Fauna Europaea import: Heterotypic synonyms

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaRelTaxonIncludeImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaRelTaxonIncludeImport.java
index 9d56b5bfcb5c68be9c794686853e0c9aa310e5a7..00d6777aca0ea6b7eafb9432c08034a4202c93a8 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaRelTaxonIncludeImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaRelTaxonIncludeImport.java
@@ -49,26 +49,26 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
        \r
        public static final String OS_NAMESPACE_TAXON = "Taxon";\r
        private static final Logger logger = Logger.getLogger(FaunaEuropaeaRelTaxonIncludeImport.class);\r
-\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
+       private static String PARENT_SYNONYM_FROM_CLAUSE = " FROM Taxon INNER JOIN Taxon AS Parent " +\r
+       " ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +\r
+       " WHERE (Taxon.TAX_TAX_IDGENUS is null) AND (Taxon.TAX_VALID = 0) " +\r
+       " AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL)";\r
+\r
+       private static String ORIGINAL_GENUS_SYNONYM_FROM_CLAUSE = " FROM Taxon INNER JOIN Taxon AS OGenus " +\r
+       " ON Taxon.TAX_TAX_IDGENUS = OGenus.TAX_ID " +\r
+       " WHERE (Taxon.TAX_TAX_IDGENUS is not null) AND (Taxon.TAX_VALID = 0) " +\r
+       " AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL)";\r
+       \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 ReferenceBase<?> sourceRef = null;\r
+//     private ReferenceBase<?> sourceRef = null;\r
 \r
        \r
-       /**\r
-        * @return the sourceRef\r
-        */\r
-       private ReferenceBase<?> getSourceRef() {\r
-               return sourceRef;\r
-       }\r
-\r
-       /**\r
-        * @param sourceRef the sourceRef to set\r
-        */\r
-       private void setSourceRef(ReferenceBase<?> sourceRef) {\r
-               this.sourceRef = sourceRef;\r
-       }\r
-\r
        /* (non-Javadoc)\r
         * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
         */\r
@@ -119,7 +119,7 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                TransactionStatus txStatus = startTransaction();\r
                \r
                TaxonBase taxon = getTaxonService().getTaxonByUuid(UUID.fromString("ac7b30dc-6207-4c71-9752-ee0fb838a271"));\r
-               setSourceRef(taxon.getSec());\r
+               ReferenceBase<?> sourceRef = taxon.getSec();\r
 \r
                TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);\r
                commitTransaction(txStatus);\r
@@ -134,7 +134,8 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                }\r
                ProfilerController.memorySnapshot();\r
                if (state.getConfig().isDoHeterotypicSynonyms()) {\r
-                       success = processHeterotypicSynonyms(state);\r
+                       success = processHeterotypicSynonyms(state, PARENT_SYNONYM_FROM_CLAUSE);\r
+                       success = processHeterotypicSynonyms(state, ORIGINAL_GENUS_SYNONYM_FROM_CLAUSE);\r
                }\r
                ProfilerController.memorySnapshot();\r
 \r
@@ -159,13 +160,13 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                String selectCount = \r
                        " SELECT count(*) ";\r
 \r
-               String selectColumns = " SELECT dbo.Taxon.UUID AS ChildUuid, Parent.UUID AS ParentUuid ";\r
+               String selectColumns = " SELECT Taxon.UUID AS ChildUuid, Parent.UUID AS ParentUuid ";\r
                \r
-               String fromClause = " 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 + " OR dbo.Taxon.TAX_AUT_ID IS NULL )";\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 dbo.Taxon.TAX_RNK_ID ASC";\r
+               String orderClause = " ORDER BY Taxon.TAX_RNK_ID ASC";\r
 \r
                String countQuery = \r
                        selectCount + fromClause;\r
@@ -325,15 +326,59 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                return success;         \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
+               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
+               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 success;         \r
+       }\r
+\r
        \r
        /** Retrieve synonyms from FauEuDB DB */\r
-       private boolean processHeterotypicSynonyms(FaunaEuropaeaImportState state) {\r
+       private boolean processHeterotypicSynonyms_(FaunaEuropaeaImportState state) {\r
 \r
                int limit = state.getConfig().getLimitSave();\r
 \r
                TransactionStatus txStatus = null;\r
 \r
-               Map<UUID, UUID> childParentMap = null;\r
+               Map<UUID, UUID> synonymAcceptedMap = null;\r
                FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
                Source source = fauEuConfig.getSource();\r
                int i = 0;\r
@@ -346,7 +391,7 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                \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
+               " 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 dbo.Taxon.TAX_RNK_ID ASC ";\r
 \r
@@ -375,33 +420,33 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                                if ((i++ % limit) == 0) {\r
                                        \r
                                        txStatus = startTransaction();\r
-                                       childParentMap = new HashMap<UUID, UUID>(limit);\r
+                                       synonymAcceptedMap = new HashMap<UUID, UUID>(limit);\r
                                        \r
                                        if(logger.isInfoEnabled()) {\r
-                                               logger.info("Synonyms retrieved: " + (i-1) ); \r
+                                               logger.info("Synonyms retrieved: " + (i-1)); \r
                                        }\r
                                }\r
 \r
-                               String childUuidStr = rs.getString("SynonymUuid");\r
-                               String parentUuidStr = rs.getString("AcceptedUuid");\r
-                               UUID childUuid = UUID.fromString(childUuidStr);\r
-                               UUID parentUuid = UUID.fromString(parentUuidStr);\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 (!childParentMap.containsKey(childUuid)) {\r
+                               if (!synonymAcceptedMap.containsKey(synonymUuid)) {\r
 \r
-                                               childParentMap.put(childUuid, parentUuid);\r
+                                               synonymAcceptedMap.put(synonymUuid, acceptedUuid);\r
 \r
                                } else {\r
                                        if(logger.isDebugEnabled()) {\r
-                                               logger.debug("Duplicated child UUID (" + childUuid + ")");\r
+                                               logger.debug("Duplicated child UUID (" + synonymUuid + ")");\r
                                        }\r
                                }\r
 \r
                                if (((i % limit) == 0 && i != 1 ) || i == count) { \r
 \r
-                                       success = createHeterotypicSynonyms(state, childParentMap);\r
+                                       success = createHeterotypicSynonyms(state, synonymAcceptedMap);\r
 \r
-                                       childParentMap = null;\r
+                                       synonymAcceptedMap = null;\r
                                        commitTransaction(txStatus);\r
 \r
                                        if(logger.isInfoEnabled()) {\r
@@ -416,25 +461,77 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                }\r
                return success;         \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
+\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
        /* Creates parent-child relationships.\r
         * Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. \r
         */\r
        private boolean createParentChildRelationships(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
+               TaxonBase taxon = getTaxonService().getTaxonByUuid(UUID.fromString("ac7b30dc-6207-4c71-9752-ee0fb838a271"));\r
+               ReferenceBase<?> sourceRef = taxon.getSec();\r
                boolean success = true;\r
                \r
-                       TaxonomicTree tree = getTaxonomicTreeFor(state, getSourceRef());\r
+                       TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);\r
                        \r
                        Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);\r
                        \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
@@ -443,28 +540,17 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                                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
@@ -503,7 +589,7 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                                                        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
@@ -522,29 +608,18 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                                                }\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
+                       if (logger.isTraceEnabled()) {\r
+                               logger.trace("End saving childSet");\r
                        }\r
 \r
                        parentValuesSet = null;\r
@@ -570,8 +645,8 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                        Set<UUID> misappliedNamesSet = fromToMap.keySet();\r
                        Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());\r
                        \r
-                       if (logger.isInfoEnabled()) {\r
-                               logger.info("Start reading misapplied names and accepted taxa");\r
+                       if (logger.isTraceEnabled()) {\r
+                               logger.trace("Start reading misapplied names and accepted taxa");\r
                        }\r
                        List<TaxonBase> misappliedNames = getTaxonService().findByUuid(misappliedNamesSet);\r
                        List<TaxonBase> acceptedTaxa = getTaxonService().findByUuid(acceptedTaxaSet);\r
@@ -580,28 +655,17 @@ public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase
                                acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);\r
                        }\r
                        \r
-                       \r
-                       if (logger.isInfoEnabled()) {\r
-                               logger.info("End reading misapplied names and accepted taxa");\r
-                       }\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
-                       }\r
-                       if (logger.isTraceEnabled()) {\r
                                for (UUID uuid : acceptedTaxaSet) {\r
                                        logger.trace("accepted taxon uuid query: " + uuid);\r
                                }\r
-                       }\r
-                       if (logger.isTraceEnabled()) {\r
                                for (TaxonBase tb : misappliedNames) {\r
                                        logger.trace("misapplied name uuid result: " + tb.getUuid());\r
                                }\r
-                       }\r
-                       if (logger.isTraceEnabled()) {\r
                                for (TaxonBase tb : acceptedTaxa) {\r
                                        logger.trace("accepted taxon uuid result: " + tb.getUuid());\r
                                }\r

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxon.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxon.java
index b76ab71f7a2c9d87f43e0f63b191ee7a762b3bee..9fb815e638e354a98acdb961adf2fa62306cbf30 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxon.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxon.java
@@ -23,8 +23,11 @@ public class FaunaEuropaeaTaxon {
        private int rankId;\r
        private int parentId;\r
        private int parentRankId;\r
+       private int grandParentId;\r
        private int grandParentRankId;\r
+       private int greatGrandParentId;\r
        private int greatGrandParentRankId;\r
+       private int greatGreatGrandParentId;\r
        private int originalGenusId;\r
        private int year;\r
        private String localName;\r
@@ -335,6 +338,48 @@ public class FaunaEuropaeaTaxon {
                this.greatGreatGrandParentName = greatGreatGrandParentName;\r
        }\r
 \r
+       /**\r
+        * @return the grandParentId\r
+        */\r
+       public int getGrandParentId() {\r
+               return grandParentId;\r
+       }\r
+\r
+       /**\r
+        * @param grandParentId the grandParentId to set\r
+        */\r
+       public void setGrandParentId(int grandParentId) {\r
+               this.grandParentId = grandParentId;\r
+       }\r
+\r
+       /**\r
+        * @return the greatGrandParentId\r
+        */\r
+       public int getGreatGrandParentId() {\r
+               return greatGrandParentId;\r
+       }\r
+\r
+       /**\r
+        * @param greatGrandParentId the greatGrandParentId to set\r
+        */\r
+       public void setGreatGrandParentId(int greatGrandParentId) {\r
+               this.greatGrandParentId = greatGrandParentId;\r
+       }\r
+\r
+       /**\r
+        * @return the greatGreatGrandParentId\r
+        */\r
+       public int getGreatGreatGrandParentId() {\r
+               return greatGreatGrandParentId;\r
+       }\r
+\r
+       /**\r
+        * @param greatGreatGrandParentId the greatGreatGrandParentId to set\r
+        */\r
+       public void setGreatGreatGrandParentId(int greatGreatGrandParentId) {\r
+               this.greatGreatGrandParentId = greatGreatGrandParentId;\r
+       }\r
+\r
 //     /**\r
 //      * @return the authorId\r
 //      */\r

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxonNameImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxonNameImport.java
index 2baac9fe46dbeb5de466f7460a3e7f6796b6af3d..f932047e2372a829641ece14a5602ce3b7e281be 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxonNameImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTaxonNameImport.java
@@ -141,9 +141,9 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
 \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 GGG5Id, GreatGreatGrandParent.TAX_NAME AS GGGP5Name, OriginalGenusTaxon.TAX_NAME AS OGenusName, " +\r
                        " Taxon.*, rank.*, author.* ";\r
                \r
                String fromClause = \r
@@ -372,9 +372,12 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                        String nameString = \r
                                buildTaxonName(fauEuTaxon, taxonBase, taxonName, false, fauEuConfig);\r
                        \r
-                       if (fauEuConfig.isDoBasionyms() && fauEuTaxon.isValid() &&\r
-                                       (fauEuTaxon.getOriginalGenusId() != 0) &&\r
-                                       (fauEuTaxon.getParentId() != fauEuTaxon.getOriginalGenusId())) {\r
+//                     if (fauEuConfig.isDoBasionyms() && fauEuTaxon.isValid() &&\r
+//                                     (fauEuTaxon.getOriginalGenusId() != 0) &&\r
+//                                     (fauEuTaxon.getParentId() != fauEuTaxon.getOriginalGenusId())) {\r
+                       if (fauEuConfig.isDoBasionyms() \r
+                                       && fauEuTaxon.getRankId() > R_SUBGENUS\r
+                                       && (fauEuTaxon.getOriginalGenusId() != 0)) {\r
                                success = createBasionym(fauEuTaxon, taxonBase, taxonName, fauEuConfig);\r
                        }\r
                }\r
@@ -507,6 +510,69 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                \r
                return stringBuilder.toString();\r
        }\r
+\r
+       /** Get actual genus id **/\r
+       private int getActualGenusId(FaunaEuropaeaTaxon fauEuTaxon) {\r
+               \r
+               int actualGenusId = -1;\r
+               int rank = fauEuTaxon.getRankId();\r
+               int parentRankId = fauEuTaxon.getParentRankId();\r
+               int grandParentRankId = fauEuTaxon.getGrandParentRankId();\r
+               int greatGrandParentRankId = fauEuTaxon.getGreatGrandParentRankId();\r
+               \r
+               if (fauEuTaxon.isValid()) { // Taxon\r
+                       \r
+                       if (rank == R_SPECIES) {\r
+\r
+                               if(parentRankId == R_SUBGENUS) {\r
+\r
+                                       actualGenusId = fauEuTaxon.getGrandParentId();\r
+       \r
+                               } else if(parentRankId == R_GENUS) {\r
+\r
+                                       actualGenusId = fauEuTaxon.getParentId();\r
+                               }\r
+\r
+                       } else if (rank == R_SUBSPECIES) {\r
+\r
+                               if(grandParentRankId == R_SUBGENUS) {\r
+\r
+                                       actualGenusId = fauEuTaxon.getGreatGrandParentId();\r
+                                       \r
+                               } else if (grandParentRankId == R_GENUS) {\r
+\r
+                                       actualGenusId = fauEuTaxon.getGrandParentId();\r
+\r
+                               }\r
+                       }\r
+               } else { // Synonym\r
+                       \r
+                       if (rank == R_SPECIES) {\r
+\r
+                               if(grandParentRankId == R_SUBGENUS) {\r
+                                       \r
+                                       actualGenusId = fauEuTaxon.getGreatGrandParentId();\r
+                                       \r
+                               } else if (grandParentRankId == R_GENUS) {\r
+                                       \r
+                                       actualGenusId = fauEuTaxon.getGrandParentId();\r
+\r
+                               }\r
+\r
+                       } else if (rank == R_SUBSPECIES) {\r
+                               \r
+                               if(greatGrandParentRankId == R_SUBGENUS) {\r
+                                       \r
+                                       actualGenusId = fauEuTaxon.getGreatGreatGrandParentId();\r
+                                       \r
+                               } else if (greatGrandParentRankId == R_GENUS) {\r
+                                       \r
+                                       actualGenusId = fauEuTaxon.getGreatGrandParentId();\r
+                               }\r
+                       }\r
+               }\r
+               return actualGenusId;\r
+       }\r
        \r
        \r
        /** Build species and subspecies names */\r