Revision 2f53c10a
Added by Andreas Müller 8 months ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupFeatureImport.java | ||
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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.util.ArrayList; |
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import javax.xml.stream.events.XMLEvent; |
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import org.apache.commons.lang.StringUtils; |
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger; |
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import org.apache.logging.log4j.LogManager; |
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import org.apache.logging.log4j.Logger; |
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import eu.etaxonomy.cdm.common.CdmUtils; |
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
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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.IntextReference; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.LanguageString; |
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/** |
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* @author a.mueller |
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* @since 30.05.2012 |
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* |
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*/ |
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public class MarkupFeatureImport extends MarkupImportBase {
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@SuppressWarnings("unused")
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(MarkupFeatureImport.class); |
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protected static final String MODS_TITLEINFO = "titleInfo"; |
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/** |
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* Creates a full description text from the mark |
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* @param cachedEvents |
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* @return |
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*/ |
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private String makeFullDescriptionText(List<XMLEvent> events) {
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String result = ""; |
| ... | ... | |
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return result; |
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} |
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/** |
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* @param state |
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* @param reader |
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* @param taxonDescription |
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* @param isDescription |
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* @param lastDescriptionElement |
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* @param next |
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* @return |
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* @throws XMLStreamException |
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*/ |
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public DescriptionElementBase makeFeatureFigureRef(MarkupImportState state, XMLEventReader reader,TaxonDescription taxonDescription, |
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boolean isDescription, DescriptionElementBase lastDescriptionElement, Reference sourceReference, XMLEvent next) throws XMLStreamException {
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FigureDataHolder figureHolder = handleFigureRef(state, reader, next); |
| ... | ... | |
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return lastDescriptionElement; |
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} |
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/** |
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* @param state |
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* @param reader |
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* @param feature |
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* @param taxonDescription |
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* @param lastDescriptionElement |
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* @param distributionList |
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* @param next |
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* @return |
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* @throws XMLStreamException |
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* @throws |
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*/ |
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private DescriptionElementBase makeFeatureString(MarkupImportState state,XMLEventReader reader, Feature feature, |
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TaxonDescription taxonDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next, Boolean isFreetext) throws XMLStreamException {
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|
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} |
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} |
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/** |
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* @param classValue |
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* @param state |
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* @param parentEvent |
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* @param parentFeature |
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* @return |
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* @throws UndefinedTransformerMethodException |
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*/ |
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private Feature makeFeature(String classValue, MarkupImportState state, XMLEvent parentEvent, Feature parentFeature) {
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UUID uuid; |
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try {
|
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classValue = String.format(classValue, parentFeature.getTitleCache()); |
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} |
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//get existing feature |
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if (classValue.endsWith(".")){
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classValue = classValue.substring(0, classValue.length() - 1); |
| ... | ... | |
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throw new IllegalStateException("RefPart has no closing tag");
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} |
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|
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/** |
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* @param state |
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* @param reader |
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* @param classValue |
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* @param feature |
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* @param next |
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* @throws XMLStreamException |
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*/ |
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private void makeFeatureHeading(MarkupImportState state, XMLEventReader reader, String classValue, Feature feature, XMLEvent next) throws XMLStreamException {
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String heading = handleHeading(state, reader, next); |
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if (StringUtils.isNotBlank(heading)) {
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} |
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} |
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/** |
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* @param state |
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* @param reader |
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* @param feature |
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* @param taxon |
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* @param next |
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* @throws XMLStreamException |
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*/ |
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private void makeFeatureWriter(MarkupImportState state,XMLEventReader reader, Feature feature, Taxon taxon, XMLEvent next) throws XMLStreamException {
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WriterDataHolder writer = handleWriter(state, reader, next); |
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if (isNotBlank(writer.writer)) {
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* @see #handleHabitat(MarkupImportState, XMLEventReader, XMLEvent) |
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*/ |
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private String handleAltitude(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
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checkNoAttributes(parentEvent); |
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Taxon taxon = state.getCurrentTaxon(); |
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// TODO which ref to take? |
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Reference sourceReference = state.getConfig().getSourceReference(); |
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boolean isTextMode = true; |
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String text = ""; |
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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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Feature feature = getFeature( |
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state, |
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MarkupTransformer.uuidExtractedAltitude, |
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"Extracted Altitude", |
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"An altitude that was extracted from a habitat text", |
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"extr. alt.", null); |
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//TODO try to make quantitative data |
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TextData altitude = TextData.NewInstance(feature); |
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altitude.putText(getDefaultLanguage(state), text); |
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altitude.addPrimaryTaxonomicSource(sourceReference); |
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TaxonDescription description = getExtractedMarkupMarkedDescription(state, taxon, sourceReference); |
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description.addElement(altitude); |
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return text; |
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} else if (next.isCharacters()) {
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if (! isTextMode) {
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String message = "String is not in text mode"; |
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fireWarningEvent(message, next, 6); |
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} else {
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text += next.asCharacters().getData(); |
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} |
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} else if (isStartingElement(next, BR)) {
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text += "<br/>"; |
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isTextMode = false; |
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} else if (isEndingElement(next, BR)) {
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isTextMode = true; |
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} else {
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String type = next.toString(); |
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String location = String.valueOf(next.getLocation().getLineNumber()); |
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System.out.println("MarkupFeatureImport.handleAltitude: Unexpected element in habitat: " + type + ": " + location);
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handleUnexpectedElement(next); |
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} |
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} |
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throw new IllegalStateException("<Habitat> has no closing tag");
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} |
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checkNoAttributes(parentEvent); |
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Taxon taxon = state.getCurrentTaxon(); |
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// TODO which ref to take? |
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Reference sourceReference = state.getConfig().getSourceReference(); |
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boolean isTextMode = true; |
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String text = ""; |
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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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Feature feature = getFeature( |
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state, |
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MarkupTransformer.uuidExtractedAltitude, |
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"Extracted Altitude", |
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"An altitude that was extracted from a habitat text", |
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"extr. alt.", null); |
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//TODO try to make quantitative data |
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TextData altitude = TextData.NewInstance(feature); |
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altitude.putText(getDefaultLanguage(state), text); |
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altitude.addPrimaryTaxonomicSource(sourceReference); |
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TaxonDescription description = getExtractedMarkupMarkedDescription(state, taxon, sourceReference); |
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description.addElement(altitude); |
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return text; |
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} else if (next.isCharacters()) {
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if (! isTextMode) {
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String message = "String is not in text mode"; |
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fireWarningEvent(message, next, 6); |
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} else {
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text += next.asCharacters().getData(); |
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} |
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} else if (isStartingElement(next, BR)) {
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text += "<br/>"; |
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isTextMode = false; |
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} else if (isEndingElement(next, BR)) {
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isTextMode = true; |
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} else {
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String type = next.toString(); |
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String location = String.valueOf(next.getLocation().getLineNumber()); |
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System.out.println("MarkupFeatureImport.handleAltitude: Unexpected element in habitat: " + type + ": " + location);
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handleUnexpectedElement(next); |
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} |
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} |
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throw new IllegalStateException("<Habitat> has no closing tag");
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} |
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private FigureDataHolder handleFigureRef(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) |
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throws XMLStreamException {
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private List<DescriptionElementBase> makeCommonNameString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException{
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List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();
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List<DescriptionElementBase> result = new ArrayList<>(); |
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checkNoAttributes(parentEvent); |
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|
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} |
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} |
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throw new IllegalStateException("closing tag is missing");
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} |
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private List<DescriptionElementBase> makeVernacularNames(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException{
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List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>(); |
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List<DescriptionElementBase> result = new ArrayList<>(); |
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checkNoAttributes(parentEvent); |
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while (reader.hasNext()) {
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| ... | ... | |
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} |
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} |
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throw new IllegalStateException("closing tag is missing");
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} |
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private void makeVernacularNamesSubHeading(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
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} |
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} |
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throw new IllegalStateException("closing tag is missing");
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} |
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private NamedArea getCommonNameArea(String text) {
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| ... | ... | |
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} |
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private List<CommonTaxonName> makeSingleVernacularName(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException{
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checkNoAttributes(parentEvent); |
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List<CommonTaxonName> result = new ArrayList<CommonTaxonName>(); |
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checkNoAttributes(parentEvent); |
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List<CommonTaxonName> result = new ArrayList<>(); |
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Language language = state.getDefaultLanguage(); |
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while (reader.hasNext()) {
|
| ... | ... | |
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} |
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} |
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private String handleHeading(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {
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private String handleHeading(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {
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checkNoAttributes(parentEvent); |
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String text = ""; |
| ... | ... | |
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} |
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} |
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throw new IllegalStateException("<String> has no closing tag");
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} |
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private List<Reference> handleReferences(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
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// attributes |
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Map<String, Attribute> attributes = getAttributes(parentEvent); |
| ... | ... | |
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} |
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throw new IllegalStateException("Some tag has no closing tag");
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} |
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} |
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} |
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