Revision 787b3ec2
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java | ||
|---|---|---|
| 227 | 227 |
public static String kINGDOM_BACTERIA_STRING = "Bacteria"; |
| 228 | 228 |
public static String KINGDOM_CHROMISTA_STRING = "Chromista"; |
| 229 | 229 |
|
| 230 |
// Animalia Ranks |
|
| 231 |
public static int Animalia_Kingdom = 10; |
|
| 232 |
public static int Animalia_Subkingdom = 20; |
|
| 233 |
public static int Animalia_Infrakingdom = 25; |
|
| 234 |
public static int Animalia_Superphylum = 28; |
|
| 235 |
public static int Animalia_Phylum = 30; |
|
| 236 |
public static int Animalia_Subphylum = 40; |
|
| 237 |
public static int Animalia_Infraphylum = 45; |
|
| 238 |
public static int Animalia_Superclass = 50; |
|
| 239 |
public static int Animalia_Class = 60; |
|
| 240 |
public static int Animalia_Subclass = 70; |
|
| 241 |
public static int Animalia_Infraclass = 80; |
|
| 242 |
public static int Animalia_Subterclass = 85; |
|
| 243 |
|
|
| 244 |
public static int Animalia_Superorder = 90; |
|
| 245 |
public static int Animalia_Order = 100; |
|
| 246 |
public static int Animalia_Suborder = 110; |
|
| 247 |
public static int Animalia_Infraorder = 120; |
|
| 248 |
public static int Animalia_Parvorder = 122; |
|
| 249 |
public static int Animalia_Section = 125; |
|
| 230 |
//ranks all kingdoms |
|
| 231 |
public static int Kingdom = 10; |
|
| 232 |
public static int Subkingdom = 20; |
|
| 233 |
public static int Phylum = 30; //Phylum and Division is same (#8541) according to ICNAFP |
|
| 234 |
public static int Division = 30; |
|
| 235 |
public static int Subphylum = 40; //See above comment |
|
| 236 |
public static int Subdivision = 40; |
|
| 237 |
public static int Class = 60; |
|
| 238 |
public static int Subclass = 70; |
|
| 239 |
public static int Order = 100; |
|
| 240 |
public static int Suborder = 110; |
|
| 241 |
public static int Family = 140; |
|
| 242 |
public static int Subfamily = 150; |
|
| 243 |
public static int Tribe = 160; |
|
| 244 |
public static int Subtribe = 170; |
|
| 245 |
public static int Genus = 180; |
|
| 246 |
public static int Subgenus = 190; |
|
| 247 |
public static int Species =220; |
|
| 248 |
public static int Subspecies = 230; |
|
| 249 |
public static int Variety = 240; |
|
| 250 |
public static int Forma = 260; |
|
| 251 |
|
|
| 252 |
//ranks some kingdoms |
|
| 253 |
public static int Infrakingdom = 25; //2,3,5,7 |
|
| 254 |
public static int Infraphylum = 45; //2,7 |
|
| 255 |
public static int Superclass = 50; //2,5,6,7 |
|
| 256 |
public static int Infraclass = 80; //2,5,6,7 |
|
| 257 |
public static int Superorder = 90; //2,3,5,6,7 |
|
| 258 |
public static int Infraorder = 120; //2,5,6,7 |
|
| 259 |
public static int Superfamily = 130; //2,5,6,7 |
|
| 260 |
public static int Bot_Section = 200; //3,4,7 |
|
| 261 |
public static int Bot_Subsection = 210; //3,4,7 |
|
| 262 |
public static int Subvariety = 250; //2,3,4,7 |
|
| 263 |
public static int Subform = 270; //2,3,4 |
|
| 264 |
public static int Forma_spec = 275; //3,4,5,7 |
|
| 265 |
|
|
| 266 |
// Animalia Ranks |
|
| 267 |
public static int Superphylum = 28; |
|
| 268 |
public static int Subterclass = 85; |
|
| 269 |
public static int Parvorder = 122; |
|
| 270 |
public static int Animalia_Section = 125; |
|
| 250 | 271 |
public static int Animalia_Subsection = 127; |
| 251 |
public static int Animalia_Superfamily = 130; |
|
| 252 |
public static int Animalia_Family = 140; |
|
| 253 |
public static int Animalia_Subfamily = 150; |
|
| 254 |
public static int Animalia_Tribe = 160; |
|
| 255 |
public static int Animalia_Subtribe = 170; |
|
| 256 |
public static int Animalia_Genus = 180; |
|
| 257 |
public static int Animalia_Subgenus = 190; |
|
| 258 |
public static int Animalia_Species =220; |
|
| 259 |
public static int Animalia_Subspecies = 230; |
|
| 260 |
public static int Animalia_Natio = 235; |
|
| 261 |
public static int Animalia_Variety = 240; |
|
| 262 |
public static int Animalia_Subvariety = 250; |
|
| 263 |
public static int Animalia_Forma = 260; |
|
| 264 |
public static int Animalia_Subform = 270; |
|
| 272 |
public static int Natio = 235; |
|
| 265 | 273 |
|
| 266 | 274 |
// Plantae Ranks |
| 267 |
public static int Plantae_Kingdom = 10; |
|
| 268 |
public static int Plantae_Subkingdom = 20; |
|
| 269 |
public static int Plantae_Infrakingdom = 25; |
|
| 270 |
public static int Plantae_Phylum = 30; //Phylum and Division is same (#8541) |
|
| 271 |
public static int Plantae_Division = 30; |
|
| 272 |
public static int Plantae_Subphylum = 40; |
|
| 273 |
public static int Plantae_Subdivision = 40; |
|
| 274 |
public static int Plantae_Class = 60; |
|
| 275 |
public static int Plantae_Subclass = 70; |
|
| 276 |
public static int Plantae_Superorder = 90; |
|
| 277 |
public static int Plantae_Order = 100; |
|
| 278 |
public static int Plantae_Suborder = 110; |
|
| 279 |
public static int Plantae_Family = 140; |
|
| 280 |
public static int Plantae_Subfamily = 150; |
|
| 281 |
public static int Plantae_Tribe = 160; |
|
| 282 |
public static int Plantae_Subtribe = 170; |
|
| 283 |
public static int Plantae_Genus = 180; |
|
| 284 |
public static int Plantae_Subgenus = 190; |
|
| 285 |
public static int Plantae_Section = 200; |
|
| 286 |
public static int Plantae_Subsection = 210; |
|
| 287 |
public static int Plantae_Series = 212; |
|
| 288 |
public static int Plantae_Subseries = 214; |
|
| 289 |
public static int Plantae_Aggregate = 216; |
|
| 290 |
public static int Plantae_Coll_Species = 218; |
|
| 291 |
public static int Plantae_Species = 220; |
|
| 292 |
public static int Plantae_Grex = 225; |
|
| 293 |
public static int Plantae_Subspecies = 230; |
|
| 294 |
public static int Plantae_Proles = 232; |
|
| 295 |
public static int Plantae_Race = 234; |
|
| 296 |
public static int Plantae_Convarietas = 236; |
|
| 297 |
public static int Plantae_Variety = 240; |
|
| 298 |
public static int Plantae_Subvariety = 250; |
|
| 299 |
public static int Plantae_Forma = 260; |
|
| 300 |
public static int Plantae_Subforma = 270; |
|
| 301 |
public static int Plantae_Forma_spec = 275; |
|
| 302 |
public static int Plantae_Taxa_infragen = 280; |
|
| 303 |
public static int Plantae_Taxa_infraspec = 285; |
|
| 304 |
|
|
| 305 |
// Fungi Ranks |
|
| 306 |
public static int Fungi_Kingdom = 10; |
|
| 307 |
public static int Fungi_Subkingdom = 20; |
|
| 308 |
public static int Fungi_Division = 30; |
|
| 309 |
public static int Fungi_Subdivision = 40; |
|
| 310 |
public static int Fungi_Class = 60; |
|
| 311 |
public static int Fungi_Subclass = 70; |
|
| 312 |
public static int Fungi_Order = 100; |
|
| 313 |
public static int Fungi_Suborder = 110; |
|
| 314 |
public static int Fungi_Family = 140; |
|
| 315 |
public static int Fungi_Subfamily = 150; |
|
| 316 |
public static int Fungi_Tribe = 160; |
|
| 317 |
public static int Fungi_Subtribe = 170; |
|
| 318 |
public static int Fungi_Genus = 180; |
|
| 319 |
public static int Fungi_Subgenus = 190; |
|
| 320 |
public static int Fungi_Section = 200; |
|
| 321 |
public static int Fungi_Subsection = 210; |
|
| 322 |
public static int Fungi_Species = 220; |
|
| 323 |
public static int Fungi_Subspecies = 230; |
|
| 324 |
public static int Fungi_Variety = 240; |
|
| 325 |
public static int Fungi_Subvariety = 250; |
|
| 326 |
public static int Fungi_Forma = 260; |
|
| 327 |
public static int Fungi_Subforma = 270; |
|
| 328 |
public static int Fungi_Forma_spec = 275; |
|
| 329 |
|
|
| 330 |
//Protozoa Ranks |
|
| 331 |
public static int Protozoa_Kingdom = 10; |
|
| 332 |
public static int Protozoa_Subkingdom = 20; |
|
| 333 |
public static int Protozoa_Infrakingdom = 35; |
|
| 334 |
public static int Protozoa_Phylum = 30; |
|
| 335 |
public static int Protozoa_Subphylum = 40; |
|
| 336 |
public static int Protozoa_Superclass = 50; |
|
| 337 |
public static int Protozoa_Class = 60; |
|
| 338 |
public static int Protozoa_Subclass = 70; |
|
| 339 |
public static int Protozoa_Infraclass = 80; |
|
| 340 |
public static int Protozoa_Superorder = 90; |
|
| 341 |
public static int Protozoa_Order = 100; |
|
| 342 |
public static int Protozoa_Suborder = 110; |
|
| 343 |
public static int Protozoa_Infraorder = 120; |
|
| 344 |
public static int Protozoa_Superfamily = 130; |
|
| 345 |
public static int Protozoa_Family = 140; |
|
| 346 |
public static int Protozoa_Subfamily = 150; |
|
| 347 |
public static int Protozoa_Tribe = 160; |
|
| 348 |
public static int Protozoa_Subtribe = 170; |
|
| 349 |
public static int Protozoa_Genus = 180; |
|
| 350 |
public static int Protozoa_Subgenus = 190; |
|
| 351 |
public static int Protozoa_Species = 220; |
|
| 352 |
public static int Protozoa_Subspecies = 230; |
|
| 353 |
public static int Protozoa_Variety = 240; |
|
| 354 |
public static int Protozoa_Forma = 260; |
|
| 355 |
|
|
| 356 |
//Bacteria Ranks |
|
| 357 |
public static int Bacteria_Kingdom = 10; |
|
| 358 |
public static int Bacteria_Subkingdom = 20; |
|
| 359 |
public static int Bacteria_Phylum = 30; |
|
| 360 |
public static int Bacteria_Subphylum = 40; |
|
| 361 |
public static int Bacteria_Superclass = 50; |
|
| 362 |
public static int Bacteria_Class = 60; |
|
| 363 |
public static int Bacteria_Subclass = 70; |
|
| 364 |
public static int Bacteria_Infraclass = 80; |
|
| 365 |
public static int Bacteria_Superorder = 90; |
|
| 366 |
public static int Bacteria_Order = 100; |
|
| 367 |
public static int Bacteria_Suborder = 110; |
|
| 368 |
public static int Bacteria_Infraorder = 120; |
|
| 369 |
public static int Bacteria_Superfamily = 130; |
|
| 370 |
public static int Bacteria_Family = 140; |
|
| 371 |
public static int Bacteria_Subfamily = 150; |
|
| 372 |
public static int Bacteria_Tribe = 160; |
|
| 373 |
public static int Bacteria_Subtribe = 170; |
|
| 374 |
public static int Bacteria_Genus = 180; |
|
| 375 |
public static int Bacteria_Subgenus = 190; |
|
| 376 |
public static int Bacteria_Species = 220; |
|
| 377 |
public static int Bacteria_Subspecies = 230; |
|
| 378 |
public static int Bacteria_Variety = 240; |
|
| 379 |
public static int Bacteria_Forma = 260; |
|
| 380 |
|
|
| 381 |
//Chromista Ranks |
|
| 382 |
public static int Chromista_Kingdom = 10; |
|
| 383 |
public static int Chromista_Subkingdom = 20; |
|
| 384 |
public static int Chromista_Infrakingdom = 25; |
|
| 385 |
public static int Chromista_Phylum = 30; |
|
| 386 |
public static int Chromista_Subphylum = 40; |
|
| 387 |
public static int Chromista_Infraphylum = 45; |
|
| 388 |
public static int Chromista_Superclass = 50; |
|
| 389 |
public static int Chromista_Class = 60; |
|
| 390 |
public static int Chromista_Subclass = 70; |
|
| 391 |
public static int Chromista_Infraclass = 80; |
|
| 392 |
public static int Chromista_Superorder = 90; |
|
| 393 |
public static int Chromista_Order = 100; |
|
| 394 |
public static int Chromista_Suborder = 110; |
|
| 395 |
public static int Chromista_Infraorder = 120; |
|
| 396 |
public static int Chromista_Superfamily = 130; |
|
| 397 |
public static int Chromista_Family = 140; |
|
| 398 |
public static int Chromista_Subfamily = 150; |
|
| 399 |
public static int Chromista_Tribe = 160; |
|
| 400 |
public static int Chromista_Subtribe = 170; |
|
| 401 |
public static int Chromista_Genus = 180; |
|
| 402 |
public static int Chromista_Subgenus = 190; |
|
| 403 |
public static int Chromista_Section = 200; |
|
| 404 |
public static int Chromista_Subsection = 210; |
|
| 405 |
public static int Chromista_Species = 220; |
|
| 406 |
public static int Chromista_Subspecies = 230; |
|
| 407 |
public static int Chromista_Variety = 240; |
|
| 408 |
public static int Chromista_Subvariety = 250; |
|
| 409 |
public static int Chromista_Forma = 260; |
|
| 275 |
public static int Series = 212; |
|
| 276 |
public static int Subseries = 214; |
|
| 277 |
public static int Aggregate = 216; |
|
| 278 |
public static int Coll_Species = 218; |
|
| 279 |
public static int Grex = 225; |
|
| 280 |
public static int Proles = 232; |
|
| 281 |
public static int Race = 234; |
|
| 282 |
public static int Convarietas = 236; |
|
| 283 |
public static int Taxa_infragen = 280; |
|
| 284 |
public static int Taxa_infraspec = 285; |
|
| 285 |
|
|
| 410 | 286 |
|
| 411 | 287 |
//NoteCategory |
| 412 | 288 |
public static int NoteCategory_description = 1; |
| ... | ... | |
| 1618 | 1494 |
return null; |
| 1619 | 1495 |
}else if (rank.equals(Rank.DOMAIN())){
|
| 1620 | 1496 |
return KINGDOM_NULL; |
| 1621 |
} |
|
| 1497 |
}else if (rank.equals(Rank.KINGDOM())) {
|
|
| 1498 |
result = Kingdom; |
|
| 1499 |
}else if (rank.equals(Rank.SUBKINGDOM())) {
|
|
| 1500 |
result = Subkingdom; |
|
| 1501 |
} else if (rank.equals(Rank.PHYLUM())) {
|
|
| 1502 |
result = Phylum; |
|
| 1503 |
}else if (rank.equals(Rank.DIVISION())) { //same as Phylum
|
|
| 1504 |
result = Division; |
|
| 1505 |
}else if (rank.equals(Rank.SUBPHYLUM())) {
|
|
| 1506 |
result = Subphylum; |
|
| 1507 |
}else if (rank.equals(Rank.SUBDIVISION())) { //same as Subphylum
|
|
| 1508 |
result = Subdivision; |
|
| 1509 |
}else if (rank.equals(Rank.CLASS())) {
|
|
| 1510 |
result = Class; |
|
| 1511 |
} else if (rank.equals(Rank.SUBCLASS())) {
|
|
| 1512 |
result = Subclass; |
|
| 1513 |
} else if (rank.equals(Rank.ORDER())) {
|
|
| 1514 |
result = Order; |
|
| 1515 |
} else if (rank.equals(Rank.SUBORDER())) {
|
|
| 1516 |
result = Suborder; |
|
| 1517 |
} else if (rank.equals(Rank.FAMILY())) {
|
|
| 1518 |
result = Family; |
|
| 1519 |
} else if (rank.equals(Rank.SUBFAMILY())) {
