Revision 1a924f2f
Added by Andreas Kohlbecker over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/iapt/IAPTExcelImport.java | ||
|---|---|---|
| 68 | 68 |
private static final Pattern nomRefPubYearExtractP = Pattern.compile("(.*?)(1[7,8,9][0-9]{2}).*$|^.*?[0-9]{1,2}([\\./])[0-1]?[0-9]\\3([0-9]{2})\\.$"); // 1700 - 1999
|
| 69 | 69 |
|
| 70 | 70 |
private MarkerType markerTypeFossil = null; |
| 71 |
private Rank rankUnrankedPseudoClass = null; |
|
| 71 |
private Rank rankUnrankedSupraGeneric = null; |
|
| 72 |
private Rank familyIncertisSedis = null; |
|
| 73 |
private AnnotationType annotationTypeCaveats = null; |
|
| 72 | 74 |
|
| 73 | 75 |
private Taxon makeTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state, |
| 74 | 76 |
TaxonNode higherTaxonNode, boolean isSynonym, boolean isFossil) {
|
| ... | ... | |
| 81 | 83 |
String nomRefStr = getValue(record, LITSTRING, true); |
| 82 | 84 |
String authorsSpelling = getValue(record, AUTHORSSPELLING, true); |
| 83 | 85 |
String notesTxt = getValue(record, NOTESTXT, true); |
| 86 |
String caveats = getValue(record, CAVEATS, true); |
|
| 84 | 87 |
|
| 85 | 88 |
String nomRefTitle = null; |
| 86 | 89 |
String nomRefDetail = null; |
| ... | ... | |
| 159 | 162 |
titleCacheCompareStr = titleCacheCompareStr.replace(" x ", " ×");
|
| 160 | 163 |
nameCompareStr = nameCompareStr.replace(" x ", " ×");
|
| 161 | 164 |
} |
| 162 |
if(taxonName.isBinomHybrid()){
|
|
| 165 |
if(taxonName.isMonomHybrid()){
|
|
| 163 | 166 |
titleCacheCompareStr = titleCacheCompareStr.replaceAll("^X ", "× ");
|
| 164 | 167 |
nameCompareStr = nameCompareStr.replace("^X ", "× ");
|
| 165 | 168 |
} |
| 169 |
if(authorStr.contains(" et ")){
|
|
| 170 |
titleCacheCompareStr = titleCacheCompareStr.replaceAll(" et ", " & ");
|
|
| 171 |
} |
|
| 166 | 172 |
if (!taxonNameTitleCache.equals(titleCacheCompareStr)) {
|
| 167 | 173 |
logger.warn(line + "The generated titleCache differs from the imported string : " + taxonNameTitleCache + " <> " + titleCacheStr + " will restore original titleCacheStr"); |
| 168 | 174 |
doRestoreTitleCacheStr = true; |
| ... | ... | |
| 197 | 203 |
notesTxt = notesTxt.replace("Notes: ", "").trim();
|
| 198 | 204 |
taxonName.addAnnotation(Annotation.NewInstance(notesTxt, AnnotationType.EDITORIAL(), Language.DEFAULT())); |
| 199 | 205 |
} |
| 206 |
if(!StringUtils.isEmpty(caveats)){
|
|
| 207 |
caveats = caveats.replace("Caveats: ", "").trim();
|
|
| 208 |
taxonName.addAnnotation(Annotation.NewInstance(caveats, annotationTypeCaveats(), Language.DEFAULT())); |
|
| 209 |
} |
|
| 210 |
// |
|
| 200 | 211 |
|
| 201 | 212 |
// Namerelations |
| 202 | 213 |
if(!StringUtils.isEmpty(authorsSpelling)){
|
| ... | ... | |
| 399 | 410 |
|
| 400 | 411 |
if(name.matches("^Plantae$|^Fungi$")){
|
| 401 | 412 |
return Rank.KINGDOM(); |
| 402 |
} else if(name.matches("Incertae sedis$|^No group assigned$")){
|
|
| 403 |
return Rank.FAMILY();
|
|
| 413 |
} else if(name.matches("^Incertae sedis$|^No group assigned$")){
|
|
| 414 |
return rankFamilyIncertisSedis();
|
|
| 404 | 415 |
} else if(name.matches(".*phyta$|.*mycota$")){
|
| 405 | 416 |
return Rank.SECTION_BOTANY(); |
| 406 | 417 |
} else if(name.matches(".*phytina$|.*mycotina$")){
|
| 407 | 418 |
return Rank.SUBSECTION_BOTANY(); |
| 408 | 419 |
} else if(name.matches("Gymnospermae$|.*ones$")){ // Monocotyledones, Dicotyledones
|
| 409 |
return rankUnrankedPseudoClass();
|
|
| 420 |
return rankUnrankedSupraGeneric();
|
|
| 410 | 421 |
} else if(name.matches(".*opsida$|.*phyceae$|.*mycetes$|.*ones$|^Musci$|^Hepaticae$")){
|
| 411 | 422 |
return Rank.CLASS(); |
| 412 | 423 |
} else if(name.matches(".*idae$|.*phycidae$|.*mycetidae$")){
|
| ... | ... | |
| 431 | 442 |
return Rank.UNKNOWN_RANK(); |
| 432 | 443 |
} |
| 433 | 444 |
|
| 434 |
private Rank rankUnrankedPseudoClass() {
|
|
| 445 |
private Rank rankUnrankedSupraGeneric() {
|
|
| 446 |
|
|
| 447 |
if(rankUnrankedSupraGeneric == null){
|
|
| 448 |
rankUnrankedSupraGeneric = Rank.NewInstance(RankClass.Suprageneric, "Unranked supra generic", " ", " "); |
|
| 449 |
getTermService().save(rankUnrankedSupraGeneric); |
|
| 450 |
} |
|
| 451 |
return rankUnrankedSupraGeneric; |
|
| 452 |
} |
|
| 453 |
|
|
| 454 |
private Rank rankFamilyIncertisSedis() {
|
|
| 455 |
|
|
| 456 |
if(familyIncertisSedis == null){
|
|
| 457 |
familyIncertisSedis = Rank.NewInstance(RankClass.Suprageneric, "Family incertis sedis", " ", " "); |
|
| 458 |
getTermService().save(familyIncertisSedis); |
|
| 459 |
} |
|
| 460 |
return familyIncertisSedis; |
|
| 461 |
} |
|
| 435 | 462 |
|
| 436 |
if(rankUnrankedPseudoClass == null){
|
|
| 437 |
rankUnrankedPseudoClass = Rank.NewInstance(RankClass.Suprageneric, "Unranked pseudo class", " ", " "); |
|
| 438 |
getTermService().save(rankUnrankedPseudoClass); |
|
| 463 |
private AnnotationType annotationTypeCaveats(){
|
|
| 464 |
if(annotationTypeCaveats == null){
|
|
| 465 |
annotationTypeCaveats = AnnotationType.NewInstance("Caveats", "Caveats", "");
|
|
| 466 |
getTermService().save(annotationTypeCaveats); |
|
| 439 | 467 |
} |
| 440 |
return rankUnrankedPseudoClass;
|
|
| 468 |
return annotationTypeCaveats;
|
|
| 441 | 469 |
} |
| 442 | 470 |
|
| 443 | 471 |
|
Also available in: Unified diff
ref #6026 multiple improvements