ref #6368 remove some further occurrences of ITaxonNameBase

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java
index f3b408363c1b1862a3da87f51831b5c3253d7fb5..245d5163376914e0f2fbb0e1e3a98e5ae26aaee3 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxExport.java
@@ -107,7 +107,7 @@ public class DwcaTaxExport extends DwcaExportBase {
                                Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);\r
                                DwcaTaxRecord record = new DwcaTaxRecord(metaRecord, config);\r
 \r
-                               INonViralName name = taxon.getName();\r
+                               TaxonName name = taxon.getName();\r
                                Taxon parent = node.getParent() == null ? null : node.getParent().getTaxon();\r
                                TaxonName basionym = name.getBasionym();\r
                                Classification classification = node.getClassification();\r
@@ -154,7 +154,7 @@ public class DwcaTaxExport extends DwcaExportBase {
                        if (type == null){ // should not happen\r
                                type = SynonymType.SYNONYM_OF();\r
                        }\r
-                       INonViralName name = synonym.getName();\r
+                       TaxonName name = synonym.getName();\r
                        //????\r
                        Taxon parent = null;\r
                        TaxonName basionym = name.getBasionym();\r
@@ -172,7 +172,7 @@ public class DwcaTaxExport extends DwcaExportBase {
                for (Taxon misappliedName : misappliedNames ){\r
                        DwcaTaxRecord record = new DwcaTaxRecord(metaRecord, config);\r
                        TaxonRelationshipType relType = TaxonRelationshipType.MISAPPLIED_NAME_FOR();\r
-                       INonViralName name = misappliedName.getName();\r
+                       TaxonName name = misappliedName.getName();\r
                        //????\r
                        Taxon parent = null;\r
                        TaxonName basionym = name.getBasionym();\r
@@ -197,7 +197,7 @@ public class DwcaTaxExport extends DwcaExportBase {
         * @param config\r
         * @param type\r
         */\r
-       private void handleTaxonBase(DwcaTaxRecord record, TaxonBase<?> taxonBase, INonViralName name,\r
+       private void handleTaxonBase(DwcaTaxRecord record, TaxonBase<?> taxonBase, TaxonName name,\r
                        Taxon acceptedTaxon, Taxon parent, TaxonName basionym, Classification classification,\r
                        RelationshipTermBase<?> relType, boolean isProParte, boolean isPartial, DwcaTaxExportConfigurator config) {\r
                record.setId(taxonBase.getId());\r

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxRecord.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxRecord.java
index 6c0d346740e3b033842ec03a88ccfc2c4e108e6b..16e507bdbd5228cde6ab8e29cc9cfbc0bcc95aa9 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxRecord.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTaxRecord.java
@@ -19,10 +19,10 @@ import org.joda.time.DateTime;
 import eu.etaxonomy.cdm.io.dwca.TermUri;\r
 import eu.etaxonomy.cdm.model.common.Language;\r
 import eu.etaxonomy.cdm.model.media.Rights;\r
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;\r
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;\r
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;\r
 import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.name.TaxonName;\r
 import eu.etaxonomy.cdm.model.taxon.Classification;\r
 \r
 /**\r
@@ -409,7 +409,7 @@ public class DwcaTaxRecord extends DwcaRecordBase{
        public String getScientificNameId() {\r
                return scientificNameId.getId();\r
        }\r
-       public void setScientificNameId(ITaxonNameBase scientificNameId) {\r
+       public void setScientificNameId(TaxonName scientificNameId) {\r
                this.scientificNameId.setId(scientificNameId);\r
        }\r
 \r

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java
index e02ced73286fa881daf1bb6bf5168b44e69a13fc..ee81ebf2101f39f84c00cbaaeaf95cf9804664b6 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java
@@ -47,7 +47,6 @@ import eu.etaxonomy.cdm.model.description.TextData;
 import eu.etaxonomy.cdm.model.location.NamedArea;
 import eu.etaxonomy.cdm.model.media.Media;
 import eu.etaxonomy.cdm.model.name.INonViralName;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
@@ -500,7 +499,7 @@ public class NormalExplicitImport extends TaxonExcelImporterBase {
      */
     private Synonym createSynonym(TaxonExcelImportState state, TaxonBase<?> taxonBase, String synonymNameStr) {
         NomenclaturalCode nc = state.getConfig().getNomenclaturalCode();
-        ITaxonNameBase name = null;
+        TaxonName name = null;
         if (nc.isKindOf(NomenclaturalCode.ICZN)){
             name = TaxonNameFactory.NewZoologicalInstance(taxonBase.getName().getRank());
         }else if (nc.isKindOf(NomenclaturalCode.ICNAFP)){

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java
index ab48110842b2f8ee849cc692934876dd56ec9210..aeef89a7a602a865a4ca87f108d7fd33711a11f4 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java
@@ -79,7 +79,6 @@ import eu.etaxonomy.cdm.model.media.MediaRepresentation;
 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;\r
 import eu.etaxonomy.cdm.model.media.Rights;\r
 import eu.etaxonomy.cdm.model.name.INonViralName;\r
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;\r
 import eu.etaxonomy.cdm.model.name.Rank;\r
 import eu.etaxonomy.cdm.model.name.TaxonName;\r
 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;\r
@@ -115,7 +114,7 @@ public class SDDImport extends XmlImportBase<SDDImportConfigurator, SDDImportSta
     private Map<String,Reference> publications = new HashMap<>();\r
     private Map<String,State> states = new HashMap<>();\r
     private Map<String,TaxonDescription> taxonDescriptions = new HashMap<>();\r
-    private Map<String,INonViralName> taxonNames = new HashMap<>();\r
+    private Map<String,TaxonName> taxonNames = new HashMap<>();\r
     private Map<String,MeasurementUnit> units = new HashMap<>();\r
     private Map<String,TaxonNode> taxonNodes = new HashMap<>();\r
     private Map<String,NamedArea> namedAreas = new HashMap<>();\r
@@ -1901,7 +1900,7 @@ public class SDDImport extends XmlImportBase<SDDImportConfigurator, SDDImportSta
 \r
                                                for (Element elNode : listNodes){\r
                                                        String idN = elNode.getAttributeValue("id");\r
-                                                       ITaxonNameBase tnb = null;\r
+                                                       TaxonName tnb = null;\r
                                                        if (!idN.equals("")) {\r
                                                                Element elTaxonName = elNode.getChild("TaxonName", sddNamespace);\r
                                                                String refTN = elTaxonName.getAttributeValue("ref");\r

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java
index 9d980c2d65adb1e9b8b0d08fbb06af0917370d74..db92c0f27f75e96ca859e08124b619d9f2d86c4a 100755 (executable)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java
@@ -45,7 +45,6 @@ import eu.etaxonomy.cdm.model.description.Feature;
 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.name.INonViralName;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.Rank;
 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
@@ -103,7 +102,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
 
         //check atomised name data for rank
         //new name will be created
-        ITaxonNameBase atomisedTaxonName = null;
+        TaxonName atomisedTaxonName = null;
         if (rank==null && unitIndexInAbcdFile>=0 && ((state.getDataHolder().getAtomisedIdentificationList() != null && !state.getDataHolder().getAtomisedIdentificationList().isEmpty())|| state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
             atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state);
             if(atomisedTaxonName!=null){
@@ -111,7 +110,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
             }
         }
         if(config.isReuseExistingTaxaWhenPossible()){
-            ITaxonNameBase parsedName = atomisedTaxonName;
+            TaxonName parsedName = atomisedTaxonName;
             if(parsedName==null){
 
                 parsedName = parseScientificName(scientificName, state, state.getReport(), rank);
@@ -150,7 +149,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
         }
 
         if(taxonName==null && atomisedTaxonName!=null){
-            taxonName = (TaxonName) atomisedTaxonName;
+            taxonName = atomisedTaxonName;
             state.getReport().addName(taxonName);
             logger.info("Created new taxon name "+taxonName);
             if(taxonName.hasProblem()){
@@ -256,10 +255,10 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
             * @return a parsed name
             */
 
-           protected ITaxonNameBase parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
+           protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
 
                NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
-               ITaxonNameBase taxonName = null;
+               TaxonName taxonName = null;
                boolean problem = false;
 
                if (logger.isDebugEnabled()){
@@ -267,25 +266,25 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
                }
 
                if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
-                   taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
+                   taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
                    if (taxonName.hasProblem()) {
                        problem = true;
                    }
                }
                else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
-                   taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
+                   taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
                    if (taxonName.hasProblem()) {
                        problem = true;
                    }
                }
                else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
-                   taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank);
+                   taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank);
                    if (taxonName.hasProblem()) {
                        problem = true;
                    }
                }
                else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
-                   taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
+                   taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
                    if (taxonName.hasProblem()) {
                        problem = true;
                    }
@@ -379,7 +378,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
                    }
                }
                else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
-                   TaxonName taxonName = (TaxonName)parseScientificName(fullName, state, state.getReport(), null);
+                   TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null);
                    if (taxonName != null){
                        return taxonName;
                    }

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportReport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportReport.java
index 9c6ca17c1f2d0c3f8f9c5244e60bbc8308d4fc25..cd24acd4bc5520e5e773d725e44b8a448d9b9bcb 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportReport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportReport.java
@@ -25,7 +25,7 @@ import java.util.Set;
 import org.apache.log4j.Logger;
 
 import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
+import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
@@ -47,7 +47,7 @@ public class SpecimenImportReport {
     private final Map<Taxon, List<UnitIdSpecimen>> taxonToAssociatedSpecimens =  new HashMap<>();
     private final Map<UnitIdSpecimen, List<UnitIdSpecimen>> derivateMap = new HashMap<>();
     private final List<UnitIdSpecimen> alreadyExistingSpecimens = new ArrayList<>();
-    private final List<ITaxonNameBase> createdNames = new ArrayList<>();
+    private final List<TaxonName> createdNames = new ArrayList<>();
     private final List<TaxonNode> createdTaxonNodes = new ArrayList<>();
     private final List<String> infoMessages = new ArrayList<>();
 
@@ -55,7 +55,7 @@ public class SpecimenImportReport {
         createdTaxa.add(taxon);
     }
 
-    public void addName(ITaxonNameBase taxonName){
+    public void addName(TaxonName taxonName){
         createdNames.add(taxonName);
     }
 
@@ -159,7 +159,7 @@ public class SpecimenImportReport {
 
         //taxon name
         out.println("---Created Taxon Names ("+createdNames.size()+")---");
-        for (ITaxonNameBase taxonName : createdNames) {
+        for (TaxonName taxonName : createdNames) {
             out.println(taxonName.getTitleCache());
         }
         out.println("\n");

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenSythesysExcelImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenSythesysExcelImport.java
index cd6e076580bb4b4307f8d6eafd1b642e03b17697..b2e95a8e5b7dd38f588d0f4e93a701891abb4b90 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenSythesysExcelImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenSythesysExcelImport.java
@@ -48,7 +48,6 @@ import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.location.NamedArea;
 import eu.etaxonomy.cdm.model.media.Media;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
@@ -393,7 +392,7 @@ public class SpecimenSythesysExcelImport  extends CdmImportBase<SpecimenSynthesy
      * @param sec
      */
     private void setTaxonName(SpecimenSynthesysExcelImportConfigurator config){
-        ITaxonNameBase taxonName = null;
+        TaxonName taxonName = null;
         Taxon taxon = null;
 
         String scientificName="";
@@ -455,7 +454,7 @@ public class SpecimenSythesysExcelImport  extends CdmImportBase<SpecimenSynthesy
                     taxonName = TaxonNameFactory.NewNonViralInstance(null);
                     taxonName.setTitleCache(scientificName, true);
                 }
-                getNameService().save((TaxonName)taxonName);
+                getNameService().save(taxonName);
                 taxon = Taxon.NewInstance(taxonName, ref); //sec set null
                 getTaxonService().save(taxon);
                 //   refreshTransaction();
@@ -509,12 +508,12 @@ public class SpecimenSythesysExcelImport  extends CdmImportBase<SpecimenSynthesy
         return (Taxon) getTaxonService().find(taxon.getUuid());
     }
 
-    private ITaxonNameBase parseScientificName(String scientificName){
+    private TaxonName parseScientificName(String scientificName){
         if (DEBUG) {
             logger.debug("in parseScientificName");
         }
         NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
-        ITaxonNameBase taxonName = null;
+        TaxonName taxonName = null;
         boolean problem=false;
 
         if (DEBUG) {
@@ -528,24 +527,24 @@ public class SpecimenSythesysExcelImport  extends CdmImportBase<SpecimenSynthesy
         }
 
         if (nomenclatureCode.toString().equals("Zoological")){
-            taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICZN,null);
+            taxonName = (TaxonName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICZN,null);
             if (taxonName.hasProblem()) {
                 problem=true;
             }
         }
         if (nomenclatureCode.toString().equals("Botanical")){
-            taxonName  = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNAFP,null);
+            taxonName  = (TaxonName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNAFP,null);
             if (taxonName.hasProblem()) {
                 problem=true;
             }}
         if (nomenclatureCode.toString().equals("Bacterial")){
-            taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNB, null);
+            taxonName = (TaxonName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNB, null);
             if (taxonName.hasProblem()) {
                 problem=true;
             }
         }
         if (nomenclatureCode.toString().equals("Cultivar")){
-            taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNCP, null);
+            taxonName = (TaxonName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNCP, null);
             if (taxonName.hasProblem()) {
                 problem=true;
             }

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXAddSources.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXAddSources.java
index 75f8fb3e29becb17e97f6514f1c9a06f74961f01..fd2e3b27e172e73e119fe487e0705d5d00336a13 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXAddSources.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXAddSources.java
@@ -19,7 +19,6 @@ import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.description.TextData;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 import eu.etaxonomy.cdm.model.reference.Reference;
@@ -188,7 +187,7 @@ public class TaxonXAddSources {
      * @param refMods
      * @param nameToBeFilled
      */
-    protected void addSource(Reference refMods, ITaxonNameBase nameToBeFilled) {
+    protected void addSource(Reference refMods, TaxonName nameToBeFilled) {
         //logger.info("addSource");
         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java
index bed3deb4d026dc251c006d8221670b20172dd49c..79c636f19e15ded6342f5d16461f527cd3b65203 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java
@@ -50,7 +50,6 @@ import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
 import eu.etaxonomy.cdm.model.description.TextData;
 import eu.etaxonomy.cdm.model.name.INonViralName;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
@@ -1583,7 +1582,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
     }
 
 
-    private boolean addFollowingTextToName(ITaxonNameBase nameToBeFilled, String followingText) {
+    private boolean addFollowingTextToName(TaxonName nameToBeFilled, String followingText) {
        if (nameToBeFilled != null && StringUtils.isNotBlank(followingText)){
                if (! followingText.matches("\\d\\.?")){
 
@@ -2139,7 +2138,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
                                 if(newNameStatus != null){
                                        nameToBeFilled.setAppendedPhrase(newNameStatus);
                                 }
-                                sourceHandler.addSource(refMods, nameToBeFilled);
+                                sourceHandler.addSource(refMods, TaxonName.castAndDeproxy(nameToBeFilled));
 
                                 if (nameToBeFilled.getNomenclaturalReference() == null) {
                                     acceptedTaxon= Taxon.NewInstance(nameToBeFilled,refMods);
@@ -2216,7 +2215,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
             }else if (childName.equalsIgnoreCase("tax:bibref")){
                logger.warn(childName + " still preliminary");
 
-               INonViralName currentName = currentMyName == null ? null : currentMyName.getTaxonName();
+               TaxonName currentName = currentMyName == null ? null : currentMyName.getTaxonName();
                boolean handled = addFollowingTextToName (currentName, childNode.getTextContent() );
                if (! handled){
                        setParticularDescription(freetext.trim(), acceptedTaxon,acceptedTaxon, refMods, getNotMarkedUpFeatureObject());
@@ -2226,7 +2225,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
             }
             if(!stringIsEmpty(freetext.trim())) {;
                 if (! freetext.matches("\\d\\.?")){
-                    INonViralName currentName = currentMyName == null ? null : currentMyName.getTaxonName();
+                    TaxonName currentName = currentMyName == null ? null : currentMyName.getTaxonName();
                        boolean handled = false;
                        if (currentName != null && !wasSynonym){
                                handled = addFollowingTextToName (currentName, childNode.getTextContent() );
@@ -2437,14 +2436,14 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
 
         boolean parseNameManually=false;
         INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();
-        ITaxonNameBase  nameToBeFilledTest ;
+        TaxonName nameToBeFilledTest ;
 
         //if selected the atomised version
         if(newName==atomisedNameStr){
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
                 addProblemNameToFile("ato",atomisedNameStr,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
-                nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode, rank);
+                nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode, rank);
                 if (nameToBeFilledTest.hasProblem()){
                     addProblemNameToFile("full",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
                     parseNameManually=true;
@@ -2454,7 +2453,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
                 addProblemNameToFile("fullversion",fullName, nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
-                nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode,rank);
+                nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode,rank);
                 parseNameManually=true;
                 if(!originalName.equalsIgnoreCase(atomisedNameStr)) {
                     addNameDifferenceToFile(originalName,atomisedNameStr);
@@ -2579,14 +2578,14 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
 
         boolean parseNameManually=false;
         INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
-        ITaxonNameBase  nameToBeFilledTest = null;
+        TaxonName  nameToBeFilledTest = null;
 
         //if selected the atomised version
         if(newName==atomisedNameStr){
             nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
                    addProblemNameToFile("ato",atomisedNameStr,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
-                nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode,rank);
+                nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode,rank);
                 if (nameToBeFilledTest.hasProblem()){
                     addProblemNameToFile("full",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
                     parseNameManually=true;
@@ -2596,7 +2595,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
             nameToBeFilledTest = parseWithExtension(parser, fullName , rank, followingText, atomisedMap);
             if (nameToBeFilledTest.hasProblem()){
                 addProblemNameToFile("fullversion",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
-                nameToBeFilledTest = parser.parseFullName(fullName, nomenclaturalCode,rank);
+                nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode,rank);
                 parseNameManually=true;
                 if(!originalName.equalsIgnoreCase(atomisedNameStr)) {
                     addNameDifferenceToFile(originalName,atomisedNameStr);
@@ -2618,7 +2617,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
 
     }
 
-    private ITaxonNameBase parseWithExtension(INonViralNameParser parser, String atomisedNameStr, Rank rank, String followingText, HashMap<String, String> atomisedMap) {
+    private TaxonName parseWithExtension(INonViralNameParser parser, String atomisedNameStr, Rank rank, String followingText, HashMap<String, String> atomisedMap) {
        Object[] nameExtensionResult = getPossibleExtension(followingText, atomisedMap, nomenclaturalCode);
 
        TaxonName name = (TaxonName)parser.parseFullName(atomisedNameStr, nomenclaturalCode, rank);
@@ -3826,7 +3825,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
         /**
          * @param nameToBeFilledTest
          */
-        public void setParsedName(ITaxonNameBase nameToBeFilledTest) {
+        public void setParsedName(TaxonName nameToBeFilledTest) {
             this.taxonName = TaxonName.castAndDeproxy(nameToBeFilledTest);
 
         }
@@ -4732,7 +4731,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
         boolean insertAsExisting =false;
         List<Taxon> existingTaxa = new ArrayList<Taxon>();
         try {
-            existingTaxa = getMatchingTaxa(tnb);
+            existingTaxa = getMatchingTaxa(TaxonName.castAndDeproxy(tnb));
         } catch (Exception e1) {
             // TODO Auto-generated catch block
             e1.printStackTrace();
@@ -4830,7 +4829,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
      * @return
      */
     @SuppressWarnings("rawtypes")
-    private List<Taxon> getMatchingTaxa(ITaxonNameBase tnb) {
+    private List<Taxon> getMatchingTaxa(TaxonName tnb) {
         //logger.info("getMatchingTaxon");
        if (tnb.getTitleCache() == null){
                tnb.setTitleCache(tnb.toString(), tnb.isProtectedTitleCache());

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NameCacheStrategyBase.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NameCacheStrategyBase.java
index 7a7ede36c1d8b664fadb68bca6e5149e3ced3df1..837c465f7c5b0629248c4952c1120e961a8ef463 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NameCacheStrategyBase.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NameCacheStrategyBase.java
@@ -24,7 +24,6 @@ import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.common.Language;
 import eu.etaxonomy.cdm.model.common.Representation;
 import eu.etaxonomy.cdm.model.name.INonViralName;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.NameRelationship;
 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
@@ -223,14 +222,14 @@ public abstract class NameCacheStrategyBase
 
     }
 
-    protected void addOriginalSpelling(List<TaggedText> tags, ITaxonNameBase name){
+    protected void addOriginalSpelling(List<TaggedText> tags, TaxonName name){
         String originalName = getOriginalNameString(name, tags);
         if (StringUtils.isNotBlank(originalName)){
             tags.add(new TaggedText(TagEnum.name, originalName));
         }
     }
 
-    private String getOriginalNameString(ITaxonNameBase currentName, List<TaggedText> originalNameTaggs) {
+    private String getOriginalNameString(TaxonName currentName, List<TaggedText> originalNameTaggs) {
         List<String> originalNameStrings = new ArrayList<>(1);
         currentName = CdmBase.deproxy(currentName);
         //Hibernate.initialize(currentName.getRelationsToThisName());
@@ -256,7 +255,7 @@ public abstract class NameCacheStrategyBase
         }
     }
 
