-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy \r
-* http://www.e-taxonomy.eu\r
-* \r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-\r
-package eu.etaxonomy.cdm.io.berlinModel.in;\r
-\r
-import java.net.URI;\r
-import java.sql.ResultSet;\r
-import java.sql.SQLException;\r
-import java.util.ArrayList;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Map;\r
-import java.util.Set;\r
-import java.util.UUID;\r
-\r
-import org.apache.commons.lang.StringUtils;\r
-import org.apache.log4j.Logger;\r
-import org.springframework.stereotype.Component;\r
-import org.springframework.transaction.TransactionStatus;\r
-\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
-import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceImportValidator;\r
-import eu.etaxonomy.cdm.io.common.IOValidator;\r
-import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;\r
-import eu.etaxonomy.cdm.io.common.Source;\r
-import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;\r
-import eu.etaxonomy.cdm.model.common.Annotation;\r
-import eu.etaxonomy.cdm.model.common.AnnotationType;\r
-import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.ExtensionType;\r
-import eu.etaxonomy.cdm.model.common.Language;\r
-import eu.etaxonomy.cdm.model.common.Marker;\r
-import eu.etaxonomy.cdm.model.common.MarkerType;\r
-import eu.etaxonomy.cdm.model.common.OriginalSourceType;\r
-import eu.etaxonomy.cdm.model.common.TermType;\r
-import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
-import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
-import eu.etaxonomy.cdm.model.description.Distribution;\r
-import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;\r
-import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
-import eu.etaxonomy.cdm.model.location.NamedArea;\r
-import eu.etaxonomy.cdm.model.location.NamedAreaLevel;\r
-import eu.etaxonomy.cdm.model.location.NamedAreaType;\r
-import eu.etaxonomy.cdm.model.reference.Reference;\r
-import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
-import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- * @created 20.03.2008\r
- */\r
-@Component\r
-public class BerlinModelOccurrenceImport extends BerlinModelImportBase {\r
- private static final String EM_AREA_NAMESPACE = "emArea";\r
-\r
- private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceImport.class);\r
-\r
- public static final String NAMESPACE = "Occurrence";\r
- \r
- \r
- private static int modCount = 5000;\r
- private static final String pluralString = "occurrences";\r
- private static final String dbTableName = "emOccurrence"; //??\r
-\r
-\r
- public BerlinModelOccurrenceImport(){\r
- super(dbTableName, pluralString);\r
- }\r
- \r
- @Override\r
- protected String getIdQuery(BerlinModelImportState state) {\r
- String result = " SELECT occurrenceId FROM " + getTableName();\r
- if (StringUtils.isNotBlank(state.getConfig().getOccurrenceFilter())){\r
- result += " WHERE " + state.getConfig().getOccurrenceFilter(); \r
- } \r
- return result;\r
- }\r
-\r
- @Override\r
- protected String getRecordQuery(BerlinModelImportConfigurator config) {\r
- String emCode = config.isIncludesAreaEmCode()? ", emArea.EMCode" : "";\r
- String strQuery = //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution \r
- " SELECT DISTINCT PTaxon.RIdentifier AS taxonId, emOccurrence.OccurrenceId, emOccurrence.Native, emOccurrence.Introduced, " +\r
- " emOccurrence.Cultivated, emOccurrence.Notes occNotes, " +\r
- " emOccurSumCat.emOccurSumCatId, emOccurSumCat.Short, emOccurSumCat.Description, " + \r
- " emOccurSumCat.OutputCode, emArea.AreaId, emArea.TDWGCode " + emCode + \r
- " FROM emOccurrence INNER JOIN " + \r
- " emArea ON emOccurrence.AreaFk = emArea.AreaId INNER JOIN " + \r
- " PTaxon ON emOccurrence.PTNameFk = PTaxon.PTNameFk AND emOccurrence.PTRefFk = PTaxon.PTRefFk LEFT OUTER JOIN " + \r
- " emOccurSumCat ON emOccurrence.SummaryStatus = emOccurSumCat.emOccurSumCatId LEFT OUTER JOIN " + \r
- " emOccurrenceSource ON emOccurrence.OccurrenceId = emOccurrenceSource.OccurrenceFk " + \r
- " WHERE (emOccurrence.OccurrenceId IN (" + ID_LIST_TOKEN + ") )" + \r
- " ORDER BY PTaxon.RIdentifier";\r
- return strQuery;\r
- }\r
-\r
- private Map<Integer, NamedArea> euroMedAreas = new HashMap<Integer, NamedArea>();\r
- \r
- \r
- @Override\r
- public void doInvoke(BerlinModelImportState state) {\r
- if (state.getConfig().isUseEmAreaVocabulary()){\r
- try {\r
- createEuroMedAreas(state);\r
- } catch (Exception e) {\r
- logger.error("Exception occurred when trying to create euroMed Areas");\r
- e.printStackTrace();\r
- state.setSuccess(false);\r
- }\r
- }\r
- super.doInvoke(state);\r
- //reset\r
- euroMedAreas = new HashMap<Integer, NamedArea>();\r
- }\r
- \r
- private TermVocabulary<NamedArea> createEuroMedAreas(BerlinModelImportState state) throws SQLException {\r
- logger.warn("Start creating E+M areas");\r
- Source source = state.getConfig().getSource();\r
- Reference<?> sourceReference = state.getConfig().getSourceReference();\r
- \r
