Revision 244c2806
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 1300 | 1300 |
} |
| 1301 | 1301 |
} |
| 1302 | 1302 |
|
| 1303 |
/** |
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| 1304 |
* Returns the <code>DisplayName</code> attribute. |
|
| 1305 |
* @param taxon The {@link TaxonBase Taxon}.
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|
| 1306 |
* @return The <code>DisplayName</code> attribute. |
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| 1307 |
* @see MethodMapper |
|
| 1308 |
*/ |
|
| 1309 |
@SuppressWarnings("unused") //used by Mapper
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|
| 1310 |
private static String getDisplayName(TaxonBase<?> taxon) {
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|
| 1311 |
TaxonName taxonName = taxon.getName(); |
|
| 1312 |
String result = getDisplayName(taxonName); |
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| 1313 |
if (isMisappliedName(taxon)){
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|
| 1314 |
result = result + " " + getAuthorString(taxon); |
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| 1315 |
} |
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| 1316 |
return result; |
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| 1317 |
} |
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| 1318 |
|
|
| 1319 | 1303 |
/** |
| 1320 | 1304 |
* Returns the <code>AuthorString</code> attribute. |
| 1321 | 1305 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
| ... | ... | |
| 1325 | 1309 |
//used by mapper |
| 1326 | 1310 |
protected static String getAuthorString(TaxonBase<?> taxon) {
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| 1327 | 1311 |
try {
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| 1328 |
String result = null; |
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| 1312 |
// For misapplied names there are special rules |
|
| 1313 |
if (isMisappliedName(taxon)){
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|
| 1314 |
return getMisappliedNameAuthorship(taxon); |
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| 1315 |
} |
|
| 1329 | 1316 |
boolean isNonViralName = false; |
| 1330 | 1317 |
String authorshipCache = null; |
| 1331 | 1318 |
TaxonName taxonName = taxon.getName(); |
| ... | ... | |
| 1333 | 1320 |
authorshipCache = taxonName.getAuthorshipCache(); |
| 1334 | 1321 |
isNonViralName = true; |
| 1335 | 1322 |
} |
| 1336 |
result = authorshipCache; |
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| 1337 |
|
|
| 1338 |
// For a misapplied names there are special rules |
|
| 1339 |
if (isMisappliedName(taxon)){
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|
| 1340 |
if (taxon.getSec() != null){
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| 1341 |
String secTitle = taxon.getSec().getTitleCache(); |
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| 1342 |
if (! secTitle.startsWith("auct")){
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|
| 1343 |
secTitle = "sensu " + secTitle; |
|
| 1344 |
}else if (secTitle.equals("auct")){ //may be removed once the title cache is generated correctly for references with title auct. #
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|
| 1345 |
secTitle = "auct."; |
|
| 1346 |
} |
|
| 1347 |
return secTitle; |
|
| 1348 |
}else if (StringUtils.isBlank(authorshipCache)) {
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// Set authorshipCache to "auct." |
|
| 1350 |
result = PesiTransformer.AUCT_STRING; |
|
| 1351 |
}else{
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|
| 1352 |
result = PesiTransformer.AUCT_STRING; |
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| 1353 |
// result = authorshipCache; |
|
| 1354 |
} |
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| 1355 |
} |
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| 1323 |
String result = authorshipCache; |
|
| 1356 | 1324 |
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| 1357 | 1325 |
if (taxonName == null){
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| 1358 | 1326 |
logger.warn("TaxonName does not exist for taxon: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
| ... | ... | |
| 1371 | 1339 |
} |
| 1372 | 1340 |
} |
| 1373 | 1341 |
|
| 1374 |
/** |
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| 1375 |
* Returns the <code>DisplayName</code> attribute. |
|
| 1376 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
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| 1377 |
* @return The <code>DisplayName</code> attribute. |
|
| 1378 |
* @see MethodMapper |
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| 1379 |
*/ |
|
| 1380 |
//used by Mapper |
|
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private static String getDisplayName(TaxonName taxonName) {
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private static String getMisappliedNameAuthorship(TaxonBase<?> taxon){
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String result; |
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String relAppendedPhrase = taxon.getAppendedPhrase(); |
|
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Reference sec = taxon.getSec(); |
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String secTitle = sec != null ? sec.getTitleCache(): null; |
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| 1347 |
if(relAppendedPhrase == null && sec == null) {
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| 1348 |
result = "auct."; |
|
| 1349 |
}else if (relAppendedPhrase != null && sec == null){
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result = relAppendedPhrase; |
|
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}else if (relAppendedPhrase == null && sec != null){
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result = "sensu " + secTitle; |
|
| 1353 |
}else{ //append!=null && sec!=null
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result = relAppendedPhrase + " " + secTitle; |
|
| 1355 |
} |
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| 1356 |
String authorship = taxon.getName().getAuthorshipCache(); |
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| 1357 |
if (isNotBlank(authorship)){
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| 1358 |
result += ", non " + authorship; |
|
| 1359 |
} |
|
| 1360 |
return result; |
|
| 1361 |
} |
|
| 1362 |
|
|
| 1363 |
/** |
|
| 1364 |
* Returns the <code>DisplayName</code> attribute. |
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| 1365 |
* @param taxon The {@link TaxonBase Taxon}.
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|
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* @return The <code>DisplayName</code> attribute. |
|
| 1367 |
* @see MethodMapper |
|
| 1368 |
*/ |
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| 1369 |
//used by Mapper |
|
| 1370 |
private static String getDisplayName(TaxonBase<?> taxon) {
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| 1371 |
boolean isMisapplied = isMisappliedName(taxon); |
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| 1372 |
TaxonName taxonName = taxon.getName(); |
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| 1373 |
String result = getDisplayName(taxonName, isMisapplied); |
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if (isMisapplied){
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| 1375 |
result = result + " " + getMisappliedNameAuthorship(taxon); |
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| 1376 |
} |
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| 1377 |
return result; |
|
| 1378 |
} |
|
| 1379 |
|
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| 1380 |
/** |
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| 1381 |
* Returns the <code>DisplayName</code> attribute. |
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| 1382 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
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| 1383 |
* @return The <code>DisplayName</code> attribute. |
|
| 1384 |
* @see MethodMapper |
|
| 1385 |
*/ |
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| 1386 |
@SuppressWarnings("unused") //used by Mapper
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|
| 1387 |
private static String getDisplayName(TaxonName taxonName) {
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| 1388 |
return getDisplayName(taxonName, false); |
|
| 1389 |
} |
|
| 1390 |
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|
| 1391 |
private static String getDisplayName(TaxonName taxonName, boolean useNameCache) {
|
|
| 1382 | 1392 |
// TODO: extension? |
| 1383 | 1393 |
if (taxonName == null) {
|
| 1384 | 1394 |
return null; |
| ... | ... | |
| 1393 | 1403 |
if (getSources(taxonName).contains(PesiSource.ERMS)){
|
| 1394 | 1404 |
result = cacheStrategy.getTitleCache(taxonName, tagRules); //according to SQL script (also in ERMS sources are not abbreviated) |
| 1395 | 1405 |
}else if (getSources(taxonName).contains(PesiSource.EM)){
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| 1396 |
result = cacheStrategy.getFullTitleCache(taxonName, tagRules); |
|
| 1406 |
if (useNameCache){
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| 1407 |
result = cacheStrategy.getNameCache(taxonName, tagRules); |
|
| 1408 |
}{
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|
| 1409 |
result = cacheStrategy.getFullTitleCache(taxonName, tagRules); |
|
| 1410 |
} |
|
| 1397 | 1411 |
}else{
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| 1398 | 1412 |
//TODO define for FE + IF and for multiple sources |
| 1399 |
result = cacheStrategy.getFullTitleCache(taxonName, tagRules); |
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| 1413 |
if (useNameCache){
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| 1414 |
result = cacheStrategy.getNameCache(taxonName, tagRules); |
|
| 1415 |
}{
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| 1416 |
result = cacheStrategy.getFullTitleCache(taxonName, tagRules); |
|
| 1417 |
} |
|
| 1400 | 1418 |
} |
| 1401 | 1419 |
return result.replaceAll("(, ?)?\\<@status@\\>.*\\</@status@\\>", "").trim();
|
| 1402 | 1420 |
} |
| ... | ... | |
| 1411 | 1429 |
|
| 1412 | 1430 |
/** |
| 1413 | 1431 |
* Returns the <code>WebShowName</code> attribute for a taxon. |
| 1414 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
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|
| 1432 |
* See {@link #getWebShowName(TaxonName)} for further explanations.
