1
|
// $Id$
|
2
|
/**
|
3
|
* Copyright (C) 2007 EDIT
|
4
|
* European Distributed Institute of Taxonomy
|
5
|
* http://www.e-taxonomy.eu
|
6
|
*
|
7
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
8
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
9
|
*/
|
10
|
|
11
|
package eu.etaxonomy.cdm.model.taxon;
|
12
|
|
13
|
import java.util.ArrayList;
|
14
|
import java.util.HashSet;
|
15
|
import java.util.Set;
|
16
|
|
17
|
import javax.persistence.Entity;
|
18
|
import javax.persistence.FetchType;
|
19
|
import javax.persistence.ManyToOne;
|
20
|
import javax.persistence.OneToMany;
|
21
|
import javax.persistence.Transient;
|
22
|
import javax.xml.bind.annotation.XmlAccessType;
|
23
|
import javax.xml.bind.annotation.XmlAccessorType;
|
24
|
import javax.xml.bind.annotation.XmlElement;
|
25
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
26
|
import javax.xml.bind.annotation.XmlIDREF;
|
27
|
import javax.xml.bind.annotation.XmlRootElement;
|
28
|
import javax.xml.bind.annotation.XmlSchemaType;
|
29
|
import javax.xml.bind.annotation.XmlType;
|
30
|
|
31
|
import org.apache.log4j.Logger;
|
32
|
import org.hibernate.annotations.Cascade;
|
33
|
import org.hibernate.annotations.CascadeType;
|
34
|
import org.hibernate.envers.Audited;
|
35
|
import org.springframework.util.Assert;
|
36
|
|
37
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
38
|
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
|
39
|
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
|
40
|
|
41
|
/**
|
42
|
* @author a.mueller
|
43
|
* @created 31.03.2009
|
44
|
* @version 1.0
|
45
|
*/
|
46
|
@XmlAccessorType(XmlAccessType.FIELD)
|
47
|
@XmlType(name = "TaxonNode", propOrder = {
|
48
|
"taxon",
|
49
|
"parent",
|
50
|
"taxonomicTree",
|
51
|
"childNodes",
|
52
|
"referenceForParentChildRelation",
|
53
|
"microReferenceForParentChildRelation",
|
54
|
"countChildren",
|
55
|
"synonymToBeUsed"
|
56
|
})
|
57
|
@XmlRootElement(name = "TaxonNode")
|
58
|
@Entity
|
59
|
@Audited
|
60
|
public class TaxonNode extends AnnotatableEntity implements ITreeNode{
|
61
|
private static final long serialVersionUID = -4743289894926587693L;
|
62
|
@SuppressWarnings("unused")
|
63
|
private static final Logger logger = Logger.getLogger(TaxonNode.class);
|
64
|
|
65
|
@XmlElement(name = "taxon")
|
66
|
@XmlIDREF
|
67
|
@XmlSchemaType(name = "IDREF")
|
68
|
@ManyToOne(fetch = FetchType.LAZY)
|
69
|
@Cascade({CascadeType.SAVE_UPDATE})
|
70
|
private Taxon taxon;
|
71
|
|
72
|
|
73
|
@XmlElement(name = "parent")
|
74
|
@XmlIDREF
|
75
|
@XmlSchemaType(name = "IDREF")
|
76
|
@ManyToOne(fetch = FetchType.LAZY)
