* 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.HashSet;
import java.util.List;
import java.util.Set;
import java.util.UUID;
-import org.apache.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.agent.Person;
import eu.etaxonomy.cdm.model.agent.Team;
import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.common.ISourceable;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.LanguageString;
-import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
-import eu.etaxonomy.cdm.model.common.OriginalSourceType;
import eu.etaxonomy.cdm.model.description.DescriptionBase;
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
+import eu.etaxonomy.cdm.model.description.DescriptionType;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
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.model.occurrence.DeterminationEvent;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
+import eu.etaxonomy.cdm.model.reference.ISourceable;
+import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
+import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
import eu.etaxonomy.cdm.model.taxon.Classification;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.term.DefinedTerm;
import eu.etaxonomy.cdm.persistence.query.MatchMode;
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
-
/**
* @author p.kelbert
- * @created 20.10.2008
+ * @since 20.10.2008
*/
public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends SpecimenImportStateBase>
extends CdmImportBase<CONFIG, STATE> {
private static final long serialVersionUID = 4423065367998125678L;
- private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
+ private static final Logger logger = LogManager.getLogger();
protected static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
private static final String COLON = ":";
+ 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();
} else {
//search for existing names
- List<TaxonName> names = getNameService().listByTitle(TaxonName.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
+ List<TaxonName> names = getNameService().listByTitleWithRestrictions(TaxonName.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
taxonName = getBestMatchingName(scientificName, names, state);
//still nothing found -> try with the atomised name full title cache
if(taxonName==null && atomisedTaxonName!=null){
- names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
+ names = getNameService().listByTitleWithRestrictions(TaxonName.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
//still nothing found -> try with the atomised name title cache
if(taxonName==null){
- names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
+ names = getNameService().listByTitleWithRestrictions(TaxonName.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
}
}
state.getReport().addName(taxonName);
logger.info("Created new taxon name "+taxonName);
}
- save(taxonName, state);
+ if (taxonName != null){
+ state.names.put(taxonName.getNameCache(), taxonName);
+ }
+ 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();
logger.debug("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
}
- if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
+ if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN"))) {
taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
if (taxonName.hasProblem()) {
problem = true;
}
}
- else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
+ else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNAFP"))) {
taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
if (taxonName.hasProblem()) {
problem = true;
}
}
- else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
- taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank);
+ else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN"))) {
+ taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNP, rank);
if (taxonName.hasProblem()) {
problem = true;
}
}
- else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
+ else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP"))) {
taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
if (taxonName.hasProblem()) {
problem = true;
taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
try {
- taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
+ taxonName.setRank(Rank.getRankByLatinName(getFromMap(atomisedMap, "Rank")));
} catch (Exception e) {
if (taxonName.getInfraSpecificEpithet() != null){
taxonName.setRank(Rank.SUBSPECIES());
return taxonName;
}
}
- else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNB.getUuid())) {
+ else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNP.getUuid())) {
TaxonName taxonName = TaxonNameFactory.NewBacterialInstance(null);
taxonName.setFullTitleCache(fullName, true);
taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
taxonName.setBasionymAuthorship(team);
}
if (taxonName.hasProblem()) {
- logger.info("pb ICNB");
+ logger.info("pb ICNP");
problem = true;
}
else {
/**
* Very fast and dirty implementation to allow handling of transient objects as described in
- * https://dev.e-taxonomy.eu/trac/ticket/3726
+ * 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)){
- return cdmRepository.getOccurrenceService().saveOrUpdate(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(Classification.class)){
}else if (cdmBase.isInstanceOf(Collection.class)){
return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
}else if (cdmBase.isInstanceOf(DescriptionBase.class)){
- return cdmRepository.getDescriptionService().saveOrUpdate(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 if (cdmBase.isInstanceOf(TaxonName.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;
}
FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
config.setSignificantIdentifier(unitId);
- Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
- if(!existingSpecimens.getRecords().isEmpty()){
- if(existingSpecimens.getRecords().size()==1){
- return existingSpecimens.getRecords().iterator().next();
- }
+ List<String> propertyPaths = new ArrayList<>();
+ propertyPaths.add("derivedFrom.*");
+ config.setPropertyPaths(propertyPaths);
+ commitTransaction(state.getTx());
+ state.setTx(startTransaction());
+ try{
+ @SuppressWarnings("rawtypes")
+ Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
+ if(!existingSpecimens.getRecords().isEmpty()){
+ if(existingSpecimens.getRecords().size()==1){
+ return existingSpecimens.getRecords().iterator().next();
+ }
+ }
+
+ }catch(NullPointerException e){
+ logger.error("searching for existing specimen creates NPE: " + config.getSignificantIdentifier());
+ e.printStackTrace();
}
+
+
return null;
}
* @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;
// for our new source.
protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
- /* List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
-
-
- if (reference != null){
- try {
- for (OriginalSourceBase<?> osb: issTmp){
- if (osb.getCitation() != null && osb.getCitation().getTitleCache().equalsIgnoreCase(reference.getTitleCache())){
- String osbDetail = osb.getCitationMicroReference();
- if ((StringUtils.isBlank(osbDetail) && StringUtils.isBlank(citationDetail))
- || (osbDetail != null && osbDetail.equalsIgnoreCase(citationDetail)) ) {
-// System.out.println("REFERENCE FOUND RETURN EXISTING SOURCE");
- return (IdentifiableSource) osb.clone();
- }
- }
- }
- } catch (CloneNotSupportedException e) {
- throw new RuntimeException(e);
- } catch (Exception e1){
- e1.printStackTrace();
- }
- }
- */
IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
return sour;
}
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();
parent = linkParentChildNode(species, subspecies, classification, state);
}
}
+ }else{
+ //handle cf. and aff. taxa
+ String genusEpithet = null;
+ if (nvname.getTitleCache().contains("cf.")){
+ genusEpithet = nvname.getTitleCache().substring(0, nvname.getTitleCache().indexOf("cf."));
+ } else if (nvname.getTitleCache().contains("aff.")){
+ genusEpithet = nvname.getTitleCache().substring(0, nvname.getTitleCache().indexOf("aff."));
+ }
+ if (genusEpithet != null){
+ genusEpithet = genusEpithet.trim();
+ TaxonName taxonName = null;
+ if (genusEpithet.contains(" ")){
+ taxonName = getOrCreateTaxonName(genusEpithet, Rank.SPECIES(), preferredFlag, state, -1);
+ }else{
+ taxonName = getOrCreateTaxonName(genusEpithet, Rank.GENUS(), preferredFlag, state, -1);
+ }
+ genus = getOrCreateTaxonForName(taxonName, state);
+ if (genus == null){
+ logger.debug("The genus should not be null " + taxonName);
+ }
+ if (preferredFlag) {
+ parent = linkParentChildNode(null, genus, classification, state);
+ }
+ }
}
if (preferredFlag && parent!=taxon ) {
linkParentChildNode(parent, taxon, classification, state);
*/
protected Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, STATE state) {
TaxonNode node =null;
+ List<String> propertyPaths = new ArrayList<>();
+ propertyPaths.add("childNodes");
if (parent != null) {
- parent = (Taxon) getTaxonService().find(parent.getUuid());
- child = (Taxon) getTaxonService().find(child.getUuid());
+
+ parent = (Taxon) getTaxonService().load(parent.getUuid(), propertyPaths);
+ child = (Taxon) getTaxonService().load(child.getUuid(), propertyPaths);
//here we do not have to check if the taxon nodes already exists
//this is done by classification.addParentChild()
//do not add child node if it already exists
}
}
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;
String preferred = identification.getPreferred();
preferredFlag = false;
- if (preferred != null){
- if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || state.getDataHolder().getIdentificationList().size()==1) {
+ if (preferred != null || state.getDataHolder().getIdentificationList().size()==1){
+ if (state.getDataHolder().getIdentificationList().size()==1){
+ preferredFlag = true;
+ }else if (preferred != null && (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1) ) {
preferredFlag = true;
}
TaxonName taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
Taxon taxon = getOrCreateTaxonForName(taxonName, state);
addTaxonNode(taxon, state,preferredFlag);
- linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate());
+ linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate(), identification.getModifier());
}
}
if (!existsInClassification(taxon,state.getClassification(), state)){
if(config.isMoveNewTaxaToDefaultClassification()){
//check if node exists in default classification
- if (!existsInClassification(taxon, state.getDefaultClassification(), state)){
- addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification());
+ if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
+ addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
}
- }
- else {
+ }else{
//add non-existing taxon to current classification
addParentTaxon(taxon, state, preferredFlag, state.getClassification());
}
+
}
}
* @param derivedFacade : the derived Unit Facade
*/
@SuppressWarnings("rawtypes")
- protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade, String identifierStr, String dateStr) {
+ protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade, String identifierStr, String dateStr, String modifier) {
SpecimenImportConfiguratorBase config = state.getConfig();
if (logger.isDebugEnabled()){
logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
}
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
+ //determinationEvent.setTaxon(taxon);
determinationEvent.setTaxonName(taxon.getName());
determinationEvent.setPreferredFlag(preferredFlag);
if (dateStr != null){
determinationEvent.setTimeperiod(TimePeriodParser.parseString(dateStr));
}
- state.getDerivedUnitBase().addDetermination(determinationEvent);
+ if (modifier != null){
+ if (modifier.equals("cf.")){
+ determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_CONFER());
+ }else if (modifier.equals("aff.")){
+ determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
+ }
+ }
+ if (config.isAddDeterminations()) {
+ state.getDerivedUnitBase().addDetermination(determinationEvent);
+ }
+
if (logger.isDebugEnabled()){
logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
if(cdmAppController == null){
cdmAppController = this;
}
- specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid());
+ specimenTypeDesignationstatus = HibernateProxyHelper.deproxy(cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid()), SpecimenTypeDesignationStatus.class);
//Designation
TaxonName name = taxon.getName();
SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
designation.setTypeStatus(specimenTypeDesignationstatus);
designation.setTypeSpecimen(state.getDerivedUnitBase());
- name.addTypeDesignation(designation, true);
+ name.addTypeDesignation(designation, false);
}
}
+ save(state.getDerivedUnitBase(), state);
for (String[] fullReference : state.getDataHolder().getReferenceList()) {
String strReference=fullReference[0];
String citationDetail = fullReference[1];
String citationURL = fullReference[2];
- List<Reference> references = getReferenceService().listByTitle(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
+ List<Reference> references = getReferenceService().listByTitleWithRestrictions(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
if (!references.isEmpty()){
Reference reference = null;
}
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 taxonDescription = null;
Set<TaxonDescription> descriptions= taxon.getDescriptions();
- if (!descriptions.isEmpty()){ taxonDescription = descriptions.iterator().next();}
-
-// for (TaxonDescription description : descriptions){
-// Set<IdentifiableSource> sources = new HashSet<>();
-// sources.addAll(description.getTaxon().getSources());
-// sources.addAll(description.getSources());
-// for (IdentifiableSource source:sources){
-// if(state.getRef().equals(source.getCitation())) {
-// taxonDescription = description;
-// }
-// }
-// }
- // }
- if (taxonDescription == null){
+ if (state.getIndividualsAssociationDescriptionPerTaxon(taxon.getUuid()) != null){
+ taxonDescription = state.getIndividualsAssociationDescriptionPerTaxon(taxon.getUuid());
+ }
+ if (taxonDescription == null && !descriptions.isEmpty() && state.getConfig().isReuseExistingDescriptiveGroups()){
+ for (TaxonDescription desc: descriptions){
+ if (desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION)){
+ taxonDescription = desc;
+ break;
+ }
+ }
+ }
+
+ if (taxonDescription == null){
taxonDescription = TaxonDescription.NewInstance(taxon, false);
+ taxonDescription.setTypes(EnumSet.of(DescriptionType.INDIVIDUALS_ASSOCIATION));
if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
}
- state.setDescriptionGroup(taxonDescription);
+ state.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
taxon.addDescription(taxonDescription);
}
//PREPARE REFERENCE QUESTIONS
- Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
+ Map<String,OriginalSourceBase> sourceMap = new HashMap<>();
List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
- Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
+ Set<OriginalSourceBase> osbSet = new HashSet<>();
if(issTmp2!=null) {
osbSet.addAll(issTmp2);
}
addToSourceMap(sourceMap, osbSet);
-// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
-// List<OriginalSourceBase<?>> res = null;
-// if(!state.isDescriptionSourcesSet()){
-// res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
-// "The current reference is "+state.getRef().getTitleCache(),getReferenceService(), state.getDataHolder().docSources);
-// state.setDescriptionRefs(res);
-// state.setDescriptionSourcesSet(true);
-// }
-// else{
-// res=state.getDescriptionRefs();
-// }
-// if(res !=null) {
-// for (OriginalSourceBase<?> sour:res){
-// if(sour.isInstanceOf(IdentifiableSource.class)){
-// try {
-// if(sourceNotLinkedToElement(taxonDescription,sour)) {
-// taxonDescription.addSource((IdentifiableSource)sour.clone());
-// }
-// } catch (CloneNotSupportedException e) {
-// logger.warn("no cloning?");
-// }
-// }else{
-// if(sourceNotLinkedToElement(taxonDescription,sour)) {
-// taxonDescription.addSource(OriginalSourceType.Import,null, null, sour.getCitation(),sour.getCitationMicroReference());
-// }
-// }
-// }
-// }
-// }
-// else {
- if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
- taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
- }
-// }
- state.setDescriptionGroup(taxonDescription);
+
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+
+ state.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
Feature feature = makeFeature(state.getDerivedUnitBase());
indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
indAssociation.setFeature(feature);
-//
-// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
-// sourceMap = new HashMap<String, OriginalSourceBase<?>>();
-//
-// issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
-// issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
-//
-// osbSet = new HashSet<OriginalSourceBase>();
-// if(issTmp2!=null) {
-// osbSet.addAll(issTmp2);
-// }
-// if(issTmp!=null) {
-// osbSet.addAll(issTmp);
-// }
-//
-//
-// addToSourceMap(sourceMap, osbSet);
-//
-// List<OriginalSourceBase<?>> sources =null;
-// if(!state.isAssociationSourcesSet()) {
-// sources = sui.askForSource(sourceMap, "descriptive element (association) ",taxon.toString(),
-// getReferenceService(),state.getDataHolder().getDocSources());
-// state.setAssociationRefs(sources);
-// state.setAssociationSourcesSet(true);
-// }
-// else{
-// sources=state.getAssociationRefs();
-// }
-// if(sources !=null) {
-// for (OriginalSourceBase<?> source: sources) {
-// if(source !=null) {
-// if(source.isInstanceOf(DescriptionElementSource.class)){
-// try {
-// if(sourceNotLinkedToElement(indAssociation,source)) {
-// indAssociation.addSource((DescriptionElementSource)source.clone());
-// }
-// } catch (CloneNotSupportedException e) {
-// logger.warn("clone forbidden?");
-// }
-// }else{
-// if(sourceNotLinkedToElement(indAssociation,source)) {
-// indAssociation.addSource(OriginalSourceType.Import,null, null, source.getCitation(),source.getCitationMicroReference());
-// }
-// try {
-// if(sourceNotLinkedToElement(state.getDerivedUnitBase(), source)) {
-// state.getDerivedUnitBase().addSource((IdentifiableSource) source.clone());
-// }
-// } catch (CloneNotSupportedException e) {
-// // TODO Auto-generated catch block
-// e.printStackTrace();
-// }
-// }
-//
-// }
-// }
-// }
-// }else {
- if(sourceNotLinkedToElement(indAssociation,state.getRef(),null)) {
- indAssociation.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
- }
- if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
- state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
- }
- for (Reference citation : determinationEvent.getReferences()) {
- if(sourceNotLinkedToElement(indAssociation,citation,null))
- {
- indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
- }
- if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
- state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
- }
- }
- // }
+
+ if(sourceNotLinkedToElement(indAssociation,state.getImportReference(state.getActualAccessPoint()),null)) {
+ indAssociation.addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getImportReference(state.getActualAccessPoint()),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
+ }
+ for (Reference citation : determinationEvent.getReferences()) {
+ if(sourceNotLinkedToElement(indAssociation,citation,null))
+ {
+ indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getImportReference(state.getActualAccessPoint()),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
+ }
+ }
taxonDescription.addElement(indAssociation);
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()){
// return getFeature("Specimen or observation");
}else{
String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
- logger.warn(String.format(message, type.getMessage()));
+ logger.warn(String.format(message, type.getLabel()));
return Feature.OBSERVATION();
// return getFeature("Specimen or observation");
}
}
-
- /**
- * @param sourceMap
- * @param osbSet
- */
- protected void addToSourceMap(Map<String, OriginalSourceBase<?>> sourceMap, Set<OriginalSourceBase> osbSet) {
- for( OriginalSourceBase<?> osb: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()) {
try{
sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
}
}
}
-
-
-}
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff