package eu.etaxonomy.cdm.io.faunaEuropaea;\r
\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_SUBGENUS;\r
-import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SPECIES;\r
-import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBSPECIES;\r
-import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_ACCEPTED;\r
-import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_NOT_ACCEPTED;\r
\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
-import java.util.Collection;\r
import java.util.HashMap;\r
import java.util.HashSet;\r
-import java.util.Iterator;\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.log4j.Logger;\r
-import org.hibernate.Session;\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.berlinModel.CdmOneToManyMapper;\r
-import eu.etaxonomy.cdm.io.berlinModel.CdmStringMapper;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;\r
-import eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase;\r
-import eu.etaxonomy.cdm.io.common.CdmSingleAttributeMapperBase;\r
import eu.etaxonomy.cdm.io.common.ICdmIO;\r
-import eu.etaxonomy.cdm.io.common.IImportConfigurator;\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.io.tcsxml.in.TcsXmlImportState;\r
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.ISourceable;\r
-import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
-import eu.etaxonomy.cdm.model.common.OriginalSource;\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.Database;\r
-import eu.etaxonomy.cdm.model.reference.Generic;\r
-import eu.etaxonomy.cdm.model.reference.PublicationBase;\r
-import eu.etaxonomy.cdm.model.reference.Publisher;\r
import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
import eu.etaxonomy.cdm.model.taxon.Synonym;\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.model.taxon.TaxonomicTree;\r
-import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
-\r
-import com.yourkit.api.Controller;\r
\r
\r
\r
\r
public static final String OS_NAMESPACE_TAXON = "Taxon";\r
private static final Logger logger = Logger.getLogger(FaunaEuropaeaRelTaxonIncludeImport.class);\r
-\r
- /* Max number of taxa to retrieve (for test purposes) */\r
- private int maxTaxa = 0;\r
- /* Max number of taxa to be saved in CDM DB with one service call */\r
- private int limit = 5000; // TODO: Make configurable\r
- /* Max number of taxa to be retrieved from CDM DB with one service call */\r
- private int limitRetrieve = 10000; // TODO: Make configurable\r
- /* Interval for progress info message when retrieving taxa */\r
- private int modCount = 10000;\r
- /* Highest taxon index in the FauEu database */\r
- private int highestTaxonIndex = 0;\r
- /* Number of times method buildParentName() has been called for one taxon */\r
- private int callCount = 0;\r
- private Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = new HashMap();\r
-\r
-\r
+ private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database\r
+ \r
+ private ReferenceBase<?> sourceRef;\r
+ private static String ALL_SYNONYM_FROM_CLAUSE = " FROM Taxon INNER JOIN Taxon AS Parent " +\r
+ " ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +\r
+ " WHERE (Taxon.TAX_VALID = 0) " +\r
+ " AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL)";\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
*/\r
protected boolean isIgnore(FaunaEuropaeaImportState state) {\r
- return ! state.getConfig().isDoTaxa();\r
+ return ! (state.getConfig().isDoTaxonomicallyIncluded() || \r
+ state.getConfig().isDoMisappliedNames() || state.getConfig().isDoHeterotypicSynonyms());\r
}\r
\r
private boolean checkTaxonStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {\r
// }\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)\r
- */\r
- protected boolean doInvokeAlter(FaunaEuropaeaImportState state) { \r
- \r
- boolean success = true;\r
- \r
- if(logger.isInfoEnabled()) { logger.info("Start making taxa..."); }\r
- \r
-// TransactionStatus txStatus = startTransaction();\r
- \r
- success = retrieveTaxa(state, fauEuTaxonMap, Q_NO_RESTRICTION);\r
- success = processTaxaFromDatabase(state, fauEuTaxonMap);\r
- \r
-// commitTransaction(txStatus);\r
- \r
- logger.info("End making taxa...");\r
- return success;\r
- }\r
-\r
- \r
protected boolean doInvoke(FaunaEuropaeaImportState state) { \r
\r
boolean success = true;\r
+\r
+ Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
+\r
+ MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);\r
+ authorStore.makeEmpty();\r
+\r
+ if(logger.isInfoEnabled()) { logger.info("Start making relationships..."); }\r
+\r
+ TransactionStatus txStatus = startTransaction();\r
\r
+ // the uuid of an accepted taxon is needed here. any accepted taxon will do.\r
+ TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));\r
+ sourceRef = taxon.getSec();\r
\r
+ TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);\r
+ commitTransaction(txStatus);\r
\r
- Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
- MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
- taxonStore.makeEmpty();\r
- MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);\r
- authorStore.makeEmpty();\r
- \r
- if(logger.isInfoEnabled()) { logger.info("Start making taxonomically included relationships..."); }\r
- \r
- // TransactionStatus txStatus = startTransaction();\r
- \r
- ProfilerController.memorySnapshot();\r
- success = retrieveChildParentUuidMap(state);\r
- success = createRelationships(state);\r
- ProfilerController.memorySnapshot();\r
- \r
- // commitTransaction(txStatus);\r
- \r
- logger.info("End making taxa...");\r
+ //ProfilerController.memorySnapshot();\r
+ if (state.getConfig().isDoTaxonomicallyIncluded()) {\r
+ success = processParentsChildren(state);\r
+ }\r
+ //ProfilerController.memorySnapshot();\r
+ if (state.getConfig().isDoMisappliedNames()) {\r
+ success = processMisappliedNames(state);\r
+ }\r
+ //ProfilerController.memorySnapshot();\r
+ if (state.getConfig().isDoHeterotypicSynonyms()) {\r
+ if(logger.isInfoEnabled()) { \r
+ logger.info("Start making heterotypic synonym relationships..."); \r
+ }\r
+ success = processHeterotypicSynonyms(state, ALL_SYNONYM_FROM_CLAUSE);\r
+ }\r
+ //ProfilerController.memorySnapshot();\r
+\r
+ logger.info("End making taxa...");\r
\r
return success;\r
}\r
\r
/** Retrieve child-parent uuid map from CDM DB */\r
- private boolean retrieveChildParentUuidMap(FaunaEuropaeaImportState state) {\r
+ private boolean processParentsChildren(FaunaEuropaeaImportState state) {\r
+\r
+ int limit = state.getConfig().getLimitSave();\r
+\r
+ TransactionStatus txStatus = null;\r
\r
- Map<UUID, UUID> childParentMap = state.getChildParentMap();\r
+ Map<UUID, UUID> childParentMap = null;\r
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
Source source = fauEuConfig.getSource();\r
int i = 0;\r
boolean success = true;\r
\r
+ String selectCount = \r
+ " SELECT count(*) ";\r
+\r
+ String selectColumns = " SELECT Taxon.UUID AS ChildUuid, Parent.UUID AS ParentUuid ";\r
+ \r
+ String fromClause = " FROM Taxon INNER JOIN Taxon AS Parent " +\r
+ " ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +\r
+ " WHERE (Taxon.TAX_VALID <> 0) AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL )";\r
+ \r
+ String orderClause = " ORDER BY Taxon.TAX_RNK_ID ASC";\r
+\r
+ String countQuery = \r
+ selectCount + fromClause;\r
+\r
+ String selectQuery = \r
+ selectColumns + fromClause + orderClause;\r
+ \r
+ if(logger.isInfoEnabled()) { logger.info("Start making taxonomically included relationships..."); }\r
+ \r
try {\r
\r
- String strQuery = \r
- " SELECT dbo.Taxon.UUID AS ChildUuid, Parent.UUID AS ParentUuid " +\r
- " FROM dbo.Taxon INNER JOIN dbo.Taxon AS Parent " +\r
- " ON dbo.Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +\r
- " WHERE (dbo.Taxon.TAX_VALID <> 0) AND (dbo.Taxon.TAX_AUT_ID <> " + A_AUCT + ")";\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("Query: " + strQuery);\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
- ResultSet rs = source.getResultSet(strQuery);\r
- \r
- while (rs.next()) {\r
+ while (rs.next()) {\r
\r
- if ((i++ % modCount) == 0 && i != 1 ) { \r
+ if ((i++ % limit) == 0) {\r
+ \r
+ txStatus = startTransaction();\r
+ childParentMap = new HashMap<UUID, UUID>(limit);\r
+ \r
if(logger.isInfoEnabled()) {\r
- logger.info("Parent-child mappings retrieved: " + (i-1)); \r
+ logger.info("Taxonomically included retrieved: " + (i-1)); \r
}\r
}\r
\r
logger.debug("Duplicated child UUID (" + childUuid + ")");\r
}\r
}\r
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
+\r
+ success = createParentChildRelationships(state, childParentMap);\r
+\r
+ childParentMap = null;\r
+ commitTransaction(txStatus);\r
+\r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("i = " + i + " - Transaction committed"); \r
+ }\r
+ }\r
}\r
\r
} catch (SQLException e) {\r
}\r
return success; \r
}\r
-\r
\r
- /** Retrieve taxa from FauEu DB and build FauEuTaxonMap only */\r
- private boolean retrieveTaxa(FaunaEuropaeaImportState state,\r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, int valid) {\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
- MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);\r
+ /** Retrieve misapplied name / accepted taxon uuid map from CDM DB */\r
+ private boolean processMisappliedNames(FaunaEuropaeaImportState state) {\r
+\r
+ int limit = state.getConfig().getLimitSave();\r
\r
+ TransactionStatus txStatus = null;\r
+\r
+ Map<UUID, UUID> childParentMap = null;\r
+ FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
Source source = fauEuConfig.getSource();\r
-// String namespace = "Taxon";\r
int i = 0;\r
boolean success = true;\r
\r
- try {\r
- \r
- String strQuery = \r
- " SELECT MAX(TAX_ID) AS TAX_ID FROM dbo.Taxon ";\r
- \r
- ResultSet rs = source.getResultSet(strQuery);\r
- while (rs.next()) {\r
- int maxTaxonId = rs.getInt("TAX_ID");\r
- highestTaxonIndex = maxTaxonId;\r
- }\r
- \r
- String top = "";\r
- if (maxTaxa > 0) {\r
- top = "TOP " + maxTaxa;\r
- }\r
+ String selectCount = \r
+ " SELECT count(*) ";\r
+\r
+ String selectColumns = " SELECT Taxon.UUID AS MisappliedUuid, Parent.UUID AS AcceptedUuid ";\r
+ \r
+ String fromClause = " FROM Taxon INNER JOIN Taxon AS Parent " +\r
+ " ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +\r
+ " WHERE (Taxon.TAX_VALID = 0) AND (Taxon.TAX_AUT_ID = " + A_AUCT + ")";\r
+ \r
+ String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";\r
+\r
+ String countQuery = \r
+ selectCount + fromClause;\r
+\r
+ String selectQuery = \r
+ selectColumns + fromClause + orderClause;\r
\r
- String validClause = "";\r
- if (valid == T_STATUS_ACCEPTED || valid == T_STATUS_NOT_ACCEPTED) {\r
- validClause = " AND " + " TAX_VALID = " + valid;\r
- }\r
+ if(logger.isInfoEnabled()) { logger.info("Start making misapplied name relationships..."); }\r
+\r
+ try {\r
+\r
+ ResultSet rs = source.getResultSet(countQuery);\r
+ rs.next();\r
+ int count = rs.getInt(1);\r
\r
- strQuery = \r
- " SELECT " + top + " 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
- validClause;\r
-\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Query: " + strQuery);\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
- rs = source.getResultSet(strQuery);\r
- \r
- while (rs.next()) {\r
\r
- if ((i++ % modCount) == 0 && i != 1 ) { \r
+ while (rs.next()) {\r
+ \r
+ if ((i++ % limit) == 0) {\r
+ \r
+ txStatus = startTransaction();\r
+ childParentMap = new HashMap<UUID, UUID>(limit);\r
+ \r
if(logger.isInfoEnabled()) {\r
- logger.info("Taxa retrieved: " + (i-1)); \r
+ logger.info("Misapplied names retrieved: " + (i-1) ); \r
}\r
}\r
\r
- int taxonId = rs.getInt("TAX_ID");\r
- String localName = rs.getString("TAX_NAME");\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 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
- int parenthesis = rs.getInt("TAX_PARENTHESIS");\r
- String autName = rs.getString("aut_name");\r
- Rank rank = null;\r
-// UUID taxonBaseUuid = UUID.randomUUID();\r
-\r
- FaunaEuropaeaTaxon fauEuTaxon = new FaunaEuropaeaTaxon();\r
-// fauEuTaxon.setUuid(taxonBaseUuid);\r
- fauEuTaxon.setLocalName(localName);\r
- fauEuTaxon.setParentId(parentId);\r
- fauEuTaxon.setOriginalGenusId(originalGenusId);\r
- fauEuTaxon.setId(taxonId);\r
- fauEuTaxon.setRankId(rankId);\r
- fauEuTaxon.setYear(year);\r
- fauEuTaxon.setAuthor(autName);\r
- if (parenthesis == P_PARENTHESIS) {\r
- fauEuTaxon.setParenthesis(true);\r
- } else {\r
- fauEuTaxon.setParenthesis(false);\r
- }\r
- if (status == T_STATUS_ACCEPTED) {\r
- fauEuTaxon.setValid(true);\r
+ String childUuidStr = rs.getString("MisappliedUuid");\r
+ String parentUuidStr = rs.getString("AcceptedUuid");\r
+ UUID childUuid = UUID.fromString(childUuidStr);\r
+ UUID parentUuid = UUID.fromString(parentUuidStr);\r
+ \r
+ if (!childParentMap.containsKey(childUuid)) {\r
+\r
+ childParentMap.put(childUuid, parentUuid);\r
+\r
} else {\r
- fauEuTaxon.setValid(false);\r
+ if(logger.isDebugEnabled()) {\r
+ logger.debug("Duplicated child UUID (" + childUuid + ")");\r
+ }\r
}\r
\r
- try {\r
- rank = FaunaEuropaeaTransformer.rankId2Rank(rs, false);\r
- } catch (UnknownCdmTypeException e) {\r
- logger.warn("Taxon (" + taxonId + ") has unknown rank (" + rankId + ") and could not be saved.");\r
- continue;\r
- } catch (NullPointerException e) {\r
- logger.warn("Taxon (" + taxonId + ") has rank null and can not be saved.");\r
- continue;\r
- }\r
- \r
- try {\r
- \r
- \r
- if (!fauEuTaxonMap.containsKey(taxonId)) {\r
- if (fauEuTaxon == null) {\r
- if (logger.isDebugEnabled()) { \r
- logger.debug("Taxon base is null. Taxon (" + taxonId + ") ignored.");\r
- }\r
- continue;\r
- }\r
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
\r
- \r
-// taxonStore.put(taxonId, taxonBase);\r
- \r
- fauEuTaxonMap.put(taxonId, fauEuTaxon);\r
- \r
-// if (logger.isDebugEnabled()) { \r
-// logger.debug("Stored taxon base (" + taxonId + ") " + localName); \r
-// }\r
- } else {\r
- logger.warn("Not imported taxon base with duplicated TAX_ID (" + taxonId + \r
- ") " + localName);\r
+ success = createMisappliedNameRelationships(state, childParentMap);\r
+\r
+ childParentMap = null;\r
+ commitTransaction(txStatus);\r
+\r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("i = " + i + " - Transaction committed"); \r
}\r
- } catch (Exception e) {\r
- logger.warn("An exception occurred when creating taxon base with id " + taxonId + \r
- ". Taxon base could not be saved.");\r
}\r
}\r
+\r
} catch (SQLException e) {\r
logger.error("SQLException:" + e);\r
success = false;\r
}\r
-\r
- return success;\r
+ return success; \r
}\r
\r
- \r
- public Map<UUID, UUID> partMap(int border, Map<UUID, UUID> map) {\r
\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Map size: " + map.size());\r
- }\r
- Set<Map.Entry<UUID, UUID>> entries = map.entrySet();\r
- Iterator<Map.Entry<UUID, UUID>> entryIter = entries.iterator();\r
- Map<UUID, UUID> partMap = new HashMap<UUID, UUID>();\r
\r
- for (int i = 0; i < border; i++) {\r
- //while (entryIter.hasNext()) {\r
+ /** Retrieve synonyms from FauEuDB DB */\r
+ private boolean processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {\r
\r
- Map.Entry<UUID, UUID> mapEntry = (Map.Entry<UUID, UUID>)entryIter.next();\r
- partMap.put(mapEntry.getKey(), mapEntry.getValue());\r
- entryIter.remove();\r
- }\r
+ FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
+ Source source = fauEuConfig.getSource();\r
+ boolean success = true;\r
+\r
+ String selectCount = \r
+ " SELECT count(*) ";\r
+\r
+ String selectColumns = " SELECT Taxon.UUID AS SynonymUuid, Parent.UUID AS AcceptedUuid ";\r
\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Map size: " + map.size());\r
- }\r
- return partMap;\r
- } \r
-\r
-// public Map<UUID, UUID> childParentMap partMap(int start, int limit, Map<UUID, UUID> childParentMap) {\r
-// \r
-// int index = 0;\r
-// \r
-// for (int i = 0; i < limit; i++) {\r
-// \r
-// int j = start + i;\r
-// \r
-// Object object = childParentMap.get(j);\r
-// if(object != null) {\r
-// childParentMap.put(index, childParentMap.get(j));\r
-// index++;\r
-// } else {\r
-// if (logger.isDebugEnabled()) { logger.debug("Object (" + j + ") is null"); }\r
-// }\r
-// }\r
-// return (Map<UUID, UUID> childParentMap)internalPartMap.values();\r
-// }\r
+ String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";\r
\r
- \r
- /** Creates parent-child relationships.\r
- * Single Parent-child pairs are retrieved via findByUUID(UUID) from CDM DB \r
- * This takes inacceptable long time. */\r
- private boolean createRelationships_(FaunaEuropaeaImportState state) {\r
+ String countQuery = \r
+ selectCount + fromClause;\r
\r
- Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
- MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
- taxonStore.makeEmpty();\r
- Map<UUID, UUID> childParentMap = state.getChildParentMap();\r
- ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();\r
+ String selectQuery = \r
+ selectColumns + fromClause + orderClause;\r
+ logger.debug(selectQuery);\r
+ \r
+ try {\r
\r
- int upperBorder = childParentMap.size();\r
- int nbrOfBlocks = 0;\r
+ ResultSet rs = source.getResultSet(countQuery);\r
+ rs.next();\r
+ int count = rs.getInt(1);\r
+ \r
+ rs = source.getResultSet(selectQuery);\r
\r
- boolean success = true;\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
+ success = storeSynonymRelationships(rs, count, state);\r
\r
- if (upperBorder < limit) { // TODO: test with critical values\r
- limit = upperBorder;\r
- } else {\r
- nbrOfBlocks = upperBorder / limit;\r
+ } catch (SQLException e) {\r
+ logger.error("SQLException:" + e);\r
+ success = false;\r
}\r
+ return success; \r
+ }\r
+ \r
+ \r
\r
- if(logger.isInfoEnabled()) { \r
- logger.info("number of child-parent pairs = " + upperBorder \r
- + ", limit = " + limit\r
- + ", number of blocks = " + nbrOfBlocks); \r
- }\r
+ \r
+ private boolean storeSynonymRelationships(ResultSet rs, int count, FaunaEuropaeaImportState state) \r
+ throws SQLException {\r
+\r
+ TransactionStatus txStatus = null;\r
+ Map<UUID, UUID> synonymAcceptedMap = null;\r
+ int i = 0;\r
+ boolean success = true;\r
+ int limit = state.getConfig().getLimitSave();\r
\r
- for (int j = 1; j <= nbrOfBlocks + 1; j++) {\r
- int offset = j - 1;\r
- int start = offset * limit;\r
+ while (rs.next()) {\r
\r
- if(logger.isInfoEnabled()) { logger.info("Processing child-parent pairs: " + start + " - " + (start + limit - 1)); }\r
+ if ((i++ % limit) == 0) {\r
\r
- if(logger.isInfoEnabled()) { \r
- logger.info("index = " + j \r
- + ", offset = " + offset\r
- + ", start = " + start); \r
- }\r
+ txStatus = startTransaction();\r
+ synonymAcceptedMap = new HashMap<UUID, UUID>(limit);\r
\r
- if (j == nbrOfBlocks + 1) {\r
- limit = upperBorder - nbrOfBlocks * limit;\r
- if(logger.isInfoEnabled()) { logger.info("number of blocks = " + nbrOfBlocks + " limit = " + limit); }\r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("Synonyms retrieved: " + (i-1)); \r
+ }\r
}\r
\r
- TransactionStatus txStatus = startTransaction();\r
- \r
- \r
-// for (int k = 1; k <= start + offset; k++) { // TODO: test borders\r
-// int k = 0;\r
+ String synonymUuidStr = rs.getString("SynonymUuid");\r
+ String acceptedUuidStr = rs.getString("AcceptedUuid");\r
+ UUID synonymUuid = UUID.fromString(synonymUuidStr);\r
+ UUID acceptedUuid = UUID.fromString(acceptedUuidStr);\r
\r
- Map<UUID, UUID> childParentPartMap = partMap(limit, childParentMap);\r
- Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);\r
- \r
- if (logger.isInfoEnabled()) {\r
- logger.info("Partmap size: " + childParentPartMap.size());\r
+ if (!synonymAcceptedMap.containsKey(synonymUuid)) {\r
+\r
+ synonymAcceptedMap.put(synonymUuid, acceptedUuid);\r
+\r
+ } else {\r
+ if(logger.isDebugEnabled()) {\r
+ logger.debug("Duplicated synonym UUID (" + synonymUuid + ")");\r
+ }\r
}\r
\r
- for (UUID childUuid : childParentPartMap.keySet()) {\r
-// for (UUID childUuid : childParentMap.keySet()) {\r
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
\r
- UUID parentUuid = childParentPartMap.get(childUuid);\r
+ success = createHeterotypicSynonyms(state, synonymAcceptedMap);\r
\r
- try {\r
- TaxonBase<?> parent = getTaxonService().findByUuid(parentUuid);\r
- if (logger.isTraceEnabled()) {\r
- logger.trace("Parent find called (" + parentUuid + ")");\r
- }\r
- TaxonBase<?> child = getTaxonService().findByUuid(childUuid);\r
- if (logger.isTraceEnabled()) {\r
- logger.trace("Child find called (" + childUuid + ")");\r
- }\r
- Taxon parentTaxon = parent.deproxy(parent, Taxon.class);\r
- Taxon childTaxon = child.deproxy(child, Taxon.class);\r
+ synonymAcceptedMap = null;\r
+ commitTransaction(txStatus);\r
\r
- if (childTaxon != null && parentTaxon != null) {\r
- \r
-// makeTaxonomicallyIncluded(state, parentTaxon, childTaxon, sourceRef, null);\r
- \r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Parent-child (" + parentUuid + "-" + childUuid + \r
- ") relationship created");\r
- }\r
- if (!childSet.contains(childTaxon)) {\r
- \r
- childSet.add(childTaxon);\r
- \r
- if (logger.isTraceEnabled()) {\r
- logger.trace("Child taxon (" + childUuid + ") added to Set");\r
- }\r
- \r
- } else {\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Duplicated child taxon (" + childUuid + ")");\r
- }\r
- }\r
- } else {\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Parent(" + parentUuid + ") or child (" + childUuid + " is null");\r
- }\r
- }\r
- \r
-// if (childTaxon != null && !childSet.contains(childTaxon)) {\r
-// childSet.add(childTaxon);\r
-// if (logger.isDebugEnabled()) {\r
-// logger.debug("Child taxon (" + childUuid + ") added to Set");\r
-// }\r
-// } else {\r
-// if (logger.isDebugEnabled()) {\r
-// logger.debug("Duplicated child taxon (" + childUuid + ")");\r
-// }\r
-// }\r
- \r
- } catch (Exception e) {\r
- logger.error("Error creating taxonomically included relationship parent-child (" + \r
- parentUuid + "-" + childUuid + ")");\r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("i = " + i + " - Transaction committed"); \r
}\r
-\r
}\r
- getTaxonService().saveTaxonAll(childSet);\r
- commitTransaction(txStatus);\r
}\r
return success;\r
}\r
- \r
- \r
+ \r
+ \r
+ \r
+ \r
+\r
/* Creates parent-child relationships.\r
* Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. \r
- * It takes about 5min to save a block of 5000 taxa.*/\r
- private boolean createRelationships(FaunaEuropaeaImportState state) {\r
-\r
- Map<UUID, UUID> childParentUuidMap = state.getChildParentMap();\r
- ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();\r
-// UUID treeUuid = state.getTree(sourceRef).getUuid();\r
-// TaxonomicTree tree = getTaxonService().getTaxonomicTreeByUuid(treeUuid);\r
-// TaxonomicTree tree = state.getTree(sourceRef);\r
-\r
- int upperBorder = childParentUuidMap.size();\r
- int nbrOfBlocks = 0;\r
-\r
+ */\r
+ private boolean createParentChildRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> childParentMap) {\r
+ //gets the taxon "Hydroscaphidae"(family)\r
+ TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));\r
+ sourceRef = taxon.getSec();\r
boolean success = true;\r
-\r
- if (upperBorder < limit) { // TODO: test with critical values\r
- limit = upperBorder;\r
- } else {\r
- nbrOfBlocks = upperBorder / limit;\r
- }\r
-\r
- if(logger.isInfoEnabled()) { \r
- logger.info("number of child-parent pairs = " + upperBorder \r
- + ", limit = " + limit\r
- + ", number of blocks = " + nbrOfBlocks); \r
- }\r
-\r
- for (int j = 1; j <= nbrOfBlocks + 1; j++) {\r
- \r
- ProfilerController.memorySnapshot();\r
- \r
- int offset = j - 1;\r
- int start = offset * limit;\r
-\r
- if(logger.isInfoEnabled()) { logger.info("Processing child-parent pairs: " + start + " - " + (start + limit - 1)); }\r
-\r
- if(logger.isInfoEnabled()) { \r
- logger.info("index = " + j \r
- + ", offset = " + offset\r
- + ", start = " + start); \r
- }\r
-\r
- if (j == nbrOfBlocks + 1) {\r
- limit = upperBorder - nbrOfBlocks * limit;\r
- if(logger.isInfoEnabled()) { logger.info("number of blocks = " + nbrOfBlocks + " limit = " + limit); }\r
- }\r
-\r
- TransactionStatus txStatus = startTransaction();\r
- //add tree to new session\r
- TaxonomicTree tree = state.getTree(sourceRef);\r
- if (tree == null){\r
- tree = makeTree(state, sourceRef);\r
- }\r
- getTaxonService().saveTaxonomicTree(tree);\r
+ int limit = state.getConfig().getLimitSave();\r
+ \r
+ TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);\r
\r
- Map<UUID, UUID> childParentPartUuidMap = partMap(limit, childParentUuidMap);\r
Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);\r
\r
- Set<UUID> childKeysSet = childParentPartUuidMap.keySet();\r
- Set<UUID> parentValuesSet = new HashSet<UUID>(childParentPartUuidMap.values());\r
+ Set<UUID> childKeysSet = childParentMap.keySet();\r
+ Set<UUID> parentValuesSet = new HashSet<UUID>(childParentMap.values());\r
\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Start reading children and parents");\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start reading children and parents");\r
}\r
- List<TaxonBase> children = getTaxonService().findByUuid(childKeysSet);\r
- List<TaxonBase> parents = getTaxonService().findByUuid(parentValuesSet);\r
- Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>();\r
+ List<TaxonBase> children = getTaxonService().find(childKeysSet);\r
+ List<TaxonBase> parents = getTaxonService().find(parentValuesSet);\r
+ Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>(parents.size());\r
for (TaxonBase taxonBase : parents){\r
parentsMap.put(taxonBase.getUuid(), taxonBase);\r
}\r
\r
- \r
- if (logger.isInfoEnabled()) {\r
- logger.info("End reading children and parents");\r
- }\r
- \r
- \r
if (logger.isTraceEnabled()) {\r
+ logger.debug("End reading children and parents");\r
for (UUID uuid : childKeysSet) {\r
logger.trace("child uuid query: " + uuid);\r
}\r
- }\r
- if (logger.isTraceEnabled()) {\r
for (UUID uuid : parentValuesSet) {\r
logger.trace("parent uuid query: " + uuid);\r
}\r
- }\r
- if (logger.isTraceEnabled()) {\r
for (TaxonBase tb : children) {\r
logger.trace("child uuid result: " + tb.getUuid());\r
}\r
- }\r
- if (logger.isTraceEnabled()) {\r
for (TaxonBase tb : parents) {\r
logger.trace("parent uuid result: " + tb.getUuid());\r
}\r
}\r
\r
UUID mappedParentUuid = null;\r
- UUID parentUuid = null;\r
UUID childUuid = null;\r
\r
for (TaxonBase child : children) {\r
try {\r
Taxon childTaxon = child.deproxy(child, Taxon.class);\r
childUuid = childTaxon.getUuid();\r
- mappedParentUuid = childParentPartUuidMap.get(childUuid);\r
+ mappedParentUuid = childParentMap.get(childUuid);\r
TaxonBase parent = null;\r
\r
TaxonBase potentialParent = parentsMap.get(mappedParentUuid);\r
// if(parentUuid.equals(mappedParentUuid)) {\r
parent = potentialParent;\r
if (logger.isDebugEnabled()) {\r
- logger.debug("Parent (" + parentUuid + ") found for child (" + childUuid + ")");\r
+ logger.debug("Parent (" + mappedParentUuid + ") found for child (" + childUuid + ")");\r
}\r
// break;\r
// }\r
\r
if (childTaxon != null && parentTaxon != null) {\r
\r
-// makeTaxonomicallyIncluded(state, parentTaxon, childTaxon, sourceRef, null, tree);\r
- makeTaxonomicallyIncluded(state, parentTaxon, childTaxon, sourceRef, null);\r
+ tree.addParentChild(parentTaxon, childTaxon, sourceRef, null);\r
\r
if (logger.isDebugEnabled()) {\r
- logger.debug("Parent-child (" + parentUuid + "-" + childUuid + \r
+ logger.debug("Parent-child (" + mappedParentUuid + "-" + childUuid + \r
") relationship created");\r
