init(CNode cn, SystemMetadata sys, Identifier id){
|
| 2718 |
|
|
this.cNode = cn;
|
| 2719 |
|
|
this.sys = sys;
|
| 2720 |
|
|
this.id = id;
|
| 2721 |
|
|
return this;
|
| 2722 |
|
|
|
| 2723 |
|
|
}
|
| 2724 |
|
|
}.init(cn, sysmeta, pid);
|
| 2725 |
|
|
// submit the task, and that's it
|
| 2726 |
10104
|
tao
|
if(executor != null) {
|
| 2727 |
|
|
executor.submit(runner);
|
| 2728 |
10102
|
tao
|
} else {
|
| 2729 |
10104
|
tao
|
logMetacat.warn("MNodeSerivce.updateSystemMetadata - since the executor service for submitting the call of cn.synchronize() is null, the system metadata change of the id "+pid.getValue()+" can't go to cn through cn.synchronize.");
|
| 2730 |
9246
|
tao
|
}
|
| 2731 |
9177
|
tao
|
}
|
| 2732 |
|
|
return success;
|
| 2733 |
|
|
}
|
| 2734 |
9190
|
tao
|
|
| 2735 |
|
|
/*
|
| 2736 |
|
|
* Determine if the current node is the authoritative node for the given pid.
|
| 2737 |
|
|
*/
|
| 2738 |
9374
|
tao
|
protected boolean isAuthoritativeNode(Identifier pid) throws InvalidRequest {
|
| 2739 |
9190
|
tao
|
boolean isAuthoritativeNode = false;
|
| 2740 |
|
|
if(pid != null && pid.getValue() != null) {
|
| 2741 |
|
|
SystemMetadata sys = HazelcastService.getInstance().getSystemMetadataMap().get(pid);
|
| 2742 |
|
|
if(sys != null) {
|
| 2743 |
|
|
NodeReference node = sys.getAuthoritativeMemberNode();
|
| 2744 |
|
|
if(node != null) {
|
| 2745 |
|
|
String nodeValue = node.getValue();
|
| 2746 |
|
|
logMetacat.debug("The authoritative node for id "+pid.getValue()+" is "+nodeValue);
|
| 2747 |
|
|
//System.out.println("The authoritative node for id "+pid.getValue()+" is "+nodeValue);
|
| 2748 |
|
|
String currentNodeId = Settings.getConfiguration().getString("dataone.nodeId");
|
| 2749 |
|
|
logMetacat.debug("The node id in metacat.properties is "+currentNodeId);
|
| 2750 |
|
|
//System.out.println("The node id in metacat.properties is "+currentNodeId);
|
| 2751 |
|
|
if(currentNodeId != null && !currentNodeId.trim().equals("") && currentNodeId.equals(nodeValue)) {
|
| 2752 |
10021
|
tao
|
logMetacat.debug("They are matching, so the authoritative mn of the object "+pid.getValue()+" is the current node");
|
| 2753 |
9190
|
tao
|
//System.out.println("They are matching");
|
| 2754 |
|
|
isAuthoritativeNode = true;
|
| 2755 |
|
|
}
|
| 2756 |
9374
|
tao
|
} else {
|
| 2757 |
|
|
throw new InvalidRequest("4869", "Coudn't find the authoritative member node in the system metadata associated with the pid "+pid.getValue());
|
| 2758 |
9190
|
tao
|
}
|
| 2759 |
9374
|
tao
|
} else {
|
| 2760 |
|
|
throw new InvalidRequest("4869", "Coudn't find the system metadata associated with the pid "+pid.getValue());
|
| 2761 |
9190
|
tao
|
}
|
| 2762 |
9374
|
tao
|
} else {
|
| 2763 |
|
|
throw new InvalidRequest("4869", "The request pid is null");
|
| 2764 |
9190
|
tao
|
}
|
| 2765 |
|
|
return isAuthoritativeNode;
|
| 2766 |
|
|
}
|
| 2767 |
6795
|
cjones
|
|
| 2768 |
9263
|
tao
|
/*
|
| 2769 |
|
|
* Rules are:
|
| 2770 |
|
|
* 1. If the session has an cn object, it is allowed.
|
| 2771 |
|
|
* 2. If it is not a cn object, the client should have approperate permission and it should also happen on the authorative node.
|
| 2772 |
9700
|
cjones
|
* 3. If it's the authoritative node, the MN Admin Subject is allowed.
|
| 2773 |
9263
|
tao
|
*/
|
| 2774 |
9997
|
tao
|
private boolean allowUpdating(Session session, Identifier pid, Permission permission) throws NotAuthorized, NotFound, InvalidRequest, ServiceFailure, NotImplemented, InvalidToken {
|
| 2775 |
9263
|
tao
|
boolean allow = false;
|
| 2776 |
9781
|
cjones
|
|
| 2777 |
9700
|
cjones
|
if( isCNAdmin (session) ) {
|
| 2778 |
9263
|
tao
|
allow = true;
|
| 2779 |
9700
|
cjones
|
|
| 2780 |
9263
|
tao
|
} else {
|
| 2781 |
9700
|
cjones
|
if( isAuthoritativeNode(pid) ) {
|
| 2782 |
|
|
|
| 2783 |
9781
|
cjones
|
// Check for admin authorization
|
| 2784 |
9700
|
cjones
|
try {
|
| 2785 |
9781
|
cjones
|
allow = isNodeAdmin(session);
|
| 2786 |
9700
|
cjones
|
|
| 2787 |
|
|
} catch (NotImplemented e) {
|
| 2788 |
|
|
logMetacat.debug("Failed to authorize the Member Node Admin Subject: " + e.getMessage());
|
| 2789 |
|
|
|
| 2790 |
|
|
} catch (ServiceFailure e) {
|
| 2791 |
|
|
logMetacat.debug("Failed to authorize the Member Node Admin Subject: " + e.getMessage());
|
| 2792 |
|
|
|
| 2793 |
|
|
}
|
| 2794 |
|
|
|
| 2795 |
9781
|
cjones
|
// Check for user authorization
|
| 2796 |
|
|
if ( !allow ) {
|
| 2797 |
|
|
allow = userHasPermission(session, pid, permission);
|
| 2798 |
9700
|
cjones
|
|
| 2799 |
9781
|
cjones
|
}
|
| 2800 |
9700
|
cjones
|
|
| 2801 |
9263
|
tao
|
} else {
|
| 2802 |
10021
|
tao
|
throw new NotAuthorized("4861", "Client can only call the request on the authoritative memember node of the object "+pid.getValue());
|
| 2803 |
9700
|
cjones
|
|
| 2804 |
9263
|
tao
|
}
|
| 2805 |
|
|
}
|
| 2806 |
|
|
return allow;
|
| 2807 |
|
|
|
| 2808 |
|
|
}
|
| 2809 |
|
|
|
| 2810 |
9478
|
tao
|
/**
|
| 2811 |
|
|
* Check if the metacat is in the read-only mode.
|
| 2812 |
|
|
* @return true if it is; otherwise false.
|
| 2813 |
|
|
*/
|
| 2814 |
|
|
protected boolean isReadOnlyMode() {
|
| 2815 |
|
|
boolean readOnly = false;
|
| 2816 |
|
|
ReadOnlyChecker checker = new ReadOnlyChecker();
|
| 2817 |
|
|
readOnly = checker.isReadOnly();
|
| 2818 |
|
|
return readOnly;
|
| 2819 |
|
|
}
|
| 2820 |
|
|
|
| 2821 |
6179
|
cjones
|
}
|