\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.Source;\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
boolean success = true;\r
if(logger.isInfoEnabled()) { logger.info("Start making taxa..."); }\r
-\r
+ \r
+ \r
+ \r
success = processTaxa(state);\r
\r
logger.info("End making taxa...");\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
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();\r
\r
String selectColumns = \r
" SELECT Parent.TAX_NAME AS P2Name, Parent.TAX_RNK_ID AS P2RankId, " +\r
- " GrandParent.TAX_NAME AS GP3Name, GrandParent.TAX_RNK_ID AS GP3RankId, " +\r
- " GreatGrandParent.TAX_NAME AS GGP4Name, GreatGrandParent.TAX_RNK_ID AS GGP4RankId, " +\r
- " GreatGreatGrandParent.TAX_NAME AS GGGP5Name, OriginalGenusTaxon.TAX_NAME AS OGenusName, " +\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
" 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
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
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 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
+ \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
fauEuTaxon.setUuid(taxonBaseUuid);\r
fauEuTaxon.setId(taxonId);\r
fauEuTaxon.setRankId(rankId);\r
+ fauEuTaxon.setLocalName(localName);\r
+ \r
fauEuTaxon.setParentId(parentId);\r
fauEuTaxon.setParentRankId(parentRankId);\r
- fauEuTaxon.setGrandParentRankId(grandParentRankId);\r
- fauEuTaxon.setGreatGrandParentRankId(greatGrandParentRankId);\r
- fauEuTaxon.setOriginalGenusId(originalGenusId);\r
- fauEuTaxon.setYear(year);\r
- fauEuTaxon.setLocalName(localName);\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
\r
ZoologicalName zooName = ZoologicalName.NewInstance(rank);\r
TeamOrPersonBase<?> author = authorStore.get(autId);\r
+ \r
zooName.setCombinationAuthorTeam(author);\r
zooName.setPublicationYear(year);\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
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
\r
if (((i % limit) == 0 && i != 1 ) || i == count) { \r
\r
- success = processTaxaSecondPass(state, taxonMap, fauEuTaxonMap);\r
- saveTaxa(state, taxonMap);\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
* Processes taxa from complete taxon store\r
*/\r
private boolean processTaxaSecondPass(FaunaEuropaeaImportState state, Map<Integer, TaxonBase<?>> taxonMap,\r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap) {\r
+ Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, Set<Synonym> synonymSet) {\r
\r
if(logger.isDebugEnabled()) { logger.debug("Processing taxa second pass..."); }\r
\r
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
- ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();\r
\r
boolean success = true;\r
\r
TaxonBase<?> taxonBase = taxonMap.get(id);\r
TaxonNameBase<?,?> taxonName = taxonBase.getName();\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, 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, 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
private boolean createBasionym(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, \r
- TaxonNameBase<?,?>taxonName, FaunaEuropaeaImportConfigurator fauEuConfig) {\r
-\r
-// if (fauEuTaxon.isParenthesis() && (fauEuTaxon.getOriginalGenusId() != 0)\r
-// && (fauEuTaxon.getParentId() != fauEuTaxon.getOriginalGenusId())) {\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, 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) {\r
\r
+ // species or subspecies name\r
String localName = fauEuTaxon.getLocalName();\r
int taxonId = fauEuTaxon.getId();\r
int parentId = fauEuTaxon.getParentId();\r
if (rank == R_SPECIES) {\r
\r
if(parentRankId == R_SUBGENUS) {\r
-\r
+ //differ between isParanthesis= true and false\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
genusOrUninomial.append(grandParentName), \r
- infraGenericEpithet.append(parentName));\r
- nameCacheStringBuilder.append(genusSubGenusPart);\r
+ infraGenericEpithet.append(parentName),\r
+ fauEuTaxon);\r
+ nameCacheStringBuilder.append(genusSubGenusPart);\r
+ \r
\r
} else if(parentRankId == R_GENUS) {\r
\r
\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
genusOrUninomial.append(greatGrandParentName), \r
- infraGenericEpithet.append(grandParentName));\r
+ infraGenericEpithet.append(grandParentName),\r
+ fauEuTaxon);\r
nameCacheStringBuilder.append(genusSubGenusPart);\r
\r
} else if (grandParentRankId == R_GENUS) {\r
\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
genusOrUninomial.append(greatGrandParentName), \r
- infraGenericEpithet.append(grandParentName));\r
+ infraGenericEpithet.append(grandParentName),\r
+ fauEuTaxon);\r
nameCacheStringBuilder.append(genusSubGenusPart);\r
\r
} else if (grandParentRankId == R_GENUS) {\r
nameCacheStringBuilder.append(genusPart);\r
\r
}\r
+ nameCacheStringBuilder.append(localName);\r
+ specificEpithet.append(localName);\r
\r
} else if (rank == R_SUBSPECIES) {\r
\r
\r
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus, \r
genusOrUninomial.append(greatGreatGrandParentName), \r
- infraGenericEpithet.append(greatGrandParentName));\r
+ infraGenericEpithet.append(greatGrandParentName),\r
+ fauEuTaxon);\r
nameCacheStringBuilder.append(genusSubGenusPart);\r
\r
} else if (greatGrandParentRankId == R_GENUS) {\r
nameCacheStringBuilder.append(grandParentName);\r
nameCacheStringBuilder.append(" ");\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
/* Concatenated taxon name string */\r
String completeString = "";\r
\r
- StringBuilder originalGenus = null;\r
- String originalGenusString = fauEuTaxon.getOriginalGenusName();\r
+ StringBuilder originalGenus = new StringBuilder("");\r
\r
- if (useOriginalGenus && originalGenusString != null) {\r
- originalGenus = new StringBuilder(originalGenusString);\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
+ 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 void saveTaxa(FaunaEuropaeaImportState state, Map<Integer, TaxonBase<?>> taxonMap) {\r
-\r
- if(logger.isDebugEnabled()) { logger.debug("Saving taxa ..."); }\r
-\r
- getTaxonService().saveTaxonAll(taxonMap.values());\r
-\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
- \r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff