1
|
/**
|
2
|
* Copyright (C) 2007 EDIT
|
3
|
* European Distributed Institute of Taxonomy
|
4
|
* http://www.e-taxonomy.eu
|
5
|
*
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
8
|
*/
|
9
|
|
10
|
package eu.etaxonomy.cdm.app.cyprus;
|
11
|
|
12
|
import java.io.File;
|
13
|
import java.io.IOException;
|
14
|
import java.net.MalformedURLException;
|
15
|
import java.net.URI;
|
16
|
import java.net.URISyntaxException;
|
17
|
import java.util.ArrayList;
|
18
|
import java.util.HashMap;
|
19
|
import java.util.HashSet;
|
20
|
import java.util.Iterator;
|
21
|
import java.util.List;
|
22
|
import java.util.Map;
|
23
|
import java.util.Set;
|
24
|
import java.util.regex.Matcher;
|
25
|
import java.util.regex.Pattern;
|
26
|
|
27
|
import org.apache.log4j.Logger;
|
28
|
import org.apache.sanselan.ImageReadException;
|
29
|
import org.apache.sanselan.Sanselan;
|
30
|
import org.apache.sanselan.common.IImageMetadata;
|
31
|
import org.apache.sanselan.common.ImageMetadata.Item;
|
32
|
import org.joda.time.DateTime;
|
33
|
import org.joda.time.format.DateTimeFormat;
|
34
|
import org.joda.time.format.DateTimeFormatter;
|
35
|
import org.springframework.transaction.TransactionStatus;
|
36
|
|
37
|
import eu.etaxonomy.cdm.api.application.CdmApplicationController;
|
38
|
import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
|
39
|
import eu.etaxonomy.cdm.app.common.CdmDestinations;
|
40
|
import eu.etaxonomy.cdm.common.UTF8;
|
41
|
import eu.etaxonomy.cdm.common.media.ImageInfo;
|
42
|
import eu.etaxonomy.cdm.database.DbSchemaValidation;
|
43
|
import eu.etaxonomy.cdm.database.ICdmDataSource;
|
44
|
import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
|
45
|
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;
|
46
|
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
|
47
|
import eu.etaxonomy.cdm.model.agent.AgentBase;
|
48
|
import eu.etaxonomy.cdm.model.agent.Institution;
|
49
|
import eu.etaxonomy.cdm.model.agent.Person;
|
50
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
51
|
import eu.etaxonomy.cdm.model.common.Language;
|
52
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
53
|
import eu.etaxonomy.cdm.model.description.Feature;
|
54
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
55
|
import eu.etaxonomy.cdm.model.description.TextData;
|
56
|
import eu.etaxonomy.cdm.model.media.ImageFile;
|
57
|
import eu.etaxonomy.cdm.model.media.Media;
|
58
|
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
|
59
|
import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
|
60
|
import eu.etaxonomy.cdm.model.media.Rights;
|
61
|
import eu.etaxonomy.cdm.model.media.RightsType;
|
62
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
63
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
64
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
65
|
|
66
|
/**
|
67
|
* @author a.mueller
|
68
|
* @created 16.12.2010
|
69
|
*/
|
70
|
public class CyprusImagesActivator {
|
71
|
private static final Logger logger = Logger.getLogger(CyprusImagesActivator.class);
|
72
|
|
73
|
//database validation status (create, update, validate ...)
