|
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.io.berlinModel.in;
|
|
11
|
|
|
12
|
import java.io.IOException;
|
|
13
|
import java.net.URI;
|
|
14
|
import java.net.URISyntaxException;
|
|
15
|
import java.sql.ResultSet;
|
|
16
|
import java.sql.SQLException;
|
|
17
|
import java.util.HashMap;
|
|
18
|
import java.util.HashSet;
|
|
19
|
import java.util.List;
|
|
20
|
import java.util.Map;
|
|
21
|
import java.util.Set;
|
|
22
|
import java.util.UUID;
|
|
23
|
|
|
24
|
import javax.validation.constraints.NotNull;
|
|
25
|
|
|
26
|
import org.apache.commons.lang.StringUtils;
|
|
27
|
import org.apache.http.HttpException;
|
|
28
|
import org.apache.log4j.Logger;
|
|
29
|
import org.springframework.stereotype.Component;
|
|
30
|
|
|
31
|
import au.com.bytecode.opencsv.CSVReader;
|
|
32
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
|
33
|
import eu.etaxonomy.cdm.common.UTF8;
|
|
34
|
import eu.etaxonomy.cdm.common.media.ImageInfo;
|
|
35
|
import eu.etaxonomy.cdm.database.update.DatabaseTypeNotSupportedException;
|
|
36
|
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
|
|
37
|
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelFactsImportValidator;
|
|
38
|
import eu.etaxonomy.cdm.io.common.IOValidator;
|
|
39
|
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
|
|
40
|
import eu.etaxonomy.cdm.io.common.Source;
|
|
41
|
import eu.etaxonomy.cdm.model.agent.AgentBase;
|
|
42
|
import eu.etaxonomy.cdm.model.agent.Person;
|
|
43
|
import eu.etaxonomy.cdm.model.agent.Team;
|
|
44
|
import eu.etaxonomy.cdm.model.common.Annotation;
|
|
45
|
import eu.etaxonomy.cdm.model.common.AnnotationType;
|
|
46
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
47
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
48
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
49
|
import eu.etaxonomy.cdm.model.common.LanguageString;
|
|
50
|
import eu.etaxonomy.cdm.model.common.Marker;
|
|
51
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
|
52
|
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
|
|
53
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
|
54
|
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
|
|
55
|
import eu.etaxonomy.cdm.model.description.Distribution;
|
|
56
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
57
|
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
|
|
58
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
59
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
60
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
61
|
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
|
|
62
|
import eu.etaxonomy.cdm.model.location.NamedAreaType;
|
|
63
|
import eu.etaxonomy.cdm.model.media.ImageFile;
|
|
64
|
import eu.etaxonomy.cdm.model.media.Media;
|
|
65
|
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
|
|
66
|
import eu.etaxonomy.cdm.model.media.Rights;
|
|
67
|
import eu.etaxonomy.cdm.model.media.RightsType;
|
|
68
|
import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
|
|
69
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
70
|
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
|
71
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
72
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
73
|
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
74
|
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
75
|
import eu.etaxonomy.cdm.model.term.Representation;
|
|
76
|
import eu.etaxonomy.cdm.model.term.TermBase;
|
|
77
|
import eu.etaxonomy.cdm.model.term.TermType;
|
|
78
|
import eu.etaxonomy.cdm.model.term.TermVocabulary;
|
|
79
|
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
|
|
80
|
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
|
|
81
|
|
|
82
|
/**
|
|
83
|
* @author a.mueller
|
|
84
|
* @since 20.03.2008
|
|
85
|
*/
|
|
86
|
@Component
|
|
87
|
public class BerlinModelFactsImport extends BerlinModelImportBase {
|
|
88
|
private static final long serialVersionUID = 4095154818163504795L;
|
|
89
|
|
|
90
|
private static final Logger logger = Logger.getLogger(BerlinModelFactsImport.class);
|
|
91
|
|
|
92
|
public static final String NAMESPACE = "Fact";
|
|
93
|
|
|
94
|
public static final String SEQUENCE_PREFIX = "ORDER: ";
|
|
95
|
|
|
96
|
private int modCount = 10000;
|
|
97
|
private static final String pluralString = "facts";
|
|
98
|
private static final String dbTableName = "Fact";
|
|
99
|
|
|
100
|
//FIXME don't use as class variable
|
|
101
|
private Map<Integer, Feature> featureMap;
|
|
102
|
|
|
103
|
public BerlinModelFactsImport(){
|
|
104
|
super(dbTableName, pluralString);
|
|
105
|
}
|
|
106
|
|
|
107
|
|
|
108
|
private TermVocabulary<Feature> getFeatureVocabulary(){
|
|
109
|
TermVocabulary<Feature> newVoc = TermVocabulary.NewInstance(TermType.Feature, "Berlin Model Import Feature Vocabulary", "Berlin Model Import Feature Vocabulary", null, null);
|
|
110
|
getVocabularyService().save(newVoc);
|
|
111
|
|
|
112
|
return newVoc;
|
|
113
|
}
|
|
114
|
|
|
115
|
private Map<Integer, Feature> invokeFactCategories(BerlinModelImportState state){
|
|
116
|
|
|
117
|
Map<Integer, Feature> result = state.getConfig().getFeatureMap();
|
|
118
|
Source source = state.getConfig().getSource();
|
|
119
|
boolean createFeatureTree = state.getConfig().isSalvador(); //for some reason feature tree creation does not work for salavdor
|
|
120
|
|
|
121
|
FeatureTree featureTree = (!createFeatureTree) ? null : FeatureTree.NewInstance(state.getConfig().getFeatureTreeUuid());
|
|
122
|
if (featureTree!= null && createFeatureTree){
|
|
123
|
featureTree.setTitleCache(state.getConfig().getFeatureTreeTitle(), true);
|
|
124
|
}
|
|
125
|
|
|
126
|
try {
|
|
127
|
//get data from database
|
|
128
|
String strQuery =
|
|
129
|
" SELECT FactCategory.* " +
|
|
130
|
" FROM FactCategory "+
|
|
131
|
" WHERE (1=1)";
|
|
132
|
if (state.getConfig().isSalvador()){
|
|
133
|
strQuery += " AND " + state.getConfig().getFactFilter().replace("factCategoryFk", "factCategoryId");
|
|
134
|
}
|
|
135
|
|
|
136
|
ResultSet rs = source.getResultSet(strQuery) ;
|
|
137
|
|
|
138
|
TermVocabulary<Feature> featureVocabulary = getFeatureVocabulary();
|
|
139
|
int i = 0;
|
|
140
|
//for each reference
|
|
141
|
while (rs.next()){
|
|
142
|
|
|
143
|
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("FactCategories handled: " + (i-1));}
|
|
144
|
|
|
145
|
int factCategoryId = rs.getInt("factCategoryId");
|
|
146
|
String factCategory = rs.getString("factCategory");
|
|
147
|
|
|
148
|
Feature feature;
|
|
149
|
try {
|
|
150
|
feature = BerlinModelTransformer.factCategory2Feature(factCategoryId);
|
|
151
|
} catch (UnknownCdmTypeException e) {
|
|
152
|
UUID featureUuid = null;
|
|
153
|
featureUuid = BerlinModelTransformer.getFeatureUuid(String.valueOf(factCategoryId+"-"+factCategory));
|
|
154
|
if (featureUuid == null){
|
|
155
|
logger.warn("New Feature (FactCategoryId: " + factCategoryId + ")");
|
|
156
|
featureUuid = UUID.randomUUID();
|
|
157
|
}
|
|
158
|
feature = getFeature(state, featureUuid, factCategory, factCategory, null, featureVocabulary);
|
|
159
|
if (state.getConfig().isSalvador()){
|
|
160
|
adaptNewSalvadorFeature(factCategoryId, feature);
|
|
161
|
}
|
|
162
|
//id
|
|
163
|
doId(state, feature, factCategoryId, "FactCategory");
|
|
164
|
|
|
165
|
//TODO
|
|
166
|
// MaxFactNumber int Checked
|
|
167
|
// ExtensionTableName varchar(100) Checked
|
|
168
|
// Description nvarchar(1000) Checked
|
|
169
|
// locExtensionFormName nvarchar(80) Checked
|
|
170
|
// RankRestrictionFk int Checked
|
|
171
|
}
|
|
172
|
|
|
173
|
result.put(factCategoryId, feature);
|
|
174
|
if (createFeatureTree && isPublicFeature(factCategoryId)){
|
|
175
|
featureTree.getRoot().addChild(FeatureNode.NewInstance(feature));
|
|
176
|
}
|
|
177
|
}
|
|
178
|
if (createFeatureTree){
|
|
179
|
featureTree.getRoot().addChild(FeatureNode.NewInstance(Feature.DISTRIBUTION()),2);
|
|
180
|
featureTree.getRoot().addChild(FeatureNode.NewInstance(Feature.NOTES()), featureTree.getRoot().getChildCount()-1);
|
|
181
|
getFeatureTreeService().save(featureTree);
|
|
182
|
}
|
|
183
|
return result;
|
|
184
|
} catch (SQLException e) {
|
|
185
|
logger.error("SQLException:" + e);
|
|
186
|
return null;
|
|
187
|
}
|
|
188
|
}
|
|
189
|
|
|
190
|
|
|
191
|
/**
|
|
192
|
* @param factCategoryId
|
|
193
|
* @param feature
|
|
194
|
*/
|
|
195
|
private void adaptNewSalvadorFeature(int factCategoryId, Feature feature) {
|
|
196
|
if (factCategoryId == 306){
|
|
197
|
addSpanishRepresentationLabel(feature, "Nombre(s) común(es)");
|
|
198
|
} else if (factCategoryId == 307){
|
|
199
|
addSpanishRepresentationLabel(feature, "Muestras de herbario");
|
|
200
|
} else if (factCategoryId == 310){
|
|
201
|
addEnglishFactCategoryName(feature, "Other references for taxon");
|
|
202
|
} else if (factCategoryId == 309){
|
|
203
|
addEnglishFactCategoryName(feature, "Report (reference) for El Salvador");
|
|
204
|
} else if (factCategoryId == 311){
|
|
205
|
addEnglishFactCategoryName(feature, "Taxon illustration references");
|
|
206
|
} else if (factCategoryId == 312){
|
|
207
|
addSpanishRepresentationLabel(feature, "Imágen");
|
|
208
|
} else if (factCategoryId == 350){
|
|
209
|
addSpanishRepresentationLabel(feature, "Descripción");
|
|
210
|
} else if (factCategoryId == 303){
|
|
211
|
addEnglishFactCategoryName(feature, "General distribution");
|
|
212
|
} else if (factCategoryId == 2000){
|
|
213
|
addEnglishFactCategoryName(feature, "Habitat in El Salvador");
|
|
214
|
} else if (factCategoryId == 302){
|
|
215
|
addSpanishRepresentationLabel(feature, "Usos");
|
|
216
|
} else if (factCategoryId == 1800){
|
|
217
|
addEnglishFactCategoryName(feature, "Specimen notes");
|
|
218
|
} else if (factCategoryId == 1900){
|
|
219
|
addEnglishFactCategoryName(feature, "Editorial notes");
|
|
220
|
}
|
|
221
|
|
|
222
|
}
|
|
223
|
|
|
224
|
|
|
225
|
/**
|
|
226
|
* @param feature
|
|
227
|
* @param string
|
|
228
|
*/
|
|
229
|
private void addSpanishRepresentationLabel(TermBase term, String label) {
|
|
230
|
term.getRepresentations().add(Representation.NewInstance(label, label, null, Language.SPANISH_CASTILIAN()));
|
|
231
|
}
|
|
232
|
|
|
233
|
/**
|
|
234
|
* @param feature
|
|
235
|
* @param string
|
|
236
|
*/
|
|
237
|
private void addEnglishFactCategoryName(Feature feature, String label) {
|
|
238
|
feature.getRepresentations().iterator().next().setLanguage(Language.SPANISH_CASTILIAN());
|
|
239
|
feature.getRepresentations().add(Representation.NewInstance(label, label, null, Language.ENGLISH()));
|
|
240
|
}
|
|
241
|
|
|
242
|
|
|
243
|
@Override
|
|
244
|
protected void doInvoke(BerlinModelImportState state) {
|
|
245
|
if (state.getConfig().isSalvador()){
|
|
246
|
invokeSpanishTermLabels();
|
|
247
|
}
|
|
248
|
featureMap = invokeFactCategories(state);
|
|
249
|
super.doInvoke(state);
|
|
250
|
return;
|
|
251
|
}
|
|
252
|
|
|
253
|
|
|
254
|
/**
|
|
255
|
*
|
|
256
|
*/
|
|
257
|
private void invokeSpanishTermLabels() {
|
|
258
|
addSpanishRepresentationLabel(Feature.NOTES(), "Notas");
|
|
259
|
addSpanishRepresentationLabel(NamedAreaLevel.DEPARTMENT(), "Departamento");
|
|
260
|
addSpanishRepresentationLabel(PresenceAbsenceTerm.NATIVE(), "nativo");
|
|
261
|
addSpanishRepresentationLabel(PresenceAbsenceTerm.CULTIVATED(), "cultivado");
|
|
262
|
addSpanishRepresentationLabel(PresenceAbsenceTerm.PRESENT(), "presente");
|
|
263
|
|
|
264
|
|
|
265
|
}
|
|
266
|
|
|
267
|
|
|
268
|
@Override
|
|
269
|
protected String getIdQuery(BerlinModelImportState state) {
|
|
270
|
String result = super.getIdQuery(state);
|
|
271
|
if (StringUtils.isNotBlank(state.getConfig().getFactFilter())){
|
|
272
|
result += " WHERE " + state.getConfig().getFactFilter();
|
|
273
|
}else{
|
|
274
|
result = super.getIdQuery(state);
|
|
275
|
}
|
|
276
|
result += getOrderBy(state.getConfig());
|
|
277
|
return result;
|
|
278
|
}
|
|
279
|
|
|
280
|
@Override
|
|
281
|
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
|
282
|
String strQuery =
|
|
283
|
" SELECT Fact.*, PTaxon.RIdentifier as taxonId, RefDetail.Details " +
|
|
284
|
" FROM Fact " +
|
|
285
|
" INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk " +
|
|
286
|
" LEFT OUTER JOIN RefDetail ON Fact.FactRefDetailFk = RefDetail.RefDetailId AND Fact.FactRefFk = RefDetail.RefFk " +
|
|
287
|
" WHERE (FactId IN (" + ID_LIST_TOKEN + "))";
|
|
288
|
strQuery += getOrderBy(config);
|
|
289
|
|
|
290
|
return strQuery;
|
|
291
|
}
|
|
292
|
|
|
293
|
|
|
294
|
private String getOrderBy(BerlinModelImportConfigurator config) {
|
|
295
|
String result;
|
|
296
|
try{
|
|
297
|
if (config.getSource().checkColumnExists("Fact", "Sequence")){
|
|
298
|
result = " ORDER By Fact.Sequence, Fact.FactId";
|
|
299
|
if (config.isSalvador()){
|
|
300
|
result = " ORDER By Fact.FactCategoryFk, Fact.Sequence, Fact.FactId";
|
|
301
|
}
|
|
302
|
}else{
|
|
303
|
result = " ORDER By Fact.FactId";
|
|
304
|
}
|
|
305
|
} catch (DatabaseTypeNotSupportedException e) {
|
|
306
|
logger.info("checkColumnExists not supported");
|
|
307
|
result = " ORDER By Fact.FactId";
|
|
308
|
}
|
|
309
|
return result;
|
|
310
|
}
|
|
311
|
|
|
312
|
@Override
|
|
313
|
public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
|
|
314
|
boolean success = true ;
|
|
315
|
Set<TaxonBase> taxaToSave = new HashSet<>();
|
|
316
|
Map<String, TaxonBase> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
|
|
317
|
Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
|
|
318
|
|
|
319
|
ResultSet rs = partitioner.getResultSet();
|
|
320
|
|
|
321
|
Reference sourceRef = state.getTransactionalSourceReference();
|
|
322
|
|
|
323
|
try{
|
|
324
|
int i = 0;
|
|
325
|
//for each fact
|
|
326
|
while (rs.next()){
|
|
327
|
try{
|
|
328
|
if ((i++ % modCount) == 0){ logger.info("Facts handled: " + (i-1));}
|
|
329
|
|
|
330
|
int factId = rs.getInt("factId");
|
|
331
|
Integer taxonId = nullSafeInt(rs, "taxonId");
|
|
332
|
Integer factRefFkInt = nullSafeInt(rs, "factRefFk");
|
|
333
|
Integer categoryFkInt = nullSafeInt(rs, "factCategoryFk");
|
|
334
|
String details = rs.getString("Details");
|
|
335
|
String fact = CdmUtils.Nz(rs.getString("Fact"));
|
|
336
|
String notes = CdmUtils.Nz(rs.getString("notes"));
|
|
337
|
Boolean doubtfulFlag = rs.getBoolean("DoubtfulFlag");
|
|
338
|
|
|
339
|
TaxonBase<?> taxonBase = getTaxon(taxonMap, taxonId, taxonId);
|
|
340
|
Feature feature = getFeature(featureMap, categoryFkInt) ;
|
|
341
|
|
|
342
|
if (taxonBase == null){
|
|
343
|
logger.warn("Taxon for Fact " + factId + " does not exist in store");
|
|
344
|
success = false;
|
|
345
|
}else{
|
|
346
|
TaxonDescription taxonDescription;
|
|
347
|
if ( (taxonDescription = getMyTaxonDescripion(taxonBase, state, categoryFkInt, taxonId, factId, fact, sourceRef)) == null){
|
|
348
|
success = false;
|
|
349
|
continue;
|
|
350
|
}
|
|
351
|
|
|
352
|
//textData
|
|
353
|
TextData textData = null;
|
|
354
|
boolean newTextData = true;
|
|
355
|
|
|
356
|
// For Cichorieae DB: If fact category is 31 (Systematics) and there is already a Systematics TextData
|
|
357
|
// description element append the fact text to the existing TextData
|
|
358
|
if(categoryFkInt.equals(31)) {
|
|
359
|
Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();
|
|
360
|
for (DescriptionElementBase descriptionElement : descriptionElements) {
|
|
361
|
String featureString = descriptionElement.getFeature().getRepresentation(Language.DEFAULT()).getLabel();
|
|
362
|
if (descriptionElement instanceof TextData && featureString.equals("Systematics")) { // TODO: test
|
|
363
|
textData = (TextData)descriptionElement;
|
|
364
|
String factTextStr = textData.getText(Language.DEFAULT());
|
|
365
|
// FIXME: Removing newlines doesn't work
|
|
366
|
if (factTextStr.contains("\\r\\n")) {
|
|
367
|
factTextStr = factTextStr.replaceAll("\\r\\n","");
|
|
368
|
}
|
|
369
|
StringBuilder factText = new StringBuilder(factTextStr);
|
|
370
|
factText.append(fact);
|
|
371
|
fact = factText.toString();
|
|
372
|
newTextData = false;
|
|
373
|
break;
|
|
374
|
}
|
|
375
|
}
|
|
376
|
}
|
|
377
|
|
|
378
|
if (taxonDescription.isImageGallery()){
|
|
379
|
newTextData = false;
|
|
380
|
textData = (TextData)taxonDescription.getElements().iterator().next();
|
|
381
|
}
|
|
382
|
if(newTextData == true) {
|
|
383
|
textData = TextData.NewInstance();
|
|
384
|
}else if (textData == null){
|
|
385
|
throw new RuntimeException("Textdata must not be null"); //does not happen, only to avoid potential NPE warnings
|
|
386
|
}
|
|
387
|
|
|
388
|
|
|
389
|
//for diptera database
|
|
390
|
if (categoryFkInt.equals(99) && notes.contains("<OriginalName>")){
|
|
391
|
fact = notes + ": " + fact ;
|
|
392
|
}
|
|
393
|
//for E+M maps
|
|
394
|
if (categoryFkInt.equals(14) && state.getConfig().isRemoveHttpMapsAnchor() && fact.contains("<a href")){
|
|
395
|
//example <a href="http://euromed.luomus.fi/euromed_map.php?taxon=280629&size=medium">distribution</a>
|
|
396
|
fact = fact.replace("<a href=\"", "").replace("\">distribution</a>", "");
|
|
397
|
}
|
|
398
|
|
|
399
|
//TODO textData.putText(fact, bmiConfig.getFactLanguage()); //doesn't work because bmiConfig.getFactLanguage() is not not a persistent Language Object
|
|
400
|
//throws in thread "main" org.springframework.dao.InvalidDataAccessApiUsageException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language; nested exception is org.hibernate.TransientObjectException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language
|
|
401
|
|
|
402
|
Language lang = Language.DEFAULT();
|
|
403
|
if (state.getConfig().isSalvador()){
|
|
404
|
lang = getSalvadorFactLanguage(categoryFkInt);
|
|
405
|
}
|
|
406
|
if (! taxonDescription.isImageGallery()){
|
|
407
|
textData.putText(lang, fact);
|
|
408
|
textData.setFeature(feature);
|
|
409
|
}
|
|
410
|
|
|
411
|
DescriptionElementBase deb = textData;
|
|
412
|
|
|
413
|
if (state.getConfig().isSalvador()){
|
|
414
|
if (categoryFkInt == 306){
|
|
415
|
NamedArea area = null; // for now we do not set an area as it can not be disabled in dataportals via css yet
|
|
416
|
deb = CommonTaxonName.NewInstance(fact, Language.SPANISH_CASTILIAN(), area);
|
|
417
|
}else if (categoryFkInt == 307){
|
|
418
|
Distribution salvadorDistribution = salvadorDistributionFromMuestrasDeHerbar((Taxon)taxonBase, fact);
|
|
419
|
if (salvadorDistribution != null){
|
|
420
|
//id
|
|
421
|
doId(state, salvadorDistribution, factId, "Fact");
|
|
422
|
mergeSalvadorDistribution(taxonDescription, salvadorDistribution);
|
|
423
|
}
|
|
424
|
}
|
|
425
|
}
|
|
426
|
|
|
427
|
//reference
|
|
428
|
Reference citation = null;
|
|
429
|
String factRefFk = String.valueOf(factRefFkInt);
|
|
430
|
if (factRefFkInt != null){
|
|
431
|
citation = refMap.get(factRefFk);
|
|
432
|
}
|
|
433
|
if (citation == null && (factRefFkInt != null)){
|
|
434
|
logger.warn("Citation not found in referenceMap: " + factRefFk);
|
|
435
|
success = false;
|
|
436
|
}
|
|
437
|
if (citation != null || StringUtils.isNotBlank(details)){
|
|
438
|
DescriptionElementSource originalSource = DescriptionElementSource.NewPrimarySourceInstance(citation, details);
|
|
439
|
deb.addSource(originalSource);
|
|
440
|
}
|
|
441
|
taxonDescription.addElement(deb);
|
|
442
|
//doubtfulFlag
|
|
443
|
if (doubtfulFlag){
|
|
444
|
deb.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), true));
|
|
445
|
}
|
|
446
|
//publisheFlag
|
|
447
|
String strPublishFlag = "publishFlag";
|
|
448
|
boolean publishFlagExists = state.getConfig().getSource().checkColumnExists(dbTableName, strPublishFlag);
|
|
449
|
if (publishFlagExists){
|
|
450
|
Boolean publishFlag = rs.getBoolean(strPublishFlag);
|
|
451
|
if (publishFlag == false){
|
|
452
|
deb.addMarker(Marker.NewInstance(MarkerType.PUBLISH(), publishFlag));
|
|
453
|
}
|
|
454
|
}
|
|
455
|
|
|
456
|
//Sequence
|
|
457
|
Integer sequence = rs.getInt("Sequence");
|
|
458
|
if (sequence != 999){
|
|
459
|
String strSequence = String.valueOf(sequence);
|
|
460
|
strSequence = SEQUENCE_PREFIX + strSequence;
|
|
461
|
//TODO make it an Extension when possible
|
|
462
|
//Extension datesExtension = Extension.NewInstance(textData, strSequence, ExtensionType.ORDER());
|
|
463
|
Annotation annotation = Annotation.NewInstance(strSequence, AnnotationType.TECHNICAL(), Language.ENGLISH());
|
|
464
|
deb.addAnnotation(annotation);
|
|
465
|
}
|
|
466
|
|
|
467
|
// if (categoryFkObj == FACT_DESCRIPTION){
|
|
468
|
// //;
|
|
469
|
// }else if (categoryFkObj == FACT_OBSERVATION){
|
|
470
|
// //;
|
|
471
|
// }else if (categoryFkObj == FACT_DISTRIBUTION_EM){
|
|
472
|
// //
|
|
473
|
// }else {
|
|
474
|
// //TODO
|
|
475
|
// //logger.warn("FactCategory " + categoryFk + " not yet implemented");
|
|
476
|
// }
|
|
477
|
|
|
478
|
//notes
|
|
479
|
doCreatedUpdatedNotes(state, deb, rs);
|
|
480
|
doId(state, deb, factId, "Fact");
|
|
481
|
|
|
482
|
//TODO
|
|
483
|
//Designation References -> unclear how to map to CDM
|
|
484
|
|
|
485
|
|
|
486
|
//sequence -> textData is not an identifiable entity therefore extensions are not possible
|
|
487
|
//fact category better
|
|
488
|
|
|
489
|
taxaToSave.add(taxonBase);
|
|
490
|
}
|
|
491
|
} catch (Exception re){
|
|
492
|
logger.error("An exception occurred during the facts import");
|
|
493
|
re.printStackTrace();
|
|
494
|
success = false;
|
|
495
|
}
|
|
496
|
//put
|
|
497
|
}
|
|
498
|
logger.info("Facts handled: " + (i-1));
|
|
499
|
logger.info("Taxa to save: " + taxaToSave.size());
|
|
500
|
getTaxonService().save(taxaToSave);
|
|
501
|
}catch(SQLException e){
|
|
502
|
throw new RuntimeException(e);
|
|
503
|
}
|
|
504
|
return success;
|
|
505
|
}
|
|
506
|
|
|
507
|
|
|
508
|
/**
|
|
509
|
* @param taxonDescription
|
|
510
|
* @param salvadorDistribution
|
|
511
|
*/
|
|
512
|
private void mergeSalvadorDistribution(TaxonDescription taxonDescription,
|
|
513
|
@NotNull Distribution newDistribution) {
|
|
514
|
|
|
515
|
Distribution existingDistribution = null;
|
|
516
|
for (DescriptionElementBase deb : taxonDescription.getElements()){
|
|
517
|
if (deb.isInstanceOf(Distribution.class)){
|
|
518
|
Distribution distribution = CdmBase.deproxy(deb, Distribution.class);
|
|
519
|
if (distribution.getArea() != null && distribution.getArea().equals(newDistribution.getArea())){
|
|
520
|
existingDistribution = distribution;
|
|
521
|
break;
|
|
522
|
}else if (distribution.getArea() == null){
|
|
523
|
logger.warn("Area for distribution is null: " + distribution.getUuid());
|
|
524
|
}
|
|
525
|
}
|
|
526
|
}
|
|
527
|
if (existingDistribution == null){
|
|
528
|
taxonDescription.addElement(newDistribution);
|
|
529
|
}else if(!existingDistribution.getStatus().equals(newDistribution.getStatus())){
|
|
530
|
//should not happen
|
|
531
|
logger.warn("Taxon has areas with different distribution states: " + taxonDescription.getTaxon().getTitleCache());
|
|
532
|
}else{
|
|
533
|
//do nothing, distribution already exists
|
|
534
|
}
|
|
535
|
}
|
|
536
|
|
|
537
|
|
|
538
|
private Map<String, NamedArea> salvadorAreaMap = null;
|
|
539
|
private Distribution salvadorDistributionFromMuestrasDeHerbar(Taxon taxon, String fact) {
|
|
540
|
if (salvadorAreaMap == null){
|
|
541
|
salvadorAreaMap = new HashMap<>();
|
|
542
|
TermVocabulary<NamedArea> salvadorAreas = getVocabulary(TermType.NamedArea, BerlinModelTransformer.uuidSalvadorAreas,
|
|
543
|
"Salvador areas", "Salvador areas", null, null, true, NamedArea.NewInstance());
|
|
544
|
getVocabularyService().save(salvadorAreas);
|
|
545
|
}
|
|
546
|
Distribution result = null;
|
|
547
|
String[] areaStrings = fact.split(":");
|
|
548
|
if (areaStrings.length > 1){
|
|
549
|
String areaString = areaStrings[0];
|
|
550
|
NamedArea area = salvadorAreaMap.get(areaString);
|
|
551
|
if (area == null){
|
|
552
|
logger.info("Added Salvador area: " + areaString);
|
|
553
|
TermVocabulary<NamedArea> voc = getVocabulary(TermType.NamedArea, BerlinModelTransformer.uuidSalvadorAreas,
|
|
554
|
"Salvador departments", "Salvador departments", null, null, true, NamedArea.NewInstance());
|
|
555
|
if (voc.getRepresentation(Language.SPANISH_CASTILIAN()) == null){
|
|
556
|
voc.addRepresentation(Representation.NewInstance("Salvador departamentos", "Salvador departamentos", "dep.", Language.SPANISH_CASTILIAN()));
|
|
557
|
getVocabularyService().saveOrUpdate(voc);
|
|
558
|
}
|
|
559
|
NamedArea newArea = NamedArea.NewInstance(areaString, areaString, null);
|
|
560
|
newArea.getRepresentations().iterator().next().setLanguage(Language.SPANISH_CASTILIAN());
|
|
561
|
newArea.setLevel(NamedAreaLevel.DEPARTMENT());
|
|
562
|
newArea.setType(NamedAreaType.ADMINISTRATION_AREA());
|
|
563
|
voc.addTerm(newArea);
|
|
564
|
getTermService().saveOrUpdate(newArea);
|
|
565
|
salvadorAreaMap.put(areaString, newArea);
|
|
566
|
area = newArea;
|
|
567
|
}
|
|
568
|
PresenceAbsenceTerm state = getSalvadorDistributionState(taxon);
|
|
569
|
result = Distribution.NewInstance(area, state);
|
|
570
|
return result;
|
|
571
|
}else{
|
|
572
|
return null;
|
|
573
|
}
|
|
574
|
}
|
|
575
|
|
|
576
|
private PresenceAbsenceTerm getSalvadorDistributionState(Taxon taxon) {
|
|
577
|
boolean hasGlobalDist = false;
|
|
578
|
for (TaxonDescription desc : taxon.getDescriptions()){
|
|
579
|
for (DescriptionElementBase deb : desc.getElements()){
|
|
580
|
if (deb.getFeature().getUuid().equals(BerlinModelTransformer.uuidFeatureDistributionGlobal)){
|
|
581
|
hasGlobalDist = true;
|
|
582
|
TextData textData = CdmBase.deproxy(deb, TextData.class);
|
|
583
|
for (LanguageString text : textData.getMultilanguageText().values()){
|
|
584
|
if (text.getText().contains("El Salvador")){
|
|
585
|
return PresenceAbsenceTerm.NATIVE();
|
|
586
|
}
|
|
587
|
}
|
|
588
|
}
|
|
589
|
}
|
|
590
|
}
|
|
591
|
if (!hasGlobalDist){
|
|
592
|
logger.warn("No global distribution found: " + taxon.getTitleCache());
|
|
593
|
}
|
|
594
|
return hasGlobalDist ? PresenceAbsenceTerm.CULTIVATED(): PresenceAbsenceTerm.PRESENT();
|
|
595
|
}
|
|
596
|
|
|
597
|
|
|
598
|
/**
|
|
599
|
* @param factId
|
|
600
|
* @return
|
|
601
|
*/
|
|
602
|
private Language getSalvadorFactLanguage(int categoryFkInt) {
|
|
603
|
if (categoryFkInt == 350){
|
|
604
|
return Language.ENGLISH();
|
|
605
|
}else if (categoryFkInt == 1800 || categoryFkInt == 1900){
|
|
606
|
return Language.UNDETERMINED();
|
|
607
|
}
|
|
608
|
return Language.SPANISH_CASTILIAN();
|
|
609
|
}
|
|
610
|
|
|
611
|
|
|
612
|
private TaxonDescription getMyTaxonDescripion(TaxonBase taxonBase, BerlinModelImportState state, Integer categoryFk, Integer taxonId, int factId, String fact, Reference sourceRef) {
|
|
613
|
Taxon taxon = null;
|
|
614
|
if ( taxonBase instanceof Taxon ) {
|
|
615
|
taxon = (Taxon) taxonBase;
|
|
616
|
}else{
|
|
617
|
logger.warn("TaxonBase " + (taxonId==null?"(null)":taxonId) + " for Fact " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
|
|
618
|
return null;
|
|
619
|
}
|
|
620
|
|
|
621
|
TaxonDescription taxonDescription = null;
|
|
622
|
Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
|
|
623
|
|
|
624
|
Media media = null;
|
|
625
|
//for diptera / salvador images
|
|
626
|
if (categoryFk == 51 || categoryFk == 312){ //TODO check also FactCategory string
|
|
627
|
media = Media.NewInstance();
|
|
628
|
taxonDescription = makeImage(state, fact, media, descriptionSet, taxon);
|
|
629
|
|
|
630
|
if (taxonDescription == null){
|
|
631
|
return null;
|
|
632
|
}
|
|
633
|
|
|
634
|
TextData textData = null;
|
|
635
|
for (DescriptionElementBase el: taxonDescription.getElements()){
|
|
636
|
if (el.isInstanceOf(TextData.class)){
|
|
637
|
textData = CdmBase.deproxy(el, TextData.class);
|
|
638
|
}
|
|
639
|
}
|
|
640
|
if (textData == null){
|
|
641
|
textData = TextData.NewInstance(Feature.IMAGE());
|
|
642
|
taxonDescription.addElement(textData);
|
|
643
|
}
|
|
644
|
textData.addMedia(media);
|
|
645
|
}
|
|
646
|
//all others (no image) -> getDescription
|
|
647
|
else{
|
|
648
|
boolean isPublic = isPublicFeature(categoryFk);
|
|
649
|
for (TaxonDescription desc: descriptionSet){
|
|
650
|
|
|
651
|
if (! desc.isImageGallery()){
|
|
652
|
if (state.getConfig().isSalvador()){
|
|
653
|
if (desc.isDefault() && isPublic || !desc.isDefault() && !isPublic){
|
|
654
|
taxonDescription = desc;
|
|
655
|
break;
|
|
656
|
}
|
|
657
|
}else{
|
|
658
|
taxonDescription = desc;
|
|
659
|
break;
|
|
660
|
}
|
|
661
|
}
|
|
662
|
}
|
|
663
|
if (taxonDescription == null){
|
|
664
|
taxonDescription = TaxonDescription.NewInstance();
|
|
665
|
if (state.getConfig().isSalvador()){
|
|
666
|
String title = "Factual data for " + taxon.getName().getTitleCache();
|
|
667
|
if (isPublic){
|
|
668
|
taxonDescription.setDefault(isPublic);
|
|
669
|
}else{
|
|
670
|
title = "Non public f" + title.substring(1);
|
|
671
|
}
|
|
672
|
taxonDescription.setTitleCache(title, true);
|
|
673
|
}else if(state.getConfig().isEuroMed()){
|
|
674
|
taxonDescription.setDefault(true);
|
|
675
|
}else{
|
|
676
|
taxonDescription.setTitleCache(sourceRef == null ? null : sourceRef.getTitleCache(), true);
|
|
677
|
}
|
|
678
|
taxon.addDescription(taxonDescription);
|
|
679
|
}
|
|
680
|
}
|
|
681
|
return taxonDescription;
|
|
682
|
}
|
|
683
|
|
|
684
|
|
|
685
|
/**
|
|
686
|
* @param categoryFk
|
|
687
|
* @return
|
|
688
|
*/
|
|
689
|
private boolean isPublicFeature(Integer categoryFk) {
|
|
690
|
return ! (categoryFk == 1800 || categoryFk == 1900 || categoryFk == 2000);
|
|
691
|
}
|
|
692
|
|
|
693
|
|
|
694
|
@Override
|
|
695
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
|
696
|
String nameSpace;
|
|
697
|
Class<?> cdmClass;
|
|
698
|
Set<String> idSet;
|
|
699
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
700
|
|
|
701
|
try{
|
|
702
|
Set<String> taxonIdSet = new HashSet<String>();
|
|
703
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
704
|
Set<String> refDetailIdSet = new HashSet<String>();
|
|
705
|
while (rs.next()){
|
|
706
|
handleForeignKey(rs, taxonIdSet, "taxonId");
|
|
707
|
handleForeignKey(rs, referenceIdSet, "FactRefFk");
|
|
708
|
handleForeignKey(rs, referenceIdSet, "PTDesignationRefFk");
|
|
709
|
handleForeignKey(rs, refDetailIdSet, "FactRefDetailFk");
|
|
710
|
handleForeignKey(rs, refDetailIdSet, "PTDesignationRefDetailFk");
|
|
711
|
}
|
|
712
|
|
|
713
|
//taxon map
|
|
714
|
nameSpace = BerlinModelTaxonImport.NAMESPACE;
|
|
715
|
cdmClass = TaxonBase.class;
|
|
716
|
idSet = taxonIdSet;
|
|
717
|
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
718
|
result.put(nameSpace, taxonMap);
|
|
719
|
|
|
720
|
//reference map
|
|
721
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
722
|
cdmClass = Reference.class;
|
|
723
|
idSet = referenceIdSet;
|
|
724
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
725
|
result.put(nameSpace, referenceMap);
|
|
726
|
|
|
727
|
//refDetail map
|
|
728
|
nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
|
|
729
|
cdmClass = Reference.class;
|
|
730
|
idSet = refDetailIdSet;
|
|
731
|
Map<String, Reference> refDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
732
|
result.put(nameSpace, refDetailMap);
|
|
733
|
|
|
734
|
} catch (SQLException e) {
|
|
735
|
throw new RuntimeException(e);
|
|
736
|
}
|
|
737
|
return result;
|
|
738
|
}
|
|
739
|
|
|
740
|
|
|
741
|
/**
|
|
742
|
* @param state
|
|
743
|
* @param media
|
|
744
|
* @param media
|
|
745
|
* @param descriptionSet
|
|
746
|
* @throws URISyntaxException
|
|
747
|
*
|
|
748
|
*/
|
|
749
|
private TaxonDescription makeImage(BerlinModelImportState state, String fact, Media media, Set<TaxonDescription> descriptionSet, Taxon taxon) {
|
|
750
|
TaxonDescription taxonDescription = null;
|
|
751
|
try {
|
|
752
|
Reference sourceRef = state.getTransactionalSourceReference();
|
|
753
|
URI uri;
|
|
754
|
URI thumbUri;
|
|
755
|
if (state.getConfig().isSalvador()){
|
|
756
|
String thumbs = "thumbs/";
|
|
757
|
String uriStrFormat = "http://media.e-taxonomy.eu/salvador/berendsohn-et-al-%s/%s.jpg";
|
|
758
|
Integer intFact = Integer.valueOf(fact);
|
|
759
|
String vol = "2009";
|
|
760
|
int page = intFact + 249;
|
|
761
|
if (intFact >= 263){
|
|
762
|
vol = "2016";
|
|
763
|
page = intFact - (intFact < 403 ? 95 : 94);
|
|
764
|
}else if (intFact >= 142){
|
|
765
|
vol = "2012";
|
|
766
|
page = intFact + (intFact < 255 ? 3 : 4);
|
|
767
|
}
|
|
768
|
|
|
769
|
String title = getSalvadorImageTitle(intFact, vol);
|
|
770
|
media.putTitle(Language.LATIN(), title);
|
|
771
|
String description = getSalvadorImageDescription(intFact);
|
|
772
|
media.putDescription(Language.SPANISH_CASTILIAN(), description);
|
|
773
|
|
|
774
|
Reference ref = getSalvadorReference(vol);
|
|
775
|
String originalName = getSalvadorImageNameInfo(intFact);
|
|
776
|
IdentifiableSource source = media.addSource(OriginalSourceType.PrimaryMediaSource, fact, "Fig.", ref, "p. " + page);
|
|
777
|
source.setOriginalNameString(originalName);
|
|
778
|
media.setArtist(getSalvadorArtist());
|
|
779
|
media.addRights(getSalvadorCopyright(vol));
|
|
780
|
String uriStr = String.format(uriStrFormat, vol, fact);
|
|
781
|
String thumbUriStr = String.format(uriStrFormat, vol, thumbs + fact);
|
|
782
|
uri = new URI(uriStr);
|
|
783
|
thumbUri = new URI(thumbUriStr);
|
|
784
|
}else{
|
|
785
|
uri = new URI(fact.trim());
|
|
786
|
thumbUri = null;
|
|
787
|
}
|
|
788
|
|
|
789
|
makeMediaRepresentation(media, uri);
|
|
790
|
if (thumbUri != null){
|
|
791
|
makeMediaRepresentation(media, thumbUri);
|
|
792
|
}
|
|
793
|
|
|
794
|
taxonDescription = taxon.getOrCreateImageGallery(sourceRef == null ? null :sourceRef.getTitleCache());
|
|
795
|
} catch (URISyntaxException e) {
|
|
796
|
logger.warn("URISyntaxException. Image could not be imported: " + fact);
|
|
797
|
return null;
|
|
798
|
}
|
|
799
|
return taxonDescription;
|
|
800
|
}
|
|
801
|
|
|
802
|
|
|
803
|
/**
|
|
804
|
* @param intFact
|
|
805
|
* @param vol
|
|
806
|
* @return
|
|
807
|
*/
|
|
808
|
private String getSalvadorImageTitle(Integer intFact, String vol) {
|
|
809
|
initSalvadorImagesFile();
|
|
810
|
String[] line = salvadorImages.get(intFact);
|
|
811
|
if (line == null){
|
|
812
|
logger.warn("Could not find salvador image metadata for " + intFact);
|
|
813
|
return String.valueOf(intFact);
|
|
814
|
}else{
|
|
815
|
String name = getSalvadorImageNameInfo(intFact);
|
|
816
|
String result = UTF8.QUOT_DBL_LEFT + name + UTF8.QUOT_DBL_RIGHT + " [Berendsohn & al. " + vol + "]";
|
|
817
|
return result;
|
|
818
|
}
|
|
819
|
}
|
|
820
|
|
|
821
|
|
|
822
|
private Map<Integer, String[]> salvadorImages = null;
|
|
823
|
private String getSalvadorImageDescription(Integer intFact) {
|
|
824
|
initSalvadorImagesFile();
|
|
825
|
String[] line = salvadorImages.get(intFact);
|
|
826
|
if (line == null){
|
|
827
|
logger.warn("Could not find salvador image metadata for " + intFact);
|
|
828
|
return String.valueOf(intFact);
|
|
829
|
}else{
|
|
830
|
int i = 2;
|
|
831
|
String result = CdmUtils.concat(" " + UTF8.EN_DASH + " ", line[i], line[i + 1]);
|
|
832
|
return result;
|
|
833
|
}
|
|
834
|
}
|
|
835
|
|
|
836
|
private String getSalvadorImageNameInfo(Integer intFact) {
|
|
837
|
initSalvadorImagesFile();
|
|
838
|
String[] line = salvadorImages.get(intFact);
|
|
839
|
if (line == null){
|
|
840
|
logger.warn("Could not find salvador image metadata for " + intFact);
|
|
841
|
return String.valueOf(intFact);
|
|
842
|
}else{
|
|
843
|
int i = 1;
|
|
844
|
String result = line[i].substring("Fig. ".length() + line[0].length()).trim();
|
|
845
|
return result;
|
|
846
|
}
|
|
847
|
}
|
|
848
|
|
|
849
|
private void initSalvadorImagesFile() {
|
|
850
|
if (salvadorImages == null){
|
|
851
|
salvadorImages = new HashMap<>();
|
|
852
|
try {
|
|
853
|
CSVReader reader = new CSVReader(CdmUtils.getUtf8ResourceReader("salvador" + CdmUtils.getFolderSeperator() + "SalvadorImages.csv"),';');
|
|
854
|
List<String[]> lines = reader.readAll();
|
|
855
|
for (String[] line : lines){
|
|
856
|
String first = line[0];
|
|
857
|
if(! "ID".equals(first)){
|
|
858
|
try {
|
|
859
|
salvadorImages.put(Integer.valueOf(first), line);
|
|
860
|
} catch (NumberFormatException e) {
|
|
861
|
logger.warn("Number not recognized: " + first);
|
|
862
|
}
|
|
863
|
}
|
|
864
|
}
|
|
865
|
reader.close();
|
|
866
|
} catch (IOException e) {
|
|
867
|
e.printStackTrace();
|
|
868
|
}
|
|
869
|
}
|
|
870
|
}
|
|
871
|
|
|
872
|
|
|
873
|
private Rights rights1;
|
|
874
|
private Rights rights2;
|
|
875
|
private Rights rights3;
|
|
876
|
|
|
877
|
private Rights getSalvadorCopyright(String vol) {
|
|
878
|
initRights();
|
|
879
|
if ("2009".equals(vol)){
|
|
880
|
return rights1;
|
|
881
|
}else if ("2012".equals(vol)){
|
|
882
|
return rights1;
|
|
883
|
}else if ("2016".equals(vol)){
|
|
884
|
return rights3;
|
|
885
|
}else{
|
|
886
|
throw new RuntimeException("Volume not recognized: " + vol);
|
|
887
|
}
|
|
888
|
}
|
|
889
|
|
|
890
|
private void initRights(){
|
|
891
|
if (rights1 == null){
|
|
892
|
String text = "(c) Jardín Botánico y Museo Botánico Berlin-Dahlem & Asociación Jardín Botánico La Laguna. Berlin, Antiguo Cuscatlán 2009.";
|
|
893
|
rights1 = Rights.NewInstance(text, Language.SPANISH_CASTILIAN(), RightsType.COPYRIGHT());
|
|
894
|
text = "(c) Jardín Botánico y Museo Botánico Berlin-Dahlem & Asociación Jardín Botánico La Laguna. Berlin, Antiguo Cuscatlán 2012.";
|
|
895
|
rights2 = Rights.NewInstance(text, Language.SPANISH_CASTILIAN(), RightsType.COPYRIGHT());
|
|
896
|
text = "(c) Jardín Botánico y Museo Botánico Berlin-Dahlem & Asociación Jardín Botánico La Laguna. Berlin, Antiguo Cuscatlán 2016.";
|
|
897
|
rights3 = Rights.NewInstance(text, Language.SPANISH_CASTILIAN(), RightsType.COPYRIGHT());
|
|
898
|
getCommonService().save(rights1);
|
|
899
|
getCommonService().save(rights2);
|
|
900
|
getCommonService().save(rights3);
|
|
901
|
}
|
|
902
|
}
|
|
903
|
|
|
904
|
private Integer salvadorArtistId;
|
|
905
|
private AgentBase<?> getSalvadorArtist() {
|
|
906
|
if (salvadorArtistId == null){
|
|
907
|
Person person = Person.NewInstance();
|
|
908
|
person.setGivenName("José Gerver");
|
|
909
|
person.setFamilyName("Molina");
|
|
910
|
salvadorArtistId = getAgentService().save(person).getId();
|
|
911
|
return person;
|
|
912
|
}else{
|
|
913
|
return getAgentService().find(salvadorArtistId);
|
|
914
|
}
|
|
915
|
}
|
|
916
|
|
|
917
|
private Integer salvadorRef1Id;
|
|
918
|
private Integer salvadorRef2Id;
|
|
919
|
private Integer salvadorRef3Id;
|
|
920
|
|
|
921
|
private Reference getSalvadorReference(String vol){
|
|
922
|
if (salvadorRef1Id == null){
|
|
923
|
makeSalvadorReferences();
|
|
924
|
}
|
|
925
|
if ("2009".equals(vol)){
|
|
926
|
return getReferenceService().find(salvadorRef1Id);
|
|
927
|
}else if ("2012".equals(vol)){
|
|
928
|
return getReferenceService().find(salvadorRef2Id);
|
|
929
|
}else if ("2016".equals(vol)){
|
|
930
|
return getReferenceService().find(salvadorRef3Id);
|
|
931
|
}else{
|
|
932
|
throw new RuntimeException("Volume not recognized: " + vol);
|
|
933
|
}
|
|
934
|
|
|
935
|
}
|
|
936
|
|
|
937
|
private void makeSalvadorReferences() {
|
|
938
|
Person walter = Person.NewTitledInstance("Berendsohn, W. G.");
|
|
939
|
walter.setGivenName("Walter G.");
|
|
940
|
walter.setFamilyName("Berendsohn");
|
|
941
|
Person katja = Person.NewTitledInstance("Gruber, Anne Kathrina");
|
|
942
|
katja.setGivenName("Anne Katharina");
|
|
943
|
katja.setFamilyName("Gruber");
|
|
944
|
Person monte = Person.NewTitledInstance("Monterrosa Salomón, J.");
|
|
945
|
Person olmedo = Person.NewTitledInstance("Olmedo Galán, P.");
|
|
946
|
Person rodriguez = Person.NewTitledInstance("Rodríguez Delcid, D");
|
|
947
|
|
|
948
|
Team team1 = Team.NewInstance();
|
|
949
|
team1.addTeamMember(walter);
|
|
950
|
team1.addTeamMember(katja);
|
|
951
|
team1.addTeamMember(monte);
|
|
952
|
|
|
953
|
Team team2 = Team.NewInstance();
|
|
954
|
team2.addTeamMember(walter);
|
|
955
|
team2.addTeamMember(katja);
|
|
956
|
team2.addTeamMember(rodriguez);
|
|
957
|
team2.addTeamMember(olmedo);
|
|
958
|
|
|
959
|
Reference vol1 = ReferenceFactory.newBook();
|
|
960
|
Reference vol2 = ReferenceFactory.newBook();
|
|
961
|
Reference vol3 = ReferenceFactory.newBook();
|
|
962
|
|
|
963
|
vol1.setAuthorship(team1);
|
|
964
|
vol2.setAuthorship(team1);
|
|
965
|
vol3.setAuthorship(team2);
|
|
966
|
|
|
967
|
vol1.setDatePublished(TimePeriodParser.parseStringVerbatim("2009"));
|
|
968
|
vol2.setDatePublished(TimePeriodParser.parseStringVerbatim("2012"));
|
|
969
|
vol3.setDatePublished(TimePeriodParser.parseStringVerbatim("2016"));
|
|
970
|
|
|
971
|
Reference englera = ReferenceFactory.newPrintSeries("Englera");
|
|
972
|
vol1.setInSeries(englera);
|
|
973
|
vol2.setInSeries(englera);
|
|
974
|
vol3.setInSeries(englera);
|
|
975
|
|
|
976
|
vol1.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 1: Angiospermae - Familias A a L");
|
|
977
|
vol2.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 2: Angiospermae - Familias M a P y Pteridophyta");
|
|
978
|
vol3.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 3: Angiospermae - Familias R a Z y Gymnospermae");
|
|
979
|
|
|
980
|
vol1.setVolume("29(1)");
|
|
981
|
vol2.setVolume("29(2)");
|
|
982
|
vol3.setVolume("29(3)");
|
|
983
|
|
|
984
|
vol1.setPages("1-438");
|
|
985
|
vol2.setVolume("1-300");
|
|
986
|
vol3.setVolume("1-356");
|
|
987
|
|
|
988
|
String placePublished = "Berlin: Botanic Garden and Botanical Museum Berlin; Antiguo Cuscatlán: Asociación Jardín Botánico La Laguna, El Salvador";
|
|
989
|
vol1.setPlacePublished(placePublished);
|
|
990
|
vol2.setPlacePublished(placePublished);
|
|
991
|
vol3.setPlacePublished(placePublished);
|
|
992
|
|
|
993
|
salvadorRef1Id = getReferenceService().save(vol1).getId();
|
|
994
|
salvadorRef2Id = getReferenceService().find(getReferenceService().saveOrUpdate(vol2)).getId();
|
|
995
|
salvadorRef3Id = getReferenceService().find(getReferenceService().saveOrUpdate(vol3)).getId();
|
|
996
|
return;
|
|
997
|
}
|
|
998
|
|
|
999
|
|
|
1000
|
/**
|
|
1001
|
* @param media
|
|
1002
|
* @param uri
|
|
1003
|
* @param imageInfo
|
|
1004
|
* @param size
|
|
1005
|
*/
|
|
1006
|
private void makeMediaRepresentation(Media media, URI uri) {
|
|
1007
|
ImageInfo imageInfo = null;
|
|
1008
|
Integer size = null;
|
|
1009
|
try {
|
|
1010
|
imageInfo = ImageInfo.NewInstance(uri, 30);
|
|
1011
|
} catch (IOException | HttpException e) {
|
|
1012
|
logger.error("Error when reading image meta: " + e + ", "+ uri.toString());
|
|
1013
|
}
|
|
1014
|
String mimeType = imageInfo == null ? null : imageInfo.getMimeType();
|
|
1015
|
String suffix = imageInfo == null ? null : imageInfo.getSuffix();
|
|
1016
|
MediaRepresentation mediaRepresentation = MediaRepresentation.NewInstance(mimeType, suffix);
|
|
1017
|
media.addRepresentation(mediaRepresentation);
|
|
1018
|
ImageFile image = ImageFile.NewInstance(uri, size, imageInfo);
|
|
1019
|
mediaRepresentation.addRepresentationPart(image);
|
|
1020
|
}
|
|
1021
|
|
|
1022
|
private TaxonBase<?> getTaxon(Map<String, TaxonBase> taxonMap, Integer taxonIdObj, Number taxonId){
|
|
1023
|
if (taxonIdObj != null){
|
|
1024
|
return taxonMap.get(String.valueOf(taxonId));
|
|
1025
|
}else{
|
|
1026
|
return null;
|
|
1027
|
}
|
|
1028
|
|
|
1029
|
}
|
|
1030
|
|
|
1031
|
private Feature getFeature(Map<Integer, Feature> featureMap, Integer categoryFkInt){
|
|
1032
|
if (categoryFkInt != null){
|
|
1033
|
return featureMap.get(categoryFkInt);
|
|
1034
|
}else{
|
|
1035
|
return null;
|
|
1036
|
}
|
|
1037
|
|
|
1038
|
}
|
|
1039
|
|
|
1040
|
@Override
|
|
1041
|
protected boolean doCheck(BerlinModelImportState state){
|
|
1042
|
IOValidator<BerlinModelImportState> validator = new BerlinModelFactsImportValidator();
|
|
1043
|
return validator.validate(state);
|
|
1044
|
}
|
|
1045
|
|
|
1046
|
@Override
|
|
1047
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
1048
|
return ! state.getConfig().isDoFacts();
|
|
1049
|
}
|
|
1050
|
|
|
1051
|
|
|
1052
|
|
|
1053
|
}
|