ref #6362 remove some further NVN occurrences

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 94a7154551e6ecc54a09025f1cd14f8b79d3dd54..2182c4eaccd9c0a21437579df0716b880e66fbc1 100644 (file)
--- 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
@@ -53,7 +53,6 @@ import eu.etaxonomy.cdm.model.name.Rank;
 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.name.ZoologicalName;
 import eu.etaxonomy.cdm.model.occurrence.Collection;
 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
@@ -105,7 +104,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
 
         //check atomised name data for rank
         //new name will be created
-        NonViralName<?> atomisedTaxonName = null;
+        TaxonNameBase<?,?> 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){
@@ -113,7 +112,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
             }
         }
         if(config.isReuseExistingTaxaWhenPossible()){
-            NonViralName<?> parsedName = atomisedTaxonName;
+            TaxonNameBase<?,?> parsedName = atomisedTaxonName;
             if(parsedName==null){
                 parsedName = parseScientificName(scientificName, state, state.getReport());
             }
@@ -220,9 +219,9 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
             * @param report the import report
             * @return a parsed name
             */
-           protected NonViralName<?> parseScientificName(String scientificName, STATE state, SpecimenImportReport report) {
+           protected TaxonNameBase<?,?> parseScientificName(String scientificName, STATE state, SpecimenImportReport report) {
                NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
-               NonViralName<?> taxonName = null;
+               TaxonNameBase<?,?> taxonName = null;
                boolean problem = false;
 
                if(DEBUG){
@@ -275,7 +274,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
             * @param state
             * @return the corresponding Botanical or Zoological or... name
             */
-           protected NonViralName<?> setTaxonNameByType(
+           protected TaxonNameBase<?,?> setTaxonNameByType(
                    HashMap<String, String> atomisedMap, String fullName, STATE state) {
                boolean problem = false;
                if(DEBUG) {
@@ -283,7 +282,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
                }
 
                if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
-                   NonViralName<ZoologicalName> taxonName = TaxonNameBase.NewZoologicalInstance(null);
+                   TaxonNameBase<?,?> taxonName = TaxonNameBase.NewZoologicalInstance(null);
                    taxonName.setFullTitleCache(fullName, true);
                    taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
                    taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
@@ -455,11 +454,11 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
 
                if (problem) {
                    logger.info("Problem im setTaxonNameByType ");
-                   NonViralName<?> taxonName = TaxonNameBase.NewNonViralInstance(null);
+                   TaxonNameBase<?,?> taxonName = TaxonNameBase.NewNonViralInstance(null);
                    taxonName.setFullTitleCache(fullName, true);
                    return taxonName;
                }
-               NonViralName<?> tn = TaxonNameBase.NewNonViralInstance(null);
+               TaxonNameBase<?,?> tn = TaxonNameBase.NewNonViralInstance(null);
                return tn;
            }
 

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/gbif/in/GbifImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/gbif/in/GbifImport.java
index 8ddfc1bcdfbd725b6741f326a1cde90677d95fad..aa9e59c4aeb7f63a657397c801fefa50f2274ea3 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/gbif/in/GbifImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/gbif/in/GbifImport.java
@@ -652,13 +652,13 @@ private void handleDeterminations(
  * @param names
  * @param item
  */
-private TaxonNameBase findBestMatchingNames(GbifResponse item, SpecimenImportStateBase state) {
+private TaxonNameBase<?,?> findBestMatchingNames(GbifResponse item, SpecimenImportStateBase state) {
    //TODO
     if (item.getScientificName() != null){
 
        List<NonViralName> names = findExistingNames(item.getScientificName().getNameCache(), state);
        if (!names.isEmpty()){
-           NonViralName<?> result = names.get(0);
+           TaxonNameBase<?,?> result = names.get(0);
            Set<DeterminationEvent> detEvents = item.getDerivedUnitFacade().baseUnit().getDeterminations();
            for (DeterminationEvent event:detEvents){
                if(event.getTaxonName().getNameCache().equals(result.getNameCache()) ){

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 a24ecfeea6dd27c0a0d21194af4e899169af697c..53bf14c109f926009d2ef1a26ed3f9c56bc0575b 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.NonViralName;
 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
 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, NonViralName<?> nameToBeFilled) {
+    protected void addSource(Reference refMods, TaxonNameBase<?,?> 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 f2c6412124a8353f370324cf64690b7ee46259af..b608a71b1c7fbd59156ceedb47cbf28cd7b6e09f 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
@@ -900,7 +900,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
      * @param acceptedTaxon: the current accepted Taxon
      * @param refMods: the current reference extracted from the MODS
      */
-    private String extractMaterialsDirect(Node materials, Taxon acceptedTaxon, Reference refMods, String event, NonViralName<?> currentName) {
+    private String extractMaterialsDirect(Node materials, Taxon acceptedTaxon, Reference refMods, String event, TaxonNameBase<?,?> currentName) {
         logger.info("extractMaterialsDirect");
         //        logger.info("acceptedTaxon: "+acceptedTaxon);
         String descr="";
@@ -2303,7 +2303,7 @@ public class TaxonXTreatmentExtractor extends TaxonXExtractor{
                     s = askSetParent(s);
                     r = askRank(s,rankListStr);
 
-                    NonViralName<?> nameToBeFilled = null;
+                    TaxonNameBase<?,?> nameToBeFilled = null;
                     if (nomenclaturalCode.equals(NomenclaturalCode.ICNAFP)){
                         nameToBeFilled = TaxonNameBase.NewBotanicalInstance(null);
                     }

diff --git a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/dto/NameCatalogueController.java b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/dto/NameCatalogueController.java
index cb00c3bea9ca2368b1f3ba482c571bab09b06d12..5d42c5073462fe317f3e4c47e1cab99737e7ff58 100644 (file)
--- a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/dto/NameCatalogueController.java
+++ b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/dto/NameCatalogueController.java
@@ -676,8 +676,7 @@ public class NameCatalogueController extends AbstractController<TaxonNameBase, I
             logger.info("doGetNameInformation()" + request.getRequestURI() + " for name uuid \""
                     + nameUuid + "\"");
             // find name by uuid
-            NonViralName<?> nvn = CdmBase.deproxy(service.load(UUID.fromString(nameUuid),
-                        NAME_INFORMATION_INIT_STRATEGY), NonViralName.class);
+            TaxonNameBase<?,?> nvn = service.load(UUID.fromString(nameUuid),NAME_INFORMATION_INIT_STRATEGY);
 
             // if search is successful then get related information, else return error
             if (nvn != null) {

diff --git a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/view/oaipmh/dwc/GetRecordView.java b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/view/oaipmh/dwc/GetRecordView.java
index 632e668ecd0aff72a4b27e285a5bb90c3bd5d636..4f9558554cea19fbccb59321b198d7fa07ba31e5 100644 (file)
--- a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/view/oaipmh/dwc/GetRecordView.java
+++ b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/view/oaipmh/dwc/GetRecordView.java
@@ -1,20 +1,19 @@
 package eu.etaxonomy.cdm.remote.view.oaipmh.dwc;\r
 \r
-import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
+import eu.etaxonomy.cdm.model.name.INonViralName;\r
 import eu.etaxonomy.cdm.model.taxon.Taxon;\r
 import eu.etaxonomy.cdm.remote.dto.dwc.SimpleDarwinRecord;\r
 import eu.etaxonomy.cdm.remote.dto.oaipmh.Metadata;\r
 \r
 public class GetRecordView extends     eu.etaxonomy.cdm.remote.view.oaipmh.ListRecordsView {\r
-       \r
+\r
 \r
        @Override\r
        public void constructMetadata(Metadata metadata, IdentifiableEntity identifiableEntity) {\r
-               SimpleDarwinRecord dc = (SimpleDarwinRecord)mapper.map(identifiableEntity, SimpleDarwinRecord.class);\r
+               SimpleDarwinRecord dc = mapper.map(identifiableEntity, SimpleDarwinRecord.class);\r
                if(identifiableEntity instanceof Taxon){\r
-                       NonViralName<?> name = HibernateProxyHelper.deproxy(((Taxon)identifiableEntity).getName(), NonViralName.class);\r
+                       INonViralName name = ((Taxon)identifiableEntity).getName();\r
                        mapper.map(name, dc);\r
                }\r
                dc.setBasisOfRecord("Taxon");\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 c7aee56170ddbc9d758a3c564504d312171ecfb4..097861aa7b9da236de9b8dac1d330d38dee2ee13 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
@@ -60,6 +60,7 @@ import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
 import eu.etaxonomy.cdm.model.name.HybridRelationship;
 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
+import eu.etaxonomy.cdm.model.name.INonViralName;
 import eu.etaxonomy.cdm.model.name.NameRelationship;
 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
@@ -798,18 +799,16 @@ public class NameServiceImpl extends IdentifiableServiceBase<TaxonNameBase,ITaxo
 
     @Override
     protected void setOtherCachesNull(TaxonNameBase name) {
-        if (name.isInstanceOf(NonViralName.class)){
-            NonViralName<?> nvn = CdmBase.deproxy(name, NonViralName.class);
-            if (! nvn.isProtectedNameCache()){
-                nvn.setNameCache(null, false);
-            }
-            if (! nvn.isProtectedAuthorshipCache()){
-                nvn.setAuthorshipCache(null, false);
-            }
-            if (! nvn.isProtectedFullTitleCache()){
-                nvn.setFullTitleCache(null, false);
-            }
+         if (! name.isProtectedNameCache()){
+             name.setNameCache(null, false);
         }
+        if (! name.isProtectedAuthorshipCache()){
+            name.setAuthorshipCache(null, false);
+        }
+        if (! name.isProtectedFullTitleCache()){
+            name.setFullTitleCache(null, false);
+        }
+
     }
 
     @Override
@@ -861,7 +860,7 @@ public class NameServiceImpl extends IdentifiableServiceBase<TaxonNameBase,ITaxo
 
         //hybrid relationships
         if (name.isInstanceOf(NonViralName.class)){
-            NonViralName nvn = CdmBase.deproxy(name, NonViralName.class);
+            INonViralName nvn = name;
             Set<HybridRelationship> parentHybridRelations = nvn.getHybridParentRelations();
             //Hibernate.initialize(parentHybridRelations);
             if (! parentHybridRelations.isEmpty()){

diff --git a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTaxaAndNamesTest.java b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTaxaAndNamesTest.java
index 807fea90485fe37047bc5ec0d95720c51291d3d3..4c60c7490d97873cfe4e05a48f4b6949f55b27b8 100644 (file)
--- a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTaxaAndNamesTest.java
+++ b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTaxaAndNamesTest.java
@@ -29,7 +29,6 @@ import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
 import eu.etaxonomy.cdm.api.service.pager.Pager;
 import eu.etaxonomy.cdm.api.service.search.ICdmMassIndexer;
 import eu.etaxonomy.cdm.common.UTF8;
-import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
 import eu.etaxonomy.cdm.model.common.Language;
 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
@@ -658,7 +657,7 @@ public class TaxonServiceSearchTaxaAndNamesTest extends CdmTransactionalIntegrat
                     nameCache = ((NonViralName<?>) list.get(i)).getNameCache();
                 } else if (list.get(i) instanceof TaxonBase) {
                     TaxonNameBase<?,?> taxonNameBase = ((TaxonBase) list.get(i)).getName();
-                    nameCache = HibernateProxyHelper.deproxy(taxonNameBase, NonViralName.class).getNameCache();
+                    nameCache = taxonNameBase.getNameCache();
                 } else {
                 }
                 logger.log(level, list.get(i).getClass() + "(" + i + ")" + ": Name Cache = " + nameCache + ", Title Cache = "