Revision aea90ab7
Added by Andreas Müller almost 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java | ||
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package eu.etaxonomy.cdm.io.greece; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.UUID; |
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import org.apache.log4j.Logger; |
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import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
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import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.INonViralName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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private static final long serialVersionUID = 2593130403213346396L; |
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private static final Logger logger = Logger.getLogger(FloraHellenicaImportBase.class); |
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private Map<UUID, Taxon> acceptedTaxonMap = new HashMap<>(); |
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private Reference sourceReference; |
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private Reference secReference; |
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private Reference secReference2; |
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@SuppressWarnings("unchecked")
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private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(this); |
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/** |
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* @param taxon |
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* @return |
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*/ |
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protected Reference getSourceCitation(SimpleExcelTaxonImportState<CONFIG> state) {
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return state.getConfig().getSourceReference(); |
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if (this.sourceReference == null){
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this.sourceReference = getPersistentReference(state.getConfig().getSourceReference()); |
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} |
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return this.sourceReference; |
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} |
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protected Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state) {
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// TODO Auto-generated method stub |
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return null; |
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if (this.secReference == null){
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this.secReference = getPersistentReference(state.getConfig().getSecReference()); |
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} |
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return this.secReference; |
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} |
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protected Reference getSecReference2(SimpleExcelTaxonImportState<CONFIG> state) {
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if (this.secReference2 == null){
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this.secReference2 = getPersistentReference(state.getConfig().getSecReference2()); |
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} |
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return this.secReference2; |
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} |
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/** |
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* @param reference |
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* @return |
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*/ |
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private Reference getPersistentReference(Reference reference) {
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Reference result = getReferenceService().find(reference.getUuid()); |
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if (result == null){
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result = reference; |
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} |
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return result; |
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} |
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*/ |
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protected Taxon getAcceptedTaxon(HashMap<String, String> record, |
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SimpleExcelTaxonImportState<CONFIG> state, String key) {
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String accStr = getValue(record, key); |
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if (accStr == null){
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return null; |
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logger.warn(message); |
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return null; |
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}else{
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accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid()); |
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initAcceptedTaxonMap(); |
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// accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid()); |
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accTaxon = acceptedTaxonMap.get(accTaxon.getUuid()); |
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} |
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return accTaxon; |
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} |
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private void initAcceptedTaxonMap() {
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if (acceptedTaxonMap.isEmpty()){
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List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null); |
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for (Taxon taxon : list){
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acceptedTaxonMap.put(taxon.getUuid(), taxon); |
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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 state |
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* @return |
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*/ |
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protected Taxon getHigherTaxon(HashMap<String, String> record, |
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SimpleExcelTaxonImportState<CONFIG> state, String key) {
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protected BotanicalName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state, String famStr) {
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String accStr = getValue(record, key); |
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if (accStr == null){
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return null; |
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} |
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accStr = accStr.trim(); |
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Taxon accTaxon = state.getHigherTaxon(accStr); |
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if (accTaxon == null){
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String message = state.getCurrentLine()+ ": Higher taxon could not be found: " + accStr; |
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logger.info(message); //not critical |
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return null; |
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}else{
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initAcceptedTaxonMap(); |
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// accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid()); |
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accTaxon = acceptedTaxonMap.get(accTaxon.getUuid()); |
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} |
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return accTaxon; |
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} |
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protected BotanicalName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state, |
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String famStr) {
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BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY()); |
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famStr = famStr.substring(0,1).toUpperCase() + famStr.substring(1).toLowerCase(); |
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name.setGenusOrUninomial(famStr); |
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name.addSource(makeOriginalSource(state)); |
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return name; |
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} |
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/** |
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* @param state |
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* @param name |
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* @return |
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*/ |
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protected <NAME extends INonViralName> NAME replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, NAME name) {
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NAME result = deduplicationHelper.getExistingName(state, name); |
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deduplicationHelper.replaceAuthorNamesAndNomRef(state, result); |
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return result; |
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} |
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/** |
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* @param state |
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* @return |
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*/ |
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@Override |
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protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {
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return IdentifiableSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, getSourceCitation(state));
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} |
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} |
Also available in: Unified diff
ref #6286 updates for Flora Hellenica import (including new image import)