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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.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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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 java.util.regex.Matcher;
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import java.util.regex.Pattern;
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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.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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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.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Extension;
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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.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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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.PolytomousKey;
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import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
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import eu.etaxonomy.cdm.model.description.PresenceTerm;
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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.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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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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/**
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* @author a.mueller
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*
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*/
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public class MarkupDocumentImportNoComponent extends MarkupImportBase {
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private static final Logger logger = Logger.getLogger(MarkupDocumentImportNoComponent.class);
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private MarkupKeyImport keyImport;
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private MarkupSpecimenImport specimenImport;
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private 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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nomenclatureImport = new MarkupNomenclatureImport(docImport, keyImport, specimenImport);
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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 (event.isEndElement()) {
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if (isEndingElement(event, elName)) {
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return;
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} else {
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if (isEndingElement(event, BIOGRAPHIES)) {
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// NOT YET IMPLEMENTED
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popUnimplemented(event.asEndElement());
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} else if (isEndingElement(event, REFERENCES)) {
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// NOT YET IMPLEMENTED
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popUnimplemented(event.asEndElement());
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} else if (isEndingElement(event, TEXT_SECTION)) {
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// NOT YET IMPLEMENTED
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popUnimplemented(event.asEndElement());
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} else if (isEndingElement(event, ADDENDA)) {
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// NOT YET IMPLEMENTED
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popUnimplemented(event.asEndElement());
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} else {
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handleUnexpectedElement(event);
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}
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}
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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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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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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<PolytomousKey>();
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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 key leads are unmatched: %s";
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message = String.format(message, 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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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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/**
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* @param taxon
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* @param lastTaxon
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*/
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private void doTaxonRelation(MarkupImportState state, Taxon taxon, Taxon lastTaxon, Location dataLocation) {
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if (state.isTaxonInClassification() == false){
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return;
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}
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Classification tree = makeTree(state, dataLocation);
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if (lastTaxon == null) {
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tree.addChildTaxon(taxon, null, null, null);
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return;
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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().size() > 0) {
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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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}else if (thisRank.isLower(lastRank)) {
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lastNode.addChildTaxon(taxon, null, 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) {
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parent.addChildTaxon(taxon, null, null, null);
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fillMissingEpithetsForTaxa(parent.getTaxon(), taxon);
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} else {
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tree.addChildTaxon(taxon, null, null, null);
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}
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} else if (thisRank.isHigher(lastRank)) {
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doTaxonRelation(state, taxon, lastNode.getParent().getTaxon(), dataLocation);
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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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}
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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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}
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}
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297
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/**
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* @param state
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* @param dataLocation
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* @return
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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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328
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private Taxon handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
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330
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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);
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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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339
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Reference<?> descriptionReference = state.getConfig().getSourceReference();
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while (reader.hasNext()) {
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XMLEvent next = readNoWhitespace(reader);
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343
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if (next.isEndElement()) {
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344
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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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349
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handleUnexpectedAttributes(parentEvent.getLocation(),attributes);
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350
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if (taxon.getName().getRank() == null){
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351
|
String warning = "No rank exists for taxon " + taxon.getTitleCache();
|
|
352
|
fireWarningEvent(warning, next, 12);
|
|
353
|
taxon.getName().setRank(Rank.UNKNOWN_RANK());
|
|
354
|
}
|
|
355
|
|
|
356
|
keyImport.makeKeyNodes(state, parentEvent, taxonTitle);
|
|
357
|
state.setCurrentTaxon(null);
|
|
358
|
state.setCurrentTaxonNum(null);
|
|
359
|
if (taxon.getName().getRank().isHigher(Rank.GENUS())){
|
|
360
|
state.setLatestGenusEpithet(null);
|
|
361
|
}else{
|
|
362
|
state.setLatestGenusEpithet(((NonViralName<?>)taxon.getName()).getGenusOrUninomial());
|
|
363
|
}
|
|
364
|
save(taxon, state);
|
|
365
|
return taxon;
|
|
366
|
} else {
|
|
367
|
if (isEndingElement(next, HEADING)) {
|
|
368
|
// NOT YET IMPLEMENTED
|
|
369
|
popUnimplemented(next.asEndElement());
|
|
370
|
} else if (isEndingElement(next, TEXT_SECTION)) {
|
|
371
|
// NOT YET IMPLEMENTED
|
|
372
|
popUnimplemented(next.asEndElement());
|
|
373
|
} else if (isEndingElement(next, REFERENCES)) {
|
|
374
|
// NOT YET IMPLEMENTED
|
|
375
|
popUnimplemented(next.asEndElement());
|
|
376
|
} else if (isEndingElement(next, FIGURE_REF)) {
|
|
377
|
// NOT YET IMPLEMENTED
|
|
378
|
popUnimplemented(next.asEndElement());
|
|
379
|
} else {
|
|
380
|
handleUnexpectedEndElement(next.asEndElement());
|
|
381
|
}
|
|
382
|
}
|
|
383
|
} else if (next.isStartElement()) {
|
|
384
|
if (isStartingElement(next, HEADING)) {
|
|
385
|
handleNotYetImplementedElement(next);
|
|
386
|
} else if (isStartingElement(next, TAXONTITLE)) {
|
|
387
|
taxonTitle = handleTaxonTitle(state, reader, next);
|
|
388
|
hasTitle = true;
|
|
389
|
} else if (isStartingElement(next, WRITER)) {
|
|
390
|
makeKeyWriter(state, reader, taxon, taxonTitle, next);
|
|
391
|
} else if (isStartingElement(next, TEXT_SECTION)) {
|
|
392
|
handleNotYetImplementedElement(next);
|
|
393
|
} else if (isStartingElement(next, KEY)) {
|
|
394
|
keyImport.handleKey(state, reader, next);
|
|
395
|
} else if (isStartingElement(next, NOMENCLATURE)) {
|
|
396
|
nomenclatureImport.handleNomenclature(state, reader, next);
|
|
397
|
hasNomenclature = true;
|
|
398
|
} else if (isStartingElement(next, FEATURE)) {
|
|
399
|
handleFeature(state, reader, next);
|
|
400
|
} else if (isStartingElement(next, NOTES)) {
|
|
401
|
// TODO is this the correct way to handle notes?
|
|
402
|
String note = handleNotes(state, reader, next);
|
|
403
|
|
|
404
|
UUID notesUuid;
|
|
405
|
try {
|
|
406
|
notesUuid = state.getTransformer().getFeatureUuid("notes");
|
|
407
|
Feature feature = getFeature(state, notesUuid, "Notes", "Notes", "note", null);
|
|
408
|
TextData textData = TextData.NewInstance(feature);
|
|
409
|
textData.putText(getDefaultLanguage(state), note);
|
|
410
|
TaxonDescription description = getTaxonDescription(taxon, descriptionReference, false, true);
|
|
411
|
description.addElement(textData);
|
|
412
|
} catch (UndefinedTransformerMethodException e) {
|
|
413
|
String message = "getFeatureUuid method not yet implemented";
|
|
414
|
fireWarningEvent(message, next, 8);
|
|
415
|
}
|
|
416
|
} else if (isStartingElement(next, REFERENCES)) {
|
|
417
|
handleNotYetImplementedElement(next);
|
|
418
|
} else if (isStartingElement(next, FIGURE_REF)) {
|
|
419
|
TaxonDescription desc = getTaxonDescription(taxon, state.getConfig().getSourceReference(), IMAGE_GALLERY, CREATE_NEW);
|
|
420
|
TextData textData;
|
|
421
|
if (desc.getElements().isEmpty()){
|
|
422
|
textData = TextData.NewInstance(Feature.IMAGE());
|
|
423
|
desc.addElement(textData);
|
|
424
|
}
|
|
425
|
textData = (TextData)desc.getElements().iterator().next();
|
|
426
|
makeFeatureFigureRef(state, reader, desc, false, textData, next);
|
|
427
|
} else if (isStartingElement(next, FIGURE)) {
|
|
428
|
handleFigure(state, reader, next);
|
|
429
|
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
430
|
FootnoteDataHolder footnote = handleFootnote(state, reader, next);
|
|
431
|
if (footnote.isRef()) {
|
|
432
|
String message = "Ref footnote not implemented here";
|
|
433
|
fireWarningEvent(message, next, 4);
|
|
434
|
} else {
|
|
435
|
registerGivenFootnote(state, footnote);
|
|
436
|
}
|
|
437
|
} else {
|
|
438
|
handleUnexpectedStartElement(next);
|
|
439
|
}
|
|
440
|
} else {
|
|
441
|
handleUnexpectedElement(next);
|
|
442
|
}
|
|
443
|
}
|
|
444
|
throw new IllegalStateException("<Taxon> has no closing tag");
|
|
445
|
}
|
|
446
|
|
|
447
|
/**
|
|
448
|
* @param state
|
|
449
|
* @param reader
|
|
450
|
* @param taxon
|
|
451
|
* @param taxonTitle
|
|
452
|
* @param next
|
|
453
|
* @throws XMLStreamException
|
|
454
|
*/
|
|
455
|
private void makeKeyWriter(MarkupImportState state, XMLEventReader reader, Taxon taxon, String taxonTitle, XMLEvent next) throws XMLStreamException {
|
|
456
|
WriterDataHolder writer = handleWriter(state, reader, next);
|
|
457
|
taxon.addExtension(writer.extension);
|
|
458
|
// TODO what if taxonTitle comes later
|
|
459
|
if (StringUtils.isNotBlank(taxonTitle)
|
|
460
|
&& writer.extension != null) {
|
|
461
|
Reference<?> sec = ReferenceFactory.newBookSection();
|
|
462
|
sec.setTitle(taxonTitle);
|
|
463
|
TeamOrPersonBase<?> author = createAuthor(writer.writer);
|
|
464
|
sec.setAuthorTeam(author);
|
|
465
|
sec.setInReference(state.getConfig()
|
|
466
|
.getSourceReference());
|
|
467
|
taxon.setSec(sec);
|
|
468
|
registerFootnotes(state, sec, writer.footnotes);
|
|
469
|
} else {
|
|
470
|
String message = "No taxontitle exists for writer";
|
|
471
|
fireWarningEvent(message, next, 6);
|
|
472
|
}
|
|
473
|
}
|
|
474
|
|
|
475
|
private String handleNotes(MarkupImportState state, XMLEventReader reader,
|
|
476
|
XMLEvent parentEvent) throws XMLStreamException {
|
|
477
|
checkNoAttributes(parentEvent);
|
|
478
|
|
|
479
|
String text = "";
|
|
480
|
while (reader.hasNext()) {
|
|
481
|
XMLEvent next = readNoWhitespace(reader);
|
|
482
|
if (isMyEndingElement(next, parentEvent)) {
|
|
483
|
return text;
|
|
484
|
} else if (next.isEndElement()) {
|
|
485
|
if (isEndingElement(next, HEADING)) {
|
|
486
|
popUnimplemented(next.asEndElement());
|
|
487
|
} else if (isEndingElement(next, WRITER)) {
|
|
488
|
popUnimplemented(next.asEndElement());
|
|
489
|
} else if (isEndingElement(next, NUM)) {
|
|
490
|
popUnimplemented(next.asEndElement());
|
|
491
|
} else {
|
|
492
|
handleUnexpectedEndElement(next.asEndElement());
|
|
493
|
}
|
|
494
|
} else if (next.isStartElement()) {
|
|
495
|
if (isStartingElement(next, HEADING)) {
|
|
496
|
handleNotYetImplementedElement(next);
|
|
497
|
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
498
|
String subheading = getCData(state, reader, next).trim();
|
|
499
|
if (! isNoteHeading(subheading)) {
|
|
500
|
fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);
|
|
501
|
}
|
|
502
|
} else if (isStartingElement(next, WRITER)) {
|
|
503
|
handleNotYetImplementedElement(next);
|
|
504
|
} else if (isStartingElement(next, NUM)) {
|
|
505
|
handleNotYetImplementedElement(next);
|
|
506
|
} else if (isStartingElement(next, STRING)) {
|
|
507
|
// TODO why multiple strings in schema?
|
|
508
|
text = makeNotesString(state, reader, text, next);
|
|
509
|
} else {
|
|
510
|
handleUnexpectedStartElement(next.asStartElement());
|
|
511
|
}
|
|
512
|
} else {
|
|
513
|
handleUnexpectedElement(next);
|
|
514
|
}
|
|
515
|
}
|
|
516
|
throw new IllegalStateException("<Notes> has no closing tag");
|
|
517
|
}
|
|
518
|
|
|
519
|
/**
|
|
520
|
* @param state
|
|
521
|
* @param reader
|
|
522
|
* @param text
|
|
523
|
* @param next
|
|
524
|
* @return
|
|
525
|
* @throws XMLStreamException
|
|
526
|
*/
|
|
527
|
private String makeNotesString(MarkupImportState state, XMLEventReader reader, String text, XMLEvent next) throws XMLStreamException {
|
|
528
|
Map<String, String> stringMap = handleString(state, reader, next, null);
|
|
529
|
if (stringMap.size() == 0){
|
|
530
|
String message = "No text available in <notes>";
|
|
531
|
fireWarningEvent(message, next, 4);
|
|
532
|
}else if (stringMap.size() > 1){
|
|
533
|
String message = "Subheadings not yet supported in <notes>";
|
|
534
|
fireWarningEvent(message, next, 4);
|
|
535
|
}else{
|
|
536
|
String firstSubheading = stringMap.keySet().iterator().next();
|
|
537
|
if ( firstSubheading != null && ! isNoteHeading (firstSubheading) ) {
|
|
538
|
String message = "Subheadings not yet supported in <notes>";
|
|
539
|
fireWarningEvent(message, next, 4);
|
|
540
|
}
|
|
541
|
}
|
|
542
|
for (String subheading : stringMap.keySet()){
|
|
543
|
text += subheading;
|
|
544
|
text += stringMap.get(subheading);
|
|
545
|
}
|
|
546
|
return text;
|
|
547
|
}
|
|
548
|
|
|
549
|
private boolean isNoteHeading(String heading) {
|
|
550
|
String excludePattern = "(i?)(Notes?):?";
|
|
551
|
return heading.matches(excludePattern);
|
|
552
|
}
|
|
553
|
|
|
554
|
/**
|
|
555
|
* @param state
|
|
556
|
* @param attributes
|
|
557
|
*/
|
|
558
|
private Taxon createTaxonAndName(MarkupImportState state,
|
|
559
|
Map<String, Attribute> attributes) {
|
|
560
|
NonViralName<?> name;
|
|
561
|
Rank rank = null; //Rank.SPECIES(); // default
|
|
562
|
boolean isCultivar = checkAndRemoveAttributeValue(attributes, CLASS, "cultivated");
|
|
563
|
if (isCultivar) {
|
|
564
|
name = CultivarPlantName.NewInstance(rank);
|
|
565
|
} else {
|
|
566
|
name = createNameByCode(state, rank);
|
|
567
|
}
|
|
568
|
Taxon taxon = Taxon.NewInstance(name, state.getConfig().getSourceReference());
|
|
569
|
if (checkAndRemoveAttributeValue(attributes, CLASS, "dubious")) {
|
|
570
|
taxon.setDoubtful(true);
|
|
571
|
} else if (checkAndRemoveAttributeValue(attributes, CLASS, "excluded")) {
|
|
572
|
taxon.setExcluded(true);
|
|
573
|
}
|
|
574
|
// TODO insufficient, new, expected
|
|
575
|
handleNotYetImplementedAttribute(attributes, CLASS);
|
|
576
|
// From old version
|
|
577
|
// MarkerType markerType = getMarkerType(state, attrValue);
|
|
578
|
// if (markerType == null){
|
|
579
|
// logger.warn("Class attribute value for taxon not yet supported: " +
|
|
580
|
// attrValue);
|
|
581
|
// }else{
|
|
582
|
// taxon.addMarker(Marker.NewInstance(markerType, true));
|
|
583
|
// }
|
|
584
|
|
|
585
|
// save(name, state);
|
|
586
|
// save(taxon, state);
|
|
587
|
return taxon;
|
|
588
|
}
|
|
589
|
|
|
590
|
private String handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
591
|
//attributes
|
|
592
|
String text = "";
|
|
593
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
594
|
String rankAttr = getAndRemoveAttributeValue(attributes, RANK);
|
|
595
|
Rank rank = makeRank(state, rankAttr, false);
|
|
596
|
String num = getAndRemoveAttributeValue(attributes, NUM);
|
|
597
|
state.setCurrentTaxonNum(num);
|
|
598
|
checkNoAttributes(attributes, parentEvent);
|
|
599
|
|
|
600
|
// TODO handle attributes
|
|
601
|
while (reader.hasNext()) {
|
|
602
|
XMLEvent next = readNoWhitespace(reader);
|
|
603
|
if (next.isEndElement()) {
|
|
604
|
if (isMyEndingElement(next, parentEvent)) {
|
|
605
|
Taxon taxon = state.getCurrentTaxon();
|
|
606
|
String titleText = null;
|
|
607
|
if (checkMandatoryText(text, parentEvent)) {
|
|
608
|
titleText = normalize(text);
|
|
609
|
UUID uuidTitle = MarkupTransformer.uuidTaxonTitle;
|
|
610
|
ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "Taxon Title ","taxon title", "title");
|
|
611
|
taxon.addExtension(titleText, titleExtension);
|
|
612
|
}
|
|
613
|
taxon.getName().setRank(rank);
|
|
614
|
// TODO check title exists
|
|
615
|
return titleText;
|
|
616
|
} else {
|
|
617
|
if (isEndingElement(next, FOOTNOTE)) {
|
|
618
|
// NOT YET IMPLEMENTED
|
|
619
|
popUnimplemented(next.asEndElement());
|
|
620
|
} else {
|
|
621
|
handleUnexpectedEndElement(next.asEndElement());
|
|
622
|
state.setUnsuccessfull();
|
|
623
|
}
|
|
624
|
}
|
|
625
|
} else if (next.isStartElement()) {
|
|
626
|
if (isStartingElement(next, FOOTNOTE)) {
|
|
627
|
handleNotYetImplementedElement(next);
|
|
628
|
}else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
629
|
handleNotYetImplementedElement(next);
|
|
630
|
} else {
|
|
631
|
handleUnexpectedStartElement(next);
|
|
632
|
state.setUnsuccessfull();
|
|
633
|
}
|
|
634
|
} else if (next.isCharacters()) {
|
|
635
|
text += next.asCharacters().getData();
|
|
636
|
|
|
637
|
} else {
|
|
638
|
handleUnexpectedElement(next);
|
|
639
|
state.setUnsuccessfull();
|
|
640
|
}
|
|
641
|
}
|
|
642
|
return null;
|
|
643
|
|
|
644
|
}
|
|
645
|
|
|
646
|
private WriterDataHolder handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
647
|
String text = "";
|
|
648
|
checkNoAttributes(parentEvent);
|
|
649
|
WriterDataHolder dataHolder = new WriterDataHolder();
|
|
650
|
List<FootnoteDataHolder> footnotes = new ArrayList<FootnoteDataHolder>();
|
|
651
|
|
|
652
|
// TODO handle attributes
|
|
653
|
while (reader.hasNext()) {
|
|
654
|
XMLEvent next = readNoWhitespace(reader);
|
|
655
|
if (isMyEndingElement(next, parentEvent)) {
|
|
656
|
text = CdmUtils.removeBrackets(text);
|
|
657
|
if (checkMandatoryText(text, parentEvent)) {
|
|
658
|
text = normalize(text);
|
|
659
|
dataHolder.writer = text;
|
|
660
|
dataHolder.footnotes = footnotes;
|
|
661
|
|
|
662
|
// Extension
|
|
663
|
UUID uuidWriterExtension = MarkupTransformer.uuidWriterExtension;
|
|
664
|
ExtensionType writerExtensionType = this
|
|
665
|
.getExtensionType(state, uuidWriterExtension,
|
|
666
|
"Writer", "writer", "writer");
|
|
667
|
Extension extension = Extension.NewInstance();
|
|
668
|
extension.setType(writerExtensionType);
|
|
669
|
extension.setValue(text);
|
|
670
|
dataHolder.extension = extension;
|
|
671
|
|
|
672
|
// Annotation
|
|
673
|
UUID uuidWriterAnnotation = MarkupTransformer.uuidWriterAnnotation;
|
|
674
|
AnnotationType writerAnnotationType = this.getAnnotationType(state, uuidWriterAnnotation, "Writer", "writer", "writer", null);
|
|
675
|
Annotation annotation = Annotation.NewInstance(text, writerAnnotationType, getDefaultLanguage(state));
|
|
676
|
dataHolder.annotation = annotation;
|
|
677
|
|
|
678
|
return dataHolder;
|
|
679
|
} else {
|
|
680
|
return null;
|
|
681
|
}
|
|
682
|
} else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
683
|
FootnoteDataHolder footNote = handleFootnoteRef(state, reader, next);
|
|
684
|
if (footNote.isRef()) {
|
|
685
|
footnotes.add(footNote);
|
|
686
|
} else {
|
|
687
|
logger.warn("Non ref footnotes not yet impelemnted");
|
|
688
|
}
|
|
689
|
} else if (next.isCharacters()) {
|
|
690
|
text += next.asCharacters().getData();
|
|
691
|
|
|
692
|
} else {
|
|
693
|
handleUnexpectedElement(next);
|
|
694
|
state.setUnsuccessfull();
|
|
695
|
}
|
|
696
|
}
|
|
697
|
throw new IllegalStateException("<writer> has no end tag");
|
|
698
|
}
|
|
699
|
|
|
700
|
private void registerFootnotes(MarkupImportState state, AnnotatableEntity entity, List<FootnoteDataHolder> footnotes) {
|
|
701
|
for (FootnoteDataHolder footNote : footnotes) {
|
|
702
|
registerFootnoteDemand(state, entity, footNote);
|
|
703
|
}
|
|
704
|
}
|
|
705
|
|
|
706
|
private void registerGivenFootnote(MarkupImportState state, FootnoteDataHolder footnote) {
|
|
707
|
state.registerFootnote(footnote);
|
|
708
|
Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.id);
|
|
709
|
if (demands != null) {
|
|
710
|
for (AnnotatableEntity entity : demands) {
|
|
711
|
attachFootnote(state, entity, footnote);
|
|
712
|
}
|
|
713
|
}
|
|
714
|
}
|
|
715
|
|
|
716
|
private void registerGivenFigure(MarkupImportState state, XMLEvent next, String id, Media figure) {
|
|
717
|
state.registerFigure(id, figure);
|
|
718
|
Set<AnnotatableEntity> demands = state.getFigureDemands(id);
|
|
719
|
if (demands != null) {
|
|
720
|
for (AnnotatableEntity entity : demands) {
|
|
721
|
attachFigure(state, next, entity, figure);
|
|
722
|
}
|
|
723
|
}
|
|
724
|
save(figure, state);
|
|
725
|
}
|
|
726
|
|
|
727
|
private void registerFootnoteDemand(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {
|
|
728
|
FootnoteDataHolder existingFootnote = state.getFootnote(footnote.ref);
