Revision 2890acf5
Added by Andreas Müller about 13 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java | ||
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import org.springframework.stereotype.Component; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.model.common.Annotation; |
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import eu.etaxonomy.cdm.model.common.AnnotationType; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| ... | ... | |
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writer = createPrintWriter(fileName, state); |
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List<TaxonNode> allNodes = getAllNodes(null); |
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int i = 0; |
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for (TaxonNode node : allNodes){
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i++; |
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Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class); |
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DwcaTaxRecord record = new DwcaTaxRecord(metaRecord, config); |
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|
| ... | ... | |
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} |
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} |
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/** |
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* @param record |
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* @param taxon |
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* @param name |
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* @param parent |
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* @param basionym |
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* @param type |
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* @return |
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*/ |
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/** |
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* @param record |
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* @param taxonBase |
| ... | ... | |
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record.setId(taxonBase.getId()); |
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record.setUuid(taxonBase.getUuid()); |
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//maybe wrong as according to the DwC-A documentation only resolvable ids are allowed, this differs from DwC documentation |
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record.setScientificNameId(name); |
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record.setScientificName(name.getTitleCache()); |
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record.setAcceptedNameUsageId(acceptedTaxon.getUuid()); |
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record.setParentNameUsageId(parent == null ? null : parent.getUuid()); |
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record.setAcceptedNameUsage(acceptedTaxon.getName() == null? acceptedTaxon.getTitleCache() : acceptedTaxon.getName().getTitleCache()); |
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//parentNameUsage |
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if (parent != null){
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record.setParentNameUsageId(parent.getUuid()); |
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record.setParentNameUsage(parent.getTitleCache()); |
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} |
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//originalNameUsage |
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// ??? - is not a name usage (concept) |
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// record.setOriginalNameUsageId(basionym.getId()); |
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if (basionym != null){
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record.setOriginalNameUsageId(basionym.getUuid()); |
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record.setOriginalNameUsage(basionym.getTitleCache()); |
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} |
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//nameAccordingTo |
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Reference<?> sec = taxonBase.getSec(); |
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if (sec == null){
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String message = "There is a taxon without sec " + taxonBase.getTitleCache() + "( " + taxonBase.getId() + ")"; |
| ... | ... | |
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record.setNameAccordingToId(taxonBase.getSec().getUuid()); |
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record.setNameAccordingTo(taxonBase.getSec().getTitleCache()); |
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} |
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record.setNamePublishedInId(name.getNomenclaturalReference() == null ? null : name.getNomenclaturalReference().getUuid()); |
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// what is the difference to id |
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record.setTaxonConceptId(taxonBase.getUuid()); |
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record.setScientificName(name.getTitleCache()); |
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// ??? |
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record.setAcceptedNameUsage(acceptedTaxon.getTitleCache()); |
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record.setParentNameUsage(parent == null ? null : parent.getTitleCache()); |
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//namePublishedIn |
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// ??? is not a nameUsage (concept) |
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record.setOriginalNameUsage(basionym == null ? null : basionym.getTitleCache()); |
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record.setNamePublishedIn(name.getNomenclaturalReference() == null ? null : name.getNomenclaturalReference().getTitleCache()); |
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if (name.getNomenclaturalReference() != null){
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record.setNamePublishedInId(name.getNomenclaturalReference().getUuid()); |
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record.setNamePublishedIn(name.getNomenclaturalReference() == null ? null : name.getNomenclaturalReference().getTitleCache()); |
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} |
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// what is the exact difference to id and acceptedNameUsageId |
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record.setTaxonConceptId(taxonBase.getUuid()); |
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//??? |
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//Classification |
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//FIXME all classification and rank specific fields are meant to represent the classification |
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//currently the information is only compiled for the exact same range but it should be compiled |
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//for all ranks above the rank of this taxon |
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//TODO we do not support this yet |
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record.setHigherClassification(null); |
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//... higher ranks |
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handleUninomialOrGenus(record, name); |
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if (name.getRank() != null && name.getRank().equals(Rank.SUBGENUS())){
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record.setSubgenus(name.getNameCache()); |
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} |
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//record.setSubgenus(name.getInfraGenericEpithet()); |
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//TODO other subgneric ranks ?? |
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record.setSubgenus(name.getInfraGenericEpithet()); |
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record.setSpecificEpithet(name.getSpecificEpithet()); |
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record.setInfraspecificEpithet(name.getInfraSpecificEpithet()); |
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record.setTaxonRank(name.getRank()); |
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if (name.getRank() != null){
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record.setVerbatimTaxonRank(name.getRank().getTitleCache());
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record.setVerbatimTaxonRank(name.getRank().getAbbreviation());
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}else{
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String message = "No rank available for " + name.getTitleCache() + "(" + name.getId() + ")";
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logger.warn(message); |
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} |
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record.setScientificNameAuthorship(name.getAuthorshipCache()); |
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// ??? - use for TextData names? |
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// ??? - use for TextData common names?
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record.setVernacularName(null); |
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record.setNomenclaturalCode(name.getNomenclaturalCode()); |
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// ??? TODO Misapplied Names, inferred synonyms |
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handleTaxonomicStatus(record, name, relType, isProParte, isPartial); |
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handleNomStatus(record, taxonBase, name); |
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// ??? |
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record.setTaxonRemarks(null); |
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// ??? which date is needed here (taxon, name, sec, ... ?) |
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// TODO we need to differentiate technical |
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String taxonRemarks = ""; |
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for (Annotation annotation : taxonBase.getAnnotations()){
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if (AnnotationType.EDITORIAL().equals(annotation.getAnnotationType())){
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taxonRemarks += CdmUtils.Nz(annotation.getText()); |
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} |
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} |
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for (Annotation annotation : name.getAnnotations()){
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if (AnnotationType.EDITORIAL().equals(annotation.getAnnotationType())){
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taxonRemarks += CdmUtils.Nz(annotation.getText()); |
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} |
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} |
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if (StringUtils.isNotBlank(taxonRemarks)){
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record.setTaxonRemarks(taxonRemarks); |
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} |
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// TODO which date is needed here (taxon, name, sec, ... ?) |
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record.setModified(taxonBase.getUpdated()); |
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// ??? |
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record.setLanguage(null); |
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|
| ... | ... | |
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//TODO |
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record.setRightsHolder(null); |
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record.setAccessRights(null); |
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//TODO currently only via default value |
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record.setBibliographicCitation(null); |
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record.setInformationWithheld(null); |
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record.setDatasetId(classification); |
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record.setDatasetName(classification.getTitleCache()); |
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//TODO |
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record.setSource(null); |
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return; |
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