- TransactionStatus txStatus = this.startTransaction();\r
- \r
- sourceReference = getSourceReference(sourceReference);\r
- \r
- TermVocabulary<NamedArea> euroMedAreas = makeEmptyEuroMedVocabulary();\r
- \r
- MarkerType eurMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurArea, "eur", "eur Area", "eur");\r
- MarkerType euroMedAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurMedArea, "EuroMedArea", "EuroMedArea", "EuroMedArea");\r
- ExtensionType isoCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidIsoCode, "IsoCode", "IsoCode", "iso");\r
- ExtensionType tdwgCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidTdwgAreaCode, "TDWG code", "TDWG Area code", "tdwg");\r
- ExtensionType mclCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidMclCode, "MCL code", "MedCheckList code", "mcl");\r
- NamedAreaLevel areaLevelTop = getNamedAreaLevel(state, BerlinModelTransformer.uuidAreaLevelTop, "Euro+Med top area level", "Euro+Med top area level. This level is only to be used for the area representing the complete Euro+Med area", "e+m top", null);\r
- NamedAreaLevel areaLevelEm1 = getNamedAreaLevel(state, BerlinModelTransformer.uuidAreaLevelFirst, "Euro+Med 1. area level", "Euro+Med 1. area level", "e+m 1.", null);\r
- NamedAreaLevel areaLevelEm2 = getNamedAreaLevel(state, BerlinModelTransformer.uuidAreaLevelSecond, "Euro+Med 2. area level", "Euro+Med 2. area level", "Euro+Med 1. area level", null);\r
- \r
- \r
- String sql = "SELECT * , CASE WHEN EMCode = 'EM' THEN 'a' ELSE 'b' END as isEM " +\r
- " FROM emArea " +\r
- " ORDER BY isEM, EMCode"; \r
- ResultSet rs = source.getResultSet(sql);\r
- \r
- NamedArea euroMedArea = null;\r
- NamedArea lastLevel2Area = null;\r
- \r
- //euroMedArea (EMCode = 'EM')\r
- rs.next();\r
- euroMedArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType, isoCodeExtType, tdwgCodeExtType, mclCodeExtType, \r
- areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel2Area);\r
- euroMedAreas.addTerm(euroMedArea);\r
- \r
- //all other areas\r
- while (rs.next()){\r
- NamedArea newArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType,\r
- isoCodeExtType, tdwgCodeExtType, mclCodeExtType, \r
- areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel2Area);\r
- euroMedAreas.addTerm(newArea);\r
- if (newArea.getPartOf().equals(euroMedArea)){\r
- lastLevel2Area = newArea;\r
- }\r
- getVocabularyService().saveOrUpdate(euroMedAreas);\r
- } \r
- \r
- commitTransaction(txStatus);\r
- logger.warn("Created E+M areas");\r
- \r
- return euroMedAreas;\r
- }\r
-\r
- /**\r
- * @param sourceReference\r
- * @return\r
- */\r
- private Reference<?> getSourceReference(Reference<?> sourceReference) {\r
- Reference<?> persistentSourceReference = getReferenceService().find(sourceReference.getUuid()); //just to be sure\r
- if (persistentSourceReference != null){\r
- sourceReference = persistentSourceReference;\r
- }\r
- return sourceReference;\r
- }\r
-\r
- /**\r
- * @param eurMarkerType\r
- * @param euroMedAreaMarkerType\r
- * @param isoCodeExtType\r
- * @param tdwgCodeExtType\r
- * @param mclCodeExtType\r
- * @param rs\r
- * @param areaLevelEm2 \r
- * @param areaLevelEm1 \r
- * @param areaLevelTop \r
- * @throws SQLException\r
- */\r
- private NamedArea makeSingleEuroMedArea(ResultSet rs, MarkerType eurMarkerType,\r
- MarkerType euroMedAreaMarkerType, ExtensionType isoCodeExtType,\r
- ExtensionType tdwgCodeExtType, ExtensionType mclCodeExtType,\r
- NamedAreaLevel areaLevelTop, NamedAreaLevel areaLevelEm1, NamedAreaLevel areaLevelEm2, \r
- Reference<?> sourceReference, NamedArea euroMedArea, NamedArea level2Area) throws SQLException {\r
- Integer areaId = rs.getInt("AreaId");\r
- String emCode = nullSafeTrim(rs.getString("EMCode"));\r
- String isoCode = nullSafeTrim(rs.getString("ISOCode"));\r
- String tdwgCode = nullSafeTrim(rs.getString("TDWGCode"));\r
- String unit = nullSafeTrim(rs.getString("Unit"));\r
-// ,[Status]\r
-// ,[OutputOrder]\r
- boolean eurMarker = rs.getBoolean("eur");\r
- boolean euroMedAreaMarker = rs.getBoolean("EuroMedArea");\r
- String notes = nullSafeTrim(rs.getString("Notes"));\r
- String mclCode = nullSafeTrim(rs.getString("MCLCode"));\r
- String geoSearch = nullSafeTrim(rs.getString("NameForGeoSearch"));\r
- \r
- if (isBlank(emCode)){\r
- emCode = unit;\r
- }\r
- \r
- //uuid\r
- UUID uuid = BerlinModelTransformer.getEMAreaUuid(emCode);\r
- NamedArea area = (NamedArea)getTermService().find(uuid);\r
- if (area == null){\r
- //label\r
- area = NamedArea.NewInstance(geoSearch, unit, emCode);\r
- if (uuid != null){\r
- area.setUuid(uuid);\r
- }else{\r
- logger.warn("Uuuid for emCode could not be defined: " + emCode);\r
- }\r
- }\r
- \r
- \r
- //code\r
- area.setIdInVocabulary(emCode);\r
- //notes\r
- if (StringUtils.isNotEmpty(notes)){\r
- area.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT()));\r
- }\r
- //markers\r
- area.addMarker(Marker.NewInstance(eurMarkerType, eurMarker));\r
- area.addMarker(Marker.NewInstance(euroMedAreaMarkerType, euroMedAreaMarker));\r
- \r
- //extensions\r
- if (isNotBlank(isoCode)){\r
- area.addExtension(isoCode, isoCodeExtType);\r
- }\r
- if (isNotBlank(tdwgCode)){\r
- area.addExtension(tdwgCode, tdwgCodeExtType);\r
- }\r
- if (isNotBlank(mclCode)){\r
- area.addExtension(mclCode, mclCodeExtType);\r
- }\r
- \r
- //type\r
- area.setType(NamedAreaType.ADMINISTRATION_AREA());\r
- \r
- //source\r
- area.addSource(OriginalSourceType.Import, String.valueOf(areaId), EM_AREA_NAMESPACE, sourceReference, null);\r
- \r
- //parent\r
- if (euroMedArea != null){\r
- if (emCode.contains("(")){\r
- area.setPartOf(level2Area);\r
- area.setLevel(areaLevelEm2);\r
- }else{\r
- area.setPartOf(euroMedArea);\r
- area.setLevel(areaLevelEm1);\r
- }\r
- }else{\r
- area.setLevel(areaLevelTop);\r
- }\r
- this.euroMedAreas.put(areaId, area);\r
- \r
- //save\r
- getTermService().saveOrUpdate(area);\r
- \r
- return area;\r
- }\r
-\r
- private String nullSafeTrim(String string) {\r
- if (string == null){\r
- return null;\r
- }else{\r
- return string.trim();\r
- }\r
- }\r
-\r
- /**\r
- * \r
- */\r
- private TermVocabulary<NamedArea> makeEmptyEuroMedVocabulary() {\r
- TermType type = TermType.NamedArea;\r
- String description = "Euro+Med area vocabulary";\r
- String label = "E+M areas";\r
- String abbrev = null;\r
- URI termSourceUri = null;\r
- TermVocabulary<NamedArea> result = TermVocabulary.NewInstance(type, description, label, abbrev, termSourceUri);\r
- getVocabularyService().save(result);\r
- return result;\r
- }\r
-\r
- @Override\r
- public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {\r
- boolean success = true;\r
- Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();\r
- \r
- Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);\r
- \r
- ResultSet rs = partitioner.getResultSet();\r
-\r
- try {\r
- //map to store the mapping of duplicate berlin model occurrences to their real distributions\r
- //duplicated may occur due to area mappings from BM areas to TDWG areas\r
- Map<Integer, String> duplicateMap = new HashMap<Integer, String>();\r
- int oldTaxonId = -1;\r
- TaxonDescription oldDescription = null;\r
- int i = 0;\r
- int countDescriptions = 0;\r
- int countDistributions = 0;\r
- int countDuplicates = 0;\r
- //for each reference\r
- while (rs.next()){\r
- \r
- if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Facts handled: " + (i-1));}\r
- \r
- int occurrenceId = rs.getInt("OccurrenceId");\r
- int newTaxonId = rs.getInt("taxonId");\r
- String notes = nullSafeTrim(rs.getString("occNotes"));\r
- \r
- Integer emStatusId = nullSafeInt(rs, "emOccurSumCatId");\r
- \r
- try {\r
- //status\r
- PresenceAbsenceTerm status = null;\r
- String alternativeStatusString = null;\r
- if (emStatusId != null){\r
- status = BerlinModelTransformer.occStatus2PresenceAbsence(emStatusId);\r
- }else{\r
- String[] stringArray = new String[]{rs.getString("Native"), rs.getString("Introduced"), rs.getString("Cultivated")};\r
- alternativeStatusString = CdmUtils.concat(",", stringArray);\r
- }\r
- \r
- Reference<?> sourceRef = state.getTransactionalSourceReference();\r
- \r
- List<NamedArea> areas = makeAreaList(state, rs, occurrenceId);\r
- \r
- //create description(elements)\r
- TaxonDescription taxonDescription = getTaxonDescription(newTaxonId, oldTaxonId, oldDescription, taxonMap, occurrenceId, sourceRef);\r
- for (NamedArea area : areas){\r
- Distribution distribution = Distribution.NewInstance(area, status);\r
- if (status == null){\r
- AnnotationType annotationType = AnnotationType.EDITORIAL();\r
- Annotation annotation = Annotation.NewInstance(alternativeStatusString, annotationType, null);\r
- distribution.addAnnotation(annotation);\r
- distribution.addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));\r
- }\r
-// distribution.setCitation(sourceRef);\r
- if (taxonDescription != null) { \r
- Distribution duplicate = checkIsNoDuplicate(taxonDescription, distribution, duplicateMap , occurrenceId);\r
- if (duplicate == null){\r
- taxonDescription.addElement(distribution); \r
- distribution.addImportSource(String.valueOf(occurrenceId), NAMESPACE, state.getTransactionalSourceReference(), null);\r
- countDistributions++; \r
- if (taxonDescription != oldDescription){ \r
- taxaToSave.add(taxonDescription.getTaxon()); \r
- oldDescription = taxonDescription; \r
- countDescriptions++; \r
- } \r
- }else{ \r
- countDuplicates++;\r
- duplicate.addImportSource(String.valueOf(occurrenceId), NAMESPACE, state.getTransactionalSourceReference(), null);\r
- logger.info("Distribution is duplicate"); }\r
- } else { \r
- logger.warn("Distribution " + area.getLabel() + " ignored. OccurrenceId = " + occurrenceId);\r
- success = false;\r
- }\r
- //notes\r
- if (isNotBlank(notes)){\r
- Annotation annotation = Annotation.NewInstance(notes, Language.DEFAULT());\r
- distribution.addAnnotation(annotation);\r
- }\r
- }\r
- } catch (UnknownCdmTypeException e) {\r
- logger.error("Unknown presenceAbsence status id: " + emStatusId); \r
- e.printStackTrace();\r
- success = false;\r
- }\r
- }\r
- \r
- logger.info("Distributions: " + countDistributions + ", Descriptions: " + countDescriptions );\r
- logger.info("Duplicate occurrences: " + (countDuplicates));\r
-\r
- logger.info("Taxa to save: " + taxaToSave.size());\r
- getTaxonService().save(taxaToSave); \r
- \r
- return success;\r
- } catch (SQLException e) {\r
- logger.error("SQLException:" + e);\r
- return false;\r
- }\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param rs\r
- * @param occurrenceId\r
- * @param tdwgCodeString\r
- * @param emCodeString\r
- * @return\r
- * @throws SQLException\r
- */\r
- //Create area list\r
- private List<NamedArea> makeAreaList(BerlinModelImportState state, ResultSet rs, int occurrenceId) throws SQLException {\r
- List<NamedArea> areas = new ArrayList<NamedArea>();\r
- \r
- if (state.getConfig().isUseEmAreaVocabulary()){\r
- Integer areaId = rs.getInt("AreaId");\r
- NamedArea area = this.euroMedAreas.get(areaId);\r
- areas.add(area);\r
- }else{\r
- String tdwgCodeString = rs.getString("TDWGCode");\r
- String emCodeString = state.getConfig().isIncludesAreaEmCode() ? rs.getString("EMCode") : null;\r
- \r
- if (tdwgCodeString != null){\r
- \r
- String[] tdwgCodes = new String[]{tdwgCodeString};\r
- if (state.getConfig().isSplitTdwgCodes()){\r
- tdwgCodes = tdwgCodeString.split(";");\r
- }\r
- \r
- for (String tdwgCode : tdwgCodes){\r
- NamedArea area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode.trim());\r
- if (area == null){\r
- area = getOtherAreas(state, emCodeString, tdwgCodeString);\r
- }\r
- if (area != null){\r
- areas.add(area);\r
- }\r
- }\r
- }\r
- \r
- if (areas.size()== 0){\r
- NamedArea area = getOtherAreas(state, emCodeString, tdwgCodeString);\r
- if (area != null){\r
- areas.add(area);\r
- }\r
- }\r
- if (areas.size() == 0){\r
- String areaId = rs.getString("AreaId");\r
- logger.warn("No areas defined for occurrence " + occurrenceId + ". EMCode: " + CdmUtils.Nz(emCodeString).trim() + ". AreaId: " + areaId );\r
- }\r
- }\r
- return areas;\r
- }\r
-\r
- @Override\r
- public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {\r
- String nameSpace;\r
- Class<?> cdmClass;\r
- Set<String> idSet;\r
- Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
- \r
- try{\r
- Set<String> taxonIdSet = new HashSet<String>();\r
- while (rs.next()){\r
- handleForeignKey(rs, taxonIdSet, "taxonId");\r
- }\r
- \r
- //taxon map\r
- nameSpace = BerlinModelTaxonImport.NAMESPACE;\r
- cdmClass = TaxonBase.class;\r
- idSet = taxonIdSet;\r
- Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
- result.put(nameSpace, objectMap);\r
-\r
- } catch (SQLException e) {\r
- throw new RuntimeException(e);\r
- }\r
- return result;\r
- }\r
-\r
-\r
-\r
- /**\r
- * Tests if a distribution with the same tdwgArea and the same status already exists in the description. \r
- * If so the old distribution is returned \r
- * @param description\r
- * @param tdwgArea\r
- * @return false, if dupplicate exists. True otherwise.\r
- */\r
- private Distribution checkIsNoDuplicate(TaxonDescription description, Distribution distribution, Map<Integer, String> duplicateMap, Integer bmDistributionId){\r
- for (DescriptionElementBase descElBase : description.getElements()){\r
- if (descElBase.isInstanceOf(Distribution.class)){\r
- Distribution oldDistr = HibernateProxyHelper.deproxy(descElBase, Distribution.class);\r
- NamedArea oldArea = oldDistr.getArea();\r
- if (oldArea != null && oldArea.equals(distribution.getArea())){\r
- PresenceAbsenceTerm oldStatus = oldDistr.getStatus();\r
- if (oldStatus != null && oldStatus.equals(distribution.getStatus())){\r
- duplicateMap.put(bmDistributionId, oldDistr.getSources().iterator().next().getIdInSource());\r
- return oldDistr;\r
- }\r
- }\r
- }\r
- }\r
- return null;\r
- }\r
- \r
- /**\r
- * Use same TaxonDescription if two records belong to the same taxon \r
- * @param newTaxonId\r
- * @param oldTaxonId\r
- * @param oldDescription\r
- * @param taxonMap\r
- * @return\r
- */\r
- private TaxonDescription getTaxonDescription(int newTaxonId, int oldTaxonId, TaxonDescription oldDescription, Map<String, TaxonBase<?>> taxonMap, int occurrenceId, Reference<?> sourceSec){\r
- TaxonDescription result = null;\r
- if (oldDescription == null || newTaxonId != oldTaxonId){\r
- TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));\r
- //TODO for testing\r
- //TaxonBase taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);\r
- Taxon taxon;\r
- if ( taxonBase instanceof Taxon ) {\r
- taxon = (Taxon) taxonBase;\r
- } else if (taxonBase != null) {\r
- logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());\r
- return null;\r
- } else {\r
- logger.warn("TaxonBase for Occurrence " + occurrenceId + " is null.");\r
- return null;\r
- } \r
- Set<TaxonDescription> descriptionSet= taxon.getDescriptions();\r
- if (descriptionSet.size() > 0) {\r
- result = descriptionSet.iterator().next(); \r
- }else{\r
- result = TaxonDescription.NewInstance();\r
- result.setTitleCache(sourceSec.getTitleCache(), true);\r
- taxon.addDescription(result);\r
- }\r
- }else{\r
- result = oldDescription;\r
- }\r
- return result;\r
- }\r
- \r
- @Override\r
- protected boolean doCheck(BerlinModelImportState state){\r
- IOValidator<BerlinModelImportState> validator = new BerlinModelOccurrenceImportValidator();\r
- return validator.validate(state);\r
- }\r
-\r
-\r
- @Override\r
- protected boolean isIgnore(BerlinModelImportState state){\r
- if (! state.getConfig().isDoOccurrence()){\r
- return true;\r
- }else{\r
- if (!this.checkSqlServerColumnExists(state.getConfig().getSource(), "emOccurrence", "OccurrenceId")){\r
- logger.error("emOccurrence table or emOccurrenceId does not exist. Must ignore occurrence import");\r
- return true;\r
- }else{\r
- return false;\r
- }\r
- }\r
- }\r
- \r
-}\r
+/**
+* Copyright (C) 2007 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+
+package eu.etaxonomy.cdm.io.berlinModel.in;
+
+import java.net.URI;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.log4j.Logger;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.TransactionStatus;
+
+import eu.etaxonomy.cdm.common.CdmUtils;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
+import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
+import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceImportValidator;
+import eu.etaxonomy.cdm.io.common.IOValidator;
+import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
+import eu.etaxonomy.cdm.io.common.Source;
+import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;
+import eu.etaxonomy.cdm.model.common.Annotation;
+import eu.etaxonomy.cdm.model.common.AnnotationType;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.ExtensionType;
+import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.common.Marker;
+import eu.etaxonomy.cdm.model.common.MarkerType;
+import eu.etaxonomy.cdm.model.common.OriginalSourceType;
+import eu.etaxonomy.cdm.model.common.TermType;
+import eu.etaxonomy.cdm.model.common.TermVocabulary;
+import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
+import eu.etaxonomy.cdm.model.description.Distribution;
+import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.location.NamedArea;
+import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
+import eu.etaxonomy.cdm.model.location.NamedAreaType;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
+
+
+/**
+ * @author a.mueller
+ * @created 20.03.2008
+ */
+@Component
+public class BerlinModelOccurrenceImport extends BerlinModelImportBase {
+ private static final String EM_AREA_NAMESPACE = "emArea";
+
+ private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceImport.class);
+
+ public static final String NAMESPACE = "Occurrence";
+
+
+ private static int modCount = 5000;
+ private static final String pluralString = "occurrences";
+ private static final String dbTableName = "emOccurrence"; //??
+
+
+ public BerlinModelOccurrenceImport(){
+ super(dbTableName, pluralString);
+ }
+
+ @Override
+ protected String getIdQuery(BerlinModelImportState state) {
+ String result = " SELECT occurrenceId FROM " + getTableName();
+ if (StringUtils.isNotBlank(state.getConfig().getOccurrenceFilter())){
+ result += " WHERE " + state.getConfig().getOccurrenceFilter();
+ }
+ return result;
+ }
+
+ @Override
+ protected String getRecordQuery(BerlinModelImportConfigurator config) {
+ String emCode = config.isIncludesAreaEmCode()? ", emArea.EMCode" : "";
+ String strQuery = //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution
+ " SELECT DISTINCT PTaxon.RIdentifier AS taxonId, emOccurrence.OccurrenceId, emOccurrence.Native, emOccurrence.Introduced, " +
+ " emOccurrence.Cultivated, emOccurrence.Notes occNotes, " +
+ " emOccurSumCat.emOccurSumCatId, emOccurSumCat.Short, emOccurSumCat.Description, " +
+ " emOccurSumCat.OutputCode, emArea.AreaId, emArea.TDWGCode " + emCode +
+ " FROM emOccurrence INNER JOIN " +
+ " emArea ON emOccurrence.AreaFk = emArea.AreaId INNER JOIN " +
+ " PTaxon ON emOccurrence.PTNameFk = PTaxon.PTNameFk AND emOccurrence.PTRefFk = PTaxon.PTRefFk LEFT OUTER JOIN " +
+ " emOccurSumCat ON emOccurrence.SummaryStatus = emOccurSumCat.emOccurSumCatId LEFT OUTER JOIN " +
+ " emOccurrenceSource ON emOccurrence.OccurrenceId = emOccurrenceSource.OccurrenceFk " +
+ " WHERE (emOccurrence.OccurrenceId IN (" + ID_LIST_TOKEN + ") )" +
+ " ORDER BY PTaxon.RIdentifier";
+ return strQuery;
+ }
+
+ private Map<Integer, NamedArea> euroMedAreas = new HashMap<Integer, NamedArea>();
+
+
+ @Override
+ public void doInvoke(BerlinModelImportState state) {
+ if (state.getConfig().isUseEmAreaVocabulary()){
+ try {
+ createEuroMedAreas(state);
+ } catch (Exception e) {
+ logger.error("Exception occurred when trying to create euroMed Areas");
+ e.printStackTrace();
+ state.setSuccess(false);
+ }
+ }
+ super.doInvoke(state);
+ //reset
+ euroMedAreas = new HashMap<Integer, NamedArea>();
+ }
+
+ private TermVocabulary<NamedArea> createEuroMedAreas(BerlinModelImportState state) throws SQLException {
+ logger.warn("Start creating E+M areas");
+ Source source = state.getConfig().getSource();
+ Reference<?> sourceReference = state.getConfig().getSourceReference();
+
+ TransactionStatus txStatus = this.startTransaction();
+
+ sourceReference = getSourceReference(sourceReference);
+
+ TermVocabulary<NamedArea> euroMedAreas = makeEmptyEuroMedVocabulary();
+
+ MarkerType eurMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurArea, "eur", "eur Area", "eur");
+ MarkerType euroMedAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidEurMedArea, "EuroMedArea", "EuroMedArea", "EuroMedArea");
+ ExtensionType isoCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidIsoCode, "IsoCode", "IsoCode", "iso");
+ ExtensionType tdwgCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidTdwgAreaCode, "TDWG code", "TDWG Area code", "tdwg");
+ ExtensionType mclCodeExtType = getExtensionType(state, BerlinModelTransformer.uuidMclCode, "MCL code", "MedCheckList code", "mcl");
+ NamedAreaLevel areaLevelTop = getNamedAreaLevel(state, BerlinModelTransformer.uuidAreaLevelTop, "Euro+Med top area level", "Euro+Med top area level. This level is only to be used for the area representing the complete Euro+Med area", "e+m top", null);
+ NamedAreaLevel areaLevelEm1 = getNamedAreaLevel(state, BerlinModelTransformer.uuidAreaLevelFirst, "Euro+Med 1. area level", "Euro+Med 1. area level", "e+m 1.", null);
+ NamedAreaLevel areaLevelEm2 = getNamedAreaLevel(state, BerlinModelTransformer.uuidAreaLevelSecond, "Euro+Med 2. area level", "Euro+Med 2. area level", "Euro+Med 1. area level", null);
+
+
+ String sql = "SELECT * , CASE WHEN EMCode = 'EM' THEN 'a' ELSE 'b' END as isEM " +
+ " FROM emArea " +
+ " ORDER BY isEM, EMCode";
+ ResultSet rs = source.getResultSet(sql);
+
+ NamedArea euroMedArea = null;
+ NamedArea lastLevel2Area = null;
+
+ //euroMedArea (EMCode = 'EM')
+ rs.next();
+ euroMedArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType, isoCodeExtType, tdwgCodeExtType, mclCodeExtType,
+ areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel2Area);
+ euroMedAreas.addTerm(euroMedArea);
+
+ //all other areas
+ while (rs.next()){
+ NamedArea newArea = makeSingleEuroMedArea(rs, eurMarkerType, euroMedAreaMarkerType,
+ isoCodeExtType, tdwgCodeExtType, mclCodeExtType,
+ areaLevelTop, areaLevelEm1 , areaLevelEm2, sourceReference, euroMedArea, lastLevel2Area);
+ euroMedAreas.addTerm(newArea);
+ if (newArea.getPartOf().equals(euroMedArea)){
+ lastLevel2Area = newArea;
+ }
+ getVocabularyService().saveOrUpdate(euroMedAreas);
+ }
+
+ commitTransaction(txStatus);
+ logger.warn("Created E+M areas");
+
+ return euroMedAreas;
+ }
+
+ /**
+ * @param sourceReference
+ * @return
+ */
+ private Reference<?> getSourceReference(Reference<?> sourceReference) {
+ Reference<?> persistentSourceReference = getReferenceService().find(sourceReference.getUuid()); //just to be sure
+ if (persistentSourceReference != null){
+ sourceReference = persistentSourceReference;
+ }
+ return sourceReference;
+ }
+
+ /**
+ * @param eurMarkerType
+ * @param euroMedAreaMarkerType
+ * @param isoCodeExtType
+ * @param tdwgCodeExtType
+ * @param mclCodeExtType
+ * @param rs
+ * @param areaLevelEm2
+ * @param areaLevelEm1
+ * @param areaLevelTop
+ * @throws SQLException
+ */
+ private NamedArea makeSingleEuroMedArea(ResultSet rs, MarkerType eurMarkerType,
+ MarkerType euroMedAreaMarkerType, ExtensionType isoCodeExtType,
+ ExtensionType tdwgCodeExtType, ExtensionType mclCodeExtType,
+ NamedAreaLevel areaLevelTop, NamedAreaLevel areaLevelEm1, NamedAreaLevel areaLevelEm2,
+ Reference<?> sourceReference, NamedArea euroMedArea, NamedArea level2Area) throws SQLException {
+ Integer areaId = rs.getInt("AreaId");
+ String emCode = nullSafeTrim(rs.getString("EMCode"));
+ String isoCode = nullSafeTrim(rs.getString("ISOCode"));
+ String tdwgCode = nullSafeTrim(rs.getString("TDWGCode"));
+ String unit = nullSafeTrim(rs.getString("Unit"));
+// ,[Status]
+// ,[OutputOrder]
+ boolean eurMarker = rs.getBoolean("eur");
+ boolean euroMedAreaMarker = rs.getBoolean("EuroMedArea");
+ String notes = nullSafeTrim(rs.getString("Notes"));
+ String mclCode = nullSafeTrim(rs.getString("MCLCode"));
+ String geoSearch = nullSafeTrim(rs.getString("NameForGeoSearch"));
+
+ if (isBlank(emCode)){
+ emCode = unit;
+ }
+
+ //uuid
+ UUID uuid = BerlinModelTransformer.getEMAreaUuid(emCode);
+ NamedArea area = (NamedArea)getTermService().find(uuid);
+ if (area == null){
+ //label
+ area = NamedArea.NewInstance(geoSearch, unit, emCode);
+ if (uuid != null){
+ area.setUuid(uuid);
+ }else{
+ logger.warn("Uuuid for emCode could not be defined: " + emCode);
+ }
+ }
+
+
+ //code
+ area.setIdInVocabulary(emCode);
+ //notes
+ if (StringUtils.isNotEmpty(notes)){
+ area.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT()));
+ }
+ //markers
+ area.addMarker(Marker.NewInstance(eurMarkerType, eurMarker));
+ area.addMarker(Marker.NewInstance(euroMedAreaMarkerType, euroMedAreaMarker));
+
+ //extensions
+ if (isNotBlank(isoCode)){
+ area.addExtension(isoCode, isoCodeExtType);
+ }
+ if (isNotBlank(tdwgCode)){
+ area.addExtension(tdwgCode, tdwgCodeExtType);
+ }
+ if (isNotBlank(mclCode)){
+ area.addExtension(mclCode, mclCodeExtType);
+ }
+
+ //type
+ area.setType(NamedAreaType.ADMINISTRATION_AREA());
+
+ //source
+ area.addSource(OriginalSourceType.Import, String.valueOf(areaId), EM_AREA_NAMESPACE, sourceReference, null);
+
+ //parent
+ if (euroMedArea != null){
+ if (emCode.contains("(")){
+ area.setPartOf(level2Area);
+ area.setLevel(areaLevelEm2);
+ }else{
+ area.setPartOf(euroMedArea);
+ area.setLevel(areaLevelEm1);
+ }
+ }else{
+ area.setLevel(areaLevelTop);
+ }
+ this.euroMedAreas.put(areaId, area);
+
+ //save
+ getTermService().saveOrUpdate(area);
+
+ return area;
+ }
+
+ private String nullSafeTrim(String string) {
+ if (string == null){
+ return null;
+ }else{
+ return string.trim();
+ }
+ }
+
+ /**
+ *
+ */
+ private TermVocabulary<NamedArea> makeEmptyEuroMedVocabulary() {
+ TermType type = TermType.NamedArea;
+ String description = "Euro+Med area vocabulary";
+ String label = "E+M areas";
+ String abbrev = null;
+ URI termSourceUri = null;
+ TermVocabulary<NamedArea> result = TermVocabulary.NewInstance(type, description, label, abbrev, termSourceUri);
+
+ result.setUuid(BerlinModelTransformer.uuidVocEuroMedAreas);
+ getVocabularyService().save(result);
+ return result;
+ }
+
+ @Override
+ public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
+ boolean success = true;
+ Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
+
+ Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
+
+ ResultSet rs = partitioner.getResultSet();
+
+ try {
+ //map to store the mapping of duplicate berlin model occurrences to their real distributions
+ //duplicated may occur due to area mappings from BM areas to TDWG areas
+ Map<Integer, String> duplicateMap = new HashMap<Integer, String>();
+ int oldTaxonId = -1;
+ TaxonDescription oldDescription = null;
+ int i = 0;
+ int countDescriptions = 0;
+ int countDistributions = 0;
+ int countDuplicates = 0;
+ //for each reference
+ while (rs.next()){
+
+ if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Facts handled: " + (i-1));}
+
+ int occurrenceId = rs.getInt("OccurrenceId");
+ int newTaxonId = rs.getInt("taxonId");
+ String notes = nullSafeTrim(rs.getString("occNotes"));
+
+ Integer emStatusId = nullSafeInt(rs, "emOccurSumCatId");
+
+ try {
+ //status
+ PresenceAbsenceTerm status = null;
+ String alternativeStatusString = null;
+ if (emStatusId != null){
+ status = BerlinModelTransformer.occStatus2PresenceAbsence(emStatusId);
+ }else{
+ String[] stringArray = new String[]{rs.getString("Native"), rs.getString("Introduced"), rs.getString("Cultivated")};
+ alternativeStatusString = CdmUtils.concat(",", stringArray);
+ }
+
+ Reference<?> sourceRef = state.getTransactionalSourceReference();
+
+ List<NamedArea> areas = makeAreaList(state, rs, occurrenceId);
+
+ //create description(elements)
+ TaxonDescription taxonDescription = getTaxonDescription(newTaxonId, oldTaxonId, oldDescription, taxonMap, occurrenceId, sourceRef);
+ for (NamedArea area : areas){
+ Distribution distribution = Distribution.NewInstance(area, status);
+ if (status == null){
+ AnnotationType annotationType = AnnotationType.EDITORIAL();
+ Annotation annotation = Annotation.NewInstance(alternativeStatusString, annotationType, null);
+ distribution.addAnnotation(annotation);
+ distribution.addMarker(Marker.NewInstance(MarkerType.PUBLISH(), false));
+ }
+// distribution.setCitation(sourceRef);
+ if (taxonDescription != null) {
+ Distribution duplicate = checkIsNoDuplicate(taxonDescription, distribution, duplicateMap , occurrenceId);
+ if (duplicate == null){
+ taxonDescription.addElement(distribution);
+ distribution.addImportSource(String.valueOf(occurrenceId), NAMESPACE, state.getTransactionalSourceReference(), null);
+ countDistributions++;
+ if (taxonDescription != oldDescription){
+ taxaToSave.add(taxonDescription.getTaxon());
+ oldDescription = taxonDescription;
+ countDescriptions++;
+ }
+ }else{
+ countDuplicates++;
+ duplicate.addImportSource(String.valueOf(occurrenceId), NAMESPACE, state.getTransactionalSourceReference(), null);
+ logger.info("Distribution is duplicate"); }
+ } else {
+ logger.warn("Distribution " + area.getLabel() + " ignored. OccurrenceId = " + occurrenceId);
+ success = false;
+ }
+ //notes
+ if (isNotBlank(notes)){
+ Annotation annotation = Annotation.NewInstance(notes, Language.DEFAULT());
+ distribution.addAnnotation(annotation);
+ }
+ }
+ } catch (UnknownCdmTypeException e) {
+ logger.error("Unknown presenceAbsence status id: " + emStatusId);
+ e.printStackTrace();
+ success = false;
+ }
+ }
+
+ logger.info("Distributions: " + countDistributions + ", Descriptions: " + countDescriptions );
+ logger.info("Duplicate occurrences: " + (countDuplicates));
+
+ logger.info("Taxa to save: " + taxaToSave.size());
+ getTaxonService().save(taxaToSave);
+
+ return success;
+ } catch (SQLException e) {
+ logger.error("SQLException:" + e);
+ return false;
+ }
+ }
+
+ /**
+ * @param state
+ * @param rs
+ * @param occurrenceId
+ * @param tdwgCodeString
+ * @param emCodeString
+ * @return
+ * @throws SQLException
+ */
+ //Create area list
+ private List<NamedArea> makeAreaList(BerlinModelImportState state, ResultSet rs, int occurrenceId) throws SQLException {
+ List<NamedArea> areas = new ArrayList<NamedArea>();
+
+ if (state.getConfig().isUseEmAreaVocabulary()){
+ Integer areaId = rs.getInt("AreaId");
+ NamedArea area = this.euroMedAreas.get(areaId);
+ areas.add(area);
+ }else{
+ String tdwgCodeString = rs.getString("TDWGCode");
+ String emCodeString = state.getConfig().isIncludesAreaEmCode() ? rs.getString("EMCode") : null;
+
+ if (tdwgCodeString != null){
+
+ String[] tdwgCodes = new String[]{tdwgCodeString};
+ if (state.getConfig().isSplitTdwgCodes()){
+ tdwgCodes = tdwgCodeString.split(";");
+ }
+
+ for (String tdwgCode : tdwgCodes){
+ NamedArea area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode.trim());
+ if (area == null){
+ area = getOtherAreas(state, emCodeString, tdwgCodeString);
+ }
+ if (area != null){
+ areas.add(area);
+ }
+ }
+ }
+
+ if (areas.size()== 0){
+ NamedArea area = getOtherAreas(state, emCodeString, tdwgCodeString);
+ if (area != null){
+ areas.add(area);
+ }
+ }
+ if (areas.size() == 0){
+ String areaId = rs.getString("AreaId");
+ logger.warn("No areas defined for occurrence " + occurrenceId + ". EMCode: " + CdmUtils.Nz(emCodeString).trim() + ". AreaId: " + areaId );
+ }
+ }
+ return areas;
+ }
+
+ @Override
+ public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
+ String nameSpace;
+ Class<?> cdmClass;
+ Set<String> idSet;
+ Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
+
+ try{
+ Set<String> taxonIdSet = new HashSet<String>();
+ while (rs.next()){
+ handleForeignKey(rs, taxonIdSet, "taxonId");
+ }
+
+ //taxon map
+ nameSpace = BerlinModelTaxonImport.NAMESPACE;
+ cdmClass = TaxonBase.class;
+ idSet = taxonIdSet;
+ Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
+ result.put(nameSpace, objectMap);
+
+ } catch (SQLException e) {
+ throw new RuntimeException(e);
+ }
+ return result;
+ }
+
+
+
+ /**
+ * Tests if a distribution with the same tdwgArea and the same status already exists in the description.
+ * If so the old distribution is returned
+ * @param description
+ * @param tdwgArea
+ * @return false, if dupplicate exists. True otherwise.
+ */
+ private Distribution checkIsNoDuplicate(TaxonDescription description, Distribution distribution, Map<Integer, String> duplicateMap, Integer bmDistributionId){
+ for (DescriptionElementBase descElBase : description.getElements()){
+ if (descElBase.isInstanceOf(Distribution.class)){
+ Distribution oldDistr = HibernateProxyHelper.deproxy(descElBase, Distribution.class);
+ NamedArea oldArea = oldDistr.getArea();
+ if (oldArea != null && oldArea.equals(distribution.getArea())){
+ PresenceAbsenceTerm oldStatus = oldDistr.getStatus();
+ if (oldStatus != null && oldStatus.equals(distribution.getStatus())){
+ duplicateMap.put(bmDistributionId, oldDistr.getSources().iterator().next().getIdInSource());
+ return oldDistr;
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Use same TaxonDescription if two records belong to the same taxon
+ * @param newTaxonId
+ * @param oldTaxonId
+ * @param oldDescription
+ * @param taxonMap
+ * @return
+ */
+ private TaxonDescription getTaxonDescription(int newTaxonId, int oldTaxonId, TaxonDescription oldDescription, Map<String, TaxonBase<?>> taxonMap, int occurrenceId, Reference<?> sourceSec){
+ TaxonDescription result = null;
+ if (oldDescription == null || newTaxonId != oldTaxonId){
+ TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));
+ //TODO for testing
+ //TaxonBase taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);
+ Taxon taxon;
+ if ( taxonBase instanceof Taxon ) {
+ taxon = (Taxon) taxonBase;
+ } else if (taxonBase != null) {
+ logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
+ return null;
+ } else {
+ logger.warn("TaxonBase for Occurrence " + occurrenceId + " is null.");
+ return null;
+ }
+ Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
+ if (descriptionSet.size() > 0) {
+ result = descriptionSet.iterator().next();
+ }else{
+ result = TaxonDescription.NewInstance();
+ result.setTitleCache(sourceSec.getTitleCache(), true);
+ taxon.addDescription(result);
+ }
+ }else{
+ result = oldDescription;
+ }
+ return result;
+ }
+
+ @Override
+ protected boolean doCheck(BerlinModelImportState state){
+ IOValidator<BerlinModelImportState> validator = new BerlinModelOccurrenceImportValidator();
+ return validator.validate(state);
+ }
+
+
+ @Override
+ protected boolean isIgnore(BerlinModelImportState state){
+ if (! state.getConfig().isDoOccurrence()){
+ return true;
+ }else{
+ if (!this.checkSqlServerColumnExists(state.getConfig().getSource(), "emOccurrence", "OccurrenceId")){
+ logger.error("emOccurrence table or emOccurrenceId does not exist. Must ignore occurrence import");
+ return true;
+ }else{
+ return false;
+ }
+ }
+ }
+
+}
BGBM BDI Projects / cdmlib-apps.git / blobdiff