|
|
729
|
if (existingFootnote != null) {
|
|
730
|
attachFootnote(state, entity, existingFootnote);
|
|
731
|
} else {
|
|
732
|
Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.ref);
|
|
733
|
if (demands == null) {
|
|
734
|
demands = new HashSet<AnnotatableEntity>();
|
|
735
|
state.putFootnoteDemands(footnote.ref, demands);
|
|
736
|
}
|
|
737
|
demands.add(entity);
|
|
738
|
}
|
|
739
|
}
|
|
740
|
|
|
741
|
private void registerFigureDemand(MarkupImportState state, XMLEvent next, AnnotatableEntity entity, String figureRef) {
|
|
742
|
Media existingFigure = state.getFigure(figureRef);
|
|
743
|
if (existingFigure != null) {
|
|
744
|
attachFigure(state, next, entity, existingFigure);
|
|
745
|
} else {
|
|
746
|
Set<AnnotatableEntity> demands = state.getFigureDemands(figureRef);
|
|
747
|
if (demands == null) {
|
|
748
|
demands = new HashSet<AnnotatableEntity>();
|
|
749
|
state.putFigureDemands(figureRef, demands);
|
|
750
|
}
|
|
751
|
demands.add(entity);
|
|
752
|
}
|
|
753
|
}
|
|
754
|
|
|
755
|
private void attachFootnote(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {
|
|
756
|
AnnotationType annotationType = this.getAnnotationType(state, MarkupTransformer.uuidFootnote, "Footnote", "An e-flora footnote", "fn", null);
|
|
757
|
Annotation annotation = Annotation.NewInstance(footnote.string, annotationType, getDefaultLanguage(state));
|
|
758
|
// TODO transient objects
|
|
759
|
entity.addAnnotation(annotation);
|
|
760
|
save(entity, state);
|
|
761
|
}
|
|
762
|
|
|
763
|
private void attachFigure(MarkupImportState state, XMLEvent next, AnnotatableEntity entity, Media figure) {
|
|
764
|
// IdentifiableEntity<?> toSave;
|
|
765
|
if (entity.isInstanceOf(TextData.class)) {
|
|
766
|
TextData deb = CdmBase.deproxy(entity, TextData.class);
|
|
767
|
deb.addMedia(figure);
|
|
768
|
// toSave = ((TaxonDescription)deb.getInDescription()).getTaxon();
|
|
769
|
} else if (entity.isInstanceOf(SpecimenOrObservationBase.class)) {
|
|
770
|
String message = "figures for specimen should be handled as Textdata";
|
|
771
|
fireWarningEvent(message, next, 4);
|
|
772
|
// toSave = ime;
|
|
773
|
} else if (entity.isInstanceOf(IdentifiableMediaEntity.class)) {
|
|
774
|
IdentifiableMediaEntity<?> ime = CdmBase.deproxy(entity, IdentifiableMediaEntity.class);
|
|
775
|
ime.addMedia(figure);
|
|
776
|
// toSave = ime;
|
|
777
|
} else {
|
|
778
|
String message = "Unsupported entity to attach media: %s";
|
|
779
|
message = String.format(message, entity.getClass().getName());
|
|
780
|
// toSave = null;
|
|
781
|
}
|
|
782
|
save(entity, state);
|
|
783
|
}
|
|
784
|
|
|
785
|
private Media handleFigure(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
786
|
// FigureDataHolder result = new FigureDataHolder();
|
|
787
|
|
|
788
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
789
|
String id = getAndRemoveAttributeValue(attributes, ID);
|
|
790
|
String type = getAndRemoveAttributeValue(attributes, TYPE);
|
|
791
|
String urlAttr = getAndRemoveAttributeValue(attributes, URL);
|
|
792
|
checkNoAttributes(attributes, parentEvent);
|
|
793
|
|
|
794
|
String urlString = null;
|
|
795
|
String legendString = null;
|
|
796
|
String titleString = null;
|
|
797
|
String numString = null;
|
|
798
|
String text = null;
|
|
799
|
if (isNotBlank(urlAttr)){
|
|
800
|
urlString = CdmUtils.Nz(state.getBaseMediaUrl()) + urlAttr;
|
|
801
|
}
|
|
802
|
while (reader.hasNext()) {
|
|
803
|
XMLEvent next = readNoWhitespace(reader);
|
|
804
|
if (isMyEndingElement(next, parentEvent)) {
|
|
805
|
if (isNotBlank(text)){
|
|
806
|
fireWarningEvent("Text not yet handled for figures: " + text, next, 4);
|
|
807
|
}
|
|
808
|
Media media = makeFigure(state, id, type, urlString, legendString, titleString, numString, next);
|
|
809
|
return media;
|
|
810
|
} else if (isStartingElement(next, FIGURE_LEGEND)) {
|
|
811
|
// TODO same as figure string ?
|
|
812
|
legendString = handleFootnoteString(state, reader, next);
|
|
813
|
} else if (isStartingElement(next, FIGURE_TITLE)) {
|
|
814
|
titleString = getCData(state, reader, next);
|
|
815
|
} else if (isStartingElement(next, URL)) {
|
|
816
|
String localUrl = getCData(state, reader, next);
|
|
817
|
String url = CdmUtils.Nz(state.getBaseMediaUrl()) + localUrl;
|
|
818
|
if (isBlank(urlString)){
|
|
819
|
urlString = url;
|
|
820
|
}
|
|
821
|
if (! url.equals(urlString)){
|
|
822
|
String message = "URL attribute and URL element differ. Attribute: %s, Element: %s";
|
|
823
|
fireWarningEvent(String.format(message, urlString, url), next, 2);
|
|
824
|
}
|
|
825
|
} else if (isStartingElement(next, NUM)) {
|
|
826
|
numString = getCData(state, reader, next);
|
|
827
|
} else if (next.isCharacters()) {
|
|
828
|
text += CdmUtils.concat("", text, next.asCharacters().getData());
|
|
829
|
} else {
|
|
830
|
fireUnexpectedEvent(next, 0);
|
|
831
|
}
|
|
832
|
}
|
|
833
|
throw new IllegalStateException("<figure> has no end tag");
|
|
834
|
}
|
|
835
|
|
|
836
|
/**
|
|
837
|
* @param state
|
|
838
|
* @param id
|
|
839
|
* @param type
|
|
840
|
* @param urlString
|
|
841
|
* @param legendString
|
|
842
|
* @param titleString
|
|
843
|
* @param numString
|
|
844
|
* @param next
|
|
845
|
*/
|
|
846
|
private Media makeFigure(MarkupImportState state, String id, String type, String urlString,
|
|
847
|
String legendString, String titleString, String numString, XMLEvent next) {
|
|
848
|
Media media = null;
|
|
849
|
boolean isFigure = false;
|
|
850
|
try {
|
|
851
|
//TODO maybe everything is a figure as it is all taken from a book
|
|
852
|
if ("lineart".equals(type)) {
|
|
853
|
isFigure = true;
|
|
854
|
// media = Figure.NewInstance(url.toURI(), null, null, null);
|
|
855
|
} else if (type == null || "photo".equals(type)
|
|
856
|
|| "signature".equals(type)
|
|
857
|
|| "others".equals(type)) {
|
|
858
|
//TODO
|
|
859
|
} else {
|
|
860
|
String message = "Unknown figure type '%s'";
|
|
861
|
message = String.format(message, type);
|
|
862
|
fireWarningEvent(message, next, 2);
|
|
863
|
}
|
|
864
|
media = docImport.getImageMedia(urlString, docImport.getReadMediaData(), isFigure);
|
|
865
|
|
|
866
|
if (media != null){
|
|
867
|
// title
|
|
868
|
if (StringUtils.isNotBlank(titleString)) {
|
|
869
|
media.putTitle(getDefaultLanguage(state), titleString);
|
|
870
|
}
|
|
871
|
// legend
|
|
872
|
if (StringUtils.isNotBlank(legendString)) {
|
|
873
|
media.addDescription(legendString, getDefaultLanguage(state));
|
|
874
|
}
|
|
875
|
if (StringUtils.isNotBlank(numString)) {
|
|
876
|
// TODO use concrete source (e.g. DAPHNIPHYLLACEAE in FM
|
|
877
|
// vol.13)
|
|
878
|
Reference<?> citation = state.getConfig().getSourceReference();
|
|
879
|
media.addSource(numString, "num", citation, null);
|
|
880
|
// TODO name used in source if available
|
|
881
|
}
|
|
882
|
// TODO which citation
|
|
883
|
if (StringUtils.isNotBlank(id)) {
|
|
884
|
media.addSource(id, null, state.getConfig().getSourceReference(), null);
|
|
885
|
} else {
|
|
886
|
String message = "Figure id should never be empty or null";
|
|
887
|
fireWarningEvent(message, next, 6);
|
|
888
|
}
|
|
889
|
|
|
890
|
// text
|
|
891
|
// do nothing
|
|
892
|
registerGivenFigure(state, next, id, media);
|
|
893
|
|
|
894
|
}else{
|
|
895
|
String message = "No media found: ";
|
|
896
|
fireWarningEvent(message, next, 4);
|
|
897
|
}
|
|
898
|
} catch (MalformedURLException e) {
|
|
899
|
String message = "Media uri has incorrect syntax: %s";
|
|
900
|
message = String.format(message, urlString);
|
|
901
|
fireWarningEvent(message, next, 4);
|
|
902
|
// } catch (URISyntaxException e) {
|
|
903
|
// String message = "Media uri has incorrect syntax: %s";
|
|
904
|
// message = String.format(message, urlString);
|
|
905
|
// fireWarningEvent(message, next, 4);
|
|
906
|
}
|
|
907
|
|
|
908
|
return media;
|
|
909
|
}
|
|
910
|
|
|
911
|
private FigureDataHolder handleFigureRef(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent)
|
|
912
|
throws XMLStreamException {
|
|
913
|
FigureDataHolder result = new FigureDataHolder();
|
|
914
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
915
|
result.ref = getAndRemoveAttributeValue(attributes, REF);
|
|
916
|
checkNoAttributes(attributes, parentEvent);
|
|
917
|
|
|
918
|
// text is not handled, needed only for debugging purposes
|
|
919
|
String text = "";
|
|
920
|
while (reader.hasNext()) {
|
|
921
|
XMLEvent next = readNoWhitespace(reader);
|
|
922
|
if (isMyEndingElement(next, parentEvent)) {
|
|
923
|
return result;
|
|
924
|
} else if (isStartingElement(next, NUM)) {
|
|
925
|
String num = getCData(state, reader, next);
|
|
926
|
result.num = num; // num is not handled during import
|
|
927
|
} else if (isStartingElement(next, FIGURE_PART)) {
|
|
928
|
result.figurePart = getCData(state, reader, next);
|
|
929
|
} else if (next.isCharacters()) {
|
|
930
|
text += next.asCharacters().getData();
