Revision 0429965c
Added by Andreas Müller almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoConabioTaxonImport.java | ||
|---|---|---|
| 17 | 17 |
import java.util.Set; |
| 18 | 18 |
import java.util.UUID; |
| 19 | 19 |
|
| 20 |
import org.apache.commons.lang3.StringUtils; |
|
| 20 | 21 |
import org.apache.log4j.Logger; |
| 21 | 22 |
import org.springframework.stereotype.Component; |
| 22 | 23 |
|
| 23 | 24 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 24 | 25 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 25 | 26 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 27 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
| 26 | 28 |
import eu.etaxonomy.cdm.model.common.Annotation; |
| 27 | 29 |
import eu.etaxonomy.cdm.model.common.AnnotationType; |
| 28 | 30 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| ... | ... | |
| 37 | 39 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 38 | 40 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 39 | 41 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 42 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
|
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import eu.etaxonomy.cdm.model.reference.Reference; |
| 41 | 44 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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import eu.etaxonomy.cdm.model.reference.ReferenceType; |
|
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 44 | 48 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| ... | ... | |
| 114 | 118 |
|
| 115 | 119 |
//Name |
| 116 | 120 |
BotanicalName speciesName = makeName(line, record, state); |
| 117 |
String statusStr = getValue(record, "EstatusNombre"); |
|
| 118 | 121 |
|
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//sec |
|
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String secRefStr = getValueNd(record, "ReferenciaNombre"); |
| 120 | 124 |
Reference sec = getSecRef(state, secRefStr, line); |
| 121 | 125 |
|
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//status |
|
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String statusStr = getValue(record, "EstatusNombre"); |
|
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TaxonBase<?> taxonBase; |
| 123 | 129 |
if ("aceptado".equals(statusStr)){
|
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taxonBase = Taxon.NewInstance(speciesName, sec); |
| ... | ... | |
| 128 | 134 |
throw new RuntimeException(line + " Status not recognized: " + statusStr); |
| 129 | 135 |
} |
| 130 | 136 |
|
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//annotation |
|
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String annotation = getValue(record, "Anotacion al Taxon"); |
| 132 | 139 |
if (annotation != null && (!annotation.equals("nom. illeg.") || !annotation.equals("nom. cons."))){
|
| 133 | 140 |
taxonBase.addAnnotation(Annotation.NewInstance(annotation, AnnotationType.EDITORIAL(), Language.SPANISH_CASTILIAN())); |
| 134 | 141 |
} |
| 135 | 142 |
|
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//id |
|
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String idCat = getValue(record, "IdCAT"); |
| 137 | 145 |
this.addOriginalSource(taxonBase, idCat, TAXON_NAMESPACE, state.getConfig().getSourceReference()); |
| 138 | 146 |
|
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//save |
|
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getTaxonService().save(taxonBase); |
| 140 | 149 |
taxonIdMap.put(idCat, taxonBase); |
| 141 | 150 |
|
| ... | ... | |
| 153 | 162 |
if (result == null && secRefStr != null){
|
| 154 | 163 |
result = ReferenceFactory.newBook(); |
| 155 | 164 |
TimePeriod tp = TimePeriodParser.parseString(secRefStr.substring(secRefStr.length()-4)); |
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String authorStr = secRefStr.substring(0, secRefStr.length()-6); |
|
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if (! (authorStr + ", " + tp.getYear()).equals(secRefStr)){
|
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String authorStrPart = secRefStr.substring(0, secRefStr.length()-6);
|
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if (! (authorStrPart + ", " + tp.getYear()).equals(secRefStr)){
|
|
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logger.warn(line + "Sec ref could not be parsed: " + secRefStr); |
| 159 | 168 |
}else{
|
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result.setDatePublished(tp); |
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} |
| 162 |
|
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if (authorStr.contains(",") || authorStr.contains("&")){
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//TODO split |
|
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Team team = Team.NewTitledInstance(authorStr, null); |
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result.setAuthorship(team); |
|
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}else if (authorStr.equals("Tropicos") || authorStr.equals("The plant list")
|
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|| authorStr.equals("APG IV")){
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result.setTitle(authorStr); |
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|
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TeamOrPersonBase<?> author = state.getAgentBase(authorStrPart); |
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if (author == null){
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if (authorStrPart.contains("&")){
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Team team = Team.NewInstance(); |
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String[] authorSplit = authorStrPart.split("&");
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String[] firstAuthorSplit = authorSplit[0].trim().split(",");
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for (String authorStr : firstAuthorSplit){
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addTeamMember(team, authorStr); |
|
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} |
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addTeamMember(team, authorSplit[1]); |
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result.setAuthorship(team); |
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state.putAgentBase(team.getTitleCache(), team); |
|
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}else if (authorStrPart.equalsIgnoreCase("Tropicos") || authorStrPart.equalsIgnoreCase("The Plant List")
|
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|| authorStrPart.equalsIgnoreCase("APG IV")){
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result.setTitle(authorStrPart); |
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}else{
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Person person = Person.NewInstance(); |
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person.setLastname(authorStrPart); |
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result.setAuthorship(person); |
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state.putAgentBase(person.getTitleCache(), person); |
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} |
|
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}else{
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Person person = Person.NewTitledInstance(authorStr); |
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result.setAuthorship(person); |
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result.setAuthorship(author); |
|
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} |
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|
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state.putReference(secRefStr, result); |
|
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}else if(secRefStr == null){
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logger.warn(line + "Empty secRefStr not yet implemented");
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return state.getConfig().getSecReference();
|
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} |
| 179 | 199 |
|
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return result; |
| ... | ... | |
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|
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|
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|
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/** |
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* @param team |
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* @param author |
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*/ |
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private void addTeamMember(Team team, String author) {
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if (StringUtils.isNotBlank(author)){
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Person person = Person.NewInstance(); |
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person.setLastname(author.trim()); |
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team.addTeamMember(person); |
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} |
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} |
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|
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/** |
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* @param record |
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* @param state |
| ... | ... | |
| 196 | 230 |
String idCat = getValue(record, "IdCAT"); |
| 197 | 231 |
String rankStr = getValue(record, "CategoriaTaxonomica"); |
| 198 | 232 |
String annotation = getValue(record, "Anotacion al Taxon"); |
| 233 |
|
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//rank |
|
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Rank rank = null; |
| 200 | 236 |
try {
|
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rank = state.getTransformer().getRankByKey(rankStr); |
| ... | ... | |
| 207 | 243 |
logger.warn(line + "Rank not recognized: " + rankStr); |
| 208 | 244 |
} |
| 209 | 245 |
|
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//name + author |
|
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String fullNameStr = nameStr + (authorStr != null ? " " + authorStr : ""); |
| 211 | 248 |
|
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BotanicalName fullName = (BotanicalName)nameParser.parseFullName(fullNameStr, NomenclaturalCode.ICNAFP, rank); |
| 213 | 250 |
if (fullName.isProtectedTitleCache()){
|
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logger.warn(line + "Name could not be parsed: " + fullNameStr ); |
| 215 | 252 |
}else{
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replaceAuthorNames(state, fullName); |
|
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replaceAuthorNamesAndNomRef(state, fullName);
|
|
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} |
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BotanicalName existingName = getExistingName(state, fullName); |
| 219 | 256 |
|
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//reference |
|
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String refNameStr = getRefNameStr(nomRefStr, refType, fullNameStr); |
| 221 | 259 |
|
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BotanicalName referencedName = (BotanicalName)nameParser.parseReferencedName(refNameStr, NomenclaturalCode.ICNAFP, rank); |
| 223 | 261 |
if (referencedName.isProtectedFullTitleCache() || referencedName.isProtectedTitleCache()){
|
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logger.warn(line + "Referenced name could not be parsed: " + refNameStr ); |
| 225 | 263 |
}else{
|
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replaceAuthorNames(state, referencedName); |
|
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addSourcesToReferences(referencedName, state); |
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replaceAuthorNamesAndNomRef(state, referencedName); |
|
| 227 | 266 |
} |
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adaptRefTypeForGeneric(referencedName, refType); |
|
| 228 | 268 |
|
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//compare nom. ref. with Borhidi |
|
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BotanicalName result= referencedName; |
| 230 | 271 |
Boolean equal = null; |
| 231 | 272 |
if (existingName != null){
|
| ... | ... | |
| 242 | 283 |
} |
| 243 | 284 |
addNomRefExtension(state, result, equal); |
| 244 | 285 |
|
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if (annotation != null && ! annotation.equals("nom. illeg.") && ! annotation.equals("nom. cons.")){
|
|
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//status |
|
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if (annotation != null && (annotation.equals("nom. illeg.") || annotation.equals("nom. cons."))){
|
|
| 246 | 288 |
try {
|
| 247 | 289 |
NomenclaturalStatusType nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(annotation, result); |
| 248 | 290 |
result.addStatus(NomenclaturalStatus.NewInstance(nomStatusType)); |
| ... | ... | |
| 258 | 300 |
|
| 259 | 301 |
|
| 260 | 302 |
|
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/** |
|
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* @param name |
|
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* @param state |
|
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*/ |
|
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private void addSourcesToReferences(BotanicalName name, SimpleExcelTaxonImportState<CONFIG> state) {
|
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Reference nomRef = (Reference)name.getNomenclaturalReference(); |
|
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if (nomRef != null){
|
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nomRef.addSource(makeOriginalSource(state)); |
|
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if (nomRef.getInReference() != null){
|
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nomRef.getInReference().addSource(makeOriginalSource(state)); |
|
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} |
|
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} |
|
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} |
|
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|
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|
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|
|
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/** |
|
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* @param referencedName |
|
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* @param refType |
|
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*/ |
|
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private void adaptRefTypeForGeneric(BotanicalName referencedName, String refTypeStr) {
|
|
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INomenclaturalReference ref = referencedName.getNomenclaturalReference(); |
|
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if (ref == null){
|
|
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return; |
|
| 327 |
} |
|
| 328 |
ReferenceType refType = refTypeByRefTypeStr(refTypeStr); |
|
| 329 |
if (ref.getType() != refType && refType == ReferenceType.Book){
|
|
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ref.setType(refType); |
|
| 331 |
} |
|
| 332 |
} |
|
| 333 |
|
|
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|
|
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private ReferenceType refTypeByRefTypeStr(String refType){
|
|
| 336 |
if ("A".equals(refType)){ //Article
|
|
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return ReferenceType.Article; |
|
| 338 |
}else if ("B".equals(refType)){ //Book
|
|
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return ReferenceType.Book; |
|
| 340 |
}else if (refType == null){ //Book
|
|
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return null; |
|
| 342 |
}else{
|
|
| 343 |
throw new IllegalArgumentException("RefType not supported " + refType);
|
|
| 344 |
} |
|
| 345 |
} |
|
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|
|
| 261 | 347 |
/** |
| 262 | 348 |
* @param nomRefStr |
| 263 | 349 |
* @param refType |
| 264 | 350 |
* @param fullNameStr |
| 265 | 351 |
* @return |
| 266 | 352 |
*/ |
| 267 |
private String getRefNameStr(String nomRefStr, String refType, String fullNameStr) {
|
|
| 353 |
private String getRefNameStr(String nomRefStr, String refTypeStr, String fullNameStr) {
|
|
| 268 | 354 |
String refNameStr = fullNameStr; |
| 269 |
if ("A".equals(refType)){ //Article
|
|
| 355 |
ReferenceType refType = refTypeByRefTypeStr(refTypeStr); |
|
| 356 |
if (refType == ReferenceType.Article){
|
|
| 270 | 357 |
refNameStr = fullNameStr + " in " + nomRefStr; |
| 271 |
}else if ("B".equals(refType)){ //Book
|
|
| 358 |
}else if (refType == ReferenceType.Book){
|
|
| 272 | 359 |
refNameStr = fullNameStr + ", " + nomRefStr; |
| 360 |
}else if (refType == null && nomRefStr != null){
|
|
| 361 |
logger.warn("RefType is null but nomRefStr exists");
|
|
| 273 | 362 |
} |
| 274 | 363 |
return refNameStr; |
| 275 | 364 |
} |
| ... | ... | |
| 302 | 391 |
* @param fullName |
| 303 | 392 |
* @return |
| 304 | 393 |
*/ |
| 305 |
@SuppressWarnings("rawtypes")
|
|
| 306 | 394 |
private BotanicalName getExistingName(SimpleExcelTaxonImportState<CONFIG> state, BotanicalName fullName) {
|
| 395 |
initExistinNames(state); |
|
| 396 |
return (BotanicalName)state.getName(fullName.getTitleCache()); |
|
| 397 |
} |
|
| 398 |
|
|
| 399 |
/** |
|
| 400 |
* @param state |
|
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*/ |
|
| 402 |
@SuppressWarnings("rawtypes")
|
|
| 403 |
private void initExistinNames(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
| 307 | 404 |
if (!nameMapIsInitialized){
|
| 308 | 405 |
List<String> propertyPaths = Arrays.asList("");
|
| 309 | 406 |
List<TaxonNameBase> existingNames = this.getNameService().list(null, null, null, null, propertyPaths); |
| ... | ... | |
| 312 | 409 |
} |
| 313 | 410 |
nameMapIsInitialized = true; |
| 314 | 411 |
} |
| 315 |
return (BotanicalName)state.getName(fullName.getTitleCache()); |
|
| 316 | 412 |
} |
| 317 | 413 |
|
| 414 |
|
|
| 415 |
|
|
| 318 | 416 |
/** |
| 319 | 417 |
* @param record |
| 320 | 418 |
* @param string |
| ... | ... | |
| 417 | 515 |
MexicoConabioImportConfigurator config = state.getConfig(); |
| 418 | 516 |
classification = Classification.NewInstance(config.getClassificationName()); |
| 419 | 517 |
classification.setUuid(config.getClassificationUuid()); |
| 420 |
classification.setReference(config.getSourceReference());
|
|
| 518 |
classification.setReference(config.getSecReference());
|
|
| 421 | 519 |
getClassificationService().save(classification); |
| 422 | 520 |
} |
| 423 | 521 |
return classification; |
Also available in: Unified diff
#5822 / #5892 Mexico rubiaceae import