|
77
|
@Cascade({CascadeType.SAVE_UPDATE})
|
78
|
private TaxonNode parent;
|
79
|
|
80
|
|
81
|
@XmlElement(name = "taxonomicTree")
|
82
|
@XmlIDREF
|
83
|
@XmlSchemaType(name = "IDREF")
|
84
|
@ManyToOne(fetch = FetchType.LAZY)
|
85
|
@Cascade({CascadeType.SAVE_UPDATE})
|
86
|
private TaxonomicTree taxonomicTree;
|
87
|
|
88
|
@XmlElementWrapper(name = "childNodes")
|
89
|
@XmlElement(name = "childNode")
|
90
|
@XmlIDREF
|
91
|
@XmlSchemaType(name = "IDREF")
|
92
|
@OneToMany(mappedBy="parent", fetch=FetchType.LAZY)
|
93
|
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
|
94
|
private Set<TaxonNode> childNodes = new HashSet<TaxonNode>();
|
95
|
|
96
|
@XmlElement(name = "reference")
|
97
|
@XmlIDREF
|
98
|
@XmlSchemaType(name = "IDREF")
|
99
|
@ManyToOne(fetch = FetchType.LAZY)
|
100
|
@Cascade({CascadeType.SAVE_UPDATE})
|
101
|
private ReferenceBase referenceForParentChildRelation;
|
102
|
|
103
|
@XmlElement(name = "microReference")
|
104
|
private String microReferenceForParentChildRelation;
|
105
|
|
106
|
@XmlElement(name = "countChildren")
|
107
|
private int countChildren;
|
108
|
|
109
|
// private Taxon originalConcept;
|
110
|
// //or
|
111
|
@XmlElement(name = "synonymToBeUsed")
|
112
|
@XmlIDREF
|
113
|
@XmlSchemaType(name = "IDREF")
|
114
|
@ManyToOne(fetch = FetchType.LAZY)
|
115
|
@Cascade({CascadeType.SAVE_UPDATE})
|
116
|
private Synonym synonymToBeUsed;
|
117
|
|
118
|
|
119
|
protected TaxonNode(){
|
120
|
super();
|
121
|
}
|
122
|
|
123
|
/**
|
124
|
* to create nodes either use TaxonomicView.addRoot() or TaxonNode.addChild();
|
125
|
* @param taxon
|
126
|
* @param taxonomicTree
|
127
|
* @deprecated setting of taxonomic tree is handled in the addTaxonNode() method,
|
128
|
* use TaxonNode(taxon) instead
|
129
|
*/
|
130
|
protected TaxonNode (Taxon taxon, TaxonomicTree taxonomicTree){
|
131
|
this(taxon);
|
132
|
setTaxonomicTree(taxonomicTree);
|
133
|
}
|
134
|
|
135
|
/**
|
136
|
* to create nodes either use TaxonomicView.addChildTaxon() or TaxonNode.addChildTaxon();
|
137
|
*
|
138
|
* @param taxon
|
139
|
*/
|
140
|
protected TaxonNode(Taxon taxon){
|
141
|
setTaxon(taxon);
|
142
|
}
|
143
|
|
144
|
|
145
|
|
146
|
//************************ METHODS **************************/
|
147
|
/**
|
148
|
* @deprecated developers should be forced to pass in null values if they choose so.
|
149
|
*/
|
150
|
@Deprecated
|
151
|
public TaxonNode addChild(Taxon taxon){
|
152
|
return addChild(taxon, null, null, null);
|
153
|
}
|
154
|
|
155
|
/**
|
156
|
* @deprecated developers should be forced to pass in null values if they choose so.
