Revision 8ef74e91
Added by Andreas Müller over 5 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelOccurrenceImport.java | ||
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| 9 | 9 |
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package eu.etaxonomy.cdm.io.berlinModel.in; |
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import java.net.URI; |
|
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import java.sql.ResultSet; |
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import java.sql.SQLException; |
| 15 | 14 |
import java.util.ArrayList; |
| ... | ... | |
| 18 | 17 |
import java.util.List; |
| 19 | 18 |
import java.util.Map; |
| 20 | 19 |
import java.util.Set; |
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import java.util.UUID; |
|
| 22 | 20 |
|
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import org.apache.commons.lang.StringUtils; |
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import org.apache.log4j.Logger; |
| 25 | 23 |
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.hibernate.HibernateProxyHelper; |
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer; |
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceImportValidator; |
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import eu.etaxonomy.cdm.io.common.CdmImportBase; |
|
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import eu.etaxonomy.cdm.io.common.IOValidator; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.io.common.Source; |
|
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import eu.etaxonomy.cdm.io.common.TdwgAreaProvider; |
| 37 | 32 |
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.ExtensionType;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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|
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.Marker; |
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
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import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
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import eu.etaxonomy.cdm.model.common.TermType; |
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import eu.etaxonomy.cdm.model.common.TermVocabulary; |
|
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
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import eu.etaxonomy.cdm.model.description.Distribution; |
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
|
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import eu.etaxonomy.cdm.model.location.NamedAreaType; |
|
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
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*/ |
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@Component |
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public class BerlinModelOccurrenceImport extends BerlinModelImportBase {
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private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceImport.class); |
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private static final long serialVersionUID = -7918122767284077183L; |
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private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceImport.class); |
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public static final String NAMESPACE = "Occurrence"; |
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private static final String EM_AREA_NAMESPACE = "emArea"; |
| ... | ... | |
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return strQuery; |
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} |
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private Map<Integer, NamedArea> euroMedAreas = new HashMap<Integer, NamedArea>();
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// private Map<Integer, NamedArea> euroMedAreas = new HashMap<>();
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@Override |
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public void doInvoke(BerlinModelImportState state) {
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if (state.getConfig().isUseEmAreaVocabulary()){
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try {
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createEuroMedAreas(state); |
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} catch (Exception e) {
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logger.error("Exception occurred when trying to create euroMed Areas");
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e.printStackTrace(); |
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state.setSuccess(false); |
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} |
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} |
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// if (state.getConfig().isUseEmAreaVocabulary()){
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// try {
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// createEuroMedAreas(state);
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// } catch (Exception e) {
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// logger.error("Exception occurred when trying to create euroMed Areas");
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// e.printStackTrace();
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// state.setSuccess(false);
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// }
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// }
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super.doInvoke(state); |
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//reset |
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euroMedAreas = new HashMap<Integer, NamedArea>();
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// euroMedAreas = new HashMap<>();
|
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} |
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private TermVocabulary<NamedArea> createEuroMedAreas(BerlinModelImportState state) throws SQLException {
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logger.warn("Start creating E+M areas");
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Source source = state.getConfig().getSource(); |
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Reference sourceReference = state.getConfig().getSourceReference(); |
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TransactionStatus txStatus = this.startTransaction(); |
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sourceReference = getSourceReference(sourceReference); |
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TermVocabulary<NamedArea> euroMedAreas = makeEmptyEuroMedVocabulary(); |
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|
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MarkerType eurMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurArea, "eur", "eur Area", "eur", getEuroMedMarkerTypeVoc()); |
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MarkerType euroMedAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurMedArea, "EuroMedArea", "EuroMedArea", "EuroMedArea", getEuroMedMarkerTypeVoc()); |
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ExtensionType isoCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidIsoCode, "IsoCode", "IsoCode", "iso"); |
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ExtensionType tdwgCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidTdwgAreaCode, "TDWG code", "TDWG Area code", "tdwg"); |
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ExtensionType mclCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidMclCode, "MCL code", "MedCheckList code", "mcl"); |
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NamedAreaLevel areaLevelTop = getNamedAreaLevel(state, BerlinModelTransformer.uuidEuroMedAreaLevelTop, "Euro+Med top area level", "Euro+Med top area level. This level is only to be used for the area representing the complete Euro+Med area", "e+m top", null); |
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NamedAreaLevel areaLevelEm1 = getNamedAreaLevel(state, BerlinModelTransformer.uuidEuroMedAreaLevelFirst, "Euro+Med 1. area level", "Euro+Med 1. area level", "e+m 1.", null); |
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NamedAreaLevel areaLevelEm2 = getNamedAreaLevel(state, BerlinModelTransformer.uuidEuroMedAreaLevelSecond, "Euro+Med 2. area level", "Euro+Med 2. area level", "Euro+Med 1. area level", null); |
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String sql = "SELECT * , CASE WHEN EMCode = 'EM' THEN 'a' ELSE 'b' END as isEM " + |
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" FROM emArea " + |
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" ORDER BY isEM, EMCode"; |
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ResultSet rs = source.getResultSet(sql); |
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|
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NamedArea euroMedArea = null; |
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NamedArea lastLevel1Area = null; |
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|
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//euroMedArea (EMCode = 'EM') |
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rs.next(); |
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euroMedArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType, isoCodeExtType, tdwgCodeExtType, mclCodeExtType, |
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areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel1Area); |
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euroMedAreas.addTerm(euroMedArea); |
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|
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//all other areas |
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while (rs.next()){
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NamedArea newArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType, |
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isoCodeExtType, tdwgCodeExtType, mclCodeExtType, |
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areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel1Area); |
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if (newArea != null){
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euroMedAreas.addTerm(newArea); |
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if (newArea.getPartOf().equals(euroMedArea)){
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lastLevel1Area = newArea; |
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} |
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} |
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} |
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emAreaFinetuning(euroMedAreas, areaLevelEm2); |
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markAreasAsHidden(state, euroMedAreas); |
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getVocabularyService().saveOrUpdate(euroMedAreas); |
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try {
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commitTransaction(txStatus); |
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} catch (Exception e) {
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e.printStackTrace(); |
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logger.error("An exception occurred when trying to commit E+M Areas");
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} |
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logger.warn("Created E+M areas");
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return euroMedAreas; |
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} |
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|
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/** |
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* @param areaLevelEm2 |
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* @param euroMedAreas2 |
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/** |
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* @param emCode |
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* @return |
|
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*/ |
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private void emAreaFinetuning(TermVocabulary<NamedArea> euroMedAreas, NamedAreaLevel areaLevelEm2) {
|
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//CZ |
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NamedArea oldArea = euroMedAreas.getTermByIdInvocabulary("Cz");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Cs"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sk"), areaLevelEm2);
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|
