Revision c561f681
Added by Andreas Müller over 7 years ago
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java | ||
|---|---|---|
| 794 | 794 |
//infra genus |
| 795 | 795 |
else if (infraGenusPattern.matcher(fullNameString).matches()){
|
| 796 | 796 |
Rank infraGenericRank; |
| 797 |
|
|
| 798 |
|
|
| 799 | 797 |
if ("[unranked]".equals(epi[1])){
|
| 800 | 798 |
infraGenericRank = Rank.INFRAGENERICTAXON(); |
| 801 | 799 |
}else{
|
| 802 |
infraGenericRank = Rank.getRankByIdInVoc(epi[1], nameToBeFilledOrig.getNomenclaturalCode()); |
|
| 800 |
String infraGenericRankMarker = epi[1]; |
|
| 801 |
if (infraGenericRankMarker.startsWith(notho)){ //#3868
|
|
| 802 |
nameToBeFilled.setBinomHybrid(true); |
|
| 803 |
infraGenericRankMarker = infraGenericRankMarker.substring(notho.length()); |
|
| 804 |
}else if(infraGenericRankMarker.startsWith("n")){
|
|
| 805 |
nameToBeFilled.setBinomHybrid(true); |
|
| 806 |
infraGenericRankMarker = infraGenericRankMarker.substring(1); |
|
| 807 |
} |
|
| 808 |
infraGenericRank = Rank.getRankByIdInVoc(infraGenericRankMarker, nameToBeFilledOrig.getNomenclaturalCode()); |
|
| 803 | 809 |
} |
| 804 | 810 |
nameToBeFilled.setRank(infraGenericRank); |
| 805 | 811 |
nameToBeFilled.setGenusOrUninomial(epi[0]); |
| ... | ... | |
| 841 | 847 |
if ("[unranked]".equals(infraSpecRankMarker)){
|
| 842 | 848 |
infraSpecificRank = Rank.INFRASPECIFICTAXON(); |
| 843 | 849 |
}else{
|
| 844 |
infraSpecificRank = Rank.getRankByIdInVoc(infraSpecRankMarker); |
|
| 850 |
String localInfraSpecRankMarker; |
|
| 851 |
if (infraSpecRankMarker.startsWith(notho)){ //#3868
|
|
| 852 |
nameToBeFilled.setTrinomHybrid(true); |
|
| 853 |
localInfraSpecRankMarker = infraSpecRankMarker.substring(notho.length()); |
|
| 854 |
}else if(infraSpecRankMarker.startsWith("n")){
|
|
| 855 |
nameToBeFilled.setTrinomHybrid(true); |
|
| 856 |
localInfraSpecRankMarker = infraSpecRankMarker.substring(1); |
|
| 857 |
}else{
|
|
| 858 |
localInfraSpecRankMarker = infraSpecRankMarker; |
|
| 859 |
} |
|
| 860 |
infraSpecificRank = Rank.getRankByIdInVoc(localInfraSpecRankMarker); |
|
| 845 | 861 |
} |
| 846 | 862 |
nameToBeFilled.setRank(infraSpecificRank); |
| 847 | 863 |
nameToBeFilled.setGenusOrUninomial(epi[0]); |
| ... | ... | |
| 934 | 950 |
nameToBeFilled.addParsingProblem(ParserProblem.UnparsableNamePart); |
| 935 | 951 |
nameToBeFilled.setTitleCache(fullNameString,true); |
| 936 | 952 |
// FIXME Quick fix, otherwise search would not deilver results for unparsable names |
| 937 |
nameToBeFilled.setNameCache(fullNameString,true); |
|
| 953 |
nameToBeFilled.setNameCache(fullNameString, true);
|
|
| 938 | 954 |
// END |
| 939 | 955 |
logger.info("no applicable parsing rule could be found for \"" + fullNameString + "\"");
|
| 940 | 956 |
} |
| ... | ... | |
| 1071 | 1087 |
fullAuthors(authorString, authors, years, clazz); |
| 1072 | 1088 |
} catch (StringNotParsableException e) {
|
| 1073 | 1089 |
nameToBeFilled.addParsingProblem(ParserProblem.UnparsableAuthorPart); |
| 1074 |
nameToBeFilled.setTitleCache(fullNameString,true); |
|
| 1090 |
nameToBeFilled.setTitleCache(fullNameString, true);
|
|
| 1075 | 1091 |