|
157
|
*/
|
158
|
@Deprecated
|
159
|
public TaxonNode addChild(Taxon taxon, ReferenceBase ref, String microReference){
|
160
|
return addChild(taxon, ref, microReference, null);
|
161
|
}
|
162
|
|
163
|
/**
|
164
|
*
|
165
|
* @param taxon
|
166
|
* @param ref
|
167
|
* @param microReference
|
168
|
* @param synonymUsed
|
169
|
* @return
|
170
|
* @deprecated use addChildTaxon() instead
|
171
|
*/
|
172
|
@Deprecated
|
173
|
public TaxonNode addChild(Taxon taxon, ReferenceBase ref, String microReference, Synonym synonymUsed){
|
174
|
return addChildTaxon(taxon, ref, microReference, synonymUsed);
|
175
|
}
|
176
|
|
177
|
|
178
|
/* (non-Javadoc)
|
179
|
* @see eu.etaxonomy.cdm.model.taxon.ITreeNode#addChildTaxon(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String, eu.etaxonomy.cdm.model.taxon.Synonym)
|
180
|
*/
|
181
|
public TaxonNode addChildTaxon(Taxon taxon, ReferenceBase citation,
|
182
|
String microCitation, Synonym synonymToBeUsed) {
|
183
|
if (this.getTaxonomicTree().isTaxonInTree(taxon)){
|
184
|
throw new IllegalArgumentException("Taxon may not be in a taxonomic view twice");
|
185
|
}
|
186
|
|
187
|
return addChildNode(new TaxonNode(taxon), citation, microCitation, synonymToBeUsed);
|
188
|
}
|
189
|
|
190
|
/**
|
191
|
*
|
192
|
* @param childNode
|
193
|
* @param ref
|
194
|
* @param microReference
|
195
|
* @param synonymUsed
|
196
|
*
|
197
|
* @deprecated use addChildNode instead
|
198
|
*/
|
199
|
@Deprecated
|
200
|
protected void addChildNote(TaxonNode childNode, ReferenceBase ref, String microReference, Synonym synonymUsed){
|
201
|
if (! childNode.getTaxonomicTree().equals(this.getTaxonomicTree())){
|
202
|
throw new IllegalArgumentException("addChildNote(): both nodes must be part of the same view");
|
203
|
}
|
204
|
childNode.setParent(this);
|
205
|
childNodes.add(childNode);
|
206
|
this.countChildren++;
|
207
|
childNode.setReferenceForParentChildRelation(ref);
|
208
|
childNode.setMicroReferenceForParentChildRelation(microReference);
|
209
|
childNode.setSynonymToBeUsed(synonymUsed);
|
210
|
}
|
211
|
|
212
|
/**
|
213
|
* Moves a taxon node to a new parent. Descendents of the node are moved as well
|
214
|
*
|
215
|
* @param childNode the taxon node to be moved to the new parent
|
216
|
* @return the child node in the state of having a new parent
|
217
|
*/
|
218
|
public TaxonNode addChildNode(TaxonNode childNode, ReferenceBase reference, String microReference, Synonym synonymToBeUsed){
|
219
|
// check if this node is a descendant of the childNode
|
220
|
if(childNode.getParent() != this && childNode.isAncestor(this)){
|
221
|
throw new IllegalAncestryException("New parent node is a descendant of the node to be moved.");
|
222
|
}
|
223
|
|
224
|
TaxonomicTree oldChildTree = childNode.getTaxonomicTree();
|
225
|
|
226
|
// remove this childNode from previous parents and trees
|
227
|
if(childNode.getParent() instanceof TaxonNode){ //child is already child
|
228
|
((TaxonNode) childNode.getParent()).removeChildNode(childNode);
|
229
|
}else if(oldChildTree != null){ //child is root in old tree
|
230
|
childNode.getTaxonomicTree().removeChildNode(childNode);
|
231
|
}
|
232
|
|
233
|
TaxonomicTree parentTree = this.getTaxonomicTree();
|
234
|
if (oldChildTree != null && ! oldChildTree.equals(parentTree)){ //oldChildTree is null if the node was just created new
|
235
|
childNode.setTaxonomicTreeRecursively(parentTree);
|
236
|
}else{
|
237
|
childNode.setTaxonomicTree(parentTree);
|
238
|
}
|
239
|
|
240
|
childNode.setParent(this);
|
241
|
childNodes.add(childNode);
|
242
|
this.countChildren++;
|
243
|
childNode.setReference(reference);
|
244
|
childNode.setMicroReference(microReference);
|
245
|
childNode.setSynonymToBeUsed(synonymToBeUsed);
|
246
|
|
247
|
return childNode;
|
248
|
}
|
249
|
|
250
|
/**
|
251
|
* @param parentTree
|
252
|
*/
|
253
|
private void setTaxonomicTreeRecursively(TaxonomicTree parentTree) {
|
254
|
this.setTaxonomicTree(parentTree);
|
255
|
for(TaxonNode childNode : this.getChildNodes()){
|
256
|
childNode.setTaxonomicTreeRecursively(parentTree);
|
257
|
}
|
258
|
}
|
259
|
|
260
|
/**
|
261
|
* This removes recursively all child nodes from this node and from this taxonomic view.
|
262
|
* TODO remove orphan nodes completely
|
263
|
*
|
264
|
* @param node
|
265
|
* @return
|
266
|
* @deprecated use removeChildNode() instead
|
267
|
*/
|
268
|
@Deprecated
|
269
|
public boolean removeChild(TaxonNode node){
|
270
|
return deleteChildNode(node);
|
271
|
}
|
272
|
|
273
|
|
274
|
/* (non-Javadoc)
|
275
|
* @see eu.etaxonomy.cdm.model.taxon.ITreeNode#removeChildNode(eu.etaxonomy.cdm.model.taxon.TaxonNode)
|
276
|
*/
|
277
|
public boolean deleteChildNode(TaxonNode node) {
|
278
|
boolean result = removeChildNode(node);
|
279
|
|
280
|
node.getTaxon().removeTaxonNode(node);
|
281
|
node.setTaxon(null);
|
282
|
|
283
|
ArrayList<TaxonNode> childNodes = new ArrayList<TaxonNode>(node.getChildNodes());
|
284
|
for(TaxonNode childNode : childNodes){
|
285
|
node.deleteChildNode(childNode);
|
286
|
}
|
287
|
|
288
|
// // two iterations because of ConcurrentModificationErrors
|
289
|
// Set<TaxonNode> removeNodes = new HashSet<TaxonNode>();
|
290
|
// for (TaxonNode grandChildNode : node.getChildNodes()) {
|
291
|
// removeNodes.add(grandChildNode);
|
292
|
// }
|
293
|
// for (TaxonNode childNode : removeNodes) {
|
294
|
// childNode.deleteChildNode(node);
|
295
|
// }
|
296
|
|
297
|
return result;
|
298
|
}
|
299
|
|
300
|
/**
|
301
|
* Removes the child node from this node. Sets the parent and the taxonomic tree of the child
|
302
|
* node to null
|
303
|
*
|
304
|
* @param childNode
|
305
|
* @return
|
306
|
*/
|
307
|
protected boolean removeChildNode(TaxonNode childNode){
|
308
|
boolean result = false;
|
309
|
|
310
|
if(childNode == null){
|
311
|
throw new IllegalArgumentException("TaxonNode may not be null");
|
312
|
}
|
313
|
if(HibernateProxyHelper.deproxy(childNode.getParent(), TaxonNode.class) != this){
|
314
|
throw new IllegalArgumentException("TaxonNode must be a child of this node");
|
315
|
}
|
316
|
|
317
|
result = childNodes.remove(childNode);
|
318
|
this.countChildren--;
|
319
|
if (this.countChildren < 0){
|
320
|
throw new IllegalStateException("children count must not be negative ");
|
321
|
}
|
322
|
childNode.setParent(null);
|
323
|
childNode.setTaxonomicTree(null);
|
324
|
|
325
|
return result;
|
326
|
}
|
327
|
|
328
|
|
329
|
/**
|
330
|
* Remove this taxonNode From its taxonomic parent
|
331
|
*
|
332
|
* @return true on success
|
333
|
*/
|
334
|
public boolean delete(){
|
335
|
if(isTopmostNode()){
|
336
|
return taxonomicTree.deleteChildNode(this);
|
337
|
}else{
|
338
|
return getParent().deleteChildNode(this);
|
339
|
}
|
340
|
}
|
341
|
|
342
|
//*********** GETTER / SETTER ***********************************/
|
343
|
|
344
|
public Taxon getTaxon() {
|
345
|
return taxon;
|
346
|
}
|
347
|
protected void setTaxon(Taxon taxon) {
|
348
|
this.taxon = taxon;
|
349
|
if (taxon != null){
|
350
|
taxon.addTaxonNode(this);
|
351
|
}
|
352
|
}
|
353
|
public ITreeNode getParent() {
|
354
|
if(isTopmostNode())
|
355
|
return getTaxonomicTree();
|
356
|
return parent;
|
357
|
}
|
358
|
protected void setParent(ITreeNode parent) {
|
359
|
if(parent instanceof TaxonomicTree)
|
360
|
this.parent = null;
|
361
|
this.parent = (TaxonNode) parent;
|
362
|
}
|
363
|
public TaxonomicTree getTaxonomicTree() {
|
364
|
return taxonomicTree;
|
365
|
}
|
366
|
//invisible part of the bidirectional relationship, for public use TaxonomicView.addRoot() or TaxonNode.addChild()
|
367
|
protected void setTaxonomicTree(TaxonomicTree taxonomicTree) {
|
368
|
this.taxonomicTree = taxonomicTree;
|
369
|
}
|
370
|
public Set<TaxonNode> getChildNodes() {
|
371
|
return childNodes;
|
372
|
}
|
373
|
|
374
|
/**
|
375
|
* Returns a set containing this node and all nodes that are descendants of this node
|
376
|
*
|
377
|
* @return
|
378
|
*/
|
379
|
protected Set<TaxonNode> getDescendants(){
|
380
|
Set<TaxonNode> nodeSet = new HashSet<TaxonNode>();
|
381
|
|
382
|
nodeSet.add(this);
|
383
|
|
384
|
for(TaxonNode childNode : getChildNodes()){
|
385
|
nodeSet.addAll(childNode.getDescendants());
|
386
|
}
|
387
|
|
388
|
return nodeSet;
|
389
|
}
|
390
|
|
391
|
/**
|
392
|
* Returns a
|
393
|
*
|
394
|
* @return
|
395
|
*/
|
396
|
protected Set<TaxonNode> getAncestors(){
|
397
|
Set<TaxonNode> nodeSet = new HashSet<TaxonNode>();
|
398
|
|
399
|
|
400
|
nodeSet.add(this);
|
401
|
|
402
|
if(this.getParent() instanceof TaxonNode){
|
403
|
nodeSet.addAll(((TaxonNode) this.getParent()).getAncestors());
|
404
|
}
|
405
|
|
406
|
return nodeSet;
|
407
|
}
|
408
|
|
409
|
// protected void setChildNodes(List<TaxonNode> childNodes) {
|
410
|
// this.childNodes = childNodes;
|
411
|
// }
|
412
|
/**
|
413
|
* The reference for the parent child relationship
|
414
|
*
|
415
|
* @see eu.etaxonomy.cdm.model.taxon.ITreeNode#getReference()
|
416
|
*/
|
417
|
public ReferenceBase getReference() {
|
418
|
return referenceForParentChildRelation;
|
419
|
}
|
420
|
|
421
|
/* (non-Javadoc)
|
422
|
* @see eu.etaxonomy.cdm.model.taxon.ITreeNode#setReference(eu.etaxonomy.cdm.model.reference.ReferenceBase)
|
423
|
*/
|
424
|
public void setReference(ReferenceBase reference) {
|
425
|
this.referenceForParentChildRelation = reference;
|
426
|
}
|
427
|
|
428
|
/**
|
429
|
* @return
|
430
|
* @deprecated use getReference instead
|
431
|
*/
|
432
|
@Deprecated
|
433
|
public ReferenceBase getReferenceForParentChildRelation() {
|
434
|
return referenceForParentChildRelation;
|
435
|
}
|
436
|
@Deprecated
|
437
|
public void setReferenceForParentChildRelation(
|
438
|
ReferenceBase referenceForParentChildRelation) {
|
439
|
this.referenceForParentChildRelation = referenceForParentChildRelation;
|
440
|
}
|
441
|
|
442
|
/**
|
443
|
*
|
444
|
*
|
445
|
* @see eu.etaxonomy.cdm.model.taxon.ITreeNode#getMicroReference()
|
446
|
*/
|
447
|
public String getMicroReference() {
|
448
|
return microReferenceForParentChildRelation;
|
449
|
}
|
450
|
|
451
|
/* (non-Javadoc)
|
452
|
* @see eu.etaxonomy.cdm.model.taxon.ITreeNode#setMicroReference(java.lang.String)
|
453
|
*/
|
454
|
public void setMicroReference(String microReference) {
|
455
|
this.microReferenceForParentChildRelation = microReference;
|
456
|
}
|
457
|
|
458
|
@Deprecated
|
459
|
public String getMicroReferenceForParentChildRelation() {
|
460
|
return microReferenceForParentChildRelation;
|
461
|
}
|
462
|
|
463
|
@Deprecated
|
464
|
public void setMicroReferenceForParentChildRelation(
|
465
|
String microReferenceForParentChildRelation) {
|
466
|
this.microReferenceForParentChildRelation = microReferenceForParentChildRelation;
|
467
|
}
|
468
|
|
469
|
|
470
|
/**
|
471
|
* @return the count of children this taxon node has
|
472
|
*/
|
473
|
public int getCountChildren() {
|
474
|
return countChildren;
|
475
|
}
|
476
|
|
477
|
/**
|
478
|
* @param countChildren
|
479
|
*/
|
480
|
protected void setCountChildren(int countChildren) {
|
481
|
this.countChildren = countChildren;
|
482
|
}
|
483
|
// public Taxon getOriginalConcept() {
|
484
|
// return originalConcept;
|
485
|
// }
|
486
|
// public void setOriginalConcept(Taxon originalConcept) {
|
487
|
// this.originalConcept = originalConcept;
|
488
|
// }
|
489
|
public Synonym getSynonymToBeUsed() {
|
490
|
return synonymToBeUsed;
|
491
|
}
|
492
|
public void setSynonymToBeUsed(Synonym synonymToBeUsed) {
|
493
|
this.synonymToBeUsed = synonymToBeUsed;
|
494
|
}
|
495
|
|
496
|
/**
|
497
|
* Whether this TaxonNode is a root node
|
498
|
* @return
|
499
|
* @deprecated use isTopmostNode() instead
|
500
|
*/
|
501
|
@Transient
|
502
|
public boolean isRootNode(){
|
503
|
return parent == null;
|
504
|
}
|
505
|
|
506
|
/**
|
507
|
* Whether this TaxonNode is a direct child of the taxonomic tree TreeNode
|
508
|
* @return
|
509
|
*/
|
510
|
@Transient
|
511
|
public boolean isTopmostNode(){
|
512
|
return parent == null;
|
513
|
}
|
514
|
|
515
|
/**
|
516
|
* Whether this TaxonNode is a descendant of the given TaxonNode
|
517
|
*
|
518
|
* Caution: use this method with care on big branches. -> performance and memory hungry
|
519
|
*
|
520
|
* Protip: Try solving your problem with the isAscendant method which traverses the tree in the
|
521
|
* other direction (up). It will always result in a rather small set of consecutive parents beeing
|
522
|
* generated.
|
523
|
*
|
524
|
* TODO implement more efficiently without generating the set of descendants first
|
525
|
*
|
526
|
* @param possibleParent
|
527
|
* @return true if this is a descendant
|
528
|
*/
|
529
|
@Transient
|
530
|
public boolean isDescendant(TaxonNode possibleParent){
|
531
|
return possibleParent.getDescendants().contains(this);
|
532
|
}
|
533
|
|
534
|
/**
|
535
|
* Whether this TaxonNode is an ascendant of the given TaxonNode
|
536
|
*
|
537
|
*
|
538
|
* @param possibleChild
|
539
|
* @return true if there are ascendants
|
540
|
*/
|
541
|
@Transient
|
542
|
public boolean isAncestor(TaxonNode possibleChild){
|
543
|
return possibleChild.getAncestors().contains(this);
|
544
|
}
|
545
|
|
546
|
/**
|
547
|
* Whether this taxon has child nodes
|
548
|
*
|
549
|
* @return true if the taxonNode has childNodes
|
550
|
*/
|
551
|
@Transient
|
552
|
public boolean hasChildNodes(){
|
553
|
return childNodes.size() > 0;
|
554
|
}
|
555
|
}
|