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/**
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* Copyright (C) 2009 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.dwca.out;
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import java.io.PrintWriter;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTime;
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import org.joda.time.Partial;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.stream.terms.TermUri;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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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.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.ICdmBase;
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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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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.location.Point;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
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/**
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* @author a.mueller
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\* @since 20.04.2011
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*
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*/
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public abstract class DwcaRecordBase {
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private static final Logger logger = Logger.getLogger(DwcaRecordBase.class);
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//TODO Collection_SEPARATOR
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protected static final CharSequence COLLECTION_SEPARATOR = "@";
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// protected static final String FIELD_ENCLOSER = "\"";
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protected static final boolean IS_FIRST = false;
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protected static final boolean IS_NOT_FIRST = true;
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// protected static final String SEP = ",";
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protected Map<String, URI> knownFields = new HashMap<>();
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protected Set<TermUri> knownTermFields = new HashSet<>();
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protected abstract void doWrite(DwcaTaxExportState state, PrintWriter writer);
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public void write(DwcaTaxExportState state, PrintWriter writer){
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if(writer == null){
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writeCsv(state);
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return;
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}
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if (this.count == 1 && state.getConfig().isHasHeaderLines() & this.isWritingHeader == false){
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this.isWritingHeader = true;
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write(state, writer);
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this.isWritingHeader = false;
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}
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doWrite(state, writer);
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}
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public void writeCsv(DwcaTaxExportState state){
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state.getResult().addWarning(this.getClass().getName() + ".writeCsv() not yet implemented!");
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}
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protected abstract void registerKnownFields();
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protected int count;
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protected boolean isWritingHeader; //should better be moved in state
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private DwcaMetaDataRecord metaDataRecord;
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protected DwcaTaxExportConfigurator config;
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private Integer id;
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private UUID uuid;
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protected DwcaRecordBase(DwcaMetaDataRecord metaDataRecord, DwcaTaxExportConfigurator config){
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this.metaDataRecord = metaDataRecord;
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this.count = metaDataRecord.inc();
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this.config = config;
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}
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public void setId(Integer id) {
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this.id = id;
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}
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public Integer getId() {
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return id;
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}
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public void setUuid(UUID uuid) {
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this.uuid = uuid;
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}
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public UUID getUuid() {
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return uuid;
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}
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protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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printNotes(notes, writer, addSeparator, fieldKey.getUriString());
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}
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protected void printNotes(Set<Annotation> notes, PrintWriter writer, boolean addSeparator, String fieldKey) {
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//FIXME handles annotations correctly
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String value = null;
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print(value, writer, addSeparator, fieldKey);
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}
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// protected void print(Object object, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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// print(object == null ? null : object.toString(), writer, addSeparator, fieldKey);
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// }
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protected void print(DwcaId dwcaId, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(dwcaId == null ? null : dwcaId.getId(), writer, addSeparator, fieldKey);
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}
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protected void print(UUID uuid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(uuid == null ? null : uuid.toString(), writer, addSeparator, fieldKey);
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}
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protected void print(AgentBase<?> agent, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(agent, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(AgentBase<?> agent, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(agent == null ? null : getAgent(agent), writer, addSeparator, fieldKey);
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}
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protected void print(Language language, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(language, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(Language language, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(language == null ? null : getLanguage(language), writer, addSeparator, fieldKey);
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}
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protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(lsid, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(LSID lsid, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(lsid == null ? null : String.valueOf(lsid.toString()), writer, addSeparator, fieldKey);
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}
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protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(rights, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(Set<Rights> rights, PrintWriter writer, boolean addSeparator, String fieldKey) {
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String rightsString = getRights(rights);
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print(rightsString, writer, addSeparator, fieldKey);
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}
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protected void print(URI uri, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(uri, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(URI uri, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(uri == null ? null : String.valueOf(uri), writer, addSeparator, fieldKey);
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}
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protected void print(Point point, PrintWriter writer, boolean addSeparator, TermUri latitudeKey, TermUri longitudeKey) {
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print(point, writer, addSeparator, latitudeKey.getUriString(), longitudeKey.getUriString());
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}
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protected void print(Point point, PrintWriter writer, boolean addSeparator, String latitudeKey, String longitudeKey) {
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if (point == null){
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String toPrint = null;
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print(toPrint, writer, addSeparator, latitudeKey);
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print(toPrint, writer, addSeparator, longitudeKey);
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}else{
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String latitude = point.getLatitude().toString();
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String longitude = point.getLongitude().toString();
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print(latitude, writer, addSeparator, latitudeKey);
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print(longitude, writer, addSeparator, longitudeKey);
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}
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}
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protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(boolValue, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(Boolean boolValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(boolValue == null ? null : String.valueOf(boolValue), writer, addSeparator, fieldKey);
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}
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protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(intValue, writer, addSeparator, fieldKey.getUriString());
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}
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protected void print(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
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}
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protected void printId(Integer intValue, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(intValue == null ? null : String.valueOf(intValue), writer, addSeparator, fieldKey);
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}
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protected void printId(UUID uuid, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(uuid == null ? null : String.valueOf(uuid), writer, addSeparator, fieldKey);
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}
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protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey) {
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print(value, writer, addSeparator, fieldKey, null);
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}
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protected void print(String value, PrintWriter writer, boolean addSeparator, TermUri fieldKey, String defaultValue) {
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print(value, writer, addSeparator, fieldKey.getUriString(), defaultValue);
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}
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protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey) {
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print(value, writer, addSeparator, fieldKey, null);
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}
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protected void print(String value, PrintWriter writer, boolean addSeparator, String fieldKey, String defaultValue) {
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if (isWritingHeader == true){
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printHeader(writer, addSeparator, fieldKey, defaultValue);
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return;
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}
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if (count == 1 && addSeparator == IS_NOT_FIRST){
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registerFieldKey(URI.create(fieldKey), defaultValue);
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}
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if (StringUtils.isBlank(defaultValue)){
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String strToPrint = addSeparator ? config.getFieldsTerminatedBy() : "";
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if (StringUtils.isNotBlank(value)){
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//Replace quotes by double quotes
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value = value.replace("\"", "\"\"");
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value = value.replace(config.getLinesTerminatedBy(), "\\r");
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//replace all line brakes according to best practices: http://code.google.com/p/gbif-ecat/wiki/BestPractices
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value = value.replace("\r\n", "\\r");
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value = value.replace("\r", "\\r");
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value = value.replace("\n", "\\r");
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strToPrint += config.getFieldsEnclosedBy() + value + config.getFieldsEnclosedBy();
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}
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writer.print(strToPrint);
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}
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}
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/**
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* @param writer
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* @param addSeparator
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* @param fieldKey
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*/
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private void printHeader(PrintWriter writer, boolean addSeparator, String fieldKey, String defaultValue) {
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if (StringUtils.isBlank(defaultValue)){
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String strToPrint = addSeparator ? config.getFieldsTerminatedBy() : "";
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int pos = fieldKey.lastIndexOf("/");
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if (pos != -1){
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fieldKey = fieldKey.substring(pos + 1);
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}
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strToPrint += fieldKey ;
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writer.print(strToPrint);
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}
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}
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protected void line(DwcaTaxExportState state, String[] csvLine, DwcaTaxExportFile table, TermUri termUri, Set<Rights> rights) {
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String rightsStr = getRights(rights);
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if (rights != null){ line(state, csvLine, table, termUri, rightsStr);}
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}
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protected void line(DwcaTaxExportState state, String[] csvLine, DwcaTaxExportFile table, TermUri termUri, Language language) {
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if (language != null){ line(state, csvLine, table, termUri, getLanguage(language));}
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}
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protected void line(DwcaTaxExportState state, String[] csvLine, DwcaTaxExportFile table, TermUri termUri, DwcaId id) {
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if (id != null){ line(state, csvLine, table, termUri, id.getId());}
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}
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protected void line(DwcaTaxExportState state, String[] csvLine, DwcaTaxExportFile table, TermUri termUri, UUID uuid) {
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if (uuid != null){ line(state, csvLine, table, termUri, uuid.toString());}
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}
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protected void line(DwcaTaxExportState state, String[] csvLine, DwcaTaxExportFile table, TermUri termUri, String string) {
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line(state, csvLine, table, termUri, string, null);
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}
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protected void line(DwcaTaxExportState state, String[] csvLine, DwcaTaxExportFile table, TermUri termUri, String string, String defaultValue) {
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try {
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csvLine[table.getIndex(termUri)] = string;
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if (count == 1 && table.getIndex(termUri) != 0){
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registerFieldKey(termUri.getUri(), defaultValue);
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}
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} catch (Exception e) {
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String message = "Unhandled exception when handling " + (termUri != null ? termUri.getUriString() : "undefined") + ": " + e.getMessage();
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state.getResult().addException(e, message);
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}
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}
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protected void registerFieldKey(URI key, String defaultValue) {
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this.metaDataRecord.addFieldEntry(key, defaultValue);
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}
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protected String getRights(Rights rights) {
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if (rights == null){
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return "";
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}else{
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//TODO
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return rights.getAbbreviatedText();
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}
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}
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protected String getLanguage(Language language) {
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if (language == null){
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return "";
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}else{
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//TODO
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return language.getIso639_2();
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}
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}
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protected String getDate(DateTime date) {
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315
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if (date == null){
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return "";
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}else{
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//TODO
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return date.toString();
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}
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}
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protected String getNomStatus(NomenclaturalStatusType nomStatus) {
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String result = DwcaTaxExportTransformer.transformToGbifNomStatus(nomStatus);
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if (result == null){
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if (nomStatus == null){
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return "";
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}else{
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return nomStatus.getLabel();
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}
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}else{
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return result;
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}
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}
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protected String getNomCode(NomenclaturalCode nomCode) {
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337
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if (nomCode == null){
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return "";
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}else{
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//TODO
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return nomCode.getTitleCache();
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}
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343
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}
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344
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345
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protected String getRank(Rank rank) {
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346
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String result = DwcaTaxExportTransformer.transformToGbifRank(rank);
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347
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if (result == null){
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348
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if (rank == null){
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349
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return "";
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}else{
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351
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return rank.getLabel();
|
|
352
|
}
|
|
353
|
}else{
|
|
354
|
return result;
|
|
355
|
}
|
|
356
|
}
|
|
357
|
|
|
358
|
protected String getSex(DefinedTerm sex) {
|
|
359
|
String result = DwcaTaxExportTransformer.transformToGbifSex(sex);
|
|
360
|
if (result == null){
|
|
361
|
if (sex == null){
|
|
362
|
return "";
|
|
363
|
}else{
|
|
364
|
return sex.getLabel();
|
|
365
|
}
|
|
366
|
}else{
|
|
367
|
return result;
|
|
368
|
}
|
|
369
|
}
|
|
370
|
|
|
371
|
protected String getLifeStage(DefinedTerm stage) {
|
|
372
|
String result = DwcaTaxExportTransformer.transformToGbifLifeStage(stage);
|
|
373
|
if (result == null){
|
|
374
|
if (stage == null){
|
|
375
|
return "";
|
|
376
|
}else{
|
|
377
|
return stage.getLabel();
|
|
378
|
}
|
|
379
|
}else{
|
|
380
|
return result;
|
|
381
|
}
|
|
382
|
}
|
|
383
|
|
|
384
|
protected String getOccurrenceStatus(PresenceAbsenceTerm status) {
|
|
385
|
String result = DwcaTaxExportTransformer.transformToGbifOccStatus(status);
|
|
386
|
if (result == null){
|
|
387
|
if (status == null){
|
|
388
|
return "";
|
|
389
|
}else{
|
|
390
|
return status.getLabel();
|
|
391
|
}
|
|
392
|
}else{
|
|
393
|
return result;
|
|
394
|
}
|
|
395
|
}
|
|
396
|
|
|
397
|
protected String getEstablishmentMeans(PresenceAbsenceTerm status) {
|
|
398
|
String result = DwcaTaxExportTransformer.transformToGbifEstablishmentMeans(status);
|
|
399
|
if (result == null){
|
|
400
|
if (status == null){
|
|
401
|
return "";
|
|
402
|
}else{
|
|
403
|
return status.getLabel();
|
|
404
|
}
|
|
405
|
}else{
|
|
406
|
return result;
|
|
407
|
}
|
|
408
|
}
|
|
409
|
|
|
410
|
|
|
411
|
|
|
412
|
protected String getAgent(AgentBase<?> agent) {
|
|
413
|
if (agent == null){
|
|
414
|
return "";
|
|
415
|
}else{
|
|
416
|
//TODO
|
|
417
|
return agent.getTitleCache();
|
|
418
|
}
|
|
419
|
}
|
|
420
|
|
|
421
|
|
|
422
|
protected String getFeature(Feature feature) {
|
|
423
|
if (feature == null){
|
|
424
|
return "";
|
|
425
|
}else{
|
|
426
|
//TODO
|
|
427
|
return feature.getTitleCache();
|
|
428
|
}
|
|
429
|
}
|
|
430
|
|
|
431
|
|
|
432
|
protected String getTimePeriod(TimePeriod period) {
|
|
433
|
if (period == null){
|
|
434
|
return "";
|
|
435
|
}else{
|
|
436
|
//TODO
|
|
437
|
return period.toString();
|
|
438
|
}
|
|
439
|
}
|
|
440
|
|
|
441
|
protected String getTimePeriodPart(TimePeriod period, boolean useEnd) {
|
|
442
|
if (period == null){
|
|
443
|
return "";
|
|
444
|
}else{
|
|
445
|
Partial date = useEnd? period.getEnd(): period.getStart();
|
|
446
|
if (date == null){
|
|
447
|
return "";
|
|
448
|
}else{
|
|
449
|
//TODO
|
|
450
|
return date.toString();
|
|
451
|
}
|
|
452
|
}
|
|
453
|
}
|
|
454
|
|
|
455
|
protected String getRights(Set<Rights> rights) {
|
|
456
|
if (rights == null || rights.isEmpty()){
|
|
457
|
return null;
|
|
458
|
}else{
|
|
459
|
String result = null;
|
|
460
|
for (Rights right: rights){
|
|
461
|
//TODO usi uri if available ??
|
|
462
|
String message = "Rights not yet fully implemented";
|
|
463
|
logger.warn(message);
|
|
464
|
result = CdmUtils.concat(COLLECTION_SEPARATOR, result, right.getAbbreviatedText());
|
|
465
|
}
|
|
466
|
return result;
|
|
467
|
}
|
|
468
|
}
|
|
469
|
|
|
470
|
|
|
471
|
protected String getDesignationType(TypeDesignationStatusBase<?> status) {
|
|
472
|
if (status == null){
|
|
473
|
return "";
|
|
474
|
}
|
|
475
|
String result;
|
|
476
|
if (status.isInstanceOf(SpecimenTypeDesignationStatus.class)){
|
|
477
|
SpecimenTypeDesignationStatus specStatus = CdmBase.deproxy(status, SpecimenTypeDesignationStatus.class);
|
|
478
|
result = DwcaTaxExportTransformer.transformSpecimenTypeStatusToGbif(specStatus);
|
|
479
|
}else{
|
|
480
|
NameTypeDesignationStatus nameStatus = CdmBase.deproxy(status, NameTypeDesignationStatus.class);
|
|
481
|
result = DwcaTaxExportTransformer.transformNameTypeStatusToGbif(nameStatus);
|
|
482
|
}
|
|
483
|
if (result == null){
|
|
484
|
return status.getLabel();
|
|
485
|
}else{
|
|
486
|
return result;
|
|
487
|
}
|
|
488
|
}
|
|
489
|
|
|
490
|
|
|
491
|
|
|
492
|
|
|
493
|
protected void addKnownField(String string, String uri) throws URISyntaxException {
|
|
494
|
this.knownFields.put(string, new URI(uri));
|
|
495
|
}
|
|
496
|
|
|
497
|
protected void addKnownField(TermUri term) throws URISyntaxException {
|
|
498
|
this.knownTermFields.add(term);
|
|
499
|
}
|
|
500
|
|
|
501
|
|
|
502
|
//*************** CSV Methods ******************/
|
|
503
|
|
|
504
|
/**
|
|
505
|
* @param state
|
|
506
|
* @param taxon
|
|
507
|
* @return
|
|
508
|
*/
|
|
509
|
protected String getId(DwcaTaxExportState state, ICdmBase cdmBase) {
|
|
510
|
if (cdmBase == null){
|
|
511
|
return "";
|
|
512
|
}
|
|
513
|
//TODO make configurable
|
|
514
|
return cdmBase.getUuid().toString();
|
|
515
|
}
|
|
516
|
}
|