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.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.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 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.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.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
\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
- /* 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
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
- taxonStore.makeEmpty();\r
+\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
+ if(logger.isInfoEnabled()) { logger.info("Start making relationships..."); }\r
\r
- //ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();\r
TransactionStatus txStatus = startTransaction();\r
\r
- TaxonBase taxon = getTaxonService().getTaxonByUuid(UUID.fromString("ac7b30dc-6207-4c71-9752-ee0fb838a271"));\r
- ReferenceBase<?> sourceRef = taxon.getSec();\r
- TaxonomicTree tree= getTaxonomicTreeFor(state, sourceRef);\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
- ProfilerController.memorySnapshot(); \r
- success = processParentsChildren(state);\r
- ProfilerController.memorySnapshot();\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
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
- " ORDER BY dbo.Taxon.TAX_RNK_ID ASC";\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++ % limit) == 0) {\r
\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 )) { \r
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
\r
- success = createRelationships(state, childParentMap);\r
+ success = createParentChildRelationships(state, childParentMap);\r
\r
childParentMap = null;\r
commitTransaction(txStatus);\r
- \r
+\r
if(logger.isInfoEnabled()) {\r
logger.info("i = " + i + " - Transaction committed"); \r
}\r
}\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
+ /** 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
+ int i = 0;\r
+ boolean success = true;\r
\r
- for (int i = 0; i < border; i++) {\r
- //while (entryIter.hasNext()) {\r
+ String selectCount = \r
+ " SELECT count(*) ";\r
\r
- Map.Entry<UUID, UUID> mapEntry = (Map.Entry<UUID, UUID>)entryIter.next();\r
- partMap.put(mapEntry.getKey(), mapEntry.getValue());\r
- entryIter.remove();\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
+ 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
+ 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) {\r
+ \r
+ txStatus = startTransaction();\r
+ childParentMap = new HashMap<UUID, UUID>(limit);\r
+ \r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("Misapplied names retrieved: " + (i-1) ); \r
+ }\r
+ }\r
+\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
+ if(logger.isDebugEnabled()) {\r
+ logger.debug("Duplicated child UUID (" + childUuid + ")");\r
+ }\r
+ }\r
+\r
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
+\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
+ }\r
+ }\r
+\r
+ } catch (SQLException e) {\r
+ logger.error("SQLException:" + e);\r
+ success = false;\r
}\r
+ return success; \r
+ }\r
+\r
+\r
+\r
+ /** Retrieve synonyms from FauEuDB DB */\r
+ private boolean processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {\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
+ 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
+ logger.debug(selectQuery);\r
+ \r
+ try {\r
+\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
+ success = storeSynonymRelationships(rs, count, state);\r
+\r
+ } catch (SQLException e) {\r
+ logger.error("SQLException:" + e);\r
+ success = false;\r
}\r
- return partMap;\r
- } \r
+ return success; \r
+ }\r
+ \r
+ \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
+ while (rs.next()) {\r
\r
+ if ((i++ % limit) == 0) {\r
+\r
+ txStatus = startTransaction();\r
+ synonymAcceptedMap = new HashMap<UUID, UUID>(limit);\r
+\r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("Synonyms retrieved: " + (i-1)); \r
+ }\r
+ }\r
+\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
+ 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
+ if (((i % limit) == 0 && i != 1 ) || i == count) { \r
+\r
+ success = createHeterotypicSynonyms(state, synonymAcceptedMap);\r
+\r
+ synonymAcceptedMap = null;\r
+ commitTransaction(txStatus);\r
+\r
+ if(logger.isInfoEnabled()) {\r
+ logger.info("i = " + i + " - Transaction committed"); \r
+ }\r
+ }\r
+ }\r
+ return success;\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, Map<UUID, UUID> childParentMap) {\r
-\r
- TaxonBase taxon = getTaxonService().getTaxonByUuid(UUID.fromString("ac7b30dc-6207-4c71-9752-ee0fb838a271"));\r
