Revision 9dc896c9
Added by Andreas Müller almost 7 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java | ||
|---|---|---|
| 50 | 50 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 51 | 51 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 53 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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|
| 53 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 54 | 54 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 55 | 55 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 56 | 56 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| ... | ... | |
| 97 | 97 |
|
| 98 | 98 |
|
| 99 | 99 |
|
| 100 |
protected TaxonNameBase<?, ?> getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
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| 101 |
TaxonNameBase<?, ?> taxonName = null;
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| 100 |
protected TaxonName getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
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| 101 |
TaxonName taxonName = null; |
|
| 102 | 102 |
SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig(); |
| 103 | 103 |
|
| 104 | 104 |
//check atomised name data for rank |
| ... | ... | |
| 121 | 121 |
if(config.isIgnoreAuthorship() && parsedName!=null){// && preferredFlag){
|
| 122 | 122 |
// do not ignore authorship for non-preferred names because they need |
| 123 | 123 |
// to be created for the determination history |
| 124 |
String nameCache = TaxonNameBase.castAndDeproxy(parsedName).getNameCache();
|
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| 125 |
List<TaxonNameBase> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
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String nameCache = TaxonName.castAndDeproxy(parsedName).getNameCache(); |
|
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List<TaxonName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null); |
|
| 126 | 126 |
if (!names.isEmpty()){
|
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taxonName = getBestMatchingName(scientificName, new ArrayList<TaxonNameBase>(names), state);
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|
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taxonName = getBestMatchingName(scientificName, new ArrayList<>(names), state); |
|
| 128 | 128 |
} |
| 129 | 129 |
if (taxonName == null && !names.isEmpty()){
|
| 130 | 130 |
taxonName = names.get(0); |
| ... | ... | |
| 132 | 132 |
|
| 133 | 133 |
} else {
|
| 134 | 134 |
//search for existing names |
| 135 |
List<TaxonNameBase> names = getNameService().listByTitle(TaxonNameBase.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
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List<TaxonName> names = getNameService().listByTitle(TaxonName.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
|
|
| 136 | 136 |
taxonName = getBestMatchingName(scientificName, names, state); |
| 137 | 137 |
//still nothing found -> try with the atomised name full title cache |
| 138 | 138 |
if(taxonName==null && atomisedTaxonName!=null){
|
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names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
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names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null); |
|
| 140 | 140 |
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state); |
| 141 | 141 |
//still nothing found -> try with the atomised name title cache |
| 142 | 142 |
if(taxonName==null){
|
| 143 |
names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
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names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null); |
|
| 144 | 144 |
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state); |
| 145 | 145 |
} |
| 146 | 146 |
} |
| ... | ... | |
| 150 | 150 |
} |
| 151 | 151 |
|
| 152 | 152 |
if(taxonName==null && atomisedTaxonName!=null){
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taxonName = (TaxonNameBase<?, ?>) atomisedTaxonName;
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taxonName = (TaxonName<?, ?>) atomisedTaxonName; |
|
| 154 | 154 |
state.getReport().addName(taxonName); |
| 155 | 155 |
logger.info("Created new taxon name "+taxonName);
|
| 156 | 156 |
if(taxonName.hasProblem()){
|
| ... | ... | |
| 179 | 179 |
return taxonName; |
| 180 | 180 |
} |
| 181 | 181 |
|
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protected TaxonNameBase<?, ?> getBestMatchingName(String scientificName, java.util.Collection<TaxonNameBase> names, STATE state){
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Set<TaxonNameBase> namesWithAcceptedTaxa = new HashSet<TaxonNameBase>();
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List<TaxonNameBase> namesWithAcceptedTaxaInClassification = new ArrayList<TaxonNameBase>();
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for (TaxonNameBase name : names) {
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protected TaxonName getBestMatchingName(String scientificName, java.util.Collection<TaxonName> names, STATE state){
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Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
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List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
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for (TaxonName name : names) {
|
|
| 186 | 186 |
if(!name.getTaxa().isEmpty()){
|
| 187 | 187 |
Set<Taxon> taxa = name.getTaxa(); |
| 188 | 188 |
for (Taxon taxon:taxa){
|
| ... | ... | |
| 224 | 224 |
} |
| 225 | 225 |
//no names with accepted taxa found -> check accepted taxa of synonyms |
| 226 | 226 |
List<Taxon> taxaFromSynonyms = new ArrayList<>(); |
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for (TaxonNameBase name : names) {
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for (TaxonName name : names) {
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|
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Set<TaxonBase> taxonBases = name.getTaxonBases(); |
| 229 | 229 |
for (TaxonBase taxonBase : taxonBases) {
|
| 230 | 230 |
if(taxonBase.isInstanceOf(Synonym.class)){
|
| ... | ... | |
| 312 | 312 |
* @param state |
| 313 | 313 |
* @return the corresponding Botanical or Zoological or... name |
| 314 | 314 |
*/ |
| 315 |
protected TaxonNameBase<?,?> setTaxonNameByType(
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protected TaxonName setTaxonNameByType( |
|
| 316 | 316 |
HashMap<String, String> atomisedMap, String fullName, STATE state) {
|
| 317 | 317 |
boolean problem = false; |
| 318 | 318 |
if (logger.isDebugEnabled()){
|
| ... | ... | |
| 320 | 320 |
} |
| 321 | 321 |
|
| 322 | 322 |
if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
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TaxonNameBase<?,?> taxonName = TaxonNameFactory.NewZoologicalInstance(null);
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TaxonName taxonName = TaxonNameFactory.NewZoologicalInstance(null); |
|
| 324 | 324 |
taxonName.setFullTitleCache(fullName, true); |
| 325 | 325 |
taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus"))); |
| 326 | 326 |
taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus"))); |
| ... | ... | |
| 379 | 379 |
} |
| 380 | 380 |
} |
| 381 | 381 |
else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
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TaxonNameBase taxonName = (TaxonNameBase)parseScientificName(fullName, state, state.getReport(), null);
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TaxonName taxonName = (TaxonName)parseScientificName(fullName, state, state.getReport(), null);
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| 383 | 383 |
if (taxonName != null){
|
| 384 | 384 |
return taxonName; |
| 385 | 385 |
} |
| ... | ... | |
| 439 | 439 |
} |
| 440 | 440 |
} |
| 441 | 441 |
else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNB.getUuid())) {
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TaxonNameBase taxonName = TaxonNameFactory.NewBacterialInstance(null);
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TaxonName taxonName = TaxonNameFactory.NewBacterialInstance(null); |
|
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taxonName.setFullTitleCache(fullName, true); |
| 444 | 444 |
taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus")); |
| 445 | 445 |
taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus"))); |
| ... | ... | |
| 478 | 478 |
} |
| 479 | 479 |
} |
| 480 | 480 |
else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
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TaxonNameBase taxonName = TaxonNameFactory.NewCultivarInstance(null);
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TaxonName taxonName = TaxonNameFactory.NewCultivarInstance(null); |
|
| 482 | 482 |
|
| 483 | 483 |
if (taxonName.hasProblem()) {
|
| 484 | 484 |
logger.info("pb ICNCP");
|
| ... | ... | |
| 492 | 492 |
|
| 493 | 493 |
if (problem) {
|
| 494 | 494 |
logger.info("Problem im setTaxonNameByType ");
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TaxonNameBase<?,?> taxonName = TaxonNameFactory.NewNonViralInstance(null);
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TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null); |
|
| 496 | 496 |
taxonName.setFullTitleCache(fullName, true); |
| 497 | 497 |
return taxonName; |
| 498 | 498 |
} |
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TaxonNameBase<?,?> tn = TaxonNameFactory.NewNonViralInstance(null);
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TaxonName tn = TaxonNameFactory.NewNonViralInstance(null); |
|
| 500 | 500 |
return tn; |
| 501 | 501 |
} |
| 502 | 502 |
|
| ... | ... | |
| 567 | 567 |
return cdmRepository.getDescriptionService().saveOrUpdate(CdmBase.deproxy(cdmBase, DescriptionBase.class)); |
| 568 | 568 |
}else if (cdmBase.isInstanceOf(TaxonBase.class)){
|
| 569 | 569 |
return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class)); |
| 570 |
}else if (cdmBase.isInstanceOf(TaxonNameBase.class)){
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return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNameBase.class));
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}else if (cdmBase.isInstanceOf(TaxonName.class)){
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return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonName.class)); |
|
| 572 | 572 |
}else if (cdmBase.isInstanceOf(TaxonNode.class)){
|
| 573 | 573 |
return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.class)); |
| 574 | 574 |
}else{
|
| ... | ... | |
| 785 | 785 |
if(rank!=null){
|
| 786 | 786 |
if (rank.isLower(Rank.GENUS() )){
|
| 787 | 787 |
String genusOrUninomial = nvname.getGenusOrUninomial(); |
| 788 |
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
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TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1); |
|
| 789 | 789 |
genus = getOrCreateTaxonForName(taxonName, state); |
| 790 | 790 |
if (genus == null){
|
| 791 | 791 |
logger.debug("The genus should not be null " + taxonName);
|
| ... | ... | |
| 799 | 799 |
String prefix = nvname.getGenusOrUninomial(); |
| 800 | 800 |
String name = nvname.getInfraGenericEpithet(); |
| 801 | 801 |
if (name != null){
|
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TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
|
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TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1); |
|
| 803 | 803 |
subgenus = getOrCreateTaxonForName(taxonName, state); |
| 804 | 804 |
if (preferredFlag) {
|
| 805 | 805 |
parent = linkParentChildNode(genus, subgenus, classification, state); |
| ... | ... | |
| 811 | 811 |
String name = nvname.getInfraGenericEpithet(); |
| 812 | 812 |
String spe = nvname.getSpecificEpithet(); |
| 813 | 813 |
if (spe != null){
|
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TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
|
|
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TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1); |
|
| 815 | 815 |
species = getOrCreateTaxonForName(taxonName, state); |
| 816 | 816 |
if (preferredFlag) {
|
| 817 | 817 |
parent = linkParentChildNode(subgenus, species, classification, state); |
| ... | ... | |
| 822 | 822 |
String prefix = nvname.getGenusOrUninomial(); |
| 823 | 823 |
String name = nvname.getSpecificEpithet(); |
| 824 | 824 |
if (name != null){
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| 825 |
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
|
|
| 825 |
TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1); |
|
| 826 | 826 |
species = getOrCreateTaxonForName(taxonName, state); |
| 827 | 827 |
if (preferredFlag) {
|
| 828 | 828 |
parent = linkParentChildNode(genus, species, classification, state); |
| ... | ... | |
| 831 | 831 |
} |
| 832 | 832 |
} |
| 833 | 833 |
if (rank.isLower(Rank.INFRASPECIES())){
|
| 834 |
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
|
|
| 834 |
TaxonName taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1); |
|
| 835 | 835 |
subspecies = getOrCreateTaxonForName(taxonName, state); |
| 836 | 836 |
if (preferredFlag) {
|
| 837 | 837 |
parent = linkParentChildNode(species, subspecies, classification, state); |
| ... | ... | |
| 891 | 891 |
return null; |
| 892 | 892 |
} |
| 893 | 893 |
|
| 894 |
protected Taxon getOrCreateTaxonForName(TaxonNameBase<?, ?> taxonNameBase, STATE state){
|
|
| 895 |
if (taxonNameBase != null){
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| 896 |
Set<Taxon> acceptedTaxa = taxonNameBase.getTaxa();
|
|
| 894 |
protected Taxon getOrCreateTaxonForName(TaxonName taxonName, STATE state){
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|
| 895 |
if (taxonName != null){
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|
| 896 |
Set<Taxon> acceptedTaxa = taxonName.getTaxa(); |
|
| 897 | 897 |
if(acceptedTaxa.size()>0){
|
| 898 | 898 |
Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next(); |
| 899 | 899 |
if(acceptedTaxa.size()>1){
|
| 900 | 900 |
String message = "More than one accepted taxon was found for taxon name: " |
| 901 |
+ taxonNameBase.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
|
|
| 901 |
+ taxonName.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase(); |
|
| 902 | 902 |
state.getReport().addInfoMessage(message); |
| 903 | 903 |
logger.warn(message); |
| 904 | 904 |
} |
| ... | ... | |
| 907 | 907 |
} |
| 908 | 908 |
} |
| 909 | 909 |
else{
|
| 910 |
Set<TaxonBase> taxonAndSynonyms = taxonNameBase.getTaxonBases();
|
|
| 910 |
Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases(); |
|
| 911 | 911 |
for (TaxonBase taxonBase : taxonAndSynonyms) {
|
| 912 | 912 |
if(taxonBase.isInstanceOf(Synonym.class)){
|
| 913 | 913 |
Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class); |
| 914 | 914 |
Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon(); |
| 915 | 915 |
if(acceptedTaxonOfSynonym == null){
|
| 916 | 916 |
String message = "No accepted taxon could be found for taxon name: " |
| 917 |
+ taxonNameBase.getTitleCache()
|
|
| 917 |
+ taxonName.getTitleCache() |
|
| 918 | 918 |
+ "!"; |
| 919 | 919 |
state.getReport().addInfoMessage(message); |
| 920 | 920 |
logger.warn(message); |
| ... | ... | |
| 925 | 925 |
} |
| 926 | 926 |
} |
| 927 | 927 |
} |
| 928 |
Taxon taxon = Taxon.NewInstance(taxonNameBase, state.getRef());
|
|
| 928 |
Taxon taxon = Taxon.NewInstance(taxonName, state.getRef()); |
|
| 929 | 929 |
save(taxon, state); |
| 930 | 930 |
state.getReport().addTaxon(taxon); |
| 931 | 931 |
logger.info("Created new taxon "+ taxon);
|
| ... | ... | |
| 988 | 988 |
state.getDataHolder().setNomenclatureCode(identification.getCode()); |
| 989 | 989 |
} |
| 990 | 990 |
} |
| 991 |
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
|
|
| 991 |
TaxonName taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i); |
|
| 992 | 992 |
Taxon taxon = getOrCreateTaxonForName(taxonName, state); |
| 993 | 993 |
addTaxonNode(taxon, state,preferredFlag); |
| 994 | 994 |
linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate()); |
| ... | ... | |
| 1099 | 1099 |
} |
| 1100 | 1100 |
specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid()); |
| 1101 | 1101 |
//Designation |
| 1102 |
TaxonNameBase<?,?> name = taxon.getName();
|
|
| 1102 |
TaxonName name = taxon.getName(); |
|
| 1103 | 1103 |
SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance(); |
| 1104 | 1104 |
|
| 1105 | 1105 |
designation.setTypeStatus(specimenTypeDesignationstatus); |
Also available in: Unified diff
fix #6368 rename table and class TaxonNameBase