From: Andreas Müller <a.mueller@bgbm.org>
Date: Wed, 15 Dec 2021 22:10:25 +0000 (+0100)
Subject: cleanup
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib-apps.git/commitdiff_plain/c5d04eba76d8159e78fc70b4d4409196c6874714

cleanup
---

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaChecklistTaxonImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaChecklistTaxonImport.java
index 0c4b0110..b144f4c4 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaChecklistTaxonImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaChecklistTaxonImport.java
@@ -23,6 +23,7 @@ import eu.etaxonomy.cdm.model.common.IdentifiableSource;
 import eu.etaxonomy.cdm.model.common.Language;
 import eu.etaxonomy.cdm.model.name.IBotanicalName;
 import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
 import eu.etaxonomy.cdm.model.reference.Reference;
 import eu.etaxonomy.cdm.model.taxon.Classification;
@@ -167,7 +168,7 @@ public class BogotaChecklistTaxonImport<CONFIG extends BogotaChecklistImportConf
         }else{
             nameStr = nameStr.replace(auctStr, "").trim();
         }
-        IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+        TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
         name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
         name = state.getDeduplicationHelper().getExistingName(name);
         if (name.isProtectedTitleCache()){
@@ -184,27 +185,14 @@ public class BogotaChecklistTaxonImport<CONFIG extends BogotaChecklistImportConf
         taxon.addMisappliedName(misApp, state.getConfig().getSecReference(), null);
     }
 
-
-    /**
-     * @param col
-     * @return
-     */
     private String getNamespace(CONFIG config) {
         return getWorksheetName(config)+"."+ ID_COL;
     }
 
-
-    /**
-     * @param state
-     * @param record
-     * @param line
-     * @param taxon
-     * @param noStr
-     */
     private void handleSingleSynonym(SimpleExcelTaxonImportState<CONFIG> state, String nameStr,
             String line, Taxon taxon, String noStr) {
         Rank rank = Rank.SPECIES();
-        IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+        TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
         name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
         name = state.getDeduplicationHelper().getExistingName(name);
         if (name.isProtectedTitleCache()){
@@ -217,14 +205,6 @@ public class BogotaChecklistTaxonImport<CONFIG extends BogotaChecklistImportConf
         taxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
     }
 
-
-    /**
-     * @param state
-     * @param line
-     * @param record
-     * @param taxon
-     * @param noStr
-     */
     private void makeInfraSpecific(SimpleExcelTaxonImportState<CONFIG> state, Map<String, String> record, String line,
             TaxonNode speciesNode, String noStr) {
         String subSpeciesStr = getValue(record, INFRASPECIFIC);
@@ -235,7 +215,7 @@ public class BogotaChecklistTaxonImport<CONFIG extends BogotaChecklistImportConf
                     split = split.replace(" None", "").trim();
                 }
                 Rank rank = Rank.SUBSPECIES();
-                IBotanicalName name = (IBotanicalName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank);
+                TaxonName name = (TaxonName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank);
                 name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
                 name = state.getDeduplicationHelper().getExistingName(name);
                 if (name.isProtectedTitleCache()){
@@ -251,13 +231,6 @@ public class BogotaChecklistTaxonImport<CONFIG extends BogotaChecklistImportConf
         }
     }
 
-    /**
-     * @param state
-     * @param line
-     * @param record
-     * @param noStr
-     * @return
-     */
     private TaxonNode makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, Map<String, String> record,
             String noStr) {
 
@@ -272,7 +245,7 @@ public class BogotaChecklistTaxonImport<CONFIG extends BogotaChecklistImportConf
 
         nameStr = CdmUtils.concat(" ", nameStr, speciesAuthorStr);
         Rank rank = Rank.SPECIES();
-        IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+        TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
         name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
         name = state.getDeduplicationHelper().getExistingName(name);
         if (name.isProtectedTitleCache()){
diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaExcludedTaxonImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaExcludedTaxonImport.java
index aed80a41..a5f19d01 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaExcludedTaxonImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaExcludedTaxonImport.java
@@ -19,8 +19,6 @@ import org.springframework.stereotype.Component;
 import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
 import eu.etaxonomy.cdm.model.agent.Person;
 import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
-import eu.etaxonomy.cdm.model.name.IBotanicalName;
-import eu.etaxonomy.cdm.model.name.INonViralName;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.Rank;
 import eu.etaxonomy.cdm.model.name.TaxonName;
@@ -114,7 +112,7 @@ public class FloraHellenicaExcludedTaxonImport<CONFIG extends FloraHellenicaImpo
             isSensuStrictu = true;
             taxonStr = taxonStr.substring(0, taxonStr.length() - "s.str.".length() ).trim();
         }
-        INonViralName name = parser.parseFullName(taxonStr, NomenclaturalCode.ICNAFP, null);
+        TaxonName name = (TaxonName)parser.parseFullName(taxonStr, NomenclaturalCode.ICNAFP, null);
         name = replaceNameAuthorsAndReferences(state, name);
         if (name.isProtectedTitleCache()){
             logger.warn(line + "Name could not be parsed: " + taxonStr);
@@ -155,7 +153,7 @@ public class FloraHellenicaExcludedTaxonImport<CONFIG extends FloraHellenicaImpo
         if (family != null){
             familyNode = family.getTaxonNodes().iterator().next();
         }else{
-            IBotanicalName name = makeFamilyName(state, familyStr);
+            TaxonName name = makeFamilyName(state, familyStr);
             name = replaceNameAuthorsAndReferences(state, name);
 
             Reference sec = getSecReference(state);
diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java
index c9fee370..a4381eed 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.java
@@ -19,8 +19,6 @@ import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;
 import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.name.IBotanicalName;
-import eu.etaxonomy.cdm.model.name.INonViralName;
 import eu.etaxonomy.cdm.model.name.Rank;
 import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
@@ -141,7 +139,7 @@ public abstract class FloraHellenicaImportBase<CONFIG extends FloraHellenicaImpo
     }
 
 
-    protected IBotanicalName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,
+    protected TaxonName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,
             String famStr) {
         TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
         famStr = famStr.substring(0,1).toUpperCase() + famStr.substring(1).toLowerCase();
@@ -150,8 +148,8 @@ public abstract class FloraHellenicaImportBase<CONFIG extends FloraHellenicaImpo
         return name;
     }
 
-    protected <NAME extends INonViralName> NAME replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, NAME name) {
-        NAME result = state.getDeduplicationHelper().getExistingName(name);
+    protected TaxonName replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, TaxonName name) {
+        TaxonName result = state.getDeduplicationHelper().getExistingName(name);
         state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(result);
         return result;
     }
diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTaxonImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTaxonImport.java
index f5787f86..d6e405c2 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTaxonImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTaxonImport.java
@@ -29,8 +29,8 @@ import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
 import eu.etaxonomy.cdm.model.description.State;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.location.NamedArea;
-import eu.etaxonomy.cdm.model.name.IBotanicalName;
 import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
 import eu.etaxonomy.cdm.model.reference.Reference;
 import eu.etaxonomy.cdm.model.taxon.Classification;
@@ -393,7 +393,7 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
             nameStr = nameStr.substring(0, nameStr.length() - "s.str.".length() ).trim();
         }
         Rank rank = isSubSpecies ? Rank.SUBSPECIES() : Rank.SPECIES();
-        IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+        TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
         if (name.isProtectedTitleCache()){
             logger.warn(line + "Name could not be parsed: " + nameStr);
         }
@@ -450,15 +450,9 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
         return CdmUtils.concat(" ", new String[]{genusStr, speciesStr, speciesAuthorStr});
     }
 
-    /**
-     * @param state
-     * @param record
-     * @param genusStr
-     * @return
-     */
     private TaxonNode makeGenusNode(SimpleExcelTaxonImportState<CONFIG> state,
             Map<String, String> record, String genusStr) {
-        IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
+        TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
         name.setGenusOrUninomial(genusStr);
         name = replaceNameAuthorsAndReferences(state, name);
         Taxon genus = Taxon.NewInstance(name, getSecReference(state));
@@ -470,22 +464,12 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
         return genusNode;
     }
 
-    /**
-     * @param state
-     * @param parentStr
-     * @return
-     */
     private TaxonNode getParent(SimpleExcelTaxonImportState<CONFIG> state, String parentStr) {
         Taxon taxon = state.getHigherTaxon(parentStr);
 
         return taxon == null ? null : taxon.getTaxonNodes().iterator().next();
     }
 
-    /**
-     * @param record
-     * @param state
-     * @return
-     */
     private TaxonNode getFamilyTaxon(Map<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {
         String familyStr = getValue(record, "Family");
         if (familyStr == null){
@@ -498,7 +482,7 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
         if (family != null){
             familyNode = family.getTaxonNodes().iterator().next();
         }else{
-            IBotanicalName name = makeFamilyName(state, familyStr);
+            TaxonName name = makeFamilyName(state, familyStr);
             name = replaceNameAuthorsAndReferences(state, name);
 
             Reference sec = getSecReference(state);
@@ -530,7 +514,7 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
         if (group != null){
             groupNode = group.getTaxonNodes().iterator().next();
         }else{
-            IBotanicalName name = makeFamilyName(state, groupStr);
+            TaxonName name = makeFamilyName(state, groupStr);
             name = replaceNameAuthorsAndReferences(state, name);
 
             Reference sec = getSecReference(state);
@@ -554,7 +538,7 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
             classification.setUuid(state.getConfig().getClassificationUuid());
             classification.getRootNode().setUuid(rootUuid);
 
-            IBotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
+            TaxonName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
             plantaeName.setGenusOrUninomial("Plantae");
             plantaeName = replaceNameAuthorsAndReferences(state, plantaeName);
 
@@ -568,11 +552,6 @@ public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfig
         return rootNode;
     }
 
-    /**
-     * @param desc
-     * @param string
-     * @param uuidUserDefinedAnnotationTypeVocabulary
-     */
     private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state,
                 TaxonDescription desc, String key, UUID uuid, String line, String id) {
         Map<String, String> record = state.getOriginalRecord();
diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/excel/RedListGefaesspflanzenTaxonExcelImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/excel/RedListGefaesspflanzenTaxonExcelImport.java
index a8902368..e7a199cb 100644
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/excel/RedListGefaesspflanzenTaxonExcelImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/excel/RedListGefaesspflanzenTaxonExcelImport.java
@@ -154,7 +154,7 @@ public class RedListGefaesspflanzenTaxonExcelImport<CONFIG extends RedListGefaes
         nameStr = normalizeNameStr(nameStr);
 
         Rank rank = Rank.SPECIES();
-        IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+        TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
         name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
         name = state.getDeduplicationHelper().getExistingName(name);
         if (name.isProtectedTitleCache()){