Revision 1cc6cd7b
Added by Andreas Müller almost 6 years ago
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImpl.java | ||
|---|---|---|
| 31 | 31 |
import org.springframework.beans.factory.annotation.Qualifier; |
| 32 | 32 |
import org.springframework.stereotype.Repository; |
| 33 | 33 |
|
| 34 |
import eu.etaxonomy.cdm.common.CdmUtils; |
|
| 35 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
|
| 34 | 36 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
| 37 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
| 35 | 38 |
import eu.etaxonomy.cdm.model.common.TreeIndex; |
| 36 | 39 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 37 | 40 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 44 | 47 |
import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao; |
| 45 | 48 |
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao; |
| 46 | 49 |
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao; |
| 47 |
import eu.etaxonomy.cdm.persistence.dto.MergeResult; |
|
| 48 | 50 |
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
| 49 | 51 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 50 | 52 |
|
| ... | ... | |
| 465 | 467 |
return result; |
| 466 | 468 |
} |
| 467 | 469 |
|
| 470 |
/** |
|
| 471 |
* {@inheritDoc}
|
|
| 472 |
*/ |
|
| 473 |
@Override |
|
| 474 |
public int countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, |
|
| 475 |
boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {
|
|
| 476 |
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT); |
|
| 477 |
if (!overwriteExisting){
|
|
| 478 |
queryStr += " AND t.sec IS NULL "; |
|
| 479 |
} |
|
| 480 |
return countResult(queryStr); |
|
| 481 |
|
|
| 482 |
} |
|
| 483 |
/** |
|
| 484 |
* @param queryStr |
|
| 485 |
* @return |
|
| 486 |
*/ |
|
| 487 |
protected int countResult(String queryStr) {
|
|
| 488 |
Query query = getSession().createQuery(queryStr); |
|
| 489 |
return ((Long)query.uniqueResult()).intValue(); |
|
| 490 |
} |
|
| 491 |
/** |
|
| 492 |
* {@inheritDoc}
|
|
| 493 |
*/ |
|
| 494 |
@Override |
|
| 495 |
public int countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, |
|
| 496 |
boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {
|
|
| 497 |
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT); |
|
| 498 |
if (!overwriteExisting){
|
|
| 499 |
queryStr += " AND syn.sec IS NULL "; |
|
| 500 |
} |
|
| 501 |
return countResult(queryStr); |
|
| 502 |
} |
|
| 503 |
|
|
| 468 | 504 |
|
| 469 | 505 |
/** |
| 470 | 506 |
* {@inheritDoc}
|
| 471 | 507 |
*/ |
| 472 | 508 |
//#3465 |
| 473 | 509 |
@Override |
| 474 |
public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail) {
|
|
| 510 |
public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, |
|
| 511 |
boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor) {
|
|
| 475 | 512 |
//for some reason this does not work, maybe because the listeners are not activated, |
| 476 |
//but also the first taxon for some reason does not get updated in terms of secundum, but only by the udpate listener
|
|
| 513 |
//but also the first taxon for some reason does not get updated in terms of secundum, but only by the update listener
|
|
| 477 | 514 |
// String where = "SELECT t.id FROM TaxonNode tn JOIN tn.taxon t " + |
| 478 | 515 |
// " WHERE tn.treeIndex like '%s%%' ORDER BY t.id"; |
| 479 | 516 |
// where = String.format(where, subTreeIndex.toString()); |
| ... | ... | |
| 485 | 522 |
// query.setParameter("newSec", newSec);
|
| 486 | 523 |
// int n = query.executeUpdate(); |
| 487 | 524 |
|
| 488 |
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
|
| 525 |
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