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|
| 1433 |
* @param taxon The {@link TaxonBase taxon}.
|
|
| 1415 | 1434 |
* @return The <code>WebShowName</code> attribute. |
| 1435 |
* @see #getWebShowName(TaxonName) |
|
| 1436 |
* @see #getDisplayName(TaxonBase) |
|
| 1437 |
* @see #getFullName(TaxonBase) |
|
| 1416 | 1438 |
* @see MethodMapper |
| 1417 | 1439 |
*/ |
| 1418 | 1440 |
@SuppressWarnings("unused")
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| 1419 | 1441 |
private static String getWebShowName(TaxonBase<?> taxon) {
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| 1420 |
TaxonName taxonName = taxon.getName(); |
|
| 1421 |
String result = getWebShowName(taxonName); |
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| 1422 |
if (isMisappliedName(taxon)){
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|
| 1423 |
result = result + " " + getAuthorString(taxon); |
|
| 1424 |
} |
|
| 1425 |
return result; |
|
| 1442 |
if (isMisappliedName(taxon)){
|
|
| 1443 |
//for misapplications the webshowname is the same as the displayname as they do not show the nom.ref. in displayname |
|
| 1444 |
return getDisplayName(taxon); |
|
| 1445 |
}else{
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|
| 1446 |
TaxonName taxonName = taxon.getName(); |
|
| 1447 |
return getWebShowName(taxonName); |
|
| 1448 |
} |
|
| 1426 | 1449 |
} |
| 1427 | 1450 |
|
| 1428 | 1451 |
/** |
| 1429 |
* Returns the <code>WebShowName</code> attribute. |
|
| 1452 |
* Returns the <code>WebShowName</code> attribute for a name. The |
|
| 1453 |
* <code>WebShowName</code> is like fullName but with |
|
| 1454 |
* tagged (<i>) name part. It is also similar to |
|
| 1455 |
* <code>DisplayName</code> but for titleCache not fullTitleCache. |
|
| 1456 |
* For misapplications it slightly differs (see {@link #getWebShowName(TaxonBase)} )
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|
| 1457 |
* |
|
| 1430 | 1458 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
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| 1431 | 1459 |
* @return The <code>WebShowName</code> attribute. |
| 1460 |
* @see #getDisplayName(TaxonName) |
|
| 1461 |
* @see #getFullName(TaxonName) |
|
| 1462 |
* @see #getWebShowName(TaxonBase) |
|
| 1432 | 1463 |
* @see MethodMapper |
| 1433 | 1464 |
*/ |
| 1434 | 1465 |
private static String getWebShowName(TaxonName taxonName) {
|
| ... | ... | |
| 1458 | 1489 |
return result; |
| 1459 | 1490 |
} |
| 1460 | 1491 |
|
| 1492 |
@SuppressWarnings("unused") //used by mapper
|
|
| 1493 |
private static String getFullName(TaxonBase<?> taxon) {
|
|
| 1494 |
if (isMisappliedName(taxon)){
|
|
| 1495 |
String result = getCacheStrategy(taxon.getName()).getTitleCache(taxon.getName()); |
|
| 1496 |
result = result + " " + getMisappliedNameAuthorship(taxon); |
|
| 1497 |
return result; |
|
| 1498 |
}else{
|
|
| 1499 |
return getFullName(taxon.getName()); |
|
| 1500 |
} |
|
| 1501 |
} |
|
| 1502 |
|
|
| 1503 |
|
|
| 1461 | 1504 |
/** |
| 1462 | 1505 |
* Returns the <code>FullName</code> attribute. |
| 1463 | 1506 |
* @param taxonName The {@link NonViralName NonViralName}.
|
| 1464 | 1507 |
* @return The <code>FullName</code> attribute. |
| 1465 | 1508 |
* @see MethodMapper |
| 1466 | 1509 |
*/ |
| 1467 |
@SuppressWarnings("unused")
|
|
| 1510 |
//used by mapper
|
|
| 1468 | 1511 |
private static String getFullName(TaxonName taxonName) {
|
| 1469 | 1512 |
//TODO extensions? |
| 1470 | 1513 |
String result = getCacheStrategy(taxonName).getTitleCache(taxonName); |
| ... | ... | |
| 1475 | 1518 |
if (isMisappliedName(taxon)){
|
| 1476 | 1519 |
result = result + " " + getAuthorString(taxon); |
| 1477 | 1520 |
} |
| 1478 |
taxon = null; |
|
| 1479 | 1521 |
} |
| 1480 | 1522 |
} |
| 1481 | 1523 |
return result; |
| ... | ... | |
| 1575 | 1617 |
try {
|
| 1576 | 1618 |
if (taxonName != null) {
|
| 1577 | 1619 |
Set<NomenclaturalStatus> states = taxonName.getStatus(); |
| 1578 |
if (states.size() == 1) {
|
|
| 1579 |
NomenclaturalStatus status = states.iterator().next(); |
|
| 1620 |
if (states.size() >= 1) {
|
|
| 1621 |
if (states.size() > 1) {
|
|
| 1622 |
String statusStr = null; |
|
| 1623 |
for (NomenclaturalStatus status: states){
|
|
| 1624 |
statusStr = CdmUtils.concat(",", statusStr, status.getType()== null? null:status.getType().getTitleCache());
|
|
| 1625 |
} |
|
| 1626 |
//a known case is ad43508a-8a10-480a-8519-2a76de2c0a0f (Labiatae Juss.) from E+M |
|
| 1627 |
logger.warn("This TaxonName has more than one nomenclatural status. This may happen in very rare cases but is not handled by the PESI data warehouse. Taxon name: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")Status:" + statusStr);
|
|
| 1628 |
} |
|
| 1629 |
NomenclaturalStatus status = states.iterator().next(); |
|
| 1580 | 1630 |
return status; |
| 1581 |
} else if (states.size() > 1) {
|
|
| 1582 |
logger.error("This TaxonName has more than one Nomenclatural Status: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1583 | 1631 |
} |
| 1584 | 1632 |
} |
| 1585 | 1633 |
} catch (Exception e) {
|
| ... | ... | |
| 2160 | 2208 |
|
| 2161 | 2209 |
mapping.addMapper(MethodMapper.NewInstance("DerivedFromGuid", this));
|
| 2162 | 2210 |
mapping.addMapper(MethodMapper.NewInstance("CacheCitation", this));
|
| 2163 |
mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because Misapllied Names are handled differently
|
|
| 2211 |
mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because misapplied names are handled differently
|
|
| 2212 |
mapping.addMapper(MethodMapper.NewInstance("FullName", this)); //For Taxon because misapplied names are handled differently
|
|
| 2164 | 2213 |
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this));
|
| 2165 | 2214 |
|
| 2166 | 2215 |
// DisplayName |
| ... | ... | |
| 2206 | 2255 |
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusFk", Types.INTEGER, PesiTransformer.T_STATUS_UNACCEPTED));
|
| 2207 | 2256 |
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusCache", Types.VARCHAR, state.getTransformer().getTaxonStatusCacheByKey( PesiTransformer.T_STATUS_UNACCEPTED)));
|
| 2208 | 2257 |
mapping.addMapper(DbStringMapper.NewInstance("AuthorshipCache", "AuthorString").setBlankToNull(true));
|
| 2258 |
mapping.addMapper(MethodMapper.NewInstance("FullName", this, TaxonName.class));
|
|
| 2209 | 2259 |
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this, TaxonName.class));
|
| 2210 | 2260 |
mapping.addMapper(MethodMapper.NewInstance("GUID", this, TaxonName.class));
|
| 2211 | 2261 |
|
| ... | ... | |
| 2230 | 2280 |
//full name |
| 2231 | 2281 |
// mapping.addMapper(DbStringMapper.NewInstance("NameCache", "WebSearchName")); //does not work as we need other cache strategy
|
| 2232 | 2282 |
mapping.addMapper(MethodMapper.NewInstance("WebSearchName", this, TaxonName.class));
|
| 2233 |
mapping.addMapper(MethodMapper.NewInstance("FullName", this, TaxonName.class));
|
|
| 2234 | 2283 |
|
| 2235 | 2284 |
//nom ref |
| 2236 | 2285 |
mapping.addMapper(MethodMapper.NewInstance("NomRefString", this, TaxonName.class));
|
Also available in: Unified diff
ref #2717 adapt export for DisplayName, WebShowName etc. to E+M requirements