|
74
|
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
75
|
|
76
|
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();
|
77
|
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
|
78
|
|
79
|
boolean testOnly = false;
|
80
|
|
81
|
private static final String path = "//media/digitalimages/EditWP6/Zypern/photos/";
|
82
|
private static final String urlPath = "http://media.bgbm.org/erez/erez?src=EditWP6/zypern/photos/";
|
83
|
|
84
|
private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper;
|
85
|
|
86
|
|
87
|
private void doImport(ICdmDataSource cdmDestination){
|
88
|
|
89
|
CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, hbm2dll);
|
90
|
TransactionStatus tx = app.startTransaction();
|
91
|
|
92
|
deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(app);
|
93
|
|
94
|
File file = new File(path);
|
95
|
String[] fileList = file.list();
|
96
|
Set<String> notFound = new HashSet<>();
|
97
|
|
98
|
String regEx = "([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(?:jpg|JPG)";
|
99
|
Pattern pattern = Pattern.compile(regEx);
|
100
|
|
101
|
for (String fileName : fileList){
|
102
|
Matcher matcher = pattern.matcher(fileName);
|
103
|
if (matcher.matches()){
|
104
|
// System.out.println(fileName);
|
105
|
String taxonName = matcher.group(1);
|
106
|
taxonName = taxonName.replace("_s_", " subsp. ").replace("_", " ");
|
107
|
Taxon taxon = getAcceptedTaxon(app, taxonName);
|
108
|
if (taxon == null){
|
109
|
if (!notFound.contains(taxonName)){
|
110
|
notFound.add(taxonName);
|
111
|
logger.warn("Taxon not found: " + taxonName);
|
112
|
}
|
113
|
}else{
|
114
|
handleTaxon(app, taxon, fileName);
|
115
|
}
|
116
|
}else{
|
117
|
if (!fileName.matches("(?:\\.erez|Thumbs\\.db.*|zypern_.*|__Keywords_template\\.txt)")){
|
118
|
logger.warn("Incorrect filename:" + fileName);
|
119
|
}
|
120
|
}
|
121
|
}
|
122
|
|
123
|
// app.getTaxonService().saveOrUpdate(taxaToSave);
|
124
|
|
125
|
if (testOnly){
|
126
|
tx.setRollbackOnly();
|
127
|
}
|
128
|
app.commitTransaction(tx);
|
129
|
}
|
130
|
|
131
|
/**
|
132
|
* @param app
|
133
|
* @param taxon
|
134
|
* @param fileName
|
135
|
*/
|
136
|
private void handleTaxon(CdmApplicationController app, Taxon taxon, String fileName) {
|
137
|
Set<String> urlStr = getAllExistingUrls(taxon);
|
138
|
String fullName = urlPath + fileName;
|
139
|
if (urlStr.contains(fullName)){
|
140
|
return;
|
141
|
}else{
|
142
|
addMedia(app, taxon, fileName);
|
143
|
}
|
144
|
}
|
145
|
|
146
|
/**
|
147
|
* @param app
|
148
|
* @param taxon
|
149
|
* @param fileName
|
150
|
*/
|
151
|
private void addMedia(CdmApplicationController app, Taxon taxon, String fileName) {
|
152
|
try {
|
153
|
String fullName = urlPath + fileName;
|
154
|
Media media = getImageMedia(fullName, null, true);
|
155
|
makeMetaData(media, fileName);
|
156
|
String title = fileName.replace("_s_"," subsp. ")
|
157
|
.replace("_"," ").replace(".jpg","").replace(".JPG","");
|
158
|
media.putTitle(Language.LATIN(), title);
|
159
|
if (!testOnly){
|
160
|
makeTextData(fileName, media, taxon);
|
161
|
}
|
162
|
|
163
|
} catch (Exception e) {
|
164
|
e.printStackTrace();
|
165
|
return;
|
166
|
}
|
167
|
}
|
168
|
|
169
|
/**
|
170
|
* @param media
|
171
|
*/
|
172
|
private void makeMetaData(Media media, String fileName) {
|
173
|
//image metadata
|
174
|
|
175
|
Map<String, String> keywords = new HashMap<>();
|
176
|
File file = new File(path + fileName);
|
177
|
String copyright = null;
|
178
|
String artistStr = null;
|
179
|
try{
|
180
|
IImageMetadata metadata = Sanselan.getMetadata(file);
|
181
|
ArrayList<?> items = metadata.getItems();
|
182
|
for (Object object : items){
|
183
|
Item item = (Item) object;
|
184
|
// System.out.println(item.getKeyword() + ": " + item.getText());
|
185
|
String keyword = item.getKeyword().toLowerCase();
|
186
|
String value =removeQuots(item.getText());
|
187
|
|
188
|
if("keywords".equals(keyword)){
|
189
|
String[] splits = value.split(":");
|
190
|
if (splits.length == 2){
|
191
|
keywords.put(splits[0].trim().toLowerCase(), splits[1].trim());
|
192
|
}else{
|
193
|
logger.warn("Keyword has not correct format and can not be parsed: " + value + " for file " + fileName);
|
194
|
}
|
195
|
}else if ("Copyright Notice".equalsIgnoreCase(keyword)){
|
196
|
copyright = value;
|
197
|
}else if ("artist".equals(keyword)){
|
198
|
artistStr = value;
|
199
|
}else if ("date time original".equalsIgnoreCase(item.getKeyword())){
|
200
|
DateTimeFormatter f = DateTimeFormat.forPattern("yyyy:MM:dd HH:mm:ss");
|
201
|
DateTime created;
|
202
|
try {
|
203
|
created = f/*.withZone(DateTimeZone.forID("Europe/Athens"))*/.parseDateTime(value);
|
204
|
media.setMediaCreated(created);
|
205
|
} catch (Exception e) {
|
206
|
logger.warn("Exception (" + e.getMessage() + ") when parsing create date " + value + " for file " + fileName);
|
207
|
}
|
208
|
}
|
209
|
}
|
210
|
} catch (ImageReadException | IOException e1) {
|
211
|
logger.warn(" Problem (" + e1.getMessage() + ") when reading metadata from file: " + fileName);
|
212
|
}
|
213
|
if (keywords.get("photographer") != null){
|
214
|
String artist = keywords.get("photographer");
|
215
|
Person person = makePerson(artist, fileName);
|
216
|
media.setArtist(person);
|
217
|
}
|
218
|
if (artistStr != null){
|
219
|
if (keywords.get("photographer") == null){
|
220
|
Person person = makePerson(artistStr, fileName);
|
221
|
media.setArtist(person);
|
222
|
}else if (!keywords.get("photographer").toLowerCase().replace(" ", "")
|
223
|
.contains(artistStr.toLowerCase().replace(" ", ""))){
|
224
|
logger.warn("Artist '" + artistStr + "' could not be handled for " + fileName);
|
225
|
}
|
226
|
}
|
227
|
if (keywords.get("locality") != null){
|
228
|
String locality = keywords.get("locality");
|
229
|
media.putDescription(Language.ENGLISH(), locality);
|
230
|
}
|
231
|
if (copyright != null){
|
232
|
if (rightsMap.get(copyright)!= null){
|
233
|
media.addRights(rightsMap.get(copyright));
|
234
|
}else{
|
235
|
AgentBase<?> agent;
|
236
|
if (copyright.equals("Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM)")){
|
237
|
agent = Institution.NewNamedInstance(copyright);
|
238
|
}else{
|
239
|
agent = makePerson(copyright, fileName);
|
240
|
}
|
241
|
Rights r = Rights.NewInstance(null, null, RightsType.COPYRIGHT());
|
242
|
r.setAgent(agent);
|
243
|
media.addRights(r);
|
244
|
rightsMap.put(copyright, r);
|
245
|
}
|
246
|
}
|
247
|
}
|
248
|
|
249
|
private static Map<String, Rights> rightsMap = new HashMap<>();
|
250
|
|
251
|
/**
|
252
|
* @param artist
|
253
|
* @return
|
254
|
*/
|
255
|
private Person makePerson(String artist, String fileName) {
|
256
|
artist = artist.trim();
|
257
|
String regEx = "((?:[A-Z]\\. ?)+)([A-Z][a-z\\-\u00E4\u00F6\u00FC]+)";
|
258
|
Matcher matcher = Pattern.compile(regEx).matcher(artist);
|
259
|
Person person = Person.NewInstance();
|
260
|
if (matcher.matches()){
|
261
|
person.setFirstname(matcher.group(1).trim());
|
262
|
person.setLastname(matcher.group(2).trim());
|
263
|
}else{
|
264
|
person.setTitleCache(artist, true);
|
265
|
logger.warn("Person could not be parsed: " + artist + " for file " + fileName);
|
266
|
}
|
267
|
|
268
|
person = (Person)deduplicationHelper.getExistingAuthor(null, person);
|
269
|
return person;
|
270
|
}
|
271
|
|
272
|
private String removeQuots(String text) {
|
273
|
if (text.startsWith("'") && text.endsWith("'")){
|
274
|
return text.substring(1, text.length() -1);
|
275
|
}else{
|
276
|
return text;
|
277
|
}
|
278
|
}
|
279
|
|
280
|
private void makeTextData(String fileStr, Media media, Taxon taxon) {
|
281
|
TaxonDescription imageGallery = taxon.getImageGallery(true);
|
282
|
TextData textData = null;
|
283
|
if (!imageGallery.getElements().isEmpty()){
|
284
|
DescriptionElementBase el = imageGallery.getElements().iterator().next();
|
285
|
if (el.isInstanceOf(TextData.class)){
|
286
|
textData = CdmBase.deproxy(el, TextData.class);
|
287
|
}else{
|
288
|
logger.warn("Image gallery had non-textdata description elmenet: " + fileStr);
|
289
|
}
|
290
|
}
|
291
|
if (textData == null){
|
292
|
textData = TextData.NewInstance();
|
293
|
textData.setFeature(Feature.IMAGE());
|
294
|
}
|
295
|
imageGallery.addElement(textData);
|
296
|
textData.addMedia(media);
|
297
|
}
|
298
|
|
299
|
/**
|
300
|
* Creates
|
301
|
* @param uriString
|
302
|
* @param readDataFromUrl
|
303
|
* @see #READ_MEDIA_DATA
|
304
|
* @return
|
305
|
* @throws MalformedURLException
|
306
|
*/
|
307
|
protected Media getImageMedia(String uriString, String uriStrThumb, boolean readMediaData) throws MalformedURLException {
|
308
|
if( uriString == null){
|
309
|
return null;
|
310
|
} else {
|
311
|
uriString = uriString.replace(" ", "%20"); //replace whitespace
|
312
|
try {
|
313
|
ImageInfo imageInfo = null;
|
314
|
URI uri = new URI(uriString);
|
315
|
|
316
|
try {
|
317
|
if (readMediaData){
|
318
|
logger.info("Read media data from: " + uri);
|
319
|
imageInfo = ImageInfo.NewInstance(uri, 0);
|
320
|
}
|
321
|
} catch (Exception e) {
|
322
|
String message = "An error occurred when trying to read image meta data for " + uri.toString() + ": " + e.getMessage();
|
323
|
logger.warn(message);
|
324
|
}
|
325
|
ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInfo);
|
326
|
|
327
|
MediaRepresentation representation = MediaRepresentation.NewInstance();
|
328
|
|
329
|
if(imageInfo != null){
|
330
|
representation.setMimeType(imageInfo.getMimeType());
|
331
|
representation.setSuffix(imageInfo.getSuffix());
|
332
|
}
|
333
|
representation.addRepresentationPart(imageFile);
|
334
|
Media media = Media.NewInstance();
|
335
|
media.addRepresentation(representation);
|
336
|
|
337
|
if (uriStrThumb != null){
|
338
|
ImageInfo imageInfoThumb = null;
|
339
|
uriStrThumb = uriStrThumb.replace(" ", "%20"); //replace whitespace
|
340
|
URI uriThumb = new URI(uriStrThumb);
|
341
|
try {
|
342
|
if (readMediaData){
|
343
|
logger.info("Read media data from: " + uriThumb);
|
344
|
imageInfoThumb = ImageInfo.NewInstance(uriThumb, 0);
|
345
|
}
|
346
|
} catch (Exception e) {
|
347
|
String message = "An error occurred when trying to read image meta data for " + uriThumb.toString() + ": " + e.getMessage();
|
348
|
logger.warn(message);
|
349
|
}
|
350
|
|
351
|
ImageFile imageFileFhumb = ImageFile.NewInstance(uriThumb, null, imageInfoThumb);
|
352
|
MediaRepresentation reprThumb = MediaRepresentation.NewInstance();
|
353
|
if(imageInfoThumb != null){
|
354
|
reprThumb.setMimeType(imageInfoThumb.getMimeType());
|
355
|
reprThumb.setSuffix(imageInfoThumb.getSuffix());
|
356
|
}
|
357
|
reprThumb.addRepresentationPart(imageFileFhumb);
|
358
|
media.addRepresentation(reprThumb);
|
359
|
}
|
360
|
|
361
|
return media;
|
362
|
} catch (URISyntaxException e1) {
|
363
|
String message = "An URISyntaxException occurred when trying to create uri from multimedia objcet string: " + uriString;
|
364
|
logger.warn(message);
|
365
|
return null;
|
366
|
}
|
367
|
}
|
368
|
}
|
369
|
|
370
|
/**
|
371
|
* @param taxon
|
372
|
* @return
|
373
|
*/
|
374
|
private Set<String> getAllExistingUrls(Taxon taxon) {
|
375
|
Set<String> result = new HashSet<>();
|
376
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
377
|
for (TaxonDescription td : descriptions){
|
378
|
if (td.isImageGallery()){
|
379
|
for (DescriptionElementBase deb : td.getElements()){
|
380
|
if (deb.isInstanceOf(TextData.class)){
|
381
|
TextData textData = CdmBase.deproxy(deb, TextData.class);
|
382
|
for (Media media :textData.getMedia()){
|
383
|
for (MediaRepresentation rep : media.getRepresentations()){
|
384
|
for (MediaRepresentationPart part : rep.getParts()){
|
385
|
URI uri = part.getUri();
|
386
|
if (uri != null){
|
387
|
String uriStr = uri.toString();
|
388
|
result.add(uriStr);
|
389
|
}
|
390
|
}
|
391
|
}
|
392
|
}
|
393
|
|
394
|
}
|
395
|
}
|
396
|
}
|
397
|
}
|
398
|
return result;
|
399
|
}
|
400
|
|
401
|
private Taxon getAcceptedTaxon(CdmApplicationController app, String taxonNameStr) {
|
402
|
|
403
|
MatchingTaxonConfigurator config = new MatchingTaxonConfigurator();
|
404
|
taxonNameStr = adaptName(taxonNameStr);
|
405
|
config.setTaxonNameTitle(taxonNameStr);
|
406
|
config.setIncludeSynonyms(false);
|
407
|
List<TaxonBase> list = app.getTaxonService().findTaxaByName(config);
|
408
|
if (list.isEmpty()){
|
409
|
// logger.warn("Taxon not found for media: " + taxonNameStr);
|
410
|
taxonNameStr = taxonNameStr.replaceFirst(" ", UTF8.HYBRID.toString() + " ");
|
411
|
list = app.getTaxonService().findTaxaByName(config);
|
412
|
if (list.isEmpty()){
|
413
|
return null;
|
414
|
}else if (list.size() > 1){
|
415
|
logger.warn("After searching for hybrids more than 1 taxon was foung: " + taxonNameStr);
|
416
|
}
|
417
|
}
|
418
|
if (list.size()>1){
|
419
|
Iterator<TaxonBase> it = list.iterator();
|
420
|
while (it.hasNext()){
|
421
|
Taxon next = (Taxon)it.next();
|
422
|
if (next.getTaxonNodes().isEmpty() && !next.getTaxonForMisappliedName().isEmpty()){
|
423
|
it.remove();
|
424
|
}
|
425
|
}
|
426
|
if (list.size()>1){
|
427
|
logger.warn("More than 1 taxon found for media: " + taxonNameStr + " . Will now try to use only taxon with taxon node.");
|
428
|
it = list.iterator();
|
429
|
while (it.hasNext()){
|
430
|
Taxon next = (Taxon)it.next();
|
431
|
if (next.getTaxonNodes().isEmpty()){
|
432
|
it.remove();
|
433
|
}
|
434
|
}
|
435
|
if (list.size()>1){
|
436
|
logger.warn("Still more than 1 taxon found for media: " + taxonNameStr);
|
437
|
}else if (list.size() < 1){
|
438
|
logger.warn("After removing nodeless taxa no taxon was left: " + taxonNameStr);
|
439
|
return null;
|
440
|
}
|
441
|
}else if (list.size() < 1){
|
442
|
logger.warn("After removing misapplications no taxon was left: " + taxonNameStr);
|
443
|
return null;
|
444
|
}
|
445
|
}
|
446
|
TaxonBase<?> taxonBase = list.get(0);
|
447
|
Taxon result;
|
448
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
449
|
result = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
|
450
|
}else{
|
451
|
result = CdmBase.deproxy(taxonBase, Taxon.class);
|
452
|
}
|
453
|
return result;
|
454
|
}
|
455
|
|
456
|
/**
|
457
|
* @param taxonNameStr
|
458
|
* @return
|
459
|
*/
|
460
|
private String adaptName(String taxonNameStr) {
|
461
|
// if (taxonNameStr.equals("Hypericum cerastoides")){
|
462
|
// taxonNameStr = "Hypericum cerastioides";
|
463
|
// }
|
464
|
return taxonNameStr;
|
465
|
}
|
466
|
|
467
|
public void test(){
|
468
|
File f = new File(path);
|
469
|
String[] list = f.list();
|
470
|
List<String> fullFileNames = new ArrayList<>();
|
471
|
for (String fileName : list){
|
472
|
fullFileNames.add(path + fileName);
|
473
|
if (! fileName.matches("([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(jpg|JPG)")){
|
474
|
System.out.println(fileName);
|
475
|
}
|
476
|
}
|
477
|
}
|
478
|
|
479
|
/**
|
480
|
* @param args
|
481
|
*/
|
482
|
public static void main(String[] args) {
|
483
|
CyprusImagesActivator me = new CyprusImagesActivator();
|
484
|
me.doImport(cdmDestination);
|
485
|
// me.test();
|
486
|
System.exit(0);
|
487
|
}
|
488
|
|
489
|
}
|