\r
import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.A_AUCT;\r
import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.P_PARENTHESIS;\r
-import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.Q_NO_RESTRICTION;\r
import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_GENUS;\r
import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SPECIES;\r
import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBGENUS;\r
\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
+import java.util.ArrayList;\r
import java.util.Collection;\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 org.springframework.stereotype.Component;\r
import org.springframework.transaction.TransactionStatus;\r
\r
-import eu.etaxonomy.cdm.api.service.IService;\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
import eu.etaxonomy.cdm.io.common.ICdmIO;\r
import eu.etaxonomy.cdm.io.common.ImportHelper;\r
import eu.etaxonomy.cdm.io.common.MapWrapper;\r
import eu.etaxonomy.cdm.io.common.Source;\r
-import eu.etaxonomy.cdm.io.profiler.ProfilerController;\r
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.OriginalSource;\r
+import eu.etaxonomy.cdm.model.common.IdentifiableSource;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
import eu.etaxonomy.cdm.model.taxon.Synonym;\r
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;\r
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;\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
/* Max number of taxa to retrieve (for test purposes) */\r
private int maxTaxa = 0;\r
- /* Interval for progress info message when retrieving taxa */\r
-// private int modCount = 10000;\r
\r
\r
/* (non-Javadoc)\r
*/\r
protected boolean doInvoke(FaunaEuropaeaImportState state) { \r
\r
- ProfilerController.memorySnapshot();\r
-\r
- TransactionStatus txStatus = null;\r
boolean success = true;\r
- \r
if(logger.isInfoEnabled()) { logger.info("Start making taxa..."); }\r
-\r
- if (state.getConfig().isUseTransactions()) {\r
- txStatus = startTransaction();\r
- }\r
\r
- success = retrieveTaxa(state);\r
-// success = processTaxaSecondPass(state);\r
-// success = saveTaxa(state, state.getHighestTaxonIndex(), state.getConfig().getLimitSave());\r
\r
- if (state.getConfig().isUseTransactions()) {\r
- commitTransaction(txStatus);\r
- }\r
+ \r
+ success = processTaxa(state);\r
\r
logger.info("End making taxa...");\r
- ProfilerController.memorySnapshot();\r
return success;\r
}\r
\r
\r
- /** Retrieve taxa from FauEu DB, fill TaxonStore */\r
- private boolean retrieveTaxa(FaunaEuropaeaImportState state) {\r
+ /** Retrieve taxa from FauEu DB, process in blocks */\r
+ private boolean processTaxa(FaunaEuropaeaImportState state) {\r
\r
int limit = state.getConfig().getLimitSave();\r
\r
+ TransactionStatus txStatus = null;\r
+\r
Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
-// MapWrapper<TaxonBase> nameStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXONNAME_STORE);\r
- MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);\r
-// Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = state.getFauEuTaxonMap();\r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);\r
- state.setFauEuTaxonMap(fauEuTaxonMap);\r
+ \r
+ Map<Integer, TaxonBase<?>> taxonMap = null;\r
+ Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = null;\r
+ /* Store for heterotypic synonyms to be save separately */\r
+ Set<Synonym> synonymSet = null;\r
\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Initial size of taxon store is: " + taxonStore.size());\r
- }\r
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();\r
\r
int i = 0;\r
boolean success = true;\r
\r
- try {\r
+ String selectCount = \r
+ " SELECT count(*) ";\r
+\r
+ String selectColumns = \r
+ " SELECT Parent.TAX_NAME AS P2Name, Parent.TAX_RNK_ID AS P2RankId, " +\r
+ " GrandParent.TAX_ID AS GP3Id, GrandParent.TAX_NAME AS GP3Name, GrandParent.TAX_RNK_ID AS GP3RankId, " +\r
+ " GreatGrandParent.TAX_ID AS GGP4Id, GreatGrandParent.TAX_NAME AS GGP4Name, GreatGrandParent.TAX_RNK_ID AS GGP4RankId, " +\r
+ " GreatGreatGrandParent.TAX_ID AS GGGP5Id, GreatGreatGrandParent.TAX_NAME AS GGGP5Name, GreatGreatGrandParent.TAX_RNK_ID AS GGGP5RankId, " +\r
+ " OriginalGenusTaxon.TAX_NAME AS OGenusName, " +\r
+ " GreatGreatGreatGrandParent.TAX_ID AS GGGGP6Id, GreatGreatGreatGrandParent.TAX_NAME AS GGGGP6Name, GreatGreatGreatGrandParent.TAX_RNK_ID AS GGGGP6RankId," +\r
+ " Taxon.*, rank.*, author.* ";\r
+ \r
+ String fromClause = \r
+ " FROM Taxon LEFT OUTER JOIN " +\r
+ " Taxon AS Parent ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID LEFT OUTER JOIN " +\r
+ " Taxon AS GrandParent ON Parent.TAX_TAX_IDPARENT = GrandParent.TAX_ID LEFT OUTER JOIN " +\r
+ " Taxon AS GreatGrandParent ON GrandParent.TAX_TAX_IDPARENT = GreatGrandParent.TAX_ID LEFT OUTER JOIN " +\r
+ " Taxon AS GreatGreatGrandParent ON GreatGrandParent.TAX_TAX_IDPARENT = GreatGreatGrandParent.TAX_ID LEFT OUTER JOIN " +\r
+ " Taxon AS GreatGreatGreatGrandParent ON GreatGreatGrandParent.TAX_TAX_IDPARENT = GreatGreatGreatGrandParent.TAX_ID LEFT OUTER JOIN " +\r
+ " Taxon AS OriginalGenusTaxon ON Taxon.TAX_TAX_IDGENUS = OriginalGenusTaxon.TAX_ID LEFT OUTER JOIN " +\r
+ " author ON Taxon.TAX_AUT_ID = author.aut_id LEFT OUTER JOIN " +\r
+ " rank ON Taxon.TAX_RNK_ID = rank.rnk_id ";\r
+\r
+ String countQuery = \r
+ selectCount + fromClause;\r
+\r
+ String selectQuery = \r
+ selectColumns + fromClause;\r
+ \r
\r
- String strQuery = \r
- " SELECT Taxon.*, rank.*, author.* " + \r
- " FROM dbo.Taxon " +\r
- " LEFT OUTER JOIN dbo.author ON dbo.Taxon.TAX_AUT_ID = dbo.author.aut_id " +\r
- " LEFT OUTER JOIN dbo.rank ON dbo.Taxon.TAX_RNK_ID = dbo.rank.rnk_id " +\r
- " WHERE (1=1)";\r
+ try {\r
\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Query: " + strQuery);\r
- }\r
- ResultSet rs = source.getResultSet(strQuery);\r
+ ResultSet rs = source.getResultSet(countQuery);\r
+ rs.next();\r
+ int count = rs.getInt(1);\r
+ \r
+ rs = source.getResultSet(selectQuery);\r
\r
+ if (logger.isInfoEnabled()) {\r
+ logger.info("Number of rows: " + count);\r
+ logger.info("Count Query: " + countQuery);\r
+ logger.info("Select Query: " + selectQuery);\r
+ }\r
+ \r
while (rs.next()) {\r
\r
-// if ((i++ % limit) == 0 && i != 1 ) { \r
-// if(logger.isInfoEnabled()) {\r
-// logger.info("Taxa retrieved: " + (i-1)); \r
-// }\r
-// }\r
+ if ((i++ % limit) == 0) {\r
+ \r
+ txStatus = startTransaction();\r
+ taxonMap = new HashMap<Integer, TaxonBase<?>>(limit);\r
+ fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);\r
+ synonymSet = new HashSet<Synonym>();\r
+ \r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("i = " + i + " - Transaction started"); \r
+ }\r
+ }\r
\r
- int taxonId = rs.getInt("TAX_ID");\r
String localName = rs.getString("TAX_NAME");\r
+ String parentName = rs.getString("P2Name");\r
+ int grandParentId = rs.getInt("GP3Id");\r
+ String grandParentName = rs.getString("GP3Name");\r
+ int greatGrandParentId = rs.getInt("GGP4Id");\r
+ String greatGrandParentName = rs.getString("GGP4Name");\r
+ int greatGreatGrandParentId = rs.getInt("GGGP5Id");\r
+ String greatGreatGrandParentName = rs.getString("GGGP5Name");\r
+ String greatGreatGreatGrandParentName = rs.getString("GGGGP6Name");\r
+ String originalGenusName = rs.getString("OGenusName");\r
+ String autName = rs.getString("aut_name");\r
+ int taxonId = rs.getInt("TAX_ID");\r
int rankId = rs.getInt("TAX_RNK_ID");\r
int parentId = rs.getInt("TAX_TAX_IDPARENT");\r
- int familyId = rs.getInt("TAX_TAX_IDFAMILY");\r
+ int parentRankId = rs.getInt("P2RankId");\r
+ int grandParentRankId = rs.getInt("GP3RankId");\r
+ int greatGrandParentRankId = rs.getInt("GGP4RankId");\r
+ int greatGreatGrandParentRankId = rs.getInt("GGGP5RankId");\r
+ int greatGreatGreatGrandParentRankId = rs.getInt("GGGGP6RankId");\r
int originalGenusId = rs.getInt("TAX_TAX_IDGENUS");\r
int autId = rs.getInt("TAX_AUT_ID");\r
int status = rs.getInt("TAX_VALID");\r
- int year = rs.getInt("TAX_YEAR");\r
- String autName = rs.getString("aut_name");\r
+ \r
+ // Avoid publication year 0 for NULL values in database.\r
+ Integer year = rs.getInt("TAX_YEAR");\r
+ if (year != null && year.intValue() == 0) {\r
+ year = null;\r
+ }\r
+ \r
+ //int familyId = rs.getInt("TAX_TAX_IDFAMILY");\r
\r
Rank rank = null;\r
int parenthesis = rs.getInt("TAX_PARENTHESIS");\r
taxonBaseUuid = UUID.randomUUID();\r
}\r
\r
-// String originalGenusName = "";\r
-// String genusName = "";\r
-// String specificEpithet = "";\r
-\r
-\r
FaunaEuropaeaTaxon fauEuTaxon = new FaunaEuropaeaTaxon();\r
fauEuTaxon.setUuid(taxonBaseUuid);\r
- fauEuTaxon.setLocalName(rs.getString("TAX_NAME"));\r
- fauEuTaxon.setParentId(rs.getInt("TAX_TAX_IDPARENT"));\r
-// fauEuTaxon.setOriginalGenusId(rs.getInt("TAX_TAX_IDGENUS"));\r
- fauEuTaxon.setId(rs.getInt("TAX_ID"));\r
- fauEuTaxon.setRankId(rs.getInt("TAX_RNK_ID"));\r
- fauEuTaxon.setYear(rs.getInt("TAX_YEAR"));\r
-// fauEuTaxon.setAuthorId(autId);\r
- fauEuTaxon.setAuthorName(rs.getString("aut_name"));\r
+ fauEuTaxon.setId(taxonId);\r
+ fauEuTaxon.setRankId(rankId);\r
+ fauEuTaxon.setLocalName(localName);\r
+ \r
+ fauEuTaxon.setParentId(parentId);\r
+ fauEuTaxon.setParentRankId(parentRankId);\r
+ fauEuTaxon.setParentName(parentName);\r
+ \r
+ fauEuTaxon.setGrandParentId(grandParentId);\r
+ fauEuTaxon.setGrandParentRankId(grandParentRankId);\r
+ fauEuTaxon.setGrandParentName(grandParentName);\r
+ \r
+ fauEuTaxon.setGreatGrandParentId(greatGrandParentId);\r
+ fauEuTaxon.setGreatGrandParentRankId(greatGrandParentRankId);\r
+ fauEuTaxon.setGreatGrandParentName(greatGrandParentName);\r
+ \r
+ fauEuTaxon.setGreatGreatGrandParentId(greatGreatGrandParentId);\r
+ fauEuTaxon.setGreatGreatGrandParentRankId(greatGreatGrandParentRankId);\r
+ fauEuTaxon.setGreatGreatGrandParentName(greatGreatGrandParentName);\r
+ \r
+ fauEuTaxon.setGreatGreatGreatGrandParentRankId(greatGreatGreatGrandParentRankId);\r
+ fauEuTaxon.setGreatGreatGreatGrandParentName(greatGreatGreatGrandParentName);\r
+ \r
+ fauEuTaxon.setOriginalGenusId(originalGenusId);\r
+ fauEuTaxon.setYear(year);\r
+ fauEuTaxon.setOriginalGenusName(originalGenusName);\r
+ fauEuTaxon.setAuthorName(autName);\r
if (parenthesis == P_PARENTHESIS) {\r
fauEuTaxon.setParenthesis(true);\r
} else {\r
fauEuTaxon.setValid(false);\r
}\r
\r
+// fauEuTaxon.setAuthorId(autId);\r
\r
try {\r
rank = FaunaEuropaeaTransformer.rankId2Rank(rs, false);\r
\r
ZoologicalName zooName = ZoologicalName.NewInstance(rank);\r
TeamOrPersonBase<?> author = authorStore.get(autId);\r
+ \r
zooName.setCombinationAuthorTeam(author);\r
zooName.setPublicationYear(year);\r
-\r
- // set local name cache\r
-// zooName.setNameCache(localName);\r
-\r
+ \r
TaxonBase<?> taxonBase;\r
\r
Synonym synonym;\r
try {\r
if ((status == T_STATUS_ACCEPTED) || (autId == A_AUCT)) { // taxon\r
if (autId == A_AUCT) { // misapplied name\r
+ zooName.setCombinationAuthorTeam(null);\r
+ zooName.setPublicationYear(null);\r
taxon = Taxon.NewInstance(zooName, auctReference);\r
if (logger.isDebugEnabled()) {\r
logger.debug("Misapplied name created (" + taxonId + ")");\r
}\r
- } else { // regular taxon\r
+ } else { // accepted taxon\r
taxon = Taxon.NewInstance(zooName, sourceReference);\r
if (logger.isDebugEnabled()) {\r
logger.debug("Taxon created (" + taxonId + ")");\r
taxonBase = taxon;\r
} else if ((status == T_STATUS_NOT_ACCEPTED) && (autId != A_AUCT)) { // synonym\r
synonym = Synonym.NewInstance(zooName, sourceReference);\r
+ //logger.info("Synonym created: " + synonym.getTitleCache() + " taxonName: " + zooName.getTitleCache());\r
if (logger.isDebugEnabled()) {\r
logger.debug("Synonym created (" + taxonId + ")");\r
}\r
ImportHelper.setOriginalSource(zooName, fauEuConfig.getSourceReference(), taxonId, "TaxonName");\r
\r
\r
- if (!taxonStore.containsId(taxonId)) {\r
+ if (!taxonMap.containsKey(taxonId)) {\r
if (taxonBase == null) {\r
if (logger.isDebugEnabled()) { \r
logger.debug("Taxon base is null. Taxon (" + taxonId + ") ignored.");\r
}\r
continue;\r
}\r
- taxonStore.put(taxonId, taxonBase);\r
+ taxonMap.put(taxonId, taxonBase);\r
fauEuTaxonMap.put(taxonId, fauEuTaxon);\r
+ \r
// if (logger.isDebugEnabled()) { \r
// logger.debug("Stored taxon base (" + taxonId + ") " + localName); \r
// }\r
e.printStackTrace();\r
}\r
\r
- if ((i++ % limit) == 0 && i != 1 ) { \r
- if(logger.isInfoEnabled()) {\r
- logger.info("Taxa retrieved: " + (i-1)); \r
- }\r
- success = processTaxaSecondPass(state);\r
- success = saveTaxa(state);\r
-\r
- if (logger.isInfoEnabled()) {\r
- logger.info("End size of taxon Store is: " + taxonStore.size());\r
- }\r
-\r
-// taxonStore.makeNewMap((IService)getTaxonService());\r
- taxonStore.makeEmpty();\r
- fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);\r
- state.setFauEuTaxonMap(fauEuTaxonMap);\r
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Final size of taxon Store is: " + taxonStore.size());\r
+ success = processTaxaSecondPass(state, taxonMap, fauEuTaxonMap, synonymSet);\r
+ if(logger.isDebugEnabled()) { logger.debug("Saving taxa ..."); }\r
+ getTaxonService().save((Collection)taxonMap.values());\r
+ getTaxonService().save((Collection)synonymSet);\r
+ \r
+ taxonMap = null;\r
+ synonymSet = null;\r
+ fauEuTaxonMap = null;\r
+ commitTransaction(txStatus);\r
+ \r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("i = " + i + " - Transaction committed"); \r
}\r
}\r
\r
/**\r
* Processes taxa from complete taxon store\r
*/\r
- private boolean processTaxaSecondPass(FaunaEuropaeaImportState state) {\r
+ private boolean processTaxaSecondPass(FaunaEuropaeaImportState state, Map<Integer, TaxonBase<?>> taxonMap,\r
+ Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, Set<Synonym> synonymSet) {\r
\r
- if(logger.isInfoEnabled()) { logger.info("Processing taxa second pass..."); }\r
+ if(logger.isDebugEnabled()) { logger.debug("Processing taxa second pass..."); }\r
\r
- Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
- MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
- ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();\r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = state.getFauEuTaxonMap();\r
-\r
+ \r
boolean success = true;\r
\r
- for (int id : taxonStore.keySet())\r
+ for (int id : taxonMap.keySet())\r
{\r
- TaxonBase<?> taxonBase = taxonStore.get(id);\r
if (logger.isDebugEnabled()) { logger.debug("Taxon # " + id); }\r
\r
+ TaxonBase<?> taxonBase = taxonMap.get(id);\r
TaxonNameBase<?,?> taxonName = taxonBase.getName();\r
- \r
FaunaEuropaeaTaxon fauEuTaxon = fauEuTaxonMap.get(id);\r
+ boolean useOriginalGenus = false;\r
+ if (taxonBase instanceof Synonym){\r
+ useOriginalGenus = true;\r
+ }\r
\r
String nameString = \r
- buildTaxonName(fauEuTaxon, taxonBase, taxonName, false, fauEuTaxonMap, fauEuConfig);\r
+ buildTaxonName(fauEuTaxon, taxonBase, taxonName, useOriginalGenus, fauEuConfig);\r
+ \r
+ if (taxonBase instanceof Synonym){\r
+ logger.info("Name of Synonym: " + nameString);\r
+ }\r
\r
- if (fauEuConfig.isDoBasionyms() && (fauEuTaxon.isValid()) &&\r
- (fauEuTaxon.getOriginalGenusId() != 0) &&\r
- (fauEuTaxon.getParentId() != fauEuTaxon.getOriginalGenusId())) {\r
- success = createBasionym(fauEuTaxon, taxonBase, taxonName, fauEuTaxonMap, fauEuConfig);\r
+ if (fauEuConfig.isDoBasionyms() \r
+ && fauEuTaxon.getRankId() > R_SUBGENUS\r
+ && (fauEuTaxon.getOriginalGenusId() != 0)) {\r
+ \r
+ Integer originalGenusId = fauEuTaxon.getOriginalGenusId();\r
+ Integer actualGenusId = getActualGenusId(fauEuTaxon);\r
+ \r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("actual genus id = " + actualGenusId + ", original genus id = " + originalGenusId);\r
+ }\r
+ \r
+ if (actualGenusId != originalGenusId && taxonBase.isInstanceOf(Taxon.class)) {\r
+ success = createBasionym(fauEuTaxon, taxonBase, taxonName, fauEuConfig, synonymSet);\r
+ } else if (fauEuTaxon.isParenthesis()) {\r
+ //the authorteam should be set in parenthesis because there should be a basionym, but we do not know it?\r
+ ZoologicalName zooName = taxonName.deproxy(taxonName, ZoologicalName.class);\r
+ zooName.setBasionymAuthorTeam(zooName.getCombinationAuthorTeam());\r
+ zooName.setCombinationAuthorTeam(null);\r
+ zooName.setOriginalPublicationYear(zooName.getPublicationYear());\r
+ zooName.setPublicationYear(null);\r
+ }\r
+ \r
}\r
}\r
return success; \r
}\r
\r
\r
- private boolean createBasionym(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, TaxonNameBase<?,?>taxonName, \r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, FaunaEuropaeaImportConfigurator fauEuConfig) {\r
-\r
-// if (fauEuTaxon.isParenthesis() && (fauEuTaxon.getOriginalGenusId() != 0)\r
-// && (fauEuTaxon.getParentId() != fauEuTaxon.getOriginalGenusId())) {\r
+ private boolean createBasionym(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, \r
+ TaxonNameBase<?,?>taxonName, FaunaEuropaeaImportConfigurator fauEuConfig,\r
+ Set<Synonym> synonymSet) {\r
\r
boolean success = true;\r
\r
try {\r
ZoologicalName zooName = taxonName.deproxy(taxonName, ZoologicalName.class);\r
- Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);\r
\r
// create basionym\r
ZoologicalName basionym = ZoologicalName.NewInstance(taxonName.getRank());\r
basionym.setCombinationAuthorTeam(zooName.getCombinationAuthorTeam());\r
+ \r
+ zooName.setOriginalPublicationYear(zooName.getPublicationYear());\r
basionym.setPublicationYear(zooName.getPublicationYear());\r
+\r
+ // add originalGenusId as source\r
+ String originalGenusIdString = "" + fauEuTaxon.getId();\r
+ IdentifiableSource basionymSource = IdentifiableSource.NewInstance(originalGenusIdString, "originalGenusId");\r
+ basionym.addSource(basionymSource);\r
+ \r
+ // add original database reference\r
+ ImportHelper.setOriginalSource(basionym, fauEuConfig.getSourceReference(), fauEuTaxon.getId(), "TaxonName");\r
+ \r
zooName.addBasionym(basionym, fauEuConfig.getSourceReference(), null, null);\r
zooName.setBasionymAuthorTeam(zooName.getCombinationAuthorTeam());\r
+ zooName.setCombinationAuthorTeam(null);\r
+ zooName.setPublicationYear(null);\r
+ zooName.setTitleCache(null); // This should (re)generate the titleCache automagically\r
if (logger.isDebugEnabled()) {\r
logger.debug("Basionym created (" + fauEuTaxon.getId() + ")");\r
}\r
\r
- // create homotypic synonym\r
- Synonym homotypicSynonym = Synonym.NewInstance(basionym, fauEuConfig.getSourceReference());\r
-// SynonymRelationship synRel = \r
-// taxon.addSynonym(homotypicSynonym, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF(), \r
-// sourceReference, null);\r
-// homotypicSynonym.addRelationship(synRel);\r
- taxon.addHomotypicSynonym(homotypicSynonym, fauEuConfig.getSourceReference(), null);\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Homotypic synonym created (" + fauEuTaxon.getId() + ")");\r
+ // create synonym\r
