Revision 786696e3
Added by Andreas Müller over 10 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcTaxonStreamItem2CdmTaxonConverter.java | ||
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*/ |
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package eu.etaxonomy.cdm.io.dwca.in; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.HashSet; |
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import java.util.List; |
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import eu.etaxonomy.cdm.io.stream.StreamItem; |
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import eu.etaxonomy.cdm.model.common.Annotation; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.Extension; |
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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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import eu.etaxonomy.cdm.model.common.LSID; |
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import eu.etaxonomy.cdm.model.common.Language; |
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* |
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*/ |
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public class DwcTaxonStreamItem2CdmTaxonConverter<CONFIG extends DwcaDataImportConfiguratorBase, STATE extends StreamImportStateBase<CONFIG, StreamImportBase>> extends PartitionableConverterBase<CONFIG, STATE> implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{
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@SuppressWarnings("unused")
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private static Logger logger = Logger.getLogger(DwcTaxonStreamItem2CdmTaxonConverter.class); |
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private static final Logger logger = Logger.getLogger(DwcTaxonStreamItem2CdmTaxonConverter.class); |
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private static final String ID = "id"; |
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// temporary key for the case that no dataset information is supplied, TODO use something better |
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//nameAccordingTo |
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MappedCdmBase<Reference> sec = getNameAccordingTo(csvTaxonRecord, resultList); |
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if (sec == null && state.getConfig().isUseSourceReferenceAsSec()){
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sec = new MappedCdmBase<Reference>(state.getTransactionalSourceReference()); |
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} |
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* @param taxonBase |
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*/ |
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private void handleIdentifiableObjects(StreamItem item,TaxonBase<?> taxonBase) {
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String references = item.get(TermUri.DC_REFERENCES); |
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if (references == null || references == "") {
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references = item.get(TermUri.DWC_NAME_PUBLISHED_IN_ID);//lorna temporary until Scratchpads move the reference to the correct place. |
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} |
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if (StringUtils.isNotBlank(references)){
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URI uri = makeUriIfIs(references); |
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if (uri != null){
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Extension.NewInstance(taxonBase, references, ExtensionType.URL()); |
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}else{
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String message = "Non-URI Dublin Core References not yet handled for taxa. References is: %s"; |
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fireWarningEvent(String.format(message, references), item, 6); |
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} |
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} |
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//TODO: Finish properly |
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String id = item.get(TermUri.CDM_SOURCE_IDINSOURCE); |
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String idNamespace = item.get(TermUri.CDM_SOURCE_IDNAMESPACE); |
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Taxon taxon = (Taxon) taxonBase; |
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taxon.addSource(OriginalSourceType.Import, id, idNamespace, ref, null); |
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} |
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} |
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/** |
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* If str is an uri it returns is as an {@link URI}. If not it returns <code>null</code>.
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* @param str |
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* @return the URI. |
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*/ |
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private URI makeUriIfIs(String str) {
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if (! str.startsWith("http:")){
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return null; |
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}else{
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try {
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URI uri = URI.create(str); |
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return uri; |
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} catch (Exception e) {
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return null; |
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} |
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} |
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} |
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|
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private void handleTdwgArea(StreamItem item, TaxonBase<?> taxonBase) {
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// TODO Auto-generated method stub |
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String tdwg_area = item.get(TermUri.DWC_COUNTRY_CODE); |
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if (tdwg_area != null){
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if(taxonBase instanceof Synonym){
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Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class); |
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Set<Taxon> acceptedTaxaList = synonym.getAcceptedTaxa(); |
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for(Taxon taxon : acceptedTaxaList){
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TaxonDescription td = getTaxonDescription(taxon, false); |
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NamedArea area = NamedArea.getAreaByTdwgAbbreviation(tdwg_area); |
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if (area == null){
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area = NamedArea.getAreaByTdwgLabel(tdwg_area); |
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} |
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
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TaxonDescription td = getTaxonDescription(taxon, false); |
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NamedArea area = NamedArea.getAreaByTdwgAbbreviation(tdwg_area); |
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if (area == null){
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area = NamedArea.getAreaByTdwgLabel(tdwg_area); |
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} |
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} |
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} |
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} |
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} |
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/** |
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//if not exists, create new |
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if (! classificationExists){
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String classificationName = StringUtils.isBlank(datasetName)? datasetId : datasetName; |
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if (classificationName.equals(NO_DATASET)){
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classificationName = "Classification (no name)"; //TODO define by config or zipfile or metadata |
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if (classificationName.equals(NO_DATASET)){
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classificationName = config.getClassificationName(); |
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//classificationName = "Classification (no name)"; //TODO define by config or zipfile or metadata |
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} |
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String classificationId = StringUtils.isBlank(datasetId)? datasetName : datasetId; |
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if (! idIsInternal){
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//references should already exist in store if not linking to external links like URLs |
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String message = "External namePublishedInIDs are not yet supported"; |
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fireWarningEvent(message, item, 4); |
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fireWarningEvent(message, item, 4);//set to DEBUG
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}else{
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newRef = ReferenceFactory.newGeneric(); //TODO handle other types if possible |
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newRef.addSource(OriginalSourceType.Import, refId, idTerm.toString(), sourceCitation, null); |
Also available in: Unified diff
merge trunk into cdm3.3 branch