import eu.etaxonomy.cdm.api.service.pager.Pager;\r
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;\r
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
+import eu.etaxonomy.cdm.model.common.CdmBase;\r
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;\r
-import eu.etaxonomy.cdm.model.description.CommonTaxonName;\r
-import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
+import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;\r
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
import eu.etaxonomy.cdm.model.media.Media;\r
import eu.etaxonomy.cdm.model.media.MediaRepresentation;\r
+import eu.etaxonomy.cdm.model.media.MediaUtils;\r
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
-import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;\r
import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;\r
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;\r
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;\r
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;\r
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
import eu.etaxonomy.cdm.persistence.query.OrderHint;\r
\r
\r
+/**\r
+ * @author a.kohlbecker\r
+ * @date 10.09.2010\r
+ *\r
+ */\r
@Service\r
@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)\r
public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService{\r
@Autowired\r
private ITaxonNameDao nameDao;\r
\r
+ @Autowired \r
+ private IDescriptionDao descriptionDao;\r
\r
@Autowired\r
private IOrderedTermVocabularyDao orderedVocabularyDao;\r
- @Autowired\r
- private IDescriptionDao descriptionDao;\r
- @Autowired\r
- private BeanInitializer defaultBeanInitializer;\r
- \r
- private Comparator<? super TaxonNode> taxonNodeComparator;\r
- @Autowired\r
- public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){\r
- this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;\r
- }\r
\r
/**\r
* Constructor\r
}\r
\r
//Move descriptions to new taxon\r
- for(TaxonDescription oldDescription : oldTaxon.getDescriptions()){\r
- \r
- TaxonDescription newDescription = TaxonDescription.NewInstance(newAcceptedTaxon);\r
- newDescription.setTitleCache("Description copied from " + oldTaxon + ". Old title: " + oldDescription.getTitleCache());\r
- \r
- for(DescriptionElementBase element : oldDescription.getElements()){\r
- newDescription.addElement(element);\r
- }\r
+ for(TaxonDescription description : oldTaxon.getDescriptions()){\r
+ description.setTitleCache("Description copied from former accepted taxon: " + oldTaxon.getTitleCache() + "(Old title: " + description.getTitleCache() + ")");\r
+ newAcceptedTaxon.addDescription(description);\r
}\r
\r
oldTaxonNode.delete();\r
* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)\r
*/\r
@Transactional(readOnly = false)\r
- public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, SynonymRelationshipType synonymRelationshipType){\r
+ public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){\r
\r
- // create a new synonym with the old acceptedName\r
- TaxonNameBase oldAcceptedTaxonName = acceptedTaxon.getName();\r
+ TaxonNameBase synonymName = synonym.getName();\r
+ synonymName.removeTaxonBase(synonym);\r
+ TaxonNameBase taxonName = acceptedTaxon.getName();\r
+ taxonName.removeTaxonBase(acceptedTaxon);\r
\r
- // store the synonyms name\r
- TaxonNameBase newAcceptedTaxonName = synonym.getName();\r
+ synonym.setName(taxonName);\r
+ acceptedTaxon.setName(synonymName);\r
\r
- // remove synonym from oldAcceptedTaxon\r
- acceptedTaxon.removeSynonym(synonym);\r
- \r
- // make synonym name the accepted taxons name\r
- acceptedTaxon.setName(newAcceptedTaxonName);\r
- \r
- // add the new synonym to the acceptedTaxon\r
- if(synonymRelationshipType == null){\r
- synonymRelationshipType = SynonymRelationshipType.SYNONYM_OF();\r
- }\r
- \r
- acceptedTaxon.addSynonymName(oldAcceptedTaxonName, synonymRelationshipType);\r
+ // the accepted taxon needs a new uuid because the concept has changed\r
+ // FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"\r
+ //acceptedTaxon.setUuid(UUID.randomUUID());\r
}\r
+ \r
\r
/*\r
* (non-Javadoc)\r
\r
return newAcceptedTaxon;\r
}\r
-\r
- public void generateTitleCache() {\r
- generateTitleCache(true);\r
- }\r
- //TODO\r
- public void generateTitleCache(boolean forceProtected) {\r
- logger.warn("generateTitleCache not yet fully implemented!");\r
+ \r
+ public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, ReferenceBase citation, String microcitation){\r
+ \r
+ // Get name from synonym\r
+ TaxonNameBase<?, ?> synonymName = synonym.getName();\r
+ \r
+ // remove synonym from taxon\r
+ toTaxon.removeSynonym(synonym);\r
+ \r
+ // Create a taxon with synonym name\r
+ Taxon fromTaxon = Taxon.NewInstance(synonymName, null);\r
+ \r
+ // Add taxon relation \r
+ fromTaxon.addTaxonRelation(toTaxon, taxonRelationshipType, citation, microcitation);\r
+ \r
+ // since we are swapping names, we have to detach the name from the synonym completely. \r
+ // Otherwise the synonym will still be in the list of typified names.\r
+ synonym.getName().removeTaxonBase(synonym);\r
+ \r
+ return fromTaxon;\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache()\r
+ */\r
+ @Override\r
+ @Transactional(readOnly = false)\r
+ public void updateTitleCache() {\r
+ Class<TaxonBase> clazz = TaxonBase.class;\r
+ super.updateTitleCache(clazz, null, null);\r
+ }\r
+ \r
@Autowired\r
protected void setDao(ITaxonDao dao) {\r
this.dao = dao;\r
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);\r
}\r
\r
+ public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {\r
+ Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);\r
+ \r
+ List<TaxonBase> results = new ArrayList<TaxonBase>();\r
+ if(numberOfResults > 0) { // no point checking again\r
+ results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber); \r
+ }\r
+ \r
+ return results;\r
+ }\r
+\r
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){\r
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);\r
\r
return heterotypicSynonymyGroups;\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)\r
+ */\r
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {\r
\r
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();\r
long numberTaxaResults = 0L;\r
\r
Class<? extends TaxonBase> clazz = null;\r
- if (configurator.isDoTaxa() && configurator.isDoSynonyms()) {\r
+ List<String> propertyPath = new ArrayList<String>();\r
+ if(configurator.getTaxonPropertyPath() != null){\r
+ propertyPath.addAll(configurator.getTaxonPropertyPath());\r
+ }\r
+ if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {\r
clazz = TaxonBase.class;\r
+ //propertyPath.addAll(configurator.getTaxonPropertyPath());\r
+ //propertyPath.addAll(configurator.getSynonymPropertyPath());\r
} else if(configurator.isDoTaxa()) {\r
clazz = Taxon.class;\r
+ //propertyPath = configurator.getTaxonPropertyPath();\r
} else if (configurator.isDoSynonyms()) {\r
clazz = Synonym.class;\r
+ //propertyPath = configurator.getSynonymPropertyPath();\r
}\r
\r
if(clazz != null){\r
- numberTaxaResults = \r
- dao.countTaxaByName(clazz, \r
- configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(),\r
- configurator.getNamedAreas());\r
- if(numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results\r
+ if(configurator.getPageSize() != null){ // no point counting if we need all anyway\r
+ numberTaxaResults = \r
+ dao.countTaxaByName(clazz, \r
+ configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(),\r
+ configurator.getNamedAreas());\r
+ }\r
+ if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results\r
taxa = dao.getTaxaByName(clazz, \r
configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(),\r
configurator.getNamedAreas(), configurator.getPageSize(), \r
- configurator.getPageNumber(), configurator.getTaxonPropertyPath());\r
+ configurator.getPageNumber(), propertyPath);\r
}\r
}\r
\r
}\r
\r
numberOfResults += numberTaxaResults;\r
- \r
+\r
// Names without taxa \r
- \r
if (configurator.isDoNamesWithoutTaxa()) {\r
int numberNameResults = 0;\r
- //FIXME implement search by area\r
+ \r
List<? extends TaxonNameBase<?,?>> names = \r
nameDao.findByName(configurator.getSearchString(), configurator.getMatchMode(), \r
- configurator.getPageSize(), configurator.getPageNumber(), null, null);\r
+ configurator.getPageSize(), configurator.getPageNumber(), null, configurator.getTaxonNamePropertyPath());\r
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }\r
if (names.size() > 0) {\r
for (TaxonNameBase<?,?> taxonName : names) {\r
}\r
\r
// Taxa from common names\r
- // FIXME the matching common names also must be returned\r
- // FIXME implement search by area\r
+ \r
if (configurator.isDoTaxaByCommonNames()) {\r
- int numberCommonNameResults = 0;\r
- List<CommonTaxonName> commonTaxonNames = \r
- descriptionDao.searchDescriptionByCommonName(configurator.getSearchString(), \r
- configurator.getMatchMode(), configurator.getPageSize(), configurator.getPageNumber());\r
- if (logger.isDebugEnabled()) { logger.debug(commonTaxonNames.size() + " matching common name(s) found"); }\r
- if (commonTaxonNames.size() > 0) {\r
- for (CommonTaxonName commonTaxonName : commonTaxonNames) {\r
- DescriptionBase description = commonTaxonName.getInDescription();\r
- description = HibernateProxyHelper.deproxy(description, DescriptionBase.class);\r
- if (description instanceof TaxonDescription) {\r
- TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);\r
- Taxon taxon = taxonDescription.getTaxon();\r
- taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);\r
- if (!results.contains(taxon) && !taxon.isMisappliedName()) {\r
- defaultBeanInitializer.initialize(taxon, configurator.getTaxonPropertyPath());\r
- results.add(taxon);\r
- numberCommonNameResults++;\r
- }\r
- } else {\r
- logger.warn("Description of " + commonTaxonName.getName() + " is not an instance of TaxonDescription");\r
- }\r
- }\r
- numberOfResults += numberCommonNameResults;\r
- } \r
+ taxa = null;\r
+ numberTaxaResults = 0;\r
+ if(configurator.getPageSize() != null){// no point counting if we need all anyway\r
+ numberTaxaResults = dao.countTaxaByCommonName(configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(), configurator.getNamedAreas());\r
+ }\r
+ if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){\r
+ taxa = dao.getTaxaByCommonName(configurator.getSearchString(), configurator.getTaxonomicTree(), configurator.getMatchMode(), configurator.getNamedAreas(), configurator.getPageSize(), configurator.getPageNumber(), configurator.getTaxonPropertyPath());\r
+ }\r
+ if(taxa != null){\r
+ results.addAll(taxa);\r
+ }\r
+ numberOfResults += numberTaxaResults;\r
+ \r
}\r
\r
- //FIXME does not work any more after model change\r
- logger.warn("Sort does currently not work on identifiable entities due to model changes (duplicated implementation of the Comparable interface).");\r
- //Collections.sort(results);\r
- return new DefaultPagerImpl<IdentifiableEntity>\r
+ return new DefaultPagerImpl<IdentifiableEntity>\r
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results);\r
}\r
\r
for(Media media : descElem.getMedia()){\r
\r
//find the best matching representation\r
- medRep.add(media.findBestMatchingRepresentation(size, height, widthOrDuration, mimeTypes));\r
+ medRep.add(MediaUtils.findBestMatchingRepresentation(media, size, height, widthOrDuration, mimeTypes));\r
\r
}\r
}\r
}\r
return medRep;\r
}\r
+\r
+ public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {\r
+ return this.dao.findById(listOfIDs);\r
+ }\r
+\r
+ public int countAllRelationships() {\r
+ return this.dao.countAllRelationships();\r
+ }\r
+\r
+ public List<Synonym> createAllInferredSynonyms(TaxonomicTree tree,\r
+ Taxon taxon) {\r
+ \r
+ return this.dao.createAllInferredSynonyms(taxon, tree);\r
+ }\r
+\r
+ public List<Synonym> createInferredSynonyms(TaxonomicTree tree, Taxon taxon, SynonymRelationshipType type) {\r
+ \r
+ return this.dao.createInferredSynonyms(taxon, tree, type);\r
+ }\r
+\r
+ public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {\r
+ \r
+ return this.dao.findIdenticalTaxonNames(propertyPath);\r
+ }\r
+ \r
+ public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {\r
+ \r
+ return this.dao.findIdenticalNamesNew(propertyPath);\r
+ }\r
+ \r
+ public String getPhylumName(TaxonNameBase name){\r
+ return this.dao.getPhylumName(name);\r
+ }\r
+ \r
+ private class TaxonAndNameComparator implements Comparator{\r
+\r
+ public int compare(Object arg0, Object arg1) {\r
+ IdentifiableEntity castArg0 = (IdentifiableEntity) arg0;\r
+ IdentifiableEntity castArg1 = (IdentifiableEntity) arg1;\r
+ return castArg0.compareTo(castArg1);\r
+ }\r
+ \r
+ }\r
+\r
+ public long deleteSynonymRelationships(Synonym syn) {\r
+ \r
+ return dao.deleteSynonymRelationships(syn);\r
+ }\r
+\r
+ \r
+ public List<SynonymRelationship> listSynonymRelationships(\r
+ TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,\r
+ List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {\r
+ Integer numberOfResults = dao.countSynonymRelationships(taxonBase, type, direction);\r
+ \r
+ List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();\r
+ if(numberOfResults > 0) { // no point checking again\r
+ results = dao.getSynonymRelationships(taxonBase, type, pageSize, pageNumber, orderHints, propertyPaths, direction); \r
+ }\r
+ return results;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.ITaxonService#matchToTaxon(eu.etaxonomy.cdm.model.name.NonViralName)\r
+ */\r
+ @Override\r
+ public Taxon findBestMatchingTaxon(String taxonName) {\r
+ \r
+ Taxon matchedTaxon = null;\r
+ try{\r
+ // 1. search for acceptet taxa\r
+ List<TaxonBase> taxonList = dao.findByNameTitleCache(Taxon.class, taxonName, null, MatchMode.EXACT, null, 0, null, null);\r
+ for(IdentifiableEntity taxonBaseCandidate : taxonList){\r
+ if(taxonBaseCandidate instanceof Taxon){\r
+ matchedTaxon = (Taxon)taxonBaseCandidate;\r
+ if(taxonList.size() > 1){\r
+ logger.info(taxonList.size() + " TaxonBases found, using first accepted Taxon: " + matchedTaxon.getTitleCache());\r
+ return matchedTaxon;\r
+ } else {\r
+ logger.info("using accepted Taxon: " + matchedTaxon.getTitleCache());\r
+ return matchedTaxon;\r
+ }\r
+ //TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found \r
+ }\r
+ }\r
+ \r
+ // 2. search for synonyms\r
+ List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, taxonName, null, MatchMode.EXACT, null, 0, null, null);\r
+ for(TaxonBase taxonBase : synonymList){\r
+ if(taxonBase instanceof Synonym){\r
+ Set<Taxon> acceptetdCandidates = ((Synonym)taxonBase).getAcceptedTaxa();\r
+ if(!acceptetdCandidates.isEmpty()){\r
+ matchedTaxon = acceptetdCandidates.iterator().next();\r
+ if(acceptetdCandidates.size() == 1){\r
+ logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxonBase.getTitleCache() + ", using first one: " + matchedTaxon.getTitleCache());\r
+ return matchedTaxon;\r
+ } else {\r
+ logger.info("using accepted Taxon " + matchedTaxon.getTitleCache() + "for synonym " + taxonBase.getTitleCache());\r
+ return matchedTaxon;\r
+ }\r
+ //TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found\r
+ }\r
+ }\r
+ }\r
+ \r
+ } catch (Exception e){\r
+ logger.error(e);\r
+ }\r
+ \r
+ return matchedTaxon;\r
+ }\r
+\r
+ @Override\r
+ public Synonym findBestMatchingSynonym(String taxonName) {\r
+ List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, taxonName, null, MatchMode.EXACT, null, 0, null, null);\r
+ if(! synonymList.isEmpty()){\r
+ Synonym result = CdmBase.deproxy(synonymList.iterator().next(), Synonym.class);\r
+ if(synonymList.size() == 1){\r
+ logger.info(synonymList.size() + " Synonym found " + result.getTitleCache() );\r
+ return result;\r
+ } else {\r
+ logger.info("Several matching synonyms found. Using first: " + result.getTitleCache());\r
+ return result;\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ \r
+ \r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff