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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.out;
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import java.io.ByteArrayOutputStream;
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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.logging.log4j.LogManager;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.model.common.CdmBase;
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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.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 CsvTaxExportRedlist extends CsvExportBaseRedlist {
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private static final long serialVersionUID = 841703025922543361L;
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private static final Logger logger = LogManager.getLogger(CsvTaxExportRedlist.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 CsvTaxExportRedlist() {
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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(CsvTaxExportStateRedlist state){
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CsvTaxExportConfiguratorRedlist 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<TaxonNode> taxonNodes = assembleTaxonNodeSet(config);
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PrintWriter writer = null;
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ByteArrayOutputStream byteArrayOutputStream;
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try {
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byteArrayOutputStream = config.getByteArrayOutputStream();
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writer = new PrintWriter(byteArrayOutputStream);
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//geographical Filter
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List<TaxonNode> filteredNodes = handleGeographicalFilter(state, selectedAreas, taxonNodes);
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//sorting List
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Collections.sort(filteredNodes, new Comparator<TaxonNode>() {
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@Override
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public int compare(TaxonNode tn1, TaxonNode tn2) {
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Taxon taxon1 = tn1.getTaxon();
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Taxon taxon2 = tn2.getTaxon();
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if(taxon1 != null && taxon2 != null){
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return taxon1.getTitleCache().compareTo(taxon2.getTitleCache());
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}
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else{
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return 0;
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}
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}
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});
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for (TaxonNode node : filteredNodes){
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Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
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CsvTaxRecordRedlist 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, taxon, classification, null, false, false, config);
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record.write(writer);
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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);
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writer.flush();
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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(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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commitTransaction(txStatus);
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return;
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}
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//TODO: Exception handling
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protected Set<TaxonNode> assembleTaxonNodeSet(CsvTaxExportConfiguratorRedlist config){
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Set<TaxonNode> taxonNodes = new HashSet<>();
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if(config != null){
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List<UUID> taxonNodeUuidSet = new ArrayList<>(config.getTaxonNodeUuids());
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List<TaxonNode> loadedNodes = getTaxonNodeService().load(taxonNodeUuidSet, null);
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taxonNodes.addAll(loadedNodes);
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}
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return taxonNodes;
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}
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//TODO: Exception handling
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private CsvTaxRecordRedlist assembleRecord(CsvTaxExportStateRedlist state) {
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if(state!=null){
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CsvTaxExportConfiguratorRedlist config = state.getConfig();
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CsvMetaDataRecordRedlist metaRecord = new CsvMetaDataRecordRedlist(true, fileName, ROW_TYPE);
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state.addMetaRecord(metaRecord);
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CsvTaxRecordRedlist record = new CsvTaxRecordRedlist(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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* Takes positive List of areas and iterates over a given taxon node
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* and their {@link Taxon} to return all {@link Taxon} with the desired
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* geographical attribute.
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*
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* <p><p>
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*
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* If selectedAreas is null all child {@link TaxonNode}s of the given taxon node will be returned.