- ReferenceBase<?> sourceRef = taxon.getSec();\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
+ int limit = state.getConfig().getLimitSave();\r
+ \r
TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);\r
\r
Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);\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
+ 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
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 (" + 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
}\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
mappedParentUuid + "-" + childUuid + ")", e);\r
}\r
\r
}\r
- if (logger.isInfoEnabled()) {\r
- logger.info("Start saving childSet");\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start saving childSet");\r
}\r
- getTaxonService().saveTaxonAll(childSet);\r
- if (logger.isInfoEnabled()) {\r
- logger.info("End saving childSet");\r
+ getTaxonService().save(childSet);\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("End saving childSet");\r
}\r
\r
parentValuesSet = null;\r
return success;\r
}\r
\r
- /**\r
- * @param state\r
- * @param sourceRef\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 TaxonomicTree getTaxonomicTreeFor(FaunaEuropaeaImportState state, ReferenceBase<?> sourceRef) {\r
+ private boolean createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {\r
+\r
+ //gets the taxon "Hydroscaphidae" (family)\r
+ \r
+ TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));\r
+ sourceRef = taxon.getSec();\r
+ boolean success = true;\r
+ int limit = state.getConfig().getLimitSave();\r
\r
- TaxonomicTree tree;\r
- UUID treeUuid = state.getTreeUuid(sourceRef);\r
- if (treeUuid == null){\r
- if(logger.isInfoEnabled()) { logger.info(".. creating new taxonomic tree"); }\r
+ Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);\r
\r
- TransactionStatus txStatus = startTransaction();\r
- tree = makeTreeMemSave(state, sourceRef);\r
- commitTransaction(txStatus);\r
+ Set<UUID> misappliedNamesSet = fromToMap.keySet();\r
+ Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());\r
\r
- } else {\r
- tree = getTaxonService().getTaxonomicTreeByUuid(treeUuid);\r
- }\r
- return tree;\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Start reading misapplied names and accepted taxa");\r
+ }\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
+ UUID mappedAcceptedTaxonUuid = null;\r
+ UUID misappliedNameUuid = null;\r
+ Taxon misappliedNameTaxon = null;\r
+ TaxonBase acceptedTaxonBase = null;\r
+ Taxon acceptedTaxon = null;\r
+\r
+ for (TaxonBase misappliedName : misappliedNames) {\r
+\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
+ }\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
+ acceptedTaxaSet = null;\r
+ misappliedNameSet = null;\r
+ misappliedNames = null;\r
+ acceptedTaxa = null;\r
+ \r
+ return success;\r
}\r
+\r
\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
+ int limit = state.getConfig().getLimitSave();\r
+ boolean success = true;\r
+\r
+ Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);\r
+\r
+ Set<UUID> synonymUuidSet = fromToMap.keySet();\r
+ Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());\r
+\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Reading synonym names and accepted taxa...");\r
+ }\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
+ 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
+ UUID mappedAcceptedTaxonUuid = null;\r
+ UUID synonymUuid = null;\r
+ Synonym synonym = null;\r
+ TaxonBase acceptedTaxonBase = null;\r
+ Taxon acceptedTaxon = null;\r
+\r
+ for (TaxonBase synonymTaxonBase : synonyms) {\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 (synonym != null && acceptedTaxon != null) {\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
+ if (logger.isDebugEnabled()) {\r
+ logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid + \r
+ ") relationship created");\r
+ }\r
+ if (synonym != null && !synonymSet.contains(synonym)) {\r
+\r
+ synonymSet.add(synonym);\r
+\r
+ if (logger.isTraceEnabled()) {\r
+ logger.trace("Synonym (" + synonymUuid + ") added to Set");\r
+ }\r
+\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
+ } catch (Exception e) {\r
+ logger.error("Error creating synonym relationship: accepted taxon-synonym (" + \r
+ mappedAcceptedTaxonUuid + "-" + synonymUuid + ")", e);\r
+ }\r
+ }\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
+ acceptedTaxaUuidSet = null;\r
+ synonymSet = null;\r
+ synonyms = null;\r
+ acceptedTaxa = null;\r
+\r
+ return success;\r
+ }\r
+\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff