* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
-
package eu.etaxonomy.cdm.io.specimen;
-
import java.util.ArrayList;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.Set;
import java.util.UUID;
-import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import eu.etaxonomy.cdm.api.application.ICdmRepository;
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.facade.DerivedUnitFacade;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.common.CdmImportBase;
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
import eu.etaxonomy.cdm.model.name.INonViralName;
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.RankClass;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
-
/**
* @author p.kelbert
* @since 20.10.2008
extends CdmImportBase<CONFIG, STATE> {
private static final long serialVersionUID = 4423065367998125678L;
- private static final Logger logger = LogManager.getLogger(SpecimenImportBase.class);
+ private static final Logger logger = LogManager.getLogger();
protected static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
protected Map<String, DefinedTerm> kindOfUnitsMap;
-
@Override
protected abstract void doInvoke(STATE state);
/**
* Handle a single unit
- * @param state
- * @param item
*/
protected abstract void handleSingleUnit(STATE state, Object item) ;
-
-
protected TaxonName getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
TaxonName taxonName = null;
SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
if (taxonName != null){
state.names.put(taxonName.getNameCache(), taxonName);
}
- if(!taxonName.isPersited()) {
+ if(!taxonName.isPersisted()) {
save(taxonName, state);
}
return taxonName;
Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
for (TaxonName name : names) {
- if(!name.getTaxa().isEmpty()){
- Set<Taxon> taxa = name.getTaxa();
- for (Taxon taxon:taxa){
- if (!taxon.getTaxonNodes().isEmpty()){
+ if(!name.getTaxonBases().isEmpty()){
+ Set<TaxonBase> taxa = name.getTaxonBases();
+ for (TaxonBase taxonBase:taxa){
+ Taxon acceptedTaxon= null;
+ if (taxonBase instanceof Synonym) {
+ Synonym syn = (Synonym) taxonBase;
+ acceptedTaxon = syn.getAcceptedTaxon();
+ }else {
+ acceptedTaxon = (Taxon)taxonBase;
+ }
+ if (!(acceptedTaxon).getTaxonNodes().isEmpty()){
//use only taxa included in a classification
- for (TaxonNode node:taxon.getTaxonNodes()){
+ for (TaxonNode node:(acceptedTaxon).getTaxonNodes()){
if (state.getClassification() != null && node.getClassification().equals(state.getClassification())){
namesWithAcceptedTaxaInClassification.add(name);
}else {
namesWithAcceptedTaxa.add(name);
}
}
-
}
}
-
}
}
String message = String.format("More than one taxon name was found for %s, maybe in other classifications!", scientificName);
}
return namesWithAcceptedTaxa.iterator().next();
}
- //no names with accepted taxa found -> check accepted taxa of synonyms
- List<Taxon> taxaFromSynonyms = new ArrayList<>();
- for (TaxonName name : names) {
- Set<TaxonBase> taxonBases = name.getTaxonBases();
- for (TaxonBase taxonBase : taxonBases) {
- if(taxonBase.isInstanceOf(Synonym.class)){
- Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
- taxaFromSynonyms.add(synonym.getAcceptedTaxon());
- }
- }
- }
- if(taxaFromSynonyms.size()>0){
- if(taxaFromSynonyms.size()>1){
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
- }
- return taxaFromSynonyms.iterator().next().getName();
- }
+// //no names with accepted taxa found -> check accepted taxa of synonyms -> this is handled in the first block now!
+// List<Taxon> taxaFromSynonyms = new ArrayList<>();
+// for (TaxonName name : names) {
+// Set<TaxonBase> taxonBases = name.getTaxonBases();
+// for (TaxonBase taxonBase : taxonBases) {
+// if(taxonBase.isInstanceOf(Synonym.class)){
+// Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
+// taxaFromSynonyms.add(synonym.getAcceptedTaxon());
+// }
+// }
+// }
+// if(taxaFromSynonyms.size()>0){
+// if(taxaFromSynonyms.size()>1){
+// state.getReport().addInfoMessage(message);
+// logger.warn(message);
+// return null;
+// }
+// return taxaFromSynonyms.iterator().next().getName();
+// }
//no accepted and no synonyms -> return one of the names and create a new taxon
if (names.isEmpty()){
return null;
return names.iterator().next();
}
}
+
/**
* Parse automatically the scientific name
* @param scientificName the scientific name to parse
* @param report the import report
* @return a parsed name
*/
-
protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
* https://dev.e-taxonomy.eu/redmine/issues/3726
*
* Not yet complete.
- *
- * @param cdmBase
- * @param state
*/
- protected UUID save(CdmBase cdmBase, SpecimenImportStateBase state) {
+ protected UUID save(CdmBase cdmBase, SpecimenImportStateBase<?,?> state) {
ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
if (cdmRepository == null){
cdmRepository = this;
if (cdmBase.isInstanceOf(LanguageString.class)){
return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
}else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
- SpecimenOrObservationBase specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
-
+ SpecimenOrObservationBase<?> specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
return cdmRepository.getOccurrenceService().saveOrUpdate(specimen);
}else if (cdmBase.isInstanceOf(Reference.class)){
return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
}else if (cdmBase.isInstanceOf(Collection.class)){
return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
}else if (cdmBase.isInstanceOf(DescriptionBase.class)){
- DescriptionBase description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
-
+ DescriptionBase<?> description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
return cdmRepository.getDescriptionService().saveOrUpdate(description);
}else if (cdmBase.isInstanceOf(TaxonBase.class)){
return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
}else{
throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
}
-
}
-
- protected SpecimenOrObservationBase findExistingSpecimen(String unitId, SpecimenImportStateBase state){
+ protected SpecimenOrObservationBase<?> findExistingSpecimen(String unitId, SpecimenImportStateBase<?,?> state){
ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
if(cdmAppController==null){
cdmAppController = this;
commitTransaction(state.getTx());
state.setTx(startTransaction());
try{
- Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
+ @SuppressWarnings("rawtypes")
+ Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
if(!existingSpecimens.getRecords().isEmpty()){
if(existingSpecimens.getRecords().size()==1){
return existingSpecimens.getRecords().iterator().next();
* @return the Institution (existing or new)
*/
protected Institution getInstitution(String institutionCode, STATE state) {
- SpecimenImportConfiguratorBase config = state.getConfig();
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
Institution institution=null;
institution = (Institution)state.institutions.get(institutionCode);
if (institution != null){
institution = Institution.NewInstance();
institution.setCode(institutionCode);
institution.setTitleCache(institutionCode, true);
- UUID uuid = save(institution, state);
+ save(institution, state);
}
-
state.institutions.put(institutionCode, institution);
return institution;
}
* @return the Collection (existing or new)
*/
protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
- SpecimenImportConfiguratorBase config = state.getConfig();
+
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
Collection collection = null;
List<Collection> collections;
collection = (Collection) state.collections.get(collectionCode);
try {
collections = getCollectionService().searchByCode(collectionCode);
} catch (Exception e) {
- collections = new ArrayList<Collection>();
+ collections = new ArrayList<>();
}
if (collections.size() > 0 && config.isReuseExistingMetaData()) {
for (Collection coll:collections){
collection =Collection.NewInstance();
collection.setCode(collectionCode);
collection.setInstitute(institution);
- collection.setTitleCache(collectionCode);
- UUID uuid = save(collection, state);
+ save(collection, state);
}
-
-
state.collections.put(collectionCode, collection);
return collection;
Taxon subspecies = null;
Taxon parent = null;
if(rank!=null){
- if (rank.isLower(Rank.GENUS() )){
+ if (rank.isLowerThan(RankClass.Genus)){
String genusOrUninomial = nvname.getGenusOrUninomial();
TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
genus = getOrCreateTaxonForName(taxonName, state);
subgenus = getOrCreateTaxonForName(taxonName, state);
if (preferredFlag) {
parent = linkParentChildNode(genus, subgenus, classification, state);
- } }
+ }
+ }
}
- if (rank.isLower(Rank.SPECIES())){
+ if (rank.isLowerThan(RankClass.Species)){
if (subgenus!=null){
String prefix = nvname.getGenusOrUninomial();
String name = nvname.getInfraGenericEpithet();
}
}
else{
- Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases();
- for (TaxonBase taxonBase : taxonAndSynonyms) {
+ @SuppressWarnings("rawtypes")
+ Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases();
+ for (TaxonBase<?> taxonBase : taxonAndSynonyms) {
if(taxonBase.isInstanceOf(Synonym.class)){
Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon();
return taxon;
}
return null;
-
}
private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
* @param derivedUnitFacade : the current derivedunitfacade
*/
protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
- SpecimenImportConfiguratorBase config = state.getConfig();
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
String scientificName = "";
boolean preferredFlag = false;
determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
}
}
- state.getDerivedUnitBase().addDetermination(determinationEvent);
+ if (config.isAddDeterminations()) {
+ state.getDerivedUnitBase().addDetermination(determinationEvent);
+ }
+
if (logger.isDebugEnabled()){
logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
}
save(state.getDerivedUnitBase(), state);
- if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
+ if (config.isAddIndividualsAssociations() && preferredFlag) {
//do not add IndividualsAssociation to non-preferred taxa
if (logger.isDebugEnabled()){
logger.debug("isDoCreateIndividualsAssociations");
}
}
-
taxonDescription.addElement(indAssociation);
save(taxonDescription, state);
state.getReport().addIndividualAssociation(taxon, state.getDataHolder().getUnitID(), state.getDerivedUnitBase());
}
- /**
- * @param derivedUnitBase2
- * @param ref2
- * @param object
- * @return
- */
private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference b, String d) {
Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
for (IdentifiableSource is:linkedSources){
}
}catch(Exception e){}
-
try{
if (c==null && d==null) {
microMatch=true;
if (microMatch && refMatch) {
return false;
}
-
-
}
return true;
}
- private <T extends OriginalSourceBase> boolean sourceNotLinkedToElement(ISourceable<T> sourcable, Reference reference, String microReference) {
+ private <T extends OriginalSourceBase> boolean sourceNotLinkedToElement(
+ ISourceable<T> sourcable, Reference reference, String microReference) {
+
Set<T> linkedSources = sourcable.getSources();
for (T is:linkedSources){
Reference unitReference = is.getCitation();
private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
SpecimenOrObservationType type = unit.getRecordBasis();
-
-
if (type.isFeatureObservation()){
return Feature.OBSERVATION();
}else if (type.isFeatureSpecimen()){
}
}
-
- /**
- * @param sourceMap
- * @param osbSet
- */
protected void addToSourceMap(Map<String, OriginalSourceBase> sourceMap, Set<OriginalSourceBase> osbSet) {
for( OriginalSourceBase osb:osbSet) {
if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
}
}
}
-
-
-
-
-}
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff