Revision 9c810b9f
Added by Andreas Müller over 12 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupDocumentImport.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.markup; |
| 11 | 11 |
|
| 12 |
import java.util.ArrayList; |
|
| 13 | 12 |
import java.util.HashMap; |
| 14 |
import java.util.HashSet; |
|
| 15 |
import java.util.Iterator; |
|
| 16 | 13 |
import java.util.LinkedList; |
| 17 |
import java.util.List; |
|
| 18 | 14 |
import java.util.Map; |
| 19 | 15 |
import java.util.Queue; |
| 20 |
import java.util.Set; |
|
| 21 | 16 |
import java.util.UUID; |
| 22 |
import java.util.regex.Matcher; |
|
| 23 |
import java.util.regex.Pattern; |
|
| 24 | 17 |
|
| 25 | 18 |
import javax.xml.stream.FactoryConfigurationError; |
| 19 |
import javax.xml.stream.Location; |
|
| 26 | 20 |
import javax.xml.stream.XMLEventReader; |
| 27 | 21 |
import javax.xml.stream.XMLStreamException; |
| 22 |
import javax.xml.stream.events.Attribute; |
|
| 28 | 23 |
import javax.xml.stream.events.StartElement; |
| 29 | 24 |
import javax.xml.stream.events.XMLEvent; |
| 30 | 25 |
|
| 31 |
import org.apache.commons.lang.CharUtils; |
|
| 32 | 26 |
import org.apache.commons.lang.StringUtils; |
| 33 | 27 |
import org.apache.log4j.Logger; |
| 34 |
import org.jdom.Attribute; |
|
| 35 |
import org.jdom.Element; |
|
| 36 | 28 |
import org.springframework.beans.factory.annotation.Autowired; |
| 37 | 29 |
import org.springframework.security.access.PermissionEvaluator; |
| 38 | 30 |
import org.springframework.security.authentication.AuthenticationManager; |
| 39 |
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; |
|
| 40 | 31 |
import org.springframework.security.core.Authentication; |
| 41 |
import org.springframework.security.core.context.SecurityContext; |
|
| 42 |
import org.springframework.security.core.context.SecurityContextHolder; |
|
| 43 | 32 |
import org.springframework.stereotype.Component; |
| 44 | 33 |
|
| 45 |
import eu.etaxonomy.cdm.common.CdmUtils; |
|
| 46 |
import eu.etaxonomy.cdm.common.ResultWrapper; |
|
| 47 |
import eu.etaxonomy.cdm.common.XmlHelp; |
|
| 48 | 34 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
| 49 | 35 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 50 |
import eu.etaxonomy.cdm.io.markup.UnmatchedLeads.UnmatchedLeadsKey; |
|
| 51 |
import eu.etaxonomy.cdm.model.agent.Person; |
|
| 52 | 36 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 53 | 37 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 54 |
import eu.etaxonomy.cdm.model.common.AnnotatableEntity; |
|
| 55 |
import eu.etaxonomy.cdm.model.common.Annotation; |
|
| 56 |
import eu.etaxonomy.cdm.model.common.AnnotationType; |
|
| 57 | 38 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 58 |
import eu.etaxonomy.cdm.model.common.Credit;
|
|
| 39 |
import eu.etaxonomy.cdm.model.common.Extension;
|
|
| 59 | 40 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| 60 |
import eu.etaxonomy.cdm.model.common.ISourceable; |
|
| 61 | 41 |
import eu.etaxonomy.cdm.model.common.Language; |
| 62 |
import eu.etaxonomy.cdm.model.common.Marker; |
|
| 63 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
|
| 42 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
|
| 64 | 43 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 65 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
|
| 66 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
| 67 | 44 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 68 |
import eu.etaxonomy.cdm.model.description.KeyStatement; |
|
| 69 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
|
| 70 |
import eu.etaxonomy.cdm.model.description.PolytomousKeyNode; |
|
| 71 | 45 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 72 | 46 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 73 | 47 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 48 |
import eu.etaxonomy.cdm.model.name.CultivarPlantName; |
|
| 74 | 49 |
import eu.etaxonomy.cdm.model.name.HomotypicalGroup; |
| 75 |
import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
|
| 76 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignation; |
|
| 77 | 50 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 51 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
|
| 52 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
|
| 78 | 53 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 79 | 54 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 80 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
|
| 81 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
|
| 82 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 83 |
import eu.etaxonomy.cdm.model.name.TypeDesignationBase; |
|
| 84 |
import eu.etaxonomy.cdm.model.occurrence.Specimen; |
|
| 85 |
import eu.etaxonomy.cdm.model.reference.IBook; |
|
| 55 |
import eu.etaxonomy.cdm.model.reference.IArticle; |
|
| 86 | 56 |
import eu.etaxonomy.cdm.model.reference.IJournal; |
| 87 | 57 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 88 | 58 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 89 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
|
| 90 | 59 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 91 | 60 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| 92 | 61 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 93 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 94 | 62 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 95 |
import eu.etaxonomy.cdm.permission.CdmPermissionEvaluator; |
|
| 96 | 63 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| 97 | 64 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| 98 | 65 |
|
| ... | ... | |
| 103 | 70 |
*/ |
| 104 | 71 |
@Component |
| 105 | 72 |
public class MarkupDocumentImport extends MarkupImportBase implements ICdmIO<MarkupImportState> {
|
| 73 |
private static final String ORIGINAL_DETERMINATION = "originalDetermination"; |
|
| 74 |
|
|
| 75 |
private static final String COLLECTION = "collection"; |
|
| 76 |
|
|
| 77 |
private static final String FULL_TYPE = "fullType"; |
|
| 78 |
|
|
| 79 |
private static final String NOT_FOUND = "notFound"; |
|
| 80 |
|
|
| 106 | 81 |
private static final Logger logger = Logger.getLogger(MarkupDocumentImport.class); |
| 107 | 82 |
|
| 108 |
private static int modCount = 30000; |
|
| 83 |
private static final boolean CREATE_NEW = true; |
|
| 84 |
private static final boolean IS_IMAGE_GALLERY = true; |
|
| 85 |
private static final boolean NO_IMAGE_GALLERY = false; |
|
| 86 |
|
|
| 87 |
private static final String ACCEPTED = "accepted"; |
|
| 88 |
private static final String ADDENDA = "addenda"; |
|
| 89 |
private static final String ALTERNATEPUBTITLE = "alternatepubtitle"; |
|
| 90 |
private static final String ANNOTATION = "annotation"; |
|
| 91 |
private static final String AUTHOR = "author"; |
|
| 92 |
private static final String BIOGRAPHIES = "biographies"; |
|
| 93 |
private static final String BOLD = "bold"; |
|
| 94 |
private static final String CHAR = "char"; |
|
| 95 |
private static final String CITATION = "citation"; |
|
| 96 |
private static final String DESTROYED = "destroyed"; |
|
| 97 |
private static final String DETAILS = "details"; |
|
| 98 |
private static final String DISTRIBUTION_LIST = "distributionList"; |
|
| 99 |
private static final String EDITION = "edition"; |
|
| 100 |
private static final String EDITORS = "editors"; |
|
| 101 |
private static final String EXAUT = "exaut"; |
|
| 102 |
private static final String FEATURE = "feature"; |
|
| 103 |
private static final String FIGURE = "figure"; |
|
| 104 |
private static final String FOOTNOTE = "footnote"; |
|
| 105 |
private static final String FULL_NAME = "fullName"; |
|
| 106 |
private static final String HEADING = "heading"; |
|
| 107 |
private static final String HABITAT_LIST = "habitatList"; |
|
| 108 |
private static final String HOMONYM = "homonym"; |
|
| 109 |
private static final String HOMOTYPES = "homotypes"; |
|
| 110 |
private static final String INFRANK = "infrank"; |
|
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private static final String INFRAUT = "infraut"; |
|
| 112 |
private static final String INFREX = "infrex"; |
|
| 113 |
private static final String INFRPARAUT = "infrparaut"; |
|
| 114 |
private static final String INFRPAREX = "infrparex"; |
|
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private static final String ISSUE = "issue"; |
|
| 116 |
private static final String ITALICS = "italics"; |
|
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private static final String KEY = "key"; |
|
| 118 |
private static final String LOST = "lost"; |
|
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private static final String META_DATA = "metaData"; |
|
| 120 |
private static final String NAME = "name"; |
|
| 121 |
private static final String NAME_TYPE = "nameType"; |
|
| 122 |
private static final String NOM = "nom"; |
|
| 123 |
private static final String NOMENCLATURE = "nomenclature"; |
|
| 124 |
private static final String NOT_SEEN = "notSeen"; |
|
| 125 |
private static final String NOTES = "notes"; |
|
| 126 |
private static final String NUM = "num"; |
|
| 127 |
private static final String PARAUT = "paraut"; |
|
| 128 |
private static final String PUBFULLNAME = "pubfullname"; |
|
| 129 |
private static final String PUBLICATION = "publication"; |
|
| 130 |
private static final String PUBNAME = "pubname"; |
|
| 131 |
private static final String PUBTITLE = "pubtitle"; |
|
| 132 |
private static final String PUBTYPE = "pubtype"; |
|
| 133 |
private static final String RANK = "rank"; |
|
| 134 |
private static final String REFERENCES = "references"; |
|
| 135 |
private static final String REF_PART = "refPart"; |
|
| 136 |
private static final String TAXON = "taxon"; |
|
| 137 |
private static final String TAXONTITLE = "taxontitle"; |
|
| 138 |
private static final String TEXT_SECTION = "textSection"; |
|
| 139 |
private static final String TYPE = "type"; |
|
| 140 |
private static final String TYPE_STATUS = "typeStatus"; |
|
| 141 |
private static final String TREATMENT = "treatment"; |
|
| 142 |
private static final String SPECIMEN_TYPE = "specimenType"; |
|
| 143 |
private static final String STRING = "string"; |
|
| 144 |
private static final String SYNONYM = "synonym"; |
|
| 145 |
private static final String UNKNOWN = "unknown"; |
|
| 146 |
private static final String USAGE = "usage"; |
|
| 147 |
private static final String VOLUME = "volume"; |
|
| 148 |
private static final String WRITER = "writer"; |
|
| 149 |
private static final String YEAR = "year"; |
|
| 150 |
|
|
| 151 |
|
|
| 109 | 152 |
private NonViralNameParserImpl parser = new NonViralNameParserImpl(); |
| 110 | 153 |
|
| 111 | 154 |
//TODO make part of state, but state is renewed when invoking the import a second time |
| ... | ... | |
| 159 | 202 |
} |
| 160 | 203 |
|
| 161 | 204 |
//publication |
| 162 |
String elName = "publication"; |
|
| 205 |
String elName = PUBLICATION; |
|
| 206 |
boolean hasPublication = false; |
|
| 163 | 207 |
while (reader.hasNext()) {
|
| 164 | 208 |
XMLEvent nextEvent = reader.nextEvent(); |
| 165 | 209 |
if (isStartingElement(nextEvent, elName)){
|
| 166 | 210 |
handlePublication(state, reader, nextEvent, elName); |
| 211 |
hasPublication = true; |
|
| 212 |
}else if (nextEvent.isEndDocument()){
|
|
| 213 |
if (!hasPublication){
|
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| 214 |
String message = "No publication root element found"; |
|
| 215 |
fireWarningEvent(message, makeLocationStr(nextEvent.getLocation()), 8); |
|
| 216 |
} |
|
| 217 |
//done |
|
| 167 | 218 |
}else{
|
| 168 | 219 |
fireSchemaConflictEventExpectedStartTag(elName, reader); |
| 169 | 220 |
} |
| ... | ... | |
| 188 | 239 |
|
| 189 | 240 |
} |
| 190 | 241 |
|
| 191 |
|
|
| 242 |
|
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| 243 |
|
|
| 192 | 244 |
return; |
| 193 | 245 |
|
| 194 | 246 |
} |
| ... | ... | |
| 199 | 251 |
private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, String elName) throws XMLStreamException {
|
| 200 | 252 |
|
| 201 | 253 |
//attributes |
| 202 |
StartElement element = currentEvent.asStartElement().asStartElement();
|
|
| 203 |
Map<String, javax.xml.stream.events.Attribute> attributes = getAttributes(element);
|
|
| 204 |
handleUnexpectedAttributes(element.getLocation(), attributes); |
|
| 254 |
StartElement element = currentEvent.asStartElement(); |
|
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Map<String, Attribute> attributes = getAttributes(element); |
|
| 256 |
handleUnexpectedAttributes(element.getLocation(), attributes, "noNamespaceSchemaLocation");
|
|
| 205 | 257 |
|
| 206 | 258 |
while (reader.hasNext()){
|
| 207 | 259 |
XMLEvent event = readNoWhitespace(reader); |
| ... | ... | |
| 210 | 262 |
if (isEndingElement(event, elName)){
|
| 211 | 263 |
return; |
| 212 | 264 |
}else{
|
| 213 |
if(isEndingElement(event, "metaData")){
|
|
| 265 |
if(isEndingElement(event, META_DATA)){
|
|
| 214 | 266 |
//NOT YET IMPLEMENTED |
| 215 |
}else if(isStartingElement(event, "treatment")){
|
|
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popUnimplemented(event.asEndElement()); |
|
| 268 |
}else if(isStartingElement(event, TREATMENT)){
|
|
| 216 | 269 |
//NOT YET IMPLEMENTED |
| 217 |
}else if(isStartingElement(event, "biographies")){
|
|
| 270 |
popUnimplemented(event.asEndElement()); |
|
| 271 |
}else if(isStartingElement(event, BIOGRAPHIES)){
|
|
| 218 | 272 |
//NOT YET IMPLEMENTED |
| 219 |
}else if(isStartingElement(event, "references")){
|
|
| 273 |
popUnimplemented(event.asEndElement()); |
|
| 274 |
}else if(isStartingElement(event, REFERENCES)){
|
|
| 220 | 275 |
//NOT YET IMPLEMENTED |
| 221 |
}else if(isStartingElement(event, "textSection")){
|
|
| 276 |
popUnimplemented(event.asEndElement()); |
|
| 277 |
}else if(isStartingElement(event, TEXT_SECTION)){
|
|
| 222 | 278 |
//NOT YET IMPLEMENTED |
| 223 |
}else if(isStartingElement(event, "addenda")){
|
|
| 279 |
popUnimplemented(event.asEndElement()); |
|
| 280 |
}else if(isStartingElement(event, ADDENDA)){
|
|
| 224 | 281 |
//NOT YET IMPLEMENTED |
| 282 |
popUnimplemented(event.asEndElement()); |
|
| 225 | 283 |
}else{
|
| 226 |
handleUnexpectedEndElement(event);
|
|
| 284 |
handleUnexpectedElement(event); |
|
| 227 | 285 |
} |
| 228 | 286 |
} |
| 229 | 287 |
}else if (event.isStartElement()){
|
| 230 |
if(isStartingElement(event, "metaData")){
|
|
| 288 |
if(isStartingElement(event, META_DATA)){
|
|
| 231 | 289 |
handleNotYetImplementedElement(event); |
| 232 |
}else if(isStartingElement(event, "treatment")){
|
|
| 290 |
}else if(isStartingElement(event, TREATMENT)){
|
|
| 233 | 291 |
handleTreatment(state, reader, event); |
| 234 |
}else if(isStartingElement(event, "biographies")){
|
|
| 292 |
}else if(isStartingElement(event, BIOGRAPHIES)){
|
|
| 235 | 293 |
handleNotYetImplementedElement(event); |
| 236 |
}else if(isStartingElement(event, "references")){
|
|
| 294 |
}else if(isStartingElement(event, REFERENCES)){
|
|
| 237 | 295 |
handleNotYetImplementedElement(event); |
| 238 |
}else if(isStartingElement(event, "textSection")){
|
|
| 296 |
}else if(isStartingElement(event, TEXT_SECTION)){
|
|
| 239 | 297 |
handleNotYetImplementedElement(event); |
| 240 |
}else if(isStartingElement(event, "addenda")){
|
|
| 298 |
}else if(isStartingElement(event, ADDENDA)){
|
|
| 241 | 299 |
handleNotYetImplementedElement(event); |
| 242 | 300 |
}else{
|
| 243 | 301 |
handleUnexpectedStartElement(event); |
| ... | ... | |
| 249 | 307 |
return; |
| 250 | 308 |
} |
| 251 | 309 |
|
| 252 |
|
|
| 253 |
|
|
| 254 |
|
|
| 310 |
private void handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 311 |
checkNoAttributes(parentEvent); |
|
| 312 |
Taxon lastTaxon = null; |
|
| 313 |
while (reader.hasNext()){
|
|
| 314 |
XMLEvent next = readNoWhitespace(reader); |
|
| 315 |
if (isStartingElement(next, TAXON)){
|
|
| 316 |
Taxon thisTaxon = handleTaxon(state, reader, next.asStartElement(), lastTaxon); |
|
| 317 |
doTaxonRelation(state, thisTaxon, lastTaxon, parentEvent.getLocation()); |
|
| 318 |
lastTaxon = thisTaxon; |
|
| 319 |
//TODO for imports spanning multiple documents ?? Still needed? |
|
| 320 |
state.getConfig().setLastTaxonUuid(lastTaxon.getUuid()); |
|
| 321 |
}else if(isMyEndingElement(next, parentEvent)){
|
|
| 322 |
return; |
|
| 323 |
}else{
|
|
| 324 |
fireSchemaConflictEventExpectedStartTag(TAXON, reader); |
|
| 325 |
state.setUnsuccessfull(); |
|
| 326 |
} |
|
| 327 |
} |
|
| 328 |
return; |
|
| 329 |
} |
|
| 330 |
|
|
| 255 | 331 |
/** |
| 256 |
* Read next event. Ignore whitespace events. |
|
| 257 |
* @param reader |
|
| 258 |
* @return |
|
| 259 |
* @throws XMLStreamException |
|
| 332 |
* @param taxon |
|
| 333 |
* @param lastTaxon |
|
| 260 | 334 |
*/ |
| 261 |
private XMLEvent readNoWhitespace(XMLEventReader reader) throws XMLStreamException {
|
|
| 262 |
XMLEvent event = reader.nextEvent(); |
|
| 263 |
while (event.isCharacters() && event.asCharacters().isWhiteSpace()){
|
|
| 264 |
event = reader.nextEvent(); |
|
| 335 |
private void doTaxonRelation(MarkupImportState state, Taxon taxon, Taxon lastTaxon, Location dataLocation) {
|
|
| 336 |
|
|
| 337 |
Classification tree = makeTree(state); |
|
| 338 |
if (lastTaxon == null){
|
|
| 339 |
tree.addChildTaxon(taxon, null, null, null); |
|
| 340 |
return; |
|
| 341 |
} |
|
| 342 |
Rank thisRank = taxon.getName().getRank(); |
|
| 343 |
Rank lastRank = lastTaxon.getName().getRank(); |
|
| 344 |
if (lastTaxon.getTaxonNodes().size() > 0){
|
|
| 345 |
TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next(); |
|
| 346 |
if (thisRank.isLower(lastRank ) ){
|
|
| 347 |
lastNode.addChildTaxon(taxon, null, null, null); |
|
| 348 |
fillMissingEpithetsForTaxa(lastTaxon, taxon); |
|
| 349 |
}else if (thisRank.equals(lastRank)){
|
|
| 350 |
TaxonNode parent = lastNode.getParent(); |
|
| 351 |
if (parent != null){
|
|
| 352 |
parent.addChildTaxon(taxon, null, null, null); |
|
| 353 |
fillMissingEpithetsForTaxa(parent.getTaxon(), taxon); |
|
| 354 |
}else{
|
|
| 355 |
tree.addChildTaxon(taxon, null, null, null); |
|
| 356 |
} |
|
| 357 |
}else if (thisRank.isHigher(lastRank)){
|
|
| 358 |
doTaxonRelation(state, taxon, lastNode.getParent().getTaxon(), dataLocation); |
|
| 359 |
// TaxonNode parentNode = handleTaxonRelation(state, taxon, lastNode.getParent().getTaxon()); |
|
| 360 |
// parentNode.addChildTaxon(taxon, null, null, null); |
|
| 361 |
} |
|
| 362 |
}else{
|
|
| 363 |
|
|
| 364 |
String message = "Last taxon has no node"; |
|
| 365 |
fireWarningEvent(message, makeLocationStr(dataLocation), 6); |
|
| 265 | 366 |
} |
| 266 |
return event; |
|
| 267 | 367 |
} |
| 268 | 368 |
|
| 269 |
private boolean handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 270 |
boolean success = true; |
|
| 271 |
while (reader.hasNext()){
|
|
| 272 |
XMLEvent next = readNoWhitespace(reader); |
|
| 273 |
if (isStartingElement(next, "taxon")){
|
|
| 274 |
handleTaxon(state, reader, next.asStartElement()); |
|
| 275 |
}else if(isMyEndingElement(next, parentEvent)){
|
|
| 276 |
return success; |
|
| 369 |
|
|
| 370 |
/** |
|
| 371 |
* @param state |
|
| 372 |
* @return |
|
| 373 |
*/ |
|
| 374 |
private Classification makeTree(MarkupImportState state) {
|
|
| 375 |
Classification result = state.getTree(null); |
|
| 376 |
if (result == null){
|
|
| 377 |
UUID uuid = state.getConfig().getClassificationUuid(); |
|
| 378 |
if (uuid == null){
|
|
| 379 |
logger.warn("No classification uuid is defined");
|
|
| 380 |
result = createNewClassification(state); |
|
| 277 | 381 |
}else{
|
| 278 |
fireSchemaConflictEventExpectedStartTag("taxon", reader);
|
|
| 279 |
success = false; |
|
| 382 |
result = getClassificationService().find(uuid); |
|
| 383 |
if (result == null){
|
|
| 384 |
result = createNewClassification(state); |
|
| 385 |
result.setUuid(uuid); |
|
| 386 |
} |
|
| 280 | 387 |
} |
| 388 |
state.putTree(null, result); |
|
| 281 | 389 |
} |
| 282 |
return success; |
|
| 390 |
save(result, state); |
|
| 391 |
return result; |
|
| 392 |
} |
|
| 393 |
|
|
| 394 |
|
|
| 395 |
private Classification createNewClassification(MarkupImportState state) {
|
|
| 396 |
Classification result; |
|
| 397 |
result = Classification.NewInstance(state.getConfig().getClassificationTitle()); |
|
| 398 |
state.putTree(null, result); |
|
| 399 |
return result; |
|
| 283 | 400 |
} |
| 284 | 401 |
|
| 285 | 402 |
|
| 286 |
private void handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
|
|
| 403 |
private Taxon handleTaxon(MarkupImportState state, XMLEventReader reader, StartElement parentEvent, Taxon lastTaxon) throws XMLStreamException {
|
|
| 404 |
//TODO progress monitoring |
|
| 405 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 406 |
Taxon taxon = createTaxonAndName(state, attributes); |
|
| 407 |
state.setCurrentTaxon(taxon); |
|
| 408 |
|
|
| 287 | 409 |
boolean hasTitle = false; |
| 288 | 410 |
boolean hasNomenclature = false; |
| 411 |
String taxonTitle = null; |
|
| 289 | 412 |
while (reader.hasNext()){
|
| 290 | 413 |
XMLEvent next = readNoWhitespace(reader); |
| 291 | 414 |
if (next.isEndElement()){
|
| 292 | 415 |
if (isMyEndingElement(next, parentEvent)){
|
| 293 |
handleMandatoryElement(hasTitle, parentEvent, "taxontitle"); |
|
| 294 |
handleMandatoryElement(hasNomenclature, parentEvent, "nomenclature"); |
|
| 295 |
//TODO check title and nomenclature exists |
|
| 296 |
return; |
|
| 416 |
checkMandatoryElement(hasTitle, parentEvent, TAXONTITLE); |
|
| 417 |
checkMandatoryElement(hasNomenclature, parentEvent, NOMENCLATURE); |
|
| 418 |
handleUnexpectedAttributes(parentEvent.getLocation(), attributes); |
|
| 419 |
state.setCurrentTaxon(null); |
|
| 420 |
save(taxon, state); |
|
| 421 |
return taxon; |
|
| 297 | 422 |
}else{
|
| 298 |
if(isEndingElement(next, "heading")){
|
|
| 423 |
if(isEndingElement(next, HEADING)){
|
|
| 299 | 424 |
//NOT YET IMPLEMENTED |
| 300 |
}else if(isStartingElement(next, "taxontitle")){
|
|
| 425 |
popUnimplemented(next.asEndElement()); |
|
| 426 |
}else if(isEndingElement(next, TEXT_SECTION)){
|
|
| 301 | 427 |
//NOT YET IMPLEMENTED |
| 302 |
}else if(isStartingElement(next, "biographies")){
|
|
| 428 |
popUnimplemented(next.asEndElement()); |
|
| 429 |
}else if(isEndingElement(next, KEY)){
|
|
| 303 | 430 |
//NOT YET IMPLEMENTED |
| 304 |
}else if(isStartingElement(next, "references")){
|
|
| 431 |
popUnimplemented(next.asEndElement()); |
|
| 432 |
}else if(isEndingElement(next, NOTES)){
|
|
| 305 | 433 |
//NOT YET IMPLEMENTED |
| 306 |
}else if(isStartingElement(next, "textSection")){
|
|
| 434 |
popUnimplemented(next.asEndElement()); |
|
| 435 |
}else if(isEndingElement(next, REFERENCES)){
|
|
| 307 | 436 |
//NOT YET IMPLEMENTED |
| 308 |
}else if(isStartingElement(next, "addenda")){
|
|
| 437 |
popUnimplemented(next.asEndElement()); |
|
| 438 |
}else if(isEndingElement(next, FIGURE)){
|
|
| 309 | 439 |
//NOT YET IMPLEMENTED |
| 440 |
popUnimplemented(next.asEndElement()); |
|
| 441 |
}else if(isEndingElement(next, FOOTNOTE)){
|
|
| 442 |
//NOT YET IMPLEMENTED |
|
| 443 |
popUnimplemented(next.asEndElement()); |
|
| 310 | 444 |
}else{
|
| 311 |
handleUnexpectedEndElement(next); |
|
| 445 |
handleUnexpectedEndElement(next.asEndElement());
|
|
| 312 | 446 |
} |
| 313 | 447 |
} |
| 314 | 448 |
}else if (next.isStartElement()){
|
| 315 |
if(isStartingElement(next, "heading")){
|
|
| 316 |
handleNotYetImplementedElement(next); |
|
| 317 |
}else if(isStartingElement(next, "taxontitle")){
|
|
| 318 |
handleTaxonTitle(state, reader, next); |
|
| 319 |
}else if(isStartingElement(next, "writer")){
|
|
| 449 |
if(isStartingElement(next, HEADING)){
|
|
| 320 | 450 |
handleNotYetImplementedElement(next); |
| 321 |
}else if(isStartingElement(next, "textsection")){
|
|
| 451 |
}else if(isStartingElement(next, TAXONTITLE)){
|
|
| 452 |
taxonTitle = handleTaxonTitle(state, reader, next); |
|
| 453 |
hasTitle = true; |
|
| 454 |
}else if(isStartingElement(next, WRITER)){
|
|
| 455 |
Extension writerExtension = handleWriter(state, reader, next); |
|
| 456 |
|
|
| 457 |
|
|
| 458 |
taxon.addExtension(writerExtension); |
|
| 459 |
}else if(isStartingElement(next, TEXT_SECTION)){
|
|
| 322 | 460 |
handleNotYetImplementedElement(next); |
| 323 |
}else if(isStartingElement(next, "key")){
|
|
| 461 |
}else if(isStartingElement(next, KEY)){
|
|
| 324 | 462 |
handleNotYetImplementedElement(next); |
| 325 |
}else if(isStartingElement(next, "feature")){
|
|
| 463 |
}else if(isStartingElement(next, NOMENCLATURE)){
|
|
| 464 |
handleNomenclature(state, reader, next, taxon); |
|
| 465 |
hasNomenclature = true; |
|
| 466 |
}else if(isStartingElement(next, FEATURE)){
|
|
| 467 |
handleFeature(state, reader, next); |
|
| 468 |
}else if(isStartingElement(next, NOTES)){
|
|
| 326 | 469 |
handleNotYetImplementedElement(next); |
| 327 |
}else if(isStartingElement(next, "notes")){
|
|
| 470 |
}else if(isStartingElement(next, REFERENCES)){
|
|
| 328 | 471 |
handleNotYetImplementedElement(next); |
| 329 |
}else if(isStartingElement(next, "references")){
|
|
| 472 |
}else if(isStartingElement(next, FIGURE)){
|
|
| 330 | 473 |
handleNotYetImplementedElement(next); |
| 331 |
}else if(isStartingElement(next, "figure")){
|
|
| 332 |
handleNotYetImplementedElement(next); |
|
| 333 |
}else if(isStartingElement(next, "footnote")){
|
|
| 474 |
}else if(isStartingElement(next, FOOTNOTE)){
|
|
| 334 | 475 |
handleNotYetImplementedElement(next); |
| 335 | 476 |
}else{
|
| 336 | 477 |
handleUnexpectedStartElement(next); |
| ... | ... | |
| 339 | 480 |
handleUnexpectedElement(next); |
| 340 | 481 |
} |
| 341 | 482 |
} |
| 342 |
return; |
|
| 483 |
//TODO handle missing end element |
|
| 484 |
throw new IllegalStateException("Taxon has no closing tag");
|
|
| 343 | 485 |
} |
| 344 | 486 |
|
| 345 |
private void handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 346 |
boolean hasTitle = false; |
|
| 487 |
|
|
| 488 |
/** |
|
| 489 |
* @param state |
|
| 490 |
* @param attributes |
|
| 491 |
*/ |
|
| 492 |
private Taxon createTaxonAndName(MarkupImportState state, Map<String, Attribute> attributes) {
|
|
| 493 |
NonViralName name; |
|
| 494 |
Rank rank = Rank.SPECIES(); //default |
|
| 495 |
if (checkAndRemoveAttributeValue(attributes, CLASS, "cultivated")){
|
|
| 496 |
name = CultivarPlantName.NewInstance(rank); |