-    private String makeOriginalNameString(ITaxonNameBase currentName, INonViralName originalName,
+    private String makeOriginalNameString(TaxonName currentName, INonViralName originalName,
             List<TaggedText> currentNameTags) {
         //use cache if necessary
         String cacheToUse = null;

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/taxon/TaxonBaseDefaultCacheStrategy.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/taxon/TaxonBaseDefaultCacheStrategy.java
index d425c54605b1165033745f4a87821fb8c0e90761..eb8a7301c0e2fe73691b18c6950b27679aa16b7f 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/taxon/TaxonBaseDefaultCacheStrategy.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/taxon/TaxonBaseDefaultCacheStrategy.java
@@ -17,7 +17,6 @@ import org.apache.commons.lang.StringUtils;
 
 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
 import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
 import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.reference.Reference;
 import eu.etaxonomy.cdm.model.taxon.Synonym;
@@ -91,7 +90,7 @@ public class TaxonBaseDefaultCacheStrategy<T extends TaxonBase>
         return tags;
     }
 
-    private <X extends ITaxonNameBase> List<TaggedText> getNameTags(T taxonBase) {
+    private <X extends TaxonName> List<TaggedText> getNameTags(T taxonBase) {
         List<TaggedText> tags = new ArrayList<>();
         TaxonName name = CdmBase.deproxy(taxonBase.getName());
 

diff --git a/cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/view/OaiPmhViewTest.java b/cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/view/OaiPmhViewTest.java
index 21be1dc1b3578a9d109d26c4a8f9ff0b75d0109e..9ba6323eb53fe7ac1c1dcea8eb10e29a771efaad 100644 (file)
--- a/cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/view/OaiPmhViewTest.java
+++ b/cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/view/OaiPmhViewTest.java
@@ -29,7 +29,7 @@ import eu.etaxonomy.cdm.api.service.pager.Pager;
 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;\r
 import eu.etaxonomy.cdm.common.UriUtils;\r
 import eu.etaxonomy.cdm.model.common.LSID;\r
-import eu.etaxonomy.cdm.model.name.ITaxonNameBase;\r
+import eu.etaxonomy.cdm.model.name.TaxonName;\r
 import eu.etaxonomy.cdm.model.taxon.Taxon;\r
 import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
 import eu.etaxonomy.cdm.model.view.AuditEvent;\r
@@ -148,7 +148,7 @@ public class OaiPmhViewTest extends UnitilsJUnit4 {
             return;\r
         }\r
 \r
-        Taxon taxon = Taxon.NewInstance((ITaxonNameBase)null, null);\r
+        Taxon taxon = Taxon.NewInstance((TaxonName)null, null);\r
         taxon.setTitleCache("TitleCache", true);\r
         taxon.setCreated(new DateTime());\r
         taxon.setLsid(new LSID("urn:lsid:example.org:taxonconcepts:1"));\r

diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java
index 7540b9aa5e8b82ce3b56e8a6df7873c8b9e2b1d4..16c9f173da9b3fcbe1f830708fd982e318739fa2 100644 (file)
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java
@@ -184,10 +184,6 @@ public class NameServiceImpl extends IdentifiableServiceBase<TaxonName,ITaxonNam
         return result;
     }
 
-
-    /* (non-Javadoc)
-     * @see eu.etaxonomy.cdm.api.service.INameService#delete(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.api.service.NameDeletionConfigurator)
-     */
     @Override
     @Transactional(readOnly = false)
     public DeleteResult delete(UUID nameUUID, NameDeletionConfigurator config) {

diff --git a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.java b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.java
index ef6838068feb014c655d1ee3abaa11b4a52ae10f..28db2089a138d1dbf4c7eb6f48391465a6e5f29c 100644 (file)
--- a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.java
+++ b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.java
@@ -764,7 +764,7 @@ public class TaxonServiceImplTest extends CdmTransactionalIntegrationTest {
 
     public final void testDeleteSynonymWithAnnotations(){
         final String[]tableNames = {
-//                "TaxonBase","TaxonBase_AUD", "TaxonNameBase","TaxonNameBase_AUD",
+//                "TaxonBase","TaxonBase_AUD", "TaxonName","TaxonName_AUD",
 //                "HomotypicalGroup","HomotypicalGroup_AUD"
         };