// FIXME Quick fix, otherwise search would not deliver results for unparsable names |
| 1076 |
nameToBeFilled.setNameCache(fullNameString,true); |
|
| 1092 |
nameToBeFilled.setNameCache(fullNameString, true);
|
|
| 1077 | 1093 |
// END |
| 1078 | 1094 |
logger.info("no applicable parsing rule could be found for \"" + fullNameString + "\"");;
|
| 1079 | 1095 |
} |
| ... | ... | |
| 1305 | 1321 |
} |
| 1306 | 1322 |
|
| 1307 | 1323 |
|
| 1308 |
//Parsing of the given full name that has been identified as hybrid already somewhere else. |
|
| 1309 |
private void parseHybrid(NonViralName nameToBeFilled, String fullNameString, Rank rank, boolean makeEmpty){
|
|
| 1310 |
logger.warn("parseHybrid --> function not yet implemented");
|
|
| 1311 |
|
|
| 1312 |
// String nonHybridName = fullNameString; |
|
| 1313 |
// boolean isMonomHybrid = isMonomHybrid(fullNameString); |
|
| 1314 |
// if (isMonomHybrid){
|
|
| 1315 |
// nonHybridName.replaceAll(hybrid, ""); |
|
| 1316 |
// } |
|
| 1317 |
// |
|
| 1318 |
// String[] split = nonHybridName.split("\\s");
|
|
| 1319 |
// parseFullName(nameToBeFilled, nonHybridName, rank, makeEmpty); |
|
| 1320 |
// |
|
| 1321 |
// nonHybridName = nonHybridName.replaceAll(hybrid, " "); |
|
| 1322 |
// |
|
| 1323 |
// boolean isBinomHybrid = isBinomHybrid(split); |
|
| 1324 |
//// boolean isTrinomHybrid = isTrinomHybrid(split); |
|
| 1325 |
// |
|
| 1326 |
// nonHybridName = nonHybridName.replaceAll(hybrid, " "); |
|
| 1327 |
// |
|
| 1328 |
// parseFullName(nameToBeFilled, nonHybridName, rank, makeEmpty); |
|
| 1329 |
// nameToBeFilled.getTitleCache(); |
|
| 1330 |
// nameToBeFilled.setMonomHybrid(isMonomHybrid); |
|
| 1331 |
// nameToBeFilled.setBinomHybrid(isBinomHybrid); |
|
| 1332 |
// nameToBeFilled.setBinomHybrid(isTrinomHybrid); |
|
| 1333 |
|
|
| 1334 |
nameToBeFilled.setTitleCache(fullNameString,true); |
|
| 1335 |
return; |
|
| 1336 |
} |
|
| 1337 |
|
|
| 1338 |
// private boolean isBinomHybrid(String[] split) {
|
|
| 1339 |
// if (){
|
|
| 1340 |
// |
|
| 1341 |
// } |
|
| 1342 |
// return false; |
|
| 1343 |
// } |
|
| 1344 |
|
|
| 1345 |
private boolean isMonomHybrid(String fullNameString) {
|
|
| 1346 |
Matcher matcher = hybridPattern.matcher(fullNameString); |
|
| 1347 |
boolean find = matcher.find(); |
|
| 1348 |
int start = matcher.start(); |
|
| 1349 |
if (find == true && start == 0){
|
|
| 1350 |
return true; |
|
| 1351 |
}else{
|
|
| 1352 |
return false; |
|
| 1353 |
} |
|
| 1354 |
} |
|
| 1355 |
|
|
| 1356 | 1324 |
// // Parsing of the given full name that has been identified as a cultivar already somwhere else. |
| 1357 | 1325 |
// // The ... cv. ... syntax is not covered here as it is not according the rules for naming cultivars. |
| 1358 | 1326 |
public BotanicalName parseCultivar(String fullName) throws StringNotParsableException{
|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImplRegExBase.java | ||
|---|---|---|
| 77 | 77 |
protected static String status = ""; |
| 78 | 78 |
|
| 79 | 79 |
//marker |
| 80 |
protected static String InfraGenusMarker = "(subgen\\.|subg\\.|sect\\.|subsect\\.|ser\\.|subser\\.|t\\.infgen\\.|\\[unranked\\])"; |
|
| 80 |
protected static String InfraGenusMarker = "(n|notho)?(subgen\\.|subg\\.|sect\\.|subsect\\.|ser\\.|subser\\.|t\\.infgen\\.|\\[unranked\\])";
|
|
| 81 | 81 |
protected static String aggrOrGroupMarker = "(aggr\\.|agg\\.|group)"; |
| 82 |
protected static String infraSpeciesMarker = "(subsp\\.|convar\\.|var\\.|subvar\\.|f\\.|subf\\.|f\\. sp\\.|f\\.spec\\.|f\\.sp\\.|\\[unranked\\]|tax\\." + fWs + "infrasp\\.)";
|
|
| 82 |
protected static String infraSpeciesMarker = "(n|notho)?(subsp\\.|convar\\.|var\\.|subvar\\.|f\\.|subf\\.|f\\.\\ssp\\.|f\\.spec\\.|f\\.sp\\.|\\[unranked\\]|tax\\." + fWs + "infrasp\\.)";
|
|
| 83 | 83 |
protected static String oldInfraSpeciesMarker = "(prol\\.|proles|race|taxon|sublusus)"; |
| 84 | 84 |
|
| 85 | 85 |
|
| ... | ... | |
| 237 | 237 |
//cultivars and hybrids |
| 238 | 238 |
protected static String cultivar = oWs + "'..+'"; //Achtung mit Hochkomma in AuthorNamen |
| 239 | 239 |
protected static String cultivarMarker = oWs + "(cv\\.|')"; |
| 240 |
protected static String hybridPart = "([xX]" + oWs + "|"+hybridSign+"|notho)"; |
|
| 241 |
protected static String hybridFull = "(" +oWs +"|"+ pStart +")" + hybridPart;
|
|
| 240 |
protected static String notho = "notho"; |
|
| 241 |
protected static String hybridPart = "([xX]" + oWs + "|"+hybridSign+"|"+notho+")"; |
|
| 242 |
protected static String noNothoHybridPart = "([xX]" + oWs + "|"+hybridSign+")"; |
|
| 243 |
protected static String hybridFull = "(" +oWs +"|"+ pStart +")" + noNothoHybridPart; //for some reason infraspecific notho ranks do not parse if notho is allowed as uninomial prefix.
|
|
| 242 | 244 |
protected static String hybridFormularSeparator = oWs + "[" + hybridSign + "xX]" + oWs; |
| 243 | 245 |
|
| 244 | 246 |
|
| ... | ... | |
| 269 | 271 |
protected static Pattern finalTeamSplitterPattern = Pattern.compile(finalTeamSplitter); |
| 270 | 272 |
protected static Pattern cultivarPattern = Pattern.compile(cultivar); |
| 271 | 273 |
protected static Pattern cultivarMarkerPattern = Pattern.compile(cultivarMarker); |
| 272 |
protected static Pattern hybridPattern = Pattern.compile(hybridFull); |
|
| 273 | 274 |
|
| 274 | 275 |
protected static Pattern genusOrSupraGenusPattern = Pattern.compile(pStart + genusOrSupraGenus + facultFullAuthorString2 + end); |
| 275 | 276 |
protected static Pattern infraGenusPattern = Pattern.compile(pStart + infraGenus + facultFullAuthorString2 + end); |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImplTest.java | ||
|---|---|---|
| 430 | 430 |
*/ |
| 431 | 431 |
@Test |
| 432 | 432 |
public final void testHybrids() {
|
| 433 |
try {
|
|
| 434 |
Method parseMethod = parser.getClass().getDeclaredMethod("parseFullName", String.class, NomenclaturalCode.class, Rank.class);
|
|
| 435 |
testName_StringNomcodeRank(parseMethod); |
|
| 436 |
} catch (Exception e) {
|
|
| 437 |
e.printStackTrace(); |
|
| 438 |
assertTrue(false); |
|
| 439 |
} |
|
| 433 |
NonViralName<?> name1; |
|
| 434 |
|
|
| 435 |
|
|
| 436 |
//Infrageneric hybrid |
|
| 437 |
name1 = parser.parseFullName("Aegilops nothosubg. Insulae Scholz", botanicCode, null);
|
|
| 438 |
assertTrue("Name must have binom hybrid bit set", name1.isBinomHybrid());
|
|
| 439 |
assertFalse("Name must not have monom hybrid bit set", name1.isMonomHybrid());
|
|
| 440 |
assertFalse("Name must not have trinom hybrid bit set", name1.isTrinomHybrid());
|
|
| 441 |
assertEquals("Infrageneric epithet must be 'Insulae'", "Insulae", name1.getInfraGenericEpithet());
|
|
| 440 | 442 |
|
| 441 | 443 |
//Species hybrid |
| 442 | 444 |
// NonViralName nameTeam1 = parser.parseFullName("Aegilops \u00D7insulae-cypri H. Scholz");
|
| 443 |
NonViralName<?> name1 = parser.parseFullName("Aegilops \u00D7insulae Scholz", botanicCode, null);
|
|
| 445 |
name1 = parser.parseFullName("Aegilops \u00D7insulae Scholz", botanicCode, null);
|
|
| 444 | 446 |
assertTrue("Name must have binom hybrid bit set", name1.isBinomHybrid());
|
| 445 | 447 |
assertFalse("Name must not have monom hybrid bit set", name1.isMonomHybrid());
|
| 446 | 448 |
assertFalse("Name must not have trinom hybrid bit set", name1.isTrinomHybrid());
|
| ... | ... | |
| 453 | 455 |
assertFalse("Name must not have trinom hybrid bit set", name1.isTrinomHybrid());
|
| 454 | 456 |
assertEquals("Uninomial must be 'Aegilops'", "Aegilops", name1.getGenusOrUninomial());
|
| 455 | 457 |
|
| 456 |
//Species hybrid |
|
| 458 |
//Subspecies hybrid with hybrid sign |
|
| 459 |
//maybe false: see http://dev.e-taxonomy.eu/trac/ticket/3868 |
|
| 457 | 460 |
name1 = parser.parseFullName("Aegilops insulae subsp. X abies Scholz", botanicCode, null);
|
| 458 | 461 |
assertFalse("Name must not have monom hybrid bit set", name1.isMonomHybrid());
|
| 459 | 462 |
assertFalse("Name must not have binom hybrid bit set", name1.isBinomHybrid());
|
| 460 | 463 |
assertTrue("Name must have trinom hybrid bit set", name1.isTrinomHybrid());
|
| 461 | 464 |
assertEquals("Infraspecific epithet must be 'abies'", "abies", name1.getInfraSpecificEpithet());
|
| 462 | 465 |
|
| 466 |
//Subspecies hybrid with notho / n |
|
| 467 |
name1 = parser.parseFullName("Aegilops insulae nothosubsp. abies Scholz", botanicCode, null);
|
|
| 468 |
assertFalse("Name must not have monom hybrid bit set", name1.isMonomHybrid());
|
|
| 469 |
assertFalse("Name must not have binom hybrid bit set", name1.isBinomHybrid());
|
|
| 470 |
assertFalse("Name must not be protected", name1.isProtectedTitleCache());
|
|
| 471 |
assertTrue("Name must have trinom hybrid bit set", name1.isTrinomHybrid());
|
|
| 472 |
assertEquals("Infraspecific epithet must be 'abies'", "abies", name1.getInfraSpecificEpithet());
|
|
| 473 |
name1 = parser.parseFullName("Aegilops insulae nsubsp. abies Scholz", botanicCode, null);
|
|
| 474 |
assertFalse("Name must not have monom hybrid bit set", name1.isMonomHybrid());
|
|
| 475 |
assertFalse("Name must not have binom hybrid bit set", name1.isBinomHybrid());
|
|
| 476 |
assertFalse("Name must not be protected", name1.isProtectedTitleCache());
|
|
| 477 |
assertTrue("Name must have trinom hybrid bit set", name1.isTrinomHybrid());
|
|
| 478 |
assertEquals("Infraspecific epithet must be 'abies'", "abies", name1.getInfraSpecificEpithet());
|
|
| 463 | 479 |
|
| 464 | 480 |
} |
| 465 | 481 |
|
Also available in: Unified diff
Implement notho rank recognition #3868