Revision bb5bac58
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java | ||
|---|---|---|
| 12 | 12 |
import java.sql.ResultSet; |
| 13 | 13 |
import java.sql.SQLException; |
| 14 | 14 |
import java.util.HashMap; |
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import java.util.HashSet; |
|
| 16 | 15 |
import java.util.List; |
| 17 | 16 |
import java.util.Map; |
| 18 | 17 |
import java.util.Set; |
| ... | ... | |
| 55 | 54 |
" SELECT DISTINCT [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name], [Family name], g.[NAME OF FUNGUS] as GenusName, c.PreferredName as SpeciesName " + |
| 56 | 55 |
" FROM [tblPESIfungi-Classification] c LEFT OUTER JOIN " + |
| 57 | 56 |
" tblGenera g ON c.PreferredNameFDCnumber = g.[RECORD NUMBER]" + |
| 58 |
// " WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";
|
|
| 59 | 57 |
" ORDER BY [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name], [Family name], GenusName, SpeciesName "; |
| 60 | 58 |
return strRecordQuery; |
| 61 | 59 |
} |
| ... | ... | |
| 77 | 75 |
String lastSubclass = ""; |
| 78 | 76 |
String lastOrder = ""; |
| 79 | 77 |
String lastFamily = ""; |
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// String lastGenus = ""; |
|
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// String lastSpecies = ""; |
|
| 82 | 78 |
|
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Taxon taxonKingdom = null; |
| 84 | 80 |
Taxon taxonPhylum = null; |
| ... | ... | |
| 87 | 83 |
Taxon taxonSubclass = null; |
| 88 | 84 |
Taxon taxonOrder = null; |
| 89 | 85 |
Taxon taxonFamily = null; |
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// Taxon taxonGenus = null; |
|
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// Taxon taxonSpecies = null; |
|
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|
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Taxon higherTaxon = null; |
| 94 | 88 |
|
| ... | ... | |
| 107 | 101 |
String subclass = rs.getString("Subclass name");
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| 108 | 102 |
String order = rs.getString("Order name");
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| 109 | 103 |
String family = rs.getString("Family name");
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// String genus = rs.getString("GenusName");
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|
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// String species = rs.getString("SpeciesName");
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|
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// if (isNewTaxon(species, lastSpecies)){
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// if (isNewTaxon(genus, lastGenus)){
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|
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if (isNewTaxon(family, lastFamily)){
|
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if (isNewTaxon(order,lastOrder)){
|
| 117 | 107 |
if (isNewTaxon(subclass,lastSubclass)){
|
| ... | ... | |
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taxonFamily = makeTaxon(state, family, Rank.FAMILY()); |
| 179 | 169 |
if (taxonFamily != null){
|
| 180 | 170 |
try{
|
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//if this shown a warning see single issue in #2826 about Glomerelllaceae (which has 2 different parents)
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//if this shows a warning see single issue in #2826 about Glomerellaceae (which has 2 different parents)
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|
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getClassification(state).addParentChild(higherTaxon, taxonFamily, null, null); |
| 183 | 173 |
}catch(IllegalStateException e){
|
| 184 | 174 |
if (e.getMessage().startsWith("The child taxon is already part of the tree")){
|
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//TaxonNode node = getClassification(state).getNode(taxonFamily); |
| 186 | 176 |
logger.warn(e.getMessage() + taxonFamily.getTitleCache() + " " + higherTaxon.getTitleCache()); |
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} |
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} |
|
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} |
| 190 | 179 |
} |
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higherTaxon = isIncertisSedis(family) ? higherTaxon : taxonFamily; |
| 192 | 181 |
lastFamily = family; |
| 193 | 182 |
getTaxonService().saveOrUpdate(higherTaxon); |
| 194 | 183 |
} |
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// else{
|
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// higherTaxon = taxonFamily; |
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// } |
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// taxonGenus = makeTaxon(state, genus, Rank.GENUS()); |
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// if (taxonGenus != null){
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// getClassification(state).addParentChild(higherTaxon, taxonGenus, null, null); |
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// } |
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// higherTaxon = isIncertisSedis(genus) ? higherTaxon : taxonGenus; |
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// lastGenus = genus; |
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// }else{
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// higherTaxon = taxonGenus; |
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// } |
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// taxonSpecies = makeTaxon(state, species, Rank.SPECIES()); |
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// if (taxonSpecies != null){
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// getClassification(state).addParentChild(higherTaxon, taxonSpecies, null, null); |
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// } |
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// higherTaxon = isIncertisSedis(species) ? higherTaxon : taxonSpecies; |
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// lastSpecies = species; |
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// getTaxonService().saveOrUpdate(higherTaxon); |
|
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// } |
|
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getTaxonService().saveOrUpdate(higherTaxon); |
| 216 | 185 |
} |
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|
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} catch (SQLException e) {
|
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e.printStackTrace(); |
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logger.error(e.getMessage()); |
| ... | ... | |
| 226 | 193 |
logger.info("End higher classification ...");
|
| 227 | 194 |
|
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return; |
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} |
| 231 | 197 |
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private boolean isIncertisSedis(String uninomial) {
|
| 234 | 199 |
return uninomial.equalsIgnoreCase(INCERTAE_SEDIS) || uninomial.equalsIgnoreCase(FOSSIL_FUNGI); |
| 235 | 200 |
} |
| 236 | 201 |
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private boolean isNewTaxon(String uninomial, String lastUninomial) {
|
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boolean result = !uninomial.equalsIgnoreCase(lastUninomial); |
| 240 | 204 |
result |= lastUninomial.equalsIgnoreCase(INCERTAE_SEDIS); |
| ... | ... | |
| 246 | 210 |
if (uninomial.equalsIgnoreCase(INCERTAE_SEDIS) || uninomial.equalsIgnoreCase(FOSSIL_FUNGI)){
|
| 247 | 211 |
return null; |
| 248 | 212 |
} |
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Taxon taxon = state.getRelatedObject(IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES, uninomial, Taxon.class);
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Taxon taxon = state.getRelatedObject(IndexFungorumImportBase.NAMESPACE_SUPRAGENERIC_NAMES, uninomial, Taxon.class);
|
|
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if (taxon == null){
|
| 251 | 215 |
if (! newRank.equals(Rank.KINGDOM())){
|
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logger.warn("Taxon not found for uninomial " + uninomial);
|
| ... | ... | |
| 262 | 226 |
return taxon; |
| 263 | 227 |
} |
| 264 | 228 |
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@Override |
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
|
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String nameSpace; |
| 269 | 232 |
Class<?> cdmClass; |
| 270 | 233 |
Set<String> idSet; |
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
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|
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try{
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Set<String> taxonNameSet = new HashSet<String>();
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// Set<String> taxonNameSet = new HashSet<>();
|
|
| 275 | 238 |
// while (rs.next()){
|
| 276 | 239 |
// handleForeignKey(rs, taxonIdSet,"tu_accfinal" ); |
| 277 | 240 |
// } |
| 278 | 241 |
|
| 279 | 242 |
//taxon map |
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nameSpace = IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES ;
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nameSpace = IndexFungorumImportBase.NAMESPACE_SUPRAGENERIC_NAMES ;
|
|
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cdmClass = TaxonBase.class; |
| 282 | 245 |
// idSet = taxonNameSet; |
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Map<String, TaxonBase<?>> taxonMap = new HashMap<String, TaxonBase<?>>();
|
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Map<String, TaxonBase<?>> taxonMap = new HashMap<>(); |
|
| 284 | 247 |
List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null); |
| 285 | 248 |
for (Taxon taxon : list){
|
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taxonMap.put(CdmBase.deproxy(taxon.getName()).getGenusOrUninomial(), taxon); |
| ... | ... | |
| 289 | 252 |
|
| 290 | 253 |
//source reference |
| 291 | 254 |
Reference sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum); |
| 292 |
Map<String, Reference> referenceMap = new HashMap<String, Reference>();
|
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Map<String, Reference> referenceMap = new HashMap<>(); |
|
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referenceMap.put(SOURCE_REFERENCE, sourceReference); |
| 294 | 257 |
result.put(NAMESPACE_REFERENCE, referenceMap); |
| 295 | 258 |
|
| ... | ... | |
| 308 | 271 |
protected boolean isIgnore(IndexFungorumImportState state){
|
| 309 | 272 |
return ! state.getConfig().isDoRelTaxa(); |
| 310 | 273 |
} |
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} |
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minor, cleanup