Revision 539b7820
Added by Andreas Müller over 5 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaSpecimenImport.java | ||
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| 73 | 73 |
extends SimpleExcelSpecimenImport<CONFIG> {
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| 74 | 74 |
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private static final long serialVersionUID = -884838817884874228L; |
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(BogotaSpecimenImport.class); |
| 77 | 78 |
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private static final String COL_TAXON_UUID = "Platform Name ID = cdmID"; |
| ... | ... | |
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@Override |
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protected void firstPass(SimpleExcelSpecimenImportState<CONFIG> state) {
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HashMap<String, String> record = state.getOriginalRecord();
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Map<String, String> record = state.getOriginalRecord(); |
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String voucherId = getValue(record, COL_VOUCHER_ID); |
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if (!isInInterval(state)){
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| ... | ... | |
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* @return |
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*/ |
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private Taxon getOrCreateNewTaxon(SimpleExcelSpecimenImportState<CONFIG> state, |
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HashMap<String, String> record, String line) {
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Map<String, String> record, String line) {
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String familyStr = record.get(COL_FAMILY); |
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String genusStr = record.get(COL_GENUS); |
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initTaxonMap(state); |
| ... | ... | |
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* @return |
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*/ |
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private TaxonName makeSpeciesName(SimpleExcelSpecimenImportState<CONFIG> state, String line) {
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HashMap<String, String> record = state.getOriginalRecord();
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Map<String, String> record = state.getOriginalRecord(); |
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String genus = record.get(COL_GENUS); |
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String species = record.get(COL_SPECIFIC_EPI); |
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String basionymAuthorStr = record.get(COL_BASIONYM_AUTHOR); |
| ... | ... | |
| 297 | 298 |
protected void handleRecordForTaxon(SimpleExcelSpecimenImportState<CONFIG> state, |
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String voucherId, String line, TaxonBase<?> taxonBase) {
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HashMap<String, String> record = state.getOriginalRecord();
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Map<String, String> record = state.getOriginalRecord(); |
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Taxon taxon = getTaxon(taxonBase); |
| 302 | 303 |
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TaxonDescription taxonDescription = getTaxonDescription(state, line, taxon); |
| ... | ... | |
| 353 | 354 |
* @return |
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*/ |
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private DerivedUnit makeSpecimen(SimpleExcelSpecimenImportState<CONFIG> state, String line, |
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HashMap<String, String> record, String voucherId, TaxonBase<?> taxonBase) {
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Map<String, String> record, String voucherId, TaxonBase<?> taxonBase) {
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DerivedUnitFacade facade = DerivedUnitFacade.NewPreservedSpecimenInstance(); |
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facade.setAccessionNumber(voucherId); |
| ... | ... | |
| 379 | 380 |
* @param name |
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*/ |
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private void makeTypus(DerivedUnit specimen, SimpleExcelSpecimenImportState<CONFIG> state, String line, |
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HashMap<String, String> record, TaxonName name) {
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Map<String, String> record, TaxonName name) {
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String typus = record.get(COL_TYPUS); |
| 384 | 385 |
if (typus != null){
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SpecimenTypeDesignationStatus status; |
| ... | ... | |
| 402 | 403 |
* @param record |
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*/ |
| 404 | 405 |
private void makeCollection(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, |
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String line, HashMap<String, String> record) {
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String line, Map<String, String> record) {
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String strCollection = record.get(COL_COLLECTION); |
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String collectionFormat = ".*\\([A-Z]{2,4}\\)";
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if (!strCollection.matches(collectionFormat)){
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| ... | ... | |
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* @param record |
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*/ |
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private void makeHabitus(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, String line, |
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HashMap<String, String> record) {
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Map<String, String> record) {
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String habitus = record.get(COL_HABITUS); |
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if (habitus != null){
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facade.setPlantDescription(habitus); |
| ... | ... | |
| 456 | 457 |
* @param voucherId |
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*/ |
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private void makeLocationFields(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, String line, |
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HashMap<String, String> record) {
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Map<String, String> record) {
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//Altitude |
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String strAltitudeFrom = record.get(COL_ALTITUDE_FROM); |
| 462 | 463 |
String strAltitudeTo = record.get(COL_ALTITUDE_TO); |
| ... | ... | |
| 595 | 596 |
* @param record |
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*/ |
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private void makeCollectorFields(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, String line, |
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HashMap<String, String> record) {
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Map<String, String> record) {
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//collector number |
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facade.setFieldNumber(record.get(COL_COLLECTOR_NUMBER)); |
| ... | ... | |
| 687 | 688 |
* @param taxonBase |
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*/ |
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private void makeDetermination(DerivedUnit specimen, SimpleExcelSpecimenImportState<CONFIG> state, String line, |
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HashMap<String, String> record, TaxonName taxonName) {
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Map<String, String> record, TaxonName taxonName) {
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DeterminationEvent determination; |
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determination = DeterminationEvent.NewInstance(taxonName, specimen); |
| ... | ... | |
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* @return |
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*/ |
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private TeamOrPersonBase<?> makeDeterminer(SimpleExcelSpecimenImportState<CONFIG> state, |
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HashMap<String, String> record, String line) {
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Map<String, String> record, String line) {
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String identifier = record.get(COL_IDENTIFIER); |
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if (identifier == null){
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return null; |
| ... | ... | |
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* @return |
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*/ |
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private TimePeriod makeIdentificationDate(SimpleExcelSpecimenImportState<CONFIG> state, |
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HashMap<String, String> record, String line) {
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Map<String, String> record, String line) {
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String strDate = record.get(COL_IDENTIFICATION_DATE); |
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if (strDate == null || strDate.equals("s.n.")){
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return null; |
| ... | ... | |
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* @return |
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*/ |
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private DefinedTerm makeDeterminationQualifier(SimpleExcelSpecimenImportState<CONFIG> state, |
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HashMap<String, String> record, String line) {
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Map<String, String> record, String line) {
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String qualifier = record.get(COL_IDENTIFICATION_QUALIFIER); |
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if (qualifier != null){
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try {
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| ... | ... | |
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* @return |
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*/ |
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private TaxonBase<?> getTaxonByCdmId(SimpleExcelSpecimenImportState<CONFIG> state, String line, |
| 838 |
HashMap<String, String> record, String noStr) {
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Map<String, String> record, String noStr) {
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String strUuidTaxon = record.get(COL_TAXON_UUID); |
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if (strUuidTaxon != null && ! state.getConfig().isOnlyNonCdmTaxa()){
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