Revision e5299170
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 247 | 247 |
rankTypeExpertsUpdateStmt = connection.prepareStatement(sql); |
| 248 | 248 |
} |
| 249 | 249 |
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| 250 |
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping) throws SQLException {
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| 250 |
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping){
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| 251 | 251 |
int count = 0; |
| 252 | 252 |
int pastCount = 0; |
| 253 | 253 |
List<TaxonBase> list; |
| ... | ... | |
| 1452 | 1452 |
/** |
| 1453 | 1453 |
* Returns the rank cache for the taxon name based on the names nomenclatural code. |
| 1454 | 1454 |
* You may not use this method for kingdoms other then Animalia, Plantae and Bacteria. |
| 1455 |
* @param taxonName |
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| 1456 |
* @return |
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*/ |
| 1458 | 1456 |
@SuppressWarnings("unused") //used by mapper
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| 1459 | 1457 |
private static String getRankCache(TaxonName taxonName, PesiExportState state) {
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| ... | ... | |
| 2081 | 2079 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
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| 2082 | 2080 |
* @return The Sources. |
| 2083 | 2081 |
*/ |
| 2084 |
private static Set<IdentifiableSource> getPesiSources(IdentifiableEntity identEntity) {
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Set<IdentifiableSource> sources = new java.util.HashSet<IdentifiableSource>();
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private static Set<IdentifiableSource> getPesiSources(IdentifiableEntity<?> identifiableEntity) {
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Set<IdentifiableSource> sources = new HashSet<>();
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| 2086 | 2084 |
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| 2087 | 2085 |
//Taxon Names |
| 2088 |
if (identEntity.isInstanceOf(TaxonName.class)){
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| 2086 |
if (identifiableEntity.isInstanceOf(TaxonName.class)){
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| 2089 | 2087 |
// Sources from TaxonName |
| 2090 |
TaxonName taxonName = CdmBase.deproxy(identEntity, TaxonName.class); |
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Set<IdentifiableSource> testSources = identEntity.getSources(); |
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| 2092 |
sources = filterPesiSources(identEntity.getSources()); |
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TaxonName taxonName = CdmBase.deproxy(identifiableEntity, TaxonName.class);
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| 2089 |
Set<IdentifiableSource> testSources = identifiableEntity.getSources();
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| 2090 |
sources = filterPesiSources(identifiableEntity.getSources());
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| 2093 | 2091 |
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| 2094 | 2092 |
if (sources.size() == 0 && testSources.size()>0){
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| 2095 | 2093 |
IdentifiableSource source = testSources.iterator().next(); |
| 2096 | 2094 |
logger.warn("There are sources, but they are no pesi sources!!!" + source.getIdInSource() + " - " + source.getIdNamespace() + " - " + source.getCitation().getTitleCache());
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| 2097 | 2095 |
} |
| 2098 | 2096 |
if (sources.size() > 1) {
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| 2099 |
logger.warn("This TaxonName has more than one Source: " + identEntity.getUuid() + " (" + identEntity.getTitleCache() + ")");
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logger.warn("This TaxonName has more than one Source: " + identifiableEntity.getUuid() + " (" + identifiableEntity.getTitleCache() + ")");
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| 2100 | 2098 |
} |
| 2101 | 2099 |
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| 2102 | 2100 |
// name has no PESI source, take sources from TaxonBase |
| ... | ... | |
| 2108 | 2106 |
} |
| 2109 | 2107 |
|
| 2110 | 2108 |
//for TaxonBases |
| 2111 |
}else if (identEntity.isInstanceOf(TaxonBase.class)){
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sources = filterPesiSources(identEntity.getSources()); |
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}else if (identifiableEntity.isInstanceOf(TaxonBase.class)){
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sources = filterPesiSources(identifiableEntity.getSources());
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| 2113 | 2111 |
} |
| 2114 | 2112 |
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| 2115 | 2113 |
/*TODO: deleted only for testing the inferred synonyms |
| ... | ... | |
| 2124 | 2122 |
|
| 2125 | 2123 |
// return all sources with a PESI reference |
| 2126 | 2124 |
private static Set<IdentifiableSource> filterPesiSources(Set<? extends IdentifiableSource> sources) {
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Set<IdentifiableSource> result = new HashSet<IdentifiableSource>();
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Set<IdentifiableSource> result = new HashSet<>(); |
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| 2128 | 2126 |
for (IdentifiableSource source : sources){
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| 2129 | 2127 |
Reference ref = source.getCitation(); |
| 2130 | 2128 |
UUID refUuid = ref.getUuid(); |
| ... | ... | |
| 2456 | 2454 |
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| 2457 | 2455 |
mapping.addMapper(MethodMapper.NewInstance("DerivedFromGuid", this));
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| 2458 | 2456 |
mapping.addMapper(MethodMapper.NewInstance("CacheCitation", this));
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| 2459 |
mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because Misallied Names are handled differently
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mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because Misapllied Names are handled differently
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| 2460 | 2458 |
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this));
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| 2461 | 2459 |
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| 2462 | 2460 |
// DisplayName |
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