|
|
| 1520 |
result = Subfamily; |
|
| 1521 |
} else if (rank.equals(Rank.TRIBE())) {
|
|
| 1522 |
result = Tribe; |
|
| 1523 |
} else if (rank.equals(Rank.SUBTRIBE())) {
|
|
| 1524 |
result = Subtribe; |
|
| 1525 |
} else if (rank.equals(Rank.GENUS())) {
|
|
| 1526 |
result = Genus; |
|
| 1527 |
} else if (rank.equals(Rank.SUBGENUS())) {
|
|
| 1528 |
result = Subgenus; |
|
| 1529 |
} else if (rank.equals(Rank.SPECIES())) {
|
|
| 1530 |
result = Species; |
|
| 1531 |
} else if (rank.equals(Rank.SUBSPECIES())) {
|
|
| 1532 |
result = Subspecies; |
|
| 1533 |
} else if (rank.equals(Rank.VARIETY())) {
|
|
| 1534 |
result = Variety; |
|
| 1535 |
} else if (rank.equals(Rank.FORM())) {
|
|
| 1536 |
result = Forma; |
|
| 1537 |
} else |
|
| 1622 | 1538 |
|
| 1623 | 1539 |
// We differentiate between Animalia and Plantae only for now. |
| 1624 | 1540 |
if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_ANIMALIA) {
|
| 1625 |
if (rank.equals(Rank.KINGDOM())) {
|
|
| 1626 |
result = Animalia_Kingdom; |
|
| 1627 |
} else if (rank.equals(Rank.SUBKINGDOM())) {
|
|
| 1628 |
result = Animalia_Subkingdom; |
|
| 1629 |
} else if (rank.equals(Rank.INFRAKINGDOM())) {
|
|
| 1630 |
result = Animalia_Infrakingdom; |
|
| 1631 |
} else if (rank.equals(Rank.SUPERPHYLUM())) {
|
|
| 1632 |
result = Animalia_Superphylum; |
|
| 1633 |
} else if (rank.equals(Rank.PHYLUM())) {
|
|
| 1634 |
result = Animalia_Phylum; |
|
| 1635 |
} else if (rank.equals(Rank.SUBPHYLUM())) {
|
|
| 1636 |
result = Animalia_Subphylum; |
|
| 1637 |
} else if (rank.equals(Rank.INFRAPHYLUM())) {
|
|
| 1638 |
result = Animalia_Infraphylum; |
|
| 1639 |
} else if (rank.equals(Rank.SUPERCLASS())) {
|
|
| 1640 |
result = Animalia_Superclass; |
|
| 1641 |
} else if (rank.equals(Rank.CLASS())) {
|
|
| 1642 |
result = Animalia_Class; |
|
| 1643 |
} else if (rank.equals(Rank.SUBCLASS())) {
|
|
| 1644 |
result = Animalia_Subclass; |
|
| 1645 |
} else if (rank.equals(Rank.INFRACLASS())) {
|
|
| 1646 |
result = Animalia_Infraclass; |
|
| 1647 |
} else if (rank.getUuid().equals(ErmsTransformer.uuidRankSubterclass)) {
|
|
| 1648 |
result = Animalia_Subterclass; |
|
| 1649 |
} else if (rank.equals(Rank.SUPERORDER())) {
|
|
| 1650 |
result = Animalia_Superorder; |
|
| 1651 |
} else if (rank.equals(Rank.ORDER())) {
|
|
| 1652 |
result = Animalia_Order; |
|
| 1653 |
} else if (rank.equals(Rank.SUBORDER())) {
|
|
| 1654 |
result = Animalia_Suborder; |
|
| 1655 |
} else if (rank.equals(Rank.INFRAORDER())) {
|
|
| 1656 |
result = Animalia_Infraorder; |
|
| 1657 |
} else if (rank.getUuid().equals(ErmsTransformer.uuidRankParvorder)) {
|
|
| 1658 |
result = Animalia_Parvorder; |
|
| 1659 |
} else if (rank.equals(Rank.SECTION_ZOOLOGY())) {
|
|
| 1660 |
result = Animalia_Section; |
|
| 1661 |
} else if (rank.equals(Rank.SUBSECTION_ZOOLOGY())) {
|
|
| 1662 |
result = Animalia_Subsection; |
|
| 1663 |
} else if (rank.equals(Rank.SUPERFAMILY())) {
|
|
| 1664 |
result = Animalia_Superfamily; |
|
| 1665 |
} else if (rank.equals(Rank.FAMILY())) {
|
|
| 1666 |
result = Animalia_Family; |
|
| 1667 |
} else if (rank.equals(Rank.SUBFAMILY())) {
|
|
| 1668 |
result = Animalia_Subfamily; |
|
| 1669 |
} else if (rank.equals(Rank.TRIBE())) {
|
|
| 1670 |
result = Animalia_Tribe; |
|
| 1671 |
} else if (rank.equals(Rank.SUBTRIBE())) {
|
|
| 1672 |
result = Animalia_Subtribe; |
|
| 1673 |
} else if (rank.equals(Rank.GENUS())) {
|
|
| 1674 |
result = Animalia_Genus; |
|
| 1675 |
} else if (rank.equals(Rank.SUBGENUS())) {
|
|
| 1676 |
result = Animalia_Subgenus; |
|
| 1677 |
} else if (rank.equals(Rank.SPECIES())) {
|
|
| 1678 |
result = Animalia_Species; |
|
| 1679 |
} else if (rank.equals(Rank.SUBSPECIES())) {
|
|
| 1680 |
result = Animalia_Subspecies; |
|
| 1681 |
// } else if (rank.equals(Rank.)) { // not yet specified
|
|
| 1682 |
// result = Animalia_Natio; |
|
| 1683 |
} else if (rank.equals(Rank.VARIETY())) {
|
|
| 1684 |
result = Animalia_Variety; |
|
| 1685 |
} else if (rank.equals(Rank.SUBVARIETY())) {
|
|
| 1686 |
result = Animalia_Subvariety; |
|
| 1687 |
} else if (rank.equals(Rank.FORM())) {
|
|
| 1688 |
result = Animalia_Forma; |
|
| 1689 |
} else if (rank.equals(Rank.SUBFORM())) {
|
|
| 1690 |
result = Animalia_Subform; |
|
| 1541 |
if (rank.equals(Rank.INFRAKINGDOM())) {result = Infrakingdom;
|
|
| 1542 |
} else if (rank.equals(Rank.SUPERPHYLUM())) {result = Superphylum;
|
|
| 1543 |
} else if (rank.equals(Rank.INFRAPHYLUM())) {result = Infraphylum;
|
|
| 1544 |
} else if (rank.equals(Rank.SUPERCLASS())) {result = Superclass;
|
|
| 1545 |
} else if (rank.equals(Rank.INFRACLASS())) {result = Infraclass;
|
|
| 1546 |
} else if (rank.getUuid().equals(ErmsTransformer.uuidRankSubterclass)) {result = Subterclass;
|
|
| 1547 |
} else if (rank.equals(Rank.SUPERORDER())) {result = Superorder;
|
|
| 1548 |
} else if (rank.equals(Rank.INFRAORDER())) {result = Infraorder;
|
|
| 1549 |
} else if (rank.getUuid().equals(ErmsTransformer.uuidRankParvorder)) {result = Parvorder;
|
|
| 1550 |
} else if (rank.equals(Rank.SECTION_ZOOLOGY())) {result = Animalia_Section;
|
|
| 1551 |
} else if (rank.equals(Rank.SUBSECTION_ZOOLOGY())) {result = Animalia_Subsection;
|
|
| 1552 |
} else if (rank.equals(Rank.SUPERFAMILY())) {result = Superfamily;
|
|
| 1553 |
} else if (rank.equals(Rank.NATIO())) {result = Natio;
|
|
| 1554 |
} else if (rank.equals(Rank.SUBVARIETY())) {result = Subvariety;
|
|
| 1555 |
} else if (rank.equals(Rank.SUBFORM())) {result = Subform;
|
|
| 1691 | 1556 |
} else {
|
| 1692 | 1557 |
//TODO Exception |
| 1693 | 1558 |
logger.warn("Rank for Kingdom Animalia not yet supported in CDM: "+ rank.getLabel());
|
| 1694 | 1559 |
return null; |
| 1695 | 1560 |
} |
| 1696 | 1561 |
} else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_PLANTAE) {
|
| 1697 |
if (rank.equals(Rank.KINGDOM())) {
|
|
| 1698 |
result = Plantae_Kingdom; |
|
| 1699 |
} else if (rank.equals(Rank.INFRAKINGDOM())) {
|
|
| 1700 |
result = Plantae_Infrakingdom; |
|
| 1701 |
} else if (rank.equals(Rank.SUBKINGDOM())) {
|
|
| 1702 |
result = Plantae_Subkingdom; |
|
| 1703 |
}else if (rank.equals(Rank.PHYLUM())) { //is same as Division (#8541)
|
|
| 1704 |
result = Plantae_Phylum; |
|
| 1705 |
}else if (rank.equals(Rank.DIVISION())) {
|
|
| 1706 |
result = Plantae_Division; |
|
| 1707 |
} else if (rank.equals(Rank.SUBPHYLUM())) {
|
|
| 1708 |
result = Plantae_Subphylum; |
|
| 1709 |
} else if (rank.equals(Rank.SUBDIVISION())) {
|
|
| 1710 |
result = Plantae_Subdivision; |
|
| 1711 |
} else if (rank.equals(Rank.CLASS())) {
|
|
| 1712 |
result = Plantae_Class; |
|
| 1713 |
} else if (rank.equals(Rank.SUBCLASS())) {
|
|
| 1714 |
result = Plantae_Subclass; |
|
| 1715 |
} else if (rank.equals(Rank.SUPERORDER())) {
|
|
| 1716 |
result = Plantae_Superorder; |
|
| 1717 |
} else if (rank.equals(Rank.ORDER())) {
|
|
| 1718 |
result = Plantae_Order; |
|
| 1719 |
} else if (rank.equals(Rank.SUBORDER())) {
|
|
| 1720 |
result = Plantae_Suborder; |
|
| 1721 |
} else if (rank.equals(Rank.FAMILY())) {
|
|
| 1722 |
result = Plantae_Family; |
|
| 1723 |
} else if (rank.equals(Rank.SUBFAMILY())) {
|
|
| 1724 |
result = Plantae_Subfamily; |
|
| 1725 |
} else if (rank.equals(Rank.TRIBE())) {
|
|
| 1726 |
result = Plantae_Tribe; |
|
| 1727 |
} else if (rank.equals(Rank.SUBTRIBE())) {
|
|
| 1728 |
result = Plantae_Subtribe; |
|
| 1729 |
} else if (rank.equals(Rank.GENUS())) {
|
|
| 1730 |
result = Plantae_Genus; |
|
| 1731 |
} else if (rank.equals(Rank.SUBGENUS())) {
|
|
| 1732 |
result = Plantae_Subgenus; |
|
| 1733 |
} else if (rank.equals(Rank.SECTION_BOTANY())) {
|
|
| 1734 |
result = Plantae_Section; |
|
| 1735 |
} else if (rank.equals(Rank.SUBSECTION_BOTANY())) {
|
|
| 1736 |
result = Plantae_Subsection; |
|
| 1737 |
} else if (rank.equals(Rank.SERIES())) {
|
|
| 1738 |
result = Plantae_Series; |
|
| 1739 |
} else if (rank.equals(Rank.SUBSERIES())) {
|
|
| 1740 |
result = Plantae_Subseries; |
|
| 1741 |
} else if (rank.equals(Rank.SPECIESAGGREGATE() )) {
|
|
| 1742 |
result = Plantae_Aggregate; |
|
| 1562 |
if (rank.equals(Rank.INFRAKINGDOM())) {result = Infrakingdom;
|
|
| 1563 |
} else if (rank.equals(Rank.SUPERORDER())) {result = Superorder;
|
|
| 1564 |
} else if (rank.equals(Rank.SECTION_BOTANY())) {result = Bot_Section;
|
|
| 1565 |
} else if (rank.equals(Rank.SUBSECTION_BOTANY())) {result = Bot_Subsection;
|
|
| 1566 |
} else if (rank.equals(Rank.SERIES())) {result = Series;
|
|
| 1567 |
} else if (rank.equals(Rank.SUBSERIES())) {result = Subseries;
|
|
| 1568 |
} else if (rank.equals(Rank.SPECIESAGGREGATE() )) {result = Aggregate;
|
|
| 1743 | 1569 |
} else if (rank.equals(Rank.SPECIESGROUP())) {
|
| 1744 | 1570 |
logger.warn("Rank Species Group not yet implemented");
|
| 1745 | 1571 |
result = null; |
| 1746 |
} else if (rank.getUuid().equals(Rank.uuidCollSpecies)) {
|
|
| 1747 |
result = Plantae_Coll_Species; |
|
| 1748 |
} else if (rank.equals(Rank.SPECIES())) {
|
|
| 1749 |
result = Plantae_Species; |
|
| 1750 |
} else if (rank.equals(Rank.SUBSPECIES())) {
|
|
| 1751 |
result = Plantae_Subspecies; |
|
| 1752 |
} else if (rank.equals(Rank.GREX())) {
|
|
| 1753 |
result = Plantae_Grex; |
|
| 1754 |
} else if (rank.getUuid().equals(Rank.uuidProles) ) {
|
|
| 1755 |
result = Plantae_Proles; |
|
| 1756 |
} else if (rank.getUuid().equals(Rank.uuidRace)) {
|
|
| 1757 |
result = Plantae_Race; |
|
| 1758 |
} else if (rank.equals(Rank.CONVAR())) {
|
|
| 1759 |
result = Plantae_Convarietas; |
|
| 1760 |
} else if (rank.equals(Rank.VARIETY())) {
|
|
| 1761 |
result = Plantae_Variety; |
|
| 1762 |
} else if (rank.equals(Rank.SUBVARIETY())) {
|
|
| 1763 |
result = Plantae_Subvariety; |
|
| 1764 |
} else if (rank.equals(Rank.FORM())) {
|
|
| 1765 |
result = Plantae_Forma; |
|
| 1766 |
} else if (rank.equals(Rank.SUBFORM())) {
|
|
| 1767 |
result = Plantae_Subforma; |
|
| 1768 |
// } else if (rank.equals(Rank.)) { // not yet specified
|
|
| 1769 |
// result = Plantae_Forma_spec; |
|
| 1770 |
} else if (rank.equals(Rank.INFRAGENERICTAXON())) {
|
|
| 1771 |
result = Plantae_Taxa_infragen; |
|
| 1772 |
} else if (rank.equals(Rank.INFRASPECIFICTAXON())) {
|
|
| 1773 |
result = Plantae_Taxa_infraspec; |
|
| 1572 |
} else if (rank.getUuid().equals(Rank.uuidCollSpecies)) {result = Coll_Species;
|
|
| 1573 |
} else if (rank.equals(Rank.GREX())) {result = Grex;
|
|
| 1574 |
} else if (rank.getUuid().equals(Rank.uuidProles) ) {result = Proles;
|
|
| 1575 |
} else if (rank.getUuid().equals(Rank.uuidRace)) {result = Race;
|
|
| 1576 |
} else if (rank.equals(Rank.CONVAR())) {result = Convarietas;
|
|
| 1577 |
} else if (rank.equals(Rank.SUBVARIETY())) {result = Subvariety;
|
|
| 1578 |
} else if (rank.equals(Rank.SUBFORM())) {result = Subform;
|
|
| 1579 |
} else if (rank.equals(Rank.SPECIALFORM())) {result = Forma_spec;
|
|
| 1580 |
} else if (rank.equals(Rank.INFRAGENERICTAXON())) {result = Taxa_infragen;
|
|
| 1581 |
} else if (rank.equals(Rank.INFRASPECIFICTAXON())) {result = Taxa_infraspec;
|
|
| 1774 | 1582 |
} else {
|
| 1775 | 1583 |
//TODO Exception |
| 1776 | 1584 |
logger.warn("Rank for Kingdom Plantae not yet supported in CDM: "+ rank.getLabel());
|
| 1777 | 1585 |
return null; |
| 1778 | 1586 |
} |
| 1587 |
} else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_FUNGI) {
|
|
| 1588 |
if (rank.equals(Rank.SECTION_BOTANY())) { result = Bot_Section;}
|
|
| 1589 |
else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Bot_Subsection;}
|
|
| 1590 |
else if (rank.equals(Rank.SUBVARIETY())) { result = Subvariety; }
|
|
| 1591 |
else if (rank.equals(Rank.SUBFORM())) { result = Subform;}
|
|
| 1592 |
else {
|
|
| 1593 |
//TODO Exception |
|
| 1594 |
logger.warn("Rank for Kingdom Fungi not yet supported in CDM: "+ rank.getLabel());
|
|
| 1595 |
return null; |
|
| 1596 |
} |
|
| 1779 | 1597 |
}else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_PROTOZOA) {
|
| 1780 |
if (rank.equals(Rank.KINGDOM())) { result = Protozoa_Kingdom; }
|
|
| 1781 |
else if (rank.equals(Rank.SUBKINGDOM())) { result = Protozoa_Subkingdom; }
|
|
| 1782 |
else if (rank.equals(Rank.INFRAKINGDOM())) { result = Protozoa_Infrakingdom; }
|
|
| 1783 |
else if (rank.equals(Rank.PHYLUM())) { result = Protozoa_Phylum; }
|
|
| 1784 |
else if (rank.equals(Rank.SUBPHYLUM())) { result = Protozoa_Subphylum; }
|
|
| 1785 |
else if (rank.equals(Rank.CLASS())) { result = Protozoa_Class; }
|
|
| 1786 |
else if (rank.equals(Rank.SUBCLASS())) { result = Protozoa_Subclass; }
|
|
| 1787 |
else if (rank.equals(Rank.ORDER())) { result = Protozoa_Order; }
|
|
| 1788 |
else if (rank.equals(Rank.SUBORDER())) { result = Protozoa_Suborder; }
|
|
| 1789 |
else if (rank.equals(Rank.INFRAORDER())) { result = Protozoa_Infraorder; }
|
|
| 1790 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Protozoa_Superfamily; }
|
|
| 1791 |
else if (rank.equals(Rank.FAMILY())) { result = Protozoa_Family; }
|
|
| 1792 |
else if (rank.equals(Rank.SUBFAMILY())) { result = Protozoa_Subfamily; }
|
|
| 1793 |
else if (rank.equals(Rank.TRIBE())) { result = Protozoa_Tribe; }
|
|
| 1794 |
else if (rank.equals(Rank.SUBTRIBE())) { result = Protozoa_Subtribe; }
|
|
| 1795 |
else if (rank.equals(Rank.GENUS())) { result = Protozoa_Genus; }
|
|
| 1796 |
else if (rank.equals(Rank.SUBGENUS())) { result = Protozoa_Subgenus; }
|
|
| 1797 |
else if (rank.equals(Rank.SPECIES())) { result = Protozoa_Species; }
|
|
| 1798 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Protozoa_Subspecies; }
|
|
| 1799 |
else if (rank.equals(Rank.VARIETY())) { result = Protozoa_Variety; }
|
|
| 1800 |
else if (rank.equals(Rank.FORM())) { result = Protozoa_Forma; }
|
|
| 1598 |
if (rank.equals(Rank.INFRAKINGDOM())) { result = Infrakingdom; }
|
|
| 1599 |
else if (rank.equals(Rank.SUPERCLASS())) { result = Superclass; }
|
|
| 1600 |
else if (rank.equals(Rank.INFRACLASS())) { result = Infraclass; }
|
|
| 1601 |
else if (rank.equals(Rank.SUPERORDER())) { result = Superorder; }
|
|
| 1602 |
else if (rank.equals(Rank.INFRAORDER())) { result = Infraorder; }
|
|
| 1603 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Superfamily; }
|
|
| 1801 | 1604 |
else {
|
| 1802 | 1605 |
//TODO Exception |
| 1803 | 1606 |
logger.warn("Rank for Kingdom Protozoa not yet supported in CDM: "+ rank.getLabel());
|
| 1804 | 1607 |
return null; |
| 1805 | 1608 |
} |
| 1806 |
} else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_FUNGI) {
|
|
| 1807 |
if (rank.equals(Rank.KINGDOM())) { result = Fungi_Kingdom; }
|
|
| 1808 |
else if (rank.equals(Rank.SUBKINGDOM())) { result = Fungi_Subkingdom; }
|
|
| 1809 |
else if (rank.equals(Rank.PHYLUM())) { result = Fungi_Division;} //Phylum and Division is same in ICNAFP
|
|
| 1810 |
else if (rank.equals(Rank.DIVISION())) { result = Fungi_Division;}
|
|
| 1811 |
else if (rank.equals(Rank.SUBDIVISION())) { result = Fungi_Subdivision;}
|
|
| 1812 |
else if (rank.equals(Rank.CLASS())) { result = Fungi_Class; }
|
|
| 1813 |
else if (rank.equals(Rank.SUBCLASS())) { result = Fungi_Subclass; }
|
|
| 1814 |
else if (rank.equals(Rank.ORDER())) { result = Fungi_Order; }
|
|
| 1815 |
else if (rank.equals(Rank.SUBORDER())) { result = Fungi_Suborder; }
|
|
| 1816 |
else if (rank.equals(Rank.FAMILY())) { result = Fungi_Family; }
|
|
| 1817 |
else if (rank.equals(Rank.SUBFAMILY())) { result = Fungi_Subfamily; }
|
|
| 1818 |
else if (rank.equals(Rank.TRIBE())) { result = Fungi_Tribe; }
|
|
| 1819 |
else if (rank.equals(Rank.SUBTRIBE())) { result = Fungi_Subtribe; }
|
|
| 1820 |
else if (rank.equals(Rank.GENUS())) { result = Fungi_Genus; }
|
|
| 1821 |
else if (rank.equals(Rank.SUBGENUS())) { result = Fungi_Subgenus; }
|
|
| 1822 |
else if (rank.equals(Rank.SECTION_BOTANY())) { result = Fungi_Section;}
|
|
| 1823 |
else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Fungi_Subsection;}
|
|
| 1824 |
else if (rank.equals(Rank.SPECIES())) { result = Fungi_Species; }
|
|
| 1825 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Fungi_Subspecies; }
|
|
| 1826 |
else if (rank.equals(Rank.VARIETY())) { result = Fungi_Variety; }
|
|
| 1827 |
else if (rank.equals(Rank.SUBVARIETY())) { result = Fungi_Subvariety; }
|
|
| 1828 |
else if (rank.equals(Rank.FORM())) { result = Fungi_Forma; }
|
|
| 1829 |
else if (rank.equals(Rank.SUBFORM())) { result = Fungi_Subforma;}
|
|
| 1830 |
else {
|
|
| 1831 |
//TODO Exception |
|
| 1832 |
logger.warn("Rank for Kingdom Fungi not yet supported in CDM: "+ rank.getLabel());
|
|
| 1833 |
return null; |
|
| 1834 |
} |
|
| 1835 | 1609 |
} else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_BACTERIA) {
|
| 1836 |
if (rank.equals(Rank.KINGDOM())) { result = Bacteria_Kingdom; }
|
|
| 1837 |
else if (rank.equals(Rank.SUBKINGDOM())) { result = Bacteria_Subkingdom; }
|
|
| 1838 |
else if (rank.equals(Rank.PHYLUM())) { result = Bacteria_Phylum; }
|
|
| 1839 |
else if (rank.equals(Rank.SUBPHYLUM())) { result = Bacteria_Subphylum; }
|
|
| 1840 |
else if (rank.equals(Rank.SUPERCLASS())) { result = Bacteria_Superclass; }
|
|
| 1841 |
else if (rank.equals(Rank.CLASS())) { result = Bacteria_Class; }
|
|
| 1842 |
else if (rank.equals(Rank.SUBCLASS())) { result = Bacteria_Subclass; }
|
|
| 1843 |
else if (rank.equals(Rank.INFRACLASS())) { result = Bacteria_Infraclass; }
|
|
| 1844 |
else if (rank.equals(Rank.SUPERORDER())) { result = Bacteria_Superorder; }
|
|
| 1845 |
else if (rank.equals(Rank.ORDER())) { result = Bacteria_Order; }
|
|
| 1846 |
else if (rank.equals(Rank.SUBORDER())) { result = Bacteria_Suborder; }
|
|
| 1847 |
else if (rank.equals(Rank.INFRAORDER())) { result = Bacteria_Infraorder; }
|
|
| 1848 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Bacteria_Superfamily; }
|
|
| 1849 |
else if (rank.equals(Rank.FAMILY())) { result = Bacteria_Family; }
|
|
| 1850 |
else if (rank.equals(Rank.SUBFAMILY())) { result = Bacteria_Subfamily; }
|
|
| 1851 |
else if (rank.equals(Rank.TRIBE())) { result = Bacteria_Tribe; }
|
|
| 1852 |
else if (rank.equals(Rank.SUBTRIBE())) { result = Bacteria_Subtribe; }
|
|
| 1853 |
