Revision 495cebda
Added by Andreas Müller almost 11 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 29 | 29 |
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.mapping.IMappingImport; |
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
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import eu.etaxonomy.cdm.io.globis.validation.GlobisSpecTaxaImportValidator; |
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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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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.location.WaterbodyOrCountry; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
|
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| ... | ... | |
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private static final String pluralString = "taxa"; |
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private static final String dbTableName = "specTax"; |
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private static final Class cdmTargetClass = Reference.class; |
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public static final String SPEC_TAX_NAMESPACE = dbTableName; |
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public static final String TYPE_NAMESPACE = dbTableName + ".SpecTypeDepository"; |
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|
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private static UUID uuidCitedTypeLocality = UUID.fromString("ca431e0a-84ec-4828-935f-df4c8f5cf880");
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private static UUID uuidCitedTypeMaterial = UUID.fromString("8395021a-e596-4a55-9794-8c03aaad9e16");
|
| ... | ... | |
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Integer acceptedTaxonId = nullSafeInt(rs, "SpecCurrspecID"); |
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String specSystaxRank = rs.getString("SpecSystaxRank");
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//ignore: CountryDummy, currentSpecies, DepositoryDisplay, DepositoryDummy, ReferenceDisplay, SpecDescriptionImageFile, all *Valid* |
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|
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try {
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|
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//source ref |
| ... | ... | |
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objectsToSave.add(acceptedTaxon); |
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} |
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|
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//makeMarker1(state, rs, name); //ignore! |
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|
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makeNotAvailable(state, rs, name); |
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|
|
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//SpecCitedTypeLocality |
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String citedTypeLocality = rs.getString("SpecCitedTypeLocality");
|
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if (isNotBlank(citedTypeLocality)){
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ExtensionType exTypeCitedTypeLoc = getExtensionType(state, uuidCitedTypeLocality, "Type locality as cited in original description", "Type locality as cited in original description", null, ExtensionType.DOI().getVocabulary()); |
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name.addExtension(citedTypeLocality, exTypeCitedTypeLoc); |
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// ExtensionType exTypeCitedTypeLoc = getExtensionType(state, uuidCitedTypeLocality, "Type locality as cited in original description", "Type locality as cited in original description", null, ExtensionType.DOI().getVocabulary()); |
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// name.addExtension(citedTypeLocality, exTypeCitedTypeLoc); |
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addNameDescription(state, name, uuidCitedTypeLocality, citedTypeLocality, "Type locality as cited in original description"); |
|
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} |
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|
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//SpecCitedTypeMaterial |
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String citedTypeMaterial = rs.getString("SpecCitedTypeMaterial");
|
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if (isNotBlank(citedTypeMaterial)){
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ExtensionType exTypeCitedTypeLoc = getExtensionType(state, uuidCitedTypeMaterial, "Type material as cited in original description", "Type locality as cited in original description", null, ExtensionType.DOI().getVocabulary());
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ExtensionType exTypeCitedTypeLoc = getExtensionType(state, uuidCitedTypeMaterial, "Type material as cited in original description", "Type material as cited in original description", null, ExtensionType.DOI().getVocabulary());
|
|
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name.addExtension(citedTypeLocality, exTypeCitedTypeLoc); |
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} |
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name.addSource(String.valueOf(specTaxId), SPEC_TAX_NAMESPACE, state.getTransactionalSourceReference(), null); |
|
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|
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namesToSave.add(name); |
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|
| ... | ... | |
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} |
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|
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private void makeNotAvailable(GlobisImportState state, ResultSet rs, ZoologicalName name) throws SQLException {
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String notAvailableStr = rs.getString("SpecNotAvailable");
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try {
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if (isNotBlank(notAvailableStr)){
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if (notAvailableStr.contains("not available") ){
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UUID uuidNotAvailableMarkerType = state.getTransformer().getMarkerTypeUuid("not available");
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MarkerType markerType = getMarkerType(state, uuidNotAvailableMarkerType, "not available", "not available", null); |
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name.addMarker(Marker.NewInstance(markerType, true)); |
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} |
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} |
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace(); |
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} |
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//Not available reason |
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//TODO make it a vocabulary |
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String notAvailableReason = rs.getString("SpecNotAvailableReason");
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if (isNotBlank(notAvailableReason)){
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UUID uuidNotAvailableReason; |
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try {
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uuidNotAvailableReason = state.getTransformer().getExtensionTypeUuid("not available reason");
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ExtensionType notAvailableReasonExtType = getExtensionType(state, uuidNotAvailableReason, "Not available reason", "Not available reason", null, null); |
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name.addExtension(notAvailableReason, notAvailableReasonExtType); |
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace(); |
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} |
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} |
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} |
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/** |
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* This method is not used anymore as according to Alexander Marker1 should be ignored. |
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* @param state |
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* @param rs |
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* @param name |
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* @throws SQLException |
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*/ |
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private void makeMarker1(GlobisImportState state, ResultSet rs, ZoologicalName name) throws SQLException {
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String marker1Str = rs.getString("Marker1");
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try {
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if (isNotBlank(marker1Str)){
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marker1Str = marker1Str.trim(); |
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if (marker1Str.contains("checked") || marker1Str.contains("berpr") ){ //überprüft
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UUID uuidCheckedMarkerType; |
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uuidCheckedMarkerType = state.getTransformer().getMarkerTypeUuid("checked");
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MarkerType markerType = getMarkerType(state, uuidCheckedMarkerType, "checked", "checked", null); |
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name.addMarker(Marker.NewInstance(markerType, true)); |
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} |
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if (marker1Str.contains("old record") || marker1Str.contains("alte Angabe") ){
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UUID uuidOldRecordMarkerType = state.getTransformer().getMarkerTypeUuid("old record");
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MarkerType markerType = getMarkerType(state, uuidOldRecordMarkerType, "checked", "checked", null); |
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name.addMarker(Marker.NewInstance(markerType, true)); |
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} |
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} |
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace(); |
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} |
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} |
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private void addNameDescription(GlobisImportState state, ZoologicalName name, UUID featureUuid, |
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String citedTypeLocality, String featureLabel) {
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Feature feature = getFeature(state, featureUuid,featureLabel,featureLabel, null, null); |
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getTaxonNameDescription(name, false, true); |
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} |
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|
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private Pattern patternAll = Pattern.compile("(.+,\\s.+)(\\(.+\\))");
|
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|
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|
| ... | ... | |
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//TODO several issues |
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if (specTypeDepositories.length == 0){
|
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Specimen specimen = makeSingleTypeSpecimen(fieldObservation); |
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makeTypeDesignation(name, rs, specimen); |
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makeTypeDesignation(name, rs, specimen, specTaxId);
|
|
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makeTypeIdInSource(state, specimen, "null", specTaxId); |
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} |
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for (String specTypeDepositoryStr : specTypeDepositories){
|
| ... | ... | |
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} |
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|
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//type Designation |
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makeTypeDesignation(name, rs, specimen); |
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makeTypeDesignation(name, rs, specimen, specTaxId);
|
|
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} |
| 283 | 365 |
|
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|
| ... | ... | |
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DerivedUnitType unitType = DerivedUnitType.Specimen; |
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(unitType); |
| 472 | 554 |
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WaterbodyOrCountry typeCountry = getCountry(state, countryString);
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NamedArea typeCountry = getCountry(state, countryString);
|
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facade.setCountry(typeCountry); |
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FieldObservation fieldObservation = facade.innerFieldObservation(); |
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return fieldObservation; |
| ... | ... | |
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* @param rs |
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* @param status |
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* @param specimen |
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* @param specTaxId |
|
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* @throws SQLException |
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*/ |
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protected void makeTypeDesignation(ZoologicalName name, ResultSet rs, Specimen specimen) throws SQLException {
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protected void makeTypeDesignation(ZoologicalName name, ResultSet rs, Specimen specimen, Integer specTaxId) throws SQLException {
|
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//type |
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String specType = rs.getString("SpecType");
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SpecimenTypeDesignationStatus status = getTypeDesigType(specType); |
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SpecimenTypeDesignationStatus status = getTypeDesigType(specType, specTaxId);
|
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|
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SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance(); |
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typeDesignation.setTypeStatus(status); |
| ... | ... | |
| 501 | 584 |
|
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|
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|
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private SpecimenTypeDesignationStatus getTypeDesigType(String specType) {
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private SpecimenTypeDesignationStatus getTypeDesigType(String specType, Integer specTaxId) {
|
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if (isBlank(specType) ){
|
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return null; |
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}else if (specType.matches("Holotype(Holotypus)?")){
|
|
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}else if (specType.matches("Holotype(.*Holotypus)?")){
|
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return SpecimenTypeDesignationStatus.HOLOTYPE(); |
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}else if (specType.matches("Neotype")){
|
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return SpecimenTypeDesignationStatus.NEOTYPE(); |
| ... | ... | |
| 513 | 596 |
}else if (specType.matches("Lectotype")){
|
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return SpecimenTypeDesignationStatus.LECTOTYPE(); |
| 515 | 598 |
}else{
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logger.warn("SpecimenTypeDesignationStatus does not match: " + specType);
|
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logger.warn("SpecimenTypeDesignationStatus does not match: " + specType + " in specTaxId " + specTaxId);
|
|
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return null; |
| 518 | 601 |
} |
| 519 | 602 |
} |
| ... | ... | |
| 613 | 696 |
String authorStr = rs.getString("SpecAuthor");
|
| 614 | 697 |
String yearStr = rs.getString("SpecYear");
|
| 615 | 698 |
String authorAndYearStr = CdmUtils.concat(", ", authorStr, yearStr);
|
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handleAuthorAndYear(authorAndYearStr, name); |
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handleAuthorAndYear(authorAndYearStr, name, specTaxId);
|
|
| 617 | 700 |
|
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name.addSource(String.valueOf(specTaxId), SPEC_TAX_NAMESPACE, state.getTransactionalSourceReference(), null); |
|
| 619 | 701 |
return name; |
| 620 | 702 |
} |
| 621 | 703 |
|
| ... | ... | |
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|
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|
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@Override |
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public Reference createObject(ResultSet rs, GlobisImportState state) |
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public Reference<?> createObject(ResultSet rs, GlobisImportState state)
|
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throws SQLException {
|
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// not needed |
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return null; |
| 724 | 806 |
} |
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|
|
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} |
Also available in: Unified diff
updates to globis import