minor, cleanup

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
index 2591f839808a4ffce60769359c724c40f6379094..68799c6700a29dc555394699e8e44eecaf28e351 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
@@ -649,6 +649,14 @@ public class CdmDestinations {
                return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
        }
 
+       public static ICdmDataSource cdm_test_caryo_spp(){
+        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
+        String cdmServer = "160.45.63.175";
+        String cdmDB = "cdm_caryo_spp";
+        String cdmUserName = "edit";
+        return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
+    }
+
        public static ICdmDataSource cdm_production_cichorieae(){
                DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
                String cdmServer = "160.45.63.171";

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
index 46ce0613df4e165c20fac7a2a7cacc59c0dbc431..fe28a14b0ad6624b19bafdb229e965077f6779a5 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
@@ -103,6 +103,14 @@ public class CdmDestinations {
         int port = 3306;
         return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null);
     }
+    public static ICdmDataSource cdm_pesi2019_final_test(){
+        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
+        String cdmServer = "127.0.0.1";
+        String cdmDB = "cdm_pesi_2019final_test";
+        String cdmUserName = "edit";
+        int port = 3306;
+        return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null);
+    }
 
        public static ICdmDataSource cdm_test_local_mysql_test(){
                DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java
index bee96fa7b86cf61cd6f69df203ea219a6093a7af..f0e063b6abdc04c4017ed90b3e6ba8fac80e13c4 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java
@@ -67,7 +67,6 @@ public class PesiFindIdenticalNamesActivator {
         sources.put(ifSourceUuid, "IF");
     }
 
-
        private void invoke(ICdmDataSource source){
 
         CdmApplicationController app = CdmIoApplicationController.NewInstance(source, DbSchemaValidation.VALIDATE, false);

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java
index 944b986fa50da9220a8cb0df117b44e66117a8e0..7a806cc46b7c2e5251a8b265aea3efea3bdf50f2 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java
@@ -12,7 +12,6 @@ package eu.etaxonomy.cdm.io.pesi.indexFungorum;
 import java.sql.ResultSet;\r
 import java.sql.SQLException;\r
 import java.util.HashMap;\r
-import java.util.HashSet;\r
 import java.util.List;\r
 import java.util.Map;\r
 import java.util.Set;\r
@@ -55,7 +54,6 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                        " SELECT DISTINCT [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name], [Family name], g.[NAME OF FUNGUS] as GenusName, c.PreferredName as SpeciesName " +\r
                        " FROM [tblPESIfungi-Classification] c  LEFT OUTER JOIN " +\r
                       " tblGenera g ON c.PreferredNameFDCnumber = g.[RECORD NUMBER]" +\r
-//                     " WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";\r
                        " ORDER BY [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name],  [Family name], GenusName, SpeciesName ";\r
                return strRecordQuery;\r
        }\r
@@ -77,8 +75,6 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                String lastSubclass = "";\r
                String lastOrder = "";\r
                String lastFamily = "";\r
-//             String lastGenus = "";\r
-//             String lastSpecies = "";\r
 \r
                Taxon taxonKingdom = null;\r
                Taxon taxonPhylum = null;\r
@@ -87,8 +83,6 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                Taxon taxonSubclass = null;\r
                Taxon taxonOrder = null;\r
                Taxon taxonFamily = null;\r
-//             Taxon taxonGenus = null;\r
-//             Taxon taxonSpecies = null;\r
 \r
                Taxon higherTaxon = null;\r
 \r
@@ -107,11 +101,7 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                                String subclass = rs.getString("Subclass name");\r
                                String order = rs.getString("Order name");\r
                                String family = rs.getString("Family name");\r
-//                             String genus = rs.getString("GenusName");\r
-//                             String species = rs.getString("SpeciesName");\r
 \r
-//                             if (isNewTaxon(species, lastSpecies)){\r
-//                                     if (isNewTaxon(genus, lastGenus)){\r
                                if (isNewTaxon(family, lastFamily)){\r
                                        if (isNewTaxon(order,lastOrder)){\r
                                                if (isNewTaxon(subclass,lastSubclass)){\r
@@ -178,44 +168,21 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                                        taxonFamily = makeTaxon(state, family, Rank.FAMILY());\r
                                        if (taxonFamily != null){\r
                                                try{\r
-                                                       //if this shown a warning see single issue in #2826 about Glomerelllaceae (which has 2 different parents)\r
+                                                       //if this shows a warning see single issue in #2826 about Glomerellaceae (which has 2 different parents)\r
                                                    getClassification(state).addParentChild(higherTaxon, taxonFamily, null, null);\r
                                                }catch(IllegalStateException e){\r
                                                        if (e.getMessage().startsWith("The child taxon is already part of the tree")){\r
                                                                //TaxonNode node = getClassification(state).getNode(taxonFamily);\r
                                                                logger.warn(e.getMessage() + taxonFamily.getTitleCache() + " " + higherTaxon.getTitleCache());\r
-\r
-                                                               }\r
+                                                       }\r
                                                }\r
                                        }\r
                                        higherTaxon = isIncertisSedis(family) ? higherTaxon : taxonFamily;\r
                                        lastFamily = family;\r
                                        getTaxonService().saveOrUpdate(higherTaxon);\r
                                }\r
-//                                             else{\r
-//                                                     higherTaxon = taxonFamily;\r
-//                                             }\r
-//                                             taxonGenus = makeTaxon(state, genus, Rank.GENUS());\r
-//                                             if (taxonGenus != null){\r
-//                                                     getClassification(state).addParentChild(higherTaxon, taxonGenus, null, null);\r
-//                                             }\r
-//                                             higherTaxon = isIncertisSedis(genus) ? higherTaxon : taxonGenus;\r
-//                                             lastGenus = genus;\r
-//                                     }else{\r
-//                                             higherTaxon = taxonGenus;\r
-//                                     }\r
-//                                     taxonSpecies = makeTaxon(state, species, Rank.SPECIES());\r
-//                                     if (taxonSpecies != null){\r
-//                                             getClassification(state).addParentChild(higherTaxon, taxonSpecies, null, null);\r
-//                                     }\r
-//                                     higherTaxon = isIncertisSedis(species) ? higherTaxon : taxonSpecies;\r
-//                                     lastSpecies = species;\r
-//                                     getTaxonService().saveOrUpdate(higherTaxon);\r
-//                             }\r
                                getTaxonService().saveOrUpdate(higherTaxon);\r
                        }\r
-\r
-\r
                } catch (SQLException e) {\r
                        e.printStackTrace();\r
                        logger.error(e.getMessage());\r
@@ -226,15 +193,12 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                logger.info("End higher classification ...");\r
 \r
                return;\r
-\r
        }\r
 \r
-\r
        private boolean isIncertisSedis(String uninomial) {\r
                return  uninomial.equalsIgnoreCase(INCERTAE_SEDIS) || uninomial.equalsIgnoreCase(FOSSIL_FUNGI);\r
        }\r
 \r
-\r
        private boolean isNewTaxon(String uninomial, String lastUninomial) {\r
                boolean result =  !uninomial.equalsIgnoreCase(lastUninomial);\r
                result |= lastUninomial.equalsIgnoreCase(INCERTAE_SEDIS);\r
@@ -246,7 +210,7 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                if (uninomial.equalsIgnoreCase(INCERTAE_SEDIS) || uninomial.equalsIgnoreCase(FOSSIL_FUNGI)){\r
                        return null;\r
                }\r
-               Taxon taxon = state.getRelatedObject(IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES, uninomial, Taxon.class);\r
+               Taxon taxon = state.getRelatedObject(IndexFungorumImportBase.NAMESPACE_SUPRAGENERIC_NAMES, uninomial, Taxon.class);\r
                if (taxon == null){\r
                        if (! newRank.equals(Rank.KINGDOM())){\r
                                logger.warn("Taxon not found for uninomial " + uninomial);\r
@@ -262,25 +226,24 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
                return taxon;\r
        }\r
 \r
-\r
        @Override\r
        public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {\r
                String nameSpace;\r
                Class<?> cdmClass;\r
                Set<String> idSet;\r
-               Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
+               Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();\r
 \r
                try{\r
-                       Set<String> taxonNameSet = new HashSet<String>();\r
+//                     Set<String> taxonNameSet = new HashSet<>();\r
 //                     while (rs.next()){\r
 //                             handleForeignKey(rs, taxonIdSet,"tu_accfinal" );\r
 //                     }\r
 \r
                        //taxon map\r
-                       nameSpace = IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES ;\r
+                       nameSpace = IndexFungorumImportBase.NAMESPACE_SUPRAGENERIC_NAMES ;\r
                        cdmClass = TaxonBase.class;\r
 //                     idSet = taxonNameSet;\r
-                       Map<String, TaxonBase<?>> taxonMap = new HashMap<String, TaxonBase<?>>();\r
+                       Map<String, TaxonBase<?>> taxonMap = new HashMap<>();\r
                        List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null);\r
                        for (Taxon taxon : list){\r
                                taxonMap.put(CdmBase.deproxy(taxon.getName()).getGenusOrUninomial(), taxon);\r
@@ -289,7 +252,7 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
 \r
                        //source reference\r
                        Reference sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);\r
-                       Map<String, Reference> referenceMap = new HashMap<String, Reference>();\r
+                       Map<String, Reference> referenceMap = new HashMap<>();\r
                        referenceMap.put(SOURCE_REFERENCE, sourceReference);\r
                        result.put(NAMESPACE_REFERENCE, referenceMap);\r
 \r
@@ -308,9 +271,4 @@ public class IndexFungorumHigherClassificationImport  extends IndexFungorumImpor
        protected boolean isIgnore(IndexFungorumImportState state){\r
                return ! state.getConfig().isDoRelTaxa();\r
        }\r
-\r
-\r
-\r
-\r
-\r
 }\r

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.java
index ac8d81287184b4a9125672a2d8ab04920aa7b8b4..238142985b9e9510e8952c6e4e00934a1afdb32b 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.java
@@ -104,7 +104,7 @@ public class IndexFungorumSpeciesImport  extends IndexFungorumImportBase {
                        if (!name.isInfraSpecific()){\r
                                    Taxon parent = getParentTaxon(state, genusId);\r
                                    if (parent == null){\r
-                           logger.warn("parent not found for name:" + preferredName + "ID(PreferredNameIFnumber)" +id+ "; GenusId(PreferredNameFDCnumber): ");\r
+                           logger.warn("Parent not found for name:" + preferredName + "; ID(PreferredNameIFnumber): " +id+ "; GenusId(PreferredNameFDCnumber): ");\r
                        }else{\r
                            classification.addParentChild(parent, taxon, null, null);\r
                        }\r