Revision 0a5679a4
Added by Andreas Müller over 6 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/GbifDistributionCsv2CdmConverter.java | ||
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| 13 | 13 |
import java.util.List; |
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import java.util.Map; |
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import java.util.Set; |
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import java.util.UUID; |
|
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|
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import org.apache.log4j.Logger; |
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|
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import eu.etaxonomy.cdm.io.common.TdwgAreaProvider; |
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
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import eu.etaxonomy.cdm.io.dwca.TermUri; |
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import eu.etaxonomy.cdm.io.stream.StreamItem; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
| ... | ... | |
| 59 | 61 |
Taxon taxon = getTaxonBase(id, item, Taxon.class, state); |
| 60 | 62 |
if (taxon != null){
|
| 61 | 63 |
|
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String locality = item.get(TermUri.DWC_LOCALITY); |
|
| 62 | 65 |
String locationId = item.get(TermUri.DWC_LOCATION_ID); |
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NamedArea area = getAreaByLocationId(item, locationId); |
|
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NamedArea area = getAreaByLocationId(item, locationId, locality, resultList);
|
|
| 64 | 67 |
if (area != null){
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(item.term, csv.get(TermUri.DWC_LOCATION_ID), area);
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(TermUri.DWC_LOCATION_ID, csv.get(TermUri.DWC_LOCATION_ID.toString()), area);
|
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resultList.add(mcb); |
| 67 | 70 |
}else if (! config.isExcludeLocality()){
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String locality = item.get(TermUri.DWC_LOCALITY); |
|
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area = getAreaByLocality(item, locality); |
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(item.term, csv.get(TermUri.DWC_LOCALITY), area);
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(TermUri.DWC_LOCALITY, csv.get(TermUri.DWC_LOCALITY.toString()), area);
|
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resultList.add(mcb); |
| 72 | 74 |
} |
| 73 | 75 |
|
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if (area != null){
|
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|
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//TODO language, area, |
|
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TaxonDescription desc = getTaxonDescription(taxon, false); |
| 78 | 79 |
|
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//TODO |
|
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PresenceAbsenceTerm status = null; |
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String establishmentMeans = item.get(TermUri.DWC_ESTABLISHMENT_MEANS); |
|
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String occurrenceStatus = item.get(TermUri.DWC_OCCURRENCE_STATUS); |
|
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if (isBlank(establishmentMeans) && isBlank(occurrenceStatus)){
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status = PresenceAbsenceTerm.PRESENT(); |
|
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}else{
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//FIXME TODO status |
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} |
|
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Distribution distribution = Distribution.NewInstance(area, status); |
| 82 | 89 |
desc.addElement(distribution); |
| 83 | 90 |
|
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//save taxon |
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(item.term, csv.get(CORE_ID), taxon); |
|
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(item.term, csv.get(CORE_ID.toString()), taxon);
|
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resultList.add(mcb); |
| 87 | 94 |
} |
| 88 | 95 |
|
| ... | ... | |
| 112 | 119 |
return result.iterator().next(); |
| 113 | 120 |
} |
| 114 | 121 |
|
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private NamedArea getAreaByLocationId(StreamItem item, String locationId) {
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private NamedArea getAreaByLocationId(StreamItem item, String locationId, String newLabel, List<MappedCdmBase<? extends CdmBase>> resultList) {
|
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String namespace = TermUri.DWC_LOCATION_ID.toString(); |
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if (locationId == null){
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if (isBlank(locationId)){
|
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return null; |
| 119 | 126 |
} |
| 120 | 127 |
List<NamedArea> result = state.get(namespace, locationId, NamedArea.class); |
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if (result.isEmpty()){
|
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//try to find in cdm |
|
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NamedArea newArea = getTdwgArea(locationId); |
|
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if (newArea == null){
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//TODO could be idInVocabulary (with not voc given), abbrevTitle of any representation, ... |
|
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// state.getCurrentIO().getTermService().listByCode |
|
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} |
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if (newArea == null){
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newArea = NamedArea.NewInstance(locationId, locationId, locationId); |
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} |
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|
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state.putMapping(namespace, locationId, newArea); |
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return newArea; |
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} |
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if (result.size() > 1){
|
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String message = "There is more than 1 cdm entity matching given locationId '%s'. I take an arbitrary one."; |
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fireWarningEvent(String.format(message, locationId), item, 4); |
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} |
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return result.iterator().next(); |
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try{
|
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if (result.isEmpty()){
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NamedArea newArea = state.getTransformer().getNamedAreaByKey(locationId); |
|
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if (newArea != null){
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return newArea; |
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} |
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//try to find in cdm |
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newArea = getTdwgArea(locationId); |
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if (newArea != null){
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return newArea; |
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} |
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|
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String label = isNotBlank(newLabel)? newLabel : locationId; |
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UUID namedAreaUuid = state.getTransformer().getNamedAreaUuid(locationId); |
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newArea = state.getCurrentIO().getNamedArea(state, namedAreaUuid, label, label, locationId, null); |
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|
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//should not happen |
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if (newArea == null){
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newArea = NamedArea.NewInstance(label, label, locationId); |
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// state.putMapping(namespace, type, newArea); |
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state.getCurrentIO().saveNewTerm(newArea); |
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(namespace, locationId, newArea); |
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resultList.add(mcb); |
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} |
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|
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|
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state.putMapping(namespace, locationId, newArea); |
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return newArea; |
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} |
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if (result.size() > 1){
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String message = "There is more than 1 cdm entity matching given locationId '%s'. I take an arbitrary one."; |
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fireWarningEvent(String.format(message, locationId), item, 4); |
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} |
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return result.iterator().next(); |
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} catch (UndefinedTransformerMethodException e) {
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String message = "GetNamedArea not yet supported by DwcA-Transformer. This should not have happend. Please contact your application developer."; |
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fireWarningEvent(message, item, 8); |
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return null; |
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} |
|
| 140 | 167 |
} |
| 141 | 168 |
|
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/** |
| ... | ... | |
| 189 | 216 |
Set<String> result = new HashSet<>(); |
| 190 | 217 |
result.add(TermUri.DWC_TAXON.toString()); |
| 191 | 218 |
result.add(TermUri.DWC_LOCATION_ID.toString()); |
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result.add(TermUri.DWC_LOCALITY.toString()); |
|
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return result; |
| 193 | 221 |
} |
| 194 | 222 |
|
Also available in: Unified diff
ref #6887 and ref #5173 improve area handling for CoL distribution import