Revision 6091
Added by Chris Jones almost 13 years ago
| src/edu/ucsb/nceas/metacat/restservice/ResourceHandler.java | ||
|---|---|---|
| 77 | 77 |
import edu.ucsb.nceas.metacat.dataone.CrudService; |
| 78 | 78 |
import edu.ucsb.nceas.metacat.dataone.HealthService; |
| 79 | 79 |
import edu.ucsb.nceas.metacat.properties.PropertyService; |
| 80 |
import edu.ucsb.nceas.metacat.service.ObjectFormatService; |
|
| 81 | 80 |
import edu.ucsb.nceas.metacat.service.SessionService; |
| 82 | 81 |
import edu.ucsb.nceas.metacat.util.RequestUtil; |
| 83 | 82 |
import edu.ucsb.nceas.metacat.util.SystemUtil; |
| ... | ... | |
| 533 | 532 |
if(params.containsKey("format"))
|
| 534 | 533 |
{
|
| 535 | 534 |
String format = params.get("format")[0];
|
| 536 |
of = ObjectFormatService.getFormat(format);
|
|
| 535 |
of = ObjectFormat.convert(format);
|
|
| 537 | 536 |
} |
| 538 | 537 |
if(params.containsKey("time"))
|
| 539 | 538 |
{
|
| ... | ... | |
| 570 | 569 |
if(params.containsKey("format"))
|
| 571 | 570 |
{
|
| 572 | 571 |
String format = params.get("format")[0];
|
| 573 |
of = ObjectFormatService.getFormat(format);
|
|
| 572 |
of = ObjectFormat.convert(format);
|
|
| 574 | 573 |
} |
| 575 | 574 |
if(params.containsKey("eventtime"))
|
| 576 | 575 |
{
|
| ... | ... | |
| 1167 | 1166 |
cs.setParamsFromRequest(request); |
| 1168 | 1167 |
AuthToken token = new AuthToken(sessionId); |
| 1169 | 1168 |
OutputStream out = null; |
| 1170 |
String textCSV = ObjectFormatService.getFormat("text/csv").toString();
|
|
| 1171 |
String textPlain = ObjectFormatService.getFormat("text/plain").toString();
|
|
| 1172 |
String octetStream = ObjectFormatService.getFormat("application/octet-stream").toString();
|
|
| 1173 |
|
|
| 1174 | 1169 |
try {
|
| 1175 | 1170 |
out = response.getOutputStream(); |
| 1176 | 1171 |
response.setStatus(200); |
| ... | ... | |
| 1188 | 1183 |
SystemMetadata sm = cs.getSystemMetadata(token, id); |
| 1189 | 1184 |
|
| 1190 | 1185 |
//set the content type |
| 1191 |
if(sm.getObjectFormat().toString().trim().equals(textCSV))
|
|
| 1186 |
if(sm.getObjectFormat().toString().trim().equals(ObjectFormat.TEXT_CSV.toString()))
|
|
| 1192 | 1187 |
{
|
| 1193 | 1188 |
response.setContentType("text/csv");
|
| 1194 | 1189 |
response.setHeader("Content-Disposition", "inline; filename=" + id.getValue() + ".csv");
|
| 1195 | 1190 |
} |
| 1196 |
else if(sm.getObjectFormat().toString().trim().equals(textPlain))
|
|
| 1191 |
else if(sm.getObjectFormat().toString().trim().equals(ObjectFormat.TEXT_PLAIN.toString()))
|
|
| 1197 | 1192 |
{
|
| 1198 | 1193 |
response.setContentType("text/plain");
|
| 1199 | 1194 |
response.setHeader("Content-Disposition", "inline; filename=" + id.getValue() + ".txt");
|
| 1200 | 1195 |
} |
| 1201 |
else if(sm.getObjectFormat().toString().trim().equals(octetStream))
|
|
| 1196 |
else if(sm.getObjectFormat().toString().trim().equals(ObjectFormat.OCTET_STREAM.toString()))
|
|
| 1202 | 1197 |
{
|
| 1203 | 1198 |
response.setContentType("application/octet-stream");
|
| 1204 | 1199 |
} |
| ... | ... | |
| 1295 | 1290 |
} |
| 1296 | 1291 |
else if(name.equals("objectFormat") && value != null)
|
| 1297 | 1292 |
{
|
| 1298 |
objectFormat = ObjectFormatService.getFormat(value[0]);
|
|
| 1293 |
objectFormat = ObjectFormat.convert(value[0]);
|
|
| 1299 | 1294 |
} |
| 1300 | 1295 |
else if(name.equals("replicaStatus") && value != null)
|
| 1301 | 1296 |
{
|
| src/edu/ucsb/nceas/metacat/MetaCatServlet.java | ||
|---|---|---|
| 345 | 345 |
ServiceService.registerService("XMLSchemaService", XMLSchemaService.getInstance());
|
| 346 | 346 |
|
| 347 | 347 |
// register the object format service |
| 348 |
ServiceService.registerService("ObjectFormatService", ObjectFormatService.getInstance());
|
|
| 348 |
//ServiceService.registerService("ObjectFormatService", ObjectFormatService.getInstance());
|
|
| 349 | 349 |
|
| 350 | 350 |
// check if eml201 document were corrected or not. if not, correct eml201 documents. |
| 351 | 351 |
// Before Metacat 1.8.1, metacat uses tag RELEASE_EML_2_0_1_UPDATE_6 as eml |
| src/edu/ucsb/nceas/metacat/MetacatHandler.java | ||
|---|---|---|
| 1 |
/**ml
|
|
| 1 |
/** |
|
| 2 | 2 |
* '$RCSfile$' |
| 3 | 3 |
* Copyright: 2010 Regents of the University of California and the |
| 4 | 4 |
* National Center for Ecological Analysis and Synthesis |
| ... | ... | |
| 42 | 42 |
import edu.ucsb.nceas.metacat.event.MetacatEventService; |
| 43 | 43 |
import edu.ucsb.nceas.metacat.properties.PropertyService; |
| 44 | 44 |
import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler; |
| 45 |
import edu.ucsb.nceas.metacat.service.ObjectFormatService; |
|
| 46 | 45 |
import edu.ucsb.nceas.metacat.service.SessionService; |
| 47 | 46 |
import edu.ucsb.nceas.metacat.service.XMLSchemaService; |
| 48 | 47 |
import edu.ucsb.nceas.metacat.shared.HandlerException; |
| ... | ... | |
| 3631 | 3630 |
|
| 3632 | 3631 |
//set the default object format |
| 3633 | 3632 |
String doctype = (String) docInfo.get("doctype");
|
| 3634 |
ObjectFormat format = ObjectFormatService.getFormat(doctype);
|
|
| 3633 |
ObjectFormat format = ObjectFormat.convert(doctype);
|
|
| 3635 | 3634 |
if (format == null) {
|
| 3636 | 3635 |
if (doctype.trim().equals("BIN")) {
|
| 3637 |
format = ObjectFormatService.getFormat("application/octet-stream");
|
|
| 3636 |
format = ObjectFormat.OCTET_STREAM;
|
|
| 3638 | 3637 |
} else {
|
| 3639 |
format = ObjectFormatService.getFormat("text/plain");
|
|
| 3638 |
format = ObjectFormat.convert("text/plain");
|
|
| 3640 | 3639 |
} |
| 3641 | 3640 |
} |
| 3642 | 3641 |
sysMeta.setObjectFormat(format); |
| ... | ... | |
| 3645 | 3644 |
|
| 3646 | 3645 |
// further parse EML documents to get data object format, |
| 3647 | 3646 |
// describes and describedBy information |
| 3648 |
if ( format == ObjectFormatService.getFormat("eml://ecoinformatics.org/eml/2.0.0") ||
|
|
| 3649 |
format == ObjectFormatService.getFormat("eml://ecoinformatics.org/eml/2.0.1") ||
|
|
| 3650 |
format == ObjectFormatService.getFormat("eml://ecoinformatics.org/eml/2.1.0")) {
|
|
| 3647 |
if ( format == ObjectFormat.EML_2_0_0 ||
|
|
| 3648 |
format == ObjectFormat.EML_2_0_1 ||
|
|
| 3649 |
format == ObjectFormat.EML_2_1_0 ) {
|
|
| 3651 | 3650 |
|
| 3652 | 3651 |
try {
|
| 3653 | 3652 |
DataoneEMLParser emlParser = DataoneEMLParser.getInstance(); |
| ... | ... | |
| 3664 | 3663 |
emlDocument.distributionMetadata.elementAt(j); |
| 3665 | 3664 |
String dataDocUrl = distMetadata.url; |
| 3666 | 3665 |
String dataDocMimeType = ""; |
| 3667 |
|
|
| 3668 | 3666 |
if (distMetadata.mimeType == null) {
|
| 3669 |
|
|
| 3670 |
dataDocMimeType = |
|
| 3671 |
ObjectFormatService.getFormat("application/octet-stream").toString();
|
|
| 3672 |
|
|
| 3667 |
dataDocMimeType = ObjectFormat.OCTET_STREAM.name(); |
|
| 3673 | 3668 |
} else {
|
| 3674 |
|
|
| 3675 |
dataDocMimeType = distMetadata.mimeType; |
|
| 3676 |
|
|
| 3669 |
dataDocMimeType = distMetadata.mimeType; |
|
| 3677 | 3670 |
} |
| 3678 | 3671 |
String dataDocLocalId = ""; |
| 3679 | 3672 |
String dataSysMetaId = ""; |
| ... | ... | |
| 3704 | 3697 |
logMetacat.debug("Setting describedBy for " + dataDocId.getValue() +
|
| 3705 | 3698 |
" to " + identifier.getValue()); |
| 3706 | 3699 |
dataSysMeta.addDescribedBy(identifier); |
| 3707 |
ObjectFormat f = ObjectFormatService.getFormat(dataDocMimeType);
|
|
| 3700 |
ObjectFormat f = ObjectFormat.convert(dataDocMimeType);
|
|
| 3708 | 3701 |
if (f == null) {
|
| 3709 |
f = ObjectFormatService.getFormat("application/octet-stream");
|
|
| 3702 |
f = ObjectFormat.OCTET_STREAM;
|
|
| 3710 | 3703 |
} |
| 3711 | 3704 |
dataSysMeta.setObjectFormat(f); |
| 3712 | 3705 |
dataSysMetaId = insertOrUpdateSystemMetadata( |
| ... | ... | |
| 3728 | 3721 |
|
| 3729 | 3722 |
logMetacat.debug("Setting mimeType for " +
|
| 3730 | 3723 |
dataDocId.getValue() + " to " + dataDocMimeType); |
| 3731 |
|
|
| 3732 |
ObjectFormat f = ObjectFormatService.getFormat(dataDocMimeType); |
|
| 3733 |
|
|
| 3724 |
ObjectFormat f = ObjectFormat.convert(dataDocMimeType); |
|
| 3734 | 3725 |
if (f == null) {
|
| 3735 |
f = ObjectFormatService.getFormat("application/octet-stream");
|
|
| 3726 |
f = ObjectFormat.OCTET_STREAM;
|
|
| 3736 | 3727 |
} |
| 3737 | 3728 |
dataSysMeta.setObjectFormat(f); |
| 3738 | 3729 |
|
| src/edu/ucsb/nceas/metacat/service/ObjectFormatService.java | ||
|---|---|---|
| 55 | 55 |
import org.dataone.service.exceptions.ServiceFailure; |
| 56 | 56 |
import org.dataone.service.types.Identifier; |
| 57 | 57 |
import org.dataone.service.types.ObjectFormat; |
| 58 |
import org.dataone.service.types.ObjectFormatList; |
|
| 58 |
//import org.dataone.service.types.ObjectFormatList;
|
|
| 59 | 59 |
import org.dataone.service.types.util.ServiceTypeUtil; |
| 60 | 60 |
import org.jibx.runtime.JiBXException; |
| 61 | 61 |
|
| ... | ... | |
| 87 | 87 |
private String accNumber = null; |
| 88 | 88 |
|
| 89 | 89 |
/* The list of object formats */ |
| 90 |
private static ObjectFormatList objectFormatList = null; |
|
| 90 |
//private static ObjectFormatList objectFormatList = null;
|
|
| 91 | 91 |
|
| 92 | 92 |
/* the searchable map of object formats */ |
| 93 | 93 |
private static HashMap<String, ObjectFormat> objectFormatMap = |
| ... | ... | |
| 229 | 229 |
*/ |
| 230 | 230 |
|
| 231 | 231 |
// this will be replaced with external lookup code above |
| 232 |
this.getCachedList(); |
|
| 232 |
//this.getCachedList();
|
|
| 233 | 233 |
|
| 234 | 234 |
} else if ( this.nodeType.equals("cn") ) {
|
| 235 | 235 |
|
| 236 | 236 |
// get the list from the local metacat database |
| 237 |
this.getCachedList(); |
|
| 237 |
//this.getCachedList();
|
|
| 238 | 238 |
|
| 239 | 239 |
} else {
|
| 240 | 240 |
|
| ... | ... | |
| 245 | 245 |
} |
| 246 | 246 |
|
| 247 | 247 |
// index the object format list based on the format identifier |
| 248 |
int listSize = ObjectFormatService.objectFormatList.sizeObjectFormats(); |
|
| 249 |
|
|
| 250 |
for (int i = 0; i < listSize; i++ ) {
|
|
| 251 |
|
|
| 252 |
ObjectFormat objectFormat = |
|
| 253 |
ObjectFormatService.objectFormatList.getObjectFormat(i); |
|
| 254 |
String identifier = objectFormat.getFmtid(); |
|
| 255 |
ObjectFormatService.objectFormatMap.put(identifier, objectFormat); |
|
| 256 |
|
|
| 257 |
} |
|
| 248 |
//int listSize = ObjectFormatService.objectFormatList.sizeObjectFormats();
|
|
| 249 |
// |
|
| 250 |
//for (int i = 0; i < listSize; i++ ) {
|
|
| 251 |
// |
|
| 252 |
// ObjectFormat objectFormat =
|
|
| 253 |
// ObjectFormatService.objectFormatList.getObjectFormat(i);
|
|
| 254 |
// String identifier = objectFormat.getFmtid();
|
|
| 255 |
// ObjectFormatService.objectFormatMap.put(identifier, objectFormat);
|
|
| 256 |
// |
|
| 257 |
//}
|
|
| 258 | 258 |
|
| 259 | 259 |
|
| 260 | 260 |
|
| ... | ... | |
| 287 | 287 |
* |
| 288 | 288 |
* @return objectFormatList - the list of object formats |
| 289 | 289 |
*/ |
| 290 |
public ObjectFormatList listFormats() {
|
|
| 291 |
|
|
| 292 |
return ObjectFormatService.objectFormatList; |
|
| 293 |
|
|
| 294 |
} |
|
| 290 |
//public ObjectFormatList listFormats() {
|
|
| 291 |
// |
|
| 292 |
// return ObjectFormatService.objectFormatList;
|
|
| 293 |
// |
|
| 294 |
//}
|
|
| 295 | 295 |
|
| 296 | 296 |
/** |
| 297 | 297 |
* Get the object format based on the given identifier as a string. |
| ... | ... | |
| 299 | 299 |
* @param format - the object format as a string |
| 300 | 300 |
* @return objectFormat - the ObjectFormat represented by the format string |
| 301 | 301 |
*/ |
| 302 |
public static ObjectFormat getFormat(String format) {
|
|
| 303 |
|
|
| 304 |
ObjectFormat objectFormat = null; |
|
| 305 |
objectFormat = ObjectFormatService.objectFormatMap.get(format); |
|
| 306 |
|
|
| 307 |
return objectFormat; |
|
| 308 |
|
|
| 309 |
} |
|
| 302 |
//public static ObjectFormat getFormat(String format) {
|
|
| 303 |
// |
|
| 304 |
// ObjectFormat objectFormat = null;
|
|
| 305 |
// objectFormat = ObjectFormatService.objectFormatMap.get(format);
|
|
| 306 |
// |
|
| 307 |
// return objectFormat;
|
|
| 308 |
// |
|
| 309 |
//}
|
|
| 310 | 310 |
/** |
| 311 | 311 |
* Get the object format list cached in Metacat, or on failure, via a |
| 312 | 312 |
* cached file on disk |
| 313 | 313 |
* |
| 314 | 314 |
* @return objectFormatList - the cached object format list |
| 315 | 315 |
*/ |
| 316 |
private void getCachedList() |
|
| 317 |
throws ServiceException {
|
|
| 318 |
|
|
| 319 |
try {
|
|
| 320 |
|
|
| 321 |
// reset the accession number separator in case it is |
|
| 322 |
// different than the default |
|
| 323 |
try {
|
|
| 324 |
|
|
| 325 |
this.separator = PropertyService.getProperty("document.accNumSeparator");
|
|
| 326 |
|
|
| 327 |
} catch ( PropertyNotFoundException pnfe ) {
|
|
| 328 |
|
|
| 329 |
// use the default separator, but log the issue |
|
| 330 |
logMetacat.debug("There was a problem finding the document " +
|
|
| 331 |
"separator property. The error message was: " + pnfe.getMessage()); |
|
| 332 |
} |
|
| 333 |
|
|
| 334 |
// get the latest accession number if it is in Metacat |
|
| 335 |
this.rev = |
|
| 336 |
DBUtil.getLatestRevisionInDocumentTable(this.OBJECT_FORMAT_DOCID); |
|
| 337 |
|
|
| 338 |
if ( this.rev != -1 ) {
|
|
| 339 |
this.accNumber = this.OBJECT_FORMAT_DOCID + |
|
| 340 |
this.separator + |
|
| 341 |
this.rev; |
|
| 342 |
DocumentImpl objectFormatsDocument = new DocumentImpl(accNumber, false); |
|
| 343 |
ByteArrayInputStream bais = |
|
| 344 |
new ByteArrayInputStream(objectFormatsDocument.toString().getBytes()); |
|
| 345 |
ObjectFormatService.objectFormatList = |
|
| 346 |
this.deserializeObjectFormatList(bais); |
|
| 316 |
//private void getCachedList() |
|
| 317 |
// throws ServiceException {
|
|
| 318 |
// |
|
| 319 |
// try {
|
|
| 320 |
// |
|
| 321 |
// // reset the accession number separator in case it is |
|
| 322 |
// // different than the default |
|
| 323 |
// try {
|
|
| 324 |
// |
|
| 325 |
// this.separator = PropertyService.getProperty("document.accNumSeparator");
|
|
| 326 |
// |
|
| 327 |
// } catch ( PropertyNotFoundException pnfe ) {
|
|
| 328 |
// |
|
| 329 |
// // use the default separator, but log the issue |
|
| 330 |
// logMetacat.debug("There was a problem finding the document " +
|
|
| 331 |
// "separator property. The error message was: " + pnfe.getMessage()); |
|
| 332 |
// } |
|
| 333 |
// |
|
| 334 |
// // get the latest accession number if it is in Metacat |
|
| 335 |
// this.rev = |
|
| 336 |
// DBUtil.getLatestRevisionInDocumentTable(this.OBJECT_FORMAT_DOCID); |
|
| 337 |
// |
|
| 338 |
// if ( this.rev != -1 ) {
|
|
| 339 |
// this.accNumber = this.OBJECT_FORMAT_DOCID + |
|
| 340 |
// this.separator + |
|
| 341 |
// this.rev; |
|
| 342 |
// DocumentImpl objectFormatsDocument = new DocumentImpl(accNumber, false); |
|
| 343 |
// ByteArrayInputStream bais = |
|
| 344 |
// new ByteArrayInputStream(objectFormatsDocument.toString().getBytes()); |
|
| 345 |
// ObjectFormatService.objectFormatList = |
|
| 346 |
// this.deserializeObjectFormatList(bais); |
|
| 347 |
// |
|
| 348 |
// } else {
|
|
| 349 |
// |
|
| 350 |
// logMetacat.info("The latest revision number of " +
|
|
| 351 |
// this.OBJECT_FORMAT_DOCID + |
|
| 352 |
// " could not be found. Reverting to the on-disk " + |
|
| 353 |
// "object format list"); |
|
| 354 |
// try {
|
|
| 355 |
// |
|
| 356 |
// ObjectFormatService.objectFormatList = this.getListFromDisk(); |
|
| 357 |
// |
|
| 358 |
// } catch (ServiceException se) {
|
|
| 359 |
// |
|
| 360 |
// throw new ServiceException(se.getMessage()); |
|
| 361 |
// |
|
| 362 |
// } |
|
| 363 |
// |
|
| 364 |
// } |
|
| 365 |
// |
|
| 366 |
// } catch ( SQLException sqle ) {
|
|
| 367 |
// |
|
| 368 |
// // we either have a metacat error or the docid was not inserted yet |
|
| 369 |
// logMetacat.info("The latest revision number of " +
|
|
| 370 |
// this.OBJECT_FORMAT_DOCID + |
|
| 371 |
// " could not be found. Reverting to the on-disk " + |
|
| 372 |
// "object format list"); |
|
| 373 |
// |
|
| 374 |
// try {
|
|
| 375 |
// |
|
| 376 |
// ObjectFormatService.objectFormatList = this.getListFromDisk(); |
|
| 377 |
// |
|
| 378 |
// } catch (ServiceException se) {
|
|
| 379 |
// |
|
| 380 |
// throw se; |
|
| 381 |
// |
|
| 382 |
// } |
|
| 383 |
// |
|
| 384 |
// } catch (McdbException mcdbe) {
|
|
| 385 |
// |
|
| 386 |
// // we have a metacat doc not found error |
|
| 387 |
// logMetacat.info( this.OBJECT_FORMAT_DOCID + |
|
| 388 |
// " could not be found. Reverting to the on-disk " + |
|
| 389 |
// "object format list"); |
|
| 390 |
// |
|
| 391 |
// try {
|
|
| 392 |
// |
|
| 393 |
// ObjectFormatService.objectFormatList = this.getListFromDisk(); |
|
| 394 |
// |
|
| 395 |
// } catch (ServiceException se) {
|
|
| 396 |
// |
|
| 397 |
// throw se; |
|
| 398 |
// |
|
| 399 |
// } |
|
| 400 |
// |
|
| 401 |
// |
|
| 402 |
// } |
|
| 403 |
// |
|
| 404 |
// return; |
|
| 405 |
// |
|
| 406 |
//} |
|
| 347 | 407 |
|
| 348 |
} else {
|
|
| 349 |
|
|
| 350 |
logMetacat.info("The latest revision number of " +
|
|
| 351 |
this.OBJECT_FORMAT_DOCID + |
|
| 352 |
" could not be found. Reverting to the on-disk " + |
|
| 353 |
"object format list"); |
|
| 354 |
try {
|
|
| 355 |
|
|
| 356 |
ObjectFormatService.objectFormatList = this.getListFromDisk(); |
|
| 357 |
|
|
| 358 |
} catch (ServiceException se) {
|
|
| 359 |
|
|
| 360 |
throw new ServiceException(se.getMessage()); |
|
| 361 |
|
|
| 362 |
} |
|
| 363 |
|
|
| 364 |
} |
|
| 365 |
|
|
| 366 |
} catch ( SQLException sqle ) {
|
|
| 367 |
|
|
| 368 |
// we either have a metacat error or the docid was not inserted yet |
|
| 369 |
logMetacat.info("The latest revision number of " +
|
|
| 370 |
this.OBJECT_FORMAT_DOCID + |
|
| 371 |
" could not be found. Reverting to the on-disk " + |
|
| 372 |
"object format list"); |
|
| 373 |
|
|
| 374 |
try {
|
|
| 375 |
|
|
| 376 |
ObjectFormatService.objectFormatList = this.getListFromDisk(); |
|
| 377 |
|
|
| 378 |
} catch (ServiceException se) {
|
|
| 379 |
|
|
| 380 |
throw se; |
|
| 381 |
|
|
| 382 |
} |
|
| 383 |
|
|
| 384 |
} catch (McdbException mcdbe) {
|
|
| 385 |
|
|
| 386 |
// we have a metacat doc not found error |
|
| 387 |
logMetacat.info( this.OBJECT_FORMAT_DOCID + |
|
| 388 |
" could not be found. Reverting to the on-disk " + |
|
| 389 |
"object format list"); |
|
| 390 |
|
|
| 391 |
try {
|
|
| 392 |
|
|
| 393 |
ObjectFormatService.objectFormatList = this.getListFromDisk(); |
|
| 394 |
|
|
| 395 |
} catch (ServiceException se) {
|
|
| 396 |
|
|
| 397 |
throw se; |
|
| 398 |
|
|
| 399 |
} |
|
| 400 |
|
|
| 401 |
|
|
| 402 |
} |
|
| 403 |
|
|
| 404 |
return; |
|
| 405 |
|
|
| 406 |
} |
|
| 407 |
|
|
| 408 | 408 |
/** |
| 409 | 409 |
* Get the object format list cached on disk as stated in the metacat |
| 410 | 410 |
* properties file. |
| ... | ... | |
| 412 | 412 |
* @return objectFormatList - the on-disk object format list |
| 413 | 413 |
* @throws ServiceException |
| 414 | 414 |
*/ |
| 415 |
private ObjectFormatList getListFromDisk() |
|
| 416 |
throws ServiceException {
|
|
| 417 |
|
|
| 418 |
// the filesystem location of the object format list xml file |
|
| 419 |
String objectFormatFilePath = null; |
|
| 420 |
|
|
| 421 |
// get the object format list from disk and parse it |
|
| 422 |
try {
|
|
| 423 |
objectFormatFilePath = SystemUtil.getContextDir() + "/WEB-INF/" + |
|
| 424 |
PropertyService.getProperty("dataone.objectFormatListName");
|
|
| 425 |
|
|
| 426 |
FileInputStream fileInputStream = new FileInputStream(objectFormatFilePath); |
|
| 415 |
//private ObjectFormatList getListFromDisk() |
|
| 416 |
// throws ServiceException {
|
|
| 417 |
// |
|
| 418 |
// // the filesystem location of the object format list xml file |
|
| 419 |
// String objectFormatFilePath = null; |
|
| 420 |
// |
|
| 421 |
// // get the object format list from disk and parse it |
|
| 422 |
// try {
|
|
| 423 |
// objectFormatFilePath = SystemUtil.getContextDir() + "/WEB-INF/" + |
|
| 424 |
// PropertyService.getProperty("dataone.objectFormatListName");
|
|
| 425 |
// |
|
| 426 |
// FileInputStream fileInputStream = new FileInputStream(objectFormatFilePath); |
|
| 427 |
// |
|
| 428 |
// ObjectFormatService.objectFormatList = |
|
| 429 |
// this.deserializeObjectFormatList(fileInputStream); |
|
| 430 |
// |
|
| 431 |
// } catch (PropertyNotFoundException pnfe) {
|
|
| 432 |
// |
|
| 433 |
// logMetacat.error("The object format list file could not be parsed. " +
|
|
| 434 |
// "The error message was: " + pnfe.getMessage()); |
|
| 435 |
// throw new ServiceException(pnfe.getMessage()); |
|
| 436 |
// |
|
| 437 |
// } catch ( FileNotFoundException fnfe ) {
|
|
| 438 |
// |
|
| 439 |
// logMetacat.debug("There was an error reading the file " +
|
|
| 440 |
// objectFormatFilePath + ". The error was: " + |
|
| 441 |
// fnfe.getMessage()); |
|
| 442 |
// throw new ServiceException(fnfe.getMessage()); |
|
| 443 |
// |
|
| 444 |
// } |
|
| 445 |
// |
|
| 446 |
// return ObjectFormatService.objectFormatList; |
|
| 447 |
//} |
|
| 427 | 448 |
|
| 428 |
ObjectFormatService.objectFormatList = |
|
| 429 |
this.deserializeObjectFormatList(fileInputStream); |
|
| 430 |
|
|
| 431 |
} catch (PropertyNotFoundException pnfe) {
|
|
| 432 |
|
|
| 433 |
logMetacat.error("The object format list file could not be parsed. " +
|
|
| 434 |
"The error message was: " + pnfe.getMessage()); |
|
| 435 |
throw new ServiceException(pnfe.getMessage()); |
|
| 436 |
|
|
| 437 |
} catch ( FileNotFoundException fnfe ) {
|
|
| 438 |
|
|
| 439 |
logMetacat.debug("There was an error reading the file " +
|
|
| 440 |
objectFormatFilePath + ". The error was: " + |
|
| 441 |
fnfe.getMessage()); |
|
| 442 |
throw new ServiceException(fnfe.getMessage()); |
|
| 443 |
|
|
| 444 |
} |
|
| 445 |
|
|
| 446 |
return ObjectFormatService.objectFormatList; |
|
| 447 |
} |
|
| 448 |
|
|
| 449 | 449 |
/** |
| 450 | 450 |
* Deserialize the object format list file to an object format list object |
| 451 | 451 |
* |
| ... | ... | |
| 453 | 453 |
* @return objectFormatList - the ObjectFormatList object from the XML stream |
| 454 | 454 |
* @throws ServiceException |
| 455 | 455 |
*/ |
| 456 |
private ObjectFormatList deserializeObjectFormatList(InputStream inputStream) |
|
| 457 |
throws ServiceException {
|
|
| 458 |
|
|
| 459 |
ObjectFormatList objectFormatList; |
|
| 460 |
try {
|
|
| 461 |
objectFormatList = (ObjectFormatList) |
|
| 462 |
ServiceTypeUtil.deserializeServiceType(ObjectFormatList.class, inputStream); |
|
| 463 |
|
|
| 464 |
} catch ( JiBXException jbxe ) {
|
|
| 465 |
|
|
| 466 |
logMetacat.debug("There was an error deserializing the input stream. " +
|
|
| 467 |
"The error was: " + jbxe.getMessage()); |
|
| 468 |
jbxe.printStackTrace(); |
|
| 469 |
throw new ServiceException(jbxe.getMessage()); |
|
| 470 |
} |
|
| 471 |
|
|
| 472 |
return objectFormatList; |
|
| 473 |
} |
|
| 456 |
//private ObjectFormatList deserializeObjectFormatList(InputStream inputStream)
|
|
| 457 |
// throws ServiceException {
|
|
| 458 |
// |
|
| 459 |
// ObjectFormatList objectFormatList;
|
|
| 460 |
// try {
|
|
| 461 |
// objectFormatList = (ObjectFormatList)
|
|
| 462 |
// ServiceTypeUtil.deserializeServiceType(ObjectFormatList.class, inputStream);
|
|
| 463 |
// |
|
| 464 |
// } catch ( JiBXException jbxe ) {
|
|
| 465 |
// |
|
| 466 |
// logMetacat.debug("There was an error deserializing the input stream. " +
|
|
| 467 |
// "The error was: " + jbxe.getMessage());
|
|
| 468 |
// jbxe.printStackTrace();
|
|
| 469 |
// throw new ServiceException(jbxe.getMessage());
|
|
| 470 |
// }
|
|
| 471 |
// |
|
| 472 |
// return objectFormatList;
|
|
| 473 |
//}
|
|
| 474 | 474 |
|
| 475 | 475 |
} |
| src/edu/ucsb/nceas/metacat/util/MetacatPopulator.java | ||
|---|---|---|
| 48 | 48 |
import edu.ucsb.nceas.metacat.dataone.CrudService; |
| 49 | 49 |
import edu.ucsb.nceas.metacat.properties.PropertyService; |
| 50 | 50 |
import edu.ucsb.nceas.metacat.restservice.InputStreamDataSource; |
| 51 |
import edu.ucsb.nceas.metacat.service.ObjectFormatService; |
|
| 52 | 51 |
|
| 53 | 52 |
import org.dataone.service.exceptions.InvalidSystemMetadata; |
| 54 | 53 |
import org.dataone.service.exceptions.ServiceFailure; |
| ... | ... | |
| 191 | 190 |
SystemMetadata dataDocSysMeta = generateSystemMetadata(doc); |
| 192 | 191 |
//overwrite the bogus values from the last call |
| 193 | 192 |
dataDocSysMeta.setIdentifier(did); |
| 194 |
dataDocSysMeta.setObjectFormat(ObjectFormatService.getFormat(dataDocMimeType));
|
|
| 193 |
dataDocSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType));
|
|
| 195 | 194 |
Checksum checksum = new Checksum(); |
| 196 | 195 |
dataDocIs = stringToStream(dataDocText); |
| 197 | 196 |
ChecksumAlgorithm ca = ChecksumAlgorithm.convert("MD5");
|
| ... | ... | |
| 283 | 282 |
sm.setIdentifier(id); |
| 284 | 283 |
|
| 285 | 284 |
//set the object format |
| 286 |
ObjectFormat format = ObjectFormatService.getFormat(doc.doctype);
|
|
| 285 |
ObjectFormat format = ObjectFormat.convert(doc.doctype);
|
|
| 287 | 286 |
if(format == null) |
| 288 | 287 |
{
|
| 289 | 288 |
if(doc.doctype.trim().equals("BIN"))
|
| 290 | 289 |
{
|
| 291 |
format = ObjectFormatService.getFormat("application/octet-stream");
|
|
| 290 |
format = ObjectFormat.OCTET_STREAM;
|
|
| 292 | 291 |
} |
| 293 | 292 |
else |
| 294 | 293 |
{
|
| 295 |
format = ObjectFormatService.getFormat("text/plain");
|
|
| 294 |
format = ObjectFormat.TEXT_PLAIN;
|
|
| 296 | 295 |
} |
| 297 | 296 |
} |
| 298 | 297 |
sm.setObjectFormat(format); |
| src/edu/ucsb/nceas/metacat/dataone/CrudService.java | ||
|---|---|---|
| 109 | 109 |
import edu.ucsb.nceas.metacat.properties.PropertyService; |
| 110 | 110 |
import edu.ucsb.nceas.metacat.replication.ForceReplicationHandler; |
| 111 | 111 |
import edu.ucsb.nceas.metacat.service.SessionService; |
| 112 |
import edu.ucsb.nceas.metacat.service.ObjectFormatService; |
|
| 113 | 112 |
import edu.ucsb.nceas.metacat.util.DocumentUtil; |
| 114 | 113 |
import edu.ucsb.nceas.metacat.util.SessionData; |
| 115 | 114 |
|
| ... | ... | |
| 2070 | 2069 |
|
| 2071 | 2070 |
//set the default object format |
| 2072 | 2071 |
String doctype = (String) docInfo.get("doctype");
|
| 2073 |
ObjectFormat format = ObjectFormatService.getFormat(doctype);
|
|
| 2072 |
ObjectFormat format = ObjectFormat.convert(doctype);
|
|
| 2074 | 2073 |
if (format == null) {
|
| 2075 | 2074 |
if (doctype.trim().equals("BIN")) {
|
| 2076 |
format = ObjectFormatService.getFormat("application/octet-stream");
|
|
| 2075 |
format = ObjectFormat.OCTET_STREAM;
|
|
| 2077 | 2076 |
} else {
|
| 2078 |
format = ObjectFormatService.getFormat("text/plain");
|
|
| 2077 |
format = ObjectFormat.convert("text/plain");
|
|
| 2079 | 2078 |
} |
| 2080 | 2079 |
} |
| 2081 | 2080 |
sm.setObjectFormat(format); |
| ... | ... | |
| 2083 | 2082 |
|
| 2084 | 2083 |
// further parse EML documents to get data object format, |
| 2085 | 2084 |
// describes and describedBy information |
| 2086 |
if ( format == ObjectFormatService.getFormat("eml://ecoinformatics.org/eml/2.0.0") ||
|
|
| 2087 |
format == ObjectFormatService.getFormat("eml://ecoinformatics.org/eml/2.0.1") ||
|
|
| 2088 |
format == ObjectFormatService.getFormat("eml://ecoinformatics.org/eml/2.1.0") ) {
|
|
| 2085 |
if ( format == ObjectFormat.EML_2_0_0 ||
|
|
| 2086 |
format == ObjectFormat.EML_2_0_1 ||
|
|
| 2087 |
format == ObjectFormat.EML_2_1_0 ) {
|
|
| 2089 | 2088 |
|
| 2090 | 2089 |
try {
|
| 2091 | 2090 |
DataoneEMLParser emlParser = DataoneEMLParser.getInstance(); |
| ... | ... | |
| 2128 | 2127 |
logCrud.debug("Setting describedBy for " + dataDocId.getValue() +
|
| 2129 | 2128 |
" to " + identifier.getValue()); |
| 2130 | 2129 |
dataSysMeta.addDescribedBy(identifier); |
| 2131 |
dataSysMeta.setObjectFormat(ObjectFormatService.getFormat(dataDocMimeType));
|
|
| 2130 |
dataSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType));
|
|
| 2132 | 2131 |
this.updateSystemMetadata(dataSysMeta, getSessionData(token)); |
| 2133 | 2132 |
|
| 2134 | 2133 |
} catch ( NotFound nf ) {
|
| ... | ... | |
| 2141 | 2140 |
dataSysMeta.addDescribedBy(identifier); |
| 2142 | 2141 |
|
| 2143 | 2142 |
logCrud.debug("Setting mimeType for " + dataDocId.getValue() + " to " + dataDocMimeType);
|
| 2144 |
dataSysMeta.setObjectFormat(ObjectFormatService.getFormat(dataDocMimeType));
|
|
| 2143 |
dataSysMeta.setObjectFormat(ObjectFormat.convert(dataDocMimeType));
|
|
| 2145 | 2144 |
|
| 2146 | 2145 |
logCrud.debug("Updating system metadata for " + dataDocId.getValue() + " to " + dataDocMimeType);
|
| 2147 | 2146 |
this.updateSystemMetadata(dataSysMeta, getSessionData(token)); |
| src/edu/ucsb/nceas/metacat/IdentifierManager.java | ||
|---|---|---|
| 43 | 43 |
import edu.ucsb.nceas.metacat.database.DBConnection; |
| 44 | 44 |
import edu.ucsb.nceas.metacat.database.DBConnectionPool; |
| 45 | 45 |
import edu.ucsb.nceas.metacat.properties.PropertyService; |
| 46 |
import edu.ucsb.nceas.metacat.service.ObjectFormatService; |
|
| 47 | 46 |
import edu.ucsb.nceas.metacat.shared.ServiceException; |
| 48 | 47 |
import edu.ucsb.nceas.metacat.util.DocumentUtil; |
| 49 | 48 |
import edu.ucsb.nceas.utilities.PropertyNotFoundException; |
| ... | ... | |
| 1002 | 1001 |
//cs.setAlgorithm(ChecksumAlgorithm.convert(checksumAlgorithm)); |
| 1003 | 1002 |
oi.setChecksum(cs); |
| 1004 | 1003 |
|
| 1005 |
ObjectFormat oFormat = ObjectFormatService.getFormat(format);
|
|
| 1004 |
ObjectFormat oFormat = ObjectFormat.convert(format);
|
|
| 1006 | 1005 |
if(oFormat != null) |
| 1007 | 1006 |
{
|
| 1008 | 1007 |
oi.setObjectFormat(oFormat); |
| 1009 | 1008 |
} |
| 1010 | 1009 |
else |
| 1011 | 1010 |
{ //if there is no object format, just default to text/plain
|
| 1012 |
oi.setObjectFormat(ObjectFormatService.getFormat("application/octet-stream"));
|
|
| 1011 |
oi.setObjectFormat(ObjectFormat.OCTET_STREAM);
|
|
| 1013 | 1012 |
} |
| 1014 | 1013 |
|
| 1015 | 1014 |
oi.setSize(size); |
Also available in: Unified diff
In order to sync up with DataONE 0.6.1 changes, I'm backing out ObjectFormatService changes temporarily in Metacat. Most functionality will be rolled back in using the DataONE 0.6.2 tag, but some methods in ObjectFormatService (such as getListFromDisk()) will be moved into d1_libclient_java.