X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib-apps.git/blobdiff_plain/94adeb1df5ede5c92bf84dc94ea987cadfa62d5e..ac9742df59656534ab277f1a5586e648692fe21e:/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java
index e157c185..5468f6fe 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java
@@ -29,6 +29,8 @@ import eu.etaxonomy.cdm.model.agent.AgentBase;
 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
 import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.name.BotanicalName;
+import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
+import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 import eu.etaxonomy.cdm.model.name.Rank;
 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
 import eu.etaxonomy.cdm.model.taxon.Synonym;
@@ -46,8 +48,6 @@ import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 @SuppressWarnings("serial")
 public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
 
-    private static final String EX = " ex ";
-
     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
 
     private static final String tableName = "Rote Liste Gefäßpflanzen";
@@ -101,31 +101,32 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
 
     private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
             throws SQLException {
-        long id = rs.getLong("NAMNR");
-        String taxNameString = rs.getString("TAXNAME");
-        String gueltString = rs.getString("GUELT");
-        String rangString = rs.getString("RANG");
-        String ep1String = rs.getString("EPI1");
-        String ep2String = rs.getString("EPI2");
-        String ep3String = rs.getString("EPI3");
-        String nomZusatzString = rs.getString("NOM_ZUSATZ");
-        String zusatzString = rs.getString("ZUSATZ");
-        String authorKombString = rs.getString("AUTOR_KOMB");
-        String authorBasiString = rs.getString("AUTOR_BASI");
-
+        long id = rs.getLong(RedListUtil.NAMNR);
+        String taxNameString = rs.getString(RedListUtil.TAXNAME);
+        String gueltString = rs.getString(RedListUtil.GUELT);
+        String rangString = rs.getString(RedListUtil.RANG);
+        String ep1String = rs.getString(RedListUtil.EPI1);
+        String ep2String = rs.getString(RedListUtil.EPI2);
+        String ep3String = rs.getString(RedListUtil.EPI3);
+        String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
+        String zusatzString = rs.getString(RedListUtil.ZUSATZ);
+        String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
+        String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
+
+        //---NAME---
         if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
-            logger.error("NAMNR: "+id+" No name found!");
+            RedListUtil.logMessage(id, "No name found!", logger);
         }
 
-        Rank rank = makeRank(state, rangString);
+        Rank rank = makeRank(id, state, rangString);
         if(rank==null){
-            logger.error("NAMNR: "+id+" Rank could not be resolved.");
+            RedListUtil.logMessage(id, "Rank could not be resolved.", logger);
         }
         BotanicalName name = BotanicalName.NewInstance(rank);
 
         //ep1 should always be present
         if(CdmUtils.isBlank(ep1String)){
-            logger.error("NAMNR: "+id+" EPI1 is empty!");
+            RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
         }
         name.setGenusOrUninomial(ep1String);
         if(!CdmUtils.isBlank(ep2String)){
@@ -137,57 +138,73 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
                 name.setInfraSpecificEpithet(ep3String);
             }
         }
+        //nomenclatural status
+        NomenclaturalStatusType status = makeNomenclaturalStatus(id, state, nomZusatzString);
+        if(status!=null){
+            name.addStatus(NomenclaturalStatus.NewInstance(status));
+        }
+
 
         //--- AUTHORS ---
         //combination author
-        if(authorKombString.contains(EX)){
+        if(authorKombString.contains(RedListUtil.EX)){
             //TODO: what happens with multiple ex authors??
-            String[] kombSplit = authorKombString.split(EX);
+            String[] kombSplit = authorKombString.split(RedListUtil.EX);
             if(kombSplit.length!=2){
-                logger.error("NAMNR: "+id+" Multiple ex combination authors found");
+                RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);
             }
             for (int i = 0; i < kombSplit.length; i++) {
                 if(i==0){
                     //first author is ex author
-                    TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, kombSplit[i]);
+                    TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
                     name.setExCombinationAuthorship(authorKomb);
                 }
                 else{
-                    TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, kombSplit[i]);
+                    TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
                     name.setCombinationAuthorship(authorKomb);
                 }
             }
         }
-        else if(authorKombString.trim().equals("auct.")){
-            logger.warn("NAMNR: "+id+" AUCT information in AUTOR_KOMB column");
+        else if(authorKombString.trim().equals(RedListUtil.AUCT)){
+            RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
         }
         else if(!CdmUtils.isBlank(authorKombString)){
-            TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, authorKombString);
+            TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
             name.setCombinationAuthorship(authorKomb);
         }
         //basionym author
-        if(authorBasiString.contains(EX)){
-            String[] basiSplit = authorBasiString.split(EX);
+        if(authorBasiString.contains(RedListUtil.EX)){
+            String[] basiSplit = authorBasiString.split(RedListUtil.EX);
             for (int i = 0; i < basiSplit.length; i++) {
                 if(basiSplit.length!=2){
-                    logger.error("NAMNR: "+id+" Multiple ex basionymn authors found");
+                    RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);
                 }
                 if(i==0){
-                    TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, basiSplit[i]);
-                    name.setExBasionymAuthorship(authorBasi);
+                    TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
+                    if(CdmUtils.isBlank(authorKombString)){
+                        name.setExCombinationAuthorship(authorBasi);
+                    }
+                    else{
+                        name.setExBasionymAuthorship(authorBasi);
+                    }
                 }
                 else{
-                    TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, basiSplit[i]);
-                    name.setBasionymAuthorship(authorBasi);
+                    TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
+                    if(CdmUtils.isBlank(authorKombString)){
+                        name.setCombinationAuthorship(authorBasi);
+                    }
+                    else{
+                        name.setBasionymAuthorship(authorBasi);
+                    }
                 }
             }
         }
-        else if(authorBasiString.trim().equals("auct.")){
+        else if(authorBasiString.trim().equals(RedListUtil.AUCT)){
             name.setAppendedPhrase(authorBasiString);
         }
         else if(!CdmUtils.isBlank(authorBasiString)){
             //this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used
-            TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(Namespace.AUTHOR_NAMESPACE, authorBasiString);
+            TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
             if(CdmUtils.isBlank(authorKombString)){
                 name.setCombinationAuthorship(authorBasi);
             }
@@ -197,7 +214,7 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
         }
 
         //check authorship consistency
-        String authorString = rs.getString("AUTOR");
+        String authorString = rs.getString(RedListUtil.AUTOR);
         String authorshipCache = name.getAuthorshipCache();
 
         if(!CdmUtils.isBlank(zusatzString)){
@@ -206,37 +223,40 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
 //        if(CdmUtils.isBlank(authorKombString) && !CdmUtils.isBlank(authorBasiString)){
 //            authorString = "("+authorString+")";
 //        }
+        if(authorString.equals(RedListUtil.AUCT)){
+            authorString = "";
+        }
         if(!authorString.equals(authorshipCache)){
-            logger.warn("NAMNR: "+id+" Authorship inconsistent! name.authorhshipCache <-> Column AUTOR: "+authorshipCache+" <-> "+authorString);
+            RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
         }
 
         //id
-        ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, Namespace.NAME_NAMESPACE);
+        ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
         state.getNameMap().put(id, name.getUuid());
 
         namesToSave.add(name);
 
         //---TAXON---
         TaxonBase taxonBase = null;
-        if(gueltString.equals("1")){
+        if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON) || (name.getAppendedPhrase()!=null && name.getAppendedPhrase().equals(RedListUtil.AUCT))){
             taxonBase = Taxon.NewInstance(name, null);
         }
-        else if(gueltString.equals("x") || gueltString.equals("b")){
+        else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
             taxonBase = Synonym.NewInstance(name, null);
         }
         if(taxonBase==null){
-            logger.error("NAMNR: "+id+" Taxon for name "+name+" could not be created.");
+            RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
             return;
         }
 
         taxaToSave.add(taxonBase);
 
         //id
-        ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, Namespace.TAXON_NAMESPACE);
+        ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_NAMESPACE);
         state.getTaxonMap().put(id, taxonBase.getUuid());
     }
 
-    private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) {
+    private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr) {
         Rank rank = null;
         try {
             rank = state.getTransformer().getRankByKey(rankStr);
@@ -244,11 +264,24 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
             e.printStackTrace();
         }
         if(rank==null){
-            logger.error(rankStr+" could not be associated to a known rank.");
+            RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
         }
         return rank;
     }
 
+    private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
+        NomenclaturalStatusType status = null;
+        try {
+            status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
+        } catch (UndefinedTransformerMethodException e) {
+            e.printStackTrace();
+        }
+        if(status==null){
+            RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
+        }
+        return status;
+    }
+
 
 
     @Override
@@ -259,10 +292,10 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
 
         try {
             while (rs.next()){
-                String authorKombString = rs.getString("AUTOR_KOMB");
+                String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
 
-                if(authorKombString.contains(EX)){
-                    String[] kombSplit = authorKombString.split(EX);
+                if(authorKombString.contains(RedListUtil.EX)){
+                    String[] kombSplit = authorKombString.split(RedListUtil.EX);
                     for (int i = 0; i < kombSplit.length; i++) {
                         if(!authorMap.containsKey(kombSplit[i])){
                             authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
@@ -273,10 +306,10 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
                     authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
                 }
 
-                String authorBasiString = rs.getString("AUTOR_BASI");
+                String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
                 //basionym author
-                if(authorBasiString.contains(EX)){
-                    String[] basiSplit = authorBasiString.split(EX);
+                if(authorBasiString.contains(RedListUtil.EX)){
+                    String[] basiSplit = authorBasiString.split(RedListUtil.EX);
                     for (int i = 0; i < basiSplit.length; i++) {
                         if(!authorMap.containsKey(basiSplit[i])){
                             authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
@@ -290,7 +323,7 @@ public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefae
         } catch (SQLException e) {
             e.printStackTrace();
         }
-        result.put(Namespace.AUTHOR_NAMESPACE, authorMap);
+        result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
 
         return result;
     }