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//Ju |
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oldArea = euroMedAreas.getTermByIdInvocabulary("Ju");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("BH"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Cg"), areaLevelEm2);
|
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Ct"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Mk"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sl"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sr"), areaLevelEm2);
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|
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//IJ |
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oldArea = euroMedAreas.getTermByIdInvocabulary("IJ");
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Ir"), areaLevelEm2);
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Jo"), areaLevelEm2);
|
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|
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//LS |
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oldArea = euroMedAreas.getTermByIdInvocabulary("LS");
|
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Le"), areaLevelEm2);
|
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makeSubterm(oldArea, euroMedAreas.getTermByIdInvocabulary("Sy"), areaLevelEm2);
|
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|
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} |
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|
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//5.Mark areas to be hidden #3979 .5 |
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private void markAreasAsHidden(BerlinModelImportState state, TermVocabulary<NamedArea> euroMedAreasVoc) {
|
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|
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try {
|
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|
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@SuppressWarnings("unchecked")
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TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary); |
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if (vocUserDefinedMarkerTypes == null){
|
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String message = "Marker type vocabulary could not be found. Hidden areas not added."; |
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logger.error(message); |
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System.out.println(message); |
|
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private NamedArea getAreaByAreaId(int areaId) {
|
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NamedArea result = null; |
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String areaIdStr = String.valueOf(areaId); |
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OrderedTermVocabulary<NamedArea> voc = getAreaVoc(); |
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for (NamedArea area : voc.getTerms()){
|
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for (IdentifiableSource source : area.getSources()){
|
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if (areaIdStr.equals(source.getIdInSource()) && BerlinModelAreaImport.NAMESPACE.equals(source.getIdNamespace())){
|
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if (result != null){
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logger.warn("Result for areaId already exists. areaId: " + areaId);
|
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} |
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result = area; |
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} |
|
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} |
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MarkerType hiddenAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidHiddenArea, |
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"Hidden Area","Used to hide distributions for the named areas in publications", null, getEuroMedMarkerTypeVoc()); |
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|
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//Add hidden area marker to Rs(C) and Rs(N) |
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs); |
|
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B); |
|
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C); |
|
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E); |
|
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N); |
|
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K); |
|
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hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W); |
|
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} catch (Exception e) {
|
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e.printStackTrace(); |
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logger.error("Exception in markAreasAsHidden: " + e.getMessage());
|
|
| 247 | 136 |
} |
| 248 |
|
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return result; |
|
| 249 | 138 |
} |
| 250 | 139 |
|
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private void hideArea(TermVocabulary<NamedArea> euroMedAreasVoc, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
|
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for (NamedArea namedArea : euroMedAreasVoc){
|
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if (namedArea.getUuid().equals(areaUuid)){
|
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namedArea.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true)); |
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return; |
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} |
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private OrderedTermVocabulary<NamedArea> areaVoc; |
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@SuppressWarnings("unchecked")
|
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private OrderedTermVocabulary<NamedArea> getAreaVoc(){
|
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if (areaVoc == null){
|
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areaVoc = (OrderedTermVocabulary<NamedArea>)getVocabularyService().find(BerlinModelTransformer.uuidVocEuroMedAreas); |
|
| 257 | 145 |
} |
| 146 |
return areaVoc; |
|
| 258 | 147 |
} |
| 259 | 148 |
|
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/** |
