/ - Diff - EDIT - EDIT Project Management

     				//Don't use (created bei Marc): DisplayName, NomRefCache
     				Integer id =( (Number)rs.getObject("RECORD NUMBER")).intValue();
     				Integer id = rs.getInt("RECORD NUMBER");
     				String preferredName = rs.getString("NAME OF FUNGUS");
     				if (StringUtils.isBlank(preferredName)){
-...
     				//author + publication
     				makeAuthorAndPublication(state, rs, name);
     				//source
     				//makeSource(state, taxon, id, NAMESPACE_GENERA );
     //				if (id != null){
     					makeSource(state, taxon, id.intValue(), NAMESPACE_GENERA );
     //				} else{
     //					makeSource(state, taxon, null,NAMESPACE_GENERA);
     //				}
     				makeSource(state, taxon, id.intValue(), NAMESPACE_GENERA );
     				getTaxonService().saveOrUpdate(taxon);
+    			}
     		} catch (Exception e) {
-...
+    	}
     	@Override
     	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
     		String nameSpace;
     //		Class<?> cdmClass;
     //		Set<String> idSet;
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
     	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(
     	        ResultSet rs, IndexFungorumImportState state) {
     	    Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
     		try{
     //			Set<String> taxonNameSet = new HashSet<>();
     			while (rs.next()){
     //				handleForeignKey(rs, taxonIdSet,"tu_accfinal" );
+    			}
     			//taxon map
     			nameSpace = NAMESPACE_SUPRAGENERIC_NAMES ;
     //			cdmClass = Taxon.class;
     //			idSet = taxonNameSet;
     		    String nameSpace = NAMESPACE_SUPRAGENERIC_NAMES ;
     			Map<String, TaxonBase<?>> taxonMap = new HashMap<>();
     			@SuppressWarnings("rawtypes")
                 List<TaxonBase> list = getTaxonService().listTaxaByName(Taxon.class, "*", null, null, null, "*", null, 1000000, null, null);
-...
     			referenceMap.put(SOURCE_REFERENCE, sourceReference);
     			result.put(NAMESPACE_REFERENCE, referenceMap);
     		} catch (SQLException e) {
     		} catch (Exception e) {
     			throw new RuntimeException(e);
+    		}
     		return result;

     import java.util.HashMap;
     import java.util.List;
     import java.util.Map;
     import java.util.Set;
     import org.apache.log4j.Logger;
     import org.springframework.stereotype.Component;
-...
+    					}
     					taxonFamily = makeTaxon(state, family, Rank.FAMILY());
     					if (taxonFamily != null){
     						try{
     					    try{
     							//if this shows a warning see single issue in #2826 about Glomerellaceae (which has 2 different parents)
     						    getClassification(state).addParentChild(higherTaxon, taxonFamily, null, null);
     						}catch(IllegalStateException e){
     							if (e.getMessage().startsWith("The child taxon is already part of the tree")){
     								//TaxonNode node = getClassification(state).getNode(taxonFamily);
     								logger.warn(e.getMessage() + taxonFamily.getTitleCache() + " " + higherTaxon.getTitleCache());
+    							}
+    						}
-...
     	@Override
     	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
     		String nameSpace;
     		Class<?> cdmClass;
     		Set<String> idSet;
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
     		try{
     //			Set<String> taxonNameSet = new HashSet<>();
     //			while (rs.next()){
     //				handleForeignKey(rs, taxonIdSet,"tu_accfinal" );
     //			}
     			//taxon map
     			nameSpace = IndexFungorumImportBase.NAMESPACE_SUPRAGENERIC_NAMES ;
     			cdmClass = TaxonBase.class;
     //			idSet = taxonNameSet;
     			Map<String, TaxonBase<?>> taxonMap = new HashMap<>();
     			List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null);
     			for (Taxon taxon : list){

     import java.sql.ResultSetMetaData;
     import java.sql.SQLException;
     import java.util.HashMap;
     import java.util.HashSet;
     import java.util.Map;
     import java.util.Set;
     import java.util.UUID;
-...
      * @author a.mueller
      * @since 27.02.2012
      */
     public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungorumImportConfigurator, IndexFungorumImportState> implements ICdmIO<IndexFungorumImportState>, IPartitionedIO<IndexFungorumImportState> {
     public abstract class IndexFungorumImportBase
             extends CdmImportBase<IndexFungorumImportConfigurator, IndexFungorumImportState>
             implements ICdmIO<IndexFungorumImportState>, IPartitionedIO<IndexFungorumImportState> {
         private static final long serialVersionUID = -729872543287390949L;
         private static final Logger logger = Logger.getLogger(IndexFungorumImportBase.class);
-...
         @Override
         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, IndexFungorumImportState state) {
             boolean success = true ;
     		Set<CdmBase> objectsToSave = new HashSet<>();
     // 		DbImportMapping<?, ?> mapping = getMapping();
     //		mapping.initialize(state, cdmTargetClass);
     		ResultSet rs = partitioner.getResultSet();
     		try{
     			while (rs.next()){
     //				success &= mapping.invoke(rs,objectsToSave);
+    			}
     		} catch (SQLException e) {
     			logger.error("SQLException:" +  e);
     			return false;
+    		}
     		partitioner.startDoSave();
     		getCommonService().save(objectsToSave);
     		return success;
             //should be overridden by subclasses if used
     		return true;
+    	}
     	protected abstract String getRecordQuery(IndexFungorumImportConfigurator config);
-...
     	/**
     	 * Returns true if i is a multiple of recordsPerTransaction
     	 * @param i
     	 * @param recordsPerTransaction
     	 * @return
     	 */
     	protected boolean loopNeedsHandling(int i, int recordsPerLoop) {
     		startTransaction();
-...
+    		}
     		ref.setVolume(volume);
     		//year   //TODO why yearOfPubl 2x exact same value
     		//year
     		String yearOfPubl = rs.getString("YEAR OF PUBLICATION");
     		String yearOnPubl = rs.getString("YEAR ON PUBLICATION");
     		String year = null;
-...
     			ref.setDatePublished(TimePeriodParser.parseStringVerbatim(year));
+    		}
     		//preliminary, set protected titlecache as Generic Cache Generation with in references currently doesn't fully work yet
     		//TODO preliminary, set protected titlecache as generic cache generation with in-references currently doesn't fully work yet
     		String titleCache = CdmUtils.concat(", ", pubAuthorStr, title);
     		if  ( StringUtils.isNotBlank(pubAuthorStr)){
     		if  (isNotBlank(pubAuthorStr)){
     			titleCache = "in " + titleCache;
+    		}
     		titleCache = CdmUtils.concat(" ", titleCache, volume);

     				//DisplayName, NomRefCache -> don't use, created by Marc
     				Integer id = (Integer)rs.getObject("PreferredNameIFnumber");
     				Integer id = rs.getInt("PreferredNameIFnumber");
     				String phylumName = rs.getString("Phylum name");
     				String preferredName = rs.getString("PreferredName");
-...
     				//save
     				getTaxonService().saveOrUpdate(taxon);
+    			}
     		} catch (Exception e) {
     			e.printStackTrace();

     public class IndexFungorumSubSpeciesImport extends IndexFungorumImportBase {
         private static final long serialVersionUID = -2877755674188760685L;
         private static final Logger logger = Logger.getLogger(IndexFungorumSpeciesImport.class);
         private static final Logger logger = Logger.getLogger(IndexFungorumSubSpeciesImport.class);
     	private static final String pluralString = "subSpecies";
-...
                 TaxonName name = infraspecificTaxon.getName();
     //            getNameService().saveOrUpdate(name);
                 String parentNameString = getParentNameInfraSpecific(name);
     //            System.out.println("Parent name string: " + parentNameString);
                 MatchingTaxonConfigurator matchingConfig = new MatchingTaxonConfigurator();
                 matchingConfig.setTaxonNameTitle(parentNameString);

     		String strRecordQuery =
     			" SELECT * " +
     			" FROM [tblSupragenericNames] " +
     //			" WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";
     			"";
     		return strRecordQuery;
+    	}
-...
     	protected void doInvoke(IndexFungorumImportState state) {
     	    logger.info("Start supra genera ...");
     		//handle source reference first
     	    //handle source reference first
     		Reference sourceReference = state.getConfig().getSourceReference();
     		getReferenceService().save(sourceReference);
-...
     				//Don't use (created by Marc): DisplayName, NomRefCache
     				Integer id = ((Number)rs.getObject(COL_RECORD_NUMBER)).intValue();
     				Integer id = rs.getInt(COL_RECORD_NUMBER);
     				String supragenericNames = rs.getString(SUPRAGENERIC_NAMES);
     				//String preferredName = rs.getString("PreferredName");
     				Integer rankFk = rs.getInt("PESI_RankFk");
     				//name
     				Rank rank = state.getTransformer().getRankByKey(String.valueOf(rankFk));
     				TaxonName name = TaxonNameFactory.NewBotanicalInstance(rank);
     				name.setGenusOrUninomial(supragenericNames);
     				/*if (preferredName != null && !preferredName.equals(supragenericNames)){
     					logger.warn("Suprageneric names and preferredName is not equal. This case is not yet handled by IF import. I take SupragenericNames for import. RECORD NUMBER" +id);
     				}*/
     				//taxon
     				Taxon taxon = Taxon.NewInstance(name, sourceReference);
     				//author + nom.ref.
     				makeAuthorAndPublication(state, rs, name);
     				//source
     //				if (id != null){
     					makeSource(state, taxon, id.intValue(), NAMESPACE_SUPRAGENERIC_NAMES );
     //				} else{
     //					makeSource(state, taxon, null, NAMESPACE_SUPRAGENERIC_NAMES);
     //				}
     				makeSource(state, taxon, id, NAMESPACE_SUPRAGENERIC_NAMES );
     				getTaxonService().saveOrUpdate(taxon);
+    			}
     		} catch (Exception e) {

Project

General

Profile

EDIT

Revision 8fb964f0

Added by Andreas Müller over 4 years ago