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Revision 6707

make default formatting a little bit easier to read

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src/edu/ucsb/nceas/metacat/dataone/SystemMetadataFactory.java
72 72

  
73 73
public class SystemMetadataFactory {
74 74

  
75
	private static Logger logMetacat = Logger
76
			.getLogger(SystemMetadataFactory.class);
75
	private static Logger logMetacat = Logger.getLogger(SystemMetadataFactory.class);
77 76

  
78 77
	/**
79 78
	 * Creates a system metadata object for insertion into metacat
......
93 92
			InsufficientKarmaException, ParseLSIDException,
94 93
			PropertyNotFoundException, BaseException, NoSuchAlgorithmException,
95 94
			JiBXException {
95
		
96 96
		logMetacat.debug("MetacatHandler.createSystemMetadata() called.");
97 97
		logMetacat.debug("provided localId: " + localId);
98 98

  
99 99
		// create system metadata for the document
100 100
		SystemMetadata sysMeta = new SystemMetadata();
101 101
		sysMeta.setSerialVersion(BigInteger.valueOf(1));
102
		int rev = IdentifierManager.getInstance().getLatestRevForLocalId(
103
				localId);
102
		int rev = IdentifierManager.getInstance().getLatestRevForLocalId(localId);
104 103
		AccessionNumber accNum = new AccessionNumber(localId, "NONE");
105 104
		String guid = null;
106 105
		try {
107 106
			// get the guid if it exists
108
			guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(),
109
					rev);
107
			guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);
110 108
		} catch (McdbDocNotFoundException dnfe) {
111 109
			// otherwise create the mapping
112
			logMetacat
113
					.debug("There was a problem getting the guid from "
110
			logMetacat.debug("There was a problem getting the guid from "
114 111
							+ "the given localId (docid and revision). The error message was: "
115 112
							+ dnfe.getMessage());
116
			logMetacat.debug("No guid in the identifier table.  adding it for "
117
					+ localId);
113
			logMetacat.debug("No guid in the identifier table.  adding it for " + localId);
118 114
			IdentifierManager.getInstance().createMapping(localId, localId);
119 115
			logMetacat.debug("Mapping created for " + localId);
120 116
			logMetacat.debug("accessionNumber: " + accNum);
121
			guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(),
122
					rev);
117
			guid = IdentifierManager.getInstance().getGUID(accNum.getDocid(), rev);
123 118
		}
124 119
		Identifier identifier = new Identifier();
125 120
		identifier.setValue(guid);
......
164 159
		} // end try()
165 160

  
166 161
		// get additional docinfo
167
		Hashtable<String, Object> docInfo = IdentifierManager.getInstance()
168
				.getDocumentInfo(localId);
162
		Hashtable<String, Object> docInfo = IdentifierManager.getInstance().getDocumentInfo(localId);
169 163
		// set the default object format
170 164
		String doctype = (String) docInfo.get("doctype");
171 165
		ObjectFormatIdentifier fmtid = null;
172 166

  
173 167
		// set the object format, fall back to defaults
174 168
		try {
175
			fmtid = ObjectFormatCache.getInstance().getFormat(doctype)
176
					.getFormatId();
177

  
169
			fmtid = ObjectFormatCache.getInstance().getFormat(doctype).getFormatId();
178 170
		} catch (NotFound nfe) {
179 171

  
180 172
			try {
......
189 181
				}
190 182

  
191 183
			} catch (NotFound nf) {
192
				logMetacat
193
						.error("There was a problem getting the default format "
184
				logMetacat.error("There was a problem getting the default format "
194 185
								+ "from the ObjectFormatCache: "
195 186
								+ nf.getMessage());
196 187
				throw nf;
......
199 190
		}
200 191

  
201 192
		sysMeta.setFormatId(fmtid);
202
		logMetacat.debug("The ObjectFormat for " + localId + " is "
203
				+ fmtid.getValue());
193
		logMetacat.debug("The ObjectFormat for " + localId + " is " + fmtid.getValue());
204 194

  
205 195
		// further parse EML documents to get data object format,
206 196
		// describes and describedBy information
......
215 205

  
216 206
			try {
217 207

  
218
				DatabaseConnectionPoolInterface connectionPool = MetacatDatabaseConnectionPoolFactory
219
						.getDatabaseConnectionPoolInterface();
220
				DataManager dataManager = DataManager.getInstance(
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						connectionPool, connectionPool.getDBAdapterName());
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				DataPackage dataPackage = dataManager
223
						.parseMetadata(inputStream);
208
				DatabaseConnectionPoolInterface connectionPool = 
209
					MetacatDatabaseConnectionPoolFactory.getDatabaseConnectionPoolInterface();
210
				DataManager dataManager = 
211
					DataManager.getInstance(connectionPool, connectionPool.getDBAdapterName());
212
				DataPackage dataPackage = dataManager.parseMetadata(inputStream);
224 213

  
225 214
				// iterate through the data objects in the EML doc and add
226 215
				// sysmeta
227
				logMetacat
228
						.debug("In createSystemMetadata() the number of data "
216
				logMetacat.debug("In createSystemMetadata() the number of data "
229 217
								+ "entities is: "
230 218
								+ dataPackage.getEntityNumber());
231 219

  
......
233 221
				for (int j = 0; j < dataPackage.getEntityList().length; j++) {
234 222

  
235 223
					String dataDocUrl = dataPackage.getEntityList()[j].getURL();
236
					String dataDocMimeType = dataPackage.getEntityList()[j]
237
							.getDataFormat();
224
					String dataDocMimeType = dataPackage.getEntityList()[j].getDataFormat();
238 225
					// default to binary
239 226
					if (dataDocMimeType == null) {
240 227
						dataDocMimeType = ObjectFormatCache.getInstance()
......
254 241
								+ ecogridPrefix.length());
255 242

  
256 243
						// look up the guid for the data
257
						String dataDocid = DocumentUtil
258
								.getSmartDocId(dataDocLocalId);
259
						int dataRev = DocumentUtil
260
								.getRevisionFromAccessionNumber(dataDocLocalId);
244
						String dataDocid = DocumentUtil.getSmartDocId(dataDocLocalId);
245
						int dataRev = DocumentUtil.getRevisionFromAccessionNumber(dataDocLocalId);
261 246

  
262 247
						SystemMetadata dataSysMeta = null;
263 248
						// check if data system metadata exists
264 249
						String dataGuidString = null;
265 250
						try {
266
							dataGuidString = IdentifierManager.getInstance()
267
									.getGUID(dataDocid, dataRev);
268
							dataSysMeta = IdentifierManager.getInstance()
269
									.getSystemMetadata(dataGuidString);
251
							dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
252
							dataSysMeta = IdentifierManager.getInstance().getSystemMetadata(dataGuidString);
270 253
						} catch (McdbDocNotFoundException nf) {
271 254
							// System metadata for data doesn't exist yet, so
272 255
							// create it
273
							logMetacat
274
									.debug("There was not an existing system metadata "
256
							logMetacat.debug("There was not an existing system metadata "
275 257
											+ "document for " + dataDocLocalId);
276 258
							try {
277 259
								logMetacat.debug("Creating a system metadata "
......
279 261
								dataSysMeta = createSystemMetadata(dataDocLocalId);
280 262

  
281 263
								// now look it up again
282
								dataGuidString = IdentifierManager
283
										.getInstance().getGUID(dataDocid,
284
												dataRev);
264
								dataGuidString = IdentifierManager.getInstance().getGUID(dataDocid, dataRev);
285 265

  
286 266
								// set the guid
287 267
								Identifier dataGuid = new Identifier();
288 268
								dataGuid.setValue(dataGuidString);
289 269

  
290 270
								// set object format
291
								logMetacat
292
										.debug("Updating system metadata for "
271
								logMetacat.debug("Updating system metadata for "
293 272
												+ dataGuid.getValue() + " to "
294 273
												+ dataDocMimeType);
295 274
								try {
296
									ObjectFormatIdentifier fmt = ObjectFormatCache
297
											.getInstance().getFormat(
298
													dataDocMimeType)
299
											.getFormatId();
275
									ObjectFormatIdentifier fmt = 
276
										ObjectFormatCache.getInstance().getFormat(dataDocMimeType).getFormatId();
300 277
									dataSysMeta.setFormatId(fmt);
301

  
302 278
								} catch (NotFound nfe) {
303
									logMetacat
304
											.debug("Couldn't find format identifier for: "
279
									logMetacat.debug("Couldn't find format identifier for: "
305 280
													+ dataDocMimeType
306 281
													+ ". Setting it to application/octet-stream.");
307 282
									ObjectFormatIdentifier newFmtid = new ObjectFormatIdentifier();
308
									newFmtid
309
											.setValue("application/octet-stream");
310

  
283
									newFmtid.setValue("application/octet-stream");
311 284
								}
312 285

  
313 286
								// update the values
314
								HazelcastService.getInstance()
315
										.getSystemMetadataMap().put(
316
												dataSysMeta.getIdentifier(),
317
												dataSysMeta);
287
								HazelcastService.getInstance().getSystemMetadataMap().put(dataSysMeta.getIdentifier(), dataSysMeta);
318 288

  
319 289
							} catch (McdbDocNotFoundException mdnf) {
320 290
								mdnf.printStackTrace();
......
348 318
				} // end for()
349 319

  
350 320
			} catch (ParserConfigurationException pce) {
351
				logMetacat
352
						.debug("There was a problem parsing the EML document. "
321
				logMetacat.debug("There was a problem parsing the EML document. "
353 322
								+ "The error message was: " + pce.getMessage());
354 323

  
355 324
			} catch (SAXException saxe) {
356
				logMetacat
357
						.debug("There was a problem traversing the EML document. "
325
				logMetacat.debug("There was a problem traversing the EML document. "
358 326
								+ "The error message was: " + saxe.getMessage());
359 327

  
360 328
			} catch (XPathExpressionException xpee) {
361
				logMetacat
362
						.debug("There was a problem searching the EML document. "
329
				logMetacat.debug("There was a problem searching the EML document. "
363 330
								+ "The error message was: " + xpee.getMessage());
364 331
			} catch (Exception e) {
365
				logMetacat
366
						.debug("There was a problem creating System Metadata. "
332
				logMetacat.debug("There was a problem creating System Metadata. "
367 333
								+ "The error message was: " + e.getMessage());
368 334
			} // end try()
369 335

  
......
390 356
			SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-DD");
391 357
			dateFormat.setTimeZone(TimeZone.getDefault());
392 358

  
393
			Date dateCreated = dateFormat.parse((String) docInfo
394
					.get("date_created"));
359
			Date dateCreated = dateFormat.parse((String) docInfo.get("date_created"));
395 360
			sysMeta.setDateUploaded(dateCreated);
396
			Date dateUpdated = dateFormat.parse((String) docInfo
397
					.get("date_updated"));
361
			Date dateUpdated = dateFormat.parse((String) docInfo.get("date_updated"));
398 362
			sysMeta.setDateSysMetadataModified(dateUpdated);
399 363

  
400 364
		} catch (ParseException pe) {
......
414 378
		return sysMeta;
415 379
	}
416 380

  
417
	/*
381
	/**
418 382
	 * Find the size (in bytes) of a stream. Note: This needs to refactored out
419 383
	 * of MetacatHandler and into a utility when stream i/o in Metacat is
420 384
	 * evaluated.

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