Revision 3cf47767
Added by Andreas Müller almost 8 years ago
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java | ||
|---|---|---|
| 1213 | 1213 |
} |
| 1214 | 1214 |
|
| 1215 | 1215 |
@Override |
| 1216 |
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) {
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|
| 1217 |
checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize, Integer pageNumber)");
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| 1216 |
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber) {
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| 1217 |
checkNotInPriorView("TaxonDaoHibernateImpl.findTaxaByName(Boolean accepted, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber)");
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|
| 1218 | 1218 |
Criteria criteria = null; |
| 1219 | 1219 |
if (clazz == null){
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| 1220 | 1220 |
criteria = getSession().createCriteria(TaxonBase.class); |
| ... | ... | |
| 1249 | 1249 |
criteria.add(Restrictions.eq("name.infraSpecificEpithet", infraSpecificEpithet));
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| 1250 | 1250 |
} |
| 1251 | 1251 |
|
| 1252 |
if(authorship == null) {
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| 1253 |
criteria.add(Restrictions.isEmpty("name.authorshipCache"));
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| 1254 |
} else if(!authorship.equals("*")) {
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| 1255 |
criteria.add(Restrictions.eq("name.authorshipCache", authorship));
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| 1256 |
} |
|
| 1257 |
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| 1252 | 1258 |
if(rank != null) {
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| 1253 | 1259 |
criteria.add(Restrictions.eq("name.rank", rank));
|
| 1254 | 1260 |
} |
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java | ||
|---|---|---|
| 166 | 166 |
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) |
| 167 | 167 |
* @return a list of TaxonBase instances |
| 168 | 168 |
*/ |
| 169 |
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber); |
|
| 169 |
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
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|
| 170 | 170 |
|
| 171 | 171 |
/** |
| 172 | 172 |
* Find taxa by searching for Taxa and Synonyms where the |
| cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.java | ||
|---|---|---|
| 699 | 699 |
@Test |
| 700 | 700 |
@DataSet |
| 701 | 701 |
public void testGetTaxonMatchingUninomial() {
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| 702 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*",null,null,null); |
|
| 702 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*",null,null,null,null);
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| 703 | 703 |
|
| 704 | 704 |
assertNotNull("findTaxaByName should return a List", result);
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| 705 | 705 |
assertEquals("findTaxaByName should return two Taxa",2,result.size());
|
| ... | ... | |
| 709 | 709 |
@Test |
| 710 | 710 |
@DataSet |
| 711 | 711 |
public void testGetTaxonMatchingSpeciesBinomial() {
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| 712 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Smerinthus", null, "kindermannii", null,null,null,null);
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| 712 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", null, "kindermannii", null,null,null,null,null);
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| 713 | 713 |
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| 714 | 714 |
assertNotNull("findTaxaByName should return a List", result);
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| 715 | 715 |
assertEquals("findTaxaByName should return one Taxon",1,result.size());
|
| ... | ... | |
| 719 | 719 |
@Test |
| 720 | 720 |
@DataSet |
| 721 | 721 |
public void testGetTaxonMatchingTrinomial() {
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| 722 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis",null,null,null); |
|
| 722 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis",null,null,null,null);
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| 723 | 723 |
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| 724 | 724 |
assertNotNull("findTaxaByName should return a List", result);
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| 725 | 725 |
assertEquals("findTaxaByName should return one Taxon",1,result.size());
|
| ... | ... | |
| 729 | 729 |
@Test |
| 730 | 730 |
@DataSet |
| 731 | 731 |
public void testNegativeMatch() {
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| 732 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null); |
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| 732 |
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null,null);
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| 733 | 733 |
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| 734 | 734 |
assertNotNull("findTaxaByName should return a List", result);