|
| 497 |
}else{
|
|
| 498 |
NomenclaturalCode nc = makeNomenclaturalCode(state); |
|
| 499 |
name = (NonViralName)nc.getNewTaxonNameInstance(rank); |
|
| 500 |
} |
|
| 501 |
Taxon taxon = Taxon.NewInstance(name, state.getConfig().getSourceReference()); |
|
| 502 |
if (checkAndRemoveAttributeValue(attributes, CLASS, "dubious")){
|
|
| 503 |
taxon.setDoubtful(true); |
|
| 504 |
}else if (checkAndRemoveAttributeValue(attributes, CLASS, "excluded")){
|
|
| 505 |
taxon.setExcluded(true); |
|
| 506 |
} |
|
| 507 |
//TODO insufficient, new, expected |
|
| 508 |
handleNotYetImplementedAttribute(attributes, CLASS); |
|
| 509 |
//From old version |
|
| 510 |
// MarkerType markerType = getMarkerType(state, attrValue); |
|
| 511 |
// if (markerType == null){
|
|
| 512 |
// logger.warn("Class attribute value for taxon not yet supported: " + attrValue);
|
|
| 513 |
// }else{
|
|
| 514 |
// taxon.addMarker(Marker.NewInstance(markerType, true)); |
|
| 515 |
// } |
|
| 516 |
|
|
| 517 |
// save(name, state); |
|
| 518 |
// save(taxon, state); |
|
| 519 |
return taxon; |
|
| 520 |
} |
|
| 521 |
|
|
| 522 |
|
|
| 523 |
/** |
|
| 524 |
* @param state |
|
| 525 |
* @return |
|
| 526 |
*/ |
|
| 527 |
private NomenclaturalCode makeNomenclaturalCode(MarkupImportState state) {
|
|
| 528 |
NomenclaturalCode nc = state.getConfig().getNomenclaturalCode(); |
|
| 529 |
if (nc == null){
|
|
| 530 |
nc = NomenclaturalCode.ICBN; //default; |
|
| 531 |
} |
|
| 532 |
return nc; |
|
| 533 |
} |
|
| 534 |
|
|
| 535 |
private String handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 536 |
String text = ""; |
|
| 537 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 538 |
String rankAttr = getAndRemoveAttributeValue(attributes, RANK); |
|
| 539 |
Rank rank = makeRank(state, rankAttr, false); |
|
| 540 |
//TODO |
|
| 541 |
// String numAttr = getAndRemoveAttributeValue(attributes, NUM); |
|
| 542 |
handleNotYetImplementedAttribute(attributes, NUM); |
|
| 543 |
checkNoAttributes(attributes, parentEvent); |
|
| 347 | 544 |
|
| 348 | 545 |
//TODO handle attributes |
| 349 | 546 |
while (reader.hasNext()){
|
| 350 | 547 |
XMLEvent next = readNoWhitespace(reader); |
| 351 | 548 |
if (next.isEndElement()){
|
| 352 | 549 |
if (isMyEndingElement(next, parentEvent)){
|
| 550 |
Taxon taxon = state.getCurrentTaxon(); |
|
| 551 |
String titleText = null; |
|
| 552 |
if (checkMandatoryText(text, parentEvent)){
|
|
| 553 |
titleText = normalize(text); |
|
| 554 |
UUID uuidTitle = MarkupTransformer.uuidTaxonTitle; |
|
| 555 |
ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "Taxon Title ", "taxon title", "title"); |
|
| 556 |
taxon.addExtension(titleText, titleExtension); |
|
| 557 |
} |
|
| 558 |
taxon.getName().setRank(rank); |
|
| 353 | 559 |
//TODO check title exists |
| 354 |
return; |
|
| 560 |
return titleText;
|
|
| 355 | 561 |
}else{
|
| 356 |
if(isEndingElement(next, "footnoteString")){
|
|
| 562 |
if(isEndingElement(next, FOOTNOTE)){
|
|
| 357 | 563 |
//NOT YET IMPLEMENTED |
| 564 |
popUnimplemented(next.asEndElement()); |
|
| 358 | 565 |
}else{
|
| 359 |
handleUnexpectedEndElement(next); |
|
| 360 |
state.setSuccessToFalse();
|
|
| 566 |
handleUnexpectedEndElement(next.asEndElement());
|
|
| 567 |
state.setUnsuccessfull();
|
|
| 361 | 568 |
} |
| 362 | 569 |
} |
| 363 | 570 |
}else if (next.isStartElement()){
|
| 364 |
if(isStartingElement(next, "footnoteString")){
|
|
| 571 |
if(isStartingElement(next, FOOTNOTE)){
|
|
| 365 | 572 |
handleNotYetImplementedElement(next); |
| 366 | 573 |
}else{
|
| 367 | 574 |
handleUnexpectedStartElement(next); |
| 368 |
state.setSuccessToFalse();
|
|
| 575 |
state.setUnsuccessfull();
|
|
| 369 | 576 |
} |
| 577 |
}else if (next.isCharacters()){
|
|
| 578 |
text +=next.asCharacters().getData(); |
|
| 579 |
|
|
| 370 | 580 |
}else{
|
| 371 | 581 |
handleUnexpectedElement(next); |
| 372 |
state.setSuccessToFalse();
|
|
| 582 |
state.setUnsuccessfull();
|
|
| 373 | 583 |
} |
| 374 | 584 |
} |
| 375 |
return; |
|
| 585 |
return null;
|
|
| 376 | 586 |
|
| 377 | 587 |
|
| 378 | 588 |
} |
| 379 |
|
|
| 380 |
|
|
| 381 |
private boolean isMyEndingElement(XMLEvent next, XMLEvent event) throws XMLStreamException {
|
|
| 382 |
return isEndingElement(next, event.asStartElement().getName().getLocalPart()); |
|
| 383 |
} |
|
| 384 |
|
|
| 385 |
|
|
| 386 |
/** |
|
| 387 |
* This comes from the old version, needs to be checked on need |
|
| 388 |
* @param state |
|
| 389 |
*/ |
|
| 390 |
private void doAllTheOldOtherStuff(MarkupImportState state) {
|
|
| 391 |
state.putTree(null, null); |
|
| 392 |
if (unmatchedLeads == null){
|
|
| 393 |
unmatchedLeads = UnmatchedLeads.NewInstance(); |
|
| 394 |
} |
|
| 395 |
state.setUnmatchedLeads(unmatchedLeads); |
|
| 396 |
|
|
| 397 |
// TransactionStatus tx = startTransaction(); |
|
| 398 |
unmatchedLeads.saveToSession(getPolytomousKeyNodeService()); |
|
| 399 |
|
|
| 589 |
|
|
| 590 |
private Extension handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 591 |
String text = ""; |
|
| 592 |
checkNoAttributes(parentEvent); |
|
| 400 | 593 |
|
| 401 |
//TODO generally do not store the reference object in the config |
|
| 402 |
Reference sourceReference = state.getConfig().getSourceReference(); |
|
| 403 |
getReferenceService().saveOrUpdate(sourceReference); |
|
| 594 |
//TODO handle attributes |
|
| 595 |
while (reader.hasNext()){
|
|
| 596 |
XMLEvent next = readNoWhitespace(reader); |
|
| 597 |
if (next.isEndElement()){
|
|
| 598 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 599 |
if (checkMandatoryText(text, parentEvent)){
|
|
| 600 |
UUID uuidWriter = MarkupTransformer.uuidWriter; |
|
| 601 |
ExtensionType titleExtensionType = this.getExtensionType(state, uuidWriter, "Writer", "writer", "writer"); |
|
| 602 |
Extension extension = Extension.NewInstance(); |
|
| 603 |
extension.setType(titleExtensionType); |
|
| 604 |
extension.setValue(normalize(text)); |
|
| 605 |
return extension; |
|
| 606 |
}else{
|
|
| 607 |
return null; |
|
| 608 |
} |
|
| 609 |
}else{
|
|
| 610 |
if(isEndingElement(next, FOOTNOTE)){
|
|
| 611 |
//NOT YET IMPLEMENTED |
|
| 612 |
popUnimplemented(next.asEndElement()); |
|
| 613 |
}else{
|
|
| 614 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 615 |
state.setUnsuccessfull(); |
|
| 616 |
} |
|
| 617 |
} |
|
| 618 |
}else if (next.isStartElement()){
|
|
| 619 |
if(isStartingElement(next, FOOTNOTE)){
|
|
| 620 |
handleNotYetImplementedElement(next); |
|
| 621 |
}else{
|
|
| 622 |
handleUnexpectedStartElement(next); |
|
| 623 |
state.setUnsuccessfull(); |
|
| 624 |
} |
|
| 625 |
}else if (next.isCharacters()){
|
|
| 626 |
text +=next.asCharacters().getData(); |
|
| 627 |
|
|
| 628 |
}else{
|
|
| 629 |
handleUnexpectedElement(next); |
|
| 630 |
state.setUnsuccessfull(); |
|
| 631 |
} |
|
| 632 |
} |
|
| 633 |
return null; |
|
| 404 | 634 |
} |
| 405 | 635 |
|
| 406 |
|
|
| 407 |
private boolean doInvoke_old(MarkupImportState state){
|
|
| 408 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>(); |
|
| 409 |
ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
|
| 410 |
|
|
| 411 |
// Element elbody= getBodyElement(state.getConfig()); |
|
| 412 |
Element elbody = null; |
|
| 413 |
List<Element> elTaxonList = elbody.getChildren(); |
|
| 414 |
|
|
| 415 |
int i = 0; |
|
| 636 |
private void handleNomenclature(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Taxon taxon) throws XMLStreamException {
|
|
| 637 |
checkNoAttributes(parentEvent); |
|
| 416 | 638 |
|
| 417 |
Set<String> unhandledTitleClassess = new HashSet<String>(); |
|
| 418 |
Set<String> unhandledNomeclatureChildren = new HashSet<String>(); |
|
| 419 |
Set<String> unhandledDescriptionChildren = new HashSet<String>(); |
|
| 420 |
|
|
| 421 |
Taxon lastTaxon = getLastTaxon(state); |
|
| 422 |
|
|
| 423 |
//for each taxon |
|
| 424 |
for (Element elTaxon : elTaxonList){
|
|
| 425 |
try {
|
|
| 426 |
if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}
|
|
| 427 |
if (! elTaxon.getName().equalsIgnoreCase("taxon")){
|
|
| 428 |
logger.warn("body has element other than 'taxon'");
|
|
| 429 |
} |
|
| 430 |
|
|
| 431 |
BotanicalName botanicalName = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 432 |
Taxon taxon = Taxon.NewInstance(botanicalName, state.getConfig().getSourceReference()); |
|
| 433 |
|
|
| 434 |
handleTaxonAttributes(elTaxon, taxon, state); |
|
| 435 |
|
|
| 436 |
|
|
| 437 |
List<Element> children = elTaxon.getChildren(); |
|
| 438 |
handleTaxonElement(state, unhandledTitleClassess, unhandledNomeclatureChildren, unhandledDescriptionChildren, taxon, children); |
|
| 439 |
handleTaxonRelation(state, taxon, lastTaxon); |
|
| 440 |
lastTaxon = taxon; |
|
| 441 |
taxaToSave.add(taxon); |
|
| 442 |
state.getConfig().setLastTaxonUuid(lastTaxon.getUuid()); |