|
|
| 489 | 526 |
if (!overwriteExisting){
|
| 490 | 527 |
queryStr += " AND t.sec IS NULL "; |
| 491 | 528 |
} |
| 492 |
return setSecundum(newSec, emptyDetail, queryStr); |
|
| 529 |
return setSecundum(newSec, emptyDetail, queryStr, monitor);
|
|
| 493 | 530 |
|
| 494 | 531 |
} |
| 495 | 532 |
|
| 496 | 533 |
@Override |
| 497 |
public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail) {
|
|
| 534 |
public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, |
|
| 535 |
boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor) {
|
|
| 498 | 536 |
|
| 499 |
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
|
| 537 |
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
|
|
| 500 | 538 |
if (!overwriteExisting){
|
| 501 | 539 |
queryStr += " AND syn.sec IS NULL "; |
| 502 | 540 |
} |
| 503 |
return setSecundum(newSec, emptyDetail, queryStr); |
|
| 541 |
return setSecundum(newSec, emptyDetail, queryStr, monitor);
|
|
| 504 | 542 |
} |
| 505 | 543 |
/** |
| 506 | 544 |
* @param newSec |
| 507 | 545 |
* @param emptyDetail |
| 508 | 546 |
* @param queryStr |
| 547 |
* @param monitor |
|
| 509 | 548 |
* @return |
| 510 | 549 |
*/ |
| 511 | 550 |
@SuppressWarnings("unchecked")
|
| 512 |
private <T extends TaxonBase<?>> Set<T> setSecundum(Reference newSec, boolean emptyDetail, String queryStr) {
|
|
| 513 |
Query query = getSession().createQuery(queryStr); |
|
| 514 |
@SuppressWarnings("unchecked")
|
|
| 515 |
List<T> synonymList = query.list(); |
|
| 516 |
MergeResult mergeResult; |
|
| 551 |
private <T extends TaxonBase<?>> Set<T> setSecundum(Reference newSec, boolean emptyDetail, String queryStr, IProgressMonitor monitor) {
|
|
| 517 | 552 |
Set<T> result = new HashSet<>(); |
| 518 |
for (T taxonBase : synonymList){
|
|
| 519 |
if (taxonBase != null){
|
|
| 520 |
taxonBase = (T) taxonDao.load(taxonBase.getUuid()); |
|
| 521 |
taxonBase.setSec(newSec); |
|
| 522 |
if (emptyDetail){
|
|
| 523 |
taxonBase.setSecMicroReference(null); |
|
| 553 |
Query query = getSession().createQuery(queryStr); |
|
| 554 |
List<List<Integer>> partitionList = splitIdList(query.list(), DEFAULT_PARTITION_SIZE); |
|
| 555 |
for (List<Integer> taxonIdList : partitionList){
|
|
| 556 |
List<TaxonBase> taxonList = taxonDao.loadList(taxonIdList, null); |
|
| 557 |
for (TaxonBase taxonBase : taxonList){
|
|
| 558 |
if (taxonBase != null){
|
|
| 559 |
taxonBase = taxonDao.load(taxonBase.getUuid()); |
|
| 560 |
taxonBase.setSec(newSec); |
|
| 561 |
if (emptyDetail){
|
|
| 562 |
taxonBase.setSecMicroReference(null); |
|
| 563 |
} |
|
| 564 |
result.add((T)CdmBase.deproxy(taxonBase)); |
|
| 565 |
monitor.worked(1); |
|
| 566 |
if (monitor.isCanceled()){
|
|
| 567 |
return result; |
|
| 568 |
} |
|
| 524 | 569 |
} |
| 525 |
result.add(taxonBase); |
|
| 526 | 570 |
} |
| 571 |
} |
|
| 572 |
return result; |
|
| 573 |
} |
|
| 527 | 574 |
|
| 575 |
private List<List<Integer>> splitIdList(List<Integer> idList, Integer size){
|
|
| 576 |
List<List<Integer>> result = new ArrayList<>(); |
|
| 577 |
for (int i = 0; (i*size)<idList.size(); i++) {
|
|
| 578 |
int upper = Math.min((i+1)*size, idList.size()); |
|
| 579 |
result.add(idList.subList(i*size, upper)); |
|
| 528 | 580 |
} |
| 529 |
return result; |
|
| 581 |
return result;
|
|
| 530 | 582 |
} |
| 531 | 583 |
|
| 532 | 584 |
|
| ... | ... | |
| 535 | 587 |
*/ |
| 536 | 588 |
@Override |
| 537 | 589 |
public Set<TaxonBase> setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish, |
| 538 |
boolean includeSharedTaxa) {
|
|
| 539 |
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
|
| 540 |
return setPublish(publish, queryStr); |
|
| 590 |
boolean includeSharedTaxa, IProgressMonitor monitor) {
|
|
| 591 |
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
|
|
| 592 |
return setPublish(publish, queryStr, monitor);
|
|
| 541 | 593 |
} |
| 542 | 594 |
|
| 543 | 595 |
/** |
| ... | ... | |
| 545 | 597 |
*/ |
| 546 | 598 |
@Override |
| 547 | 599 |
public Set<TaxonBase> setPublishForSubtreeSynonyms(TreeIndex subTreeIndex, boolean publish, |
| 548 |
boolean includeSharedTaxa) {
|
|
| 549 |
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
|
| 550 |
return setPublish(publish, queryStr); |
|
| 600 |
boolean includeSharedTaxa, IProgressMonitor monitor) {
|
|
| 601 |
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
|
|
| 602 |
return setPublish(publish, queryStr, monitor);
|
|
| 551 | 603 |
} |
| 552 | 604 |
|
| 605 |
private static final int DEFAULT_PARTITION_SIZE = 100; |
|
| 553 | 606 |
/** |
| 554 | 607 |
* @param publish |
| 555 | 608 |
* @param queryStr |
| 556 | 609 |
* @return |
| 557 | 610 |
*/ |
| 558 |
private <T extends TaxonBase<?>> Set<T> setPublish(boolean publish, String queryStr) {
|
|
| 611 |
private <T extends TaxonBase<?>> Set<T> setPublish(boolean publish, String queryStr, IProgressMonitor monitor) {
|
|
| 612 |
Set<T> result = new HashSet<>(); |
|
| 559 | 613 |
Query query = getSession().createQuery(queryStr); |
| 560 | 614 |
@SuppressWarnings("unchecked")
|
| 561 |
List<T> taxonList = query.list(); |
|
| 562 |
Set<T> result = new HashSet<>(); |
|
| 563 |
for (T taxon : taxonList){
|
|
| 564 |
taxon = (T)taxonDao.load(taxon.getUuid()); |
|
| 565 |
taxon.setPublish(publish); |
|
| 566 |
result.add(taxon); |
|
| 615 |
List<List<Integer>> partitionList = splitIdList(query.list(), DEFAULT_PARTITION_SIZE); |
|
| 616 |
for (List<Integer> taxonIdList : partitionList){
|
|
| 617 |
List<TaxonBase> taxonList = taxonDao.loadList(taxonIdList, null); |
|
| 618 |
for (TaxonBase taxonBase : taxonList){
|
|
| 619 |
if (taxonBase != null){
|
|
| 620 |
taxonBase.setPublish(publish); |
|
| 621 |
result.add((T)CdmBase.deproxy(taxonBase)); |
|
| 622 |
monitor.worked(1); |
|
| 623 |
if (monitor.isCanceled()){
|
|
| 624 |
return result; |
|
| 625 |
} |
|
| 626 |
} |
|
| 627 |
} |
|
| 567 | 628 |
} |
| 568 | 629 |
return result; |
| 569 | 630 |
} |
| ... | ... | |
| 574 | 635 |
* @param subTreeIndex |
| 575 | 636 |
* @return |
| 576 | 637 |
*/ |
| 577 |
private String synonymForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex) {
|
|
| 578 |
String queryStr = "SELECT syn "
|
|
| 638 |
private String synonymForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex, SelectMode mode) {
|
|
| 639 |
String queryStr = "SELECT " + mode.hql("syn")
|
|
| 579 | 640 |
+ " FROM TaxonNode tn JOIN tn.taxon t JOIN t.synonyms syn" |
| 580 | 641 |
+ " WHERE tn.treeIndex like '%s%%' "; |
| 581 | 642 |
if (!includeSharedTaxa){
|
| ... | ... | |
| 586 | 647 |
return queryStr; |
| 587 | 648 |
} |
| 588 | 649 |
|
| 589 |
private String acceptedForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex) {
|
|
| 590 |
String queryStr = "SELECT t " |
|
| 650 |
private enum SelectMode{
|
|
| 651 |
COUNT(" count(*) "),
|
|
| 652 |
ID ("id "),
|
|
| 653 |
UUID("uuid "),
|
|
| 654 |
FULL("");
|
|
| 655 |
private String hql; |
|
| 656 |
SelectMode(String hql){
|
|
| 657 |
this.hql = hql; |
|
| 658 |
} |
|
| 659 |
public String hql(String prefix){
|
|
| 660 |
switch (this){
|
|
| 661 |
case ID: |
|
| 662 |
case UUID: |
|
| 663 |
return CdmUtils.Nz(prefix)+"." + hql; |
|
| 664 |
case FULL: |
|
| 665 |
return CdmUtils.Nz(prefix) + hql; |
|
| 666 |
case COUNT: |
|
| 667 |
default: return hql; |
|
| 668 |
} |
|
| 669 |
|
|
| 670 |
} |
|
| 671 |
} |
|
| 672 |
|
|
| 673 |
private String acceptedForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex, SelectMode mode) {
|
|
| 674 |
String queryStr = "SELECT " + mode.hql("t")
|
|
| 591 | 675 |
+ " FROM TaxonNode tn JOIN tn.taxon t " |
| 592 | 676 |
+ " WHERE tn.treeIndex like '%s%%' "; |
| 593 | 677 |
if (!includeSharedTaxa){
|
| ... | ... | |
| 599 | 683 |
} |
| 600 | 684 |
|
| 601 | 685 |
|
| 686 |
|
|
| 602 | 687 |
} |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonNodeDao.java | ||
|---|---|---|
| 15 | 15 |
import java.util.Set; |
| 16 | 16 |
import java.util.UUID; |
| 17 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
|
| 18 | 19 |
import eu.etaxonomy.cdm.model.common.TreeIndex; |
| 19 | 20 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 20 | 21 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 123 | 124 |
* @param treeIndexSet set of taxon node tree indexes |
| 124 | 125 |
* @return map with treeindex and uuidAndTitleCache of the represented taxon |
| 125 | 126 |
*/ |
| 126 |
Map<TreeIndex, UuidAndTitleCache<?>> taxonUuidsForTreeIndexes(Collection<TreeIndex> treeIndexSet); |
|
| 127 |
public Map<TreeIndex, UuidAndTitleCache<?>> taxonUuidsForTreeIndexes(Collection<TreeIndex> treeIndexSet); |
|
| 128 |
|
|
| 127 | 129 |
|
| 128 |
/** |
|
| 129 |
* @param ref |
|
| 130 |
* @return |
|
| 131 |
*/ |
|
| 132 |
public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail); |
|
| 133 | 130 |
|
| 134 | 131 |
/** |
| 135 |
* @param ref |
|
| 132 |
* @param subTreeIndex |
|
| 133 |
* @param newSec |
|
| 134 |
* @param overwriteExistingAccepted |
|
| 135 |
* @param includeSharedTaxa |
|
| 136 |
* @param emptySecundumDetail |
|
| 137 |
* @return |
|
| 136 | 138 |
*/ |
| 137 |
public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail); |
|
| 139 |
public int countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, |
|
| 140 |
boolean overwriteExistingAccepted, boolean includeSharedTaxa, boolean emptySecundumDetail); |
|
| 138 | 141 |
|
| 139 | 142 |
/** |
| 140 | 143 |
* @param subTreeIndex |
| 141 |
* @param publish |
|
| 144 |
* @param newSec |
|
| 145 |
* @param overwriteExistingSynonyms |
|
| 142 | 146 |
* @param includeSharedTaxa |
| 147 |
* @param emptySecundumDetail |
|
| 143 | 148 |
* @return |
| 144 | 149 |
*/ |
| 145 |
public Set<TaxonBase> setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish, boolean includeSharedTaxa); |
|
| 150 |
public int countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, |
|
| 151 |
boolean overwriteExistingSynonyms, boolean includeSharedTaxa, boolean emptySecundumDetail); |
|
| 146 | 152 |
|
| 147 | 153 |
/** |
| 148 | 154 |
* @param subTreeIndex |
| 149 |
* @param publish |
|
| 155 |
* @param newSec |
|
| 156 |
* @param overwriteExisting |
|
| 150 | 157 |
* @param includeSharedTaxa |
| 158 |
* @param emptyDetail |
|
| 159 |
* @param monitor |
|
| 151 | 160 |
* @return |
| 152 | 161 |
*/ |
| 162 |
public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor); |
|
| 163 |
|
|
| 164 |
public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor); |
|
| 165 |
|
|
| 166 |
public Set<TaxonBase> setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish, boolean includeSharedTaxa, IProgressMonitor monitor); |
|
| 167 |
|
|
| 153 | 168 |
public Set<TaxonBase> setPublishForSubtreeSynonyms(TreeIndex subTreeIndex, boolean publish, |
| 154 |
boolean includeSharedTaxa); |
|
| 169 |
boolean includeSharedTaxa, IProgressMonitor monitor);
|
|
| 155 | 170 |
|
| 156 | 171 |
/** |
| 157 | 172 |
* @param parent |
| 158 | 173 |
* @return |
| 159 | 174 |
*/ |
| 160 |