else if (rank.equals(Rank.GENUS())) { result = Bacteria_Genus; }
|
|
| 1854 |
else if (rank.equals(Rank.SUBGENUS())) { result = Bacteria_Subgenus; }
|
|
| 1855 |
else if (rank.equals(Rank.SPECIES())) { result = Bacteria_Species; }
|
|
| 1856 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Bacteria_Subspecies; }
|
|
| 1857 |
else if (rank.equals(Rank.VARIETY())) { result = Bacteria_Variety; }
|
|
| 1858 |
else if (rank.equals(Rank.FORM())) { result = Bacteria_Forma; }
|
|
| 1610 |
if (rank.equals(Rank.SUPERCLASS())) { result = Superclass; }
|
|
| 1611 |
else if (rank.equals(Rank.INFRACLASS())) { result = Infraclass; }
|
|
| 1612 |
else if (rank.equals(Rank.SUPERORDER())) { result = Superorder; }
|
|
| 1613 |
else if (rank.equals(Rank.INFRAORDER())) { result = Infraorder; }
|
|
| 1614 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Superfamily; }
|
|
| 1859 | 1615 |
else {
|
| 1860 | 1616 |
//TODO Exception |
| 1861 | 1617 |
logger.warn("Rank for Kingdom Bacteria not yet supported in CDM: "+ rank.getLabel());
|
| 1862 | 1618 |
return null; |
| 1863 | 1619 |
} |
| 1864 | 1620 |
}else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_CHROMISTA) {
|
| 1865 |
if (rank.equals(Rank.KINGDOM())) { result = Chromista_Kingdom; }
|
|
| 1866 |
else if (rank.equals(Rank.SUBKINGDOM())) { result = Chromista_Subkingdom; }
|
|
| 1867 |
else if (rank.equals(Rank.INFRAKINGDOM())) { result = Chromista_Infrakingdom; }
|
|
| 1868 |
else if (rank.equals(Rank.PHYLUM())) { result = Chromista_Phylum; }
|
|
| 1869 |
else if (rank.equals(Rank.SUBPHYLUM())) { result = Chromista_Subphylum; }
|
|
| 1870 |
else if (rank.equals(Rank.INFRAPHYLUM())) { result = Chromista_Infraphylum; }
|
|
| 1871 |
else if (rank.equals(Rank.SUPERCLASS())) { result = Chromista_Superclass; }
|
|
| 1872 |
else if (rank.equals(Rank.CLASS())) { result = Chromista_Class; }
|
|
| 1873 |
else if (rank.equals(Rank.SUBCLASS())) { result = Chromista_Subclass; }
|
|
| 1874 |
else if (rank.equals(Rank.SUPERORDER())) { result = Chromista_Superorder; }
|
|
| 1875 |
else if (rank.equals(Rank.ORDER())) { result = Chromista_Order; }
|
|
| 1876 |
else if (rank.equals(Rank.SUBORDER())) { result = Chromista_Suborder; }
|
|
| 1877 |
else if (rank.equals(Rank.INFRAORDER())) { result = Chromista_Infraorder; }
|
|
| 1878 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Chromista_Superfamily; }
|
|
| 1879 |
else if (rank.equals(Rank.FAMILY())) { result = Chromista_Family; }
|
|
| 1880 |
else if (rank.equals(Rank.SUBFAMILY())) { result = Chromista_Subfamily; }
|
|
| 1881 |
else if (rank.equals(Rank.TRIBE())) { result = Chromista_Tribe; }
|
|
| 1882 |
else if (rank.equals(Rank.SUBTRIBE())) { result = Chromista_Subtribe; }
|
|
| 1883 |
else if (rank.equals(Rank.GENUS())) { result = Chromista_Genus; }
|
|
| 1884 |
else if (rank.equals(Rank.SUBGENUS())) { result = Chromista_Subgenus; }
|
|
| 1885 |
else if (rank.equals(Rank.SECTION_BOTANY())) { result = Chromista_Section;}
|
|
| 1886 |
else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Chromista_Subsection;}
|
|
| 1887 |
else if (rank.equals(Rank.SPECIES())) { result = Chromista_Species; }
|
|
| 1888 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Chromista_Subspecies; }
|
|
| 1889 |
else if (rank.equals(Rank.VARIETY())) { result = Chromista_Variety; }
|
|
| 1890 |
else if (rank.equals(Rank.SUBVARIETY())) { result = Chromista_Subvariety; }
|
|
| 1891 |
else if (rank.equals(Rank.FORM())) { result = Chromista_Forma; }
|
|
| 1621 |
if (rank.equals(Rank.INFRAKINGDOM())) { result = Infrakingdom; }
|
|
| 1622 |
else if (rank.equals(Rank.INFRAPHYLUM())) { result = Infraphylum; }
|
|
| 1623 |
else if (rank.equals(Rank.SUPERCLASS())) { result = Superclass; }
|
|
| 1624 |
else if (rank.equals(Rank.INFRACLASS())) { result = Infraclass; }
|
|
| 1625 |
else if (rank.equals(Rank.SUPERORDER())) { result = Superorder; }
|
|
| 1626 |
else if (rank.equals(Rank.INFRAORDER())) { result = Infraorder; }
|
|
| 1627 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Superfamily; }
|
|
| 1628 |
else if (rank.equals(Rank.SECTION_BOTANY())) { result = Bot_Section;}
|
|
| 1629 |
else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Bot_Subsection;}
|
|
| 1630 |
else if (rank.equals(Rank.SUBVARIETY())) { result = Subvariety; }
|
|
| 1892 | 1631 |
else {
|
| 1893 | 1632 |
//TODO Exception |
| 1894 | 1633 |
logger.warn("Rank for Kingdom Chromista not yet supported in CDM: "+ rank.getLabel());
|
Also available in: Unified diff
ref #8509 cleanup rank handling in PesiTranformer