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* @param state
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*
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* @param selectedAreas
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* @param taxonNodes
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* @return
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*/
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protected List<TaxonNode> handleGeographicalFilter(CsvTaxExportStateRedlist state, List<NamedArea> selectedAreas,
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Set<TaxonNode> taxonNodes) {
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List<TaxonNode> filteredNodes = new ArrayList<>();
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List<TaxonNode> allNodes = new ArrayList<>();
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for (TaxonNode node : taxonNodes){
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if(node.getTaxon()!=null){
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allNodes.add(node);
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}
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allNodes.addAll(getTaxonNodeService().loadChildNodesOfTaxonNode(node, null, true,
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state.getConfig().isIncludeUnpublished(), null));
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}
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//Geographical filter
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if(selectedAreas != null && !selectedAreas.isEmpty() && selectedAreas.size() < 16){
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for (TaxonNode node : allNodes){
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Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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for (TaxonDescription description : descriptions){
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for (DescriptionElementBase el : description.getElements()){
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if (el.isInstanceOf(Distribution.class) ){
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Distribution distribution = CdmBase.deproxy(el, Distribution.class);
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NamedArea area = distribution.getArea();
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for(NamedArea selectedArea:selectedAreas){
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if(selectedArea.getUuid().equals(area.getUuid())){
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filteredNodes.add(node);
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}
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}
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}
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}
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}
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}
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}else{
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filteredNodes = allNodes;
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}
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return filteredNodes;
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}
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/**
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* handles misapplied {@link Taxon}
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* @param taxon
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* @param writer
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* @param classification
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* @param metaRecord
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* @param config
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*/
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private void handleMisapplication(Taxon taxon, PrintWriter writer, Classification classification, CsvTaxRecordRedlist record, CsvTaxExportConfiguratorRedlist config) {
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Set<TaxonRelationship> misappliedNameRels = taxon.getMisappliedNameRelations();
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for (TaxonRelationship misappliedNameRel : misappliedNameRels ){
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// CsvTaxRecordRedlist record = new CsvTaxRecordRedlist(metaRecord, config);
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Taxon misappliedName = misappliedNameRel.getFromTaxon();
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INonViralName name = misappliedName.getName();
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if (! this.recordExists(misappliedName)){
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handleTaxonBase(record, misappliedName, name, taxon, classification,
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misappliedNameRel.getType(), false, false, config);
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record.write(writer);
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this.addExistingRecord(misappliedName);
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}
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}
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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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* @param record the concrete information record
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* @param taxonBase {@link Taxon}
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* @param name
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* @param acceptedTaxon
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* @param parent
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* @param basionym
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* @param isPartial
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* @param isProParte
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* @param config
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* @param type
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*/
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private void handleTaxonBase(CsvTaxRecordRedlist record,TaxonBase<?> taxonBase,
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INonViralName name, Taxon acceptedTaxon, Classification classification,
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RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial,
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CsvTaxExportConfiguratorRedlist config) {
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List<Feature> features = config.getFeatures();
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record.setHeadLinePrinted(config.isHasHeaderLines());
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if(features != null) {
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record.setPrintFeatures(features);
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}
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config.setHasHeaderLines(false);
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record.setDatasetName(classification.getTitleCache());
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record.setScientificName(name.getTitleCache());
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record.setScientificNameId(name.getUuid().toString());
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handleTaxonomicStatus(record, name, relType, isProParte, isPartial);
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//synonyms
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handleSynonyms(record,(Taxon) taxonBase);
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//distribution
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handleDiscriptionData(record, (Taxon) taxonBase);
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if(features!= null) {
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List<List<String>> featureCells = new ArrayList<List<String>>(features.size());
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for(int i = 0; i < features.size(); i++) {
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featureCells.add(new ArrayList<String>());
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}
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handleRelatedRedlistStatus(record, (Taxon)taxonBase, false, featureCells, features);
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handleRelatedRedlistStatus(record, (Taxon)taxonBase, true, featureCells, features);
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}
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return;
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}
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private void handleTaxonomicStatus(
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CsvTaxRecordRedlist record,
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INonViralName name,
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RelationshipTermBase<?> type,
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boolean isProParte,
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boolean isPartial) {
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if (type == null){
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record.setTaxonomicStatus(name.getNameType().acceptedTaxonStatusLabel());
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}else{
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String status = name.getNameType().synonymStatusLabel();
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if (type.equals(SynonymType.HETEROTYPIC_SYNONYM_OF())){
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status = "heterotypicSynonym";
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}else if(type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
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status = "homotypicSynonym";
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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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if (isProParte){
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status = "proParteSynonym";
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}else if (isPartial){
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String message = "Partial synonym is not part of the gbif toxonomic status vocabulary";
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logger.warn(message);
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status = "partialSynonym";
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}
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record.setTaxonomicStatus(status);
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}
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}
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private void handleSynonyms(CsvTaxRecordRedlist record, Taxon taxon) {
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Set<Synonym> synonyms = taxon.getSynonyms();
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ArrayList<String> synonymLabels = new ArrayList<>();
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for (Synonym synonym :synonyms ){
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SynonymType type = synonym.getType();
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if (type == null){ // should not happen
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type = SynonymType.SYNONYM_OF();
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}
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INonViralName name = synonym.getName();
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synonymLabels.add(name.getTitleCache());
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}
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record.setSynonyms(synonymLabels);
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}
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private void handleDiscriptionData(CsvTaxRecordRedlist record, Taxon taxon) {
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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ArrayList<String> distributions = new ArrayList<String>();
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for (TaxonDescription description : descriptions){
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for (DescriptionElementBase el : description.getElements()){
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if (el.isInstanceOf(Distribution.class) ){
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Distribution distribution = CdmBase.deproxy(el, Distribution.class);
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NamedArea area = distribution.getArea();
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distributions.add(area.getTitleCache());
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}
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}
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}
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record.setCountryCode(distributions);
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}
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private void handleRedlistStatus(CsvTaxRecordRedlist record, Taxon taxon, List<List<String>> featureCells, List<Feature> features){
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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for (TaxonDescription description : descriptions){
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for (DescriptionElementBase el : description.getElements()){
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if(el.isInstanceOf(CategoricalData.class)){
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CategoricalData categoricalData = CdmBase.deproxy(el, CategoricalData.class);
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for(State state:categoricalData.getStatesOnly()){
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Feature stateFeature = categoricalData.getFeature();
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// find matching feature and put data into according cell
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for(int i = 0; i < features.size(); i++) {
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if(features.get(i).equals(stateFeature)){
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List<String> cell = featureCells.get(i);
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cell.add(state.toString());
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}
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}
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}
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}else if(el.isInstanceOf(TextData.class)){
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TextData textData = CdmBase.deproxy(el, TextData.class);
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Feature textFeature = textData.getFeature();
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// find matching feature and put data into according cell
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for(int i = 0; i < features.size(); i++) {
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if(features.get(i).equals(textFeature)){
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List<String> cell = featureCells.get(i);
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String text = textData.getText(Language.GERMAN());
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text = text.replaceAll(System.getProperty("line.separator"), "");
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text = text.replaceAll(" ", " ");
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cell.add(text);
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}
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}
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}
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}
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}
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record.setFeatures(featureCells);
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}
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private void handleRelatedRedlistStatus(CsvTaxRecordRedlist record, Taxon taxon, boolean relationFrom, List<List<String>> featureCells, List<Feature> features) {
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if (relationFrom) {
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handleRedlistStatus(record, taxon, featureCells, features);
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}
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389
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Set<TaxonRelationship> taxRels;
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if(relationFrom){
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taxRels = taxon.getRelationsFromThisTaxon();
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}else{
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taxRels = taxon.getRelationsToThisTaxon();
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}
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for (TaxonRelationship taxRel:taxRels){
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if(taxRel.getType().equals(TaxonRelationshipType.CONGRUENT_TO())){
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Taxon relatedTaxon;
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if(relationFrom){
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relatedTaxon = taxRel.getToTaxon();
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}else{
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relatedTaxon = taxRel.getFromTaxon();
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}
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handleRedlistStatus(record, relatedTaxon, featureCells, features);
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}
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}
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}
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408
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409
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@Override
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protected boolean doCheck(CsvTaxExportStateRedlist state) {
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boolean result = true;
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logger.warn("No check implemented for " + this.ioName);
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return result;
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}
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415
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|
416
|
@Override
|
417
|
protected boolean isIgnore(CsvTaxExportStateRedlist state) {
|
418
|
return ! state.getConfig().isDoTaxa();
|
419
|
}
|
420
|
|
421
|
|
422
|
|
423
|
|
424
|
}
|