Revision 9dc896c9
Added by Andreas Müller almost 7 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXNomenclatureImport.java | ||
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| 33 | 33 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonName; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
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unlazySynonym(config, taxon); |
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Set<Synonym> synList = taxon.getSynonyms(); |
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for (Synonym syn : synList){
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TaxonNameBase<?,?> nameBase = syn.getName();
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TaxonName nameBase = syn.getName(); |
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if (nameBase != null){
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if (nameBase.isNonViral()){
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if (nameBase.getNameCache().equals(synName)){
|
| ... | ... | |
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* @param taxonBase |
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* @return |
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*/ |
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private boolean doNomenclaturalType(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonNameBase taxonName){
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private boolean doNomenclaturalType(TaxonXImportConfigurator config, Element elNomenclature, Namespace nsTaxonx, TaxonName taxonName){
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boolean success = true; |
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if (taxonName == null){
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logger.warn("taxonName is null");
|
| ... | ... | |
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} |
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private boolean doSpecimenType(TaxonXImportConfigurator config, Element elType, Element elTypeLoc, TaxonNameBase taxonName){
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private boolean doSpecimenType(TaxonXImportConfigurator config, Element elType, Element elTypeLoc, TaxonName taxonName){
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Reference citation = null; |
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String citationMicroReference = null; |
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String originalNameString = null; |
| ... | ... | |
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return true; |
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} |
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private boolean doNameType(Element elType, TaxonNameBase taxonName, TaxonXImportConfigurator config){
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private boolean doNameType(Element elType, TaxonName taxonName, TaxonXImportConfigurator config){
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boolean success = true; |
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//type |
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String text = elType.getTextNormalize(); |
| ... | ... | |
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// logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));
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// success = false; |
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// }else{
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// TaxonNameBase childType = getChildrenNameType(taxonName, taxonNameStr, authorStr);
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// TaxonName childType = getChildrenNameType(taxonName, taxonNameStr, authorStr); |
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// if (childType != null){
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// return doNameTypeDesignation(taxonName, childType, status); |
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// }else{
|
| ... | ... | |
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String uninomial = epis[0].trim(); |
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String specEpi = epis[1].trim(); |
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Pager<TaxonNameBase> nameTypes = getNameService().searchNames(uninomial, null, specEpi, null, Rank.SPECIES(), null, null, null, null);
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Pager<TaxonName> nameTypes = getNameService().searchNames(uninomial, null, specEpi, null, Rank.SPECIES(), null, null, null, null); |
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List<INonViralName> result = new ArrayList<>(); |
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for (TaxonNameBase nt : nameTypes.getRecords()){
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for (TaxonName nt : nameTypes.getRecords()){
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if (compareAuthorship(nt, authorStr)){
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result.add(nt); |
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success &= doNameTypeDesignation(taxonName, nt, status/*, isLectoType*/); |
| ... | ... | |
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} |
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// private TaxonNameBase getChildrenNameType(TaxonNameBase name, String typeStr, String authorStr){
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// TaxonNameBase result = null;
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// private TaxonName getChildrenNameType(TaxonName name, String typeStr, String authorStr){
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// TaxonName result = null; |
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// Set<TaxonBase> list = name.getTaxonBases(); |
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// for (TaxonBase taxonBase : list){
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// Taxon taxon; |
| ... | ... | |
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} |
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private boolean doNameTypeDesignation(TaxonNameBase name, TaxonNameBase type, NameTypeDesignationStatus status/*, boolean isLectoType*/){
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private boolean doNameTypeDesignation(TaxonName name, TaxonName type, NameTypeDesignationStatus status/*, boolean isLectoType*/){
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Reference citation = null; |
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String citationMicroReference = null; |
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String originalNameString = null; |
| ... | ... | |
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*/ |
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private HashMap<DerivedUnit, SpecimenTypeDesignationStatus> doElTypeLoc(Element elTypeLoc, |
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SimpleSpecimen simpleSpecimen, |
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TaxonNameBase<?,?> taxonName,
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TaxonName taxonName, |
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TaxonXImportConfigurator config){
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HashMap<DerivedUnit, SpecimenTypeDesignationStatus> result = new HashMap<DerivedUnit, SpecimenTypeDesignationStatus>(); |
| ... | ... | |
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String[] collectionStrings = typeLocStatus.substring(pos).split(",");
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for(String collectionString : collectionStrings){
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if (taxonBase != null){
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TaxonNameBase<?, ?> taxonName = taxonBase.getName();
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TaxonName<?,?> taxonName = taxonBase.getName();
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if (taxonName != null){
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Reference citation = null; |
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String citationMicroReference = null; |
| ... | ... | |
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/** |
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* TODO Preliminary to avoid laizy loading errors |
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*/ |
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private void unlazyTypeDesignation(TaxonXImportConfigurator config, TaxonNameBase taxonNameBase){
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private void unlazyTypeDesignation(TaxonXImportConfigurator config, TaxonName taxonName){
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TransactionStatus txStatus = startTransaction(); |
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//INameService taxonNameService = config.getCdmAppController().getNameService(); |
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INameService taxonNameService = getNameService(); |
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taxonNameService.save(taxonNameBase);
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Set<TaxonNameBase> typifiedNames = taxonNameBase.getHomotypicalGroup().getTypifiedNames();
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for(TaxonNameBase typifiedName: typifiedNames){
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taxonNameService.save(taxonName); |
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Set<TaxonName> typifiedNames = taxonName.getHomotypicalGroup().getTypifiedNames();
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for(TaxonName typifiedName: typifiedNames){
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typifiedName.getTypeDesignations().size(); |
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} |
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//taxonNameService.saveTaxonName(taxonNameBase);
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//taxonNameService.saveTaxonName(taxonName); |
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commitTransaction(txStatus); |
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} |
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Also available in: Unified diff
fix #6368 rename table and class TaxonNameBase