|
| 443 |
|
|
| 444 |
} catch (Exception e) {
|
|
| 445 |
logger.warn("Exception occurred in Sapindacea taxon import: " + e);
|
|
| 446 |
e.printStackTrace(); |
|
| 639 |
while (reader.hasNext()){
|
|
| 640 |
XMLEvent next = readNoWhitespace(reader); |
|
| 641 |
if (isStartingElement(next, HOMOTYPES)){
|
|
| 642 |
handleHomotypes(state, reader, next.asStartElement(), taxon); |
|
| 643 |
}else if(isMyEndingElement(next, parentEvent)){
|
|
| 644 |
return; |
|
| 645 |
}else{
|
|
| 646 |
fireSchemaConflictEventExpectedStartTag(HOMOTYPES, reader); |
|
| 647 |
state.setUnsuccessfull(); |
|
| 447 | 648 |
} |
| 448 |
|
|
| 449 | 649 |
} |
| 450 |
|
|
| 451 |
System.out.println(state.getUnmatchedLeads().toString()); |
|
| 452 |
logger.warn("There are taxa with attributes 'excluded' and 'dubious'");
|
|
| 453 |
|
|
| 454 |
logger.info("Children for nomenclature are: " + unhandledNomeclatureChildren);
|
|
| 455 |
logger.info("Children for description are: " + unhandledDescriptionChildren);
|
|
| 456 |
logger.info("Children for homotypes are: " + unhandledHomotypeChildren);
|
|
| 457 |
logger.info("Children for nom are: " + unhandledNomChildren);
|
|
| 458 |
|
|
| 459 |
|
|
| 460 |
//invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap); |
|
| 461 |
logger.info(i + " taxa handled. Saving ..."); |
|
| 462 |
getTaxonService().saveOrUpdate(taxaToSave); |
|
| 463 |
getFeatureTreeService().saveOrUpdateFeatureNodesAll(state.getFeatureNodesToSave()); |
|
| 464 |
state.getFeatureNodesToSave().clear(); |
|
| 465 |
// commitTransaction(tx); |
|
| 466 |
|
|
| 467 |
logger.info("end makeTaxa ...");
|
|
| 468 |
logger.info("start makeKey ...");
|
|
| 469 |
// invokeDoKey(state); |
|
| 470 |
logger.info("end makeKey ...");
|
|
| 471 |
|
|
| 472 |
return success.getValue(); |
|
| 650 |
return; |
|
| 473 | 651 |
} |
| 474 | 652 |
|
| 475 |
|
|
| 476 | 653 |
|
| 477 | 654 |
|
| 478 |
private void handleTaxonAttributes(Element elTaxon, Taxon taxon, MarkupImportState state) {
|
|
| 479 |
List<Attribute> attrList = elTaxon.getAttributes(); |
|
| 480 |
for (Attribute attr : attrList){
|
|
| 481 |
String attrName = attr.getName(); |
|
| 482 |
String attrValue = attr.getValue(); |
|
| 483 |
if ("class".equals(attrName)){
|
|
| 484 |
if (attrValue.equalsIgnoreCase("dubious") || attrValue.equalsIgnoreCase("DUBIOUS GENUS") || attrValue.equalsIgnoreCase("DOUBTFUL SPECIES") ){
|
|
| 485 |
taxon.setDoubtful(true); |
|
| 655 |
private void handleHomotypes(MarkupImportState state, XMLEventReader reader, StartElement parentEvent, Taxon taxon) throws XMLStreamException {
|
|
| 656 |
checkNoAttributes(parentEvent); |
|
| 657 |
|
|
| 658 |
HomotypicalGroup homotypicalGroup = null; |
|
| 659 |
|
|
| 660 |
boolean hasNom = false; |
|
| 661 |
while (reader.hasNext()){
|
|
| 662 |
XMLEvent next = readNoWhitespace(reader); |
|
| 663 |
if (next.isEndElement()){
|
|
| 664 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 665 |
checkMandatoryElement(hasNom, parentEvent, NOM); |
|
| 666 |
return; |
|
| 486 | 667 |
}else{
|
| 487 |
MarkerType markerType = getMarkerType(state, attrValue); |
|
| 488 |
if (markerType == null){
|
|
| 489 |
logger.warn("Class attribute value for taxon not yet supported: " + attrValue);
|
|
| 668 |
if(isEndingElement(next, NAME_TYPE)){
|
|
| 669 |
state.setNameType(false); |
|
| 670 |
//NOT YET IMPLEMENTED |
|
| 671 |
popUnimplemented(next.asEndElement()); |
|
| 672 |
}else if(isEndingElement(next, NOTES)){
|
|
| 673 |
//NOT YET IMPLEMENTED |
|
| 674 |
popUnimplemented(next.asEndElement()); |
|
| 490 | 675 |
}else{
|
| 491 |
taxon.addMarker(Marker.NewInstance(markerType, true));
|
|
| 676 |
handleUnexpectedEndElement(next.asEndElement());
|
|
| 492 | 677 |
} |
| 493 | 678 |
} |
| 494 |
}else if ("num".equals(attrName)){
|
|
| 495 |
logger.warn("num not yet supported");
|
|
| 679 |
}else if (next.isStartElement()){
|
|
| 680 |
if(isStartingElement(next, NOM)){
|
|
| 681 |
homotypicalGroup = handleNom(state, reader, next, homotypicalGroup); |
|
| 682 |
hasNom = true; |
|
| 683 |
}else if(isStartingElement(next, NAME_TYPE)){
|
|
| 684 |
state.setNameType(true); |
|
| 685 |
handleNotYetImplementedElement(next); |
|
| 686 |
}else if(isStartingElement(next, SPECIMEN_TYPE)){
|
|
| 687 |
handleSpecimenType(state, reader, next, homotypicalGroup); |
|
| 688 |
}else if(isStartingElement(next, NOTES)){
|
|
| 689 |
handleNotYetImplementedElement(next); |
|
| 690 |
}else{
|
|
| 691 |
handleUnexpectedStartElement(next); |
|
| 692 |
} |
|
| 496 | 693 |
}else{
|
| 497 |
logger.warn("Attribute " + attrName + " not yet supported for element taxon");
|
|
| 694 |
handleUnexpectedElement(next);
|
|
| 498 | 695 |
} |
| 499 | 696 |
} |
| 500 |
|
|
| 501 |
} |
|
| 502 |
|
|
| 503 |
|
|
| 504 |
private Taxon getLastTaxon(MarkupImportState state) {
|
|
| 505 |
if (state.getConfig().getLastTaxonUuid() == null){
|
|
| 506 |
return null; |
|
| 507 |
}else{
|
|
| 508 |
return (Taxon)getTaxonService().find(state.getConfig().getLastTaxonUuid()); |
|
| 509 |
} |
|
| 697 |
//TODO handle missing end element |
|
| 698 |
throw new IllegalStateException("Homotypes has no closing tag");
|
|
| 699 |
|
|
| 510 | 700 |
} |
| 511 | 701 |
|
| 512 | 702 |
|
| 513 |
// private void invokeDoKey(SapindaceaeImportState state) {
|
|
| 514 |
// TransactionStatus tx = startTransaction(); |
|
| 515 |
// |
|
| 516 |
// Set<FeatureNode> nodesToSave = new HashSet<FeatureNode>(); |
|
| 517 |
// ITaxonService taxonService = getTaxonService(); |
|
| 518 |
// ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
|
| 519 |
// |
|
| 520 |
// Element elbody= getBodyElement(state.getConfig()); |
|
| 521 |
// List<Element> elTaxonList = elbody.getChildren(); |
|
| 522 |
// |
|
| 523 |
// int i = 0; |
|
| 524 |
// |
|
| 525 |
// //for each taxon |
|
| 526 |
// for (Element elTaxon : elTaxonList){
|
|
| 527 |
// if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}
|
|
| 528 |
// if (! elTaxon.getName().equalsIgnoreCase("taxon")){
|
|
| 529 |
// continue; |
|
| 530 |
// } |
|
| 531 |
// |
|
| 532 |
// List<Element> children = elTaxon.getChildren("key");
|
|
| 533 |
// for (Element element : children){
|
|
| 534 |
// handleKeys(state, element, null); |
|
| 535 |
// } |
|
| 536 |
// nodesToSave.add(taxon); |
|
| 537 |
// |
|
| 538 |
// } |
|
| 539 |
// |
|
| 540 |
// } |
|
| 541 |
|
|
| 542 |
|
|
| 543 |
// body/taxon/* |
|
| 544 |
private void handleTaxonElement(MarkupImportState state, Set<String> unhandledTitleClassess, Set<String> unhandledNomeclatureChildren, Set<String> unhandledDescriptionChildren, Taxon taxon, List<Element> children) {
|
|
| 545 |
AnnotatableEntity lastEntity = null; |
|
| 546 |
for (Element element : children){
|
|
| 547 |
String elName = element.getName(); |
|
| 548 |
|
|
| 549 |
if (elName.equalsIgnoreCase("title")){
|
|
| 550 |
handleTitle(state, element, taxon, unhandledTitleClassess); |
|
| 551 |
lastEntity = null; |
|
| 552 |
}else if(elName.equalsIgnoreCase("nomenclature")){
|
|
| 553 |
handleNomenclature(state, element, taxon, unhandledNomeclatureChildren); |
|
| 554 |
lastEntity = null; |
|
| 555 |
}else if(elName.equalsIgnoreCase("description")){
|
|
| 556 |
handleDescription(state, element, taxon, unhandledDescriptionChildren); |
|
| 557 |
lastEntity = null; |
|
| 558 |
}else if(elName.equalsIgnoreCase("habitatecology")){
|
|
| 559 |
lastEntity = handleEcology(state, element, taxon); |
|
| 560 |
}else if(elName.equalsIgnoreCase("distribution")){
|
|
| 561 |
lastEntity = handleDistribution(state, element, taxon); |
|
| 562 |
}else if(elName.equalsIgnoreCase("uses")){
|
|
| 563 |
lastEntity = handleUses(state, element, taxon); |
|
| 564 |
}else if(elName.equalsIgnoreCase("notes")){
|
|
| 565 |
lastEntity = handleTaxonNotes(state, element, taxon); |
|
| 566 |
}else if(elName.equalsIgnoreCase("chromosomes")){
|
|
| 567 |
lastEntity = handleChromosomes(state, element, taxon); |
|
| 568 |
}else if(elName.equalsIgnoreCase("vernacularnames")){
|
|
| 569 |
handleVernaculars(state, element, taxon); |
|
| 570 |
}else if(elName.equalsIgnoreCase("key")){
|
|
| 571 |
lastEntity = handleKeys(state, element, taxon); |
|
| 572 |
}else if(elName.equalsIgnoreCase("references")){
|
|
| 573 |
handleReferences(state, element, taxon, lastEntity); |
|
| 574 |
lastEntity = null; |
|
| 575 |
}else if(elName.equalsIgnoreCase("taxon")){
|
|
| 576 |
logger.warn("A taxon should not be part of a taxon");
|
|
| 577 |
}else if(elName.equalsIgnoreCase("homotypes")){
|
|
| 578 |
logger.warn("Homotypes should be included in the nomenclature flag but is child of taxon [XPath: body/taxon/homotypes]");
|
|
| 703 |
private void handleSpecimenType(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, HomotypicalGroup homotypicalGroup) throws XMLStreamException {
|
|
| 704 |
//attributes |
|
| 705 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 706 |
String typeStatus = getAndRemoveAttributeValue(attributes, TYPE_STATUS); |
|
| 707 |
String notSeen = getAndRemoveAttributeValue(attributes, NOT_SEEN); |
|
| 708 |
String unknown = getAndRemoveAttributeValue(attributes, UNKNOWN); |
|
| 709 |
String notFound = getAndRemoveAttributeValue(attributes, NOT_FOUND); |
|
| 710 |
String destroyed = getAndRemoveAttributeValue(attributes, DESTROYED); |
|
| 711 |
String lost = getAndRemoveAttributeValue(attributes, LOST); |
|
| 712 |
checkNoAttributes(attributes, parentEvent); |
|
| 713 |
if (StringUtils.isNotEmpty(typeStatus)){
|
|
| 714 |
//TODO |
|
| 715 |
//currently not needed |
|
| 716 |
} else if (StringUtils.isNotEmpty(notSeen)){
|
|
| 717 |
handleNotYetImplementedAttribute(attributes, NOT_SEEN); |
|
| 718 |
}else if (StringUtils.isNotEmpty(unknown)){
|
|
| 719 |
handleNotYetImplementedAttribute(attributes, UNKNOWN); |
|
| 720 |
}else if (StringUtils.isNotEmpty(notFound)){
|
|
| 721 |
handleNotYetImplementedAttribute(attributes, NOT_FOUND); |
|
| 722 |
}else if (StringUtils.isNotEmpty(destroyed)){
|
|
| 723 |
handleNotYetImplementedAttribute(attributes, DESTROYED); |
|
| 724 |
}else if (StringUtils.isNotEmpty(lost)){
|
|
| 725 |
handleNotYetImplementedAttribute(attributes, LOST); |
|
| 726 |
} |
|
| 727 |
|
|
| 728 |
//elements |
|
| 729 |
while (reader.hasNext()){
|
|
| 730 |
XMLEvent next = readNoWhitespace(reader); |
|
| 731 |
if (next.isEndElement()){
|
|
| 732 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 733 |
return; |
|
| 734 |
}else{
|
|
| 735 |
if(isEndingElement(next, FULL_TYPE)){
|
|
| 736 |
//NOT YET IMPLEMENTED |
|
| 737 |
popUnimplemented(next.asEndElement()); |
|
| 738 |
}else if(isEndingElement(next,TYPE_STATUS)){
|
|
| 739 |
//NOT YET IMPLEMENTED |
|
| 740 |
popUnimplemented(next.asEndElement()); |
|
| 741 |
}else if(isEndingElement(next, COLLECTION)){
|
|
| 742 |
//NOT YET IMPLEMENTED |
|
| 743 |
popUnimplemented(next.asEndElement()); |
|
| 744 |
}else if(isEndingElement(next, ORIGINAL_DETERMINATION)){
|
|
| 745 |
//NOT YET IMPLEMENTED |
|
| 746 |
popUnimplemented(next.asEndElement()); |
|
| 747 |
}else if(isEndingElement(next, SPECIMEN_TYPE)){
|
|
| 748 |
//NOT YET IMPLEMENTED |
|
| 749 |
popUnimplemented(next.asEndElement()); |
|
| 750 |
}else if(isEndingElement(next, CITATION)){
|
|
| 751 |
//NOT YET IMPLEMENTED |
|
| 752 |
popUnimplemented(next.asEndElement()); |
|
| 753 |
}else if(isEndingElement(next, NOTES)){
|
|
| 754 |
//NOT YET IMPLEMENTED |
|
| 755 |
popUnimplemented(next.asEndElement()); |
|
| 756 |
}else if(isEndingElement(next, ANNOTATION)){
|
|
| 757 |
//NOT YET IMPLEMENTED |
|
| 758 |
popUnimplemented(next.asEndElement()); |
|
| 759 |
}else{
|
|
| 760 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 761 |
} |
|
| 762 |
} |
|
| 763 |
}else if (next.isStartElement()){
|
|
| 764 |
if(isStartingElement(next, FULL_TYPE)){
|
|
| 765 |
handleNotYetImplementedElement(next); |
|
| 766 |
// homotypicalGroup = handleNom(state, reader, next, taxon, homotypicalGroup); |
|
| 767 |
}else if(isStartingElement(next, TYPE_STATUS)){
|
|
| 768 |
handleNotYetImplementedElement(next); |
|
| 769 |
}else if(isStartingElement(next, COLLECTION)){
|
|
| 770 |
handleNotYetImplementedElement(next); |
|
| 771 |
// handleName(state, reader, next, name); |
|
| 772 |
}else if(isStartingElement(next, ORIGINAL_DETERMINATION)){
|
|
| 773 |
handleNotYetImplementedElement(next); |
|
| 774 |
}else if(isStartingElement(next, SPECIMEN_TYPE)){
|
|
| 775 |
handleNotYetImplementedElement(next); |
|
| 776 |
}else if(isStartingElement(next, NOTES)){
|
|
| 777 |
handleNotYetImplementedElement(next); |
|
| 778 |
}else if(isStartingElement(next, ANNOTATION)){
|
|
| 779 |
handleNotYetImplementedElement(next); |
|
| 780 |
}else{
|
|
| 781 |
handleUnexpectedStartElement(next); |
|
| 782 |
} |
|
| 579 | 783 |
}else{
|
| 580 |
logger.warn("Unexpected child for taxon: " + elName);
|
|
| 784 |
handleUnexpectedElement(next);
|
|
| 581 | 785 |
} |
| 582 | 786 |
} |
| 583 |
} |
|
| 584 |
|
|
| 585 |
|
|
| 586 |
private void handleVernaculars(MarkupImportState state, Element elVernacular, Taxon taxon) {
|
|
| 587 |
verifyNoAttribute(elVernacular); |
|
| 588 |
verifyNoChildren(elVernacular, false); |
|
| 589 |
String value = elVernacular.getTextNormalize(); |
|
| 590 |
Feature feature = Feature.COMMON_NAME(); |
|
| 591 |
value = replaceStart(value, "Noms vernaculaires"); |
|
| 592 |
String[] dialects = value.split(";");
|
|
| 593 |
for (String singleDialect : dialects){
|
|
| 594 |
handleSingleDialect(taxon, singleDialect, feature, state); |
|
| 595 |
} |
|
| 596 |
return; |
|
| 787 |
//TODO handle missing end element |
|
| 788 |
throw new IllegalStateException("Nom has no closing tag"); // TODO Auto-generated method stub
|
|
| 789 |
|
|
| 597 | 790 |
} |
| 598 | 791 |
|
| 599 | 792 |
|
| 600 |
private void handleSingleDialect(Taxon taxon, String singleDialect, Feature feature, MarkupImportState state) {
|
|
| 601 |
singleDialect = singleDialect.trim(); |
|
| 602 |
TaxonDescription description = getDescription(taxon); |
|
| 603 |
String reDialect = "\\(dial\\.\\s.*\\)"; |
|
| 604 |
// String reDialect = "\\(.*\\)"; |
|
| 605 |
Pattern patDialect = Pattern.compile(reDialect); |
|
| 606 |
Matcher matcher = patDialect.matcher(singleDialect); |
|
| 607 |
if (matcher.find()){
|
|
| 608 |
String dialect = singleDialect.substring(matcher.start(), matcher.end()); |
|
| 609 |
dialect = dialect.replace("(dial. ", "").replace(")", "");
|
|
| 610 |
|
|
| 611 |
Language language = null; |
|
| 612 |
try {
|
|
| 613 |
language = this.getLanguage(state, state.getTransformer().getLanguageUuid(dialect), dialect, dialect, dialect); |
|
| 614 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 615 |
logger.error(e.getMessage()); |
|
| 616 |
} |
|
| 617 |
|
|
| 618 |
String commonNames = singleDialect.substring(0, matcher.start()); |
|
| 619 |
String[] splitNames = commonNames.split(",");
|
|
| 620 |
for (String commonNameString : splitNames){
|
|
| 621 |
commonNameString = commonNameString.trim(); |
|
| 622 |
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language); |
|
| 623 |
description.addElement(commonName); |
|
| 624 |
} |
|
| 793 |
private HomotypicalGroup handleNom(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, |
|
| 794 |
HomotypicalGroup homotypicalGroup) throws XMLStreamException {
|
|
| 795 |
HomotypicalGroup resultHomGroup = null; |
|
| 796 |
boolean isSynonym = false; |
|
| 797 |
boolean isNameType = state.isNameType(); |
|
| 798 |
//attributes |
|
| 799 |
String classValue = getClassOnlyAttribute(parentEvent); |
|
| 800 |
if (! isNameType && ACCEPTED.equalsIgnoreCase(classValue)){
|
|
| 801 |
isSynonym = false; |
|
| 802 |
}else if (! isNameType && SYNONYM.equalsIgnoreCase(classValue)){
|
|
| 803 |
isSynonym = true; |
|
| 804 |
}else if (isNameType && NAME_TYPE.equalsIgnoreCase(classValue)){
|
|
| 805 |
handleNotYetImplementedAttributeValue(parentEvent, CLASS, classValue); |
|
| 625 | 806 |
}else{
|
| 626 |
logger.warn("No dialect match: " + singleDialect);
|
|
| 807 |
//TODO Not yet implemented |
|
| 808 |
fireUnexpectedAttributeValue(parentEvent, CLASS, classValue); |
|
| 627 | 809 |
} |
| 628 |
} |
|
| 629 |
|
|
| 630 |
|
|
| 631 |
private void handleReferences(MarkupImportState state, Element elReferences, Taxon taxon, AnnotatableEntity lastEntity) {
|
|
| 632 |
verifyNoAttribute(elReferences); |
|
| 633 |
verifyNoChildren(elReferences, true); |
|
| 634 |
String refString = elReferences.getTextNormalize(); |
|
| 635 |
if (lastEntity == null){
|
|
| 636 |
logger.warn("No last entity defined: " + refString);
|
|
| 637 |
return; |
|
| 638 |
} |
|
| 639 |
|
|
| 640 |
Annotation annotation = Annotation.NewInstance(refString, AnnotationType.EDITORIAL(), Language.DEFAULT()); |
|
| 641 |
lastEntity.addAnnotation(annotation); |
|
| 642 |
} |
|
| 643 |
|
|
| 644 |
|
|
| 645 |
private PolytomousKey handleKeys(MarkupImportState state, Element elKey, Taxon taxon) {
|
|
| 646 |
UnmatchedLeads openKeys = state.getUnmatchedLeads(); |
|
| 647 |
|
|
| 648 |
//title |
|
| 649 |
String title = makeKeyTitle(elKey); |
|
| 650 |
|
|
| 651 |
//key |
|
| 652 |
PolytomousKey key = PolytomousKey.NewTitledInstance(title); |
|
| 653 |
|
|
| 654 |
//TODO add covered taxa etc. |
|
| 655 |
verifyNoAttribute(elKey); |
|
| 810 |
NonViralName name = makeName(state.getCurrentTaxon(), homotypicalGroup, isSynonym); |
|
| 656 | 811 |
|
| 657 |
//notes |
|
| 658 |
makeKeyNotes(elKey, key); |
|
| 659 | 812 |
|
| 660 |
//keycouplets |
|
| 661 |
List<Element> keychoices = new ArrayList<Element>(); |
|
| 662 |
keychoices.addAll(elKey.getChildren("keycouplet"));
|
|
| 663 |
keychoices.addAll(elKey.getChildren("keychoice"));
|
|
| 664 |
|
|
| 665 |
|
|
| 666 |
for (Element elKeychoice : keychoices){
|
|
| 667 |
handleKeyChoices(state, openKeys, key, elKeychoice, taxon); |
|
| 668 |
elKey.removeContent(elKeychoice); |
|
| 813 |
while (reader.hasNext()){
|
|
| 814 |
XMLEvent next = readNoWhitespace(reader); |
|
| 815 |
if (next.isEndElement()){
|
|
| 816 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 817 |
// logger.warn(name.getTitleCache()); |
|
| 818 |
return resultHomGroup; |
|
| 819 |
}else{
|
|
| 820 |
if(isEndingElement(next, FULL_NAME)){
|
|
| 821 |
//NOT YET IMPLEMENTED |
|
| 822 |
popUnimplemented(next.asEndElement()); |
|
| 823 |
}else if(isEndingElement(next, NUM)){
|
|
| 824 |
//NOT YET IMPLEMENTED |
|
| 825 |
popUnimplemented(next.asEndElement()); |
|
| 826 |
}else if(isEndingElement(next, HOMONYM)){
|
|
| 827 |
//NOT YET IMPLEMENTED |
|
| 828 |
popUnimplemented(next.asEndElement()); |
|
| 829 |
}else if(isEndingElement(next, NOTES)){
|
|
| 830 |
//NOT YET IMPLEMENTED |
|
| 831 |
popUnimplemented(next.asEndElement()); |
|
| 832 |
}else if(isEndingElement(next, ANNOTATION)){
|
|
| 833 |
//NOT YET IMPLEMENTED |
|
| 834 |
popUnimplemented(next.asEndElement()); |
|
| 835 |
}else{
|
|
| 836 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 837 |
} |
|
| 838 |
} |
|
| 839 |
}else if (next.isStartElement()){
|
|
| 840 |
if(isStartingElement(next, FULL_NAME)){
|
|
| 841 |
handleNotYetImplementedElement(next); |
|
| 842 |
// homotypicalGroup = handleNom(state, reader, next, taxon, homotypicalGroup); |
|
| 843 |
}else if(isStartingElement(next, NUM)){
|
|
| 844 |
handleNotYetImplementedElement(next); |
|
| 845 |
}else if(isStartingElement(next, NAME)){
|
|
| 846 |
handleName(state, reader, next, name); |
|
| 847 |
}else if(isStartingElement(next, CITATION)){
|
|
| 848 |
handleCitation(state, reader, next, name); |
|
| 849 |
}else if(isStartingElement(next, HOMONYM)){
|
|
| 850 |
handleNotYetImplementedElement(next); |
|
| 851 |
}else if(isStartingElement(next, NOTES)){
|
|
| 852 |
handleNotYetImplementedElement(next); |
|
| 853 |
}else if(isStartingElement(next, ANNOTATION)){
|
|
| 854 |
handleNotYetImplementedElement(next); |
|
| 855 |
}else{
|
|
| 856 |
handleUnexpectedStartElement(next); |
|
| 857 |
} |
|
| 858 |
}else{
|
|
| 859 |
handleUnexpectedElement(next); |
|
| 860 |
} |
|
| 669 | 861 |
} |
| 862 |
//TODO handle missing end element |
|
| 863 |
throw new IllegalStateException("Nom has no closing tag");
|
|
| 670 | 864 |
|
| 671 |
// |
|
| 672 |
verifyNoChildren(elKey); |
|
| 673 |
logger.info("Unmatched leads after key handling:" + openKeys.toString());
|
|
| 674 |
|
|
| 675 |
|
|
| 676 |
if (state.getConfig().isDoPrintKeys()){
|
|
| 677 |
key.print(System.err); |
|
| 678 |
} |
|
| 679 |
getPolytomousKeyService().save(key); |
|
| 680 |
return key; |
|
| 681 | 865 |
} |
| 682 | 866 |
|
| 683 |
|
|
| 684 | 867 |
/** |
| 685 |
* @param state |
|
| 686 |
* @param elKey |
|
| 687 |
* @param openKeys |
|
| 688 |
* @param key |
|
| 689 |
* @param elKeychoice |
|
| 690 |
* @param taxon |
|
| 868 |
* Returns the (empty) name with the correct homotypical group depending on the taxon status |
|
| 869 |
* @param taxon |
|
| 870 |
* @param homotypicalGroup |
|
| 871 |
* @param isSynonym |
|
| 872 |
* @return |
|
| 691 | 873 |
*/ |
| 692 |
private void handleKeyChoices(MarkupImportState state, UnmatchedLeads openKeys, PolytomousKey key, Element elKeychoice, Taxon taxon) {
|
|
| 874 |
private NonViralName makeName(Taxon taxon,HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
|
| 875 |
NonViralName name; |
|
| 876 |
if (isSynonym){
|
|
| 877 |
Rank defaultRank = Rank.SPECIES(); //can be any |
|
| 878 |
name = BotanicalName.NewInstance(defaultRank, homotypicalGroup); |
|
| 879 |
SynonymRelationshipType synonymType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(); |
|
| 880 |
if (taxon.getHomotypicGroup().equals(homotypicalGroup)){
|
|
| 881 |
synonymType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF(); |
|
| 882 |
} |
|
| 883 |
taxon.addSynonymName(name, synonymType); |
|
| 884 |
}else{
|
|
| 885 |
name = (NonViralName)taxon.getName(); |
|
| 886 |
} |
|
| 887 |
return name; |
|
| 888 |
} |
|
| 889 |
|
|
| 890 |
private void handleName(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, NonViralName name) throws XMLStreamException {
|
|
| 891 |
//attributes |
|
| 892 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 893 |
String classValue = getAndRemoveRequiredAttributeValue(parentEvent, attributes, CLASS); |
|
| 894 |
checkNoAttributes(attributes, parentEvent); |
|
| 693 | 895 |
|
| 694 |
//char Attribute |
|
| 695 |
//TODO it's still unclear if char is a feature and needs to be a new attribute |
|
| 696 |
//or if it is handled as question. Therefore both cases are handled but feature |
|
| 697 |
//is finally not yet set |
|
| 698 |
KeyStatement question = handleKeychoiceChar(state, elKeychoice); |
|
| 699 |
Feature feature = handleKeychoiceCharAsFeature(state, elKeychoice); |
|
| 896 |
//Ranks: family, subfamily, tribus, genus, subgenus, section, subsection, species, subspecies, variety, subvariety, forma |
|
| 897 |
//infrank, exaut, paraut, author, infrparaut, infraut, infrex, status, notes |
|
| 700 | 898 |
|
| 701 |
//lead
|
|
| 702 |
List<PolytomousKeyNode> childNodes = handleKeychoiceLeads(state, key, elKeychoice, taxon, question, feature);
|
|
| 899 |
//ranks
|
|
| 900 |
Rank rank = makeRank(state, classValue, false);
|
|
| 703 | 901 |
|
| 704 |
//num -> match with unmatched leads |
|
| 705 |
handleKeychoiceNum(openKeys, key, elKeychoice, childNodes); |
|
| 706 |
|
|
| 707 |
//others |
|
| 708 |
verifyNoAttribute(elKeychoice); |
|
| 709 |
} |
|
| 710 |
|
|
| 711 |
|
|
| 712 |
/** |
|
| 713 |
* @param openKeys |
|
| 714 |
* @param key |
|
| 715 |
* @param elKeychoice |
|
| 716 |
* @param childNodes |
|
| 717 |
*/ |
|
| 718 |
private void handleKeychoiceNum(UnmatchedLeads openKeys, PolytomousKey key, Element elKeychoice, List<PolytomousKeyNode> childNodes) {
|
|
| 719 |
Attribute numAttr = elKeychoice.getAttribute("num");
|
|
| 720 |
String num = CdmUtils.removeTrailingDot(numAttr == null? "":numAttr.getValue()); |
|
| 721 |
UnmatchedLeadsKey okk = UnmatchedLeadsKey.NewInstance(key, num); |
|
| 722 |
Set<PolytomousKeyNode> matchingNodes = openKeys.getNodes(okk); |
|
| 723 |
for (PolytomousKeyNode matchingNode : matchingNodes){
|
|
| 724 |
for (PolytomousKeyNode childNode : childNodes){
|
|
| 725 |
matchingNode.addChild(childNode); |
|
| 726 |
} |
|
| 727 |
openKeys.removeNode(okk, matchingNode); |
|
| 728 |
} |
|
| 729 |
if (matchingNodes.isEmpty()){
|
|
| 730 |
for (PolytomousKeyNode childNode : childNodes){
|
|
| 731 |
key.getRoot().addChild(childNode); |
|
| 902 |
String text = ""; |
|
| 903 |
while (reader.hasNext()){
|
|
| 904 |
XMLEvent next = readNoWhitespace(reader); |
|
| 905 |
if (isStartingElement(next, ANNOTATION)){
|
|
| 906 |
handleNotYetImplementedElement(next); |
|
| 907 |
// handleAnnotation(state, reader, next); |
|
| 908 |
}else if(isMyEndingElement(next, parentEvent)){
|
|
| 909 |
doNameEnd(name, rank, text, classValue, next, state); |
|
| 910 |
return; |
|
| 911 |
}else if (next.isCharacters()){
|
|
| 912 |
text += next.asCharacters().getData(); |
|
| 913 |
}else if (next.isEndElement()){
|
|
| 914 |
if(isEndingElement(next, ANNOTATION)){
|
|
| 915 |
//NOT YET IMPLEMENTED |
|
| 916 |
popUnimplemented(next.asEndElement()); |
|
| 917 |
}else{
|
|
| 918 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 919 |
} |
|
| 920 |
}else{
|
|
| 921 |
fireSchemaConflictEventExpectedStartTag("annotation", reader);
|
|
| 922 |
state.setUnsuccessfull(); |
|
| 732 | 923 |
} |
| 733 | 924 |
} |
| 925 |
return; |
|
| 734 | 926 |
|
| 735 |
elKeychoice.removeAttribute("num");
|
|
| 736 | 927 |
} |
| 737 | 928 |
|
| 738 | 929 |
|
| 739 | 930 |
/** |
| 740 | 931 |
* @param state |
| 741 |
* @param key |
|
| 742 |
* @param elKeychoice |
|
| 743 |
* @param taxon |
|
| 744 |
* @param feature |
|
| 932 |
* @param classValue |
|
| 933 |
* @param byAbbrev |
|
| 745 | 934 |
* @return |
| 746 | 935 |
*/ |
| 747 |
private List<PolytomousKeyNode> handleKeychoiceLeads( MarkupImportState state, PolytomousKey key, Element elKeychoice, Taxon taxon, KeyStatement question, Feature feature) {
|
|
| 748 |
List<PolytomousKeyNode> childNodes = new ArrayList<PolytomousKeyNode>(); |
|
| 749 |
List<Element> leads = elKeychoice.getChildren("lead");
|
|
| 750 |
for(Element elLead : leads){
|
|
| 751 |
PolytomousKeyNode childNode = handleLead(state, key, elLead, taxon, question, feature); |
|
| 752 |
childNodes.add(childNode); |
|
| 936 |
private Rank makeRank(MarkupImportState state, String value, boolean byAbbrev) {
|
|
| 937 |
Rank rank = null; |
|
| 938 |
if (StringUtils.isBlank(value)){
|
|
| 939 |
return null; |
|
| 753 | 940 |
} |
| 754 |
return childNodes; |
|
| 755 |
} |
|
| 756 |
|
|
| 757 |
|
|
| 758 |
/** |
|
| 759 |
* @param state |
|
| 760 |
* @param elKeychoice |
|
| 761 |
* @return |
|
| 762 |
*/ |
|
| 763 |
private KeyStatement handleKeychoiceChar(MarkupImportState state, Element elKeychoice) {
|
|
| 764 |
KeyStatement statement = null; |
|
| 765 |
Attribute charAttr = elKeychoice.getAttribute("char");
|
|
| 766 |
if (charAttr != null){
|
|
| 767 |
String charStr = charAttr.getValue(); |
|
| 768 |
if (StringUtils.isNotBlank(charStr)){
|
|
| 769 |
statement = KeyStatement.NewInstance(charStr); |
|
| 941 |
try {
|
|
| 942 |
boolean useUnknown = true; |
|
| 943 |
NomenclaturalCode nc = makeNomenclaturalCode(state); |
|
| 944 |
if (byAbbrev){
|
|
| 945 |
rank = Rank.getRankByAbbreviation(value, nc, useUnknown); |
|
| 946 |
}else{
|
|
| 947 |
rank = Rank.getRankByEnglishName(value, nc, useUnknown); |
|
| 948 |
} |
|
| 949 |
if (rank.equals(Rank.UNKNOWN_RANK())){
|
|
| 950 |
rank = null; |
|
| 770 | 951 |
} |
| 771 |
elKeychoice.removeAttribute("char");
|
|
| 952 |
} catch (UnknownCdmTypeException e) {
|
|
| 953 |
//doNothing |
|
| 772 | 954 |
} |
| 773 |
return statement;
|
|
| 955 |
return rank;
|
|
| 774 | 956 |
} |
| 775 | 957 |
|
| 776 |
/** |
|
| 777 |
* @param state |
|
| 778 |
* @param elKeychoice |
|
| 779 |
* @return |
|
| 780 |
*/ |
|
| 781 |
private Feature handleKeychoiceCharAsFeature(MarkupImportState state, Element elKeychoice) {
|
|
| 782 |
Feature feature = null; |
|
| 783 |
Attribute charAttr = elKeychoice.getAttribute("char");
|
|
| 784 |
if (charAttr != null){
|
|
| 785 |
String charStr = charAttr.getValue(); |
|
| 786 |
feature = getFeature(charStr, state); |
|
| 787 |
elKeychoice.removeAttribute("char");
|
|
| 958 |
private void doNameEnd(NonViralName name, Rank rank, String text, String classValue, XMLEvent xmlEvent, MarkupImportState state) {
|
|
| 959 |
Location location = xmlEvent.getLocation(); |
|
| 960 |
if (rank != null){
|
|
| 961 |
name.setRank(rank); |
|
| 962 |
if (rank.isSupraGeneric() || rank.isGenus()){
|
|
| 963 |
name.setGenusOrUninomial(text); |
|
| 964 |
}else if (rank.isInfraGeneric()){
|
|
| 965 |
name.setInfraGenericEpithet(text); |
|
| 966 |
}else if (rank.isSpecies()){
|
|
| 967 |
name.setSpecificEpithet(text); |
|
| 968 |
}else if (rank.isInfraSpecific()){
|
|
| 969 |
name.setInfraSpecificEpithet(text); |
|
| 970 |
}else{
|
|
| 971 |
String message = "Invalid rank '%s'. Can't decide which epithet to fill with '%s'"; |
|
| 972 |
message = String.format(message, rank.getTitleCache(), text); |
|
| 973 |
fireWarningEvent(message, makeLocationStr(location), 4); |
|
| 974 |
} |
|
| 975 |
}else{
|
|
| 976 |
//infrank, infrparaut, infraut, infrex, notes |
|
| 977 |
//DONE: status, exaut, paraut, author, |
|
| 978 |
|
|
| 979 |
//STATUS |
|
| 980 |
if (classValue.equalsIgnoreCase("status")){
|
|
| 981 |
try {
|
|
| 982 |
NomenclaturalStatusType nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(text); |
|
| 983 |
name.addStatus(NomenclaturalStatus.NewInstance(nomStatusType)); |
|
| 984 |
} catch (UnknownCdmTypeException e) {
|
|
| 985 |
String message = "Nom. status could not be recognized in '%s'"; |
|
| 986 |
message = String.format(message, text); |
|
| 987 |
fireWarningEvent(message, makeLocationStr(location), 2); |
|
| 988 |
} |
|
| 989 |
//NOTES |
|
| 990 |
}else if(classValue.equalsIgnoreCase(NOTES)){
|
|
| 991 |
handleNotYetImplementedAttributeValue(xmlEvent, CLASS, classValue); |
|
| 992 |
|
|
| 993 |
//Authors |
|
| 994 |
}else if(classValue.equalsIgnoreCase(AUTHOR)){
|
|
| 995 |
//TODO parse |
|
| 996 |
TeamOrPersonBase author = Team.NewTitledInstance(text, text); |
|
| 997 |
name.setCombinationAuthorTeam(author); |
|
| 998 |
}else if(classValue.equalsIgnoreCase(EXAUT)){
|
|
| 999 |
//TODO parse |
|
| 1000 |
TeamOrPersonBase exAuthor = Team.NewTitledInstance(text, text); |
|
| 1001 |
name.setExCombinationAuthorTeam(exAuthor); |
|
| 1002 |
}else if(classValue.equalsIgnoreCase(PARAUT)){
|
|
| 1003 |
//TODO parse |
|
| 1004 |
TeamOrPersonBase parAuthor = Team.NewTitledInstance(text, text); |
|
| 1005 |
name.setBasionymAuthorTeam(parAuthor); |
|
| 1006 |
}else if(classValue.equalsIgnoreCase("parexaut")){
|
|
| 1007 |
//TODO parse |
|
| 1008 |
TeamOrPersonBase parExAuthor = Team.NewTitledInstance(text, text); |
|
| 1009 |
name.setExBasionymAuthorTeam(parExAuthor); |
|
| 1010 |
}else if(classValue.equalsIgnoreCase(INFRPARAUT)){
|
|
| 1011 |
//TODO infrparaut <-> paraut |
|
| 1012 |
//TODO parse |
|
| 1013 |
TeamOrPersonBase parAuthor = Team.NewTitledInstance(text, text); |
|
| 1014 |
name.setBasionymAuthorTeam(parAuthor); |
|
| 1015 |
}else if(classValue.equalsIgnoreCase(INFRAUT)){
|
|
| 1016 |
//TODO infraut <-> author |
|
| 1017 |
//TODO parse |
|
| 1018 |
TeamOrPersonBase author = Team.NewTitledInstance(text, text); |
|
| 1019 |
name.setCombinationAuthorTeam(author); |
|
| 1020 |
}else if(classValue.equalsIgnoreCase(INFREX)){
|
|
| 1021 |
//TODO infrex <-> exaut |
|
| 1022 |
//TODO parse |
|
| 1023 |
TeamOrPersonBase exAuthor = Team.NewTitledInstance(text, text); |
|
| 1024 |
name.setExCombinationAuthorTeam(exAuthor); |
|
| 1025 |
}else if(classValue.equalsIgnoreCase(INFRPAREX)){
|
|
| 1026 |
//TODO infrparex <-> parexaut |
|
| 1027 |
//TODO parse |
|
| 1028 |
TeamOrPersonBase exParAuthor = Team.NewTitledInstance(text, text); |
|
| 1029 |
name.setExBasionymAuthorTeam(exParAuthor); |
|
| 1030 |
}else if(classValue.equalsIgnoreCase(INFRANK)){
|
|
| 1031 |
if (classValue.equalsIgnoreCase(INFRANK)){
|
|
| 1032 |
rank = makeRank(state, text, true); |
|
| 1033 |
if (rank == null){
|
|
| 1034 |
//TODO make event |
|
| 1035 |
logger.warn("Rank not recognized: " + text);
|
|
| 1036 |
} |
|
| 1037 |
} |
|
| 1038 |
|
|
| 1039 |
}else{
|
|
| 1040 |
String message = "Nom.class attribute has unhandled value '%s'"; |
|
| 1041 |
message = String.format(message, classValue); |
|
| 1042 |
fireWarningEvent(message, makeLocationStr(location), 2); |
|
| 1043 |
} |
|
| 788 | 1044 |
} |
| 789 |
return feature; |
|
| 790 | 1045 |
} |
| 791 | 1046 |
|
| 1047 |
// public void handleNameNotRank(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, String classValue, NonViralName name) throws XMLStreamException {
|
|
| 1048 |
// if (ACCEPTED.equalsIgnoreCase(classValue)){
|
|
| 1049 |
// }else if (SYNONYM.equalsIgnoreCase(classValue)){
|
|
| 1050 |
// }else{
|
|
| 1051 |
// //TODO Not yet implemented |
|
| 1052 |
// handleNotYetImplementedAttributeValue(parentEvent, CLASS, classValue); |
|
| 1053 |
// } |
|
| 1054 |
// } |
|
| 1055 |
|
|
| 1056 |
|
|
| 1057 |
private void handleCitation(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, NonViralName name) throws XMLStreamException {
|
|
| 1058 |
String classValue = getClassOnlyAttribute(parentEvent); |
|
| 792 | 1059 |
|
| 793 |
private PolytomousKeyNode handleLead(MarkupImportState state, PolytomousKey key, Element elLead, Taxon taxon, KeyStatement question, Feature feature) {
|
|
| 794 |
PolytomousKeyNode node = PolytomousKeyNode.NewInstance(); |
|
| 795 |
//TODO the char attribute in the keychoice is more a feature than a question |
|
| 796 |
//needs to be discussed on model side |
|
| 797 |
node.setQuestion(question); |
|
| 798 |
// node.setFeature(feature); |
|
| 799 |
|
|
| 800 |
//text |
|
| 801 |
String text = handleLeadText(elLead, node); |
|
| 802 |
|
|
| 803 |
//num |
|
| 804 |
handleLeadNum(elLead, text); |
|
| 805 |
|
|
| 806 |
//goto |
|
| 807 |
handleLeadGoto(state, key, elLead, taxon, node); |
|
| 1060 |
state.setCitation(true); |
|
| 1061 |
boolean hasRefPart = false; |
|
| 1062 |
Reference reference = ReferenceFactory.newGeneric(); |
|
| 1063 |
Map<String, String> refMap = new HashMap<String, String>(); |
|
| 1064 |
while (reader.hasNext()){
|
|
| 1065 |
XMLEvent next = readNoWhitespace(reader); |
|
| 1066 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 1067 |
checkMandatoryElement(hasRefPart, parentEvent.asStartElement(), REF_PART); |
|
| 1068 |
reference = createReference(state, refMap, next); |
|
| 1069 |
String microReference = refMap.get(DETAILS); |
|
| 1070 |
doCitation(state, name, classValue, reference, microReference, parentEvent); |
|
| 1071 |
state.setCitation(false); |
|
| 1072 |
return; |
|
| 1073 |
}else if(isStartingElement(next, REF_PART)){
|
|
| 1074 |
handleRefPart(state, reader, next, refMap); |
|
| 1075 |
hasRefPart = true; |
|
| 1076 |
}else{
|
|
| 1077 |
handleUnexpectedElement(next); |
|
| 1078 |
} |
|
| 1079 |
} |
|
| 1080 |
throw new IllegalStateException("Citation has no closing tag");
|
|
| 808 | 1081 |
|
| 809 |
//others |
|
| 810 |
verifyNoAttribute(elLead); |
|
Also available in: Unified diff
improvements to markup import