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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.markup;
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import java.net.MalformedURLException;
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import java.net.URL;
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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 javax.xml.stream.Location;
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import javax.xml.stream.XMLEventReader;
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import javax.xml.stream.XMLStreamException;
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import javax.xml.stream.events.Attribute;
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import javax.xml.stream.events.StartElement;
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import javax.xml.stream.events.XMLEvent;
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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 eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
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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.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeStatus;
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/**
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* @author a.mueller
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*/
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public class MarkupDocumentImportNoComponent extends MarkupImportBase {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(MarkupDocumentImportNoComponent.class);
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private final MarkupKeyImport keyImport;
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private final MarkupModsImport modsImport;
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private final MarkupSpecimenImport specimenImport;
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private final MarkupNomenclatureImport nomenclatureImport;
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public MarkupDocumentImportNoComponent(MarkupDocumentImport docImport) {
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super(docImport);
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this.keyImport = new MarkupKeyImport(docImport);
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this.specimenImport = new MarkupSpecimenImport(docImport);
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this.nomenclatureImport = new MarkupNomenclatureImport(docImport, specimenImport);
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this.modsImport = new MarkupModsImport(docImport);
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this.featureImport = new MarkupFeatureImport(docImport, specimenImport, nomenclatureImport, keyImport);
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}
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public void doInvoke(MarkupImportState state) throws XMLStreamException {
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XMLEventReader reader = state.getReader();
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// publication (= root element)
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String elName = PUBLICATION;
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boolean hasPublication = false;
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while (reader.hasNext()) {
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XMLEvent nextEvent = reader.nextEvent();
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if (isStartingElement(nextEvent, elName)) {
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handlePublication(state, reader, nextEvent, elName);
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hasPublication = true;
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} else if (nextEvent.isEndDocument()) {
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if (!hasPublication) {
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String message = "No publication root element found";
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fireWarningEvent(message, nextEvent, 8);
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}
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// done
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} else {
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fireSchemaConflictEventExpectedStartTag(elName, reader);
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}
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}
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return;
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}
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private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, String elName) throws XMLStreamException {
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// attributes
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StartElement element = currentEvent.asStartElement();
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Map<String, Attribute> attributes = getAttributes(element);
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String lang = getAndRemoveAttributeValue(attributes, "lang");
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if (lang != null){
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Language language = getTermService().getLanguageByIso(lang);
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state.setDefaultLanguage(language);
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}
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handleUnexpectedAttributes(element.getLocation(), attributes, "noNamespaceSchemaLocation");
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while (reader.hasNext()) {
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XMLEvent event = readNoWhitespace(reader);
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// TODO cardinality of alternative
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if (isEndingElement(event, elName)) {
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return;
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} else if (event.isStartElement()) {
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if (isStartingElement(event, META_DATA)) {
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handleMetaData(state, reader, event);
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} else if (isStartingElement(event, TREATMENT)) {
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handleTreatment(state, reader, event);
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} else if (isStartingElement(event, BIOGRAPHIES)) {
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handleNotYetImplementedElement(event);
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} else if (isStartingElement(event, REFERENCES)) {
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handleNotYetImplementedElement(event);
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} else if (isStartingElement(event, TEXT_SECTION)) {
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handleNotYetImplementedElement(event);
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} else if (isStartingElement(event, ADDENDA)) {
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handleNotYetImplementedElement(event);
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} else {
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handleUnexpectedStartElement(event);
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}
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} else {
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handleUnexpectedElement(event);
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}
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}
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throw new IllegalStateException("Publication has no ending element");
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}
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private void handleMetaData(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
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checkNoAttributes(parentEvent);
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while (reader.hasNext()) {
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XMLEvent next = readNoWhitespace(reader);
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if (isMyEndingElement(next, parentEvent)) {
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return;
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} else if (isStartingElement(next, DEFAULT_MEDIA_URL)) {
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String baseUrl = getCData(state, reader, next);
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try {
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new URL(baseUrl);
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state.setBaseMediaUrl(baseUrl);
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} catch (MalformedURLException e) {
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String message = "defaultMediaUrl '%s' is not a valid URL";
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message = String.format(message, baseUrl);
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fireWarningEvent(message, next, 8);
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}
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} else if (isStartingElement(next, MODS)){
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modsImport.handleMods(state, reader, next);
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} else {
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handleUnexpectedElement(next);
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}
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}
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throw new IllegalStateException("MetaData has no ending element");
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}
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private void handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
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checkNoAttributes(parentEvent);
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Taxon lastTaxon = null;
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while (reader.hasNext()) {
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XMLEvent next = readNoWhitespace(reader);
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if (isMyEndingElement(next, parentEvent)) {
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Set<PolytomousKeyNode> keyNodesToSave = state.getPolytomousKeyNodesToSave();
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//better save the key then the nodes
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Set<PolytomousKey> keySet = new HashSet<>();
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for (PolytomousKeyNode node : keyNodesToSave){
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PolytomousKey key = node.getKey();
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keySet.add(key);
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}
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save(keySet, state);
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//unmatched key leads
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UnmatchedLeads unmatched = state.getUnmatchedLeads();
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if (unmatched.size() > 0){
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String message = "The following %d key leads are unmatched: %s";
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message = String.format(message, unmatched.size(), state.getUnmatchedLeads().toString());
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fireWarningEvent(message, next, 6);
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}
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// save(keyNodesToSave, state);
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return;
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} else if (isStartingElement(next, TAXON)) {
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state.setCurrentTaxonExcluded(false);
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Taxon thisTaxon = handleTaxon(state, reader, next.asStartElement());
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doTaxonRelation(state, thisTaxon, lastTaxon, parentEvent.getLocation());
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if (state.isTaxonInClassification() == true){
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lastTaxon = thisTaxon;
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// TODO for imports spanning multiple documents ?? Still needed?
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state.getConfig().setLastTaxonUuid(lastTaxon.getUuid());
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}
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} else if (isStartingElement(next, ADDENDA)) {
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handleNotYetImplementedElement(next);
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} else {
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handleUnexpectedElement(next);
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}
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}
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return;
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}
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private TaxonNode doTaxonRelation(MarkupImportState state, Taxon taxon, Taxon lastTaxon, Location dataLocation) {
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if (state.isTaxonInClassification() == false){
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return null;
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}
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boolean excluded = state.isCurrentTaxonExcluded();
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TaxonNode node;
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Classification tree = makeTree(state, dataLocation);
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if (lastTaxon == null) {
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node = tree.addChildTaxon(taxon, null, null);
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if (excluded){
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node.setStatus(TaxonNodeStatus.EXCLUDED);
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}
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return node;
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}
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Rank thisRank = taxon.getName().getRank();
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Rank lastRank = lastTaxon.getName().getRank();
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if (lastRank == null){
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String message = "Last rank was null. Can't create tree correctly";
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fireWarningEvent(message, makeLocationStr(dataLocation), 12);
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}
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if (!lastTaxon.getTaxonNodes().isEmpty()) {
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TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next();
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if (thisRank == null){
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String message = "Rank is undefined for taxon '%s'. Can't create classification without rank.";
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message = String.format(message, taxon.getName().getTitleCache());
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fireWarningEvent(message, makeLocationStr(dataLocation), 6);
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node = null;
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}else if (thisRank.isLower(lastRank)) {
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node = null;
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node = lastNode.addChildTaxon(taxon, null, null);
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fillMissingEpithetsForTaxa(lastTaxon, taxon);
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} else if (thisRank.equals(lastRank)) {
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TaxonNode parent = lastNode.getParent();
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if (parent != null && parent.getTaxon() != null) {
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node = parent.addChildTaxon(taxon, null, null);
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fillMissingEpithetsForTaxa(parent.getTaxon(), taxon);
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} else {
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node = tree.addChildTaxon(taxon, null, null);
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}
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} else if (thisRank.isHigher(lastRank)) {
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TaxonNode parent = lastNode.getParent();
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if (parent != null){
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node = doTaxonRelation(state, taxon, parent.getTaxon(), dataLocation);
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}else{
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String warning = "No parent available for lastNode. Classification can not be build correctly. Maybe the rank was missing for the lastNode";
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fireWarningEvent(warning, makeLocationStr(dataLocation), 16);
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//TODO what to do in this case (haven't spend time to think about yet
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node = null;
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}
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// TaxonNode parentNode = handleTaxonRelation(state, taxon,
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// lastNode.getParent().getTaxon());
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// parentNode.addChildTaxon(taxon, null, null, null);
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}else{
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fireWarningEvent("Unhandled case", makeLocationStr(dataLocation), 8);
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node = null;
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}
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} else {
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String message = "Last taxon has no node";
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fireWarningEvent(message, makeLocationStr(dataLocation), 6);
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node = null;
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}
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if (excluded){
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if (node != null){
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node.setStatus(TaxonNodeStatus.EXCLUDED);
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}else{
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fireWarningEvent("Taxon is excluded but no taxon node can be created", makeLocationStr(dataLocation), 4);
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}
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}
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return node;
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}
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private Classification makeTree(MarkupImportState state, Location dataLocation) {
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Classification result = state.getTree(null);
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if (result == null) {
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UUID uuid = state.getConfig().getClassificationUuid();
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if (uuid == null) {
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String message = "No classification uuid is defined";
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fireWarningEvent(message, makeLocationStr(dataLocation), 6);
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result = createNewClassification(state);
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} else {
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result = getClassificationService().find(uuid);
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if (result == null) {
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result = createNewClassification(state);
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result.setUuid(uuid);
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}
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}
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state.putTree(null, result);
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}
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save(result, state);
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return result;
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}
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private Classification createNewClassification(MarkupImportState state) {
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Classification result = Classification.NewInstance(state.getConfig().getClassificationName(), getDefaultLanguage(state));
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state.putTree(null, result);
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return result;
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}
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private Taxon handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
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// TODO progress monitoring
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Map<String, Attribute> attributes = getAttributes(parentEvent);
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Taxon taxon = createTaxonAndName(state, attributes, parentEvent);
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state.setCurrentTaxon(taxon);
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state.addNewFeatureSorterLists(taxon.getUuid().toString());
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boolean hasTitle = false;
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boolean hasNomenclature = false;
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String taxonTitle = null;
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319
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320
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Reference sourceReference = state.getConfig().getSourceReference();
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while (reader.hasNext()) {
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XMLEvent next = readNoWhitespace(reader);
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323
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if (isMyEndingElement(next, parentEvent)) {
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// checkMandatoryElement(hasTitle, parentEvent, TAXONTITLE);
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checkMandatoryElement(hasNomenclature, parentEvent, NOMENCLATURE);
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boolean inClassification = getAndRemoveBooleanAttributeValue(next, attributes, "inClassification", true);
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state.setTaxonInClassification(inClassification);
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handleUnexpectedAttributes(parentEvent.getLocation(),attributes);
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if (taxon.getName().getRank() == null){
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String warning = "No rank exists for taxon " + taxon.getTitleCache();
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fireWarningEvent(warning, next, 12);
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taxon.getName().setRank(Rank.UNKNOWN_RANK());
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}
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//hybrid
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if (state.isTaxonIsHybrid() && !taxon.getName().isHybrid()){
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fireWarningEvent("Taxon is hybrid but name is not a hybrid name", next, 4);
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}
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state.setTaxonIsHybrid(false);
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keyImport.makeKeyNodes(state, parentEvent, taxonTitle);
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state.setCurrentTaxon(null);
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state.setCurrentTaxonNum(null);
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if (taxon.getName().getRank().isHigher(Rank.GENUS())){
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state.setLatestGenusEpithet(null);
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}else{
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state.setLatestGenusEpithet(taxon.getName().getGenusOrUninomial());
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}
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save(taxon, state);
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return taxon;
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350
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} else if (next.isStartElement()) {
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351
|
if (isStartingElement(next, HEADING)) {
|
|
352
|
handleNotYetImplementedElement(next);
|
|
353
|
} else if (isStartingElement(next, TAXONTITLE)) {
|
|
354
|
taxonTitle = handleTaxonTitle(state, reader, next);
|
|
355
|
hasTitle = true;
|
|
356
|
} else if (isStartingElement(next, WRITER)) {
|
|
357
|
makeKeyWriter(state, reader, taxon, taxonTitle, next);
|
|
358
|
} else if (isStartingElement(next, TEXT_SECTION)) {
|
|
359
|
handleNotYetImplementedElement(next);
|
|
360
|
} else if (isStartingElement(next, KEY)) {
|
|
361
|
keyImport.handleKey(state, reader, next);
|
|
362
|
} else if (isStartingElement(next, NOMENCLATURE)) {
|
|
363
|
nomenclatureImport.handleNomenclature(state, reader, next);
|
|
364
|
hasNomenclature = true;
|
|
365
|
} else if (isStartingElement(next, FEATURE)) {
|
|
366
|
featureImport.handleFeature(state, reader, next);
|
|
367
|
} else if (isStartingElement(next, NOTES)) {
|
|
368
|
// TODO is this the correct way to handle notes?
|
|
369
|
String note = handleNotes(state, reader, next);
|
|
370
|
|
|
371
|
UUID notesUuid;
|
|
372
|
try {
|
|
373
|
notesUuid = state.getTransformer().getFeatureUuid("notes");
|
|
374
|
Feature feature = getFeature(state, notesUuid, "Notes", "Notes", "note", null);
|
|
375
|
TextData textData = TextData.NewInstance(feature);
|
|
376
|
textData.addPrimaryTaxonomicSource(sourceReference);
|
|
377
|
textData.putText(getDefaultLanguage(state), note);
|
|
378
|
TaxonDescription description = getDefaultTaxonDescription(taxon, false, true, sourceReference);
|
|
379
|
description.addElement(textData);
|
|
380
|
} catch (UndefinedTransformerMethodException e) {
|
|
381
|
String message = "getFeatureUuid method not yet implemented";
|
|
382
|
fireWarningEvent(message, next, 8);
|
|
383
|
}
|
|
384
|
} else if (isStartingElement(next, REFERENCES)) {
|
|
385
|
handleNotYetImplementedElement(next);
|
|
386
|
} else if (isStartingElement(next, FIGURE_REF)) {
|
|
387
|
TaxonDescription desc = getTaxonDescription(taxon, sourceReference, IMAGE_GALLERY, CREATE_NEW);
|
|
388
|
TextData textData;
|
|
389
|
if (desc.getElements().isEmpty()){
|
|
390
|
textData = TextData.NewInstance(Feature.IMAGE());
|
|
391
|
textData.addPrimaryTaxonomicSource(sourceReference);
|
|
392
|
desc.addElement(textData);
|
|
393
|
}
|
|
394
|
textData = (TextData)desc.getElements().iterator().next();
|
|
395
|
featureImport.makeFeatureFigureRef(state, reader, desc, false, textData, sourceReference, next);
|
|
396
|
} else if (isStartingElement(next, FIGURE)) {
|
|
397
|
handleFigure(state, reader, next, specimenImport, nomenclatureImport);
|
|
398
|
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
399
|
FootnoteDataHolder footnote = handleFootnote(state, reader, next, specimenImport, nomenclatureImport);
|
|
400
|
if (footnote.isRef()) {
|
|
401
|
String message = "Ref footnote not implemented here";
|
|
402
|
fireWarningEvent(message, next, 4);
|
|
403
|
} else {
|
|
404
|
registerGivenFootnote(state, footnote);
|
|
405
|
}
|
|
406
|
} else {
|
|
407
|
handleUnexpectedStartElement(next);
|
|
408
|
}
|
|
409
|
} else {
|
|
410
|
handleUnexpectedElement(next);
|
|
411
|
}
|
|
412
|
}
|
|
413
|
throw new IllegalStateException("<Taxon> has no closing tag");
|
|
414
|
}
|
|
415
|
|
|
416
|
/**
|
|
417
|
* @param state
|
|
418
|
* @param reader
|
|
419
|
* @param taxon
|
|
420
|
* @param taxonTitle
|
|
421
|
* @param next
|
|
422
|
* @throws XMLStreamException
|
|
423
|
*/
|
|
424
|
private void makeKeyWriter(MarkupImportState state, XMLEventReader reader, Taxon taxon, String taxonTitle, XMLEvent next) throws XMLStreamException {
|
|
425
|
WriterDataHolder writer = handleWriter(state, reader, next);
|
|
426
|
if (state.getConfig().isHandleWriterManually()){
|
|
427
|
fireWarningEvent("<Writer> is expected to be handled manually", next, 1);
|
|
428
|
}else{
|
|
429
|
taxon.addExtension(writer.extension);
|
|
430
|
// TODO what if taxonTitle comes later
|
|
431
|
taxonTitle = taxonTitle != null ? taxonTitle : taxon.getName() == null ? null : taxon.getName().getNameCache();
|
|
432
|
if (writer.extension != null) {
|
|
433
|
if (StringUtils.isBlank(taxonTitle)){
|
|
434
|
fireWarningEvent("No taxon title defined for writer. Please add sec.title manually.", next, 6);
|
|
435
|
taxonTitle = null;
|
|
436
|
}
|
|
437
|
Reference sec = ReferenceFactory.newBookSection();
|
|
438
|
sec.setTitle(taxonTitle);
|
|
439
|
TeamOrPersonBase<?> author = createAuthor(state, writer.writer);
|
|
440
|
sec.setAuthorship(author);
|
|
441
|
sec.setInReference(state.getConfig().getSourceReference());
|
|
442
|
taxon.setSec(sec);
|
|
443
|
registerFootnotes(state, sec, writer.footnotes);
|
|
444
|
} else {
|
|
445
|
String message = "There is no writer extension defined";
|
|
446
|
fireWarningEvent(message, next, 6);
|
|
447
|
}
|
|
448
|
}
|
|
449
|
}
|
|
450
|
|
|
451
|
private String handleNotes(MarkupImportState state, XMLEventReader reader,
|
|
452
|
XMLEvent parentEvent) throws XMLStreamException {
|
|
453
|
checkNoAttributes(parentEvent);
|
|
454
|
|
|
455
|
String text = "";
|
|
456
|
while (reader.hasNext()) {
|
|
457
|
XMLEvent next = readNoWhitespace(reader);
|
|
458
|
if (isMyEndingElement(next, parentEvent)) {
|
|
459
|
return text;
|
|
460
|
} else if (next.isStartElement()) {
|
|
461
|
if (isStartingElement(next, HEADING)) {
|
|
462
|
handleNotYetImplementedElement(next);
|
|
463
|
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
464
|
String subheading = getCData(state, reader, next).trim();
|
|
465
|
if (! isNoteHeading(subheading)) {
|
|
466
|
fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);
|
|
467
|
}
|
|
468
|
} else if (isStartingElement(next, WRITER)) {
|
|
469
|
handleNotYetImplementedElement(next);
|
|
470
|
} else if (isStartingElement(next, NUM)) {
|
|
471
|
handleNotYetImplementedElement(next);
|
|
472
|
} else if (isStartingElement(next, STRING)) {
|
|
473
|
// TODO why multiple strings in schema?
|
|
474
|
text = makeNotesString(state, reader, text, next);
|
|
475
|
} else {
|
|
476
|
handleUnexpectedStartElement(next.asStartElement());
|
|
477
|
}
|
|
478
|
} else {
|
|
479
|
handleUnexpectedElement(next);
|
|
480
|
}
|
|
481
|
}
|
|
482
|
throw new IllegalStateException("<Notes> has no closing tag");
|
|
483
|
}
|
|
484
|
|
|
485
|
/**
|
|
486
|
* @param state
|
|
487
|
* @param reader
|
|
488
|
* @param text
|
|
489
|
* @param next
|
|
490
|
* @return
|
|
491
|
* @throws XMLStreamException
|
|
492
|
*/
|
|
493
|
private String makeNotesString(MarkupImportState state, XMLEventReader reader, String text, XMLEvent next) throws XMLStreamException {
|
|
494
|
Map<String, SubheadingResult> stringMap = handleString(state, reader, next, null);
|
|
495
|
if (stringMap.size() == 0){
|
|
496
|
String message = "No text available in <notes>";
|
|
497
|
fireWarningEvent(message, next, 4);
|
|
498
|
}else if (stringMap.size() > 1){
|
|
499
|
String message = "Subheadings not yet supported in <notes>";
|
|
500
|
fireWarningEvent(message, next, 4);
|
|
501
|
}else{
|
|
502
|
String firstSubheading = stringMap.keySet().iterator().next();
|
|
503
|
if ( firstSubheading != null && ! isNoteHeading (firstSubheading) ) {
|
|
504
|
String message = "Subheadings not yet supported in <notes>";
|
|
505
|
fireWarningEvent(message, next, 4);
|
|
506
|
}
|
|
507
|
}
|
|
508
|
for (String subheading : stringMap.keySet()){
|
|
509
|
text += subheading;
|
|
510
|
text += stringMap.get(subheading);
|
|
511
|
}
|
|
512
|
return text;
|
|
513
|
}
|
|
514
|
|
|
515
|
private boolean isNoteHeading(String heading) {
|
|
516
|
String excludePattern = "(i?)(Notes?):?";
|
|
517
|
return heading.matches(excludePattern);
|
|
518
|
}
|
|
519
|
|
|
520
|
/**
|
|
521
|
* @param state
|
|
522
|
* @param attributes
|
|
523
|
* @param event
|
|
524
|
*/
|
|
525
|
private Taxon createTaxonAndName(MarkupImportState state,
|
|
526
|
Map<String, Attribute> attributes, StartElement event) {
|
|
527
|
|
|
528
|
INonViralName name;
|
|
529
|
Rank rank = null; //Rank.SPECIES(); // default
|
|
530
|
boolean isCultivar = checkAndRemoveAttributeValue(attributes, CLASS, "cultivated");
|
|
531
|
|
|
532
|
if (isCultivar) {
|
|
533
|
name = TaxonNameFactory.NewCultivarInstance(rank);
|
|
534
|
} else {
|
|
535
|
name = createNameByCode(state, rank);
|
|
536
|
}
|
|
537
|
Taxon taxon = Taxon.NewInstance(name, state.getConfig().getSourceReference());
|
|
538
|
if (checkAndRemoveAttributeValue(attributes, CLASS, "dubious")) {
|
|
539
|
taxon.setDoubtful(true);
|
|
540
|
} else if (checkAndRemoveAttributeValue(attributes, CLASS, "excluded")) {
|
|
541
|
state.setCurrentTaxonExcluded(true);
|
|
542
|
}
|
|
543
|
state.setTaxonIsHybrid(checkAndRemoveAttributeValue(attributes, CLASS, "hybrid"));
|
|
544
|
|
|
545
|
// TODO insufficient, new, expected
|
|
546
|
handleNotYetImplementedAttribute(attributes, CLASS, event);
|
|
547
|
// From old version
|
|
548
|
// MarkerType markerType = getMarkerType(state, attrValue);
|
|
549
|
// if (markerType == null){
|
|
550
|
// logger.warn("Class attribute value for taxon not yet supported: " +
|
|
551
|
// attrValue);
|
|
552
|
// }else{
|
|
553
|
// taxon.addMarker(Marker.NewInstance(markerType, true));
|
|
554
|
// }
|
|
555
|
|
|
556
|
// save(name, state);
|
|
557
|
// save(taxon, state);
|
|
558
|
return taxon;
|
|
559
|
}
|
|
560
|
|
|
561
|
private String handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
562
|
//attributes
|
|
563
|
String text = "";
|
|
564
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
565
|
String rankAttr = getAndRemoveAttributeValue(attributes, RANK);
|
|
566
|
Rank rank = makeRank(state, rankAttr, false);
|
|
567
|
String num = getAndRemoveAttributeValue(attributes, NUM);
|
|
568
|
state.setCurrentTaxonNum(num);
|
|
569
|
checkNoAttributes(attributes, parentEvent);
|
|
570
|
|
|
571
|
// TODO handle attributes
|
|
572
|
while (reader.hasNext()) {
|
|
573
|
XMLEvent next = readNoWhitespace(reader);
|
|
574
|
if (next.isEndElement()) {
|
|
575
|
if (isMyEndingElement(next, parentEvent)) {
|
|
576
|
Taxon taxon = state.getCurrentTaxon();
|
|
577
|
String titleText = null;
|
|
578
|
if (state.getConfig().isDoExtensionForTaxonTitle() && checkMandatoryText(text, parentEvent)) {
|
|
579
|
titleText = normalize(text);
|
|
580
|
UUID uuidTitle = MarkupTransformer.uuidTaxonTitle;
|
|
581
|
ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "Taxon Title ","taxon title", "title");
|
|
582
|
taxon.addExtension(titleText, titleExtension);
|
|
583
|
}
|
|
584
|
taxon.getName().setRank(rank);
|
|
585
|
// TODO check title exists
|
|
586
|
return titleText;
|
|
587
|
} else {
|
|
588
|
if (isEndingElement(next, FOOTNOTE)) {
|
|
589
|
// NOT YET IMPLEMENTED
|
|
590
|
popUnimplemented(next.asEndElement());
|
|
591
|
} else {
|
|
592
|
handleUnexpectedEndElement(next.asEndElement());
|
|
593
|
state.setUnsuccessfull();
|
|
594
|
}
|
|
595
|
}
|
|
596
|
} else if (next.isStartElement()) {
|
|
597
|
if (isStartingElement(next, FOOTNOTE)) {
|
|
598
|
handleNotYetImplementedElement(next);
|
|
599
|
}else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
600
|
handleNotYetImplementedElement(next);
|
|
601
|
} else {
|
|
602
|
handleUnexpectedStartElement(next);
|
|
603
|
state.setUnsuccessfull();
|
|
604
|
}
|
|
605
|
} else if (next.isCharacters()) {
|
|
606
|
text += next.asCharacters().getData();
|
|
607
|
|
|
608
|
} else {
|
|
609
|
handleUnexpectedElement(next);
|
|
610
|
state.setUnsuccessfull();
|
|
611
|
}
|
|
612
|
}
|
|
613
|
return null;
|
|
614
|
|
|
615
|
}
|
|
616
|
|
|
617
|
|
|
618
|
}
|