+ Synonym synonym = Synonym.NewInstance(basionym, fauEuConfig.getSourceReference());\r
+ \r
+ if (fauEuTaxon.isValid()) { // Taxon\r
+\r
+ // homotypic synonym\r
+ Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);\r
+ taxon.addHomotypicSynonym(synonym, fauEuConfig.getSourceReference(), null);\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Homotypic synonym created (" + fauEuTaxon.getId() + ")");\r
+ }\r
+\r
+ } else { // Synonym\r
+ \r
+ // heterotypic synonym\r
+ // synonym relationship to the accepted taxon is created later\r
+ synonymSet.add(synonym);\r
+ \r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Heterotypic synonym stored (" + fauEuTaxon.getId() + ")");\r
+ }\r
}\r
\r
- buildTaxonName(fauEuTaxon, homotypicSynonym, basionym, true, fauEuTaxonMap, fauEuConfig);\r
\r
+ buildTaxonName(fauEuTaxon, synonym, basionym, true, fauEuConfig);\r
} catch (Exception e) {\r
logger.warn("Exception occurred when creating basionym for " + fauEuTaxon.getId());\r
e.printStackTrace();\r
private String buildNameTitleCache(String nameString, boolean useOriginalGenus, FaunaEuropaeaTaxon fauEuTaxon) {\r
\r
StringBuilder titleCacheStringBuilder = new StringBuilder(nameString);\r
- int year = fauEuTaxon.getYear();\r
- if (year != 0) { // TODO: Ignore authors like xp, xf, etc?\r
+ Integer year = fauEuTaxon.getYear();\r
+ if (year != null) { // TODO: Ignore authors like xp, xf, etc?\r
titleCacheStringBuilder.append(" ");\r
if ((fauEuTaxon.isParenthesis() == true) && !useOriginalGenus) {\r
titleCacheStringBuilder.append("(");\r
\r
StringBuilder stringBuilder = new StringBuilder();\r
\r
- if(useOriginalGenus == true) {\r
+ if(useOriginalGenus) {\r
stringBuilder.append(originalGenusName);\r
genusOrUninomial.delete(0, genusOrUninomial.length());\r
genusOrUninomial.append(originalGenusName);\r
}\r
\r
\r
- private String genusSubGenusPart(StringBuilder originalGenusName, boolean useOriginalGenus,\r
+ private String genusSubGenusPart(StringBuilder originalGenusName, boolean useOriginalGenus, \r
StringBuilder genusOrUninomial,\r
- StringBuilder infraGenericEpithet) {\r
+ StringBuilder infraGenericEpithet,\r
+ FaunaEuropaeaTaxon fauEuTaxon) {\r
\r
StringBuilder stringBuilder = new StringBuilder();\r
\r
stringBuilder.append(genusPart(originalGenusName, useOriginalGenus, genusOrUninomial));\r
\r
- if (useOriginalGenus == true) {\r
+ // The infraGenericEpithet is set to empty only if the original genus should be used and\r
+ // the actualGenusId is not the originalGenusId.\r
+ // This differentiation is relevant for synonyms and for basionyms.\r
+ // InfraGenericEpithets of accepted taxa are not touched at all.\r
+ Integer originalGenusId = fauEuTaxon.getOriginalGenusId();\r
+ Integer actualGenusId = getActualGenusId(fauEuTaxon);\r
+ if (useOriginalGenus && originalGenusId != actualGenusId && \r
+ originalGenusId.intValue() > 0 &&\r
+ actualGenusId.intValue() > 0) {\r
infraGenericEpithet.delete(0, infraGenericEpithet.length());\r
stringBuilder.append(" ");\r
return stringBuilder.toString();\r
\r
return stringBuilder.toString();\r
}\r
+\r
+ /** Get actual genus id **/\r
+ private Integer getActualGenusId(FaunaEuropaeaTaxon fauEuTaxon) {\r
+ Integer actualGenusId = null;\r
+ HashMap<Integer, Integer> ranks = new HashMap<Integer, Integer>();\r
+ ranks.put(fauEuTaxon.getParentRankId(), fauEuTaxon.getParentId());\r
+ ranks.put(fauEuTaxon.getGrandParentRankId(), fauEuTaxon.getGrandParentId());\r
+ ranks.put(fauEuTaxon.getGreatGrandParentRankId(), fauEuTaxon.getGreatGrandParentId());\r
+ ranks.put(fauEuTaxon.getGreatGreatGrandParentRankId(), fauEuTaxon.getGreatGreatGrandParentId());\r
+ ranks.put(fauEuTaxon.getGreatGreatGreatGrandParentRankId(), fauEuTaxon.getGreatGreatGreatGrandParentId());\r
+ \r
+ actualGenusId = ranks.get(R_GENUS);\r
+\r
+ return actualGenusId;\r
+ }\r
\r
\r
/** Build species and subspecies names */\r
- private String buildLowerTaxonName(StringBuilder originalGenus, boolean useOriginalGenus,\r
+ private String buildLowerTaxonName(StringBuilder originalGenus, boolean useOriginalGenus, \r
StringBuilder genusOrUninomial, StringBuilder infraGenericEpithet, \r
StringBuilder specificEpithet, StringBuilder infraSpecificEpithet,\r
- FaunaEuropaeaTaxon fauEuTaxon, Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap) {\r
+ FaunaEuropaeaTaxon fauEuTaxon) {\r
\r
+ // species or subspecies name\r
+ String localName = fauEuTaxon.getLocalName();\r
+ int taxonId = fauEuTaxon.getId();\r
+ int parentId = fauEuTaxon.getParentId();\r
StringBuilder nameCacheStringBuilder = new StringBuilder();\r
\r
- int rank = fauEuTaxon.getRankId();\r
- int parentId = fauEuTaxon.getParentId();\r
- FaunaEuropaeaTaxon parent = fauEuTaxonMap.get(parentId);\r
- if (parent == null) {\r
- nameCacheStringBuilder.append(fauEuTaxon.getLocalName());\r
+// FaunaEuropaeaTaxon parent = fauEuTaxonMap.get(parentId);\r
+ if (parentId == 0) {\r
+ nameCacheStringBuilder.append(localName);\r
if (logger.isInfoEnabled()) {\r
- logger.info("Parent of (" + fauEuTaxon.getId() + ") is null");\r
+ logger.info("Parent of (" + taxonId + ") is null");\r
}\r
return nameCacheStringBuilder.toString();\r
}\r
- int grandParentId = parent.getParentId();\r
- FaunaEuropaeaTaxon grandParent = fauEuTaxonMap.get(grandParentId);\r
- int greatGrandParentId = grandParent.getParentId();\r
- FaunaEuropaeaTaxon greatGrandParent = fauEuTaxonMap.get(greatGrandParentId);\r
+ \r
+ String parentName = fauEuTaxon.getParentName();\r
+ String grandParentName = fauEuTaxon.getGrandParentName();\r
+ String greatGrandParentName = fauEuTaxon.getGreatGrandParentName();\r
+ int rank = fauEuTaxon.getRankId();\r
+ int parentRankId = fauEuTaxon.getParentRankId();\r
+ int grandParentRankId = fauEuTaxon.getGrandParentRankId();\r
+ int greatGrandParentRankId = fauEuTaxon.getGreatGrandParentRankId();\r
+// int grandParentId = fauEuTaxon.getGrandParentId();\r
+// int greatGrandParentId = grandParent.getParentId();\r
\r
\r
if (fauEuTaxon.isValid()) { // Taxon\r
\r
if (rank == R_SPECIES) {\r
\r
- if(parent.getRankId() == R_SUBGENUS) {\r
-\r
+ if(parentRankId == R_SUBGENUS) {\r
+ //differ between isParanthesis= true and false\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(grandParent.getLocalName()), \r
- infraGenericEpithet.append(parent.getLocalName()));\r
- nameCacheStringBuilder.append(genusSubGenusPart);\r
+ genusOrUninomial.append(grandParentName), \r
+ infraGenericEpithet.append(parentName),\r
+ fauEuTaxon);\r
+ nameCacheStringBuilder.append(genusSubGenusPart);\r
+ \r
\r
- } else if(parent.getRankId() == R_GENUS) {\r
+ } else if(parentRankId == R_GENUS) {\r
\r
String genusPart = genusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(parent.getLocalName()));\r
+ genusOrUninomial.append(parentName));\r
nameCacheStringBuilder.append(genusPart);\r
}\r
- nameCacheStringBuilder.append(fauEuTaxon.getLocalName());\r
- specificEpithet.append(fauEuTaxon.getLocalName());\r
+ nameCacheStringBuilder.append(localName);\r
+ specificEpithet.append(localName);\r
\r
} else if (rank == R_SUBSPECIES) {\r
\r
- if(grandParent.getRankId() == R_SUBGENUS) {\r
+ if(grandParentRankId == R_SUBGENUS) {\r
\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(greatGrandParent.getLocalName()), \r
- infraGenericEpithet.append(grandParent.getLocalName()));\r
+ genusOrUninomial.append(greatGrandParentName), \r
+ infraGenericEpithet.append(grandParentName),\r
+ fauEuTaxon);\r
nameCacheStringBuilder.append(genusSubGenusPart);\r
\r
- } else if (grandParent.getRankId() == R_GENUS) {\r
+ } else if (grandParentRankId == R_GENUS) {\r
\r
String genusPart = genusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(grandParent.getLocalName()));\r
+ genusOrUninomial.append(grandParentName));\r
nameCacheStringBuilder.append(genusPart);\r
\r
}\r
- nameCacheStringBuilder.append(parent.getLocalName());\r
+ nameCacheStringBuilder.append(parentName);\r
nameCacheStringBuilder.append(" ");\r
- nameCacheStringBuilder.append(fauEuTaxon.getLocalName());\r
- specificEpithet.append(parent.getLocalName());\r
- infraSpecificEpithet.append(fauEuTaxon.getLocalName());\r
+ nameCacheStringBuilder.append(localName);\r
+ specificEpithet.append(parentName);\r
+ infraSpecificEpithet.append(localName);\r
}\r
} else { // Synonym\r
\r
if (rank == R_SPECIES) {\r
\r
- if(grandParent.getRankId() == R_SUBGENUS) {\r
+ if(grandParentRankId == R_SUBGENUS) {\r
\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(greatGrandParent.getLocalName()), \r
- infraGenericEpithet.append(grandParent.getLocalName()));\r
+ genusOrUninomial.append(greatGrandParentName), \r
+ infraGenericEpithet.append(grandParentName),\r
+ fauEuTaxon);\r
nameCacheStringBuilder.append(genusSubGenusPart);\r
\r
- } else if (grandParent.getRankId() == R_GENUS) {\r
+ } else if (grandParentRankId == R_GENUS) {\r
\r
String genusPart = genusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(grandParent.getLocalName()));\r
+ genusOrUninomial.append(grandParentName));\r
nameCacheStringBuilder.append(genusPart);\r
\r
}\r
+ nameCacheStringBuilder.append(localName);\r
+ specificEpithet.append(localName);\r
\r
} else if (rank == R_SUBSPECIES) {\r
\r
- int greatGreatGrandParentId = grandParent.getParentId();\r
- FaunaEuropaeaTaxon greatGreatGrandParent = fauEuTaxonMap.get(greatGreatGrandParentId);\r
+ String greatGreatGrandParentName = fauEuTaxon.getGreatGreatGrandParentName();\r
\r
- if(greatGrandParent.getRankId() == R_SUBGENUS) {\r
+ if(greatGrandParentRankId == R_SUBGENUS) {\r
\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(greatGreatGrandParent.getLocalName()), \r
- infraGenericEpithet.append(greatGrandParent.getLocalName()));\r
+ genusOrUninomial.append(greatGreatGrandParentName), \r
+ infraGenericEpithet.append(greatGrandParentName),\r
+ fauEuTaxon);\r
nameCacheStringBuilder.append(genusSubGenusPart);\r
\r
- } else if (greatGrandParent.getRankId() == R_GENUS) {\r
+ } else if (greatGrandParentRankId == R_GENUS) {\r
\r
String genusPart = genusPart(originalGenus, useOriginalGenus, \r
- genusOrUninomial.append(greatGreatGrandParent.getLocalName()));\r
+ genusOrUninomial.append(greatGreatGrandParentName));\r
nameCacheStringBuilder.append(genusPart);\r
}\r
\r
- nameCacheStringBuilder.append(grandParent.getLocalName());\r
+ nameCacheStringBuilder.append(grandParentName);\r
nameCacheStringBuilder.append(" ");\r
- specificEpithet.append(grandParent.getLocalName());\r
+ specificEpithet.append(grandParentName);\r
+ nameCacheStringBuilder.append(localName);\r
+ infraSpecificEpithet.append(localName);\r
}\r
\r
- nameCacheStringBuilder.append(fauEuTaxon.getLocalName());\r
- infraSpecificEpithet.append(fauEuTaxon.getLocalName());\r
+ \r
\r
}\r
\r
\r
/** Build taxon's name parts and caches */\r
private String buildTaxonName(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, TaxonNameBase<?,?>taxonName,\r
- boolean useOriginalGenus, Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, FaunaEuropaeaImportConfigurator fauEuConfig) {\r
+ boolean useOriginalGenus, FaunaEuropaeaImportConfigurator fauEuConfig) {\r
\r
/* Local taxon name string */\r
String localString = "";\r
/* Concatenated taxon name string */\r
String completeString = "";\r
\r
- StringBuilder originalGenus = new StringBuilder(fauEuTaxon.getOriginalGenusName()); \r
+ StringBuilder originalGenus = new StringBuilder("");\r
+ \r
StringBuilder genusOrUninomial = new StringBuilder();\r
StringBuilder infraGenericEpithet = new StringBuilder(); \r
StringBuilder specificEpithet = new StringBuilder();\r
StringBuilder infraSpecificEpithet = new StringBuilder();\r
\r
localString = fauEuTaxon.getLocalName();\r
-\r
int rank = fauEuTaxon.getRankId();\r
+ \r
+ // determine genus: this also works for cases of synonyms since the accepted taxon is its parent\r
+ String originalGenusString = null;\r
+ if (useOriginalGenus && ! "".equals(fauEuTaxon.getOriginalGenusName())) {\r
+ originalGenusString = fauEuTaxon.getOriginalGenusName();\r
+ } else {\r
+ originalGenusString = determineOriginalGenus(fauEuTaxon);\r
+ }\r
+\r
+ if (originalGenusString != null) {\r
+ originalGenus = new StringBuilder(originalGenusString);\r
+ }\r
\r
if(logger.isDebugEnabled()) { \r
logger.debug("Local taxon name (rank = " + rank + "): " + localString); \r
}\r
\r
if (rank < R_SPECIES) {\r
+ // subgenus or above\r
\r
completeString = localString;\r
if (rank == R_SUBGENUS) {\r
+ // subgenus part\r
infraGenericEpithet.append(localString);\r
+ \r
+ // genus part\r
+ genusOrUninomial.append(originalGenus);\r
+ \r
+ completeString = originalGenus + " ("+ localString + ")";\r
} else {\r
+ // genus or above\r
genusOrUninomial.append(localString);\r
}\r
\r
} else {\r
+ // species or below\r
\r
taxonBase = taxonBase.deproxy(taxonBase, TaxonBase.class);\r
\r
-// completeString = \r
-// buildLowerTaxonName(originalGenus, useOriginalGenus,\r
-// genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet,\r
-// fauEuTaxon, fauEuTaxonMap);\r
-// \r
-// completeString = (String) CdmUtils.removeDuplicateWhitespace(completeString.trim());\r
+ completeString = \r
+ buildLowerTaxonName(originalGenus, useOriginalGenus, \r
+ genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet,\r
+ fauEuTaxon);\r
+ \r
+ completeString = (String) CdmUtils.removeDuplicateWhitespace(completeString.trim());\r
\r
}\r
- setCompleteTaxonName(completeString, useOriginalGenus,\r
+ return setCompleteTaxonName(completeString, useOriginalGenus,\r
genusOrUninomial.toString(), infraGenericEpithet.toString(), \r
specificEpithet.toString(), infraSpecificEpithet.toString(),\r
fauEuTaxon, taxonBase, fauEuConfig);\r
- return completeString;\r
+ \r
}\r
\r
\r
+ /**\r
+ * Determines the original genus name by searching the taxon with rank Genus.\r
+ * @param fauEuTaxon\r
+ * @return\r
+ */\r
+ private String determineOriginalGenus(FaunaEuropaeaTaxon fauEuTaxon) {\r
+ String originalGenus = null;\r
+\r
+ HashMap<Integer, String> ranks = new HashMap<Integer, String>();\r
+ ranks.put(fauEuTaxon.getParentRankId(), fauEuTaxon.getParentName());\r
+ ranks.put(fauEuTaxon.getGrandParentRankId(), fauEuTaxon.getGrandParentName());\r
+ ranks.put(fauEuTaxon.getGreatGrandParentRankId(), fauEuTaxon.getGreatGrandParentName());\r
+ ranks.put(fauEuTaxon.getGreatGreatGrandParentRankId(), fauEuTaxon.getGreatGreatGrandParentName());\r
+ ranks.put(fauEuTaxon.getGreatGreatGreatGrandParentRankId(), fauEuTaxon.getGreatGreatGreatGrandParentName());\r
+ \r
+ originalGenus = ranks.get(R_GENUS);\r
+\r
+ return originalGenus;\r
+ }\r
+\r
/** Sets name parts and caches */\r
- private boolean setCompleteTaxonName(String concatString, boolean useOriginalGenus,\r
+ private String setCompleteTaxonName(String concatString, boolean useOriginalGenus,\r
String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, \r
FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, FaunaEuropaeaImportConfigurator fauEuConfig) {\r
\r
ZoologicalName zooName = (ZoologicalName)taxonName;\r
\r
if (!genusOrUninomial.equals("")) {\r
- zooName.setGenusOrUninomial(genusOrUninomial);\r
+ zooName.setGenusOrUninomial(emptyToNull(genusOrUninomial));\r
if (logger.isDebugEnabled()) { \r
logger.debug("genusOrUninomial: " + genusOrUninomial); \r
}\r
}\r
- if (!infraGenericEpithet.equals("")) {\r
- zooName.setInfraGenericEpithet(infraGenericEpithet);\r
+ \r
+ //if ((!infraGenericEpithet.equals("") && fauEuTaxon.isParenthesis()) || (!infraGenericEpithet.equals("") && fauEuTaxon.)) {\r
+ if (fauEuTaxon.getParentRankId() == R_SUBGENUS || fauEuTaxon.getRankId() == R_SUBGENUS ||\r
+ fauEuTaxon.getGrandParentRankId() == R_SUBGENUS || fauEuTaxon.getGreatGrandParentRankId() == R_SUBGENUS) {\r
+ zooName.setInfraGenericEpithet(emptyToNull(infraGenericEpithet));\r
if (logger.isDebugEnabled()) { \r
logger.debug("infraGenericEpithet: " + infraGenericEpithet); \r
}\r
}\r
- if (!specificEpithet.equals("")) {\r
- zooName.setSpecificEpithet(specificEpithet);\r
+ if ((fauEuTaxon.getRankId() == R_SPECIES || fauEuTaxon.getRankId() == R_SUBSPECIES)) {\r
+ zooName.setSpecificEpithet(emptyToNull(specificEpithet));\r
if (logger.isDebugEnabled()) { \r
logger.debug("specificEpithet: " + specificEpithet); \r
}\r
}\r
- if (!infraSpecificEpithet.equals("")) {\r
- zooName.setInfraSpecificEpithet(infraSpecificEpithet);\r
+ if (fauEuTaxon.getRankId() == R_SUBSPECIES) {\r
+ zooName.setInfraSpecificEpithet(emptyToNull(infraSpecificEpithet));\r
if (logger.isDebugEnabled()) { \r
logger.debug("infraSpecificEpithet: " + infraSpecificEpithet); \r
}\r
}\r
-\r
- zooName.setNameCache(concatString);\r
- String titleCache = buildNameTitleCache(concatString, useOriginalGenus, fauEuTaxon);\r
- zooName.setTitleCache(titleCache);\r
+ //TODO: use generate NameCache\r
+ //zooName.setNameCache(concatString);\r
+ String result = zooName.getNameCache();\r
+// zooName.generateTitle();\r
+ //String titleCache = buildNameTitleCache(concatString, useOriginalGenus, fauEuTaxon);\r
+ //zooName.setTitleCache(titleCache);\r
//titleCache = buildNameFullTitleCache(concatString, fauEuConfig);\r
- zooName.setFullTitleCache(titleCache); // TODO: Add reference, NC status\r
+// zooName.generateFullTitle();\r
+ //zooName.setFullTitleCache(titleCache); // TODO: Add reference, NC status\r
\r
// ImportHelper.setOriginalSource(taxonName, fauEuConfig.getSourceReference(), \r
// fauEuTaxon.getId(), "TaxonName");\r
-\r
- titleCache = buildTaxonTitleCache(concatString, fauEuConfig.getSourceReference());\r
- taxonBase.setTitleCache(titleCache);\r
- \r
+// taxonBase.setSec(fauEuConfig.getSourceReference());\r
+// taxonBase.generateTitle();\r
+ //titleCache = buildTaxonTitleCache(concatString, fauEuConfig.getSourceReference());\r
+ //taxonBase.setTitleCache(titleCache);\r
+ \r
if (logger.isDebugEnabled()) { \r
- logger.debug("Name stored: " + concatString); \r
+ logger.debug("Name stored: " + result); \r
}\r
- return success;\r
+ return result;\r
}\r
\r
- \r
- protected boolean saveTaxa(FaunaEuropaeaImportState state) {\r
-\r
- boolean success = true;\r
-\r
- Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
- MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
- TransactionStatus txStatus = null;\r
-\r
- if(logger.isInfoEnabled()) { logger.info("Saving taxa ..."); }\r
-\r
- if (state.getConfig().isUseTransactions()) {\r
- txStatus = startTransaction();\r
- }\r
-\r
- getTaxonService().saveTaxonAll(taxonStore.objects());\r
-\r
- if (state.getConfig().isUseTransactions()) {\r
- commitTransaction(txStatus);\r
+ /**\r
+ * Ensures that empty strings are translated to null.\r
+ * @param genusOrUninomial\r
+ * @return\r
+ */\r
+ private String emptyToNull(String text) {\r
+ if (CdmUtils.isEmpty(text)) {\r
+ return null;\r
+ } else {\r
+ return text;\r
}\r
-\r
- return success;\r
}\r
- \r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff