Merge branch 'master' of ssh://dev.e-taxonomy.eu/var/git/cdmlib-apps

diff --combined app-import/src/main/java/eu/etaxonomy/cdm/io/lichenes/LichenesGeneraTaxonImport.java
index 3012758eafc95db002cb8a1a602b79fb147040ae,93c4d60df71a67177db1f5bc695ed14bedf4451c..bcc62cee654a2ca1df55d5aa2f584cef7f3d9f39
--- 1/app-import/src/main/java/eu/etaxonomy/cdm/io/lichenes/LichenesGeneraTaxonImport.java
--- 2/app-import/src/main/java/eu/etaxonomy/cdm/io/lichenes/LichenesGeneraTaxonImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/lichenes/LichenesGeneraTaxonImport.java
@@@ -56,7 -56,7 +56,7 @@@ public class LichenesGeneraTaxonImport<
        private static final String INCERTAE_SEDIS = "Incertae sedis";
  
        private static UUID rootUuid = UUID.fromString("61187f71-96d1-419d-958b-25ab4c01a93c");
-     
+ 
      private  static List<String> expectedKeys= Arrays.asList(new String[]{
              "SORT","GENUS_X","PHYLUM","SUBPHYLUM","CLASS","SUBCLASS","ORDER","SUBORDER","FAMILY",
              "FAM_SYNONYMS","SUBFAMILY","GENUS","SYNONYMS","SPECIES","REFERENCES","MOLECULAR","NOTES"
@@@ -64,7 -64,7 +64,7 @@@
  
      private Reference sourceReference;
      private Reference secReference;
-   
+ 
      private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
  
  //    @Override
@@@ -108,15 -108,15 +108,15 @@@
          Taxon genusTaxon = Taxon.NewInstance(genusName, sec);
          genusName.addSource(makeOriginalSource(state));
          genusTaxon.addSource(makeOriginalSource(state));
-         
+ 
          makeSynonyms(state, line, record, genusTaxon, "SYNONYMS");
-         
+ 
          //TODO reference  => for now we don't use it
-         
+ 
          makeNotes(genusTaxon, record, line);
          TaxonNode genusNode = parentNode.addChildTaxon(genusTaxon, null, null);
          getTaxonNodeService().saveOrUpdate(genusNode);
-         
+ 
          return genusTaxon;
      }
  
@@@ -145,13 -145,13 +145,13 @@@
                        nameStr = nameStr.replace(", non Tayloriella Kylin (Rhodophyta)".trim(), "");
                }
                if (nameStr.endsWith("[nom. illeg.]")) {
-                       result[1] = "nom. illeg."; 
+                       result[1] = "nom. illeg.";
                        result[0] = nameStr.replace("[nom. illeg.]".trim(), "");
                }else if (nameStr.endsWith("[nom. inval.]")) {
-                       result[1] = "nom. inval."; 
+                       result[1] = "nom. inval.";
                        result[0] = nameStr.replace("[nom. inval.]".trim(), "");
                }else if (nameStr.endsWith("[nom. cons. prop.]")) {
-                       result[1] = "nom. cons. prop."; 
+                       result[1] = "nom. cons. prop.";
                        result[0] = nameStr.replace("[nom. cons. prop.]".trim(), "");
                }else{
                        result[0] = nameStr;
@@@ -163,7 -163,7 +163,7 @@@
        String notesStr = getValue(record, "NOTES");
        if (isNotBlank(notesStr)) {
                if (notesStr.startsWith("Notes.")) {
 -                      notesStr = notesStr.substring(6);
 +                      notesStr = notesStr.substring(6).trim();
                }
                //TODO or handle as fact of type "Notes"
                genusTaxon.addAnnotation(Annotation.NewInstance(notesStr, AnnotationType.EDITORIAL(), Language.ENGLISH()));
@@@ -173,12 -173,12 +173,12 @@@
        private void checkParsed(TaxonName name, String nameStr, String line) {
                if (name.isProtectedTitleCache() || name.isProtectedFullTitleCache() || name.isProtectedNameCache()) {
                        logger.warn(line + "Name could not be parsed: " + nameStr);
-               }       
+               }
        }
  