}\r
- if (!childSet.contains(childTaxon)) {\r
+ if (childTaxon != null && !childSet.contains(childTaxon)) {\r
\r
childSet.add(childTaxon);\r
\r
}\r
} else {\r
if (logger.isDebugEnabled()) {\r
- logger.debug("Parent(" + parentUuid + ") or child (" + childUuid + " is null");\r
- }\r
- }\r
- \r
- if (childTaxon != null && !childSet.contains(childTaxon)) {\r
- childSet.add(childTaxon);\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Child taxon (" + childUuid + ") added to Set");\r
- }\r
- } else {\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Duplicated child taxon (" + childUuid + ")");\r
+ logger.debug("Parent(" + mappedParentUuid + ") or child (" + childUuid + " is null");\r
}\r
}\r
\r
} catch (Exception e) {\r
logger.error("Error creating taxonomically included relationship parent-child (" + \r
- parentUuid + "-" + childUuid + ")");\r
+ mappedParentUuid + "-" + childUuid + ")", e);\r
}\r
\r
}\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Start saving childSet");\r
- }\r
- getTaxonService().saveTaxonAll(childSet);\r
- if (logger.isInfoEnabled()) {\r
- logger.info("End saving childSet");\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start saving childSet");\r
}\r
-// getTaxonService().clear();\r
-// if (logger.isInfoEnabled()) {\r
-// logger.info("End clearing session");\r
-// }\r
- commitTransaction(txStatus);\r
- if (logger.isInfoEnabled()) {\r
- logger.info("End commit transaction");\r
+ getTaxonService().save(childSet);\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("End saving childSet");\r
}\r
+\r
parentValuesSet = null;\r
childSet = null;\r
- childParentPartUuidMap = null;\r
children = null;\r
parents = null;\r
- }\r
+ tree = null;\r
+ \r
return success;\r
}\r
\r
- \r
- /* Creates parent-child relationships.\r
- * Taxon bases are retrieved in blocks from CDM DB.\r
- * Parent is retrieved from CDM DB via original source id if not found in current block.\r
- * In case of blocksize = 20.000 this takes ca. 1-2 hours per block.\r
- * */\r
- private boolean createRelationships_old(FaunaEuropaeaTaxon fauEuTaxon,\r
- TaxonBase<?> taxonBase, TaxonNameBase<?,?> taxonName, List<Taxon> taxa,\r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) {\r
- \r
- int parentId = fauEuTaxon.getParentId();\r
- int taxonId = fauEuTaxon.getId();\r
- FaunaEuropaeaTaxon parentFauEuTaxon = fauEuTaxonMap.get(parentId);\r
- if (parentFauEuTaxon == null) {\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Parent taxon is null (" + parentId + ")");\r
- }\r
- return false;\r
- }\r
-// UUID parentUuid = parentFauEuTaxon.getUuid();\r
- Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
- MapWrapper<TaxonBase> parentTaxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
- ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();\r
+ /* Creates misapplied name relationships.\r
+ * Misapplied name-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. \r
+ */\r
+ private boolean createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {\r
\r
- TaxonBase<?> parentTaxonBase = null;\r
- \r
-// for (TaxonBase<?> potentialParentTaxon : taxonBases) {\r
-// if(potentialParentTaxon.getUuid().equals(parentUuid)) {\r
-// parentTaxonBase = potentialParentTaxon;\r
-// break;\r
-// }\r
-// }\r
-// if (parentTaxonBase == null) { \r
-// parentTaxonBase = getTaxonService().getTaxonByUuid(parentUuid); \r
-// }\r
+ //gets the taxon "Hydroscaphidae" (family)\r
\r
- // TODO: Copy parents from taxonBases to parentTaxonStore\r
+ TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));\r
+ sourceRef = taxon.getSec();\r
+ boolean success = true;\r
+ int limit = state.getConfig().getLimitSave();\r
\r
- if (parentTaxonStore.containsId(parentId)) {\r
- parentTaxonBase = parentTaxonStore.get(parentId);\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Parent (" + parentId + ") found in parent taxon store");\r
+ Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);\r
+ \r
+ Set<UUID> misappliedNamesSet = fromToMap.keySet();\r
+ Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());\r
+ \r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start reading misapplied names and accepted taxa");\r
}\r
-// } else {\r
-// for (TaxonBase<?> potentialParentTaxon : taxonBases) {\r
-// if(potentialParentTaxon.getId() == parentId) {\r
-// parentTaxonBase = potentialParentTaxon;\r
-// if (logger.isInfoEnabled()) {\r
-// logger.info("Parent (" + parentId + ") found in taxon base list");\r
-// }\r
-// break;\r
-// }\r
-// }\r
- }\r
- if (parentTaxonBase == null) {\r
- ISourceable sourceable = \r
- getCommonService().getSourcedObjectByIdInSource(TaxonBase.class, Integer.toString(parentId), OS_NAMESPACE_TAXON);\r
- parentTaxonBase = ((IdentifiableEntity)sourceable).deproxy(sourceable, TaxonBase.class);\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Parent (" + parentId + ") retrieved from DB via original source id");\r
+ List<TaxonBase> misappliedNames = getTaxonService().find(misappliedNamesSet);\r
+ List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaSet);\r
+ Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());\r
+ for (TaxonBase taxonBase : acceptedTaxa){\r
+ acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);\r
+ }\r
+ \r
+ if (logger.isTraceEnabled()) {\r
+ logger.info("End reading misapplied names and accepted taxa");\r
+ for (UUID uuid : misappliedNamesSet) {\r
+ logger.trace("misapplied name uuid query: " + uuid);\r
+ }\r
+ for (UUID uuid : acceptedTaxaSet) {\r
+ logger.trace("accepted taxon uuid query: " + uuid);\r
+ }\r
+ for (TaxonBase tb : misappliedNames) {\r
+ logger.trace("misapplied name uuid result: " + tb.getUuid());\r
+ }\r
+ for (TaxonBase tb : acceptedTaxa) {\r
+ logger.trace("accepted taxon uuid result: " + tb.getUuid());\r
+ }\r
}\r
- }\r
- \r
- if (!parentTaxonStore.containsId(parentId)) {\r
- parentTaxonStore.put(parentId, parentTaxonBase);\r
- }\r
-\r
-\r
- \r
- Taxon parentTaxon = parentTaxonBase.deproxy(parentTaxonBase, Taxon.class);\r
\r
- boolean success = true;\r
- \r
-// if (!fauEuTaxon.isValid()) { // FauEu Synonym\r
+ UUID mappedAcceptedTaxonUuid = null;\r
+ UUID misappliedNameUuid = null;\r
+ Taxon misappliedNameTaxon = null;\r
+ TaxonBase acceptedTaxonBase = null;\r
+ Taxon acceptedTaxon = null;\r
\r
-// } else if (fauEuTaxon.isValid()) { // FauEu Taxon\r
- \r
- Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);\r
+ for (TaxonBase misappliedName : misappliedNames) {\r
\r
- try {\r
- // add this taxon as child to parent\r
- if (parentTaxon != null) {\r
-// makeTaxonomicallyIncluded(state, parentTaxon, taxon, sourceRef, null);\r
- if (logger.isDebugEnabled()) {\r
- logger.debug("Parent-child (" + parentId + "-" + taxonId + \r
- ") relationship created");\r
+ try {\r
+ misappliedNameTaxon = misappliedName.deproxy(misappliedName, Taxon.class);\r
+ misappliedNameUuid = misappliedNameTaxon.getUuid();\r
+ mappedAcceptedTaxonUuid = fromToMap.get(misappliedNameUuid);\r
+ acceptedTaxonBase = null;\r
+ \r
+ acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + misappliedNameUuid + ")");\r
+ }\r
+ \r
+ acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);\r
+ \r
+ if (misappliedNameTaxon != null && acceptedTaxon != null) {\r
+ \r
+ acceptedTaxon.addMisappliedName(misappliedNameTaxon, sourceRef, null);\r
+ \r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Accepted taxon / misapplied name (" + mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + \r
+ ") relationship created");\r
+ }\r
+ if (!misappliedNameSet.contains(misappliedNameTaxon)) {\r
+ \r
+ misappliedNameSet.add(misappliedNameTaxon);\r
+ \r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");\r
+ }\r
+ \r
+ } else {\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");\r
+ }\r
+ }\r
+ } else {\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + misappliedNameUuid + " is null");\r
+ }\r
}\r
+ \r
+ if (misappliedNameTaxon != null && !misappliedNameSet.contains(misappliedNameTaxon)) {\r
+ misappliedNameSet.add(misappliedNameTaxon);\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");\r
+ }\r
+ } else {\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");\r
+ }\r
+ }\r
+ \r
+ } catch (Exception e) {\r
+ logger.error("Error creating misapplied name relationship accepted taxon-misapplied name (" + \r
+ mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + ")", e);\r
}\r
\r
- } catch (Exception e) {\r
- logger.error("Error creating taxonomically included relationship Parent-child (" + \r
- parentId + "-" + taxonId + ")");\r
}\r
- \r
- \r
-// }\r
- \r
- return success;\r
- }\r
- \r
-\r
- private boolean makeTaxonomicallyIncluded(FaunaEuropaeaImportState state, Taxon toTaxon, Taxon fromTaxon, \r
- ReferenceBase citation, String microCitation){\r
- boolean success = true;\r
- ReferenceBase sec = toTaxon.getSec();\r
- sec = CdmBase.deproxy(sec, ReferenceBase.class);\r
- sec = citation;\r
- TaxonomicTree tree = state.getTree(sec);\r
- \r
- \r
- \r
-// Session session = getTaxonService().getSession();\r
- \r
-// if (session.contains(sec)) {\r
-// logger.debug("Sec contained in session. Id = " + sec.getId());\r
-// } else {\r
-// logger.info("Sec not contained in session. Id = " + sec.getId());\r
-// getReferenceService().merge(sec);\r
-// }\r
- \r
- if (tree == null){\r
- tree = makeTree(state, sec);\r
- }\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start saving misappliedNameSet");\r
+ }\r
+ getTaxonService().save(misappliedNameSet);\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("End saving misappliedNameSet");\r
+ }\r
\r
-// if (session.contains(tree)) {\r
-// logger.debug("Taxonomic tree contained in session. Id = " + tree.getId());\r
-// } else {\r
-// logger.info("Taxonomic tree not contained in session. Id = " + tree.getId());\r
-// UUID treeUuid = state.getTree(sec).getUuid();\r
-// tree = getTaxonService().getTaxonomicTreeByUuid(treeUuid);\r
-// logger.info("Tree retrieved");\r
-// }\r
+ acceptedTaxaSet = null;\r
+ misappliedNameSet = null;\r
+ misappliedNames = null;\r
+ acceptedTaxa = null;\r
\r
- success = tree.addParentChild(toTaxon, fromTaxon, citation, microCitation);\r
return success;\r
}\r
\r
\r
-// public int calculateBlockSize(int limit, int upperBorder) {\r
-//\r
-// int blockSize = 0;\r
-// \r
-// if (upperBorder < limit) {\r
-// limit = upperBorder;\r
-// } else {\r
-// blockSize = upperBorder / limit;\r
-// }\r
-// }\r
- \r
- \r
- private boolean processTaxaFromDatabase(FaunaEuropaeaImportState state,\r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap) {\r
-\r
- if(logger.isInfoEnabled()) { logger.info("Processing taxa second pass..."); }\r
+ /* Creates heterotypic synonym relationships.\r
+ * Synonym-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. \r
+ */\r
+ private boolean createHeterotypicSynonyms(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {\r
\r
- MapWrapper<TaxonBase> taxonBaseMap = new MapWrapper<TaxonBase>(null);\r
+ int limit = state.getConfig().getLimitSave();\r
+ boolean success = true;\r
\r
- int nbrOfTaxa = getTaxonService().count(Taxon.class);\r
- int n = 0;\r
+ Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);\r
\r
- boolean success = true;\r
+ Set<UUID> synonymUuidSet = fromToMap.keySet();\r
+ Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());\r
\r
- if (nbrOfTaxa < limit) { // TODO: test with critical values\r
- limit = nbrOfTaxa;\r
- } else {\r
- n = nbrOfTaxa / limit;\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Reading synonym names and accepted taxa...");\r
}\r
-\r
- if(logger.isInfoEnabled()) { \r
- logger.info("number of taxa = " + nbrOfTaxa \r
- + ", limit = " + limit\r
- + ", n = " + n); \r
+ List<TaxonBase> synonyms = getTaxonService().find(synonymUuidSet);\r
+ List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaUuidSet);\r
+ Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());\r
+ for (TaxonBase taxonBase : acceptedTaxa){\r
+ acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);\r
}\r
\r
- // process taxa in chunks of <=limit\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("End reading synonyms names and accepted taxa");\r
+ for (UUID uuid : synonymUuidSet) {\r
+ logger.trace("synonym uuid query: " + uuid);\r
+ }\r
+ for (UUID uuid : acceptedTaxaUuidSet) {\r
+ logger.trace("accepted taxon uuid query: " + uuid);\r
+ }\r
+ for (TaxonBase tb : synonyms) {\r
+ logger.trace("synonym uuid result: " + tb.getUuid());\r
+ }\r
+ for (TaxonBase tb : acceptedTaxa) {\r
+ logger.trace("accepted taxon uuid result: " + tb.getUuid());\r
+ }\r
+ }\r
\r
- for (int j = 1; j <= n + 1; j++)\r
- {\r
- int offset = j - 1;\r
- int start = offset * limit;\r
+ UUID mappedAcceptedTaxonUuid = null;\r
+ UUID synonymUuid = null;\r
+ Synonym synonym = null;\r
+ TaxonBase acceptedTaxonBase = null;\r
+ Taxon acceptedTaxon = null;\r
\r
- if(logger.isInfoEnabled()) { logger.info("Processing taxa: " + start + " - " + (start + limit - 1)); }\r
+ for (TaxonBase synonymTaxonBase : synonyms) {\r
\r
- if(logger.isInfoEnabled()) { \r
- logger.info("index = " + j \r
- + ", offset = " + offset\r
- + ", start = " + start); \r
- }\r
+ try {\r
+ synonym = synonymTaxonBase.deproxy(synonymTaxonBase, Synonym.class);\r
+ synonymUuid = synonym.getUuid();\r
+ mappedAcceptedTaxonUuid = fromToMap.get(synonymUuid);\r
+ acceptedTaxonBase = null;\r
+\r
+ acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + synonymUuid + ")");\r
+ }\r
+ acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);\r
\r
- if (j == n + 1) {\r
- limit = nbrOfTaxa - n * limit;\r
- if(logger.isInfoEnabled()) { logger.info("n = " + n + " limit = " + limit); }\r
- }\r
+ if (synonym != null && acceptedTaxon != null) {\r
\r
- TransactionStatus txStatus = startTransaction();\r
- \r
- List<Taxon> taxa = getTaxonService().getAllTaxa(limit, start);\r
- if(logger.isInfoEnabled()) { \r
- logger.info(taxa.size() + " taxa retrieved from CDM DB"); \r
- }\r
+ //TODO: in case original genus exists must add synonym to original genus instead of to accepted taxon\r
+ acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());\r
\r
- for (TaxonBase taxonBase : taxa) {\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid + \r
+ ") relationship created");\r
+ }\r
+ if (synonym != null && !synonymSet.contains(synonym)) {\r
\r
- TaxonNameBase<?,?> taxonName = taxonBase.getName();\r
+ synonymSet.add(synonym);\r
\r
- FaunaEuropaeaTaxon fauEuTaxon = findFauEuTaxonByOriginalSourceId(taxonBase, fauEuTaxonMap);\r
- \r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Synonym (" + synonymUuid + ") added to Set");\r
+ }\r
\r
- if (logger.isDebugEnabled()) { \r
- logger.debug("Taxon # " + fauEuTaxon.getId()); \r
+ } else {\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Duplicated synonym (" + synonymUuid + ")");\r
+ }\r
+ }\r
+ } else {\r
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + synonymUuid + " is null");\r
+ }\r
}\r
- //createRelationships(fauEuTaxon, taxonBase, taxonName, taxa, fauEuTaxonMap, state);\r
+ } catch (Exception e) {\r
+ logger.error("Error creating synonym relationship: accepted taxon-synonym (" + \r
+ mappedAcceptedTaxonUuid + "-" + synonymUuid + ")", e);\r
}\r
-\r
- getTaxonService().saveTaxonAll(taxa);\r
- taxa = null;\r
- \r
- commitTransaction(txStatus);\r
- \r
- // empty parent taxon store\r
-// Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
-// MapWrapper<TaxonBase> parentTaxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
-// parentTaxonStore.makeEmpty();\r
}\r
- return success;\r
- }\r
-\r
-\r
- private FaunaEuropaeaTaxon findFauEuTaxonByOriginalSourceId(TaxonBase<?> taxonBase, \r
- Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap) {\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start saving synonymSet");\r
+ }\r
+ getTaxonService().save(synonymSet);\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("End saving synonymSet");\r
+ }\r
\r
- Set set = taxonBase.getSources();\r
- Object[] array = set.toArray();\r
- if (array.length == 0) { return null; }\r
- OriginalSource os = (OriginalSource) taxonBase.getSources().toArray()[0];\r
- String taxonBaseIdStr = os.getIdInSource();\r
- int taxonBaseId = Integer.parseInt(taxonBaseIdStr);\r
- FaunaEuropaeaTaxon fauEuTaxon = fauEuTaxonMap.get(taxonBaseId); \r
+ acceptedTaxaUuidSet = null;\r
+ synonymSet = null;\r
+ synonyms = null;\r
+ acceptedTaxa = null;\r
\r
- return fauEuTaxon;\r
+ return success;\r
}\r
\r
- \r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff