1
|
/**
|
2
|
* '$RCSfile$'
|
3
|
* Copyright: 2000 Regents of the University of California and the
|
4
|
* National Center for Ecological Analysis and Synthesis
|
5
|
*
|
6
|
* '$Author: $'
|
7
|
* '$Date: 2009-06-13 15:28:13 +0300 $'
|
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
|
package edu.ucsb.nceas.metacat.dataone;
|
24
|
|
25
|
import java.io.ByteArrayOutputStream;
|
26
|
import java.io.File;
|
27
|
import java.io.FileNotFoundException;
|
28
|
import java.io.FileOutputStream;
|
29
|
import java.io.IOException;
|
30
|
import java.io.InputStream;
|
31
|
import java.io.OutputStream;
|
32
|
import java.io.PrintWriter;
|
33
|
import java.sql.SQLException;
|
34
|
import java.util.Date;
|
35
|
import java.util.Enumeration;
|
36
|
import java.util.Hashtable;
|
37
|
import java.util.Timer;
|
38
|
import java.util.List;
|
39
|
|
40
|
import javax.servlet.ServletContext;
|
41
|
import javax.servlet.http.HttpServletRequest;
|
42
|
import javax.servlet.http.HttpServletResponse;
|
43
|
|
44
|
import org.apache.commons.io.IOUtils;
|
45
|
import org.apache.log4j.Logger;
|
46
|
import org.dataone.service.exceptions.IdentifierNotUnique;
|
47
|
import org.dataone.service.exceptions.InsufficientResources;
|
48
|
import org.dataone.service.exceptions.InvalidRequest;
|
49
|
import org.dataone.service.exceptions.InvalidSystemMetadata;
|
50
|
import org.dataone.service.exceptions.InvalidToken;
|
51
|
import org.dataone.service.exceptions.NotAuthorized;
|
52
|
import org.dataone.service.exceptions.NotFound;
|
53
|
import org.dataone.service.exceptions.NotImplemented;
|
54
|
import org.dataone.service.exceptions.ServiceFailure;
|
55
|
import org.dataone.service.exceptions.UnsupportedType;
|
56
|
import org.dataone.service.mn.MemberNodeCrud;
|
57
|
import org.dataone.service.types.AuthToken;
|
58
|
import org.dataone.service.types.Checksum;
|
59
|
import org.dataone.service.types.DescribeResponse;
|
60
|
import org.dataone.service.types.Identifier;
|
61
|
import org.dataone.service.types.LogRecordSet;
|
62
|
import org.dataone.service.types.SystemMetadata;
|
63
|
import org.dataone.service.types.ObjectList;
|
64
|
import org.dataone.service.types.ObjectFormat;
|
65
|
import org.jibx.runtime.BindingDirectory;
|
66
|
import org.jibx.runtime.IBindingFactory;
|
67
|
import org.jibx.runtime.IMarshallingContext;
|
68
|
import org.jibx.runtime.IUnmarshallingContext;
|
69
|
import org.jibx.runtime.JiBXException;
|
70
|
|
71
|
import com.gc.iotools.stream.is.InputStreamFromOutputStream;
|
72
|
|
73
|
import edu.ucsb.nceas.metacat.AccessionNumberException;
|
74
|
import edu.ucsb.nceas.metacat.MetacatResultSet;
|
75
|
import edu.ucsb.nceas.metacat.MetacatResultSet.Document;
|
76
|
import edu.ucsb.nceas.metacat.DocumentImpl;
|
77
|
import edu.ucsb.nceas.metacat.EventLog;
|
78
|
import edu.ucsb.nceas.metacat.IdentifierManager;
|
79
|
import edu.ucsb.nceas.metacat.McdbDocNotFoundException;
|
80
|
import edu.ucsb.nceas.metacat.McdbException;
|
81
|
import edu.ucsb.nceas.metacat.MetacatHandler;
|
82
|
import edu.ucsb.nceas.metacat.client.InsufficientKarmaException;
|
83
|
import edu.ucsb.nceas.metacat.properties.PropertyService;
|
84
|
import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler;
|
85
|
import edu.ucsb.nceas.metacat.service.SessionService;
|
86
|
import edu.ucsb.nceas.metacat.util.DocumentUtil;
|
87
|
import edu.ucsb.nceas.metacat.util.SessionData;
|
88
|
import edu.ucsb.nceas.utilities.ParseLSIDException;
|
89
|
import edu.ucsb.nceas.utilities.PropertyNotFoundException;
|
90
|
|
91
|
/**
|
92
|
*
|
93
|
* Implements DataONE MemberNode CRUD API for Metacat.
|
94
|
*
|
95
|
* @author Matthew Jones
|
96
|
*/
|
97
|
public class CrudService implements MemberNodeCrud {
|
98
|
|
99
|
/*private ServletContext servletContext;
|
100
|
private HttpServletRequest request;
|
101
|
private HttpServletResponse response;*/
|
102
|
|
103
|
private static CrudService crudService = null;
|
104
|
|
105
|
private MetacatHandler handler;
|
106
|
private Hashtable<String, String[]> params;
|
107
|
Logger logMetacat = null;
|
108
|
|
109
|
private String metacatUrl;
|
110
|
|
111
|
/**
|
112
|
* singleton accessor
|
113
|
*/
|
114
|
public static CrudService getInstance()
|
115
|
{
|
116
|
if(crudService == null)
|
117
|
{
|
118
|
crudService = new CrudService();
|
119
|
}
|
120
|
|
121
|
return crudService;
|
122
|
}
|
123
|
|
124
|
/**
|
125
|
* Initializes new instance by setting servlet context,request and response.