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| 735 | 735 |
assertTrue("findTaxaByName should return an empty List",result.isEmpty());
|
| cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonListController.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.remote.controller; |
| 11 | 11 |
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| 12 |
import io.swagger.annotations.Api; |
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| 13 |
|
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| 14 | 12 |
import java.io.IOException; |
| 15 | 13 |
import java.util.ArrayList; |
| 16 | 14 |
import java.util.Arrays; |
| ... | ... | |
| 47 | 45 |
import eu.etaxonomy.cdm.api.service.search.SearchResult; |
| 48 | 46 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 49 | 47 |
import eu.etaxonomy.cdm.model.common.DefinedTerm; |
| 48 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
|
| 50 | 49 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 51 | 50 |
import eu.etaxonomy.cdm.model.common.Language; |
| 52 | 51 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 53 | 52 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 54 | 53 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm; |
| 55 | 54 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 55 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 56 | 56 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 57 | 57 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 58 | 58 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
| 63 | 63 |
import eu.etaxonomy.cdm.remote.controller.util.PagerParameters; |
| 64 | 64 |
import eu.etaxonomy.cdm.remote.editor.DefinedTermBaseList; |
| 65 | 65 |
import eu.etaxonomy.cdm.remote.editor.MatchModePropertyEditor; |
| 66 |
import eu.etaxonomy.cdm.remote.editor.RankPropertyEditor; |
|
| 66 | 67 |
import eu.etaxonomy.cdm.remote.editor.TermBaseListPropertyEditor; |
| 67 | 68 |
import eu.etaxonomy.cdm.remote.editor.UuidList; |
| 69 |
import io.swagger.annotations.Api; |
|
| 68 | 70 |
|
| 69 | 71 |
/** |
| 70 | 72 |
* TODO write controller documentation |
| ... | ... | |
| 92 | 94 |
setInitializationStrategy(Arrays.asList(new String[]{"$","name.nomenclaturalReference"}));
|
| 93 | 95 |
} |
| 94 | 96 |
|
| 95 |
/* (non-Javadoc) |
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| 96 |
* @see eu.etaxonomy.cdm.remote.controller.BaseListController#setService(eu.etaxonomy.cdm.api.service.IService) |
|
| 97 |
*/ |
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| 98 | 97 |
@Override |
| 99 | 98 |
@Autowired |
| 100 | 99 |
public void setService(ITaxonService service) {
|
| ... | ... | |
| 117 | 116 |
super.initBinder(binder); |
| 118 | 117 |
binder.registerCustomEditor(DefinedTermBaseList.class, new TermBaseListPropertyEditor<NamedArea>(termService)); |
| 119 | 118 |
binder.registerCustomEditor(MatchMode.class, new MatchModePropertyEditor()); |
| 119 |
binder.registerCustomEditor(Rank.class, new RankPropertyEditor()); |
|
| 120 | 120 |
|
| 121 | 121 |
} |
| 122 | 122 |
|
| ... | ... | |
| 440 | 440 |
HttpServletRequest request, |
| 441 | 441 |
HttpServletResponse response)throws IOException {
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| 442 | 442 |
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| 443 |
logger.info("doFindBestMatchingTaxon : " + requestPathAndQuery(request) );
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| 444 |
|
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| 443 | 445 |
Taxon bestMatchingTaxon = service.findBestMatchingTaxon(taxonName); |
| 444 | 446 |
|
| 445 | 447 |
return bestMatchingTaxon; |
| ... | ... | |
| 497 | 499 |
return service.findByIdentifier(type, identifier, definedTerm , subTree, matchMode, includeEntity, pagerParams.getPageSize(), pagerParams.getPageIndex(), initializationStrategy); |
| 498 | 500 |
} |
| 499 | 501 |
|
| 502 |
@RequestMapping(value = "doFindByNameParts", method = RequestMethod.GET) |
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| 503 |
public Pager<TaxonBase> doFindByNameParts( |
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@RequestParam(value = "genusOrUninomial", required = false) String genusOrUninomial, |
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| 505 |
@RequestParam(value = "infragenericEpithet", required = false) String infragenericEpithet, |
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| 506 |
@RequestParam(value = "specificEpithet", required = false) String specificEpithet, |
|
| 507 |
@RequestParam(value = "infraspecificEpithet", required = false) String infraspecificEpithet, |
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| 508 |
@RequestParam(value = "authorship", required = false) String authorship, |
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| 509 |
@RequestParam(value = "rankUuid", required = false) UUID rankUuid, |
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| 510 |
@RequestParam(value = "pageNumber", required = false) Integer pageNumber, |
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| 511 |
@RequestParam(value = "pageSize", required = false) Integer pageSize, |
