import java.util.ArrayList;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import eu.etaxonomy.cdm.model.common.LanguageString;
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;
protected Map<String, DefinedTerm> kindOfUnitsMap;
+
@Override
protected abstract void doInvoke(STATE 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.isPersited()) {
+ save(taxonName, state);
+ }
return taxonName;
}
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") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNAFP")) {
+ 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;
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.
*
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();
- }
- }
+ 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;
}
// 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;
}
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
String preferred = identification.getPreferred();
preferredFlag = false;
if (preferred != null || state.getDataHolder().getIdentificationList().size()==1){
- if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || 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());
}
}
* @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);
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()){
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);
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();
// 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);
}
+
+
}
BGBM BDI Projects / cdmlib.git / blobdiff