1
|
/**
|
2
|
* Copyright (C) 2009 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
|
package eu.etaxonomy.cdm.io.pesi.out;
|
10
|
|
11
|
import java.sql.Connection;
|
12
|
import java.sql.PreparedStatement;
|
13
|
import java.util.ArrayList;
|
14
|
import java.util.List;
|
15
|
|
16
|
import org.apache.log4j.Logger;
|
17
|
import org.springframework.stereotype.Component;
|
18
|
import org.springframework.transaction.TransactionStatus;
|
19
|
|
20
|
import eu.etaxonomy.cdm.io.common.Source;
|
21
|
import eu.etaxonomy.cdm.io.common.mapping.out.DbAnnotationMapper;
|
22
|
import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedIntegerMapper;
|
23
|
import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedStringMapper;
|
24
|
import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;
|
25
|
import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
|
26
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
27
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
28
|
import eu.etaxonomy.cdm.model.common.RelationshipBase;
|
29
|
import eu.etaxonomy.cdm.model.name.HybridRelationship;
|
30
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
31
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
32
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
33
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
34
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
35
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
36
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
37
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
38
|
|
39
|
/**
|
40
|
* The export class for relations between {@link eu.etaxonomy.cdm.model.taxon.TaxonBase TaxonBases}.<p>
|
41
|
* Inserts into DataWarehouse database table <code>RelTaxon</code>.
|
42
|
* @author e.-m.lee
|
43
|
* @since 23.02.2010
|
44
|
*/
|
45
|
@Component
|
46
|
public class PesiRelTaxonExport extends PesiExportBase {
|
47
|
|
48
|
private static final long serialVersionUID = 67808745337549629L;
|
49
|
private static final Logger logger = Logger.getLogger(PesiRelTaxonExport.class);
|
50
|
|
51
|
private static final Class<? extends CdmBase> standardMethodParameter = RelationshipBase.class;
|
52
|
|
53
|
private static int modCount = 1000;
|
54
|
private static final String dbTableName = "RelTaxon";
|
55
|
private static final String pluralString = "Relationships";
|
56
|
private static PreparedStatement synonymsStmt;
|
57
|
|
58
|
private PesiExportMapping mapping;
|
59
|
private PesiExportMapping synonymMapping;
|
60
|
private PesiExportMapping taxonNodeMapping;
|
61
|
|
62
|
public PesiRelTaxonExport() {
|
63
|
super();
|
64
|
}
|
65
|
|
66
|
@Override
|
67
|
public Class<? extends CdmBase> getStandardMethodParameter() {
|
68
|
return standardMethodParameter;
|
69
|
}
|
70
|
|
71
|
@Override
|
72
|
protected void doInvoke(PesiExportState state) {
|
73
|
try {
|
74
|
logger.info("*** Started Making " + pluralString + " ...");
|
75
|
|
76
|
doDelete(state);
|
77
|
|
78
|
Connection connection = state.getConfig().getDestination().getConnection();
|
79
|
String synonymsSql = "UPDATE Taxon SET KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?";
|
80
|
synonymsStmt = connection.prepareStatement(synonymsSql);
|
81
|
|
82
|
// Stores whether this invoke was successful or not.
|
83
|
boolean success = true;
|
84
|
|
85
|
// PESI: Clear the database table RelTaxon.
|
86
|
//doDelete(state); -> done by stored procedure
|
87
|
|
88
|
// Get specific mappings: (CDM) Relationship -> (PESI) RelTaxon
|
89
|
mapping = getMapping();
|
90
|
mapping.initialize(state);
|
91
|
|
92
|
// Get specific mappings: (CDM) Synonym -> (PESI) RelTaxon
|
93
|
synonymMapping = getSynonymMapping();
|
94
|
synonymMapping.initialize(state);
|
95
|
|
96
|
// Get specific mappings: (CDM) Synonym -> (PESI) RelTaxon
|
97
|
taxonNodeMapping = getTaxonNodeMapping();
|
98
|
taxonNodeMapping.initialize(state);
|
99
|
|
100
|
|
101
|
//Export taxon relations
|
102
|
success &= doPhase01(state, mapping);
|
103
|
|
104
|
//Export taxon nodes
|
105
|
success &= doPhase01b(state, taxonNodeMapping);
|
106
|
|
107
|
// Export name relations
|
108
|
success &= doPhase02(state, mapping);
|
109
|
|
110
|
// Export synonym relations (directly attached to taxa)
|
111
|
success &= doPhase03(state, synonymMapping);
|
112
|
|
113
|
if (! success){
|
114
|
state.getResult().addError("An unknown error occurred in PesiRelTaxonExport");
|
115
|
}
|
116
|
} catch (Exception e) {
|
117
|
e.printStackTrace();
|
118
|
logger.error(e.getMessage());
|
119
|
state.getResult().addException(e);
|
120
|
return;
|
121
|
}
|
122
|
}
|
123
|
|
124
|
private boolean doPhase03(PesiExportState state, PesiExportMapping synonymMapping) {
|
125
|
logger.info("PHASE 3: Direct Synonym Relationships ...");
|
126
|
|
127
|
boolean success = true;
|
128
|
int limit = state.getConfig().getLimitSave();
|
129
|
// Start transaction
|
130
|
TransactionStatus txStatus = startTransaction(true);
|
131
|
logger.debug("Started new transaction. Fetching some synonyms (max: " + limit + ") ...");
|
132
|
|
133
|
List<Synonym> list;
|
134
|
|
135
|
//taxon relations
|
136
|
int partitionCount = 0;
|
137
|
int totalCount = 0;
|
138
|
while ((list = getNextTaxonPartition(Synonym.class, limit, partitionCount++, null))!= null) {
|
139
|
totalCount = totalCount + list.size();
|
140
|
logger.info("Read " + list.size() + " PESI synonyms. Limit: " + limit + ". Total: " + totalCount );
|
141
|
// if (list.size() > 0){
|
142
|
// logger.warn("First relation type is " + list.get(0).getType().getTitleCache());
|
143
|
// }
|
144
|
for (Synonym synonym : list){
|
145
|
try {
|
146
|
synonymMapping.invoke(synonym);
|
147
|
} catch (Exception e) {
|
148
|
logger.error(e.getMessage() + ". Synonym: " + synonym.getUuid());
|
149
|
e.printStackTrace();
|
150
|
}
|
151
|
}
|
152
|
|
153
|
commitTransaction(txStatus);
|
154
|
txStatus = startTransaction();
|
155
|
}
|
156
|
commitTransaction(txStatus);
|
157
|
return success;
|
158
|
}
|
159
|
|
160
|
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping) {
|
161
|
logger.info("PHASE 1: Taxon Relationships ...");
|
162
|
boolean success = true;
|
163
|
|
164
|
int limit = state.getConfig().getLimitSave();
|
165
|
// Start transaction
|
166
|
TransactionStatus txStatus = startTransaction(true);
|
167
|
logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
168
|
|
169
|
List<RelationshipBase<?,?,?>> list;
|
170
|
|
171
|
//taxon relations
|
172
|
int partitionCount = 0;
|
173
|
int totalCount = 0;
|
174
|
while ((list = getNextTaxonRelationshipPartition(limit, partitionCount++, null)) != null) {
|
175
|
totalCount = totalCount + list.size();
|
176
|
logger.info("Read " + list.size() + " PESI relations. Limit: " + limit + ". Total: " + totalCount );
|
177
|
// if (list.size() > 0){
|
178
|
// logger.warn("First relation type is " + list.get(0).getType().getTitleCache());
|
179
|
// }
|
180
|
for (RelationshipBase<?,?,?> rel : list){
|
181
|
try {
|
182
|
mapping.invoke(rel);
|
183
|
} catch (Exception e) {
|
184
|
logger.error(e.getMessage() + ". Relationship: " + rel.getUuid());
|
185
|
e.printStackTrace();
|
186
|
}
|
187
|
}
|
188
|
|
189
|
commitTransaction(txStatus);
|
190
|
txStatus = startTransaction();
|
191
|
}
|
192
|
commitTransaction(txStatus);
|
193
|
return success;
|
194
|
}
|
195
|
|
196
|
private boolean doPhase01b(PesiExportState state, PesiExportMapping taxonNodeMapping) {
|
197
|
logger.info("PHASE 1b: Taxonnodes ...");
|
198
|
boolean success = true;
|
199
|
|
200
|
int limit = state.getConfig().getLimitSave();
|
201
|
// Start transaction
|
202
|
TransactionStatus txStatus = startTransaction(true);
|
203
|
logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
204
|
|
205
|
List<TaxonNode> list;
|
206
|
|
207
|
//taxon nodes
|
208
|
int partitionCount = 0;
|
209
|
int totalCount = 0;
|
210
|
while ((list = getNextTaxonNodePartition(limit, partitionCount++, null)) != null) {
|
211
|
totalCount = totalCount + list.size();
|
212
|
logger.info("Read " + list.size() + " PESI taxon nodes. Limit: " + limit + ". Total: " + totalCount );
|
213
|
for (TaxonNode tn : list){
|
214
|
try {
|
215
|
taxonNodeMapping.invoke(tn);
|
216
|
} catch (Exception e) {
|
217
|
logger.error(e.getMessage() + ". TaxonNode: " + tn.getUuid());
|
218
|
e.printStackTrace();
|
219
|
}
|
220
|
}
|
221
|
|
222
|
commitTransaction(txStatus);
|
223
|
txStatus = startTransaction();
|
224
|
}
|
225
|
commitTransaction(txStatus);
|
226
|
return success;
|
227
|
}
|
228
|
|
229
|
private boolean doPhase02(PesiExportState state, PesiExportMapping mapping2) {
|
230
|
logger.info("PHASE 2: Name Relationships ...");
|
231
|
boolean success = true;
|
232
|
|
233
|
int limit = state.getConfig().getLimitSave();
|
234
|
// Start transaction
|
235
|
TransactionStatus txStatus = startTransaction(true);
|
236
|
logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
237
|
|
238
|
//name relations
|
239
|
List<NameRelationship> list;
|
240
|
int partitionCount = 0;
|
241
|
while ((list = getNextNameRelationshipPartition(NameRelationship.class, limit, partitionCount++, null)) != null ) {
|
242
|
txStatus = handleNameRelationList(state, txStatus, list);
|
243
|
}
|
244
|
//hybrid relations
|
245
|
List<HybridRelationship> hybridList;
|
246
|
partitionCount = 0;
|
247
|
while ((hybridList = getNextNameRelationshipPartition(HybridRelationship.class, limit, partitionCount++, null)) != null ) {
|
248
|
txStatus = handleNameRelationList(state, txStatus, hybridList);
|
249
|
}
|
250
|
commitTransaction(txStatus);
|
251
|
logger.info("End PHASE 2: Name Relationships ...");
|
252
|
state.setCurrentFromObject(null);
|
253
|
state.setCurrentToObject(null);
|
254
|
return success;
|
255
|
}
|
256
|
|
257
|
private TransactionStatus handleNameRelationList(PesiExportState state, TransactionStatus txStatus,
|
258
|
List<? extends RelationshipBase<?,?,?>> list) {
|
259
|
for (RelationshipBase<?,?,?> rel : list){
|
260
|
try {
|
261
|
TaxonName name1;
|
262
|
TaxonName name2;
|
263
|
if (rel.isInstanceOf(HybridRelationship.class)){
|
264
|
HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class);
|
265
|
name1 = hybridRel.getParentName();
|
266
|
name2 = hybridRel.getHybridName();
|
267
|
}else if (rel.isInstanceOf(NameRelationship.class)){
|
268
|
NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class);
|
269
|
name1 = nameRel.getFromName();
|
270
|
name2 = nameRel.getToName();
|
271
|
}else{
|
272
|
logger.warn ("Only hybrid- and name-relationships allowed here");
|
273
|
continue;
|
274
|
}
|
275
|
List<IdentifiableEntity> fromList = new ArrayList<>();
|
276
|
List<IdentifiableEntity> toList = new ArrayList<>();
|
277
|
makeList(name1, fromList);
|
278
|
makeList(name2, toList);
|
279
|
|
280
|
for (IdentifiableEntity<?> fromEntity : fromList){
|
281
|
for (IdentifiableEntity<?> toEntity : toList){
|
282
|
//TODO set entities to state
|
283
|
state.setCurrentFromObject(fromEntity);
|
284
|
state.setCurrentToObject(toEntity);
|
285
|
mapping.invoke(rel);
|
286
|
}
|
287
|
}
|
288
|
fromList = null;
|
289
|
toList = null;
|
290
|
|
291
|
} catch (Exception e) {
|
292
|
logger.error(e.getMessage() + ". Relationship: " + rel.getUuid());
|
293
|
e.printStackTrace();
|
294
|
}
|
295
|
}
|
296
|
commitTransaction(txStatus);
|
297
|
txStatus = startTransaction();
|
298
|
return txStatus;
|
299
|
}
|
300
|
|
301
|
private void makeList(TaxonName name, List<IdentifiableEntity> list) {
|
302
|
if (! hasPesiTaxon(name)){
|
303
|
list.add(name);
|
304
|
}else{
|
305
|
for (TaxonBase<?> taxon: getPesiTaxa(name)){
|
306
|
list.add(taxon);
|
307
|
}
|
308
|
}
|
309
|
}
|
310
|
|
311
|
/**
|
312
|
* Deletes all entries of database tables related to <code>RelTaxon</code>.
|
313
|
* @param state The {@link PesiExportState PesiExportState}.
|
314
|
* @return Whether the delete operation was successful or not.
|
315
|
*/
|
316
|
protected boolean doDelete(PesiExportState state) {
|
317
|
PesiExportConfigurator pesiConfig = state.getConfig();
|
318
|
|
319
|
Source destination = pesiConfig.getDestination();
|
320
|
|
321
|
// Clear RelTaxon
|
322
|
String sql = "DELETE FROM " + dbTableName;
|
323
|
destination.update(sql);
|
324
|
return true;
|
325
|
}
|
326
|
|
327
|
/**
|
328
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.
|
329
|
* @param relationship The {@link RelationshipBase Relationship}.
|
330
|
* @param state The {@link PesiExportState PesiExportState}.
|
331
|
* @return The <code>TaxonFk1</code> attribute.
|
332
|
* @see MethodMapper
|
333
|
*/
|
334
|
@SuppressWarnings("unused")
|
335
|
private static Integer getTaxonFk1(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
336
|
return getObjectFk(relationship, state, true);
|
337
|
}
|
338
|
|
339
|
/**
|
340
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.
|
341
|
* @param relationship The {@link RelationshipBase Relationship}.
|
342
|
* @param state The {@link PesiExportState PesiExportState}.
|
343
|
* @return The <code>TaxonFk1</code> attribute.
|
344
|
* @see MethodMapper
|
345
|
*/
|
346
|
@SuppressWarnings("unused")
|
347
|
private static Integer getTaxonFk1(Synonym synonym, PesiExportState state) {
|
348
|
return synonym.getAcceptedTaxon().getId();
|
349
|
}
|
350
|
/**
|
351
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>Synonym</code>.
|
352
|
* @param synonym The {@link Synonym synonym}.
|
353
|
* @param state The {@link PesiExportState PesiExportState}.
|
354
|
* @return The <code>TaxonFk1</code> attribute.
|
355
|
* @see MethodMapper
|
356
|
*/
|
357
|
@SuppressWarnings("unused")
|
358
|
private static Integer getSynonym(Synonym synonym, PesiExportState state) {
|
359
|
return state.getDbId(synonym);
|
360
|
}
|
361
|
|
362
|
/**
|
363
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>Synonym</code>.
|
364
|
* @param synonym The {@link Synonym synonym}.
|
365
|
* @param state The {@link PesiExportState PesiExportState}.
|
366
|
* @return The <code>TaxonFk1</code> attribute.
|
367
|
* @see MethodMapper
|
368
|
*/
|
369
|
@SuppressWarnings("unused")
|
370
|
private static Integer getParent(TaxonNode taxonNode, PesiExportState state) {
|
371
|
TaxonNode parent = taxonNode == null? null : taxonNode.getParent();
|
372
|
Taxon parentTaxon = parent == null? null: parent.getTaxon();
|
373
|
return state.getDbId(parentTaxon);
|
374
|
}
|
375
|
|
376
|
/**
|
377
|
* Returns the <code>TaxonFk2</code> attribute. It corresponds to a CDM <code>SynonymRelationship</code>.
|
378
|
* @param relationship The {@link RelationshipBase Relationship}.
|
379
|
* @param state The {@link PesiExportState PesiExportState}.
|
380
|
* @return The <code>TaxonFk2</code> attribute.
|
381
|
* @see MethodMapper
|
382
|
*/
|
383
|
@SuppressWarnings("unused")
|
384
|
private static Integer getTaxonFk2(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
385
|
return getObjectFk(relationship, state, false);
|
386
|
}
|
387
|
|
388
|
/**
|
389
|
* Returns the <code>RelTaxonQualifierFk</code> attribute.
|
390
|
* @param relationship The {@link RelationshipBase Relationship}.
|
391
|
* @return The <code>RelTaxonQualifierFk</code> attribute.
|
392
|
* @see MethodMapper
|
393
|
*/
|
394
|
@SuppressWarnings("unused")
|
395
|
private static Integer getRelTaxonQualifierFk(RelationshipBase<?, ?, ?> relationship) {
|
396
|
return PesiTransformer.taxonRelation2RelTaxonQualifierFk(relationship);
|
397
|
}
|
398
|
|
399
|
@SuppressWarnings("unused")
|
400
|
private static Integer getRelTaxonQualifierFk(Synonym synonym) {
|
401
|
return PesiTransformer.synonym2RelTaxonQualifierFk(synonym);
|
402
|
}
|
403
|
|
404
|
/**
|
405
|
* Returns the <code>RelQualifierCache</code> attribute.
|
406
|
* @param relationship The {@link RelationshipBase Relationship}.
|
407
|
* @return The <code>RelQualifierCache</code> attribute.
|
408
|
* @see MethodMapper
|
409
|
*/
|
410
|
@SuppressWarnings("unused")
|
411
|
private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
412
|
String result = null;
|
413
|
NomenclaturalCode code = null;
|
414
|
Taxon taxon = null;
|
415
|
TaxonName name= null;
|
416
|
if (relationship.isInstanceOf(TaxonRelationship.class)){
|
417
|
TaxonRelationship rel = CdmBase.deproxy(relationship, TaxonRelationship.class);
|
418
|
taxon = rel.getToTaxon();
|
419
|
name = taxon.getName();
|
420
|
code = name.getNameType();
|
421
|
}else if (relationship.isInstanceOf(NameRelationship.class)){
|
422
|
NameRelationship rel = CdmBase.deproxy(relationship, NameRelationship.class);
|
423
|
name = rel.getFromName();
|
424
|
code =name.getNameType();
|
425
|
}else if (relationship.isInstanceOf(HybridRelationship.class)){
|
426
|
HybridRelationship rel = CdmBase.deproxy(relationship, HybridRelationship.class);
|
427
|
name = rel.getParentName();
|
428
|
code = name.getNameType();
|
429
|
}
|
430
|
if (code != null) {
|
431
|
result = state.getConfig().getTransformer().getCacheByRelationshipType(relationship, code);
|
432
|
} else {
|
433
|
logger.error("NomenclaturalCode is NULL while creating the following relationship: " + relationship.getUuid());
|
434
|
}
|
435
|
return result;
|
436
|
}
|
437
|
|
438
|
|
439
|
/**
|
440
|
* Returns the database key of an object in the given relationship.
|
441
|
* @param relationship {@link RelationshipBase RelationshipBase}.
|
442
|
* @param state {@link PesiExportState PesiExportState}.
|
443
|
* @param isFrom A boolean value indicating whether the database key of the parent or child in this relationship is searched. <code>true</code> means the child is searched. <code>false</code> means the parent is searched.
|
444
|
* @return The database key of an object in the given relationship.
|
445
|
*/
|
446
|
private static Integer getObjectFk(RelationshipBase<?, ?, ?> relationship, PesiExportState state, boolean isFrom) {
|
447
|
TaxonBase<?> taxonBase = null;
|
448
|
if (relationship.isInstanceOf(TaxonRelationship.class)) {
|
449
|
TaxonRelationship tr = (TaxonRelationship)relationship;
|
450
|
taxonBase = (isFrom) ? tr.getFromTaxon(): tr.getToTaxon();
|
451
|
} else if (relationship.isInstanceOf(NameRelationship.class) || relationship.isInstanceOf(HybridRelationship.class)) {
|
452
|
if (isFrom){
|
453
|
return state.getDbId(state.getCurrentFromObject());
|
454
|
}else{
|
455
|
return state.getDbId(state.getCurrentToObject());
|
456
|
}
|
457
|
}
|
458
|
if (taxonBase != null) {
|
459
|
if (! isPesiTaxon(taxonBase)){
|
460
|
logger.warn("Related taxonBase is not a PESI taxon. Taxon: " + taxonBase.getId() + "/" + taxonBase.getUuid() + "; TaxonRel: " + relationship.getId() + "(" + relationship.getType().getTitleCache() + ")");
|
461
|
return null;
|
462
|
}else{
|
463
|
return state.getDbId(taxonBase);
|
464
|
}
|
465
|
|
466
|
}
|
467
|
logger.warn("No taxon found in state for relationship: " + relationship.toString());
|
468
|
return null;
|
469
|
}
|
470
|
|
471
|
@SuppressWarnings("unused") //for synonym mapping
|
472
|
private static String getSynonymTypeCache(Synonym synonym, PesiExportState state) {
|
473
|
String result = null;
|
474
|
NomenclaturalCode code = null;
|
475
|
code = synonym.getAcceptedTaxon().getName().getNameType();
|
476
|
|
477
|
if (code != null) {
|
478
|
result = state.getConfig().getTransformer().getCacheBySynonymType(synonym, code);
|
479
|
} else {
|
480
|
logger.error("NomenclaturalCode is NULL while creating the following synonym: " + synonym.getUuid());
|
481
|
}
|
482
|
return result;
|
483
|
}
|
484
|
|
485
|
/**
|
486
|
* Returns the CDM to PESI specific export mappings.
|
487
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
488
|
*/
|
489
|
PesiExportMapping getMapping() {
|
490
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
491
|
|
492
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getTaxonFk1", standardMethodParameter, PesiExportState.class));
|
493
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getTaxonFk2", standardMethodParameter, PesiExportState.class));
|
494
|
mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this));
|
495
|
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this, RelationshipBase.class, PesiExportState.class));
|
496
|
mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));
|
497
|
|
498
|
return mapping;
|
499
|
}
|
500
|
|
501
|
/**
|
502
|
* Returns the CDM to PESI specific export mappings.
|
503
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
504
|
*/
|
505
|
PesiExportMapping getSynonymMapping() {
|
506
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
507
|
|
508
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getSynonym", Synonym.class, PesiExportState.class));
|
509
|
mapping.addMapper(DbObjectMapper.NewInstance("acceptedTaxon", "TaxonFk2"));
|
510
|
mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this, Synonym.class));
|
511
|
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this.getClass(), "getSynonymTypeCache", Synonym.class, PesiExportState.class));
|
512
|
mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));
|
513
|
|
514
|
return mapping;
|
515
|
}
|
516
|
|
517
|
PesiExportMapping getTaxonNodeMapping() {
|
518
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
519
|
|
520
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getParent", TaxonNode.class, PesiExportState.class));
|
521
|
mapping.addMapper(DbObjectMapper.NewInstance("taxon", "TaxonFk1"));
|
522
|
mapping.addMapper(DbFixedIntegerMapper.NewInstance(101, "RelTaxonQualifierFk"));
|
523
|
mapping.addMapper(DbFixedStringMapper.NewInstance("is taxonomically included in", "RelQualifierCache"));
|
524
|
// mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));
|
525
|
|
526
|
return mapping;
|
527
|
}
|
528
|
|
529
|
|
530
|
|
531
|
@Override
|
532
|
protected boolean doCheck(PesiExportState state) {
|
533
|
return true;
|
534
|
}
|
535
|
|
536
|
@Override
|
537
|
protected boolean isIgnore(PesiExportState state) {
|
538
|
return ! state.getConfig().isDoRelTaxa();
|
539
|
}
|
540
|
}
|