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Revision d2c73605

Added by Katja Luther almost 12 years ago

ID d2c736053103cc75f24d17713a66cbae10bcbce6
Parent aa125d85
Child 1c7c3662

     		while ((list = getNextTaxonPartition(Taxon.class, limit, partitionCount++, propPath )) != null   ) {
     			logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");
     			logger.warn("Start snapshot, beginning of loop, fetched " + list.size() + " " + pluralString);
     			if (partitionCount % 10 == 0){
     				logger.warn("Start snapshot, beginning of loop, fetched " + list.size() + " " + pluralString);
     				ProfilerController.memorySnapshot();
+    			}
     			for (Taxon taxon : list) {

     			if (! isPesiTaxon(taxonBase)){
     				it.remove();
+    			}
     			taxonBase = null;
+    		}
     		return list;
-...
     			SynonymRelationship synRel = CdmBase.deproxy(rel, SynonymRelationship.class);
     			taxonBase = synRel.getSynonym();
     			taxon = synRel.getAcceptedTaxon();
     			synRel = null;
     		}else if (rel.isInstanceOf(TaxonRelationship.class)){
     			TaxonRelationship taxRel = CdmBase.deproxy(rel, TaxonRelationship.class);
     			taxonBase = taxRel.getFromTaxon();
     			taxon = taxRel.getToTaxon();
     			taxRel = null;
     		}else{
     			logger.warn ("Only synonym - and taxon-relationships alowed here");
     			return false;
-...
     			Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
     			for (Marker marker : taxon.getMarkers()){
     				if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){
     					taxon = null;
     					return false;
     				//probably not needed any more after #2786 was fixed
     				}else if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){
     					logger.warn("Misapplied common name still exists");
     					taxon = null;
     					return false;
+    				}
-...
     			if (! taxon.isMisapplication()){
     				for (Marker marker : taxon.getMarkers()){
     					if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){
     						taxon = null;
     						return false;
+    					}
+    				}
-...
     			//handle misapplied names
     			}else{
     				if (excludeMisappliedNames){
     					taxon = null;
     					return false;
+    				}
     				for (Marker marker : taxon.getMarkers()){
     					//probably not needed any more after #2786 was fixed
     					if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){
     						logger.warn("Misapplied common name still exists");
     						taxon = null;
     						return false;
+    					}
+    				}
-...
     					if (taxRel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
     //						logger.warn(taxRel.getUuid() + "; " + taxRel.getToTaxon().getUuid() + " + " + taxRel.getToTaxon().getTitleCache());
     						if (isPesiTaxon(taxRel.getToTaxon(), true)){
     							taxon = null;
     							return true;
+    						}
+    					}
+    				}
     				if (logger.isDebugEnabled()){ logger.debug("Misapplied name has no accepted PESI taxon: " +  taxon.getUuid() + ", (" +  taxon.getTitleCache() + ")");}
     				taxon = null;
     				return false;
+    			}
     		//handle synonyms
-...
+    				}
+    			}
     			if (!hasAcceptedPesiTaxon) {if (logger.isDebugEnabled()){logger.debug("Synonym has no accepted PESI taxon: " +  synonym.getUuid() + ", (" +  synonym.getTitleCache() + ")");}}
     			synonym = null;
     			return hasAcceptedPesiTaxon;
     		}else {
     			throw new RuntimeException("Unknown taxon base type: " + taxonBase.getClass());
-...
     	static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {
     	protected static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {
     		NonViralNameDefaultCacheStrategy cacheStrategy;
     		if (taxonName.isInstanceOf(ZoologicalName.class)){
     			cacheStrategy = zooNameStrategy;

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiRelTaxonExport.java
215	215	}
216	216	list = null;
217	217	logger.info("End PHASE 2: Name Relationships ...");
218
	218	state.setCurrentFromObject(null);
	219	state.setCurrentToObject(null);
219	220	return success;
220	221	}
221	222
...	...
421	422	// SynonymNameRelationship
422	423	success &= saveNameRelationships(state, synonym);
423	424	}
	425	state.setCurrentFromObject(null);
424	426	return success;
425	427	}
426	428
...	...
439	441	state.setCurrentToObject(taxonBase);
440	442	isFrom = false;
441	443	success &= saveOneSideNameRelation(state, isFrom, nameRelations);
442
	444	state.setCurrentToObject(null);
443	445	return success;
444	446	}
445	447
...	...
474	476	doCount(count++, modCount, pluralString);
475	477	success &= mapping.invoke(nameRelation);
476	478	}
	479	state.setCurrentFromObject(null);
	480	state.setCurrentToObject(null);
477	481	return success;
478	482	}
479	483

     import org.springframework.stereotype.Component;
     import org.springframework.transaction.TransactionStatus;
     import com.yourkit.api.Controller;
     import eu.etaxonomy.cdm.api.service.TaxonServiceImpl;
     import eu.etaxonomy.cdm.common.CdmUtils;
     import eu.etaxonomy.cdm.io.common.Source;
-...
     		logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
     		int partitionCount = 0;
     		while ((list = getNextTaxonPartition(null, limit, partitionCount++, null)) != null   ) {
     		logger.warn("Taking snapshot at the beginning of phase 1 of taxonExport");
     		ProfilerController.memorySnapshot();
     		while ((list = getNextTaxonPartition(null, limit, partitionCount++, null)) != null   ) {
     			logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");
     			for (TaxonBase<?> taxon : list) {
     				doCount(count++, modCount, pluralString);
-...
     				validatePhaseOne(taxon, nvn);
     				taxon = null;
     				nvn = null;
     				taxonName = null;
+    			}
     			// Commit transaction
     			commitTransaction(txStatus);
     			logger.debug("Committed transaction.");
     			logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
     			pastCount = count;
     			/*logger.warn("Taking snapshot at the end of the loop of phase 1 of taxonExport");
     			ProfilerController.memorySnapshot();
     			*/
     			// Start transaction
     			txStatus = startTransaction(true);
     			logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
-...
+    		}
     		logger.warn("Taking snapshot at the end of phase 1 of taxonExport");
     		ProfilerController.memorySnapshot();
     		// Commit transaction
     		commitTransaction(txStatus);
     		txStatus = null;
     		logger.debug("Committed transaction.");
     		list = null;
     		logger.warn("Taking snapshot at the end of phase 1 of taxonExport");
     		ProfilerController.memorySnapshot();
     		return success;
+    	}
-...
+    		}
     		list = null;
     		logger.warn("Taking snapshot at the end of phase 3 of taxonExport");
     		ProfilerController.memorySnapshot();
     		// Commit transaction
     		commitTransaction(txStatus);
     		logger.debug("Committed transaction.");
     		logger.warn("Taking snapshot at the end of phase 3 of taxonExport, number of partitions: " + partitionCount);
     		ProfilerController.memorySnapshot();
     		return success;
+    	}
-...
     		String inferredSynonymPluralString = "Inferred Synonyms";
     		// Start transaction
     		Taxon acceptedTaxon = null;
     		TransactionStatus txStatus = startTransaction(true);
     		logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
     		List<TaxonBase> taxonList = null;
-...
     			logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
     			inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,
     					synRelMapping, taxonList,
     					inferredSynonymsDataToBeSaved));
     					synRelMapping, taxonList));
     			doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);
     			// Commit transaction
-...
     			logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
     			inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,
     					synRelMapping, taxonList,
     					inferredSynonymsDataToBeSaved));
     					synRelMapping, taxonList));
+    			;
     			doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);
     			// Commit transaction
-...
     	 */
     	private HashMap<Integer, TaxonNameBase<?, ?>> createInferredSynonymsForTaxonList(PesiExportState state,
     			PesiExportMapping mapping, PesiExportMapping synRelMapping,
     			 List<TaxonBase> taxonList,
     			HashMap<Integer, TaxonNameBase<?, ?>> inferredSynonymsDataToBeSaved) {
     			 List<TaxonBase> taxonList) {
     		Taxon acceptedTaxon;
     		Classification classification = null;
     		List<Synonym> inferredSynonyms = null;
     		boolean localSuccess = true;
     		HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
     		for (TaxonBase<?> taxonBase : taxonList) {
     			if (taxonBase.isInstanceOf(Taxon.class)) { // this should always be the case since we should have fetched accepted taxon only, but you never know...
-...
+    										}
+    									}
     									// Add Rank Data and KingdomFk to hashmap for later saving
     									inferredSynonymsDataToBeSaved.put(synonym.getId(), synonym.getName());
+    								}
+    							}
-...
     			NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
     			String result = cacheStrategy.getFullTitleCache(nvn, tagRules);
     			cacheStrategy = null;
     			nvn = null;
     			return result.replaceAll("\\<@status@\\>.*\\</@status@\\>", "");
+    		}
+    	}
-...
     			HTMLTagRules tagRules = new HTMLTagRules().addRule(TagEnum.name, "i");
     			NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
     			return cacheStrategy.getTitleCache(nvn, tagRules);
     			String result = cacheStrategy.getTitleCache(nvn, tagRules);
     			cacheStrategy = null;
     			nvn = null;
     			return result;
+    		}
+    	}
-...
     		NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
     		NonViralNameDefaultCacheStrategy strategy = getCacheStrategy(nvn);
     		String result = strategy.getNameCache(nvn);
     		strategy = null;
     		nvn = null;
     		return result;
+    	}
-...
     				if (isMisappliedName(taxon)){
     					result = result + " " + getAuthorString(taxon);
+    				}
     				taxon = null;
+    			}
+    		}
     		taxa = null;
     		nvn = null;
     		return result;
+    	}
-...
+    			}
     		} catch (Exception e) {
     			e.printStackTrace();
     			logger.error("An error occurs while creating idInSource..." + taxonName.getUuid() + " (" + taxonName.getTitleCache()+ e.getMessage());
+    		}
     		if (result == null) {
-...
+    	}
     	private static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {
     	protected static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {
     		taxonName = CdmBase.deproxy(taxonName, TaxonNameBase.class);
     		NonViralNameDefaultCacheStrategy<?> cacheStrategy;
     		if (taxonName.isInstanceOf(ZoologicalName.class)){

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Revision d2c73605

Added by Katja Luther almost 12 years ago