Revision e1d0f581
Added by Andreas Müller over 5 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonImport.java | ||
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*/ |
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@Component |
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public class BerlinModelTaxonImport extends BerlinModelImportBase {
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/** |
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* |
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*/ |
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private static final String LAST_SCRUTINY_FK = "lastScrutinyFk"; |
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private static final long serialVersionUID = -1186364983750790695L; |
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonImport.class); |
| ... | ... | |
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String sqlFrom = " FROM PTaxon pt "; |
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if (config.isEuroMed()){
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sqlFrom = " FROM PTaxon AS pt " + |
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" INNER JOIN v_cdm_exp_taxaAll AS em ON pt.RIdentifier = em.RIdentifier " + |
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" LEFT OUTER JOIN Reference r ON pt.LastScrutinyFk = r.RefId "; |
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sqlSelect += " , em.MA, r.RefCache as LastScrutiny "; |
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" INNER JOIN v_cdm_exp_taxaAll AS em ON pt.RIdentifier = em.RIdentifier "; |
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if (!config.isUseLastScrutinyAsSec()){
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sqlFrom += " LEFT OUTER JOIN Reference r ON pt.LastScrutinyFk = r.RefId "; |
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} |
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sqlSelect += " , em.MA "; |
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if (!config.isUseLastScrutinyAsSec()){
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sqlSelect += ", r.RefCache as LastScrutiny "; |
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} |
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} |
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|
| ... | ... | |
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uuid = rs.getString("UUID");
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} |
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TaxonName taxonName = null; |
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taxonName = taxonNameMap.get(String.valueOf(nameFk)); |
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Reference reference = null; |
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String refFk = String.valueOf(refFkInt); |
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reference = refMap.get(refFk); |
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String refFkStr = String.valueOf(refFkInt); |
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reference = refMap.get(refFkStr); |
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Reference lastScrutinyRef = null; |
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if (state.getConfig().isUseLastScrutinyAsSec() && resultSetHasColumn(rs,LAST_SCRUTINY_FK)){
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Integer lastScrutinyFk = nullSafeInt(rs,LAST_SCRUTINY_FK); |
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if (lastScrutinyFk != null){
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String lastScrutinyFkStr = String.valueOf(lastScrutinyFk); |
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if (lastScrutinyFkStr != null){
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lastScrutinyRef = refMap.get(lastScrutinyFkStr); |
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if (lastScrutinyRef == null){
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logger.warn("Last scrutiny reference "+lastScrutinyFkStr+" could not be found "
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+ "for taxon " + taxonId); |
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} |
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if(!StringUtils.right(refFkStr, 5).equals("00000")){
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logger.warn("Unexpected secFk " + refFkStr + " for taxon with last scrutiny. Taxon id " + taxonId);
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} |
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} |
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} |
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} |
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if(! config.isIgnoreNull()){
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if (taxonName == null ){
|
| ... | ... | |
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success = false; |
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continue; //next taxon |
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}else if (reference == null ){
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logger.warn("Reference belonging to taxon could not be found in store. Taxon will not be imported");
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logger.warn("Sec Reference belonging to taxon could not be found in store. Taxon will not be imported");
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success = false; |
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continue; //next taxon |
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} |
| ... | ... | |
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TaxonBase<?> taxonBase; |
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Synonym synonym; |
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Taxon taxon; |
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Reference sec = lastScrutinyRef != null? lastScrutinyRef: reference; |
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try {
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logger.debug(statusFk); |
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if (statusFk == T_STATUS_ACCEPTED || statusFk == T_STATUS_UNRESOLVED |
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|| statusFk == T_STATUS_PRO_PARTE_SYN || statusFk == T_STATUS_PARTIAL_SYN ){
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taxon = Taxon.NewInstance(taxonName, reference);
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taxon = Taxon.NewInstance(taxonName, sec);
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taxonBase = taxon; |
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if (statusFk == T_STATUS_UNRESOLVED){
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taxon.setTaxonStatusUnknown(true); |
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} |
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//TODO marker for pp and partial? |
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}else if (statusFk == T_STATUS_SYNONYM ){
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synonym = Synonym.NewInstance(taxonName, reference);
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synonym = Synonym.NewInstance(taxonName, sec);
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taxonBase = synonym; |
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// if (statusFk == T_STATUS_PRO_PARTE_SYN){
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// synonym.setProParte(true); |
| ... | ... | |
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} |
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} |
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// |
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if (resultSetHasColumn(rs, "LastScrutiny")){
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// does not exist anymore as we use last scrutiny now as sec ref
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if (!state.getConfig().isUseLastScrutinyAsSec() && resultSetHasColumn(rs, "LastScrutiny")){
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String lastScrutiny = rs.getString("LastScrutiny");
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//TODO strange, why not Extension last scrutiny? To match PESI? Is there a difference |
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//to LastScrutinyFK and SpeciesExpertFK? |
| ... | ... | |
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while (rs.next()){
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handleForeignKey(rs, nameIdSet, "PTNameFk"); |
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handleForeignKey(rs, referenceIdSet, "PTRefFk"); |
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if (state.getConfig().isUseLastScrutinyAsSec() && resultSetHasColumn(rs, LAST_SCRUTINY_FK)){
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handleForeignKey(rs, referenceIdSet, LAST_SCRUTINY_FK); |
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} |
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} |
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//name map |
| ... | ... | |
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return ! state.getConfig().isDoTaxa(); |
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} |
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} |
Also available in: Unified diff
ref #3992, ref #7713, ref #3990 Atomize last scrutiny references