Revision 2c298347
Added by Patrick Plitzner over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java | ||
|---|---|---|
| 169 | 169 |
|
| 170 | 170 |
//Gesamtliste |
| 171 | 171 |
TaxonBase<?> taxonBase = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class); |
| 172 |
taxonBase.setSec(gesamtListeClassification.getReference()); |
|
| 172 | 173 |
Taxon parent = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, Taxon.class); |
| 173 | 174 |
if(parent!=null && !parent.isInstanceOf(Taxon.class)){
|
| 174 | 175 |
RedListUtil.logMessage(id, parent+" is no taxon but is a parent of "+taxonBase+" (Gesamtliste)", logger); |
| ... | ... | |
| 182 | 183 |
Taxon family = (Taxon) state.getRelatedObject(RedListUtil.FAMILY_NAMESPACE_GESAMTLISTE, familieString); |
| 183 | 184 |
gesamtListeClassification.addParentChild(family, HibernateProxyHelper.deproxy(taxonBase, Taxon.class), null, null); |
| 184 | 185 |
//Buttler/Checklist taxon |
| 185 |
if(CdmUtils.isNotBlank(clTaxonString) && clTaxonString.equals("b")){
|
|
| 186 |
if(CdmUtils.isNotBlank(clTaxonString) && clTaxonString.equals(RedListUtil.CL_TAXON_B)){
|
|
| 186 | 187 |
checklistClassification.addParentChild(family, HibernateProxyHelper.deproxy(taxonBase, Taxon.class), null, null); |
| 188 |
taxonBase.setSec(checklistClassification.getReference()); |
|
| 187 | 189 |
} |
| 188 | 190 |
if(family.getTaxonNodes().isEmpty()){
|
| 189 | 191 |
gesamtListeClassification.addChildTaxon(family, null, null); |
| ... | ... | |
| 198 | 200 |
else{
|
| 199 | 201 |
createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBase, parent); |
| 200 | 202 |
//Buttler/Checklist taxon |
| 201 |
if(CdmUtils.isNotBlank(clTaxonString) && clTaxonString.equals("b")){
|
|
| 202 |
if(taxonBase.isInstanceOf(Taxon.class)){
|
|
| 203 |
createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBase, parent);
|
|
| 203 |
if(CdmUtils.isNotBlank(clTaxonString) && clTaxonString.equals(RedListUtil.CL_TAXON_B)){
|
|
| 204 |
if(!checklistClassification.isTaxonInTree(parent)){
|
|
| 205 |
RedListUtil.logInfoMessage(id, parent+" is parent taxon but is not in checklist. Skipping child "+taxonBase, logger);
|
|
| 204 | 206 |
} |
| 205 |
else if(taxonBase.isInstanceOf(Synonym.class)){
|
|
| 206 |
//if it is a synonym it is already added to the accepted taxon |
|
| 207 |
//so we just change the sec reference |
|
| 208 |
taxonBase.setSec(checklistClassification.getReference()); |
|
| 209 |
taxonBase.setTitleCache(null); |
|
| 207 |
else{
|
|
| 208 |
if(taxonBase.isInstanceOf(Taxon.class)){
|
|
| 209 |
createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBase, parent); |
|
| 210 |
} |
|
| 211 |
else if(taxonBase.isInstanceOf(Synonym.class)){
|
|
| 212 |
//if it is a synonym it is already added to the accepted taxon |
|
| 213 |
//so we just change the sec reference |
|
| 214 |
taxonBase.setSec(checklistClassification.getReference()); |
|
| 215 |
taxonBase.setTitleCache(null); |
|
| 216 |
} |
|
| 210 | 217 |
} |
| 211 | 218 |
|
| 212 | 219 |
} |
| 213 | 220 |
} |
| 221 |
taxonBase.setTitleCache(null, false);//refresh title cache |
|
| 214 | 222 |
|
| 215 | 223 |
//add taxa for concept relationships to E, W, K, AW, AO, R, O, S |
| 216 | 224 |
addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, relationE, taxonBase, id, state); |
| ... | ... | |
| 325 | 333 |
} |
| 326 | 334 |
//set sec reference |
| 327 | 335 |
taxonBase.setSec(classification.getReference()); |
| 328 |
taxonBase.setTitleCache(null, false);//refresh title cache |
|
| 329 | 336 |
} |
| 330 | 337 |
|
| 331 | 338 |
@Override |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 166 | 166 |
//---TAXON--- |
| 167 | 167 |
TaxonBase<?> taxonBase = importTaxon(rs, name, state); |
| 168 | 168 |
if(taxonBase==null){
|
| 169 |
RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
|
|
| 169 |
RedListUtil.logMessage(id, "!SERIOUS ERROR! Taxon for name "+name+" could not be created!", logger);
|
|
| 170 | 170 |
return; |
| 171 | 171 |
} |
| 172 | 172 |
|
| ... | ... | |
| 235 | 235 |
taxonBase = Synonym.NewInstance(name, null); |
| 236 | 236 |
} |
| 237 | 237 |
else{
|
| 238 |
RedListUtil.logMessage(id, "Taxon was not created!! Unknown value for "+RedListUtil.GUELT+"!", logger); |
|
| 238 | 239 |
return null; |
| 239 | 240 |
} |
| 240 | 241 |
|
| ... | ... | |
| 615 | 616 |
else if(rankStr.equals("KMB")){
|
| 616 | 617 |
return getRank(state, RedListUtil.uuidRankCombination, "Combination", "Combination", "", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific); |
| 617 | 618 |
} |
| 619 |
else if(rankStr.equals("'FO")){
|
|
| 620 |
return getRank(state, RedListUtil.uuidRankForme, "Forme'", "Forme'", "", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific); |
|
| 621 |
} |
|
| 618 | 622 |
else{
|
| 619 | 623 |
rank = state.getTransformer().getRankByKey(rankStr); |
| 620 | 624 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListUtil.java | ||
|---|---|---|
| 50 | 50 |
public static final UUID uuidRankLusus = UUID.fromString("4c8e12f6-2c16-4eda-a7d9-2fd247dcce789");
|
| 51 | 51 |
public static final UUID uuidRankSubspeciesPrincipes = UUID.fromString("b6b9351b-6beb-431d-8c7a-d30fe0cf3a90");
|
| 52 | 52 |
public static final UUID uuidRankCombination = UUID.fromString("ec2c580e-416a-4ecf-85df-d03641f3bd64");
|
| 53 |
public static final UUID uuidRankForme = UUID.fromString("05b4f66f-5559-4e44-bbb8-70744a5ea64a");
|
|
| 53 | 54 |
|
| 54 | 55 |
public static final String NAME_NAMESPACE = "name"; |
| 55 | 56 |
public static final String AUTHOR_NAMESPACE = "author"; |
| ... | ... | |
| 71 | 72 |
public static final String GUELT_BASIONYM = "b"; |
| 72 | 73 |
public static final String GUELT_SYNONYM = "x"; |
| 73 | 74 |
public static final String GUELT_ACCEPTED_TAXON = "1"; |
| 75 |
public static final String CL_TAXON_B = "b"; |
|
| 76 |
public static final String CL_TAXON_K = "k"; |
|
| 74 | 77 |
public static final String HYB_X = "x"; |
| 75 | 78 |
public static final String HYB_XF = "xf"; |
| 76 | 79 |
public static final String HYB_XS = "xs"; |
| ... | ... | |
| 86 | 89 |
public static final String NAMNR = "NAMNR"; |
| 87 | 90 |
public static final String SEQNUM = "SEQNUM"; |
| 88 | 91 |
public static final String GUELT = "GUELT"; |
| 89 |
public static final String LOWER = "LOWER"; |
|
| 92 |
public static final String LOWER = "LOWER_G";
|
|
| 90 | 93 |
public static final String AUTOR_BASI = "AUTOR_BASI"; |
| 91 | 94 |
public static final String AUTOR_KOMB = "AUTOR_KOMB"; |
| 92 | 95 |
public static final String ZUSATZ = "ZUSATZ"; |
| ... | ... | |
| 120 | 123 |
public static final String AO = "AO"; |
| 121 | 124 |
public static final String R = "R"; |
| 122 | 125 |
public static final String O = "O"; |
| 123 |
public static final String S = "S"; |
|
| 126 |
public static final String S = "S1"; |
|
| 127 |
public static final String S2 = "S2"; |
|
| 124 | 128 |
|
| 125 | 129 |
public static void logMessage(long id, String message, Logger logger){
|
| 126 | 130 |
logger.error(NAMNR+": "+id+" "+message); |
Also available in: Unified diff
ref #5448 Add new rank "forme"