|
|
931
|
} else {
|
|
932
|
fireUnexpectedEvent(next, 0);
|
|
933
|
}
|
|
934
|
}
|
|
935
|
throw new IllegalStateException("<figureRef> has no end tag");
|
|
936
|
}
|
|
937
|
|
|
938
|
private FootnoteDataHolder handleFootnote(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
939
|
FootnoteDataHolder result = new FootnoteDataHolder();
|
|
940
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
941
|
result.id = getAndRemoveAttributeValue(attributes, ID);
|
|
942
|
// result.ref = getAndRemoveAttributeValue(attributes, REF);
|
|
943
|
checkNoAttributes(attributes, parentEvent);
|
|
944
|
|
|
945
|
while (reader.hasNext()) {
|
|
946
|
XMLEvent next = readNoWhitespace(reader);
|
|
947
|
if (isStartingElement(next, FOOTNOTE_STRING)) {
|
|
948
|
String string = handleFootnoteString(state, reader, next);
|
|
949
|
result.string = string;
|
|
950
|
} else if (isMyEndingElement(next, parentEvent)) {
|
|
951
|
return result;
|
|
952
|
} else {
|
|
953
|
fireUnexpectedEvent(next, 0);
|
|
954
|
}
|
|
955
|
}
|
|
956
|
return result;
|
|
957
|
}
|
|
958
|
|
|
959
|
private FootnoteDataHolder handleFootnoteRef(MarkupImportState state,
|
|
960
|
XMLEventReader reader, XMLEvent parentEvent)
|
|
961
|
throws XMLStreamException {
|
|
962
|
FootnoteDataHolder result = new FootnoteDataHolder();
|
|
963
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
964
|
result.ref = getAndRemoveAttributeValue(attributes, REF);
|
|
965
|
checkNoAttributes(attributes, parentEvent);
|
|
966
|
|
|
967
|
// text is not handled, needed only for debugging purposes
|
|
968
|
String text = "";
|
|
969
|
while (reader.hasNext()) {
|
|
970
|
XMLEvent next = readNoWhitespace(reader);
|
|
971
|
// if (isStartingElement(next, FOOTNOTE_STRING)){
|
|
972
|
// String string = handleFootnoteString(state, reader, next);
|
|
973
|
// result.string = string;
|
|
974
|
// }else
|
|
975
|
if (isMyEndingElement(next, parentEvent)) {
|
|
976
|
return result;
|
|
977
|
} else if (next.isCharacters()) {
|
|
978
|
text += next.asCharacters().getData();
|
|
979
|
|
|
980
|
} else {
|
|
981
|
fireUnexpectedEvent(next, 0);
|
|
982
|
}
|
|
983
|
}
|
|
984
|
return result;
|
|
985
|
}
|
|
986
|
|
|
987
|
|
|
988
|
|
|
989
|
private String handleFootnoteString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
990
|
boolean isTextMode = true;
|
|
991
|
String text = "";
|
|
992
|
while (reader.hasNext()) {
|
|
993
|
XMLEvent next = readNoWhitespace(reader);
|
|
994
|
if (isMyEndingElement(next, parentEvent)) {
|
|
995
|
return text;
|
|
996
|
} else if (next.isEndElement()) {
|
|
997
|
if (isEndingElement(next, FULL_NAME)) {
|
|
998
|
popUnimplemented(next.asEndElement());
|
|
999
|
} else if (isEndingElement(next, BR)) {
|
|
1000
|
isTextMode = true;
|
|
1001
|
} else if (isHtml(next)) {
|
|
1002
|
text += getXmlTag(next);
|
|
1003
|
} else {
|
|
1004
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1005
|
}
|
|
1006
|
} else if (next.isStartElement()) {
|
|
1007
|
if (isStartingElement(next, FULL_NAME)) {
|
|
1008
|
handleNotYetImplementedElement(next);
|
|
1009
|
} else if (isStartingElement(next, GATHERING)) {
|
|
1010
|
text += specimenImport.handleInLineGathering(state, reader, next);
|
|
1011
|
} else if (isStartingElement(next, REFERENCES)) {
|
|
1012
|
text += " " + handleInLineReferences(state, reader, next)+ " ";
|
|
1013
|
} else if (isStartingElement(next, BR)) {
|
|
1014
|
text += "<br/>";
|
|
1015
|
isTextMode = false;
|
|
1016
|
} else if (isStartingElement(next, NOMENCLATURE)) {
|
|
1017
|
handleNotYetImplementedElement(next);
|
|
1018
|
} else if (isHtml(next)) {
|
|
1019
|
text += getXmlTag(next);
|
|
1020
|
} else {
|
|
1021
|
handleUnexpectedStartElement(next.asStartElement());
|
|
1022
|
}
|
|
1023
|
} else if (next.isCharacters()) {
|
|
1024
|
if (!isTextMode) {
|
|
1025
|
String message = "footnoteString is not in text mode";
|
|
1026
|
fireWarningEvent(message, next, 6);
|
|
1027
|
} else {
|
|
1028
|
text += next.asCharacters().getData().trim();
|
|
1029
|
// getCData(state, reader, next); does not work as we have inner tags like <references>
|
|
1030
|
}
|
|
1031
|
} else {
|
|
1032
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1033
|
}
|
|
1034
|
}
|
|
1035
|
throw new IllegalStateException("<footnoteString> has no closing tag");
|
|
1036
|
|
|
1037
|
}
|
|
1038
|
|
|
1039
|
private String handleInLineReferences(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1040
|
checkNoAttributes(parentEvent);
|
|
1041
|
|
|
1042
|
boolean hasReference = false;
|
|
1043
|
String text = "";
|
|
1044
|
while (reader.hasNext()) {
|
|
1045
|
XMLEvent next = readNoWhitespace(reader);
|
|
1046
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1047
|
checkMandatoryElement(hasReference, parentEvent.asStartElement(), REFERENCE);
|
|
1048
|
return text;
|
|
1049
|
} else if (isStartingElement(next, REFERENCE)) {
|
|
1050
|
text += handleInLineReference(state, reader, next);
|
|
1051
|
hasReference = true;
|
|
1052
|
} else {
|
|
1053
|
handleUnexpectedElement(next);
|
|
1054
|
}
|
|
1055
|
}
|
|
1056
|
throw new IllegalStateException("<References> has no closing tag");
|
|
1057
|
}
|
|
1058
|
|
|
1059
|
private String handleInLineReference(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {
|
|
1060
|
Reference<?> reference = nomenclatureImport.handleReference(state, reader, parentEvent);
|
|
1061
|
String result = "<cdm:ref uuid='%s'>%s</ref>";
|
|
1062
|
result = String.format(result, reference.getUuid(), reference.getTitleCache());
|
|
1063
|
save(reference, state);
|
|
1064
|
return result;
|
|
1065
|
}
|
|
1066
|
|
|
1067
|
private void handleFeature(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1068
|
Map<String, Attribute> attrs = getAttributes(parentEvent);
|
|
1069
|
Boolean isFreetext = getAndRemoveBooleanAttributeValue(parentEvent, attrs, IS_FREETEXT, false);
|
|
1070
|
String classValue =getAndRemoveRequiredAttributeValue(parentEvent, attrs, CLASS);
|
|
1071
|
checkNoAttributes(attrs, parentEvent);
|
|
1072
|
|
|
1073
|
|
|
1074
|
Feature feature = makeFeature(classValue, state, parentEvent, null);
|
|
1075
|
Taxon taxon = state.getCurrentTaxon();
|
|
1076
|
TaxonDescription taxonDescription = getTaxonDescription(taxon, state.getConfig().getSourceReference(), NO_IMAGE_GALLERY, CREATE_NEW);
|
|
1077
|
// TextData figureHolderTextData = null; //for use with one TextData for
|
|
1078
|
// all figure only
|
|
1079
|
|
|
1080
|
boolean isDescription = feature.equals(Feature.DESCRIPTION());
|
|
1081
|
DescriptionElementBase lastDescriptionElement = null;
|
|
1082
|
|
|
1083
|
while (reader.hasNext()) {
|
|
1084
|
XMLEvent next = readNoWhitespace(reader);
|
|
1085
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1086
|
state.putFeatureToGeneralSorterList(feature);
|
|
1087
|
return;
|
|
1088
|
} else if (isEndingElement(next, DISTRIBUTION_LIST) || isEndingElement(next, HABITAT_LIST)) {
|
|
1089
|
// only handle list elements
|
|
1090
|
} else if (isStartingElement(next, HEADING)) {
|
|
1091
|
makeFeatureHeading(state, reader, classValue, feature, next);
|
|
1092
|
} else if (isStartingElement(next, WRITER)) {
|
|
1093
|
makeFeatureWriter(state, reader, feature, taxon, next);
|
|
1094
|
// } else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {
|
|
1095
|
// if (!feature.equals(Feature.DISTRIBUTION())) {
|
|
1096
|
// String message = "Distribution locality only allowed for feature of type 'distribution'";
|
|
1097
|
// fireWarningEvent(message, next, 4);
|
|
1098
|
// }
|
|
1099
|
// handleDistributionLocality(state, reader, next);
|
|
1100
|
} else if (isStartingElement(next, DISTRIBUTION_LIST) || isStartingElement(next, HABITAT_LIST)) {
|
|
1101
|
// only handle single list elements
|
|
1102
|
} else if (isStartingElement(next, HABITAT)) {
|
|
1103
|
if (!(feature.equals(Feature.HABITAT())
|
|
1104
|
|| feature.equals(Feature.HABITAT_ECOLOGY())
|
|
1105
|
|| feature.equals(Feature.ECOLOGY()))) {
|
|
1106
|
String message = "Habitat only allowed for feature of type 'habitat','habitat ecology' or 'ecology'";
|
|
1107
|
fireWarningEvent(message, next, 4);
|
|
1108
|
}
|
|
1109
|
handleHabitat(state, reader, next);
|
|
1110
|
} else if (isStartingElement(next, CHAR)) {
|
|
1111
|
List<TextData> textDataList = handleChar(state, reader, next, null);
|
|
1112
|
for (TextData textData : textDataList){
|
|
1113
|
taxonDescription.addElement(textData);
|
|
1114
|
}
|
|
1115
|
} else if (isStartingElement(next, STRING)) {
|
|
1116
|
lastDescriptionElement = makeFeatureString(state, reader,feature, taxonDescription, lastDescriptionElement,next, isFreetext);
|
|
1117
|
} else if (isStartingElement(next, FIGURE_REF)) {
|
|
1118
|
lastDescriptionElement = makeFeatureFigureRef(state, reader, taxonDescription, isDescription, lastDescriptionElement, next);
|
|
1119
|
} else if (isStartingElement(next, REFERENCES)) {
|
|
1120
|
// TODO details/microcitation ??
|
|
1121
|
|
|
1122
|
List<Reference<?>> refs = handleReferences(state, reader, next);
|
|
1123
|
if (!refs.isEmpty()) {
|
|
1124
|
// TODO
|
|
1125
|
Reference<?> descriptionRef = state.getConfig().getSourceReference();
|
|
1126
|
TaxonDescription description = getTaxonDescription(taxon, descriptionRef, false, true);
|
|
1127
|
TextData featurePlaceholder = docImport.getFeaturePlaceholder(state, description, feature, true);
|
|
1128
|
for (Reference<?> citation : refs) {
|
|
1129
|
featurePlaceholder.addSource(null, null, citation, null);
|
|
1130
|
}
|
|
1131
|
} else {
|
|
1132
|
String message = "No reference found in references";
|
|
1133
|
fireWarningEvent(message, next, 6);
|
|
1134
|
}
|
|
1135
|
} else if (isStartingElement(next, NUM)) {
|
|
1136
|
//TODO
|
|
1137
|
handleNotYetImplementedElement(next);
|
|
1138
|
} else if (isEndingElement(next, NUM)) {
|
|
1139
|
//TODO
|
|
1140
|
popUnimplemented(next.asEndElement());
|
|
1141
|
} else {
|
|
1142
|
handleUnexpectedElement(next);
|
|
1143
|
}
|
|
1144
|
}
|
|
1145
|
throw new IllegalStateException("<Feature> has no closing tag");
|
|
1146
|
}
|
|
1147
|
|
|
1148
|
/**
|
|
1149
|
* @param state
|
|
1150
|
* @param reader
|
|
1151
|
* @param taxonDescription
|
|
1152
|
* @param isDescription
|
|
1153
|
* @param lastDescriptionElement
|
|
1154
|
* @param next
|
|
1155
|
* @return
|
|
1156
|
* @throws XMLStreamException
|
|
1157
|
*/
|
|
1158
|
private DescriptionElementBase makeFeatureFigureRef(MarkupImportState state, XMLEventReader reader,TaxonDescription taxonDescription,
|
|
1159
|
boolean isDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next) throws XMLStreamException {
|
|
1160
|
FigureDataHolder figureHolder = handleFigureRef(state, reader, next);
|
|
1161
|
Feature figureFeature = getFeature(state, MarkupTransformer.uuidFigures, "Figures", "Figures", "Fig.",null);
|
|
1162
|
if (isDescription) {
|
|
1163
|
TextData figureHolderTextData = null;
|
|
1164
|
// if (figureHolderTextData == null){
|
|
1165
|
figureHolderTextData = TextData.NewInstance(figureFeature);
|
|
1166
|
if (StringUtils.isNotBlank(figureHolder.num)) {
|
|
1167
|
String annotationText = "<num>" + figureHolder.num.trim() + "</num>";
|
|
1168
|
Annotation annotation = Annotation.NewInstance(annotationText, AnnotationType.TECHNICAL(), getDefaultLanguage(state));
|
|
1169
|
figureHolderTextData.addAnnotation(annotation);
|
|
1170
|
}
|
|
1171
|
if (StringUtils.isNotBlank(figureHolder.figurePart)) {
|
|
1172
|
String annotationText = "<figurePart>"+ figureHolder.figurePart.trim() + "</figurePart>";
|
|
1173
|
Annotation annotation = Annotation.NewInstance(annotationText,AnnotationType.EDITORIAL(), getDefaultLanguage(state));
|
|
1174
|
figureHolderTextData.addAnnotation(annotation);
|
|
1175
|
}
|
|
1176
|
// if (StringUtils.isNotBlank(figureText)){
|
|
1177
|
// figureHolderTextData.putText(language, figureText);
|
|
1178
|
// }
|
|
1179
|
taxonDescription.addElement(figureHolderTextData);
|
|
1180
|
// }
|
|
1181
|
registerFigureDemand(state, next, figureHolderTextData, figureHolder.ref);
|
|
1182
|
} else {
|
|
1183
|
if (lastDescriptionElement == null) {
|
|
1184
|
String message = "No description element created yet that can be referred by figure. Create new TextData instead";
|
|
1185
|
fireWarningEvent(message, next, 4);
|
|
1186
|
lastDescriptionElement = TextData.NewInstance(figureFeature);
|
|
1187
|
taxonDescription.addElement(lastDescriptionElement);
|
|
1188
|
}
|
|
1189
|
registerFigureDemand(state, next, lastDescriptionElement, figureHolder.ref);
|
|
1190
|
}
|
|
1191
|
return lastDescriptionElement;
|
|
1192
|
}
|
|
1193
|
|
|
1194
|
/**
|
|
1195
|
* @param state
|
|
1196
|
* @param reader
|
|
1197
|
* @param feature
|
|
1198
|
* @param taxonDescription
|
|
1199
|
* @param lastDescriptionElement
|
|
1200
|
* @param distributionList
|
|
1201
|
* @param next
|
|
1202
|
* @return
|
|
1203
|
* @throws XMLStreamException
|
|
1204
|
*/
|
|
1205
|
private DescriptionElementBase makeFeatureString(MarkupImportState state,XMLEventReader reader, Feature feature,
|
|
1206
|
TaxonDescription taxonDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next, Boolean isFreetext) throws XMLStreamException {
|
|
1207
|
|
|
1208
|
//for specimen only
|
|
1209
|
if (feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.MATERIALS_EXAMINED())){
|
|
1210
|
|
|
1211
|
List<DescriptionElementBase> specimens = specimenImport.handleMaterialsExamined(state, reader, next, feature);
|
|
1212
|
for (DescriptionElementBase specimen : specimens){
|
|
1213
|
taxonDescription.addElement(specimen);
|
|
1214
|
lastDescriptionElement = specimen;
|
|
1215
|
}
|
|
1216
|
state.setCurrentCollector(null);
|
|
1217
|
|
|
1218
|
return lastDescriptionElement;
|
|
1219
|
}else{
|
|
1220
|
|
|
1221
|
//others
|
|
1222
|
Map<String, String> subheadingMap = handleString(state, reader, next, feature);
|
|
1223
|
for (String subheading : subheadingMap.keySet()) {
|
|
1224
|
Feature subheadingFeature = feature;
|
|
1225
|
if (StringUtils.isNotBlank(subheading) && subheadingMap.size() > 1) {
|
|
1226
|
subheadingFeature = makeFeature(subheading, state, next, null);
|
|
1227
|
}
|
|
1228
|
if (feature.equals(Feature.COMMON_NAME()) && (isFreetext == null || !isFreetext)){
|
|
1229
|
List<DescriptionElementBase> commonNames = makeVernacular(state, subheading, subheadingMap.get(subheading));
|
|
1230
|
for (DescriptionElementBase commonName : commonNames){
|
|
1231
|
taxonDescription.addElement(commonName);
|
|
1232
|
lastDescriptionElement = commonName;
|
|
1233
|
}
|
|
1234
|
}else {
|
|
1235
|
TextData textData = TextData.NewInstance(subheadingFeature);
|
|
1236
|
textData.putText(getDefaultLanguage(state), subheadingMap.get(subheading));
|
|
1237
|
taxonDescription.addElement(textData);
|
|
1238
|
lastDescriptionElement = textData;
|
|
1239
|
// TODO how to handle figures when these data are split in
|
|
1240
|
// subheadings
|
|
1241
|
}
|
|
1242
|
}
|
|
1243
|
return lastDescriptionElement;
|
|
1244
|
}
|
|
1245
|
}
|
|
1246
|
|
|
1247
|
private List<DescriptionElementBase> makeVernacular(MarkupImportState state, String subheading, String commonNameString) throws XMLStreamException {
|
|
1248
|
List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();
|
|
1249
|
String[] splits = commonNameString.split(",");
|
|
1250
|
for (String split : splits){
|
|
1251
|
split = split.trim();
|
|
1252
|
if (! split.matches(".*\\(.*\\)\\.?")){
|
|
1253
|
fireWarningEvent("Common name string '"+split+"' does not match given pattern", state.getReader().peek(), 4);
|
|
1254
|
}
|
|
1255
|
|
|
1256
|
String name = split.replaceAll("\\(.*\\)", "").replace(".", "").trim();
|
|
1257
|
String languageStr = split.replaceFirst(".*\\(", "").replaceAll("\\)\\.?", "").trim();
|
|
1258
|
|
|
1259
|
Language language = null;
|
|
1260
|
if (StringUtils.isNotBlank(languageStr)){
|
|
1261
|
try {
|
|
1262
|
UUID langUuid = state.getTransformer().getLanguageUuid(languageStr);
|
|
1263
|
TermVocabulary<?> voc = null;
|
|
1264
|
language = getLanguage(state, langUuid, languageStr, languageStr, null, voc);
|
|
1265
|
if (language == null){
|
|
1266
|
logger.warn("Language " + languageStr + " not recognized by transformer");
|
|
1267
|
}
|
|
1268
|
} catch (UndefinedTransformerMethodException e) {
|
|
1269
|
throw new RuntimeException(e);
|
|
1270
|
}
|
|
1271
|
}
|
|
1272
|
NamedArea area = null;
|
|
1273
|
CommonTaxonName commonTaxonName = CommonTaxonName.NewInstance(name, language, area);
|
|
1274
|
result.add(commonTaxonName);
|
|
1275
|
}
|
|
1276
|
|
|
1277
|
return result;
|
|
1278
|
}
|
|
1279
|
|
|
1280
|
/**
|
|
1281
|
* @param state
|
|
1282
|
* @param reader
|
|
1283
|
* @param feature
|
|
1284
|
* @param taxon
|
|
1285
|
* @param next
|
|
1286
|
* @throws XMLStreamException
|
|
1287
|
*/
|
|
1288
|
private void makeFeatureWriter(MarkupImportState state,XMLEventReader reader, Feature feature, Taxon taxon, XMLEvent next) throws XMLStreamException {
|
|
1289
|
WriterDataHolder writer = handleWriter(state, reader, next);
|
|
1290
|
if (isNotBlank(writer.writer)) {
|
|
1291
|
// TODO
|
|
1292
|
Reference<?> ref = state.getConfig().getSourceReference();
|
|
1293
|
TaxonDescription description = getTaxonDescription(taxon, ref,
|
|
1294
|
false, true);
|
|
1295
|
TextData featurePlaceholder = docImport.getFeaturePlaceholder(state,
|
|
1296
|
description, feature, true);
|
|
1297
|
featurePlaceholder.addAnnotation(writer.annotation);
|
|
1298
|
registerFootnotes(state, featurePlaceholder, writer.footnotes);
|
|
1299
|
} else {
|
|
1300
|
String message = "Writer element is empty";
|
|
1301
|
fireWarningEvent(message, next, 4);
|
|
1302
|
}
|
|
1303
|
}
|
|
1304
|
|
|
1305
|
/**
|
|
1306
|
* @param state
|
|
1307
|
* @param reader
|
|
1308
|
* @param classValue
|
|
1309
|
* @param feature
|
|
1310
|
* @param next
|
|
1311
|
* @throws XMLStreamException
|
|
1312
|
*/
|
|
1313
|
private void makeFeatureHeading(MarkupImportState state, XMLEventReader reader, String classValue, Feature feature, XMLEvent next) throws XMLStreamException {
|
|
1314
|
String heading = handleHeading(state, reader, next);
|
|
1315
|
if (StringUtils.isNotBlank(heading)) {
|
|
1316
|
if (!heading.equalsIgnoreCase(classValue)) {
|
|
1317
|
try {
|
|
1318
|
if (!feature.equals(state.getTransformer().getFeatureByKey(
|
|
1319
|
heading))) {
|
|
1320
|
UUID headerFeatureUuid = state.getTransformer()
|
|
1321
|
.getFeatureUuid(heading);
|
|
1322
|
if (!feature.getUuid().equals(headerFeatureUuid)) {
|
|
1323
|
String message = "Feature heading '%s' differs from feature class '%s' and can not be transformed to feature";
|
|
1324
|
message = String.format(message, heading,
|
|
1325
|
classValue);
|
|
1326
|
fireWarningEvent(message, next, 1);
|
|
1327
|
}
|
|
1328
|
}
|
|
1329
|
} catch (UndefinedTransformerMethodException e) {
|
|
1330
|
throw new RuntimeException(e);
|
|
1331
|
}
|
|
1332
|
} else {
|
|
1333
|
// do nothing
|
|
1334
|
}
|
|
1335
|
}
|
|
1336
|
}
|
|
1337
|
|
|
1338
|
private List<Reference<?>> handleReferences(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1339
|
// attributes
|
|
1340
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
1341
|
String bibliography = getAndRemoveAttributeValue(attributes,
|
|
1342
|
BIBLIOGRAPHY);
|
|
1343
|
String serialsAbbreviations = getAndRemoveAttributeValue(attributes,
|
|
1344
|
SERIALS_ABBREVIATIONS);
|
|
1345
|
if (isNotBlank(bibliography) || isNotBlank(serialsAbbreviations)) {
|
|
1346
|
String message = "Attributes not yet implemented for <references>";
|
|
1347
|
fireWarningEvent(message, parentEvent, 4);
|
|
1348
|
}
|
|
1349
|
|
|
1350
|
List<Reference<?>> result = new ArrayList<Reference<?>>();
|
|
1351
|
|
|
1352
|
// elements
|
|
1353
|
while (reader.hasNext()) {
|
|
1354
|
XMLEvent next = readNoWhitespace(reader);
|
|
1355
|
if (next.isEndElement()) {
|
|
1356
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1357
|
return result;
|
|
1358
|
} else {
|
|
1359
|
if (isEndingElement(next, HEADING)) {
|
|
1360
|
// NOT YET IMPLEMENTED
|
|
1361
|
popUnimplemented(next.asEndElement());
|
|
1362
|
} else if (isEndingElement(next, WRITER)) {
|
|
1363
|
// NOT YET IMPLEMENTED
|
|
1364
|
popUnimplemented(next.asEndElement());
|
|
1365
|
} else if (isEndingElement(next, FOOTNOTE)) {
|
|
1366
|
// NOT YET IMPLEMENTED
|
|
1367
|
popUnimplemented(next.asEndElement());
|
|
1368
|
} else if (isEndingElement(next, STRING)) {
|
|
1369
|
// NOT YET IMPLEMENTED
|
|
1370
|
popUnimplemented(next.asEndElement());
|
|
1371
|
} else if (isEndingElement(next, REF_NUM)) {
|
|
1372
|
// NOT YET IMPLEMENTED
|
|
1373
|
popUnimplemented(next.asEndElement());
|
|
1374
|
} else {
|
|
1375
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1376
|
}
|
|
1377
|
}
|
|
1378
|
} else if (next.isStartElement()) {
|
|
1379
|
if (isStartingElement(next, HEADING)) {
|
|
1380
|
handleNotYetImplementedElement(next);
|
|
1381
|
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
1382
|
String subheading = getCData(state, reader, next).trim();
|
|
1383
|
String excludePattern = "(i?)(References?|Literature):?";
|
|
1384
|
if (!subheading.matches(excludePattern)) {
|
|
1385
|
fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);
|
|
1386
|
}
|
|
1387
|
} else if (isStartingElement(next, WRITER)) {
|
|
1388
|
handleNotYetImplementedElement(next);
|
|
1389
|
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
1390
|
handleNotYetImplementedElement(next);
|
|
1391
|
} else if (isStartingElement(next, STRING)) {
|
|
1392
|
handleNotYetImplementedElement(next);
|
|
1393
|
} else if (isStartingElement(next, REF_NUM)) {
|
|
1394
|
handleNotYetImplementedElement(next);
|
|
1395
|
} else if (isStartingElement(next, REFERENCE)) {
|
|
1396
|
Reference<?> ref = nomenclatureImport.handleReference(state, reader, next);
|
|
1397
|
result.add(ref);
|
|
1398
|
} else {
|
|
1399
|
handleUnexpectedStartElement(next);
|
|
1400
|
}
|
|
1401
|
} else {
|
|
1402
|
handleUnexpectedElement(next);
|
|
1403
|
}
|
|
1404
|
}
|
|
1405
|
throw new IllegalStateException("<References> has no closing tag");
|
|
1406
|
}
|
|
1407
|
|
|
1408
|
private void handleHabitat(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1409
|
checkNoAttributes(parentEvent);
|
|
1410
|
Taxon taxon = state.getCurrentTaxon();
|
|
1411
|
// TODO which ref to take?
|
|
1412
|
Reference<?> ref = state.getConfig().getSourceReference();
|
|
1413
|
|
|
1414
|
String text = "";
|
|
1415
|
while (reader.hasNext()) {
|
|
1416
|
XMLEvent next = readNoWhitespace(reader);
|
|
1417
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1418
|
TaxonDescription description = getTaxonDescription(taxon, ref,
|
|
1419
|
false, true);
|
|
1420
|
UUID uuidExtractedHabitat = MarkupTransformer.uuidExtractedHabitat;
|
|
1421
|
Feature feature = getFeature(
|
|
1422
|
state,
|
|
1423
|
uuidExtractedHabitat,
|
|
1424
|
"Extracted Habitat",
|
|
1425
|
"An structured habitat that was extracted from a habitat text",
|
|
1426
|
"extr. habit.", null);
|
|
1427
|
TextData habitat = TextData.NewInstance(feature);
|
|
1428
|
habitat.putText(getDefaultLanguage(state), text);
|
|
1429
|
description.addElement(habitat);
|
|
1430
|
|
|
1431
|
return;
|
|
1432
|
} else if (next.isStartElement()) {
|
|
1433
|
if (isStartingElement(next, ALTITUDE)) {
|
|
1434
|
text = text.trim() + getTaggedCData(state, reader, next);
|
|
1435
|
} else if (isStartingElement(next, LIFE_CYCLE_PERIODS)) {
|
|
1436
|
handleNotYetImplementedElement(next);
|
|
1437
|
} else {
|
|
1438
|
handleUnexpectedStartElement(next.asStartElement());
|
|
1439
|
}
|
|
1440
|
} else if (next.isCharacters()) {
|
|
1441
|
text += next.asCharacters().getData();
|
|
1442
|
} else {
|
|
1443
|
handleUnexpectedElement(next);
|
|
1444
|
}
|
|
1445
|
}
|
|
1446
|
throw new IllegalStateException("<Habitat> has no closing tag");
|
|
1447
|
}
|
|
1448
|
|
|
1449
|
private String getTaggedCData(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
1450
|
checkNoAttributes(parentEvent);
|
|
1451
|
|
|
1452
|
String text = getXmlTag(parentEvent);
|
|
1453
|
while (reader.hasNext()) {
|
|
1454
|
XMLEvent next = readNoWhitespace(reader);
|
|
1455
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1456
|
text += getXmlTag(next);
|
|
1457
|
return text;
|
|
1458
|
} else if (next.isStartElement()) {
|
|
1459
|
text += getTaggedCData(state, reader, next);
|
|
1460
|
} else if (next.isEndElement()) {
|
|
1461
|
text += getTaggedCData(state, reader, next);
|
|
1462
|
} else if (next.isCharacters()) {
|
|
1463
|
text += next.asCharacters().getData();
|
|
1464
|
} else {
|
|
1465
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1466
|
}
|
|
1467
|
}
|
|
1468
|
throw new IllegalStateException("Some tag has no closing tag");
|
|
1469
|
}
|
|
1470
|
|
|
1471
|
private String handleDistributionLocality(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {
|
|
1472
|
Map<String, Attribute> attributes = getAttributes(parentEvent);
|
|
1473
|
String classValue = getAndRemoveRequiredAttributeValue(parentEvent, attributes, CLASS);
|
|
1474
|
String statusValue =getAndRemoveAttributeValue(attributes, STATUS);
|
|
1475
|
String frequencyValue =getAndRemoveAttributeValue(attributes, FREQUENCY);
|
|
1476
|
|
|
1477
|
|
|
1478
|
Taxon taxon = state.getCurrentTaxon();
|
|
1479
|
// TODO which ref to take?
|
|
1480
|
Reference<?> ref = state.getConfig().getSourceReference();
|
|
1481
|
|
|
1482
|
String text = "";
|
|
1483
|
while (reader.hasNext()) {
|
|
1484
|
XMLEvent next = readNoWhitespace(reader);
|
|
1485
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1486
|
if (StringUtils.isNotBlank(text)) {
|
|
1487
|
String label = CdmUtils.removeTrailingDot(normalize(text));
|
|
1488
|
TaxonDescription description = getTaxonDescription(taxon, ref, false, true);
|
|
1489
|
NamedAreaLevel level = makeNamedAreaLevel(state,classValue, next);
|
|
1490
|
|
|
1491
|
//status
|
|
1492
|
PresenceAbsenceTermBase<?> status = null;
|
|
1493
|
if (isNotBlank(statusValue)){
|
|
1494
|
try {
|
|
1495
|
status = state.getTransformer().getPresenceTermByKey(statusValue);
|
|
1496
|
if (status == null){
|
|
1497
|
//TODO
|
|
1498
|
String message = "The presence/absence status '%s' could not be transformed to an CDM status";
|
|
1499
|
fireWarningEvent(String.format(message, statusValue), next, 4);
|
|
1500
|
}
|
|
1501
|
} catch (UndefinedTransformerMethodException e) {
|
|
1502
|
throw new RuntimeException(e);
|
|
1503
|
}
|
|
1504
|
}else{
|
|
1505
|
status = PresenceTerm.PRESENT();
|
|
1506
|
}
|
|
1507
|
//frequency
|
|
1508
|
if (isNotBlank(frequencyValue)){
|
|
1509
|
String message = "The frequency attribute is currently not yet available in CDM";
|
|
1510
|
fireWarningEvent(message, parentEvent, 6);
|
|
1511
|
}
|
|
1512
|
|
|
1513
|
NamedArea higherArea = null;
|
|
1514
|
List<NamedArea> areas = new ArrayList<NamedArea>();
|
|
1515
|
|
|
1516
|
String patSingleArea = "([^,\\(]{3,})";
|
|
1517
|
String patSeparator = "(,|\\sand\\s)";
|
|
1518
|
String hierarchiePattern = String.format("%s\\((%s(%s%s)*)\\)",patSingleArea, patSingleArea, patSeparator, patSingleArea);
|
|
1519
|
Pattern patHierarchie = Pattern.compile(hierarchiePattern, Pattern.CASE_INSENSITIVE);
|
|
1520
|
Matcher matcher = patHierarchie.matcher(label);
|
|
1521
|
if (matcher.matches()){
|
|
1522
|
String higherAreaStr = matcher.group(1).trim();
|
|
1523
|
higherArea = makeArea(state, higherAreaStr, level);
|
|
1524
|
String[] innerAreas = matcher.group(2).split(patSeparator);
|
|
1525
|
for (String innerArea : innerAreas){
|
|
1526
|
if (isNotBlank(innerArea)){
|
|
1527
|
NamedArea singleArea = makeArea(state, innerArea.trim(), level);
|
|
1528
|
areas.add(singleArea);
|
|
1529
|
NamedArea partOf = singleArea.getPartOf();
|
|
1530
|
// if (partOf == null){
|
|
1531
|
// singleArea.setPartOf(higherArea);
|
|
1532
|
// }
|
|
1533
|
}
|
|
1534
|
}
|
|
1535
|
}else{
|
|
1536
|
NamedArea singleArea = makeArea(state, label, level);
|
|
1537
|
areas.add(singleArea);
|
|
1538
|
}
|
|
1539
|
|
|
1540
|
for (NamedArea area : areas){
|
|
1541
|
//create distribution
|
|
1542
|
Distribution distribution = Distribution.NewInstance(area,status);
|
|
1543
|
description.addElement(distribution);
|
|
1544
|
}
|
|
1545
|
} else {
|
|
1546
|
String message = "Empty distribution locality";
|
|
1547
|
fireWarningEvent(message, next, 4);
|
|
1548
|
}
|
|
1549
|
return text;
|
|
1550
|
} else if (isStartingElement(next, COORDINATES)) {
|
|
1551
|
//TODO
|
|
1552
|
handleNotYetImplementedElement(next);
|
|
1553
|
} else if (isEndingElement(next, COORDINATES)) {
|
|
1554
|
//TODO
|
|
1555
|
popUnimplemented(next.asEndElement());
|
|
1556
|
} else if (next.isCharacters()) {
|
|
1557
|
text += next.asCharacters().getData();
|
|
1558
|
} else {
|
|
1559
|
handleUnexpectedElement(next);
|
|
1560
|
}
|
|
1561
|
}
|
|
1562
|
throw new IllegalStateException("<DistributionLocality> has no closing tag");
|
|
1563
|
}
|
|
1564
|
|
|
1565
|
private String handleHeading(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {
|
|
1566
|
checkNoAttributes(parentEvent);
|
|
1567
|
|
|
1568
|
String text = "";
|
|
1569
|
while (reader.hasNext()) {
|
|
1570
|
XMLEvent next = readNoWhitespace(reader);
|
|
1571
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1572
|
return text;
|
|
1573
|
} else if (next.isStartElement()) {
|
|
1574
|
if (isStartingElement(next, FOOTNOTE)) {
|
|
1575
|
handleNotYetImplementedElement(next);
|
|
1576
|
} else {
|
|
1577
|
handleUnexpectedStartElement(next.asStartElement());
|
|
1578
|
}
|
|
1579
|
} else if (next.isCharacters()) {
|
|
1580
|
text += next.asCharacters().getData();
|
|
1581
|
} else {
|
|
1582
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1583
|
}
|
|
1584
|
}
|
|
1585
|
throw new IllegalStateException("<String> has no closing tag");
|
|
1586
|
|
|
1587
|
}
|
|
1588
|
|
|
1589
|
/**
|
|
1590
|
* Handle string
|
|
1591
|
* @param state
|
|
1592
|
* @param reader
|
|
1593
|
* @param parentEvent
|
|
1594
|
* @param feature only needed for distributionLocalities
|
|
1595
|
* @return
|
|
1596
|
* @throws XMLStreamException
|
|
1597
|
*/
|
|
1598
|
private Map<String, String> handleString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature feature)throws XMLStreamException {
|
|
1599
|
// attributes
|
|
1600
|
String classValue = getClassOnlyAttribute(parentEvent, false);
|
|
1601
|
if (StringUtils.isNotBlank(classValue)) {
|
|
1602
|
String message = "class attribute for <string> not yet implemented";
|
|
1603
|
fireWarningEvent(message, parentEvent, 2);
|
|
1604
|
}
|
|
1605
|
|
|
1606
|
// subheadings
|
|
1607
|
Map<String, String> subHeadingMap = new HashMap<String, String>();
|
|
1608
|
String currentSubheading = null;
|
|
1609
|
|
|
1610
|
boolean isTextMode = true;
|
|
1611
|
String text = "";
|
|
1612
|
while (reader.hasNext()) {
|
|
1613
|
XMLEvent next = readNoWhitespace(reader);
|
|
1614
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1615
|
putCurrentSubheading(subHeadingMap, currentSubheading, text);
|
|
1616
|
return subHeadingMap;
|
|
1617
|
} else if (isStartingElement(next, BR)) {
|
|
1618
|
text += "<br/>";
|
|
1619
|
isTextMode = false;
|
|
1620
|
} else if (isEndingElement(next, BR)) {
|
|
1621
|
isTextMode = true;
|
|
1622
|
} else if (isHtml(next)) {
|
|
1623
|
text += getXmlTag(next);
|
|
1624
|
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
1625
|
text = putCurrentSubheading(subHeadingMap,currentSubheading, text);
|
|
1626
|
// TODO footnotes
|
|
1627
|
currentSubheading = getCData(state, reader, next).trim();
|
|
1628
|
} else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {
|
|
1629
|
if (feature != null && !feature.equals(Feature.DISTRIBUTION())) {
|
|
1630
|
String message = "Distribution locality only allowed for feature of type 'distribution'";
|
|
1631
|
fireWarningEvent(message, next, 4);
|
|
1632
|
}
|
|
1633
|
text += handleDistributionLocality(state, reader, next);
|
|
1634
|
} else if (next.isCharacters()) {
|
|
1635
|
if (! isTextMode) {
|
|
1636
|
String message = "String is not in text mode";
|
|
1637
|
fireWarningEvent(message, next, 6);
|
|
1638
|
} else {
|
|
1639
|
text += next.asCharacters().getData();
|
|
1640
|
}
|
|
1641
|
} else if (isStartingElement(next, HEADING)) {
|
|
1642
|
//TODO
|
|
1643
|
handleNotYetImplementedElement(next);
|
|
1644
|
} else if (isStartingElement(next, VERNACULAR_NAMES)) {
|
|
1645
|
//TODO
|
|
1646
|
handleNotYetImplementedElement(next);
|
|
1647
|
} else if (isEndingElement(next, HEADING)) {
|
|
1648
|
//TODO
|
|
1649
|
popUnimplemented(next.asEndElement());
|
|
1650
|
} else if (isStartingElement(next, QUOTE)) {
|
|
1651
|
//TODO
|
|
1652
|
handleNotYetImplementedElement(next);
|
|
1653
|
} else if (isEndingElement(next, QUOTE)) {
|
|
1654
|
//TODO
|
|
1655
|
popUnimplemented(next.asEndElement());
|
|
1656
|
} else if (isStartingElement(next, DEDICATION)) {
|
|
1657
|
//TODO
|
|
1658
|
handleNotYetImplementedElement(next);
|
|
1659
|
} else if (isEndingElement(next, DEDICATION)) {
|
|
1660
|
//TODO
|
|
1661
|
popUnimplemented(next.asEndElement());
|
|
1662
|
} else if (isStartingElement(next, TAXONTYPE)) {
|
|
1663
|
//TODO
|
|
1664
|
handleNotYetImplementedElement(next);
|
|
1665
|
} else if (isEndingElement(next, TAXONTYPE)) {
|
|
1666
|
//TODO
|
|
1667
|
popUnimplemented(next.asEndElement());
|
|
1668
|
} else if (isStartingElement(next, FULL_NAME)) {
|
|
1669
|
//TODO
|
|
1670
|
handleNotYetImplementedElement(next);
|
|
1671
|
} else if (isEndingElement(next, FULL_NAME)) {
|
|
1672
|
//TODO
|
|
1673
|
popUnimplemented(next.asEndElement());
|
|
1674
|
}else if (isStartingElement(next, REFERENCES)) {
|
|
1675
|
//TODO
|
|
1676
|
handleNotYetImplementedElement(next);
|
|
1677
|
} else if (isEndingElement(next, REFERENCES)) {
|
|
1678
|
//TODO
|
|
1679
|
popUnimplemented(next.asEndElement());
|
|
1680
|
} else if (isStartingElement(next, GATHERING)) {
|
|
1681
|
//TODO
|
|
1682
|
handleNotYetImplementedElement(next);
|
|
1683
|
} else if (isEndingElement(next, GATHERING)) {
|
|
1684
|
//TODO
|
|
1685
|
popUnimplemented(next.asEndElement());
|
|
1686
|
} else if (isStartingElement(next, ANNOTATION)) {
|
|
1687
|
//TODO //TODO test handleSimpleAnnotation
|
|
1688
|
handleNotYetImplementedElement(next);
|
|
1689
|
} else if (isEndingElement(next, ANNOTATION)) {
|
|
1690
|
//TODO
|
|
1691
|
popUnimplemented(next.asEndElement());
|
|
1692
|
} else if (isStartingElement(next, HABITAT)) {
|
|
1693
|
//TODO
|
|
1694
|
handleNotYetImplementedElement(next);
|
|
1695
|
} else if (isEndingElement(next, HABITAT)) {
|
|
1696
|
//TODO
|
|
1697
|
popUnimplemented(next.asEndElement());
|
|
1698
|
} else if (isStartingElement(next, FIGURE_REF)) {
|
|
1699
|
//TODO
|
|
1700
|
handleNotYetImplementedElement(next);
|
|
1701
|
} else if (isEndingElement(next, FIGURE_REF)) {
|
|
1702
|
//TODO
|
|
1703
|
popUnimplemented(next.asEndElement());
|
|
1704
|
} else if (isStartingElement(next, FIGURE)) {
|
|
1705
|
//TODO
|
|
1706
|
handleNotYetImplementedElement(next);
|
|
1707
|
} else if (isEndingElement(next, FIGURE)) {
|
|
1708
|
//TODO
|
|
1709
|
popUnimplemented(next.asEndElement());
|
|
1710
|
} else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
1711
|
//TODO
|
|
1712
|
handleNotYetImplementedElement(next);
|
|
1713
|
} else if (isEndingElement(next, FOOTNOTE_REF)) {
|
|
1714
|
//TODO
|
|
1715
|
popUnimplemented(next.asEndElement());
|
|
1716
|
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
1717
|
//TODO
|
|
1718
|
handleNotYetImplementedElement(next);
|
|
1719
|
} else if (isEndingElement(next, FOOTNOTE)) {
|
|
1720
|
//TODO
|
|
1721
|
popUnimplemented(next.asEndElement());
|
|
1722
|
} else if (isStartingElement(next, WRITER)) {
|
|
1723
|
//TODO
|
|
1724
|
handleNotYetImplementedElement(next);
|
|
1725
|
} else if (isEndingElement(next, WRITER)) {
|
|
1726
|
//TODO
|
|
1727
|
popUnimplemented(next.asEndElement());
|
|
1728
|
} else if (isStartingElement(next, DATES)) {
|
|
1729
|
//TODO
|
|
1730
|
handleNotYetImplementedElement(next);
|
|
1731
|
} else if (isEndingElement(next, DATES)) {
|
|
1732
|
//TODO
|
|
1733
|
popUnimplemented(next.asEndElement());
|
|
1734
|
} else {
|
|
1735
|
handleUnexpectedElement(next);
|
|
1736
|
}
|
|
1737
|
}
|
|
1738
|
throw new IllegalStateException("<String> has no closing tag");
|
|
1739
|
}
|
|
1740
|
|
|
1741
|
/**
|
|
1742
|
* @param subHeadingMap
|
|
1743
|
* @param currentSubheading
|
|
1744
|
* @param text
|
|
1745
|
* @return
|
|
1746
|
*/
|
|
1747
|
private String putCurrentSubheading(Map<String, String> subHeadingMap, String currentSubheading, String text) {
|
|
1748
|
if (StringUtils.isNotBlank(text)) {
|
|
1749
|
text = removeStartingMinus(text);
|
|
1750
|
subHeadingMap.put(currentSubheading, text.trim());
|
|
1751
|
}
|
|
1752
|
return "";
|
|
1753
|
}
|
|
1754
|
|
|
1755
|
private String removeStartingMinus(String string) {
|
|
1756
|
string = replaceStart(string, "-");
|
|
1757
|
string = replaceStart(string, "\u002d");
|
|
1758
|
string = replaceStart(string, "\u2013");
|
|
1759
|
string = replaceStart(string, "\u2014");
|
|
1760
|
string = replaceStart(string, "--");
|
|
1761
|
return string;
|
|
1762
|
}
|
|
1763
|
|
|
1764
|
/**
|
|
1765
|
* @param value
|
|
1766
|
* @param replacementString
|
|
1767
|
*/
|
|
1768
|
private String replaceStart(String value, String replacementString) {
|
|
1769
|
if (value.startsWith(replacementString) ){
|
|
1770
|
value = value.substring(replacementString.length()).trim();
|
|
1771
|
}
|
|
1772
|
while (value.startsWith("-") || value.startsWith("\u2014") ){
|
|
1773
|
value = value.substring("-".length()).trim();
|
|
1774
|
}
|
|
1775
|
return value;
|
|
1776
|
}
|
|
1777
|
|
|
1778
|
private String getXmlTag(XMLEvent event) {
|
|
1779
|
String result;
|
|
1780
|
if (event.isStartElement()) {
|
|
1781
|
result = "<" + event.asStartElement().getName().getLocalPart()
|
|
1782
|
+ ">";
|
|
1783
|
} else if (event.isEndElement()) {
|
|
1784
|
result = "</" + event.asEndElement().getName().getLocalPart() + ">";
|
|
1785
|
} else {
|
|
1786
|
String message = "Only start or end elements are allowed as Html tags";
|
|
1787
|
throw new IllegalStateException(message);
|
|
1788
|
}
|
|
1789
|
return result;
|
|
1790
|
}
|
|
1791
|
|
|
1792
|
protected static final List<String> htmlList = Arrays.asList("sub", "sup",
|
|
1793
|
"ol", "ul", "li", "i", "b", "table", "br","tr","td");
|
|
1794
|
|
|
1795
|
private boolean isHtml(XMLEvent event) {
|
|
1796
|
if (event.isStartElement()) {
|
|
1797
|
String tag = event.asStartElement().getName().getLocalPart();
|
|
1798
|
return htmlList.contains(tag);
|
|
1799
|
} else if (event.isEndElement()) {
|
|
1800
|
String tag = event.asEndElement().getName().getLocalPart();
|
|
1801
|
return htmlList.contains(tag);
|
|
1802
|
} else {
|
|
1803
|
return false;
|
|
1804
|
}
|
|
1805
|
|
|
1806
|
}
|
|
1807
|
|
|
1808
|
/**
|
|
1809
|
* Handle the char or subchar element. As
|
|
1810
|
* @param state the import state
|
|
1811
|
* @param reader
|
|
1812
|
* @param parentEvent
|
|
1813
|
* @param parentFeature in case of subchars we need to attache the newly created feature to a parent feature, should be <code>null</code>
|
|
1814
|
* for top level chars.
|
|
1815
|
* @return List of TextData. Not a single one as the recursive TextData will also be returned
|
|
1816
|
* @throws XMLStreamException
|
|
1817
|
*/
|
|
1818
|
private List<TextData> handleChar(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature parentFeature) throws XMLStreamException {
|
|
1819
|
List<TextData> result = new ArrayList<TextData>();
|
|
1820
|
String classValue = getClassOnlyAttribute(parentEvent);
|
|
1821
|
Feature feature = makeFeature(classValue, state, parentEvent, parentFeature);
|
|
1822
|
|
|
1823
|
boolean isTextMode = true;
|
|
1824
|
String text = "";
|
|
1825
|
while (reader.hasNext()) {
|
|
1826
|
XMLEvent next = readNoWhitespace(reader);
|
|
1827
|
if (isMyEndingElement(next, parentEvent)) {
|
|
1828
|
state.putFeatureToCharSorterList(feature);
|
|
1829
|
TextData textData = TextData.NewInstance(feature);
|
|
1830
|
textData.putText(getDefaultLanguage(state), text);
|
|
1831
|
result.add(textData);
|
|
1832
|
return result;
|
|
1833
|
} else if (isStartingElement(next, FIGURE_REF)) {
|
|
1834
|
//TODO
|
|
1835
|
handleNotYetImplementedElement(next);
|
|
1836
|
} else if (isStartingElement(next, FOOTNOTE_REF)) {
|
|
1837
|
//TODO
|
|
1838
|
handleNotYetImplementedElement(next);
|
|
1839
|
} else if (isStartingElement(next, BR)) {
|
|
1840
|
text += "<br/>";
|
|
1841
|
isTextMode = false;
|
|
1842
|
} else if (isEndingElement(next, BR)) {
|
|
1843
|
isTextMode = true;
|
|
1844
|
} else if (isHtml(next)) {
|
|
1845
|
text += getXmlTag(next);
|
|
1846
|
} else if (next.isStartElement()) {
|
|
1847
|
if (isStartingElement(next, ANNOTATION)) {
|
|
1848
|
handleNotYetImplementedElement(next); //TODO test handleSimpleAnnotation
|
|
1849
|
} else if (isStartingElement(next, ITALICS)) {
|
|
1850
|
handleNotYetImplementedElement(next);
|
|
1851
|
} else if (isStartingElement(next, BOLD)) {
|
|
1852
|
handleNotYetImplementedElement(next);
|
|
1853
|
} else if (isStartingElement(next, FIGURE)) {
|
|
1854
|
handleFigure(state, reader, next);
|
|
1855
|
} else if (isStartingElement(next, SUB_CHAR)) {
|
|
1856
|
List<TextData> textData = handleChar(state, reader, next, feature);
|
|
1857
|
result.addAll(textData);
|
|
1858
|
} else if (isStartingElement(next, FOOTNOTE)) {
|
|
1859
|
FootnoteDataHolder footnote = handleFootnote(state, reader, next);
|
|
1860
|
if (footnote.isRef()) {
|
|
1861
|
String message = "Ref footnote not implemented here";
|
|
1862
|
fireWarningEvent(message, next, 4);
|
|
1863
|
} else {
|
|
1864
|
registerGivenFootnote(state, footnote);
|
|
1865
|
}
|
|
1866
|
} else {
|
|
1867
|
handleUnexpectedStartElement(next.asStartElement());
|
|
1868
|
}
|
|
1869
|
} else if (next.isCharacters()) {
|
|
1870
|
if (!isTextMode) {
|
|
1871
|
String message = "String is not in text mode";
|
|
1872
|
fireWarningEvent(message, next, 6);
|
|
1873
|
} else {
|
|
1874
|
text += next.asCharacters().getData();
|
|
1875
|
}
|
|
1876
|
} else {
|
|
1877
|
handleUnexpectedEndElement(next.asEndElement());
|
|
1878
|
}
|
|
1879
|
}
|
|
1880
|
throw new IllegalStateException("RefPart has no closing tag");
|
|
1881
|
}
|
|
1882
|
|
|
1883
|
/**
|
|
1884
|
* @param classValue
|
|
1885
|
* @param state
|
|
1886
|
* @param parentEvent
|
|
1887
|
* @param parentFeature
|
|
1888
|
* @return
|
|
1889
|
* @throws UndefinedTransformerMethodException
|
|
1890
|
*/
|
|
1891
|
private Feature makeFeature(String classValue, MarkupImportState state, XMLEvent parentEvent, Feature parentFeature) {
|
|
1892
|
UUID uuid;
|
|
1893
|
try {
|
|
1894
|
String featureText = StringUtils.capitalize(classValue);
|
|
1895
|
if (parentFeature != null){
|
|
1896
|
featureText = "<%s>" + featureText;
|
|
1897
|
featureText = String.format(featureText, parentFeature.getTitleCache());
|
|
1898
|
classValue = "<%s>" + classValue;
|
|
1899
|
classValue = String.format(classValue, parentFeature.getTitleCache());
|
|
1900
|
}
|
|
1901
|
|
|
1902
|
|
|
1903
|
Feature feature = state.getTransformer().getFeatureByKey(classValue);
|
|
1904
|
if (feature != null) {
|
|
1905
|
return feature;
|
|
1906
|
}
|
|
1907
|
uuid = state.getTransformer().getFeatureUuid(classValue);
|
|
1908
|
|
|
1909
|
if (uuid == null){
|
|
1910
|
uuid = state.getUnknownFeatureUuid(classValue);
|
|
1911
|
}
|
|
1912
|
|
|
1913
|
if (uuid == null) {
|
|
1914
|
// TODO
|
|
1915
|
String message = "Uuid is not defined for '%s'";
|
|
1916
|
message = String.format(message, classValue);
|
|
1917
|
if (! message.contains("<")){
|
|
1918
|
//log only top level features
|
|
1919
|
fireWarningEvent(message, parentEvent, 8);
|
|
1920
|
}
|
|
1921
|
uuid = UUID.randomUUID();
|
|
1922
|
state.putUnknownFeatureUuid(classValue, uuid);
|
|
1923
|
}
|
|
1924
|
|
|
1925
|
// TODO eFlora vocabulary
|
|
1926
|
TermVocabulary<Feature> voc = null;
|
|
1927
|
feature = getFeature(state, uuid, featureText, featureText, classValue, voc);
|
|
1928
|
if (parentFeature != null){
|
|
1929
|
parentFeature.addIncludes(feature);
|
|
1930
|
save(parentFeature, state);
|
|
1931
|
}
|
|
1932
|
save(feature, state);
|
|
1933
|
|
|
1934
|
if (feature == null) {
|
|
1935
|
throw new NullPointerException(classValue + " not recognized as a feature");
|
|
1936
|
}
|
|
1937
|
// state.putFeatureToCurrentList(feature);
|
|
1938
|
return feature;
|
|
1939
|
} catch (Exception e) {
|
|
1940
|
String message = "Could not create feature for %s: %s";
|
|
1941
|
message = String.format(message, classValue, e.getMessage());
|
|
1942
|
fireWarningEvent(message, parentEvent, 4);
|
|
1943
|
state.putUnknownFeatureUuid(classValue, null);
|
|
1944
|
// e.printStackTrace();
|
|
1945
|
return Feature.UNKNOWN();
|
|
1946
|
}
|
|
1947
|
}
|
|
1948
|
|
|
1949
|
}
|