|
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.redlist.gefaesspflanzen;
|
|
11
|
|
|
12
|
import java.sql.ResultSet;
|
|
13
|
import java.sql.SQLException;
|
|
14
|
import java.util.HashMap;
|
|
15
|
import java.util.HashSet;
|
|
16
|
import java.util.Map;
|
|
17
|
import java.util.Set;
|
|
18
|
import java.util.regex.Matcher;
|
|
19
|
import java.util.regex.Pattern;
|
|
20
|
|
|
21
|
import org.apache.log4j.Logger;
|
|
22
|
import org.springframework.stereotype.Component;
|
|
23
|
|
|
24
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
|
25
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
|
26
|
import eu.etaxonomy.cdm.io.common.DbImportBase;
|
|
27
|
import eu.etaxonomy.cdm.io.common.IPartitionedIO;
|
|
28
|
import eu.etaxonomy.cdm.io.common.ImportHelper;
|
|
29
|
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
|
|
30
|
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
|
|
31
|
import eu.etaxonomy.cdm.model.agent.AgentBase;
|
|
32
|
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
|
|
33
|
import eu.etaxonomy.cdm.model.common.Annotation;
|
|
34
|
import eu.etaxonomy.cdm.model.common.AnnotationType;
|
|
35
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
36
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
37
|
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
|
|
38
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
39
|
import eu.etaxonomy.cdm.model.name.BotanicalName;
|
|
40
|
import eu.etaxonomy.cdm.model.name.CultivarPlantName;
|
|
41
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
|
42
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
|
|
43
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
|
|
44
|
import eu.etaxonomy.cdm.model.name.NonViralName;
|
|
45
|
import eu.etaxonomy.cdm.model.name.Rank;
|
|
46
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
47
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
48
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
49
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
50
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
|
51
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
|
52
|
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
|
|
53
|
|
|
54
|
/**
|
|
55
|
*
|
|
56
|
* @author pplitzner
|
|
57
|
* @date Mar 1, 2016
|
|
58
|
*
|
|
59
|
*/
|
|
60
|
|
|
61
|
@Component
|
|
62
|
@SuppressWarnings("serial")
|
|
63
|
public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
|
|
64
|
|
|
65
|
private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
|
|
66
|
|
|
67
|
private static final String tableName = "Rote Liste Gefäßpflanzen";
|
|
68
|
|
|
69
|
private static final String pluralString = "names";
|
|
70
|
|
|
71
|
private static final boolean STRICT_TITLE_CHECK = false;
|
|
72
|
|
|
73
|
public RedListGefaesspflanzenImportNames() {
|
|
74
|
super(tableName, pluralString);
|
|
75
|
}
|
|
76
|
|
|
77
|
@Override
|
|
78
|
protected String getIdQuery(RedListGefaesspflanzenImportState state) {
|
|
79
|
return "SELECT NAMNR "
|
|
80
|
+ "FROM V_TAXATLAS_D20_EXPORT t "
|
|
81
|
+ " ORDER BY NAMNR";
|
|
82
|
}
|
|
83
|
|
|
84
|
@Override
|
|
85
|
protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
|
|
86
|
String result = " SELECT * "
|
|
87
|
+ " FROM V_TAXATLAS_D20_EXPORT t "
|
|
88
|
+ " WHERE t.NAMNR IN (@IDSET)";
|
|
89
|
result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
|
|
90
|
return result;
|
|
91
|
}
|
|
92
|
|
|
93
|
@Override
|
|
94
|
protected void doInvoke(RedListGefaesspflanzenImportState state) {
|
|
95
|
super.doInvoke(state);
|
|
96
|
}
|
|
97
|
|
|
98
|
|
|
99
|
@Override
|
|
100
|
public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
|
|
101
|
ResultSet rs = partitioner.getResultSet();
|
|
102
|
Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
|
|
103
|
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
|
|
104
|
try {
|
|
105
|
while (rs.next()){
|
|
106
|
makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);
|
|
107
|
|
|
108
|
}
|
|
109
|
} catch (SQLException e) {
|
|
110
|
e.printStackTrace();
|
|
111
|
}
|
|
112
|
|
|
113
|
getNameService().saveOrUpdate(namesToSave);
|
|
114
|
getTaxonService().saveOrUpdate(taxaToSave);
|
|
115
|
return true;
|
|
116
|
}
|
|
117
|
|
|
118
|
private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
|
|
119
|
throws SQLException {
|
|
120
|
long id = rs.getLong(RedListUtil.NAMNR);
|
|
121
|
String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
|
|
122
|
String relationE = rs.getString(RedListUtil.E);
|
|
123
|
String relationW = rs.getString(RedListUtil.W);
|
|
124
|
String relationK = rs.getString(RedListUtil.K);
|
|
125
|
String relationAW = rs.getString(RedListUtil.AW);
|
|
126
|
String relationAO = rs.getString(RedListUtil.AO);
|
|
127
|
String relationR = rs.getString(RedListUtil.R);
|
|
128
|
String relationO = rs.getString(RedListUtil.O);
|
|
129
|
String relationS = rs.getString(RedListUtil.S);
|
|
130
|
|
|
131
|
//---NAME---
|
|
132
|
NonViralName<?> name = importName(state, rs, namesToSave);
|
|
133
|
|
|
134
|
|
|
135
|
//--- AUTHORS ---
|
|
136
|
importAuthors(state, rs, name);
|
|
137
|
|
|
138
|
//---TAXON---
|
|
139
|
TaxonBase<?> taxonBase = importTaxon(rs, name);
|
|
140
|
if(taxonBase==null){
|
|
141
|
RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
|
|
142
|
return;
|
|
143
|
}
|
|
144
|
|
|
145
|
//---CONCEPT RELATIONSHIPS---
|
|
146
|
//E, W, K, AW, AO, R, O, S
|
|
147
|
cloneTaxon(taxonBase, relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxaToSave, id, state);
|
|
148
|
cloneTaxon(taxonBase, relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxaToSave, id, state);
|
|
149
|
cloneTaxon(taxonBase, relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxaToSave, id, state);
|
|
150
|
cloneTaxon(taxonBase, relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxaToSave, id, state);
|
|
151
|
cloneTaxon(taxonBase, relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxaToSave, id, state);
|
|
152
|
cloneTaxon(taxonBase, relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxaToSave, id, state);
|
|
153
|
cloneTaxon(taxonBase, relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxaToSave, id, state);
|
|
154
|
cloneTaxon(taxonBase, relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxaToSave, id, state);
|
|
155
|
//checklist
|
|
156
|
TaxonBase<?> checklistTaxon = null;
|
|
157
|
if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
|
|
158
|
checklistTaxon = (TaxonBase<?>) taxonBase.clone();
|
|
159
|
if(checklistTaxon.isInstanceOf(Taxon.class)){
|
|
160
|
TaxonRelationship relation = HibernateProxyHelper.deproxy(checklistTaxon, Taxon.class).addTaxonRelation(HibernateProxyHelper.deproxy(taxonBase, Taxon.class), TaxonRelationshipType.CONGRUENT_TO(), null, null);
|
|
161
|
relation.setDoubtful(true);
|
|
162
|
}
|
|
163
|
|
|
164
|
ImportHelper.setOriginalSource(checklistTaxon, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
|
|
165
|
taxaToSave.add(checklistTaxon);
|
|
166
|
}
|
|
167
|
|
|
168
|
//NOTE: the source has to be added after cloning or otherwise the clone would also get the source
|
|
169
|
ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
|
|
170
|
taxaToSave.add(taxonBase);
|
|
171
|
}
|
|
172
|
|
|
173
|
private void cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String relationString, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
|
|
174
|
if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
|
|
175
|
Taxon clonedTaxon = null;
|
|
176
|
|
|
177
|
if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
|
|
178
|
clonedTaxon = HibernateProxyHelper.deproxy(gesamtListeTaxon.clone(), Taxon.class);
|
|
179
|
}
|
|
180
|
else if(gesamtListeTaxon.isInstanceOf(Synonym.class)){
|
|
181
|
clonedTaxon = Taxon.NewInstance(gesamtListeTaxon.getName(), gesamtListeTaxon.getSec());
|
|
182
|
}
|
|
183
|
else{
|
|
184
|
RedListUtil.logMessage(id, "Taxon base "+gesamtListeTaxon+" is neither taxon nor synonym! Taxon could not be cloned", logger);
|
|
185
|
return;
|
|
186
|
}
|
|
187
|
ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace);
|
|
188
|
taxaToSave.add(clonedTaxon);
|
|
189
|
}
|
|
190
|
}
|
|
191
|
|
|
192
|
private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name) throws SQLException {
|
|
193
|
|
|
194
|
long id = rs.getLong(RedListUtil.NAMNR);
|
|
195
|
String taxNameString = rs.getString(RedListUtil.TAXNAME);
|
|
196
|
String gueltString = rs.getString(RedListUtil.GUELT);
|
|
197
|
String trivialString = rs.getString(RedListUtil.TRIVIAL);
|
|
198
|
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
|
|
199
|
String hybString = rs.getString(RedListUtil.HYB);
|
|
200
|
String florString = rs.getString(RedListUtil.FLOR);
|
|
201
|
String atlasIdxString = rs.getString(RedListUtil.ATLAS_IDX);
|
|
202
|
String kartString = rs.getString(RedListUtil.KART);
|
|
203
|
String rl2015String = rs.getString(RedListUtil.RL2015);
|
|
204
|
String ehrdString = rs.getString(RedListUtil.EHRD);
|
|
205
|
String wisskString = rs.getString(RedListUtil.WISSK);
|
|
206
|
|
|
207
|
TaxonBase<?> taxonBase = null;
|
|
208
|
if(authorBasiString.trim().contains(RedListUtil.AUCT)){
|
|
209
|
taxonBase = Taxon.NewInstance(name, null);
|
|
210
|
taxonBase.setAppendedPhrase(RedListUtil.AUCT);
|
|
211
|
}
|
|
212
|
else if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON)){
|
|
213
|
taxonBase = Taxon.NewInstance(name, null);
|
|
214
|
}
|
|
215
|
else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
|
|
216
|
taxonBase = Synonym.NewInstance(name, null);
|
|
217
|
}
|
|
218
|
else{
|
|
219
|
return null;
|
|
220
|
}
|
|
221
|
|
|
222
|
//common name
|
|
223
|
if(taxonBase.isInstanceOf(Taxon.class) && trivialString!=null){
|
|
224
|
Taxon taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
|
|
225
|
TaxonDescription description = TaxonDescription.NewInstance(taxon);
|
|
226
|
description.addElement(CommonTaxonName.NewInstance(trivialString, Language.GERMAN()));
|
|
227
|
}
|
|
228
|
|
|
229
|
//add annotations
|
|
230
|
addAnnotation(RedListUtil.FLOR+": "+florString, taxonBase);
|
|
231
|
addAnnotation(RedListUtil.ATLAS_IDX+": "+atlasIdxString, taxonBase);
|
|
232
|
addAnnotation(RedListUtil.KART+": "+kartString, taxonBase);
|
|
233
|
addAnnotation(RedListUtil.RL2015+": "+rl2015String, taxonBase);
|
|
234
|
addAnnotation(RedListUtil.EHRD+": "+ehrdString, taxonBase);
|
|
235
|
addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase);
|
|
236
|
|
|
237
|
//check taxon name consistency
|
|
238
|
checkTaxonConsistency(id, taxNameString, hybString, taxonBase);
|
|
239
|
return taxonBase;
|
|
240
|
}
|
|
241
|
|
|
242
|
private void addAnnotation(String string, TaxonBase<?> taxonBase) {
|
|
243
|
if(CdmUtils.isNotBlank(string)){
|
|
244
|
taxonBase.addAnnotation(Annotation.NewInstance(string, AnnotationType.TECHNICAL(), Language.GERMAN()));
|
|
245
|
}
|
|
246
|
}
|
|
247
|
|
|
248
|
private void importAuthors(RedListGefaesspflanzenImportState state, ResultSet rs, NonViralName<?> name) throws SQLException {
|
|
249
|
|
|
250
|
long id = rs.getLong(RedListUtil.NAMNR);
|
|
251
|
String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
|
|
252
|
String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
|
|
253
|
String zusatzString = rs.getString(RedListUtil.ZUSATZ);
|
|
254
|
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
|
|
255
|
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
|
|
256
|
String hybString = rs.getString(RedListUtil.HYB);
|
|
257
|
|
|
258
|
//combination author
|
|
259
|
if(authorKombString.contains(RedListUtil.EX)){
|
|
260
|
//TODO: what happens with multiple ex authors??
|
|
261
|
String[] kombSplit = authorKombString.split(RedListUtil.EX);
|
|
262
|
if(kombSplit.length!=2){
|
|
263
|
RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);
|
|
264
|
}
|
|
265
|
for (int i = 0; i < kombSplit.length; i++) {
|
|
266
|
if(i==0){
|
|
267
|
//first author is ex author
|
|
268
|
TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
|
|
269
|
name.setExCombinationAuthorship(authorKomb);
|
|
270
|
}
|
|
271
|
else{
|
|
272
|
TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
|
|
273
|
name.setCombinationAuthorship(authorKomb);
|
|
274
|
}
|
|
275
|
}
|
|
276
|
}
|
|
277
|
else if(authorKombString.trim().contains(RedListUtil.AUCT)){
|
|
278
|
RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
|
|
279
|
}
|
|
280
|
else if(CdmUtils.isNotBlank(authorKombString)){
|
|
281
|
TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
|
|
282
|
name.setCombinationAuthorship(authorKomb);
|
|
283
|
}
|
|
284
|
//basionym author
|
|
285
|
if(authorBasiString.contains(RedListUtil.EX)){
|
|
286
|
String[] basiSplit = authorBasiString.split(RedListUtil.EX);
|
|
287
|
for (int i = 0; i < basiSplit.length; i++) {
|
|
288
|
if(basiSplit.length!=2){
|
|
289
|
RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);
|
|
290
|
}
|
|
291
|
if(i==0){
|
|
292
|
TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
|
|
293
|
if(CdmUtils.isBlank(authorKombString)){
|
|
294
|
name.setExCombinationAuthorship(authorBasi);
|
|
295
|
}
|
|
296
|
else{
|
|
297
|
name.setExBasionymAuthorship(authorBasi);
|
|
298
|
}
|
|
299
|
}
|
|
300
|
else{
|
|
301
|
TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
|
|
302
|
if(CdmUtils.isBlank(authorKombString)){
|
|
303
|
name.setCombinationAuthorship(authorBasi);
|
|
304
|
}
|
|
305
|
else{
|
|
306
|
name.setBasionymAuthorship(authorBasi);
|
|
307
|
}
|
|
308
|
}
|
|
309
|
}
|
|
310
|
}
|
|
311
|
else if(CdmUtils.isNotBlank(authorBasiString)){
|
|
312
|
//this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used
|
|
313
|
TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
|
|
314
|
if(CdmUtils.isBlank(authorKombString)){
|
|
315
|
name.setCombinationAuthorship(authorBasi);
|
|
316
|
}
|
|
317
|
else{
|
|
318
|
name.setBasionymAuthorship(authorBasi);
|
|
319
|
}
|
|
320
|
}
|
|
321
|
|
|
322
|
//check authorship consistency
|
|
323
|
String authorString = rs.getString(RedListUtil.AUTOR);
|
|
324
|
checkNameConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, hybString, name);
|
|
325
|
}
|
|
326
|
|
|
327
|
private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
|
|
328
|
|
|
329
|
long id = rs.getLong(RedListUtil.NAMNR);
|
|
330
|
String taxNameString = rs.getString(RedListUtil.TAXNAME);
|
|
331
|
String rangString = rs.getString(RedListUtil.RANG);
|
|
332
|
String ep1String = rs.getString(RedListUtil.EPI1);
|
|
333
|
String ep2String = rs.getString(RedListUtil.EPI2);
|
|
334
|
String ep3String = rs.getString(RedListUtil.EPI3);
|
|
335
|
String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
|
|
336
|
String hybString = rs.getString(RedListUtil.HYB);
|
|
337
|
String formelString = rs.getString(RedListUtil.FORMEL);
|
|
338
|
|
|
339
|
if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
|
|
340
|
RedListUtil.logMessage(id, "No name found!", logger);
|
|
341
|
}
|
|
342
|
|
|
343
|
NonViralName<?> name = null;
|
|
344
|
Rank rank = makeRank(id, state, rangString, ep3String!=null);
|
|
345
|
//cultivar
|
|
346
|
if(rank!= null && rank.equals(Rank.CULTIVAR())){
|
|
347
|
CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank);
|
|
348
|
cultivar.setGenusOrUninomial(ep1String);
|
|
349
|
cultivar.setSpecificEpithet(ep2String);
|
|
350
|
cultivar.setCultivarName(ep3String);
|
|
351
|
name = cultivar;
|
|
352
|
}
|
|
353
|
//botanical names
|
|
354
|
else{
|
|
355
|
name = BotanicalName.NewInstance(rank);
|
|
356
|
|
|
357
|
//ep1 should always be present
|
|
358
|
if(CdmUtils.isBlank(ep1String)){
|
|
359
|
RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
|
|
360
|
}
|
|
361
|
name.setGenusOrUninomial(ep1String);
|
|
362
|
if(CdmUtils.isNotBlank(ep2String)){
|
|
363
|
if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
|
|
364
|
name.setInfraGenericEpithet(ep2String);
|
|
365
|
}
|
|
366
|
else{
|
|
367
|
name.setSpecificEpithet(ep2String);
|
|
368
|
}
|
|
369
|
}
|
|
370
|
if(CdmUtils.isNotBlank(ep3String)){
|
|
371
|
name.setInfraSpecificEpithet(ep3String);
|
|
372
|
}
|
|
373
|
|
|
374
|
|
|
375
|
//nomenclatural status
|
|
376
|
if(CdmUtils.isNotBlank(nomZusatzString)){
|
|
377
|
NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
|
|
378
|
if(statusType!=null){
|
|
379
|
NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType);
|
|
380
|
//special case for invalid names where the DB entry contains
|
|
381
|
//additional information in brackets e.g. "nom. inval. (sine basion.)"
|
|
382
|
if(statusType.equals(NomenclaturalStatusType.INVALID())){
|
|
383
|
Pattern pattern = Pattern.compile("\\((.*?)\\)");
|
|
384
|
Matcher matcher = pattern.matcher(nomZusatzString);
|
|
385
|
if (matcher.find()){
|
|
386
|
status.setRuleConsidered(matcher.group(1));
|
|
387
|
}
|
|
388
|
}
|
|
389
|
name.addStatus(status);
|
|
390
|
}
|
|
391
|
}
|
|
392
|
//hybrid
|
|
393
|
if(CdmUtils.isNotBlank(hybString)){
|
|
394
|
//save hybrid formula
|
|
395
|
if(CdmUtils.isNotBlank(formelString)){
|
|
396
|
Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
|
|
397
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
|
398
|
name.addAnnotation(annotation);
|
|
399
|
}
|
|
400
|
|
|
401
|
if(hybString.equals(RedListUtil.HYB_X)){
|
|
402
|
name.setBinomHybrid(true);
|
|
403
|
}
|
|
404
|
else if(hybString.equals(RedListUtil.HYB_G)){
|
|
405
|
name.setMonomHybrid(true);
|
|
406
|
}
|
|
407
|
else if(hybString.equals(RedListUtil.HYB_XF)){
|
|
408
|
name.setHybridFormula(true);
|
|
409
|
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
|
410
|
RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger);
|
|
411
|
}
|
|
412
|
else if(ep2String.contains(RedListUtil.HYB_SIGN)){
|
|
413
|
String[] split = ep2String.split(RedListUtil.HYB_SIGN);
|
|
414
|
if(split.length!=2){
|
|
415
|
RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep2String, logger);
|
|
416
|
}
|
|
417
|
String hybridFormula1 = ep1String+" "+split[0].trim();
|
|
418
|
String hybridFormula2 = ep1String+" "+split[1].trim();
|
|
419
|
if(CdmUtils.isNotBlank(ep3String)){
|
|
420
|
hybridFormula1 += " "+ep3String;
|
|
421
|
hybridFormula2 += " "+ep3String;
|
|
422
|
}
|
|
423
|
String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
|
|
424
|
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
|
|
425
|
}
|
|
426
|
else if(ep3String.contains(RedListUtil.HYB_SIGN)){
|
|
427
|
String[] split = ep3String.split(RedListUtil.HYB_SIGN);
|
|
428
|
if(split.length!=2){
|
|
429
|
RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep3String, logger);
|
|
430
|
}
|
|
431
|
String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
|
|
432
|
String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
|
|
433
|
String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
|
|
434
|
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
|
|
435
|
}
|
|
436
|
}
|
|
437
|
else if(hybString.equals(RedListUtil.HYB_N)){
|
|
438
|
name = NonViralNameParserImpl.NewInstance().parseFullName(taxNameString);
|
|
439
|
}
|
|
440
|
else if(hybString.equals(RedListUtil.HYB_GF)){
|
|
441
|
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
|
442
|
name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String);
|
|
443
|
}
|
|
444
|
else{
|
|
445
|
RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
|
|
446
|
}
|
|
447
|
}
|
|
448
|
else if(hybString.equals(RedListUtil.HYB_XS)){
|
|
449
|
//nothing to do
|
|
450
|
}
|
|
451
|
else{
|
|
452
|
logger.error("HYB value "+hybString+" not yet handled");
|
|
453
|
}
|
|
454
|
}
|
|
455
|
}
|
|
456
|
//add source
|
|
457
|
ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
|
|
458
|
|
|
459
|
namesToSave.add(name);
|
|
460
|
return name;
|
|
461
|
}
|
|
462
|
|
|
463
|
private void checkNameConsistency(long id, String nomZusatzString, String taxZusatzString,
|
|
464
|
String zusatzString, String authorString, String hybString, NonViralName<?> name) {
|
|
465
|
String authorshipCache = name.getAuthorshipCache();
|
|
466
|
if(hybString.equals(RedListUtil.HYB_XF)){
|
|
467
|
if(name.getHybridChildRelations().isEmpty()){
|
|
468
|
RedListUtil.logMessage(id, "Hybrid formula but no hybrid child relations: "+name.getTitleCache(), logger);
|
|
469
|
return;
|
|
470
|
}
|
|
471
|
return;
|
|
472
|
}
|
|
473
|
|
|
474
|
if(CdmUtils.isNotBlank(zusatzString)){
|
|
475
|
authorString = authorString.replace(", "+zusatzString, "");
|
|
476
|
}
|
|
477
|
if(CdmUtils.isNotBlank(nomZusatzString)){
|
|
478
|
authorString = authorString.replace(", "+nomZusatzString, "");
|
|
479
|
}
|
|
480
|
if(CdmUtils.isNotBlank(taxZusatzString)){
|
|
481
|
authorString = authorString.replace(", "+taxZusatzString, "");
|
|
482
|
}
|
|
483
|
if(authorString.equals(RedListUtil.AUCT)){
|
|
484
|
authorString = "";
|
|
485
|
}
|
|
486
|
if(STRICT_TITLE_CHECK){
|
|
487
|
if(!authorString.equals(authorshipCache)){
|
|
488
|
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
|
|
489
|
}
|
|
490
|
}
|
|
491
|
else{
|
|
492
|
if(CdmUtils.isNotBlank(authorString) && !authorString.startsWith(authorshipCache)){
|
|
493
|
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
|
|
494
|
}
|
|
495
|
}
|
|
496
|
}
|
|
497
|
|
|
498
|
private void checkTaxonConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase) {
|
|
499
|
String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim();
|
|
500
|
taxNameString = taxNameString.trim();
|
|
501
|
taxNameString.replaceAll(" +", " ");
|
|
502
|
|
|
503
|
if(taxNameString.endsWith("agg.")){
|
|
504
|
taxNameString = taxNameString.replace("agg.", "aggr.");
|
|
505
|
}
|
|
506
|
|
|
507
|
if(hybString.equals(RedListUtil.HYB_X)){
|
|
508
|
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);//hybrid sign has no space after it in titleCache for binomial hybrids
|
|
509
|
taxNameString = taxNameString.replace(" x ", " "+RedListUtil.HYB_SIGN);//in some cases a standard 'x' is used
|
|
510
|
}
|
|
511
|
else if(hybString.equals(RedListUtil.HYB_G)){
|
|
512
|
taxNameString = taxNameString.replace("X ", RedListUtil.HYB_SIGN);
|
|
513
|
}
|
|
514
|
else if(hybString.equals(RedListUtil.HYB_GF)){
|
|
515
|
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN, " x");
|
|
516
|
}
|
|
517
|
|
|
518
|
if(taxNameString.endsWith("- Gruppe")){
|
|
519
|
taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
|
|
520
|
}
|
|
521
|
if(taxNameString.endsWith("- group")){
|
|
522
|
taxNameString = taxNameString.replaceAll("- group", "species group");
|
|
523
|
}
|
|
524
|
|
|
525
|
taxNameString = taxNameString.replace("[ranglos]", "[unranked]");
|
|
526
|
if(STRICT_TITLE_CHECK){
|
|
527
|
if(!taxNameString.trim().equals(nameCache)){
|
|
528
|
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
529
|
}
|
|
530
|
}
|
|
531
|
else{
|
|
532
|
if(!taxNameString.startsWith(nameCache)){
|
|
533
|
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
534
|
}
|
|
535
|
}
|
|
536
|
}
|
|
537
|
|
|
538
|
private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr, boolean hasSpecificEpithet) {
|
|
539
|
Rank rank = null;
|
|
540
|
try {
|
|
541
|
if(rankStr.equals("ORA")){
|
|
542
|
//special handling for ORA because of two possibilities
|
|
543
|
if(hasSpecificEpithet){
|
|
544
|
return Rank.UNRANKED_INFRASPECIFIC();
|
|
545
|
}
|
|
546
|
else{
|
|
547
|
return Rank.UNRANKED_INFRAGENERIC();
|
|
548
|
}
|
|
549
|
}
|
|
550
|
else{
|
|
551
|
rank = state.getTransformer().getRankByKey(rankStr);
|
|
552
|
}
|
|
553
|
} catch (UndefinedTransformerMethodException e) {
|
|
554
|
e.printStackTrace();
|
|
555
|
}
|
|
556
|
if(rank==null){
|
|
557
|
RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
|
|
558
|
}
|
|
559
|
return rank;
|
|
560
|
}
|
|
561
|
|
|
562
|
private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
|
|
563
|
NomenclaturalStatusType status = null;
|
|
564
|
try {
|
|
565
|
status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
|
|
566
|
} catch (UndefinedTransformerMethodException e) {
|
|
567
|
e.printStackTrace();
|
|
568
|
}
|
|
569
|
if(status==null){
|
|
570
|
RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
|
|
571
|
}
|
|
572
|
return status;
|
|
573
|
}
|
|
574
|
|
|
575
|
|
|
576
|
|
|
577
|
@Override
|
|
578
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
|
|
579
|
RedListGefaesspflanzenImportState state) {
|
|
580
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
581
|
Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
|
|
582
|
|
|
583
|
try {
|
|
584
|
while (rs.next()){
|
|
585
|
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
|
|
586
|
|
|
587
|
if(authorKombString.contains(RedListUtil.EX)){
|
|
588
|
String[] kombSplit = authorKombString.split(RedListUtil.EX);
|
|
589
|
for (int i = 0; i < kombSplit.length; i++) {
|
|
590
|
if(!authorMap.containsKey(kombSplit[i])){
|
|
591
|
authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
|
|
592
|
}
|
|
593
|
}
|
|
594
|
}
|
|
595
|
else if(CdmUtils.isNotBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
|
|
596
|
authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
|
|
597
|
}
|
|
598
|
|
|
599
|
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
|
|
600
|
//basionym author
|
|
601
|
if(authorBasiString.contains(RedListUtil.EX)){
|
|
602
|
String[] basiSplit = authorBasiString.split(RedListUtil.EX);
|
|
603
|
for (int i = 0; i < basiSplit.length; i++) {
|
|
604
|
if(!authorMap.containsKey(basiSplit[i])){
|
|
605
|
authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
|
|
606
|
}
|
|
607
|
}
|
|
608
|
}
|
|
609
|
else if(CdmUtils.isNotBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
|
|
610
|
authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
|
|
611
|
}
|
|
612
|
}
|
|
613
|
} catch (SQLException e) {
|
|
614
|
e.printStackTrace();
|
|
615
|
}
|
|
616
|
result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
|
|
617
|
|
|
618
|
return result;
|
|
619
|
}
|
|
620
|
|
|
621
|
@Override
|
|
622
|
protected boolean doCheck(RedListGefaesspflanzenImportState state) {
|
|
623
|
return false;
|
|
624
|
}
|
|
625
|
|
|
626
|
@Override
|
|
627
|
protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
|
|
628
|
return false;
|
|
629
|
}
|
|
630
|
|
|
631
|
}
|