fix #6364 use TaxonNameFactory for viral and bacterial names

diff --git a/cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifJsonOccurrenceParser.java b/cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifJsonOccurrenceParser.java
index 640b90119c382a2fe31772a85455393a1af4c637..84471f4737ce27fedc9875f3bb22a0c3cba03a77 100644 (file)
--- a/cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifJsonOccurrenceParser.java
+++ b/cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifJsonOccurrenceParser.java
@@ -252,11 +252,11 @@ public class GbifJsonOccurrenceParser {
                             } else if (string.equals(NomenclaturalCode.ICNAFP.getTitleCache())) {
                                 name = TaxonNameBase.NewBotanicalInstance(rank);
                             } else if (string.equals(NomenclaturalCode.ICNB.getTitleCache())){
-                                name = TaxonNameBase.NewBacterialInstance(rank);
+                                name = TaxonNameFactory.NewBacterialInstance(rank);
                             } else if (string.equals(NomenclaturalCode.ICNCP.getTitleCache())){
                                 name = TaxonNameFactory.NewCultivarInstance(rank);
                             } else if (string.equals(NomenclaturalCode.ICVCN.getTitleCache())){
-                                name = TaxonNameBase.NewViralInstance(rank);
+                                name = TaxonNameFactory.NewViralInstance(rank);
                             } else {
                             }
                         }else {
@@ -268,7 +268,7 @@ public class GbifJsonOccurrenceParser {
                                 } else if (record.getString(KINGDOM).equals(FUNGI)){
                                     name = TaxonNameBase.NewBotanicalInstance(rank);
                                 } else if (record.getString(KINGDOM).equals(BACTERIA)){
-                                    name = TaxonNameBase.NewBacterialInstance(rank);
+                                    name = TaxonNameFactory.NewBacterialInstance(rank);
                                 } else{
                                     name = TaxonNameBase.NewNonViralInstance(rank);
                                 }

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 76bbdf251419544dcd8697d6ebc573a68a02b20c..e061a1fe1a5eba62d6a76473526c3e07c59e079e 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
@@ -402,7 +402,7 @@ public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STA
                    }
                }
                else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNB.getUuid())) {
-                   NonViralName<BacterialName> taxonName = TaxonNameBase.NewBacterialInstance(null);
+                   NonViralName<BacterialName> taxonName = TaxonNameFactory.NewBacterialInstance(null);
                    taxonName.setFullTitleCache(fullName, true);
                    taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
                    taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java
index e3da481ef3ecccfa4e5082366133a68d8e220b8c..a0092a553970a324bfcea67ad3bdb179b443bcd7 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java
@@ -147,10 +147,10 @@ public enum NomenclaturalCode implements IEnumTerm<NomenclaturalCode> {
                        result = TaxonNameFactory.NewCultivarInstance(rank);\r
                        break;\r
                case ICNB:\r
-                       result = TaxonNameBase.NewBacterialInstance(rank);\r
+                       result = TaxonNameFactory.NewBacterialInstance(rank);\r
                        break;\r
                case ICVCN:\r
-                       result = TaxonNameBase.NewViralInstance(rank);\r
+                       result = TaxonNameFactory.NewViralInstance(rank);\r
                        break;\r
                default:\r
                        logger.warn("Unknown nomenclatural code: " + this.getUuid());\r

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
index 3f21edc172fa1c2ed1c9e74ccca2c7ecabb3702c..ff49acbeb4107e3311f83f50631f3df811b5c4d9 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
@@ -550,53 +550,6 @@ public abstract class TaxonNameBase<T extends TaxonNameBase<?,?>, S extends INam
     }
 
 
-    /**
-     * Creates a new viral taxon name instance only containing its {@link Rank rank}.
-     *
-     * @param   rank  the rank to be assigned to <i>this</i> viral taxon name
-     * @see     #ViralName(Rank)
-     */
-    public static ViralName NewViralInstance(Rank rank){
-        return new ViralName(rank);
-    }
-
-    /**
-     * Creates a new bacterial taxon name instance
-     * only containing its {@link Rank rank} and
-     * the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
-     *
-     * @param  rank  the rank to be assigned to <i>this</i> bacterial taxon name
-     * @see    #NewInstance(Rank, HomotypicalGroup)
-     * @see    #BacterialName(Rank, HomotypicalGroup)
-     * @see    eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
-     * @see    eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
-     * @see    eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
-     */
-    public static BacterialName NewBacterialInstance(Rank rank){
-        return new BacterialName(rank, null);
-    }
-
-    /**
-     * Creates a new bacterial taxon name instance
-     * only containing its {@link Rank rank},
-     * its {@link HomotypicalGroup homotypical group} and
-     * the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
-     * The new bacterial taxon name instance will be also added to the set of
-     * bacterial taxon names belonging to this homotypical group.
-     *
-     * @param  rank  the rank to be assigned to <i>this</i> bacterial taxon name
-     * @param  homotypicalGroup  the homotypical group to which <i>this</i> bacterial taxon name belongs
-     * @see    #NewInstance(Rank)
-     * @see    #BacterialName(Rank, HomotypicalGroup)
-     * @see    eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
-     * @see    eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
-     * @see    eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
-     */
-    public static BacterialName NewBacterialInstance(Rank rank, HomotypicalGroup homotypicalGroup){
-        return new BacterialName(rank, homotypicalGroup);
-    }
-
-
     /**
      * Creates a new zoological taxon name instance
      * only containing its {@link Rank rank} and

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java
index d2f219e981794f880cd17a3bfb84c2f99a6a0d38..28fc12e7a37251dd20a043b804e7749a7fe6bcf4 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java
@@ -105,7 +105,7 @@ public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase impl
                        }else if ( isZoologicalName /*&& ! isBotanicalName*/ && !isBacteriologicalName && !isCultivatedPlantName){
                                result = TaxonNameBase.NewZoologicalInstance(rank);
                        }else if ( isZoologicalName && ! isBotanicalName && !isBacteriologicalName && !isCultivatedPlantName){
-                               result = TaxonNameBase.NewBacterialInstance(rank);
+                               result = TaxonNameFactory.NewBacterialInstance(rank);
                        }else {
                                result =  TaxonNameBase.NewNonViralInstance(rank);
                        }
@@ -123,7 +123,7 @@ public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase impl
                                break;
                        case ICNB:
                                logger.warn("ICNB not yet implemented");
-                               result = TaxonNameBase.NewBacterialInstance(rank);
+                               result = TaxonNameFactory.NewBacterialInstance(rank);
                                break;
                        case ICVCN:
                                logger.error("Viral name is not a NonViralName !!");

diff --git a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BacterialNameTest.java b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BacterialNameTest.java
index 94c0ee981fa43a73b1301e7a32b286b49987cefc..8e12af0a06b3bd805ae4d7a6cb1cae21a5055c9d 100644 (file)
--- a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BacterialNameTest.java
+++ b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BacterialNameTest.java
@@ -37,7 +37,7 @@ public class BacterialNameTest {
         */\r
        @Before\r
        public void setUp() throws Exception {\r
-               bacterialName1 = TaxonNameBase.NewBacterialInstance(Rank.SPECIES());\r
+               bacterialName1 = TaxonNameFactory.NewBacterialInstance(Rank.SPECIES());\r
        }\r
 \r
 //****************** TESTS ******************************************/\r

diff --git a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/ViralNameTest.java b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/ViralNameTest.java
index 9e5d44ff405de51afdd61a4003e9b27cb8cbbcca..39e66fd8955ec7782599c84942953c980d9915a3 100644 (file)
--- a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/ViralNameTest.java
+++ b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/ViralNameTest.java
@@ -37,7 +37,7 @@ public class ViralNameTest {
         */\r
        @Before\r
        public void setUp() throws Exception {\r
-               viralName1 = ViralName.NewViralInstance(Rank.SPECIES());\r
+               viralName1 = TaxonNameFactory.NewViralInstance(Rank.SPECIES());\r
        }\r
 \r
 //****************** TESTS ******************************************/\r

diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java
index 22ab38b22eb3da3198abca2bc03b1aec6bd311a4..df16bd970ff90ad65870294c3a0a139ab2d8ce47 100644 (file)
--- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java
+++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java
@@ -812,7 +812,7 @@ public class FullCoverageDataGenerator {
 
 
        private void createTaxonName(List<CdmBase> cdmBases) {
-               BacterialName bacName = TaxonNameBase.NewBacterialInstance(Rank.GENUS());
+               BacterialName bacName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());
                bacName.setSubGenusAuthorship("sub Genus author");
                bacName.setNameApprobation("nameApprobation");
                handleIdentifiableEntity(bacName);
@@ -864,7 +864,7 @@ public class FullCoverageDataGenerator {
                                getReference(), "p,22", "original name", false, true);
                handleAnnotatableEntity(specimenDesig);
 
-               ViralName viralName = ViralName.NewViralInstance(Rank.GENUS());
+               ViralName viralName = TaxonNameFactory.NewViralInstance(Rank.GENUS());
                viralName.setAcronym("acronym");
                handleIdentifiableEntity(viralName);