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| 512 |
HttpServletRequest request, |
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| 513 |
HttpServletResponse response)throws IOException {
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| 514 |
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| 515 |
logger.info("doFindByNameParts : " + requestPathAndQuery(request) );
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| 516 |
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if (genusOrUninomial == null && infragenericEpithet == null && specificEpithet == null && infraspecificEpithet == null){
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response.sendError(404 , "At least 1 name part must be defined " ); |
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| 519 |
return null; |
|
| 520 |
} |
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| 521 |
|
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| 522 |
Rank rank = null; |
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| 523 |
if (rankUuid != null){
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| 524 |
rank = findRank(rankUuid); |
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| 525 |
} |
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| 526 |
|
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| 527 |
Pager<TaxonBase> result = service.findTaxaByName(null, genusOrUninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, authorship, rank, pageSize, pageNumber); |
|
| 528 |
|
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| 529 |
return result; |
|
| 530 |
} |
|
| 531 |
|
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| 532 |
|
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| 533 |
private Rank findRank(UUID rankUuid) {
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| 534 |
Rank rank = null; |
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if(rankUuid != null){
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| 536 |
DefinedTermBase<?> definedTermBase = termService.find(rankUuid); |
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if(definedTermBase instanceof Rank){
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| 538 |
rank = (Rank) definedTermBase; |
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| 539 |
} else {
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| 540 |
throw new IllegalArgumentException("DefinedTermBase is not a Rank");
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| 541 |
} |
|
| 542 |
} |
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| 543 |
return rank; |
|
| 544 |
} |
|
| 545 |
|
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| 500 | 546 |
} |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ITaxonService.java | ||
|---|---|---|
| 483 | 483 |
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) |
| 484 | 484 |
* @return a list of TaxonBase instances |
| 485 | 485 |
*/ |
| 486 |
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber); |
|
| 486 |
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
|
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| 487 | 487 |
|
| 488 | 488 |
/** |
| 489 | 489 |
* Returns a list of TaxonBase instances where the |
| ... | ... | |
| 500 | 500 |
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) |
| 501 | 501 |
* @return a List of TaxonBase instances |
| 502 | 502 |
*/ |
| 503 |
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber); |
|
| 503 |
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
|
|
| 504 | 504 |
|
| 505 | 505 |
/** |
| 506 | 506 |
* Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances) |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java | ||
|---|---|---|
| 451 | 451 |
} |
| 452 | 452 |
|
| 453 | 453 |
@Override |
| 454 |
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 454 |
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 455 | 455 |
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank); |
| 456 | 456 |
|
| 457 | 457 |
List<TaxonBase> results = new ArrayList<TaxonBase>(); |
| 458 | 458 |
if(numberOfResults > 0) { // no point checking again
|
| 459 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber); |
|
| 459 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, authorship, rank, pageSize, pageNumber);
|
|
| 460 | 460 |
} |
| 461 | 461 |
|
| 462 | 462 |
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results); |
| 463 | 463 |
} |
| 464 | 464 |
|
| 465 | 465 |
@Override |
| 466 |
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 466 |
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize,Integer pageNumber) {
|
|
| 467 | 467 |
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank); |
| 468 | 468 |
|
| 469 | 469 |
List<TaxonBase> results = new ArrayList<TaxonBase>(); |
| 470 | 470 |
if(numberOfResults > 0) { // no point checking again
|
| 471 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber); |
|
| 471 |
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, authorship, rank, pageSize, pageNumber);
|
|
| 472 | 472 |
} |
| 473 | 473 |
|
| 474 | 474 |
return results; |
Also available in: Unified diff
#5958 Implement name part search as web service