import java.util.ArrayList;
+import java.util.EnumSet;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
+import java.util.UUID;
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
+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.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.common.CdmImportBase;
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
import eu.etaxonomy.cdm.model.agent.AgentBase;
+import eu.etaxonomy.cdm.model.agent.Institution;
+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.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.LanguageString;
import eu.etaxonomy.cdm.model.description.DescriptionBase;
-import eu.etaxonomy.cdm.model.name.BacterialName;
-import eu.etaxonomy.cdm.model.name.BotanicalName;
-import eu.etaxonomy.cdm.model.name.CultivarPlantName;
+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.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.name.ZoologicalName;
+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.name.TaxonNameFactory;
import eu.etaxonomy.cdm.model.occurrence.Collection;
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
+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.Synonym;
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> {
+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);
+
+ protected static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
+
+ private static final String COLON = ":";
+
+ protected Map<String, DefinedTerm> kindOfUnitsMap;
+
- @SuppressWarnings("unused")
- private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
- protected final boolean DEBUG = true;
@Override
protected abstract void doInvoke(STATE state);
* @param state
* @param item
*/
- @SuppressWarnings("rawtypes")
protected abstract void handleSingleUnit(STATE state, Object item) ;
- protected TaxonNameBase<?, ?> getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
- TaxonNameBase<?, ?> taxonName = null;
- SpecimenImportConfiguratorBase config = (SpecimenImportConfiguratorBase) state.getConfig();
+ protected TaxonName getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
+ TaxonName taxonName = null;
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
//check atomised name data for rank
//new name will be created
- NonViralName<?> atomisedTaxonName = null;
- if (rank==null && unitIndexInAbcdFile>=0 && (state.getDataHolder().getAtomisedIdentificationList() != null || state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
+ TaxonName atomisedTaxonName = null;
+ if (rank==null && unitIndexInAbcdFile>=0 && ((state.getDataHolder().getAtomisedIdentificationList() != null && !state.getDataHolder().getAtomisedIdentificationList().isEmpty())|| state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state);
if(atomisedTaxonName!=null){
rank = atomisedTaxonName.getRank();
}
}
if(config.isReuseExistingTaxaWhenPossible()){
- NonViralName<?> parsedName = atomisedTaxonName;
+ TaxonName parsedName = atomisedTaxonName;
if(parsedName==null){
- parsedName = parseScientificName(scientificName, state, state.getReport());
+
+ parsedName = parseScientificName(scientificName, state, state.getReport(), rank);
+
}
- if(config.isIgnoreAuthorship() && parsedName!=null && preferredFlag){
+ atomisedTaxonName = parsedName;
+ if(config.isIgnoreAuthorship() && parsedName!=null){// && preferredFlag){
// do not ignore authorship for non-preferred names because they need
// to be created for the determination history
- String nameCache = parsedName.getNameCache();
- List<NonViralName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
- taxonName = getBestMatchingName(scientificName, new ArrayList<TaxonNameBase>(names), state);
- }
- else {
+ String nameCache = TaxonName.castAndDeproxy(parsedName).getNameCache();
+ List<TaxonName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
+ if (!names.isEmpty()){
+ taxonName = getBestMatchingName(scientificName, new ArrayList<>(names), state);
+ }
+ if (taxonName == null && !names.isEmpty()){
+ taxonName = names.get(0);
+ }
+
+ } else {
//search for existing names
- List<TaxonNameBase> names = getNameService().listByTitle(TaxonNameBase.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(TaxonNameBase.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(TaxonNameBase.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);
}
}
+
}
+
}
if(taxonName==null && atomisedTaxonName!=null){
}
else if(taxonName==null){
//create new taxon name
- taxonName = NonViralName.NewInstance(rank);
+
+ if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP)){
+ taxonName = TaxonNameFactory.NewBotanicalInstance(rank);
+ }else if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN)){
+ taxonName = TaxonNameFactory.NewZoologicalInstance(rank);
+ }else{
+ taxonName = TaxonNameFactory.NewNonViralInstance(rank);
+ }
taxonName.setFullTitleCache(scientificName,true);
taxonName.setTitleCache(scientificName, true);
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.isPersited()) {
+ save(taxonName, state);
+ }
return taxonName;
}
- protected TaxonNameBase<?, ?> getBestMatchingName(String scientificName, java.util.Collection<TaxonNameBase> names, STATE state){
- List<TaxonNameBase> namesWithAcceptedTaxa = new ArrayList<TaxonNameBase>();
- for (TaxonNameBase name : names) {
+ protected TaxonName getBestMatchingName(String scientificName, java.util.Collection<TaxonName> names, STATE state){
+ Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
+ List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
+ for (TaxonName name : names) {
if(!name.getTaxa().isEmpty()){
- namesWithAcceptedTaxa.add(name);
+ Set<Taxon> taxa = name.getTaxa();
+ for (Taxon taxon:taxa){
+ if (!taxon.getTaxonNodes().isEmpty()){
+ //use only taxa included in a classification
+ for (TaxonNode node:taxon.getTaxonNodes()){
+ if (state.getClassification() != null && node.getClassification().equals(state.getClassification())){
+ namesWithAcceptedTaxaInClassification.add(name);
+ }else {
+ namesWithAcceptedTaxa.add(name);
+ }
+ }
+
+ }
+ }
+
}
}
- String message = "More than one taxon name was found for "+scientificName+"!";
- //check for names with accepted taxa
+ String message = String.format("More than one taxon name was found for %s, maybe in other classifications!", scientificName);
+ //check for names with accepted taxa in classification
+ if(namesWithAcceptedTaxaInClassification.size()>0){
+ if(namesWithAcceptedTaxaInClassification.size()>1){
+
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return namesWithAcceptedTaxaInClassification.iterator().next();
+ }
+ //check for any names with accepted taxa
if(namesWithAcceptedTaxa.size()>0){
if(namesWithAcceptedTaxa.size()>1){
+
state.getReport().addInfoMessage(message);
logger.warn(message);
return null;
return namesWithAcceptedTaxa.iterator().next();
}
//no names with accepted taxa found -> check accepted taxa of synonyms
- List<Taxon> taxaFromSynonyms = new ArrayList<Taxon>();
- for (TaxonNameBase name : names) {
+ 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.addAll(synonym.getAcceptedTaxa());
+ taxaFromSynonyms.add(synonym.getAcceptedTaxon());
}
}
}
}
return taxaFromSynonyms.iterator().next().getName();
}
- return null;
+ //no accepted and no synonyms -> return one of the names and create a new taxon
+ if (names.isEmpty()){
+ return null;
+ }else{
+ return names.iterator().next();
+ }
}
/**
* Parse automatically the scientific name
* @param report the import report
* @return a parsed name
*/
- protected NonViralName<?> parseScientificName(String scientificName, STATE state, SpecimenImportReport report) {
+
+ protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
+
NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
- NonViralName<?> taxonName = null;
+ TaxonName taxonName = null;
boolean problem = false;
- if(DEBUG){
- logger.info("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
+ if (logger.isDebugEnabled()){
+ logger.debug("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
}
- if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, null);
+ 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")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, null);
+ 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 = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, null);
+ 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")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, null);
+ 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;
}
* @param state
* @return the corresponding Botanical or Zoological or... name
*/
- protected NonViralName<?> setTaxonNameByType(
+ protected TaxonName setTaxonNameByType(
HashMap<String, String> atomisedMap, String fullName, STATE state) {
boolean problem = false;
- if(DEBUG) {
- logger.info("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
+ if (logger.isDebugEnabled()){
+ logger.debug("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
}
- if (state.getDataHolder().getNomenclatureCode().equals("Zoological")) {
- NonViralName<ZoologicalName> taxonName = ZoologicalName.NewInstance(null);
+ if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
+ TaxonName taxonName = TaxonNameFactory.NewZoologicalInstance(null);
taxonName.setFullTitleCache(fullName, true);
taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
return taxonName;
}
}
- else if (state.getDataHolder().getNomenclatureCode().equals("Botanical")) {
- BotanicalName taxonName = (BotanicalName) parseScientificName(fullName, state, state.getReport());
+ else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
+ TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null);
if (taxonName != null){
return taxonName;
}
else{
- taxonName = BotanicalName.NewInstance(null);
+ taxonName = TaxonNameFactory.NewBotanicalInstance(null);
}
taxonName.setFullTitleCache(fullName, true);
taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
return taxonName;
}
}
- else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial")) {
- NonViralName<BacterialName> taxonName = BacterialName.NewInstance(null);
+ 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.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
taxonName.setBasionymAuthorship(team);
}
if (taxonName.hasProblem()) {
- logger.info("pb ICNB");
+ logger.info("pb ICNP");
problem = true;
}
else {
}
}
else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
- CultivarPlantName taxonName = CultivarPlantName.NewInstance(null);
+ TaxonName taxonName = TaxonNameFactory.NewCultivarInstance(null);
if (taxonName.hasProblem()) {
logger.info("pb ICNCP");
if (problem) {
logger.info("Problem im setTaxonNameByType ");
- NonViralName<?> taxonName = NonViralName.NewInstance(null);
+ TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);
taxonName.setFullTitleCache(fullName, true);
return taxonName;
}
- NonViralName<?> tn = NonViralName.NewInstance(null);
+ TaxonName tn = TaxonNameFactory.NewNonViralInstance(null);
return tn;
}
/**
* 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 void save(CdmBase cdmBase, SpecimenImportStateBase state) {
- ICdmApplicationConfiguration cdmRepository = state.getConfig().getCdmAppController();
+ protected UUID save(CdmBase cdmBase, SpecimenImportStateBase state) {
+ ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
if (cdmRepository == null){
cdmRepository = this;
}
if (cdmBase.isInstanceOf(LanguageString.class)){
- cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
+ return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
}else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
- 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)){
- cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
+ return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
}else if (cdmBase.isInstanceOf(Classification.class)){
- cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
+ return cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
}else if (cdmBase.isInstanceOf(AgentBase.class)){
- cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
+ return cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
}else if (cdmBase.isInstanceOf(Collection.class)){
- cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
+ return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
}else if (cdmBase.isInstanceOf(DescriptionBase.class)){
- 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)){
- cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
- }else if (cdmBase.isInstanceOf(TaxonNameBase.class)){
- cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNameBase.class));
- }else{
+ return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonName.class)){
+ return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonName.class));
+ }else if (cdmBase.isInstanceOf(TaxonNode.class)){
+ return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.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){
- ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
+ 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{
+ 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;
}
protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
+ /**
+ * getFacade : get the DerivedUnitFacade based on the recordBasis
+ * @param state
+ *
+ * @return DerivedUnitFacade
+ */
+ protected DerivedUnitFacade getFacade(STATE state) {
+ if (logger.isDebugEnabled()){
+ logger.info("getFacade()");
+ }
+ SpecimenOrObservationType type = null;
+
+ // create specimen
+ if (NB((state.getDataHolder().getRecordBasis())) != null) {
+ if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
+ type = SpecimenOrObservationType.PreservedSpecimen;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
+ type = SpecimenOrObservationType.Observation;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
+ type = SpecimenOrObservationType.Fossil;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
+ type = SpecimenOrObservationType.LivingSpecimen;
+ }
+ if (type == null) {
+ logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
+ type = SpecimenOrObservationType.DerivedUnit;
+ }
+ // TODO fossils?
+ } else {
+ logger.info("The basis of record is null");
+ type = SpecimenOrObservationType.DerivedUnit;
+ }
+ DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
+ return derivedUnitFacade;
+ }
+
+ /**
+ * Look if the Institution does already exist
+ * @param institutionCode: a string with the institutioncode
+ * @param config : the configurator
+ * @return the Institution (existing or new)
+ */
+ protected Institution getInstitution(String institutionCode, STATE state) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ Institution institution=null;
+ institution = (Institution)state.institutions.get(institutionCode);
+ if (institution != null){
+ return institution;
+ }
+ List<Institution> institutions;
+ try {
+ institutions = getAgentService().searchInstitutionByCode(institutionCode);
+
+ } catch (Exception e) {
+ institutions = new ArrayList<Institution>();
+ logger.warn(e);
+ }
+ if (institutions.size() > 0 && config.isReuseExistingMetaData()) {
+ for (Institution institut:institutions){
+ try{
+ if (institut.getCode().equalsIgnoreCase(institutionCode)) {
+ institution=institut;
+ break;
+ }
+ }catch(Exception e){logger.warn("no institution code in the db");}
+ }
+ }
+ if (logger.isDebugEnabled()){
+ if(institution !=null) {
+ logger.info("getinstitution " + institution.toString());
+ }
+ }
+ if (institution == null){
+ // create institution
+ institution = Institution.NewInstance();
+ institution.setCode(institutionCode);
+ institution.setTitleCache(institutionCode, true);
+ UUID uuid = save(institution, state);
+ }
+
+
+ state.institutions.put(institutionCode, institution);
+ return institution;
+ }
+
+ /**
+ * Look if the Collection does already exist
+ * @param collectionCode
+ * @param collectionCode: a string
+ * @param config : the configurator
+ * @return the Collection (existing or new)
+ */
+ protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ Collection collection = null;
+ List<Collection> collections;
+ collection = (Collection) state.collections.get(collectionCode);
+ if (collection != null){
+ return collection;
+ }
+ try {
+ collections = getCollectionService().searchByCode(collectionCode);
+ } catch (Exception e) {
+ collections = new ArrayList<Collection>();
+ }
+ if (collections.size() > 0 && config.isReuseExistingMetaData()) {
+ for (Collection coll:collections){
+ if (coll.getCode() != null && coll.getInstitute() != null
+ && coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
+ collection = coll;
+ break;
+ }
+ }
+ }
+
+ if(collection == null){
+ collection =Collection.NewInstance();
+ collection.setCode(collectionCode);
+ collection.setInstitute(institution);
+ collection.setTitleCache(collectionCode);
+ UUID uuid = save(collection, state);
+ }
+
+
+
+ state.collections.put(collectionCode, collection);
+
+ return collection;
+ }
+
+ /**
+ * @param reference
+ * @param citationDetail
+ * @return
+ */
+ //FIXME this method is highly critical, because
+ // * it will have serious performance and memory problems with large databases
+ // (databases may easily have >1 Mio source records)
+ // * it does not make sense to search for existing sources and then clone them
+ // we need to search for existing references instead and use them (if exist)
+ // for our new source.
+ protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
+
+ IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
+ return sour;
+ }
+
+ /**
+ * Add the hierarchy for a Taxon(add higher taxa)
+ * @param classification
+ * @param taxon: a taxon to add as a node
+ * @param state: the ABCD import state
+ */
+ protected void addParentTaxon(Taxon taxon, STATE state, boolean preferredFlag, Classification classification){
+ INonViralName nvname = taxon.getName();
+ Rank rank = nvname.getRank();
+ Taxon genus =null;
+ Taxon subgenus =null;
+ Taxon species = null;
+ Taxon subspecies = null;
+ Taxon parent = null;
+ if(rank!=null){
+ if (rank.isLower(Rank.GENUS() )){
+ String genusOrUninomial = nvname.getGenusOrUninomial();
+ TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, 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 (rank.isLower(Rank.SUBGENUS())){
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getInfraGenericEpithet();
+ if (name != null){
+ TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
+ subgenus = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(genus, subgenus, classification, state);
+ } }
+ }
+ if (rank.isLower(Rank.SPECIES())){
+ if (subgenus!=null){
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getInfraGenericEpithet();
+ String spe = nvname.getSpecificEpithet();
+ if (spe != null){
+ TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
+ species = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(subgenus, species, classification, state);
+ }
+ }
+ }
+ else{
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getSpecificEpithet();
+ if (name != null){
+ TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
+ species = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(genus, species, classification, state);
+ }
+ }
+ }
+ }
+ if (rank.isLower(Rank.INFRASPECIES())){
+ TaxonName taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
+ subspecies = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ 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);
+ }
+ }
+
+ /**
+ * Link a parent to a child and save it in the current classification
+ * @param parent: the higher Taxon
+ * @param child : the lower (or current) Taxon
+ * return the Taxon from the new created Node
+ * @param classification
+ * @param 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().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
+ if(hasTaxonNodeInClassification(child, classification)){
+ return child;
+ }
+ else{
+ node = classification.addParentChild(parent, child, state.getRef(), "");
+ save(node, state);
+ }
+ }
+ else {
+ if (child == null){
+ logger.debug("The child should not be null!");
+ }
+ child = (Taxon) getTaxonService().find(child.getUuid());
+ //do not add child node if it already exists
+ if(hasTaxonNodeInClassification(child, classification)){
+ return child;
+ }
+ else{
+ node = classification.addChildTaxon(child, state.getRef(), null);
+ save(node, state);
+ }
+ }
+ if(node!=null){
+ state.getReport().addTaxonNode(node);
+ return node.getTaxon();
+ }
+ String message = "Could not create taxon node for " +child;
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+
+ protected Taxon getOrCreateTaxonForName(TaxonName taxonName, STATE state){
+ if (taxonName != null){
+ Set<Taxon> acceptedTaxa = taxonName.getTaxa();
+ if(acceptedTaxa.size()>0){
+ Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
+ if(acceptedTaxa.size()>1){
+ String message = "More than one accepted taxon was found for taxon name: "
+ + taxonName.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ }
+ else{
+ return firstAcceptedTaxon;
+ }
+ }
+ else{
+ 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();
+ if(acceptedTaxonOfSynonym == null){
+ String message = "No accepted taxon could be found for taxon name: "
+ + taxonName.getTitleCache()
+ + "!";
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ }
+ else{
+ return acceptedTaxonOfSynonym;
+ }
+ }
+ }
+ }
+ Taxon taxon = Taxon.NewInstance(taxonName, state.getRef());
+ save(taxon, state);
+ state.getReport().addTaxon(taxon);
+ logger.info("Created new taxon "+ taxon);
+ return taxon;
+ }
+ return null;
+
+ }
+
+ private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
+ if(taxon.getTaxonNodes()!=null){
+ for (TaxonNode node : taxon.getTaxonNodes()){
+ if(node.getClassification().equals(classification)){
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * HandleIdentifications : get the scientific names present in the ABCD
+ * document and store link them with the observation/specimen data
+ * @param state: the current ABCD import state
+ * @param derivedUnitFacade : the current derivedunitfacade
+ */
+ protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+
+
+ String scientificName = "";
+ boolean preferredFlag = false;
+
+ if (state.getDataHolder().getNomenclatureCode() == ""){
+ if (config.getNomenclaturalCode() != null){
+ if (config.getNomenclaturalCode() != null){
+ state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
+
+ }
+ }
+ }
+
+ for (int i = 0; i < state.getDataHolder().getIdentificationList().size(); i++) {
+ Identification identification = state.getDataHolder().getIdentificationList().get(i);
+ scientificName = identification.getScientificName().replaceAll(" et ", " & ");
+
+ String preferred = identification.getPreferred();
+ preferredFlag = false;
+ 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;
+ }
+
+ }
+ if (identification.getCode() != null){
+ if (identification.getCode().indexOf(':') != -1) {
+ state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
+ }
+ else{
+ state.getDataHolder().setNomenclatureCode(identification.getCode());
+ }
+ }
+ 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(), identification.getModifier());
+ }
+ }
+
+ /**
+ * @param taxon : a taxon to add as a node
+ * @param state : the ABCD import state
+ */
+ protected void addTaxonNode(Taxon taxon, STATE state, boolean preferredFlag) {
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
+ logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
+ //only add nodes if not already existing in current classification or default classification
+
+ //check if node exists in current classification
+ //NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
+ if (!existsInClassification(taxon,state.getClassification(), state)){
+ if(config.isMoveNewTaxaToDefaultClassification()){
+ //check if node exists in default classification
+ if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
+ addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
+ }
+ }else{
+ //add non-existing taxon to current classification
+ addParentTaxon(taxon, state, preferredFlag, state.getClassification());
+ }
+
+ }
+ }
+
+
+ private boolean existsInClassification(Taxon taxon, Classification classification, STATE state){
+ boolean exist = false;
+ ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
+ if(cdmAppController==null){
+ cdmAppController = this;
+ }
+ if (classification != null){
+ if (!taxon.getTaxonNodes().isEmpty()){
+ for (TaxonNode node:taxon.getTaxonNodes()){
+ if (node.getClassification().equals(classification)){
+ return true;
+ }
+ }
+ }
+// we do not need this because we already searched for taxa in db in the previous steps
+// List<UuidAndTitleCache<TaxonNode>> uuidAndTitleCacheOfAllTaxa = cdmAppController.getClassificationService().getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification.getUuid());
+// if (uuidAndTitleCacheOfAllTaxa != null){
+// for (UuidAndTitleCache p : uuidAndTitleCacheOfAllTaxa){
+// try{
+// if(p.getTitleCache().equals(taxon.getTitleCache())) {
+// exist = true;
+// }
+// }
+// catch(Exception e){
+// logger.warn("TaxonNode doesn't seem to have a taxon");
+// }
+// }
+// }
+ }
+ return exist;
+ }
+
+ /**
+ * join DeterminationEvent to the Taxon Object
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param preferredFlag :if the current name is preferred
+ * @param derivedFacade : the derived Unit Facade
+ */
+ @SuppressWarnings("rawtypes")
+ 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);
+
+
+ determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
+ if (state.getPersonStore().get(identifierStr) != null){
+ determinationEvent.setActor((AgentBase)state.getPersonStore().get(identifierStr));
+ } else if (identifierStr != null){
+ Person identifier = Person.NewTitledInstance(identifierStr);
+ determinationEvent.setActor(identifier);
+ }
+ if (dateStr != null){
+ determinationEvent.setTimeperiod(TimePeriodParser.parseString(dateStr));
+ }
+ if (modifier != null){
+ if (modifier.equals("cf.")){
+ determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_CONFER());
+ }else if (modifier.equals("aff.")){
+ determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
+ }
+ }
+ state.getDerivedUnitBase().addDetermination(determinationEvent);
+
+ if (logger.isDebugEnabled()){
+ logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
+ }
+ for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().getStatusList()) {
+ if (specimenTypeDesignationstatus != null) {
+ if (logger.isDebugEnabled()){
+ logger.debug("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
+ }
+
+ ICdmRepository cdmAppController = config.getCdmAppController();
+ if(cdmAppController == null){
+ cdmAppController = this;
+ }
+ 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);
+ }
+ }
+ 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().listByTitleWithRestrictions(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
+
+ if (!references.isEmpty()){
+ Reference reference = null;
+ for (Reference refe: references) {
+ if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
+ reference =refe;
+ break;
+ }
+ }
+ if (reference ==null){
+ reference = ReferenceFactory.newGeneric();
+ reference.setTitleCache(strReference, true);
+ save(reference, state);
+ }
+ determinationEvent.addReference(reference);
+ }
+ }
+ save(state.getDerivedUnitBase(), state);
+
+ if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
+ //do not add IndividualsAssociation to non-preferred taxa
+ if (logger.isDebugEnabled()){
+ logger.debug("isDoCreateIndividualsAssociations");
+ }
+
+ makeIndividualsAssociation(state, taxon, determinationEvent);
+
+ save(state.getDerivedUnitBase(), state);
+ }
+ }
+
+ /**
+ * create and link each association (specimen, observation..) to the accepted taxon
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param determinationEvent:the determinationevent
+ */
+ protected void makeIndividualsAssociation(STATE state, Taxon taxon, DeterminationEvent determinationEvent) {
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
+ SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
+
+ if (logger.isDebugEnabled()){
+ logger.info("MAKE INDIVIDUALS ASSOCIATION");
+ }
+
+ TaxonDescription taxonDescription = null;
+ Set<TaxonDescription> descriptions= taxon.getDescriptions();
+ 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.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
+ taxon.addDescription(taxonDescription);
+ }
+
+ //PREPARE REFERENCE QUESTIONS
+
+ 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<>();
+ if(issTmp2!=null) {
+ osbSet.addAll(issTmp2);
+ }
+ if(issTmp!=null) {
+ osbSet.addAll(issTmp);
+ }
+
+
+ addToSourceMap(sourceMap, osbSet);
+
+
+ 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(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);
+
+ save(taxonDescription, state);
+ save(taxon, state);
+ state.getReport().addDerivate(state.getDerivedUnitBase(), config);
+ 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){
+ Reference a = is.getCitation();
+ String c = is.getCitationMicroReference();
+
+ boolean refMatch=false;
+ boolean microMatch=false;
+
+ try{
+ if (a==null && b==null) {
+ refMatch=true;
+ }
+ if (a!=null && b!=null) {
+ if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
+
+
+ try{
+ if (c==null && d==null) {
+ microMatch=true;
+ }
+ if(c!=null && d!=null) {
+ if(c.equalsIgnoreCase(d)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
+
+ if (microMatch && refMatch) {
+ return false;
+ }
+
+
+ }
+ return true;
+ }
+
+ 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();
+ String unitMicroReference = is.getCitationMicroReference();
+
+ boolean refMatch=false;
+ boolean microMatch=false;
+
+ try{
+ if (unitReference==null && reference==null) {
+ refMatch=true;
+ }
+ if (unitReference!=null && reference!=null) {
+ if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
+
+ try{
+ if (unitMicroReference==null && microReference==null) {
+ microMatch=true;
+ }
+ if(unitMicroReference!=null && microReference!=null) {
+ if(unitMicroReference.equalsIgnoreCase(microReference)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
+
+ if (microMatch && refMatch) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * look for the Feature object (FieldObs, Specimen,...)
+ * @param unit : a specimen or obersvation base
+ * @return the corresponding Feature
+ */
+ private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
+ SpecimenOrObservationType type = unit.getRecordBasis();
+
+
+
+ if (type.isFeatureObservation()){
+ return Feature.OBSERVATION();
+ }else if (type.isFeatureSpecimen()){
+ return Feature.SPECIMEN();
+ }else if (type == SpecimenOrObservationType.DerivedUnit){
+ return Feature.OBSERVATION();
+ // 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.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) {
+ if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
+ try{
+ sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
+ }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
+ } else if(osb.getCitation()!=null){
+ try{
+ sourceMap.put(osb.getCitation().getTitleCache(),osb);
+ }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
+ }
+ }
+ }
+
+
-}
\ No newline at end of file
+}
BGBM BDI Projects / cdmlib.git / blobdiff