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* @param oldArea |
|
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* @param namedArea |
|
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* @param areaLevelEm2 |
|
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*/ |
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private void makeSubterm(NamedArea oldArea, NamedArea namedArea, NamedAreaLevel areaLevelEm2) {
|
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namedArea.setLevel(areaLevelEm2); |
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namedArea.setPartOf(oldArea); |
|
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} |
|
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|
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/** |
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* @param sourceReference |
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* @return |
|
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*/ |
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private Reference getSourceReference(Reference sourceReference) {
|
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Reference persistentSourceReference = getReferenceService().find(sourceReference.getUuid()); //just to be sure |
|
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if (persistentSourceReference != null){
|
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sourceReference = persistentSourceReference; |
|
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} |
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return sourceReference; |
|
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} |
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|
|
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/** |
|
| 283 |
* @param eurMarkerType |
|
| 284 |
* @param euroMedAreaMarkerType |
|
| 285 |
* @param isoCodeExtType |
|
| 286 |
* @param tdwgCodeExtType |
|
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* @param mclCodeExtType |
|
| 288 |
* @param rs |
|
| 289 |
* @param areaLevelEm2 |
|
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* @param areaLevelEm1 |
|
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* @param areaLevelTop |
|
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* @throws SQLException |
|
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*/ |
|
| 294 |
private NamedArea makeSingleEuroMedArea(ResultSet rs, MarkerType eurMarkerType, |
|
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MarkerType euroMedAreaMarkerType, ExtensionType isoCodeExtType, |
|
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ExtensionType tdwgCodeExtType, ExtensionType mclCodeExtType, |
|
| 297 |
NamedAreaLevel areaLevelTop, NamedAreaLevel areaLevelEm1, NamedAreaLevel areaLevelEm2, |
|
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Reference sourceReference, NamedArea euroMedArea, NamedArea level1Area) throws SQLException {
|
|
| 299 |
Integer areaId = rs.getInt("AreaId");
|
|
| 300 |
String emCode = nullSafeTrim(rs.getString("EMCode"));
|
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| 301 |
String isoCode = nullSafeTrim(rs.getString("ISOCode"));
|
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| 302 |
String tdwgCode = nullSafeTrim(rs.getString("TDWGCode"));
|
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String unit = nullSafeTrim(rs.getString("Unit"));
|
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| 304 |
// ,[Status] |
|
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// ,[OutputOrder] |
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boolean eurMarker = rs.getBoolean("eur");
|
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| 307 |
boolean euroMedAreaMarker = rs.getBoolean("EuroMedArea");
|
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| 308 |
String notes = nullSafeTrim(rs.getString("Notes"));
|
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| 309 |
String mclCode = nullSafeTrim(rs.getString("MCLCode"));
|
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| 310 |
String geoSearch = nullSafeTrim(rs.getString("NameForGeoSearch"));
|
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| 311 |
|
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| 312 |
|
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| 313 |
|
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| 314 |
if (isBlank(emCode)){
|
|
| 315 |
emCode = unit; |
|
| 316 |
} |
|
| 317 |
|
|
| 318 |
//uuid |
|
| 319 |
UUID uuid = BerlinModelTransformer.getEMAreaUuid(emCode); |
|
| 320 |
NamedArea area = (NamedArea)getTermService().find(uuid); |
|
| 321 |
if (area == null){
|
|
| 322 |
//label |
|
| 323 |
area = NamedArea.NewInstance(geoSearch, unit, emCode); |
|
| 324 |
if (uuid != null){
|
|
| 325 |
area.setUuid(uuid); |
|
| 326 |
}else{
|
|
| 327 |
if (areaId == 211 || areaId == 213){ //Additional Azores and Canary Is. area are merged into primary area, see also area.addSource part below
|
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| 328 |
return null; |
|
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} |
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logger.warn("Uuid for emCode could not be defined: " + emCode);
|
|
| 331 |
} |
|
| 332 |
} |
|
| 333 |
|
|
| 334 |
|
|
| 335 |
//code |
|
| 336 |
area.setIdInVocabulary(emCode); |
|
| 337 |
//notes |
|
| 338 |
if (StringUtils.isNotEmpty(notes)){
|
|
| 339 |
area.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT())); |
|
| 340 |
} |
|
| 341 |
//markers |
|
| 342 |
area.addMarker(Marker.NewInstance(eurMarkerType, eurMarker)); |
|
| 343 |
area.addMarker(Marker.NewInstance(euroMedAreaMarkerType, euroMedAreaMarker)); |
|
| 344 |
|
|
| 345 |
//extensions |
|
| 346 |
if (isNotBlank(isoCode)){
|
|
| 347 |
area.addExtension(isoCode, isoCodeExtType); |
|
| 348 |
} |
|
| 349 |
if (isNotBlank(tdwgCode)){
|
|
| 350 |
area.addExtension(tdwgCode, tdwgCodeExtType); |
|
| 351 |
} |
|
| 352 |
if (isNotBlank(mclCode)){
|
|
| 353 |
area.addExtension(mclCode, mclCodeExtType); |
|
| 354 |
} |
|
| 355 |
|
|
| 356 |
//type |
|
| 357 |
area.setType(NamedAreaType.ADMINISTRATION_AREA()); |
|
| 358 |
|
|
| 359 |
//source |
|
| 360 |
area.addSource(OriginalSourceType.Import, String.valueOf(areaId), EM_AREA_NAMESPACE, sourceReference, null); |
|
| 361 |
//add duplicate area ids for canary |
|
| 362 |
if (areaId == 624){ //Canary Is.
|
|
| 363 |
area.addSource(OriginalSourceType.Import, String.valueOf(213), EM_AREA_NAMESPACE, sourceReference, null); |
|
| 364 |
} |
|
| 365 |
if (areaId == 210){//Azores
|
|
| 366 |
area.addSource(OriginalSourceType.Import, String.valueOf(211), EM_AREA_NAMESPACE, sourceReference, null); |
|
| 367 |
} |
|
| 368 |
|
|
| 369 |
//parent |
|
| 370 |
if (euroMedArea != null){
|
|
| 371 |
if (emCode.contains("(")){
|
|
| 372 |
area.setPartOf(level1Area); |
|
| 373 |
area.setLevel(areaLevelEm2); |
|
| 374 |
}else{
|
|
| 375 |
area.setPartOf(euroMedArea); |
|
| 376 |
area.setLevel(areaLevelEm1); |
|
| 377 |
} |
|
| 378 |
}else{
|
|
| 379 |
area.setLevel(areaLevelTop); |
|
| 380 |
} |
|
| 381 |
this.euroMedAreas.put(areaId, area); |
|
| 382 |
|
|
| 383 |
//save |
|
| 384 |
getTermService().saveOrUpdate(area); |
|
| 385 |
|
|
| 386 |
return area; |
|
| 387 |
} |
|
| 388 | 149 |
|
| 389 | 150 |
private String nullSafeTrim(String string) {
|
| 390 | 151 |
if (string == null){
|
| ... | ... | |
| 394 | 155 |
} |
| 395 | 156 |
} |
| 396 | 157 |
|
| 397 |
/** |
|
| 398 |
* |
|
| 399 |
*/ |
|
| 400 |
private TermVocabulary<NamedArea> makeEmptyEuroMedVocabulary() {
|
|
| 401 |
TermType type = TermType.NamedArea; |
|
| 402 |
String description = "Euro+Med area vocabulary"; |
|
| 403 |
String label = "E+M areas"; |
|
| 404 |
String abbrev = null; |
|
| 405 |
URI termSourceUri = null; |
|
| 406 |
OrderedTermVocabulary<NamedArea> result = OrderedTermVocabulary.NewInstance(type, description, label, abbrev, termSourceUri); |
|
| 407 |
|
|
| 408 |
result.setUuid(BerlinModelTransformer.uuidVocEuroMedAreas); |
|
| 409 |
getVocabularyService().save(result); |
|
| 410 |
return result; |
|
| 411 |
} |
|
| 412 |
|
|
| 413 | 158 |
@Override |
| 414 | 159 |
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
|
| 415 | 160 |
boolean success = true; |
| 416 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
|
|
| 161 |
Set<TaxonBase> taxaToSave = new HashSet<>(); |
|
| 417 | 162 |
|
| 418 | 163 |
Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE); |
| 419 | 164 |
|
| ... | ... | |
| 422 | 167 |
try {
|
| 423 | 168 |
//map to store the mapping of duplicate berlin model occurrences to their real distributions |
| 424 | 169 |
//duplicated may occur due to area mappings from BM areas to TDWG areas |
| 425 |
Map<Integer, String> duplicateMap = new HashMap<Integer, String>();
|
|
| 170 |
Map<Integer, String> duplicateMap = new HashMap<>(); |
|
| 426 | 171 |
int oldTaxonId = -1; |
| 427 | 172 |
TaxonDescription oldDescription = null; |
| 428 | 173 |
int i = 0; |
| ... | ... | |
| 453 | 198 |
|
| 454 | 199 |
Reference sourceRef = state.getTransactionalSourceReference(); |
| 455 | 200 |
|
| 456 |
List<NamedArea> areas = makeAreaList(state, rs, occurrenceId);
|
|
| 201 |
List<NamedArea> areas = makeAreaList(state, partitioner, rs, occurrenceId);
|
|
| 457 | 202 |
|
| 458 | 203 |
//create description(elements) |
| 459 | 204 |
TaxonDescription taxonDescription = getTaxonDescription(newTaxonId, oldTaxonId, oldDescription, taxonMap, occurrenceId, sourceRef); |
| ... | ... | |
| 513 | 258 |
|
| 514 | 259 |
/** |
| 515 | 260 |
* @param state |
| 261 |
* @param partitioner |
|
| 516 | 262 |
* @param rs |
| 517 | 263 |
* @param occurrenceId |
| 518 | 264 |
* @param tdwgCodeString |
| ... | ... | |
| 521 | 267 |
* @throws SQLException |
| 522 | 268 |
*/ |
| 523 | 269 |
//Create area list |
| 524 |
private List<NamedArea> makeAreaList(BerlinModelImportState state, ResultSet rs, int occurrenceId) throws SQLException {
|
|
| 525 |
List<NamedArea> areas = new ArrayList<NamedArea>(); |
|
| 270 |
private List<NamedArea> makeAreaList(BerlinModelImportState state, ResultSetPartitioner partitioner, ResultSet rs, int occurrenceId) throws SQLException {
|
|
| 271 |
|
|
| 272 |
List<NamedArea> areas = new ArrayList<>(); |
|
| 526 | 273 |
|
| 527 | 274 |
if (state.getConfig().isUseEmAreaVocabulary()){
|
| 528 |
Integer areaId = rs.getInt("AreaId");
|
|
| 529 |
NamedArea area = this.euroMedAreas.get(areaId); |
|
| 275 |
Integer areaId = rs.getInt("AreaId");
|
|
| 276 |
NamedArea area = getAreaByAreaId(areaId); |
|
| 277 |
if (area == null){
|
|
| 278 |
logger.warn("Area for areaId " + areaId + " not found.");
|
|
| 279 |
} |
|
| 530 | 280 |
areas.add(area); |
| 531 | 281 |
}else{
|
| 532 | 282 |
String tdwgCodeString = rs.getString("TDWGCode");
|
| ... | ... | |
| 566 | 316 |
|
| 567 | 317 |
@Override |
| 568 | 318 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 569 |
String nameSpace; |
|
| 570 |
Class<?> cdmClass; |
|
| 571 |
Set<String> idSet; |
|
| 572 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
|
| 573 | 319 |
|
| 574 | 320 |
try{
|
| 321 |
|
|
| 322 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 575 | 323 |
Set<String> taxonIdSet = new HashSet<String>(); |
| 576 | 324 |
while (rs.next()){
|
| 577 | 325 |
handleForeignKey(rs, taxonIdSet, "taxonId"); |
| 578 | 326 |
} |
| 579 | 327 |
|
| 580 | 328 |
//taxon map |
| 581 |
nameSpace = BerlinModelTaxonImport.NAMESPACE; |
|
| 582 |
cdmClass = TaxonBase.class; |
|
| 583 |
idSet = taxonIdSet; |
|
| 584 |
Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 329 |
String nameSpace = BerlinModelTaxonImport.NAMESPACE;
|
|
| 330 |
Class<?> cdmClass = TaxonBase.class;
|
|
| 331 |
Set<String> idSet = taxonIdSet;
|
|
| 332 |
Map<String, ? extends CdmBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 585 | 333 |
result.put(nameSpace, objectMap); |
| 586 | 334 |
|
| 335 |
return result; |
|
| 587 | 336 |
} catch (SQLException e) {
|
| 588 | 337 |
throw new RuntimeException(e); |
| 589 | 338 |
} |
| 590 |
return result; |
|
| 591 | 339 |
} |
| 592 | 340 |
|
| 593 | 341 |
|
| 594 |
|
|
| 595 | 342 |
/** |
| 596 | 343 |
* Tests if a distribution with the same tdwgArea and the same status already exists in the description. |
| 597 | 344 |
* If so the old distribution is returned |
Also available in: Unified diff
ref #7346 use E+M area vocabulary for common names