List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(UuidAndTitleCache<TaxonNode> parent); |
|
| 175 |
public List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(UuidAndTitleCache<TaxonNode> parent); |
|
| 176 |
|
|
| 161 | 177 |
|
| 162 | 178 |
} |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImpl.java | ||
|---|---|---|
| 825 | 825 |
if (config.getNewSecundum() != null){
|
| 826 | 826 |
newSec = refService.load(config.getNewSecundum().getUuid()); |
| 827 | 827 |
} |
| 828 |
if (subTree != null){
|
|
| 829 |
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex()); |
|
| 830 |
Long count = dao.countChildrenOf(subTree, subTree.getClassification(), true); |
|
| 831 |
int intCount = count.intValue(); |
|
| 832 |
monitor.beginTask("Update Secundum Reference", intCount);
|
|
| 833 |
} |
|
| 834 |
|
|
| 835 | 828 |
|
| 836 | 829 |
if (config.getSubtreeUuid() == null){
|
| 837 | 830 |
result.setError(); |
| ... | ... | |
| 845 | 838 |
result.addException(new NullPointerException("Subtree does not exist"));
|
| 846 | 839 |
monitor.done(); |
| 847 | 840 |
return result; |
| 841 |
}else{
|
|
| 842 |
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex()); |
|
| 843 |
int count = config.isIncludeAcceptedTaxa() ? dao.countSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail()):0; |
|
| 844 |
count += config.isIncludeSynonyms() ? dao.countSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail()) :0; |
|
| 845 |
// Long count = dao.countChildrenOf(subTree, subTree.getClassification(), true); |
|
| 846 |
monitor.beginTask("Update Secundum Reference", count);
|
|
| 848 | 847 |
} |
| 849 | 848 |
|
| 850 |
|
|
| 851 | 849 |
//Reference ref = config.getNewSecundum(); |
| 852 | 850 |
if (config.isIncludeAcceptedTaxa()){
|
| 853 | 851 |
monitor.subTask("Update Accepted Taxa");
|
| 854 | 852 |
|
| 855 |
Set<TaxonBase> updatedTaxa = dao.setSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail()); |
|
| 853 |
Set<TaxonBase> updatedTaxa = dao.setSecundumForSubtreeAcceptedTaxa(subTreeIndex, newSec, config.isOverwriteExistingAccepted(), config.isIncludeSharedTaxa(), config.isEmptySecundumDetail(), monitor);
|
|
| 856 | 854 |
result.addUpdatedObjects(updatedTaxa); |
| 857 | 855 |
} |
| 858 | 856 |
if (config.isIncludeSynonyms()){
|
| 859 | 857 |
monitor.subTask("Update Synonyms");
|
| 860 |
Set<TaxonBase> updatedSynonyms = dao.setSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail()); |
|
| 858 |
Set<TaxonBase> updatedSynonyms = dao.setSecundumForSubtreeSynonyms(subTreeIndex, newSec, config.isOverwriteExistingSynonyms(), config.isIncludeSharedTaxa() , config.isEmptySecundumDetail(), monitor);
|
|
| 861 | 859 |
result.addUpdatedObjects(updatedSynonyms); |
| 862 | 860 |
} |
| 863 | 861 |
|
| ... | ... | |
| 897 | 895 |
|
| 898 | 896 |
if (includeAcceptedTaxa){
|
| 899 | 897 |
monitor.subTask("Update Accepted Taxa");
|
| 900 |
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa); |
|
| 898 |
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, monitor);
|
|
| 901 | 899 |
// taxonService.saveOrUpdate(updatedTaxa); |
| 902 | 900 |
result.addUpdatedObjects(updatedTaxa); |
| 903 | 901 |
} |
| 904 | 902 |
if (includeSynonyms){
|
| 905 | 903 |
monitor.subTask("Update Synonyms");
|
| 906 |
Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa); |
|
| 904 |
Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, monitor);
|
|
| 907 | 905 |
// taxonService.saveOrUpdate(updatedSynonyms); |
| 908 | 906 |
result.addUpdatedObjects(updatedSynonyms); |
| 909 | 907 |
} |
Also available in: Unified diff
ref #6359, ref #3740 (setSubtree) add progress monitor progress computation, first version of partitioning