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/**
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* Copyright (C) 2007 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.csv.redlist.demo;
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import java.io.ByteArrayOutputStream;
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import java.io.FileNotFoundException;
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import java.io.PrintWriter;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashSet;
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import java.util.List;
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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.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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/**
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* @author a.oppermann
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* @since 18.10.2012
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*/
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@Component
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public class CsvDemoExport extends CsvDemoBase {
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private static final long serialVersionUID = 8265935377927091897L;
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private static final Logger logger = LogManager.getLogger(CsvDemoExport.class);
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private static final String ROW_TYPE = "http://rs.tdwg.org/dwc/terms/Taxon";
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private static final String fileName = "RedlistCoreTax.csv";
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public CsvDemoExport() {
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super();
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this.ioName = this.getClass().getSimpleName();
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}
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/** Retrieves data from a CDM DB and serializes them CDM to CSV.
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* Starts with root taxa and traverses the classification to retrieve
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* children taxa, synonyms, relationships, descriptive data, red list
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* status (features).
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* Taxa that are not part of the classification are not found.
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*
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* @param exImpConfig
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* @param dbname
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* @param filename
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*/
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@Override
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protected void doInvoke(CsvDemoExportState state){
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CsvDemoExportConfigurator config = state.getConfig();
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TransactionStatus txStatus = startTransaction(true);
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List<NamedArea> selectedAreas = config.getNamedAreas();
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Set<Classification> classificationSet = assembleClassificationSet(config);
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IProgressMonitor progressMonitor = null;
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if(config.getProgressMonitor() != null) {
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progressMonitor = config.getProgressMonitor();
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}
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PrintWriter writer = null;
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try {
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//json/xml result list
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List<CsvDemoRecord> recordList = null;
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if(config.getRecordList() != null){
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recordList = config.getRecordList();
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performJsonXMLPagination(state, config, txStatus, classificationSet, recordList);
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}
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try {
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switch(config.getTarget()) {
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case FILE:
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if(!config.getDestination().isDirectory()){
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writer = new PrintWriter(config.getDestination());
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}
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break;
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case EXPORT_DATA:
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exportStream = new ByteArrayOutputStream();
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writer = new PrintWriter(exportStream);
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break;
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default :
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break;
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}
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if(writer != null) {
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performCSVExport(state, config, txStatus, classificationSet, progressMonitor, writer);
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}
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} catch (FileNotFoundException e) {
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e.printStackTrace();
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}
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} catch (ClassCastException e) {
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e.printStackTrace();
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}
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finally{
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if (exportStream != null){
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state.getResult().addExportData(getByteArray());
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}
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if(writer != null){
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writer.close();
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}
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this.clearExistingRecordIds();
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}
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return;
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}
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private void performJsonXMLPagination(CsvDemoExportState state, CsvDemoExportConfigurator config,
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TransactionStatus txStatus, Set<Classification> classificationSet, List<CsvDemoRecord> recordList) {
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Classification classification = null;
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for(Classification c : classificationSet){
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classification = c;
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//this sets the total amount of records for pagination
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config.setTaxonNodeListSize(getTaxonNodeService().countAllNodesForClassification(c));
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}
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//calculate pagination
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int start = config.getPageSize() * config.getPageNumber();
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List<TaxonNode> result = getTaxonNodeService().listAllNodesForClassification(classification, start, config.getPageSize());
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for (TaxonNode node : result){
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Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
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CsvDemoRecord record = assembleRecord(state);
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INonViralName name = taxon.getName();
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config.setClassificationTitleCache(classification.getTitleCache());
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if (! this.recordExists(taxon)){
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handleTaxonBase(record, taxon, name, classification, null, false, false, config, node);
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recordList.add(record);
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this.addExistingRecord(taxon);
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}
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}
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commitTransaction(txStatus);
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}
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private void performCSVExport(CsvDemoExportState state, CsvDemoExportConfigurator config,
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TransactionStatus txStatus, Set<Classification> classificationSet, IProgressMonitor progressMonitor,
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PrintWriter writer) {
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//obtain chuncks of taxonNodes
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int totalWork = 0;
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int work = 0;
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int limit = 500;
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int end = 500;
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int start = 0;
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//TODO: Questionable if this information is really necessary, with respect to memory usage
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Classification classification = null;
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for(Classification c : classificationSet){
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classification = c;
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totalWork = getTaxonNodeService().countAllNodesForClassification(c);
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if(progressMonitor != null) {
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progressMonitor.beginTask("", totalWork);
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}
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List<TaxonNode> result = new ArrayList<>();
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int totalNodes = getTaxonNodeService().count(TaxonNode.class);
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for(int i = 0 ; i < totalNodes; i++){
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//geographical Filter
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// List<TaxonNode> taxonNodes = handleGeographicalFilter(state, classificationSet, config, limit, start);
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result = getTaxonNodeService().listAllNodesForClassification(classification, start, limit);
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logger.info(result.size());
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for (TaxonNode node : result){
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Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
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CsvDemoRecord record = assembleRecord(state);
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INonViralName name = taxon.getName();
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// Classification classification = node.getClassification();
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config.setClassificationTitleCache(classification.getTitleCache());
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if (! this.recordExists(taxon)){
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handleTaxonBase(record, taxon, name, classification, null, false, false, config, node);
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//if(config.getDestination() != null){
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record.write(writer);
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//}
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this.addExistingRecord(taxon);
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}
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//misapplied names
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//handleMisapplication(taxon, writer, classification, record, config, node);
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if(progressMonitor !=null) {
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if(work < totalWork-1) {
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progressMonitor.worked(1);
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}
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work++;
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}
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}
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if(writer != null){
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writer.flush();
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commitTransaction(txStatus);
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txStatus = startTransaction(true);
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}
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//get next 1000 results
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if(result.size()%limit == 0){
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//increase only once to avoid same row
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if(i==0){
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start++;
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}
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start = start + limit;
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end = end + limit;
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result = null;
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}else{
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break;
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}
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}
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}
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}
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//TODO: Exception handling
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/**
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*
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* @param config
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*/
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protected Set<Classification> assembleClassificationSet(CsvDemoExportConfigurator config){
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if(config != null){
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Set<UUID> classificationUuidSet = config.getClassificationUuids();
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List<Classification> classificationList = getClassificationService().find(classificationUuidSet);
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Set<Classification> classificationSet = new HashSet<>();
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classificationSet.addAll(classificationList);
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return classificationSet;
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}
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return null;
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}
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//TODO: Exception handling
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/**
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* @param state
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*/
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private CsvDemoRecord assembleRecord(CsvDemoExportState state) {
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if(state!=null){
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CsvDemoExportConfigurator config = state.getConfig();
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CsvDemoMetaDataRecord metaRecord = new CsvDemoMetaDataRecord(true, fileName, ROW_TYPE);
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state.addMetaRecord(metaRecord);
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CsvDemoRecord record = new CsvDemoRecord(metaRecord, config);
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return record;
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}
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return null;
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}
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/**
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* handles the information record for the actual {@link Taxon} including {@link Classification classification}, Taxon Name, Taxon ID,
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* Taxon Status, Synonyms, {@link Feature features} data
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*
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* @param record the concrete information record
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*/
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private void handleTaxonBase(CsvDemoRecord record, TaxonBase<?> taxonBase,
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INonViralName name, Classification classification,
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RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial,
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CsvDemoExportConfigurator config, TaxonNode node) {
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Taxon taxon = (Taxon) taxonBase;
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List<Feature> features = config.getFeatures();
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if(config.getDestination() != null){
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record.setHeadLinePrinted(config.isHasHeaderLines());
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if(config.isRedlistFeatures()){
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if(features != null){
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record.setPrintFeatures(features);
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}
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}
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config.setHasHeaderLines(false);
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}
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if(config.isClassification()){
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record.setDatasetName(classification.getTitleCache());
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}
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if(config.isTaxonName()){
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record.setScientificName(name.getNameCache());
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}
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if(config.isTaxonNameID()){
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record.setScientificNameId(name.getUuid().toString());
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}
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if(config.isAuthor()){
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String authorshipCache = name.getAuthorshipCache();
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if(authorshipCache == null){
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authorshipCache = "";
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}
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record.setAuthorName(authorshipCache);
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}
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if(config.isRank()){
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String rank;
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if(taxon.getName().getRank() == null){
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rank = "";
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}else{
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rank = taxon.getName().getRank().toString();
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}
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record.setRank(rank);
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}
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if(config.isTaxonStatus()){
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handleTaxonomicStatus(record, name, relType, isProParte, isPartial);
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}
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if(config.isAcceptedName()){
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//TODO write routine for accepted Name
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}
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if(config.isTaxonConceptID()){
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UUID taxonUuid = taxonBase.getUuid();
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if(taxonUuid == null){
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taxonUuid = UUID.fromString("");
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}
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record.setTaxonConceptID(taxonUuid.toString());
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}
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337
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if(config.isParentID()){
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String parentUUID;
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if(node.getParent().getTaxon() == null){
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parentUUID = "";
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}else{
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parentUUID = node.getParent().getTaxon().getUuid().toString();
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}
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record.setParentUUID(parentUUID);
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}
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346
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if(config.isLastChange()){
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String lastChange;
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348
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if(taxon.getUpdated() == null){
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lastChange = "";
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}else{
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lastChange = taxon.getUpdated().toString();
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}
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record.setLastChange(lastChange);
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}
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355
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if(config.isSynonyms()){
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handleSynonyms(record,taxon);
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}
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358
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if(config.isDistributions()){
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359
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handleDiscriptionData(record, taxon);
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360
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}
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361
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if(config.isRedlistFeatures()){
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362
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if(features!= null) {
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363
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364
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List<List<String>> featureCells = new ArrayList<>(features.size());
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365
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for(int i = 0; i < features.size(); i++) {
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366
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featureCells.add(new ArrayList<>());
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367
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}
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368
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handleRelatedRedlistStatus(record, taxon, false, featureCells, features);
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handleRelatedRedlistStatus(record, taxon, true, featureCells, features);
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370
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}
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371
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}
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372
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373
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if(config.isExternalID()){
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374
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Set<IdentifiableSource> sources = taxonBase.getSources();
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375
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for(IdentifiableSource source:sources){
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376
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Reference citation = source.getCitation();
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377
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/*
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378
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* TODO: handle this more generic.
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379
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* see ticket #4040
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380
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*
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381
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*/
|
382
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if(citation.getId() == 22){
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383
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String idInSource = source.getIdInSource();
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384
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if(idInSource == null){
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385
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idInSource = "";
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386
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}
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387
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record.setExternalID(idInSource);
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388
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389
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}
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390
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}
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391
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}
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392
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}
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393
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|
394
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private void handleTaxonomicStatus(
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395
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CsvDemoRecord record,
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396
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INonViralName name,
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397
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RelationshipTermBase<?> type,
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398
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boolean isProParte,
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399
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boolean isPartial) {
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400
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if (type == null && name.getNameType()!= null && name.getNameType().acceptedTaxonStatusLabel() != null){
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401
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String acceptedTaxonStatusLabel = name.getNameType().acceptedTaxonStatusLabel();
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402
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if(StringUtils.isEmpty(acceptedTaxonStatusLabel)){
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403
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acceptedTaxonStatusLabel="";
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404
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}
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405
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record.setTaxonomicStatus(acceptedTaxonStatusLabel);
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406
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}else if(name.getNameType() != null && name.getNameType().synonymStatusLabel() != null){
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407
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String status = name.getNameType().synonymStatusLabel();
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408
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if (type.equals(SynonymType.HETEROTYPIC_SYNONYM_OF())){
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status = "heterotypicSynonym";
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410
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}else if(type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
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status = "homotypicSynonym";
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412
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}else if(type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
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status = "misapplied";
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}else if(type.equals(TaxonRelationshipType.PRO_PARTE_MISAPPLIED_NAME_FOR())){
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status = "proParteMisapplied";
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}
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417
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if (isProParte){
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418
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status = "proParteSynonym";
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419
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}else if (isPartial){
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420
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String message = "Partial synonym is not part of the gbif toxonomic status vocabulary";
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421
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logger.warn(message);
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status = "partialSynonym";
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423
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}
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424
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425
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record.setTaxonomicStatus(status);
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426
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}
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427
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}
|
428
|
|
429
|
/**
|
430
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* This method concatenates several synonyms in a list.
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431
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*/
|
432
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private void handleSynonyms(CsvDemoRecord record, Taxon taxon) {
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433
|
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434
|
Set<Synonym> synonyms = taxon.getSynonyms();
|
435
|
ArrayList<String> synonymLabels = new ArrayList<>();
|
436
|
for (Synonym synonym :synonyms ){
|
437
|
SynonymType type = synonym.getType();
|
438
|
if (type == null){ // should not happen
|
439
|
type = SynonymType.SYNONYM_OF();
|
440
|
}
|
441
|
INonViralName name = synonym.getName();
|
442
|
synonymLabels.add(name.getTitleCache());
|
443
|
}
|
444
|
record.setSynonyms(synonymLabels);
|
445
|
}
|
446
|
|
447
|
private void handleDiscriptionData(CsvDemoRecord record, Taxon taxon) {
|
448
|
|
449
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
450
|
ArrayList<String> distributions = new ArrayList<String>();
|
451
|
for (TaxonDescription description : descriptions){
|
452
|
for (DescriptionElementBase el : description.getElements()){
|
453
|
if (el.isInstanceOf(Distribution.class) ){
|
454
|
Distribution distribution = CdmBase.deproxy(el, Distribution.class);
|
455
|
NamedArea area = distribution.getArea();
|
456
|
distributions.add(area.getTitleCache());
|
457
|
}
|
458
|
|
459
|
}
|
460
|
}
|
461
|
record.setCountryCode(distributions);
|
462
|
}
|
463
|
|
464
|
private void handleRedlistStatus(CsvDemoRecord record, Taxon taxon, List<List<String>> featureCells, List<Feature> features){
|
465
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
466
|
|
467
|
for (TaxonDescription description : descriptions){
|
468
|
for (DescriptionElementBase el : description.getElements()){
|
469
|
if(el.isInstanceOf(CategoricalData.class)){
|
470
|
CategoricalData categoricalData = CdmBase.deproxy(el, CategoricalData.class);
|
471
|
for(State state:categoricalData.getStatesOnly()){
|
472
|
Feature stateFeature = categoricalData.getFeature();
|
473
|
// find matching feature and put data into according cell
|
474
|
for(int i = 0; i < features.size(); i++) {
|
475
|
if(features.get(i).equals(stateFeature)){
|
476
|
List<String> cell = featureCells.get(i);
|
477
|
cell.add(state.toString());
|
478
|
}
|
479
|
}
|
480
|
}
|
481
|
}else if(el.isInstanceOf(TextData.class)){
|
482
|
TextData textData = CdmBase.deproxy(el, TextData.class);
|
483
|
Feature textFeature = textData.getFeature();
|
484
|
// find matching feature and put data into according cell
|
485
|
for(int i = 0; i < features.size(); i++) {
|
486
|
if(features.get(i).equals(textFeature)){
|
487
|
List<String> cell = featureCells.get(i);
|
488
|
String text = textData.getText(Language.GERMAN());
|
489
|
text = text.replaceAll(System.getProperty("line.separator"), "");
|
490
|
text = text.replaceAll(" ", " ");
|
491
|
cell.add(text);
|
492
|
|
493
|
}
|
494
|
}
|
495
|
}
|
496
|
}
|
497
|
}
|
498
|
record.setFeatures(featureCells);
|
499
|
}
|
500
|
|
501
|
private void handleRelatedRedlistStatus(CsvDemoRecord record, Taxon taxon, boolean relationFrom, List<List<String>> featureCells, List<Feature> features) {
|
502
|
|
503
|
if (relationFrom) {
|
504
|
handleRedlistStatus(record, taxon, featureCells, features);
|
505
|
}
|
506
|
|
507
|
Set<TaxonRelationship> taxRels;
|
508
|
if(relationFrom){
|
509
|
taxRels = taxon.getRelationsFromThisTaxon();
|
510
|
}else{
|
511
|
taxRels = taxon.getRelationsToThisTaxon();
|
512
|
}
|
513
|
for (TaxonRelationship taxRel:taxRels){
|
514
|
if(taxRel.getType().equals(TaxonRelationshipType.CONGRUENT_TO())){
|
515
|
Taxon relatedTaxon;
|
516
|
if(relationFrom){
|
517
|
relatedTaxon = taxRel.getToTaxon();
|
518
|
}else{
|
519
|
relatedTaxon = taxRel.getFromTaxon();
|
520
|
}
|
521
|
handleRedlistStatus(record, relatedTaxon, featureCells, features);
|
522
|
}
|
523
|
}
|
524
|
}
|
525
|
|
526
|
private void sortTaxonNodes(List<TaxonNode> taxonNodes) {
|
527
|
Collections.sort(taxonNodes, new Comparator<TaxonNode>() {
|
528
|
|
529
|
@Override
|
530
|
public int compare(TaxonNode tn1, TaxonNode tn2) {
|
531
|
Taxon taxon1 = tn1.getTaxon();
|
532
|
Taxon taxon2 = tn2.getTaxon();
|
533
|
if(taxon1 != null && taxon2 != null){
|
534
|
return taxon1.getTitleCache().compareTo(taxon2.getTitleCache());
|
535
|
}
|
536
|
else{
|
537
|
return 0;
|
538
|
}
|
539
|
}
|
540
|
});
|
541
|
}
|
542
|
|
543
|
@Override
|
544
|
protected boolean doCheck(CsvDemoExportState state) {
|
545
|
boolean result = true;
|
546
|
logger.warn("No check implemented for " + this.ioName);
|
547
|
return result;
|
548
|
}
|
549
|
|
550
|
@Override
|
551
|
protected boolean isIgnore(CsvDemoExportState state) {
|
552
|
return ! state.getConfig().isDoTaxa();
|
553
|
}
|
554
|
|
555
|
@Override
|
556
|
public byte[] getByteArray() {
|
557
|
if (this.exportStream != null){
|
558
|
return this.exportStream.toByteArray();
|
559
|
}
|
560
|
return null;
|
561
|
}
|
562
|
}
|