Revision 86c8aa4d
Added by Andreas Müller over 15 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXNomenclatureImport.java | ||
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| 50 | 50 |
public class TaxonXNomenclatureImport extends CdmIoBase<IImportConfigurator> implements ICdmIO<IImportConfigurator> {
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private static final Logger logger = Logger.getLogger(TaxonXNomenclatureImport.class); |
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@SuppressWarnings("unused")
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private static int modCount = 10000; |
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public TaxonXNomenclatureImport(){
|
| ... | ... | |
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for (Element elSynonymy : elSynonymyList){
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String synonymName = elSynonymy.getChildTextTrim("name");
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if (elSynonymy.getChild("type", nsTaxonx) != null || elSynonymy.getChild("type_loc", nsTaxonx) != null){
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Synonym synonym = getSynonym(config, taxon, synonymName);
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Synonym synonym = getSynonym(txConfig, taxon, synonymName);
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if (synonym != null){
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isChanged |= doNomenclaturalType(txConfig, elSynonymy, nsTaxonx, synonym.getName()); |
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} |
| ... | ... | |
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return true; |
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} |
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private Synonym getSynonym(IImportConfigurator config, Taxon taxon, String synName){
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private Synonym getSynonym(TaxonXImportConfigurator config, Taxon taxon, String synName){
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Synonym result = null; |
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unlazySynonym(config, taxon); |
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Set<Synonym> synList = taxon.getSynonyms(); |
| ... | ... | |
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return syn; //only first synonym is returned |
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} |
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} |
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logger.warn("Synonym ("+synName+ ")not found for taxon " + taxon.getTitleCache());
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logger.warn("Synonym ("+synName+ ")not found for taxon " + taxon.getTitleCache() + getBracketSourceName(config));
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return result; |
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} |
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|
| ... | ... | |
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SimpleSpecimen simpleSpecimen = SimpleSpecimen.NewInstance(); |
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//elType |
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if (elType != null){
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doElType(elType, simpleSpecimen); |
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doElType(elType, simpleSpecimen, config);
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}//elType |
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//typeLoc |
| ... | ... | |
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return false; |
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} |
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private boolean doElType(Element elType, SimpleSpecimen simpleSpecimen){
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private boolean doElType(Element elType, SimpleSpecimen simpleSpecimen, TaxonXImportConfigurator config){
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//type |
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String text = elType.getTextNormalize(); |
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if (text.endsWith(";")){
|
| ... | ... | |
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} |
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String[] type = text.split(";");
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if (type.length != 3 ){
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logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize());
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if (text.equals("")){
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logger.info("<nomenclature><type> is empty: " + getBracketSourceName(config));
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}else{
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logger.warn("<nomenclature><type> is of unsupported format: " + elType.getTextNormalize() + getBracketSourceName(config));
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} |
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simpleSpecimen.setTitleCache(elType.getTextNormalize()); |
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}else{
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String strLocality = type[0].trim(); |
| ... | ... | |
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typeLocStatus = typeLocStatus.trim(); |
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int pos = typeLocStatus.indexOf(" ");
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if (pos == -1){
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logger.warn("Unknown format for type_loc : " + typeLocStatus);
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logger.warn("Unknown format or empty type_loc : '" +typeLocStatus + "'" + getBracketSourceName(config));
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result.put(originalSpecimen, null); |
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}else{
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String statusString = typeLocStatus.substring(0,pos); |
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TypeDesignationStatus status = getStatusByStatusString(statusString.trim()); |
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TypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config);
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//TODO |
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//String[] collectionStrings = typeLocStatus.substring(pos).split(",");
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String tmpCollString = typeLocStatus.substring(pos).trim(); |
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//for(String collectionString : collectionStrings){
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if (tmpCollString.contains("typ")){
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logger.warn("Is this really only a collection string?");
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logger.warn("Is this really only a collection string? : " + tmpCollString + getBracketSourceName(config));
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} |
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Specimen specimen; |
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specimen = (Specimen)originalSpecimen.clone(); |
| ... | ... | |
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logger.warn("Unknown format: " + typeLocStatus);
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}else{
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String statusString = typeLocStatus.substring(0,pos); |
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TypeDesignationStatus status = getStatusByStatusString(statusString.trim()); |
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TypeDesignationStatus status = getStatusByStatusString(statusString.trim(), config);
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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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* @param statusString |
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* @return TypeDesignationStatus |
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*/ |
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private static TypeDesignationStatus getStatusByStatusString(String statusString){
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private static TypeDesignationStatus getStatusByStatusString(String statusString, TaxonXImportConfigurator config){
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TypeDesignationStatus result = null; |
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if (statusString == null || "".equals(statusString.trim())){
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return null; |
| ... | ... | |
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} |
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result = statusMap.get(statusString); |
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if (statusString.equals("type")){
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logger.info("No type designation type");
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logger.info("No type designation type" + getBracketSourceName(config));
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}else if (result == null){
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logger.warn("Unknown type status string: " + statusString);
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logger.warn("Unknown type status string: " + statusString + getBracketSourceName(config));
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} |
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return result; |
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} |
| ... | ... | |
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//taxonService.saveTaxon(taxon); |
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commitTransaction(txStatus); |
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} |
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private static String getBracketSourceName(TaxonXImportConfigurator config){
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return "(" + config.getSourceNameString() + ")";
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} |
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} |
Also available in: Unified diff
io TaxonX minor changes (v2.0)