Revision ec02b2a3
Added by Andreas Müller about 12 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupDocumentImport.java | ||
|---|---|---|
| 12 | 12 |
import java.util.ArrayList; |
| 13 | 13 |
import java.util.HashMap; |
| 14 | 14 |
import java.util.HashSet; |
| 15 |
import java.util.Iterator; |
|
| 15 | 16 |
import java.util.LinkedList; |
| 16 | 17 |
import java.util.List; |
| 17 | 18 |
import java.util.Map; |
| ... | ... | |
| 24 | 25 |
import javax.xml.stream.FactoryConfigurationError; |
| 25 | 26 |
import javax.xml.stream.XMLEventReader; |
| 26 | 27 |
import javax.xml.stream.XMLStreamException; |
| 28 |
import javax.xml.stream.events.StartElement; |
|
| 27 | 29 |
import javax.xml.stream.events.XMLEvent; |
| 28 | 30 |
|
| 29 | 31 |
import org.apache.commons.lang.CharUtils; |
| ... | ... | |
| 31 | 33 |
import org.apache.log4j.Logger; |
| 32 | 34 |
import org.jdom.Attribute; |
| 33 | 35 |
import org.jdom.Element; |
| 36 |
import org.springframework.beans.factory.annotation.Autowired; |
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| 37 |
import org.springframework.security.access.PermissionEvaluator; |
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| 38 |
import org.springframework.security.authentication.AuthenticationManager; |
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| 39 |
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; |
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import org.springframework.security.core.Authentication; |
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import org.springframework.security.core.context.SecurityContext; |
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import org.springframework.security.core.context.SecurityContextHolder; |
|
| 34 | 43 |
import org.springframework.stereotype.Component; |
| 35 | 44 |
|
| 36 | 45 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| ... | ... | |
| 83 | 92 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 84 | 93 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 85 | 94 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 95 |
import eu.etaxonomy.cdm.permission.CdmPermissionEvaluator; |
|
| 86 | 96 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| 87 | 97 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| 88 | 98 |
|
| ... | ... | |
| 102 | 112 |
private UnmatchedLeads unmatchedLeads; |
| 103 | 113 |
|
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|
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//TODO remove preliminary |
|
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@Autowired |
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private AuthenticationManager authenticationManager; |
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private Authentication authentication; |
|
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private PermissionEvaluator permissionEvaluator; |
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|
|
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public MarkupDocumentImport(){
|
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super(); |
| 123 |
System.out.println("TODO remove preliminary authentication");
|
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// UsernamePasswordAuthenticationToken token = new UsernamePasswordAuthenticationToken("admin", "0000");
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// authentication = authenticationManager.authenticate(token); |
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// SecurityContext context = SecurityContextHolder.getContext(); |
|
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// context.setAuthentication(authentication); |
|
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// permissionEvaluator = new CdmPermissionEvaluator(); |
|
| 107 | 129 |
} |
| 108 | 130 |
|
| 109 | 131 |
|
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@Override |
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public boolean doCheck(MarkupImportState state){
|
| 112 | 134 |
state.setCheck(true); |
| 113 |
boolean result = doInvoke(state);
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doInvoke(state); |
|
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state.setCheck(false); |
| 115 |
return result;
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return state.isSuccess();
|
|
| 116 | 138 |
} |
| 117 | 139 |
|
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@Override |
| 119 |
public boolean doInvoke(MarkupImportState state){
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public void doInvoke(MarkupImportState state){
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fireProgressEvent("Start import markup document", "Before start of document");
|
| 121 | 143 |
fireWarningEvent("Test a warning", "At start", 17);
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| 122 |
boolean success = false; |
|
| 123 | 144 |
|
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Queue<CdmBase> outputStream = new LinkedList<CdmBase>(); |
| 125 | 146 |
|
| ... | ... | |
| 133 | 154 |
state.setReader(reader); |
| 134 | 155 |
//start document |
| 135 | 156 |
if (! validateStartOfDocument(reader)){
|
| 136 |
return false; |
|
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state.setUnsuccessfull(); |
|
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return; |
|
| 137 | 159 |
} |
| 138 | 160 |
|
| 139 | 161 |
//publication |
| 140 | 162 |
String elName = "publication"; |
| 141 | 163 |
while (reader.hasNext()) {
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| 142 |
if (isStartingElement(reader, elName)){
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success &= handlePublication(reader, elName); |
|
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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); |
|
| 144 | 167 |
}else{
|
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fireSchemaConflictEventExpectedStartTag(elName, reader); |
| 146 | 169 |
} |
| ... | ... | |
| 151 | 174 |
// parseSAX(state, handler); |
| 152 | 175 |
|
| 153 | 176 |
} catch (FactoryConfigurationError e1) {
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// TODO Auto-generated catch block |
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fireWarningEvent("Some error occurred while setting up xml factory. Data can't be imported", "Start", 16);
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success = false;
|
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state.setUnsuccessfull();
|
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} catch (XMLStreamException e1) {
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// TODO Auto-generated catch block |
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fireWarningEvent("An XMLStreamException occurred while parsing. Data can't be imported", "Start", 16);
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success = false;
|
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state.setUnsuccessfull();
|
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// } catch (ParserConfigurationException e) {
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// fireWarningEvent("A ParserConfigurationException occurred while parsing. Data can't be imported", "Start", 16);
|
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// } catch (SAXException e) {
|
| ... | ... | |
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} |
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|
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return success;
|
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return; |
|
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|
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} |
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|
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|
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private boolean handlePublication(XMLEventReader reader, String elName) throws XMLStreamException {
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boolean success = true; |
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XMLEvent event = reader.nextEvent(); |
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if (isEndingElement(event, elName)){
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//TODO cardinality of alternative |
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return success; |
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}else if(isStartingElement(event, "metaData")){
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|
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}else if(isStartingElement(event, "treatment")){
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}else if(isStartingElement(event, "biographies")){
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}else if(isStartingElement(event, "references")){
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}else if(isStartingElement(event, "metaData")){
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}else if(isStartingElement(event, "metaData")){
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}else if(isStartingElement(event, "metaData")){
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private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, String elName) throws XMLStreamException {
|
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|
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//attributes |
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StartElement element = currentEvent.asStartElement().asStartElement(); |
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Map<String, javax.xml.stream.events.Attribute> attributes = getAttributes(element); |
|
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// if (attributes.hasNext()){
|
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// handleUnexpectedAttributes(element.getLocation(), attributes); |
|
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// } |
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|
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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, "metaData")){
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//NOT YET IMPLEMENTED |
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}else if(isStartingElement(event, "treatment")){
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//NOT YET IMPLEMENTED |
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}else if(isStartingElement(event, "biographies")){
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//NOT YET IMPLEMENTED |
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}else if(isStartingElement(event, "references")){
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//NOT YET IMPLEMENTED |
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}else if(isStartingElement(event, "textSection")){
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//NOT YET IMPLEMENTED |
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}else if(isStartingElement(event, "addenda")){
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//NOT YET IMPLEMENTED |
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}else{
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handleUnexpectedEndElement(event); |
|
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} |
|
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} |
|
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}else if (event.isStartElement()){
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if(isStartingElement(event, "metaData")){
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handleNotYetImplementedElement(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, "textSection")){
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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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} |
|
| 196 | 250 |
} |
| 197 |
return success;
|
|
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return; |
|
| 198 | 252 |
} |
| 199 |
|
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| 200 | 253 |
|
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|
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|
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|
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/** |
|
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* Read next event. Ignore whitespace events. |
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* @param reader |
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* @return |
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* @throws XMLStreamException |
|
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*/ |
|
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private XMLEvent readNoWhitespace(XMLEventReader reader) throws XMLStreamException {
|
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XMLEvent event = reader.nextEvent(); |
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while (event.isCharacters() && event.asCharacters().isWhiteSpace()){
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event = reader.nextEvent(); |
|
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} |
|
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return event; |
|
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} |
|
| 201 | 270 |
|
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private boolean handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
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boolean success = true; |
|
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while (reader.hasNext()){
|
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XMLEvent next = readNoWhitespace(reader); |
|
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if (isStartingElement(next, "taxon")){
|
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handleTaxon(state, reader, next.asStartElement()); |
|
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}else if(isMyEndingElement(next, parentEvent)){
|
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return success; |
|
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}else{
|
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fireSchemaConflictEventExpectedStartTag("taxon", reader);
|
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success = false; |
|
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} |
|
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} |
|
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return success; |
|
| 285 |
} |
|
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|
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|
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private void handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
|
|
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boolean hasTitle = false; |
|
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boolean hasNomenclature = false; |
|
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while (reader.hasNext()){
|
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XMLEvent next = readNoWhitespace(reader); |
|
| 293 |
if (next.isEndElement()){
|
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if (isMyEndingElement(next, parentEvent)){
|
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handleMandatoryElement(hasTitle, parentEvent, "taxontitle"); |
|
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handleMandatoryElement(hasNomenclature, parentEvent, "nomenclature"); |
|
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//TODO check title and nomenclature exists |
|
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return; |
|
| 299 |
}else{
|
|
| 300 |
if(isEndingElement(next, "heading")){
|
|
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//NOT YET IMPLEMENTED |
|
| 302 |
}else if(isStartingElement(next, "taxontitle")){
|
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//NOT YET IMPLEMENTED |
|
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}else if(isStartingElement(next, "biographies")){
|
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//NOT YET IMPLEMENTED |
|
| 306 |
}else if(isStartingElement(next, "references")){
|
|
| 307 |
//NOT YET IMPLEMENTED |
|
| 308 |
}else if(isStartingElement(next, "textSection")){
|
|
| 309 |
//NOT YET IMPLEMENTED |
|
| 310 |
}else if(isStartingElement(next, "addenda")){
|
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| 311 |
//NOT YET IMPLEMENTED |
|
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}else{
|
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handleUnexpectedEndElement(next); |
|
| 314 |
} |
|
| 315 |
} |
|
| 316 |
}else if (next.isStartElement()){
|
|
| 317 |
if(isStartingElement(next, "heading")){
|
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| 318 |
handleNotYetImplementedElement(next); |
|
| 319 |
}else if(isStartingElement(next, "taxontitle")){
|
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| 320 |
handleTaxonTitle(state, reader, next); |
|
| 321 |
}else if(isStartingElement(next, "writer")){
|
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| 322 |
handleNotYetImplementedElement(next); |
|
| 323 |
}else if(isStartingElement(next, "textsection")){
|
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handleNotYetImplementedElement(next); |
|
| 325 |
}else if(isStartingElement(next, "key")){
|
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handleNotYetImplementedElement(next); |
|
| 327 |
}else if(isStartingElement(next, "feature")){
|
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handleNotYetImplementedElement(next); |
|
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}else if(isStartingElement(next, "notes")){
|
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handleNotYetImplementedElement(next); |
|
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}else if(isStartingElement(next, "references")){
|
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| 332 |
handleNotYetImplementedElement(next); |
|
| 333 |
}else if(isStartingElement(next, "figure")){
|
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| 334 |
handleNotYetImplementedElement(next); |
|
| 335 |
}else if(isStartingElement(next, "footnote")){
|
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handleNotYetImplementedElement(next); |
|
| 337 |
}else{
|
|
| 338 |
handleUnexpectedStartElement(next); |
|
| 339 |
} |
|
| 340 |
}else{
|
|
| 341 |
handleUnexpectedElement(next); |
|
| 342 |
} |
|
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} |
|
| 344 |
return; |
|
| 345 |
} |
|
| 346 |
|
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| 347 |
private void handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
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boolean hasTitle = false; |
|
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|
|
| 350 |
//TODO handle attributes |
|
| 351 |
while (reader.hasNext()){
|
|
| 352 |
XMLEvent next = readNoWhitespace(reader); |
|
| 353 |
if (next.isEndElement()){
|
|
| 354 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 355 |
//TODO check title exists |
|
| 356 |
return; |
|
| 357 |
}else{
|
|
| 358 |
if(isEndingElement(next, "footnoteString")){
|
|
| 359 |
//NOT YET IMPLEMENTED |
|
| 360 |
}else{
|
|
| 361 |
handleUnexpectedEndElement(next); |
|
| 362 |
state.setSuccessToFalse(); |
|
| 363 |
} |
|
| 364 |
} |
|
| 365 |
}else if (next.isStartElement()){
|
|
| 366 |
if(isStartingElement(next, "footnoteString")){
|
|
| 367 |
handleNotYetImplementedElement(next); |
|
| 368 |
}else{
|
|
| 369 |
handleUnexpectedStartElement(next); |
|
| 370 |
state.setSuccessToFalse(); |
|
| 371 |
} |
|
| 372 |
}else{
|
|
| 373 |
handleUnexpectedElement(next); |
|
| 374 |
state.setSuccessToFalse(); |
|
| 375 |
} |
|
| 376 |
} |
|
| 377 |
return; |
|
| 378 |
|
|
| 379 |
|
|
| 380 |
} |
|
| 381 |
|
|
| 382 |
|
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| 383 |
private boolean isMyEndingElement(XMLEvent next, XMLEvent event) throws XMLStreamException {
|
|
| 384 |
return isEndingElement(next, event.asStartElement().getName().getLocalPart()); |
|
| 385 |
} |
|
| 386 |
|
|
| 387 |
|
|
| 202 | 388 |
/** |
| 203 | 389 |
* This comes from the old version, needs to be checked on need |
| 204 | 390 |
* @param state |
Also available in: Unified diff
newest developments for document markup (including success -> state)