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/**
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* Copyright (C) 2016 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.specimen;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.UUID;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
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import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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/**
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* @author k.luther
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* @since 15.07.2016
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*/
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public abstract class SpecimenImportConfiguratorBase<CONFIG extends SpecimenImportConfiguratorBase, STATE extends SpecimenImportStateBase<CONFIG,STATE>, InputStream>
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extends ImportConfiguratorBase<STATE, InputStream> {
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private static final long serialVersionUID = 4741134251527063988L;
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public SpecimenImportConfiguratorBase(IInputTransformer transformer) {
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super(transformer);
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}
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private boolean ignoreImportOfExistingSpecimen = true;
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private boolean reuseExistingTaxaWhenPossible = true;
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private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<>();
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private Map<String, Team> titleCacheTeam;
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private Map<String, Person> titleCachePerson;
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private boolean ignoreAuthorship = false;
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private boolean removeCountryFromLocalityText = false;
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protected OccurenceQuery query ;
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private boolean addMediaAsMediaSpecimen = false;
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private boolean reuseExistingMetaData = true;
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private String sourceReferenceTitle = null;
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private String taxonReference = null;
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private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;
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private boolean reuseExistingDescriptiveGroups = false;
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private String defaultAuthor="";
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private boolean allowReuseOtherClassifications =true;
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private boolean deduplicateReferences = false;
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private boolean deduplicateClassifications = false;
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private boolean moveNewTaxaToDefaultClassification = true;
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private boolean mapUnitIdToCatalogNumber = true;
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private boolean mapUnitIdToAccessionNumber = false;
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private boolean mapUnitIdToBarcode = false;
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private boolean overwriteExistingSpecimens = false;
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private boolean downloadSequenceData = false;
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private SpecimenOrObservationType type;
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private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();
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protected Map<String,UUID> namedAreaDecisions = new HashMap<>();
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private URI reportUri;
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public SpecimenOrObservationType getType() {
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return type;
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}
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public void setType(SpecimenOrObservationType type) {
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this.type = type;
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}
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public boolean isIgnoreImportOfExistingSpecimen() {
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return ignoreImportOfExistingSpecimen;
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}
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public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {
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this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;
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}
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public Map<String, Team> getTitleCacheTeam() {
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return titleCacheTeam;
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}
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public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {
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this.titleCacheTeam = titleCacheTeam;
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}
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public Map<String, Person> getTitleCachePerson() {
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return titleCachePerson;
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}
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public void setTitleCachePerson(Map<String, Person> titleCachePerson) {
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this.titleCachePerson = titleCachePerson;
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}
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public OccurenceQuery getQuery() {
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return query;
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}
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public void setQuery(OccurenceQuery query) {
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this.query = query;
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}
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public String getTaxonReference() {
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return taxonReference;
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}
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public void setTaxonReference(String taxonReference) {
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this.taxonReference = taxonReference;
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}
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public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {
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return addIndividualsAssociationsSuchAsSpecimenAndObservations;
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}
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public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(
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boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {
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this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;
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}
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public boolean isReuseExistingDescriptiveGroups() {
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return reuseExistingDescriptiveGroups;
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}
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public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {
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this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;
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}
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public String getDefaultAuthor() {
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return defaultAuthor;
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}
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public void setDefaultAuthor(String defaultAuthor) {
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this.defaultAuthor = defaultAuthor;
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}
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public boolean isAllowReuseOtherClassifications() {
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return allowReuseOtherClassifications;
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}
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public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {
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this.allowReuseOtherClassifications = allowReuseOtherClassifications;
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}
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public boolean isDeduplicateReferences() {
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return deduplicateReferences;
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}
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public void setDeduplicateReferences(boolean deduplicateReferences) {
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this.deduplicateReferences = deduplicateReferences;
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}
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public boolean isDeduplicateClassifications() {
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return deduplicateClassifications;
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}
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public void setDeduplicateClassifications(boolean deduplicateClassifications) {
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this.deduplicateClassifications = deduplicateClassifications;
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}
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public boolean isMoveNewTaxaToDefaultClassification() {
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return moveNewTaxaToDefaultClassification;
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}
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public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {
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this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;
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}
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public boolean isMapUnitIdToCatalogNumber() {
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return mapUnitIdToCatalogNumber;
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}
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public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {
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this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;
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}
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public boolean isMapUnitIdToAccessionNumber() {
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return mapUnitIdToAccessionNumber;
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}
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public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {
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this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;
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}
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public boolean isMapUnitIdToBarcode() {
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return mapUnitIdToBarcode;
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}
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public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {
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this.mapUnitIdToBarcode = mapUnitIdToBarcode;
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}
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public Map<String, UUID> getNamedAreaDecisions() {
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return namedAreaDecisions;
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}
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public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {
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this.namedAreaDecisions = namedAreaDecisions;
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}
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public void putNamedAreaDecision(String areaStr,UUID uuid){
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this.namedAreaDecisions.put(areaStr,uuid);
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}
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public UUID getNamedAreaDecision(String areaStr){
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return namedAreaDecisions.get(areaStr);
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}
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public Map<UUID, UUID> getTaxonToDescriptionMap() {
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return taxonToDescriptionMap;
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}
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public SpecimenUserInteraction getSpecimenUserInteraction() {
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return specimenUserInteraction;
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}
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public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {
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this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;
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}
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public void setIgnoreAuthorship(boolean ignoreAuthorship) {
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this.ignoreAuthorship = ignoreAuthorship;
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}
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public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {
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this.removeCountryFromLocalityText = removeCountryFromLocalityText;
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}
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public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {
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this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
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}
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public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {
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this.overwriteExistingSpecimens = overwriteExistingSpecimens;
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}
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public boolean isOverwriteExistingSpecimens(){
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return overwriteExistingSpecimens;
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}
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public boolean isReuseExistingTaxaWhenPossible() {
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return reuseExistingTaxaWhenPossible;
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}
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public void setTeams(Map<String, Team> titleCacheTeam) {
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this.titleCacheTeam = titleCacheTeam;
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}
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public Team getTeam(String titleCache){
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return titleCacheTeam.get(titleCache);
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}
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public Map<String, Team> getTeams(){
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return titleCacheTeam;
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}
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public void setPersons(Map<String, Person> titleCachePerson) {
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this.titleCachePerson = titleCachePerson;
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}
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public Map<String, Person> getPersons(){
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return titleCachePerson;
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}
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public Person getPerson(String titleCache){
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return titleCachePerson.get(titleCache);
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}
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public boolean isAddMediaAsMediaSpecimen(){
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return addMediaAsMediaSpecimen;
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}
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public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){
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this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
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}
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public boolean isIgnoreAuthorship() {
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return ignoreAuthorship;
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}
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public boolean isRemoveCountryFromLocalityText() {
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return removeCountryFromLocalityText;
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}
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public OccurenceQuery getOccurenceQuery(){
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return query;
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}
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public void setOccurenceQuery(OccurenceQuery query){
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this.query = query;
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}
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public boolean isReuseExistingMetaData() {
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return reuseExistingMetaData;
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}
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public void setReuseExistingMetaData(boolean reuseExistingMetaData) {
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this.reuseExistingMetaData = reuseExistingMetaData;
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}
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public void setReportUri(URI reportUri) {
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this.reportUri = reportUri;
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}
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public URI getReportUri() {
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return reportUri;
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}
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@Override
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public String getSourceReferenceTitle(){
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return this.sourceReferenceTitle;
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}
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@Override
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public void setSourceReferenceTitle(String name){
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this.sourceReferenceTitle=name;
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}
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@Override
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public boolean isValid(){
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return true;
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}
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public boolean isDownloadSequenceData() {
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return downloadSequenceData;
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}
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public void setDownloadSequenceData(boolean downloadSequenceData) {
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this.downloadSequenceData = downloadSequenceData;
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}
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}
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