|
126
|
* TODO: remove dependency on Servlet infrastructure
|
127
|
* TODO: Make this a real service, and make it a Singleton
|
128
|
*/
|
129
|
public CrudService() {
|
130
|
//change crud service into a singleton. dont pass servlet data structures here
|
131
|
logMetacat = Logger.getLogger(CrudService.class);
|
132
|
try
|
133
|
{
|
134
|
String server = PropertyService.getProperty("server.name");
|
135
|
String port = PropertyService.getProperty("server.httpPort");
|
136
|
String context = PropertyService.getProperty("application.context");
|
137
|
metacatUrl = "http://" + server + ":" + port + "/" + context;
|
138
|
logMetacat.debug("Initializing CrudService with url " + metacatUrl);
|
139
|
}
|
140
|
catch(Exception e)
|
141
|
{
|
142
|
logMetacat.error("Could not find servlet url in CrudService: " + e.getMessage());
|
143
|
e.printStackTrace();
|
144
|
throw new RuntimeException("Error getting servlet url in CrudService: " + e.getMessage());
|
145
|
}
|
146
|
|
147
|
/*this.servletContext = servletContext;
|
148
|
this.request = request;
|
149
|
this.response = response;*/
|
150
|
|
151
|
params = new Hashtable<String, String[]>();
|
152
|
|
153
|
handler = new MetacatHandler(new Timer());
|
154
|
|
155
|
}
|
156
|
|
157
|
/**
|
158
|
* return the context url CrudService is using.
|
159
|
*/
|
160
|
public String getContextUrl()
|
161
|
{
|
162
|
return metacatUrl;
|
163
|
}
|
164
|
|
165
|
/**
|
166
|
* set the params for this service from an HttpServletRequest param list
|
167
|
*/
|
168
|
public void setParamsFromRequest(HttpServletRequest request)
|
169
|
{
|
170
|
Enumeration paramlist = request.getParameterNames();
|
171
|
while (paramlist.hasMoreElements()) {
|
172
|
String name = (String) paramlist.nextElement();
|
173
|
String[] value = (String[])request.getParameterValues(name);
|
174
|
params.put(name, value);
|
175
|
}
|
176
|
}
|
177
|
|
178
|
/**
|
179
|
* set the parameter values needed for this request
|
180
|
*/
|
181
|
public void setParameter(String name, String[] value)
|
182
|
{
|
183
|
params.put(name, value);
|
184
|
}
|
185
|
|
186
|
public Identifier create(AuthToken token, Identifier guid,
|
187
|
InputStream object, SystemMetadata sysmeta) throws InvalidToken,
|
188
|
ServiceFailure, NotAuthorized, IdentifierNotUnique, UnsupportedType,
|
189
|
InsufficientResources, InvalidSystemMetadata, NotImplemented {
|
190
|
|
191
|
logMetacat.debug("Starting CrudService.create()...");
|
192
|
|
193
|
// authenticate & get user info
|
194
|
SessionData sessionData = getSessionData(token);
|
195
|
String username = sessionData.getUserName();
|
196
|
String[] groups = sessionData.getGroupNames();
|
197
|
|
198
|
// verify that guid == SystemMetadata.getIdentifier()
|
199
|
logMetacat.debug("Comparing guid|sysmeta_guid: " + guid.getValue() + "|" + sysmeta.getIdentifier().getValue());
|
200
|
if (!guid.getValue().equals(sysmeta.getIdentifier().getValue())) {
|
201
|
throw new InvalidSystemMetadata("1180",
|
202
|
"GUID in method call does not match GUID in system metadata.");
|
203
|
}
|
204
|
|
205
|
logMetacat.debug("Checking if identifier exists...");
|
206
|
// Check that the identifier does not already exist
|
207
|
IdentifierManager im = IdentifierManager.getInstance();
|
208
|
if (im.identifierExists(guid.getValue())) {
|
209
|
throw new IdentifierNotUnique("1120",
|
210
|
"GUID is already in use by an existing object.");
|
211
|
}
|
212
|
|
213
|
// Check if we are handling metadata or data
|
214
|
boolean isScienceMetadata = isScienceMetadata(sysmeta);
|
215
|
|
216
|
if (isScienceMetadata) {
|
217
|
// CASE METADATA:
|
218
|
try {
|
219
|
this.insertDocument(object, guid, sessionData);
|
220
|
} catch (IOException e) {
|
221
|
String msg = "Could not create string from XML stream: " +
|
222
|
" " + e.getMessage();
|
223
|
logMetacat.debug(msg);
|
224
|
throw new ServiceFailure("1190", msg);
|
225
|
}
|
226
|
|
227
|
} else {
|
228
|
// DEFAULT CASE: DATA (needs to be checked and completed)
|
229
|
insertDataObject(object, guid, sessionData);
|
230
|
|
231
|
}
|
232
|
|
233
|
// For Metadata and Data, insert the system metadata into the object store too
|
234
|
insertSystemMetadata(sysmeta, sessionData);
|
235
|
|
236
|
logMetacat.debug("Returning from CrudService.create()");
|
237
|
return guid;
|
238
|
}
|
239
|
|
240
|
/**
|
241
|
* update an existing object with a new object. Change the system metadata
|
242
|
* to reflect the changes and update it as well.
|
243
|
*/
|
244
|
public Identifier update(AuthToken token, Identifier guid,
|
245
|
InputStream object, Identifier obsoletedGuid, SystemMetadata sysmeta)
|
246
|
throws InvalidToken, ServiceFailure, NotAuthorized, IdentifierNotUnique,
|
247
|
UnsupportedType, InsufficientResources, NotFound, InvalidSystemMetadata,
|
248
|
NotImplemented {
|
249
|
try
|
250
|
{
|
251
|
SessionData sessionData = getSessionData(token);
|
252
|
|
253
|
//find the old systemmetadata (sm.old) document id (the one linked to obsoletedGuid)
|
254
|
SystemMetadata sm = getSystemMetadata(token, obsoletedGuid);
|
255
|
//change sm.old's obsoletedBy field
|
256
|
List l = sm.getObsoletedByList();
|
257
|
l.add(guid);
|
258
|
sm.setObsoletedByList(l);
|
259
|
//update sm.old
|
260
|
updateSystemMetadata(sm, sessionData);
|
261
|
|
262
|
//change the obsoletes field of the new systemMetadata (sm.new) to point to the id of the old one
|
263
|
sysmeta.addObsolete(obsoletedGuid);
|
264
|
//insert sm.new
|
265
|
insertSystemMetadata(sysmeta, sessionData);
|
266
|
|
267
|
boolean isScienceMetadata = isScienceMetadata(sysmeta);
|
268
|
if(isScienceMetadata)
|
269
|
{
|
270
|
//update the doc
|
271
|
updateDocument(object, obsoletedGuid, guid, sessionData);
|
272
|
}
|
273
|
else
|
274
|
{
|
275
|
//update a data file, not xml
|
276
|
insertDataObject(object, guid, sessionData);
|
277
|
}
|
278
|
return guid;
|
279
|
}
|
280
|
catch(Exception e)
|
281
|
{
|
282
|
throw new ServiceFailure("1030", "Error updating document in CrudService: " + e.getMessage());
|
283
|
}
|
284
|
}
|
285
|
|
286
|
/**
|
287
|
* set the permission on the document
|
288
|
* @param token
|
289
|
* @param principal
|
290
|
* @param permission
|
291
|
* @param permissionType
|
292
|
* @param permissionOrder
|
293
|
* @return
|
294
|
*/
|
295
|
public void setAccess(AuthToken token, Identifier id, String principal, String permission,
|
296
|
String permissionType, String permissionOrder)
|
297
|
throws ServiceFailure
|
298
|
{
|
299
|
try
|
300
|
{
|
301
|
IdentifierManager im = IdentifierManager.getInstance();
|
302
|
String docid = im.getLocalId(id.getValue());
|
303
|
final SessionData sessionData = getSessionData(token);
|
304
|
String permNum = "0";
|
305
|
if(permission == "read")
|
306
|
{
|
307
|
permNum = "4";
|
308
|
}
|
309
|
else if(permission == "write")
|
310
|
{
|
311
|
permNum = "6";
|
312
|
}
|
313
|
handler.setAccess(metacatUrl, sessionData.getUserName(), docid,
|
314
|
principal, permNum, permissionType, permissionOrder);
|
315
|
}
|
316
|
catch(Exception e)
|
317
|
{
|
318
|
throw new ServiceFailure("1000", "Could not set access on the document with id " + id.getValue());
|
319
|
}
|
320
|
}
|
321
|
|
322
|
/**
|
323
|
* Retrieve the list of objects present on the MN that match the calling
|
324
|
* parameters. This method is required to support the process of Member
|
325
|
* Node synchronization. At a minimum, this method should be able to
|
326
|
* return a list of objects that match:
|
327
|
* startTime <= SystemMetadata.dateSysMetadataModified
|
328
|
* but is expected to also support date range (by also specifying endTime),
|
329
|
* and should also support slicing of the matching set of records by
|
330
|
* indicating the starting index of the response (where 0 is the index
|
331
|
* of the first item) and the count of elements to be returned.
|
332
|
*
|
333
|
* @see http://mule1.dataone.org/ArchitectureDocs/mn_api_replication.html#MN_replication.listObjects
|
334
|
* @param token
|
335
|
* @param startTime
|
336
|
* @param endTime
|
337
|
* @param objectFormat
|
338
|
* @param replicaStatus
|
339
|
* @param start
|
340
|
* @param count
|
341
|
* @return ObjectList
|
342
|
* @throws NotAuthorized
|
343
|
* @throws InvalidRequest
|
344
|
* @throws NotImplemented
|
345
|
* @throws ServiceFailure
|
346
|
* @throws InvalidToken
|
347
|
*/
|
348
|
public ObjectList listObjects(AuthToken token, Date startTime, Date endTime,
|
349
|
ObjectFormat objectFormat, boolean replicaStatus, int start, int count)
|
350
|
throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken
|
351
|
{
|
352
|
ObjectList ol = new ObjectList();
|
353
|
final SessionData sessionData = getSessionData(token);
|
354
|
try
|
355
|
{
|
356
|
params.clear();
|
357
|
params.put("returndoctype", new String[] {"http://dataone.org/service/types/SystemMetadata/0.1"});
|
358
|
params.put("qformat", new String[] {"xml"});
|
359
|
params.put("returnfield", new String[] {"dateUploaded", "originMemberNode",
|
360
|
"identifier", "objectFormat", "dateSysMetadataModified"});
|
361
|
params.put("anyfield", new String[] {"%"});
|
362
|
|
363
|
System.out.println("listing objects");
|
364
|
MetacatResultSet rs = handler.query(metacatUrl, params, sessionData.getUserName(),
|
365
|
sessionData.getGroupNames(), sessionData.getId());
|
366
|
List docs = rs.getDocuments();
|
367
|
System.out.println("docs size: " + docs.size());
|
368
|
for(int i=0; i<docs.size(); i++)
|
369
|
{
|
370
|
Document d = (Document)docs.get(i);
|
371
|
//System.out.println(d.toString());
|
372
|
}
|
373
|
|
374
|
//do an squery on metacat to return systemMetadata docs where
|
375
|
//sm.dateSysMetadataModified >= startTime
|
376
|
//sm.dateSysMetadataModified <= endTime
|
377
|
//further slice the returned dataset if replicaStatus is false.
|
378
|
//if start != 0, return only the documents with index >= start
|
379
|
//if the number of results is > count, return the first count docs
|
380
|
}
|
381
|
catch(Exception e)
|
382
|
{
|
383
|
e.printStackTrace();
|
384
|
throw new ServiceFailure("1580", "Error retrieving ObjectList: " + e.getMessage());
|
385
|
}
|
386
|
return ol;
|
387
|
}
|
388
|
|
389
|
/**
|
390
|
* Call listObjects with the default values for replicaStatus (true), start (0),
|
391
|
* and count (1000).
|
392
|
* @param token
|
393
|
* @param startTime
|
394
|
* @param endTime
|
395
|
* @param objectFormat
|
396
|
* @return
|
397
|
* @throws NotAuthorized
|
398
|
* @throws InvalidRequest
|
399
|
* @throws NotImplemented
|
400
|
* @throws ServiceFailure
|
401
|
* @throws InvalidToken
|
402
|
*/
|
403
|
public ObjectList listObjects(AuthToken token, Date startTime, Date endTime,
|
404
|
ObjectFormat objectFormat)
|
405
|
throws NotAuthorized, InvalidRequest, NotImplemented, ServiceFailure, InvalidToken
|
406
|
{
|
407
|
return listObjects(token, startTime, endTime, objectFormat, true, 0, 1000);
|
408
|
}
|
409
|
|
410
|
/**
|
411
|
* Delete a document. NOT IMPLEMENTED
|
412
|
*/
|
413
|
public Identifier delete(AuthToken token, Identifier guid)
|
414
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
415
|
NotImplemented {
|
416
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
417
|
}
|
418
|
|
419
|
/**
|
420
|
* describe a document. NOT IMPLEMENTED
|
421
|
*/
|
422
|
public DescribeResponse describe(AuthToken token, Identifier guid)
|
423
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
424
|
NotImplemented {
|
425
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
426
|
}
|
427
|
|
428
|
/**
|
429
|
* get a document with a specified guid.
|
430
|
*/
|
431
|
public InputStream get(AuthToken token, Identifier guid)
|
432
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
433
|
NotImplemented {
|
434
|
|
435
|
// Retrieve the session information from the AuthToken
|
436
|
// If the session is expired, then the user is 'public'
|
437
|
final SessionData sessionData = getSessionData(token);
|
438
|
|
439
|
// Look up the localId for this global identifier
|
440
|
IdentifierManager im = IdentifierManager.getInstance();
|
441
|
try {
|
442
|
final String localId = im.getLocalId(guid.getValue());
|
443
|
|
444
|
final InputStreamFromOutputStream<String> objectStream =
|
445
|
new InputStreamFromOutputStream<String>() {
|
446
|
|
447
|
@Override
|
448
|
public String produce(final OutputStream dataSink) throws Exception {
|
449
|
|
450
|
try {
|
451
|
handler.readFromMetacat(metacatUrl, null,
|
452
|
dataSink, localId, "xml",
|
453
|
sessionData.getUserName(),
|
454
|
sessionData.getGroupNames(), true, params);
|
455
|
} catch (PropertyNotFoundException e) {
|
456
|
throw new ServiceFailure("1030", e.getMessage());
|
457
|
} catch (ClassNotFoundException e) {
|
458
|
throw new ServiceFailure("1030", e.getMessage());
|
459
|
} catch (IOException e) {
|
460
|
throw new ServiceFailure("1030", e.getMessage());
|
461
|
} catch (SQLException e) {
|
462
|
throw new ServiceFailure("1030", e.getMessage());
|
463
|
} catch (McdbException e) {
|
464
|
throw new ServiceFailure("1030", e.getMessage());
|
465
|
} catch (ParseLSIDException e) {
|
466
|
throw new NotFound("1020", e.getMessage());
|
467
|
} catch (InsufficientKarmaException e) {
|
468
|
throw new NotAuthorized("1000", "Not authorized for get().");
|
469
|
}
|
470
|
|
471
|
return "Completed";
|
472
|
}
|
473
|
};
|
474
|
return objectStream;
|
475
|
|
476
|
} catch (McdbDocNotFoundException e) {
|
477
|
throw new NotFound("1020", e.getMessage());
|
478
|
}
|
479
|
}
|
480
|
|
481
|
/**
|
482
|
* get the checksum for a document. NOT IMPLEMENTED
|
483
|
*/
|
484
|
public Checksum getChecksum(AuthToken token, Identifier guid)
|
485
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
486
|
InvalidRequest, NotImplemented {
|
487
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
488
|
}
|
489
|
|
490
|
/**
|
491
|
* get the checksum for a document. NOT IMPLEMENTED
|
492
|
*/
|
493
|
public Checksum getChecksum(AuthToken token, Identifier guid,
|
494
|
String checksumAlgorithm) throws InvalidToken, ServiceFailure,
|
495
|
NotAuthorized, NotFound, InvalidRequest, NotImplemented {
|
496
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
497
|
}
|
498
|
|
499
|
/**
|
500
|
* get log records. NOT IMPLEMENTED
|
501
|
*/
|
502
|
public LogRecordSet getLogRecords(AuthToken token, Date fromDate, Date toDate)
|
503
|
throws InvalidToken, ServiceFailure, NotAuthorized, InvalidRequest,
|
504
|
NotImplemented {
|
505
|
throw new NotImplemented("1000", "This method not yet implemented.");
|
506
|
}
|
507
|
|
508
|
/**
|
509
|
* get the system metadata for a document with a specified guid.
|
510
|
*/
|
511
|
public SystemMetadata getSystemMetadata(AuthToken token, Identifier guid)
|
512
|
throws InvalidToken, ServiceFailure, NotAuthorized, NotFound,
|
513
|
InvalidRequest, NotImplemented {
|
514
|
|
515
|
logMetacat.debug("CrudService.getSystemMetadata - for guid: " + guid.getValue());
|
516
|
|
517
|
// Retrieve the session information from the AuthToken
|
518
|
// If the session is expired, then the user is 'public'
|
519
|
final SessionData sessionData = getSessionData(token);
|
520
|
|
521
|
// TODO: Check access control rules
|
522
|
|
523
|
try {
|
524
|
IdentifierManager im = IdentifierManager.getInstance();
|
525
|
final String localId = im.getSystemMetadataId(guid.getValue());
|
526
|
|
527
|
// Read system metadata from metacat's db
|
528
|
final InputStreamFromOutputStream<String> objectStream =
|
529
|
new InputStreamFromOutputStream<String>() {
|
530
|
|
531
|
@Override
|
532
|
public String produce(final OutputStream dataSink) throws Exception {
|
533
|
try {
|
534
|
handler.readFromMetacat(metacatUrl, null,
|
535
|
dataSink, localId, "xml",
|
536
|
sessionData.getUserName(),
|
537
|
sessionData.getGroupNames(), true, params);
|
538
|
} catch (PropertyNotFoundException e) {
|
539
|
throw new ServiceFailure("1030", e.getMessage());
|
540
|
} catch (ClassNotFoundException e) {
|
541
|
throw new ServiceFailure("1030", e.getMessage());
|
542
|
} catch (IOException e) {
|
543
|
throw new ServiceFailure("1030", e.getMessage());
|
544
|
} catch (SQLException e) {
|
545
|
throw new ServiceFailure("1030", e.getMessage());
|
546
|
} catch (McdbException e) {
|
547
|
throw new ServiceFailure("1030", e.getMessage());
|
548
|
} catch (ParseLSIDException e) {
|
549
|
throw new NotFound("1020", e.getMessage());
|
550
|
} catch (InsufficientKarmaException e) {
|
551
|
throw new NotAuthorized("1000", "Not authorized for get().");
|
552
|
}
|
553
|
|
554
|
return "Completed";
|
555
|
}
|
556
|
};
|
557
|
|
558
|
// Deserialize the xml to create a SystemMetadata object
|
559
|
SystemMetadata sysmeta = deserializeSystemMetadata(objectStream);
|
560
|
return sysmeta;
|
561
|
|
562
|
} catch (McdbDocNotFoundException e) {
|
563
|
//e.printStackTrace();
|
564
|
throw new NotFound("1000", e.getMessage());
|
565
|
}
|
566
|
}
|
567
|
|
568
|
/*
|
569
|
* Look up the information on the session using the token provided in
|
570
|
* the AuthToken. The Session should have all relevant user information.
|
571
|
* If the session has expired or is invalid, the 'public' session will
|
572
|
* be returned, giving the user anonymous access.
|
573
|
*/
|
574
|
private static SessionData getSessionData(AuthToken token) {
|
575
|
SessionData sessionData = null;
|
576
|
String sessionId = "PUBLIC";
|
577
|
if (token != null) {
|
578
|
sessionId = token.getToken();
|
579
|
}
|
580
|
|
581
|
// if the session id is registered in SessionService, get the
|
582
|
// SessionData for it. Otherwise, use the public session.
|
583
|
if (SessionService.isSessionRegistered(sessionId)) {
|
584
|
sessionData = SessionService.getRegisteredSession(sessionId);
|
585
|
} else {
|
586
|
sessionData = SessionService.getPublicSession();
|
587
|
}
|
588
|
|
589
|
return sessionData;
|
590
|
}
|
591
|
|
592
|
/**
|
593
|
* Determine if a given object should be treated as an XML science metadata
|
594
|
* object.
|
595
|
*
|
596
|
* TODO: This test should be externalized in a configuration dictionary rather than being hardcoded.
