ref #6794 reduce calls to isLower and isHigher in Rank class in app-import

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.java
index ff66489ed7c64166da6bb28e5a6cd324e6ee215f..364de98c18b0d755195d4af996ae9ed14ea190c6 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/IopiActivator.java
@@ -260,7 +260,7 @@ public class IopiActivator {
                if (rank.equals(Rank.FAMILY())){\r
                        family = name.getGenusOrUninomial();\r
                        taxonName = name.getGenusOrUninomial();\r
-               }else if (rank.isHigher(Rank.GENUS())){\r
+               }else if (rank.isSupraGeneric()){\r
                        taxonName = name.getGenusOrUninomial();\r
                }else if (rank.isGenus()){\r
                        genus = name.getGenusOrUninomial();\r

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoAizoaceaeExcelImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoAizoaceaeExcelImport.java
index f61a7114a1c75adc2ae31ea83c2c3bd3ab1193cd..da6d8803aac98a7d5d5b122cba7b36f43eaca92d 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoAizoaceaeExcelImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoAizoaceaeExcelImport.java
@@ -31,6 +31,7 @@ import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.RankClass;
 import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.reference.Reference;
 import eu.etaxonomy.cdm.model.reference.ReferenceType;
@@ -583,7 +584,7 @@ public class CaryoAizoaceaeExcelImport extends SimpleExcelTaxonImport<CaryoAizoa
                         String genus = child.getName().getGenusOrUninomial();
                         UUID parentUuid = taxonMapping.get(genus);
                         parent = getParent(parentUuid, row);
-                    }else if (rank.isLower(Rank.SPECIES())){
+                    }else if (rank.isLowerThan(RankClass.Species)){
                         String speciesName = child.getName().getGenusOrUninomial() + " " + child.getName().getSpecificEpithet();
                         UUID parentUuid = taxonMapping.get(speciesName);
                         parent = getParent(parentUuid, row);

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/casearia/CaseariaTaxonImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/casearia/CaseariaTaxonImport.java
index 1e9d5d93fd5e8c165af7c93cff56a1d0910c741c..dfcf196119c3beca921c0544c9e518aec383b38a 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/casearia/CaseariaTaxonImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/casearia/CaseariaTaxonImport.java
@@ -31,6 +31,7 @@ import eu.etaxonomy.cdm.model.common.Language;
 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.RankClass;
 import eu.etaxonomy.cdm.model.name.TaxonName;
 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
 import eu.etaxonomy.cdm.model.reference.Reference;
@@ -377,7 +378,7 @@ public class CaseariaTaxonImport extends SimpleExcelTaxonImport<CaseariaImportCo
             }
         }
         if (isBlank(infraSpecRank)){
-            if (rank.isLower(Rank.SPECIES())){
+            if (rank.isLowerThan(RankClass.Species)){
                 logger.warn(row +  "No infraspce marker given but rank is lower than species");
             }
         }else if ("subsp.".equals(infraSpecRank)){
@@ -499,7 +500,7 @@ public class CaseariaTaxonImport extends SimpleExcelTaxonImport<CaseariaImportCo
                         String genus = child.getName().getGenusOrUninomial();
                         UUID parentUuid = taxonMapping.get(genus);
                         parent = getParent(parentUuid, row);
-                    }else if (rank.isLower(Rank.SPECIES())){
+                    }else if (rank.isLowerThan(RankClass.Species)){
                         String speciesName = child.getName().getGenusOrUninomial() + " " + child.getName().getSpecificEpithet();
                         UUID parentUuid = taxonMapping.get(speciesName);
                         parent = getParent(parentUuid, row);

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java
index 771b5cc521690ff9103b33139d7fefd28fb851b9..15a17333277b5fa4799b25d52f61303f65a1263d 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java
@@ -217,7 +217,7 @@ public class EdaphobaseTaxonImport extends EdaphobaseImportBase {
             setNamePart(grandParentNameStr, parentParentRank, name);
             Rank grandParentParentRank = makeRank(state, grandGrandParentRankStr);
             setNamePart(grandGrandParentNameStr, grandParentParentRank, name);
-            if (grandParentParentRank != null && grandParentParentRank.isLower(Rank.GENUS()) || isBlank(name.getGenusOrUninomial()) && !name.isProtectedNameCache()){
+            if (grandParentParentRank != null && grandParentParentRank.isLowerThan(RankClass.Genus) || isBlank(name.getGenusOrUninomial()) && !name.isProtectedNameCache()){
                 logger.warn("Grand-Grandparent rank is lower than genus for " +
                         name.getTitleCache() + " (edapho-id: " + id + "; cdm-id: " + name.getId() + ")");
             }

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/euromed/IpniImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/euromed/IpniImport.java
index 3266da8c7e9acba7a3736dd537376feee3b14ef3..592b7112383c51305a576adb05eefcc7e3e44252 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/euromed/IpniImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/euromed/IpniImport.java
@@ -236,9 +236,10 @@ public class IpniImport<CONFIG extends IpniImportConfigurator>
         TaxonNode result = null;
         for (TaxonNode child : genusNode.getChildNodes()){
             Rank childRank = child.getTaxon().getName().getRank();
-            if (childRank.isHigher(Rank.SPECIES())){
+            if (childRank.isSupraSpecific()){
                 result = getSpecies(state, line, taxonName, child);
-            }else if (childRank.isHigher(Rank.SPECIES())){
+            }else if (childRank.isSupraSpecific()){
+                //TODO why do we check for supraSpecific 2x here??
                 //do nothing
             }else if (childRank.equals(Rank.SPECIES()) && specEpi.equals(child.getTaxon().getName().getSpecificEpithet())){
                     result = child;

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/phycobank/IAPTExcelImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/phycobank/IAPTExcelImport.java
index 0b89318dd0ef335eaa4995112a3e565c4c04c33e..fe1d403ac9890a60f44872ab792595190a01787a 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/phycobank/IAPTExcelImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/phycobank/IAPTExcelImport.java
@@ -394,7 +394,7 @@ public class IAPTExcelImport<CONFIG extends IAPTImportConfigurator> extends Simp
         // Types
         if(!StringUtils.isEmpty(typeStr)){
 
-            if(taxonName.getRank().isSpecies() || taxonName.getRank().isLower(Rank.SPECIES())) {
+            if(taxonName.getRank().isSpecies() || taxonName.getRank().isLowerThan(RankClass.Species)) {
                 makeSpecimenTypeData(typeStr, taxonName, regNumber, state, false);
             } else {
                 makeNameTypeData(typeStr, taxonName, regNumber, state);
@@ -403,7 +403,7 @@ public class IAPTExcelImport<CONFIG extends IAPTImportConfigurator> extends Simp
 
         getTaxonService().save(taxon);
 
-        if(taxonName.getRank().equals(Rank.SPECIES()) || taxonName.getRank().isLower(Rank.SPECIES())){
+        if(taxonName.getRank().equals(Rank.SPECIES()) || taxonName.getRank().isLowerThan(RankClass.Species)){
             // try to find the genus, it should have been imported already, Genera are coming first in the import file
             Taxon genus = ((IAPTImportState)state).getGenusTaxonMap().get(taxonName.getGenusOrUninomial());
             if(genus != null){

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/out/BfnXmlTaxonNameExport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/out/BfnXmlTaxonNameExport.java
index 618afebcecd706d194742f76176e03232276c1eb..1dcac31e41c3f5f8bb8dd49d3df32789095c14ae 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/out/BfnXmlTaxonNameExport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/out/BfnXmlTaxonNameExport.java
@@ -36,6 +36,7 @@ import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.description.TextData;
 import eu.etaxonomy.cdm.model.name.INonViralName;
 import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.RankClass;
 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
 import eu.etaxonomy.cdm.model.taxon.Classification;
 import eu.etaxonomy.cdm.model.taxon.Synonym;
@@ -298,7 +299,7 @@ public class BfnXmlTaxonNameExport extends BfnXmlExportBase {
 
         //epitheton1-2
         addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial());
-        if(rank.isLower(Rank.GENUS())){
+        if(rank.isLowerThan(RankClass.Genus)){
             String epitheton2 = name.getInfraGenericEpithet();
             if(epitheton2==null){
                 epitheton2 = name.getSpecificEpithet();
@@ -307,7 +308,7 @@ public class BfnXmlTaxonNameExport extends BfnXmlExportBase {
         }
         //epitheton3
         String epitheton3 = null;
-        if(rank.isLower(Rank.SPECIES())){
+        if(rank.isLowerThan(RankClass.Species)){
             epitheton3 = name.getInfraSpecificEpithet();
         }
         if(epitheton3==null){