remove dipteraH2

[cdmlib-apps.git] / app-import / src / main / java / eu / etaxonomy / cdm / app / wp6 / diptera / DipteraPostImportUpdater.java

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.java
index 8ecce27764a9793d379eaace2268c562d07bdf3a..60422021e3390d9be0acf1ff1f6271ee86a1aeb9 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.java
@@ -68,7 +68,7 @@ public class DipteraPostImportUpdater {
                        int modCount = 100;\r
                        int page = 0;\r
                        int count = cdmApp.getTaxonService().count(Taxon.class);\r
-                       List<TaxonBase> taxonList = cdmApp.getTaxonService().list(Taxon.class, 100000, page, null, null);\r
+                       List<Taxon> taxonList = cdmApp.getTaxonService().list(Taxon.class, 100000, page, null, null);\r
                        List<TaxonNameBase> nameList = cdmApp.getNameService().list(null, 100000, page, null, null);\r
                        Map<String, TaxonNameBase> nameMap = new HashMap<String, TaxonNameBase>();\r
                        Map<String, TaxonNameBase> nameDuplicateMap = new HashMap<String, TaxonNameBase>();\r
@@ -76,40 +76,36 @@ public class DipteraPostImportUpdater {
                        \r
                        int i = 0;\r
                        \r
-                       Taxon taxon;\r
-                       for (TaxonBase taxonBase : taxonList){\r
+                       for (Taxon taxon : taxonList){\r
                                if ((i++ % modCount) == 0){ logger.warn("taxa handled: " + (i-1));}\r
                                \r
-                               if (taxonBase.isInstanceOf(Taxon.class)){\r
-                                       taxon = CdmBase.deproxy(taxonBase, Taxon.class);\r
-                                       Set<TextData> citations = getCitations(taxon);\r
-                                       for (TextData citation : citations){\r
-                                               Language language = Language.DEFAULT();\r
-                                               String text = citation.getText(language);\r
-                                               String originalNameString = parseOriginalNameString(text);\r
-                                               String newText = parseNewText(text);\r
-                                               citation.removeText(language);\r
-                                               citation.putText(language, newText);\r
-                                               TaxonNameBase<?,?> scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap);\r
-                                               \r
-                                               Set<DescriptionElementSource> sources = citation.getSources();\r
-                                               if (sources.size() > 1){\r
-                                                       logger.warn("There are more then 1 sources for a description");\r
-                                               }else if (sources.size() == 0){\r
-                                                       DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);\r
-                                                       citation.addSource(source);\r
-                                                       sources = citation.getSources();\r
-                                               }\r
-                                               for (DescriptionElementSource source : sources){\r
-                                                       if (scientificName != null){\r
-                                                               source.setNameUsedInSource(scientificName);\r
-                                                       }else{\r
-                                                               source.setOriginalNameString(originalNameString);\r
-                                                       }\r
+                               Set<TextData> citations = getCitations(taxon);\r
+                               for (TextData citation : citations){\r
+                                       Language language = Language.DEFAULT();\r
+                                       String text = citation.getText(language);\r
+                                       String originalNameString = parseOriginalNameString(text);\r
+                                       String newText = parseNewText(text);\r
+                                       citation.removeText(language);\r
+                                       citation.putText(language, newText);\r
+                                       TaxonNameBase<?,?> scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap);\r
+                                       \r
+                                       Set<DescriptionElementSource> sources = citation.getSources();\r
+                                       if (sources.size() > 1){\r
+                                               logger.warn("There are more then 1 sources for a description");\r
+                                       }else if (sources.size() == 0){\r
+                                               DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);\r
+                                               citation.addSource(source);\r
+                                               sources = citation.getSources();\r
+                                       }\r
+                                       for (DescriptionElementSource source : sources){\r
+                                               if (scientificName != null){\r
+                                                       source.setNameUsedInSource(scientificName);\r
+                                               }else{\r
+                                                       source.setOriginalNameString(originalNameString);\r
                                                }\r
-                                               \r
-                                               citationsToSave.add(citation);\r
                                        }\r
+                                       \r
+                                       citationsToSave.add(citation);\r
                                }\r
                        }\r
                                \r