|
597
|
*
|
598
|
* @param sysmeta the SystemMetadata describig the object
|
599
|
* @return true if the object should be treated as science metadata
|
600
|
*/
|
601
|
private boolean isScienceMetadata(SystemMetadata sysmeta) {
|
602
|
boolean scimeta = false;
|
603
|
switch (sysmeta.getObjectFormat()) {
|
604
|
case EML_2_1_0: scimeta = true; break;
|
605
|
case EML_2_0_1: scimeta = true; break;
|
606
|
case EML_2_0_0: scimeta = true; break;
|
607
|
case FGDC_STD_001_1_1999: scimeta = true; break;
|
608
|
case FGDC_STD_001_1998: scimeta = true; break;
|
609
|
case NCML_2_2: scimeta = true; break;
|
610
|
}
|
611
|
|
612
|
return scimeta;
|
613
|
}
|
614
|
|
615
|
/**
|
616
|
* insert a data doc
|
617
|
* @param object
|
618
|
* @param guid
|
619
|
* @param sessionData
|
620
|
* @throws ServiceFailure
|
621
|
*/
|
622
|
private void insertDataObject(InputStream object, Identifier guid,
|
623
|
SessionData sessionData) throws ServiceFailure {
|
624
|
|
625
|
String username = sessionData.getUserName();
|
626
|
String[] groups = sessionData.getGroupNames();
|
627
|
|
628
|
// generate guid/localId pair for object
|
629
|
logMetacat.debug("Generating a guid/localId mapping");
|
630
|
IdentifierManager im = IdentifierManager.getInstance();
|
631
|
String localId = im.generateLocalId(guid.getValue(), 1);
|
632
|
|
633
|
try {
|
634
|
logMetacat.debug("Case DATA: starting to write to disk.");
|
635
|
if (DocumentImpl.getDataFileLockGrant(localId)) {
|
636
|
|
637
|
// Save the data file to disk using "localId" as the name
|
638
|
try {
|
639
|
String datafilepath = PropertyService.getProperty("application.datafilepath");
|
640
|
|
641
|
File dataDirectory = new File(datafilepath);
|
642
|
dataDirectory.mkdirs();
|
643
|
|
644
|
File newFile = writeStreamToFile(dataDirectory, localId, object);
|
645
|
|
646
|
// TODO: Check that the file size matches SystemMetadata
|
647
|
// long size = newFile.length();
|
648
|
// if (size == 0) {
|
649
|
// throw new IOException("Uploaded file is 0 bytes!");
|
650
|
// }
|
651
|
|
652
|
// Register the file in the database (which generates an exception
|
653
|
// if the localId is not acceptable or other untoward things happen
|
654
|
try {
|
655
|
logMetacat.debug("Registering document...");
|
656
|
System.out.println("inserting data object: localId: " + localId);
|
657
|
DocumentImpl.registerDocument(localId, "BIN", localId,
|
658
|
username, groups);
|
659
|
logMetacat.debug("Registration step completed.");
|
660
|
} catch (SQLException e) {
|
661
|
//newFile.delete();
|
662
|
logMetacat.debug("SQLE: " + e.getMessage());
|
663
|
e.printStackTrace(System.out);
|
664
|
throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());
|
665
|
} catch (AccessionNumberException e) {
|
666
|
//newFile.delete();
|
667
|
logMetacat.debug("ANE: " + e.getMessage());
|
668
|
e.printStackTrace(System.out);
|
669
|
throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());
|
670
|
} catch (Exception e) {
|
671
|
//newFile.delete();
|
672
|
logMetacat.debug("Exception: " + e.getMessage());
|
673
|
e.printStackTrace(System.out);
|
674
|
throw new ServiceFailure("1190", "Registration failed: " + e.getMessage());
|
675
|
}
|
676
|
|
677
|
logMetacat.debug("Logging the creation event.");
|
678
|
EventLog.getInstance().log(metacatUrl,
|
679
|
username, localId, "create");
|
680
|
|
681
|
// Schedule replication for this data file
|
682
|
logMetacat.debug("Scheduling replication.");
|
683
|
ForceReplicationHandler frh = new ForceReplicationHandler(
|
684
|
localId, "insert", false, null);
|
685
|
|
686
|
} catch (PropertyNotFoundException e) {
|
687
|
throw new ServiceFailure("1190", "Could not lock file for writing:" + e.getMessage());
|
688
|
}
|
689
|
|
690
|
}
|
691
|
} catch (Exception e) {
|
692
|
// Could not get a lock on the document, so we can not update the file now
|
693
|
throw new ServiceFailure("1190", "Failed to lock file: " + e.getMessage());
|
694
|
}
|
695
|
}
|
696
|
|
697
|
/**
|
698
|
* write a file to a stream
|
699
|
* @param dir
|
700
|
* @param fileName
|
701
|
* @param data
|
702
|
* @return
|
703
|
* @throws ServiceFailure
|
704
|
*/
|
705
|
private File writeStreamToFile(File dir, String fileName, InputStream data)
|
706
|
throws ServiceFailure {
|
707
|
|
708
|
File newFile = new File(dir, fileName);
|
709
|
logMetacat.debug("Filename for write is: " + newFile.getAbsolutePath());
|
710
|
|
711
|
try {
|
712
|
if (newFile.createNewFile()) {
|
713
|
// write data stream to desired file
|
714
|
OutputStream os = new FileOutputStream(newFile);
|
715
|
long length = IOUtils.copyLarge(data, os);
|
716
|
os.flush();
|
717
|
os.close();
|
718
|
} else {
|
719
|
logMetacat.debug("File creation failed, or file already exists.");
|
720
|
throw new ServiceFailure("1190", "File already exists: " + fileName);
|
721
|
}
|
722
|
} catch (FileNotFoundException e) {
|
723
|
logMetacat.debug("FNF: " + e.getMessage());
|
724
|
throw new ServiceFailure("1190", "File not found: " + fileName + " "
|
725
|
+ e.getMessage());
|
726
|
} catch (IOException e) {
|
727
|
logMetacat.debug("IOE: " + e.getMessage());
|
728
|
throw new ServiceFailure("1190", "File was not written: " + fileName
|
729
|
+ " " + e.getMessage());
|
730
|
}
|
731
|
|
732
|
return newFile;
|
733
|
}
|
734
|
|
735
|
/**
|
736
|
* insert a systemMetadata doc
|
737
|
*/
|
738
|
private void insertSystemMetadata(SystemMetadata sysmeta, SessionData sessionData)
|
739
|
throws ServiceFailure {
|
740
|
logMetacat.debug("Starting to insert SystemMetadata...");
|
741
|
|
742
|
// generate guid/localId pair for sysmeta
|
743
|
Identifier sysMetaGuid = new Identifier();
|
744
|
sysMetaGuid.setValue(DocumentUtil.generateDocumentId(1));
|
745
|
sysmeta.setDateSysMetadataModified(new Date());
|
746
|
|
747
|
String xml = new String(serializeSystemMetadata(sysmeta).toByteArray());
|
748
|
String localId = insertDocument(xml, sysMetaGuid, sessionData);
|
749
|
//insert the system metadata doc id into the identifiers table to
|
750
|
//link it to the data or metadata document
|
751
|
IdentifierManager.getInstance().createSystemMetadataMapping(sysmeta.getIdentifier().getValue(), sysMetaGuid.getValue());
|
752
|
}
|
753
|
|
754
|
/**
|
755
|
* update a systemMetadata doc
|
756
|
*/
|
757
|
private void updateSystemMetadata(SystemMetadata sm, SessionData sessionData)
|
758
|
throws ServiceFailure
|
759
|
{
|
760
|
try
|
761
|
{
|
762
|
String smId = IdentifierManager.getInstance().getSystemMetadataId(sm.getIdentifier().getValue());
|
763
|
sm.setDateSysMetadataModified(new Date());
|
764
|
String xml = new String(serializeSystemMetadata(sm).toByteArray());
|
765
|
Identifier id = new Identifier();
|
766
|
id.setValue(smId);
|
767
|
String localId = updateDocument(xml, id, null, sessionData);
|
768
|
IdentifierManager.getInstance().updateSystemMetadataMapping(sm.getIdentifier().getValue(), localId);
|
769
|
}
|
770
|
catch(Exception e)
|
771
|
{
|
772
|
throw new ServiceFailure("1030", "Error updating system metadata: " + e.getMessage());
|
773
|
}
|
774
|
}
|
775
|
|
776
|
/**
|
777
|
* insert a document
|
778
|
* NOTE: this method shouldn't be used from the update or create() methods.
|
779
|
* we shouldn't be putting the science metadata or data objects into memory.
|
780
|
*/
|
781
|
private String insertDocument(String xml, Identifier guid, SessionData sessionData)
|
782
|
throws ServiceFailure
|
783
|
{
|
784
|
return insertOrUpdateDocument(xml, guid, sessionData, "insert");
|
785
|
}
|
786
|
|
787
|
/**
|
788
|
* insert a document from a stream
|
789
|
*/
|
790
|
private String insertDocument(InputStream is, Identifier guid, SessionData sessionData)
|
791
|
throws IOException, ServiceFailure
|
792
|
{
|
793
|
//HACK: change this eventually. we should not be converting the stream to a string
|
794
|
String xml = IOUtils.toString(is);
|
795
|
return insertDocument(xml, guid, sessionData);
|
796
|
}
|
797
|
|
798
|
/**
|
799
|
* update a document
|
800
|
* NOTE: this method shouldn't be used from the update or create() methods.
|
801
|
* we shouldn't be putting the science metadata or data objects into memory.
|
802
|
*/
|
803
|
private String updateDocument(String xml, Identifier obsoleteGuid, Identifier guid, SessionData sessionData)
|
804
|
throws ServiceFailure
|
805
|
{
|
806
|
return insertOrUpdateDocument(xml, obsoleteGuid, sessionData, "update");
|
807
|
}
|
808
|
|
809
|
/**
|
810
|
* update a document from a stream
|
811
|
*/
|
812
|
private String updateDocument(InputStream is, Identifier obsoleteGuid, Identifier guid, SessionData sessionData)
|
813
|
throws IOException, ServiceFailure
|
814
|
{
|
815
|
//HACK: change this eventually. we should not be converting the stream to a string
|
816
|
String xml = IOUtils.toString(is);
|
817
|
String localId = updateDocument(xml, obsoleteGuid, guid, sessionData);
|
818
|
IdentifierManager im = IdentifierManager.getInstance();
|
819
|
if(guid != null)
|
820
|
{
|
821
|
im.createMapping(guid.getValue(), localId);
|
822
|
}
|
823
|
return localId;
|
824
|
}
|
825
|
|
826
|
/**
|
827
|
* insert a document, return the id of the document that was inserted
|
828
|
*/
|
829
|
private String insertOrUpdateDocument(String xml, Identifier guid, SessionData sessionData, String insertOrUpdate)
|
830
|
throws ServiceFailure {
|
831
|
logMetacat.debug("Starting to insert xml document...");
|
832
|
IdentifierManager im = IdentifierManager.getInstance();
|
833
|
|
834
|
// generate guid/localId pair for sysmeta
|
835
|
String localId = null;
|
836
|
if(insertOrUpdate.equals("insert"))
|
837
|
{
|
838
|
localId = im.generateLocalId(guid.getValue(), 1);
|
839
|
}
|
840
|
else
|
841
|
{
|
842
|
//localid should already exist in the identifier table, so just find it
|
843
|
try
|
844
|
{
|
845
|
localId = im.getLocalId(guid.getValue());
|
846
|
//increment the revision
|
847
|
String docid = localId.substring(0, localId.lastIndexOf("."));
|
848
|
String revS = localId.substring(localId.lastIndexOf(".") + 1, localId.length());
|
849
|
int rev = new Integer(revS).intValue();
|
850
|
rev++;
|
851
|
docid = docid + "." + rev;
|
852
|
localId = docid;
|
853
|
}
|
854
|
catch(McdbDocNotFoundException e)
|
855
|
{
|
856
|
throw new ServiceFailure("1030", "CrudService.insertOrUpdateDocument(): " +
|
857
|
"guid " + guid.getValue() + " should have been in the identifier table, but it wasn't: " + e.getMessage());
|
858
|
}
|
859
|
}
|
860
|
logMetacat.debug("Metadata guid|localId: " + guid.getValue() + "|" +
|
861
|
localId);
|
862
|
|
863
|
String[] action = new String[1];
|
864
|
action[0] = insertOrUpdate;
|
865
|
params.put("action", action);
|
866
|
String[] docid = new String[1];
|
867
|
docid[0] = localId;
|
868
|
params.put("docid", docid);
|
869
|
String[] doctext = new String[1];
|
870
|
doctext[0] = xml;
|
871
|
logMetacat.debug(doctext[0]);
|
872
|
params.put("doctext", doctext);
|
873
|
|
874
|
// TODO: refactor handleInsertOrUpdateAction() to not output XML directly
|
875
|
// onto output stream, or alternatively, capture that and parse it to
|
876
|
// generate the right exceptions
|
877
|
//ByteArrayOutputStream output = new ByteArrayOutputStream();
|
878
|
//PrintWriter pw = new PrintWriter(output);
|
879
|
String result = handler.handleInsertOrUpdateAction(metacatUrl, null,
|
880
|
null, params, sessionData.getUserName(), sessionData.getGroupNames());
|
881
|
//String outputS = new String(output.toByteArray());
|
882
|
logMetacat.debug("CrudService.insertDocument - Metacat returned: " + result);
|
883
|
// if (!(outputS.indexOf("<success>") > 0 && outputS.indexOf(localId) > 0)) {
|
884
|
// throw new ServiceFailure(1190, outputS);
|
885
|
// }
|
886
|
logMetacat.debug("Finsished inserting xml document with id " + localId);
|
887
|
return localId;
|
888
|
}
|
889
|
|
890
|
/**
|
891
|
* serialize a system metadata doc
|
892
|
* @param sysmeta
|
893
|
* @return
|
894
|
* @throws ServiceFailure
|
895
|
*/
|
896
|
public static ByteArrayOutputStream serializeSystemMetadata(SystemMetadata sysmeta)
|
897
|
throws ServiceFailure {
|
898
|
IBindingFactory bfact;
|
899
|
ByteArrayOutputStream sysmetaOut = null;
|
900
|
try {
|
901
|
bfact = BindingDirectory.getFactory(SystemMetadata.class);
|
902
|
IMarshallingContext mctx = bfact.createMarshallingContext();
|
903
|
sysmetaOut = new ByteArrayOutputStream();
|
904
|
mctx.marshalDocument(sysmeta, "UTF-8", null, sysmetaOut);
|
905
|
} catch (JiBXException e) {
|
906
|
throw new ServiceFailure("1190", "Failed to serialize and insert SystemMetadata: " + e.getMessage());
|
907
|
}
|
908
|
|
909
|
return sysmetaOut;
|
910
|
}
|
911
|
|
912
|
/**
|
913
|
* deserialize a system metadata doc
|
914
|
* @param xml
|
915
|
* @return
|
916
|
* @throws ServiceFailure
|
917
|
*/
|
918
|
public static SystemMetadata deserializeSystemMetadata(InputStream xml)
|
919
|
throws ServiceFailure {
|
920
|
try {
|
921
|
IBindingFactory bfact = BindingDirectory.getFactory(SystemMetadata.class);
|
922
|
IUnmarshallingContext uctx = bfact.createUnmarshallingContext();
|
923
|
SystemMetadata sysmeta = (SystemMetadata) uctx.unmarshalDocument(xml, null);
|
924
|
return sysmeta;
|
925
|
} catch (JiBXException e) {
|
926
|
throw new ServiceFailure("1190", "Failed to serialize and insert SystemMetadata: " + e.getMessage());
|
927
|
}
|
928
|
}
|
929
|
}
|