-       private void makeSynonyms(SimpleExcelTaxonImportState<CONFIG> state, 
+       private void makeSynonyms(SimpleExcelTaxonImportState<CONFIG> state,
                String line, Map<String, String> record, Taxon accepted, String fieldName) {
-         
+ 
        String synonymsStr = getValue(record, fieldName);
        if (isBlank(synonymsStr)) {
                return;
@@@ -192,7 -192,7 +192,7 @@@
                for (String singleSynonymStr: splits) {
                        String[] split2 = parseNomStatus(singleSynonymStr);
                singleSynonymStr = split2[0];
-               
+ 
                        TaxonName synonymName = (TaxonName)parser.parseFullName(singleSynonymStr, state.getConfig().getNomenclaturalCode(), null);
                        checkParsed(TaxonName.castAndDeproxy(synonymName), singleSynonymStr, line);
                        makeStatusAndHomonym(state, synonymName, split2);
@@@ -201,7 -201,7 +201,7 @@@
                Synonym synonym = Synonym.NewInstance(synonymName, accepted.getSec());
                accepted.addSynonym(synonym, SynonymType.SYNONYM_OF());
                        synonymName.addSource(makeOriginalSource(state));
-                       synonym.addSource(makeOriginalSource(state));    
+                       synonym.addSource(makeOriginalSource(state));
                }
        }
        }
@@@ -214,7 -214,7 +214,7 @@@
        private String lastSubOrder = "";
        private String lastFamily = "";
        private String lastSubFamily = "";
-       
+ 
        private Taxon taxonPhylum = null;
        private Taxon taxonSubphylum = null;
        private Taxon taxonClass = null;
@@@ -223,7 -223,7 +223,7 @@@
        private Taxon taxonSubOrder = null;
        private Taxon taxonFamily = null;
        private Taxon taxonSubFamily = null;
-       
+ 
        private TaxonNode getParentNode(Map<String, String> record, SimpleExcelTaxonImportState<CONFIG> state, String line) {
  
            Taxon higherTaxon = null;
@@@ -237,7 -237,7 +237,7 @@@
                String suborder = Nz(getValue(record, "SUBORDER"));
                String family = Nz(getValue(record, "FAMILY"));
                String subfamily = Nz(getValue(record, "SUBFAMILY"));
-               
+ 
                if (isNewTaxon(subfamily, lastSubFamily)){
                        if (isNewTaxon(family, lastFamily)){
                                if (isNewTaxon(suborder, lastSubOrder)){
@@@ -257,7 -257,7 +257,7 @@@
                                                                        taxonSubphylum = makeHigherTaxon(state, subphylum, Rank.SUBPHYLUM());
                                                                        if (taxonSubphylum != null){  //no null expected
                                                                                classification.addParentChild(higherTaxon,taxonSubphylum, null, null);
-                                                                       }       
+                                                                       }
                                                                        higherTaxon = isIncertisSedis(subphylum) ? higherTaxon : taxonSubphylum;
                                                                        lastSubphylum = subphylum;
                                                                }else{
@@@ -323,7 -323,7 +323,7 @@@
                }else {
                        higherTaxon = taxonSubFamily;
                }
-                       
+ 
                getTaxonService().saveOrUpdate(higherTaxon);
  
                return higherTaxon.getTaxonNode(classification);
@@@ -343,13 -343,13 +343,13 @@@
                result |= lastUninomial.equalsIgnoreCase(INCERTAE_SEDIS);
                return result;
        }
-       
+ 
        private Taxon makeHigherTaxon(SimpleExcelTaxonImportState<CONFIG> state, String nameStr, Rank rank) {
                if (isBlank(nameStr) || nameStr.equalsIgnoreCase(INCERTAE_SEDIS)){
                        return null;
                }
                //name
-               INonViralName name = parser.parseFullName(nameStr, NomenclaturalCode.Fungi, rank); 
+               INonViralName name = parser.parseFullName(nameStr, NomenclaturalCode.Fungi, rank);
                replaceNameAuthorsAndReferences(state, name);
                //taxon
                Reference secRef = getSecReference(state);
@@@ -358,9 -358,9 +358,9 @@@
          taxon.addSource(makeOriginalSource(state));
                return taxon;
        }
-       
+ 
      private TaxonNode rootNode;
-     
+ 
      private TaxonNode getClassification(SimpleExcelTaxonImportState<CONFIG> state) {
          if (rootNode == null){
              Reference sec = getSecReference(state);
@@@ -401,7 -401,7 +401,7 @@@
      private void replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, INonViralName name) {
          dedupHelper().replaceAuthorNamesAndNomRef(state, name);
      }
-     
+ 
      private ImportDeduplicationHelper<SimpleExcelTaxonImportState<CONFIG>> dedupHelper;
        private ImportDeduplicationHelper<SimpleExcelTaxonImportState<CONFIG>> dedupHelper() {
        if (dedupHelper == null) {
@@@ -409,10 -409,11 +409,11 @@@
        }
        return dedupHelper;
      }
-       
+ 
+     @Override
      protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {
        String noStr = getValue(state.getOriginalRecord(), "SORT");
          return IdentifiableSource.NewDataImportInstance(noStr, "SORT", state.getConfig().getSourceReference());
      }
-     
+ 
  }