Revision 6b381b7d
Added by Andreas Müller almost 7 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java | ||
|---|---|---|
| 45 | 45 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.name.INonViralName; |
| 48 |
import eu.etaxonomy.cdm.model.name.ITaxonNameBase; |
|
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 50 | 49 |
import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| ... | ... | |
| 103 | 102 |
|
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//check atomised name data for rank |
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//new name will be created |
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ITaxonNameBase atomisedTaxonName = null;
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TaxonName atomisedTaxonName = null;
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if (rank==null && unitIndexInAbcdFile>=0 && ((state.getDataHolder().getAtomisedIdentificationList() != null && !state.getDataHolder().getAtomisedIdentificationList().isEmpty())|| state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
|
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atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state); |
| 109 | 108 |
if(atomisedTaxonName!=null){
|
| ... | ... | |
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} |
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} |
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if(config.isReuseExistingTaxaWhenPossible()){
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ITaxonNameBase parsedName = atomisedTaxonName;
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TaxonName parsedName = atomisedTaxonName;
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if(parsedName==null){
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|
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parsedName = parseScientificName(scientificName, state, state.getReport(), rank); |
| ... | ... | |
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} |
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|
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if(taxonName==null && atomisedTaxonName!=null){
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taxonName = (TaxonName) atomisedTaxonName;
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taxonName = atomisedTaxonName; |
|
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state.getReport().addName(taxonName); |
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logger.info("Created new taxon name "+taxonName);
|
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if(taxonName.hasProblem()){
|
| ... | ... | |
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* @return a parsed name |
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*/ |
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|
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protected ITaxonNameBase parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
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protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
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|
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NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance(); |
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ITaxonNameBase taxonName = null;
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TaxonName taxonName = null;
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boolean problem = false; |
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|
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if (logger.isDebugEnabled()){
|
| ... | ... | |
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} |
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|
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if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
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taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank); |
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
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|
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if (taxonName.hasProblem()) {
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problem = true; |
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} |
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} |
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else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
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taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank); |
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
|
|
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if (taxonName.hasProblem()) {
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problem = true; |
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} |
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} |
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else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
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taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank); |
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank);
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|
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if (taxonName.hasProblem()) {
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problem = true; |
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} |
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} |
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else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
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taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank); |
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taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
|
|
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if (taxonName.hasProblem()) {
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problem = true; |
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} |
| ... | ... | |
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} |
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} |
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else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
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TaxonName taxonName = (TaxonName)parseScientificName(fullName, state, state.getReport(), null);
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TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null); |
|
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if (taxonName != null){
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return taxonName; |
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} |
Also available in: Unified diff
ref #6368 remove some further occurrences of ITaxonNameBase