Rework Fauna Europaea taxa import

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / faunaEuropaea / FaunaEuropaeaTaxonNameImport.java

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 f8604342cc81d18b79bf4c6da129f7320761ab2b..7dfad14707ea17940cef70ee4162ab47796a7b62 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
@@ -138,16 +138,17 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
        private boolean retrieveTaxa(FaunaEuropaeaImportState state) {\r
 \r
                int limit = state.getConfig().getLimitSave();\r
-               \r
+\r
                Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
 //             MapWrapper<TaxonBase> nameStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXONNAME_STORE);\r
                MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
                MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);\r
 //             Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = state.getFauEuTaxonMap();\r
                Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);\r
+               state.setFauEuTaxonMap(fauEuTaxonMap);\r
 \r
                if (logger.isInfoEnabled()) {\r
-                       logger.info("Initial size of taxon Store is: " + taxonStore.size());\r
+                       logger.info("Initial size of taxon store is: " + taxonStore.size());\r
                }\r
                FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();\r
                ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();\r
@@ -157,7 +158,7 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                boolean success = true;\r
 \r
                try {\r
-                       \r
+\r
                        String strQuery = \r
                                " SELECT Taxon.*, rank.*, author.* " + \r
                                " FROM dbo.Taxon " +\r
@@ -169,13 +170,13 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                logger.debug("Query: " + strQuery);\r
                        }\r
                        ResultSet rs = source.getResultSet(strQuery);\r
-                       \r
+\r
                        while (rs.next()) {\r
 \r
 //                             if ((i++ % limit) == 0 && i != 1 ) { \r
-//                                     if(logger.isInfoEnabled()) {\r
-//                                             logger.info("Taxa retrieved: " + (i-1)); \r
-//                                     }\r
+//                             if(logger.isInfoEnabled()) {\r
+//                             logger.info("Taxa retrieved: " + (i-1)); \r
+//                             }\r
 //                             }\r
 \r
                                int taxonId = rs.getInt("TAX_ID");\r
@@ -188,7 +189,7 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                int status = rs.getInt("TAX_VALID");\r
                                int year = rs.getInt("TAX_YEAR");\r
                                String autName = rs.getString("aut_name");\r
-                               \r
+\r
                                Rank rank = null;\r
                                int parenthesis = rs.getInt("TAX_PARENTHESIS");\r
                                UUID taxonBaseUuid = null;\r
@@ -197,12 +198,12 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                } else {\r
                                        taxonBaseUuid = UUID.randomUUID();\r
                                }\r
-                               \r
+\r
 //                             String originalGenusName = "";\r
 //                             String genusName = "";\r
 //                             String specificEpithet = "";\r
 \r
-                               \r
+\r
                                FaunaEuropaeaTaxon fauEuTaxon = new FaunaEuropaeaTaxon();\r
                                fauEuTaxon.setUuid(taxonBaseUuid);\r
                                fauEuTaxon.setLocalName(rs.getString("TAX_NAME"));\r
@@ -224,7 +225,7 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                        fauEuTaxon.setValid(false);\r
                                }\r
 \r
-                               \r
+\r
                                try {\r
                                        rank = FaunaEuropaeaTransformer.rankId2Rank(rs, false);\r
                                } catch (UnknownCdmTypeException e) {\r
@@ -234,7 +235,7 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                        logger.warn("Taxon (" + taxonId + ") has rank null and can not be saved.");\r
                                        continue;\r
                                }\r
-                               \r
+\r
                                ReferenceBase<?> sourceReference = fauEuConfig.getSourceReference();\r
                                ReferenceBase<?> auctReference = fauEuConfig.getAuctReference();\r
 \r
@@ -245,7 +246,7 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
 \r
                                // set local name cache\r
 //                             zooName.setNameCache(localName);\r
-                               \r
+\r
                                TaxonBase<?> taxonBase;\r
 \r
                                Synonym synonym;\r
@@ -276,11 +277,11 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                        }\r
 \r
                                        taxonBase.setUuid(taxonBaseUuid);\r
-                                       \r
+\r
                                        ImportHelper.setOriginalSource(taxonBase, fauEuConfig.getSourceReference(), taxonId, OS_NAMESPACE_TAXON);\r
                                        ImportHelper.setOriginalSource(zooName, fauEuConfig.getSourceReference(), taxonId, "TaxonName");\r
-                                       \r
-                                       \r
+\r
+\r
                                        if (!taxonStore.containsId(taxonId)) {\r
                                                if (taxonBase == null) {\r
                                                        if (logger.isDebugEnabled()) { \r
@@ -291,7 +292,7 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                                taxonStore.put(taxonId, taxonBase);\r
                                                fauEuTaxonMap.put(taxonId, fauEuTaxon);\r
 //                                             if (logger.isDebugEnabled()) { \r
-//                                                     logger.debug("Stored taxon base (" + taxonId + ") " + localName); \r
+//                                             logger.debug("Stored taxon base (" + taxonId + ") " + localName); \r
 //                                             }\r
                                        } else {\r
                                                logger.warn("Not imported taxon base with duplicated TAX_ID (" + taxonId + \r
@@ -300,24 +301,31 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                                } catch (Exception e) {\r
                                        logger.warn("An exception occurred when creating taxon base with id " + taxonId + \r
                                        ". Taxon base could not be saved.");\r
+                                       e.printStackTrace();\r
                                }\r
-                       }\r
-                       \r
-                       if ((i++ % limit) == 0 && i != 1 ) { \r
-                               if(logger.isInfoEnabled()) {\r
-                                       logger.info("Taxa retrieved: " + (i-1)); \r
-                               }\r
-                               success = processTaxaSecondPass(state);\r
-                               success = saveTaxa(state, state.getHighestTaxonIndex(), limit);\r
-                               \r
-                               if (logger.isInfoEnabled()) {\r
-                                       logger.info("Final size of taxon Store is: " + taxonStore.size());\r
+\r
+                               if ((i++ % limit) == 0 && i != 1 ) { \r
+                                       if(logger.isInfoEnabled()) {\r
+                                               logger.info("Taxa retrieved: " + (i-1)); \r
+                                       }\r
+                                       success = processTaxaSecondPass(state);\r
+                                       success = saveTaxa(state);\r
+\r
+                                       if (logger.isInfoEnabled()) {\r
+                                               logger.info("End size of taxon Store is: " + taxonStore.size());\r
+                                       }\r
+\r
+//                                     taxonStore.makeNewMap((IService)getTaxonService());\r
+                                       taxonStore.makeEmpty();\r
+                                       fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);\r
+                                       state.setFauEuTaxonMap(fauEuTaxonMap);\r
+\r
+                                       if (logger.isInfoEnabled()) {\r
+                                               logger.info("Final size of taxon Store is: " + taxonStore.size());\r
+                                       }\r
                                }\r
-                               \r
-                               taxonStore.makeNewMap((IService)getTaxonService());\r
-//                             taxonStore.makeEmpty();\r
-                       }\r
 \r
+                       }\r
                } catch (SQLException e) {\r
                        logger.error("SQLException:" +  e);\r
                        success = false;\r
@@ -645,12 +653,12 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
 \r
                        taxonBase = taxonBase.deproxy(taxonBase, TaxonBase.class);\r
 \r
-                       completeString = \r
-                               buildLowerTaxonName(originalGenus, useOriginalGenus,\r
-                                               genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet,\r
-                                               fauEuTaxon, fauEuTaxonMap);\r
-                       \r
-                       completeString = (String) CdmUtils.removeDuplicateWhitespace(completeString.trim());\r
+//                     completeString = \r
+//                             buildLowerTaxonName(originalGenus, useOriginalGenus,\r
+//                                             genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet,\r
+//                                             fauEuTaxon, fauEuTaxonMap);\r
+//                     \r
+//                     completeString = (String) CdmUtils.removeDuplicateWhitespace(completeString.trim());\r
 \r
                }\r
                setCompleteTaxonName(completeString, useOriginalGenus,\r
@@ -713,7 +721,30 @@ public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {
                }\r
                return success;\r
        }\r
+\r
        \r
+       protected boolean saveTaxa(FaunaEuropaeaImportState state) {\r
+\r
+               boolean success = true;\r
+\r
+               Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();\r
+               MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);\r
+               TransactionStatus txStatus = null;\r
+\r
+               if(logger.isInfoEnabled()) { logger.info("Saving taxa ..."); }\r
+\r
+               if (state.getConfig().isUseTransactions()) {\r
+                       txStatus = startTransaction();\r
+               }\r
+\r
+               getTaxonService().saveTaxonAll(taxonStore.objects());\r
+\r
+               if (state.getConfig().isUseTransactions()) {\r
+                       commitTransaction(txStatus);\r
+               }\r
+\r
+               return success;\r
+       }\r
        \r
 \r
 }\r