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; |
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import eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
|
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
|
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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; |
| ... | ... | |
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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; |
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import eu.etaxonomy.cdm.persistence.dto.MergeResult; |
|
| 48 | 50 |
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 50 | 52 |
|
| ... | ... | |
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return result; |
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} |
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|
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/** |
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* {@inheritDoc}
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*/ |
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@Override |
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public int countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, |
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boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {
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String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT); |
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if (!overwriteExisting){
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queryStr += " AND t.sec IS NULL "; |
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} |
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return countResult(queryStr); |
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|
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} |
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/** |
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* @param queryStr |
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* @return |
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*/ |
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protected int countResult(String queryStr) {
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Query query = getSession().createQuery(queryStr); |
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return ((Long)query.uniqueResult()).intValue(); |
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} |
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/** |
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* {@inheritDoc}
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*/ |
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@Override |
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public int countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, |
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boolean overwriteExisting, boolean includeSharedTaxa, boolean emptySecundumDetail) {
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String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.COUNT); |
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if (!overwriteExisting){
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queryStr += " AND syn.sec IS NULL "; |
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} |
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return countResult(queryStr); |
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} |
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|
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/** |
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* {@inheritDoc}
|
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*/ |
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//#3465 |
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@Override |
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public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail) {
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public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, |
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boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor) {
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//for some reason this does not work, maybe because the listeners are not activated, |
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//but also the first taxon for some reason does not get updated in terms of secundum, but only by the udpate listener
|
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//but also the first taxon for some reason does not get updated in terms of secundum, but only by the update listener
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// String where = "SELECT t.id FROM TaxonNode tn JOIN tn.taxon t " + |
| 478 | 515 |
// " WHERE tn.treeIndex like '%s%%' ORDER BY t.id"; |
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// where = String.format(where, subTreeIndex.toString()); |
| ... | ... | |
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// query.setParameter("newSec", newSec);
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// int n = query.executeUpdate(); |
| 487 | 524 |
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String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
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String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
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if (!overwriteExisting){
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queryStr += " AND t.sec IS NULL "; |
| 491 | 528 |
} |
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return setSecundum(newSec, emptyDetail, queryStr); |
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return setSecundum(newSec, emptyDetail, queryStr, monitor);
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| 493 | 530 |
|
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} |
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|
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@Override |
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public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail) {
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public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, |
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boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail, IProgressMonitor monitor) {
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String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
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String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
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if (!overwriteExisting){
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queryStr += " AND syn.sec IS NULL "; |
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} |
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return setSecundum(newSec, emptyDetail, queryStr); |
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return setSecundum(newSec, emptyDetail, queryStr, monitor);
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} |
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/** |
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* @param newSec |
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* @param emptyDetail |
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* @param queryStr |
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* @param monitor |
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* @return |
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*/ |
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@SuppressWarnings("unchecked")
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private <T extends TaxonBase<?>> Set<T> setSecundum(Reference newSec, boolean emptyDetail, String queryStr) {
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Query query = getSession().createQuery(queryStr); |
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@SuppressWarnings("unchecked")
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List<T> synonymList = query.list(); |
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MergeResult mergeResult; |
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private <T extends TaxonBase<?>> Set<T> setSecundum(Reference newSec, boolean emptyDetail, String queryStr, IProgressMonitor monitor) {
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Set<T> result = new HashSet<>(); |
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for (T taxonBase : synonymList){
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if (taxonBase != null){
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taxonBase = (T) taxonDao.load(taxonBase.getUuid()); |
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taxonBase.setSec(newSec); |
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if (emptyDetail){
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taxonBase.setSecMicroReference(null); |
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Query query = getSession().createQuery(queryStr); |
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List<List<Integer>> partitionList = splitIdList(query.list(), DEFAULT_PARTITION_SIZE); |
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for (List<Integer> taxonIdList : partitionList){
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List<TaxonBase> taxonList = taxonDao.loadList(taxonIdList, null); |
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for (TaxonBase taxonBase : taxonList){
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if (taxonBase != null){
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taxonBase = taxonDao.load(taxonBase.getUuid()); |
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taxonBase.setSec(newSec); |
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if (emptyDetail){
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taxonBase.setSecMicroReference(null); |
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} |
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result.add((T)CdmBase.deproxy(taxonBase)); |
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monitor.worked(1); |
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if (monitor.isCanceled()){
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return result; |
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} |
|
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} |
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result.add(taxonBase); |
|
| 526 | 570 |
} |
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} |
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return result; |
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} |
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private List<List<Integer>> splitIdList(List<Integer> idList, Integer size){
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List<List<Integer>> result = new ArrayList<>(); |
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for (int i = 0; (i*size)<idList.size(); i++) {
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int upper = Math.min((i+1)*size, idList.size()); |
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result.add(idList.subList(i*size, upper)); |
|
| 528 | 580 |
} |
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return result; |
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return result;
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} |
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|
| ... | ... | |
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*/ |
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@Override |
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public Set<TaxonBase> setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish, |
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boolean includeSharedTaxa) {
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String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
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return setPublish(publish, queryStr); |
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boolean includeSharedTaxa, IProgressMonitor monitor) {
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String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
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return setPublish(publish, queryStr, monitor);
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} |
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|
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/** |
| ... | ... | |
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*/ |
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@Override |
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public Set<TaxonBase> setPublishForSubtreeSynonyms(TreeIndex subTreeIndex, boolean publish, |
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boolean includeSharedTaxa) {
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String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex); |
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return setPublish(publish, queryStr); |
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boolean includeSharedTaxa, IProgressMonitor monitor) {
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String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex, SelectMode.ID);
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return setPublish(publish, queryStr, monitor);
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} |
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private static final int DEFAULT_PARTITION_SIZE = 100; |
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/** |
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* @param publish |
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* @param queryStr |
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* @return |
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*/ |
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private <T extends TaxonBase<?>> Set<T> setPublish(boolean publish, String queryStr) {
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private <T extends TaxonBase<?>> Set<T> setPublish(boolean publish, String queryStr, IProgressMonitor monitor) {
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Set<T> result = new HashSet<>(); |
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Query query = getSession().createQuery(queryStr); |
| 560 | 614 |
@SuppressWarnings("unchecked")
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List<T> taxonList = query.list(); |
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Set<T> result = new HashSet<>(); |
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for (T taxon : taxonList){
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taxon = (T)taxonDao.load(taxon.getUuid()); |
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taxon.setPublish(publish); |
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result.add(taxon); |
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List<List<Integer>> partitionList = splitIdList(query.list(), DEFAULT_PARTITION_SIZE); |
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for (List<Integer> taxonIdList : partitionList){
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List<TaxonBase> taxonList = taxonDao.loadList(taxonIdList, null); |
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for (TaxonBase taxonBase : taxonList){
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if (taxonBase != null){
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taxonBase.setPublish(publish); |
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result.add((T)CdmBase.deproxy(taxonBase)); |
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monitor.worked(1); |
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if (monitor.isCanceled()){
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return result; |
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} |
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} |
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} |
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} |
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return result; |
| 569 | 630 |
} |
| ... | ... | |
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* @param subTreeIndex |
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* @return |
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*/ |
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private String synonymForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex) {
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String queryStr = "SELECT syn "
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private String synonymForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex, SelectMode mode) {
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String queryStr = "SELECT " + mode.hql("syn")
|
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+ " FROM TaxonNode tn JOIN tn.taxon t JOIN t.synonyms syn" |
| 580 | 641 |
+ " WHERE tn.treeIndex like '%s%%' "; |
| 581 | 642 |
if (!includeSharedTaxa){
|
| ... | ... | |
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return queryStr; |
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} |
| 588 | 649 |
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private String acceptedForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex) {
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String queryStr = "SELECT t " |
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private enum SelectMode{
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COUNT(" count(*) "),
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ID ("id "),
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UUID("uuid "),
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FULL("");
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private String hql; |
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SelectMode(String hql){
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this.hql = hql; |
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} |
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public String hql(String prefix){
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switch (this){
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case ID: |
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case UUID: |
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return CdmUtils.Nz(prefix)+"." + hql; |
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case FULL: |
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return CdmUtils.Nz(prefix) + hql; |
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case COUNT: |
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default: return hql; |
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} |
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|
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} |
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} |
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private String acceptedForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex, SelectMode mode) {
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String queryStr = "SELECT " + mode.hql("t")
|
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| 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 |
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|
|
| 602 | 687 |
} |
Also available in: Unified diff
ref #6359, ref #3740 (setSubtree) add progress monitor progress computation, first version of partitioning