ref #7666 adding NARROW NO-BREAK after doubtful marker

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / tcsxml / in / TcsXmlTaxonRelationsImport.java

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonRelationsImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonRelationsImport.java
index ab1d46b4130e1985e67d2b3973b3f47543a4d169..9b93679bd1eb439a91549484439d28c30e78f427 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonRelationsImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/in/TcsXmlTaxonRelationsImport.java
@@ -36,8 +36,8 @@ import eu.etaxonomy.cdm.model.common.OriginalSourceType;
 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;\r
 import eu.etaxonomy.cdm.model.description.CommonTaxonName;\r
 import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
-import eu.etaxonomy.cdm.model.name.NonViralName;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
+import eu.etaxonomy.cdm.model.name.TaxonName;\r
+import eu.etaxonomy.cdm.model.name.TaxonNameFactory;\r
 import eu.etaxonomy.cdm.model.reference.Reference;\r
 import eu.etaxonomy.cdm.model.taxon.Classification;\r
 import eu.etaxonomy.cdm.model.taxon.Synonym;\r
@@ -87,7 +87,7 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
 \r
                logger.info("start make taxon relations ...");\r
                MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE);\r
-               MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE);\r
+               MapWrapper<TaxonName> taxonNameMap = (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE);\r
                MapWrapper<Reference> referenceMap = (MapWrapper<Reference>)state.getStore(ICdmIO.REFERENCE_STORE);\r
 \r
                Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();\r
@@ -95,7 +95,7 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
                ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);\r
                String childName;\r
                boolean obligatory;\r
-               String idNamespace = "TaxonRelation";\r
+               String idNamespace = "TaxonRelationDTO";\r
 \r
                TcsXmlImportConfigurator config = state.getConfig();\r
                Element elDataSet = super.getDataSetElement(config);\r
@@ -149,7 +149,7 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
        }\r
 \r
        private int makeBasionymRelations(TcsXmlImportState state,\r
-                       MapWrapper<TaxonBase> taxonMap, MapWrapper<TaxonNameBase> taxonNameMap, Set<TaxonBase> taxonStore,\r
+                       MapWrapper<TaxonBase> taxonMap, MapWrapper<TaxonName> taxonNameMap, Set<TaxonBase> taxonStore,\r
                        Element elTaxonName, Namespace tcsNamespace,\r
                        ResultWrapper<Boolean> success) {\r
 \r
@@ -169,15 +169,15 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
                        Element elBasionym = XmlHelp.getSingleChildElement(success, elBasionymRelationships, childName, tcsNamespace, obligatory);\r
 \r
                        String id = elTaxonName.getAttributeValue("id");\r
-                       TaxonNameBase name = taxonNameMap.get(removeVersionOfRef(id));\r
+                       TaxonName name = taxonNameMap.get(removeVersionOfRef(id));\r
 \r
                        TaxonBase taxonBase = (TaxonBase)name.getTaxonBases().iterator().next();\r
 \r
                        String ref = elBasionym.getAttributeValue("ref");\r
-                       TaxonNameBase basionymName = taxonNameMap.get(removeVersionOfRef(ref));\r
+                       TaxonName basionymName = taxonNameMap.get(removeVersionOfRef(ref));\r
 \r
                        if (basionymName != null){\r
-                               basionymName = HibernateProxyHelper.deproxy(basionymName, TaxonNameBase.class);\r
+                               basionymName = HibernateProxyHelper.deproxy(basionymName, TaxonName.class);\r
                                TaxonBase basionym;\r
                                if (basionymName.getTaxonBases().isEmpty()){\r
                                         basionym = Synonym.NewInstance(basionymName, null);\r
@@ -214,7 +214,7 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
 \r
 \r
                        } else{\r
-                               basionymName = NonViralName.NewInstance(name.getRank());\r
+                               basionymName = TaxonNameFactory.NewNonViralInstance(name.getRank());\r
                                childName = "RelatedName";\r
                                obligatory = true;\r
                                Element elName = XmlHelp.getSingleChildElement(success, elBasionym, childName, tcsNamespace, obligatory);\r
@@ -376,8 +376,8 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
                                                                success.setValue(false);\r
                                                        }else{\r
                                                                Synonym synonym = (Synonym)fromTaxon;\r
-                                                               TaxonNameBase<?,?> synName = synonym.getName();\r
-                                                               TaxonNameBase<?,?> accName = taxonTo.getName();\r
+                                                               TaxonName synName = synonym.getName();\r
+                                                               TaxonName accName = taxonTo.getName();\r
                                                                if (synName != null && accName != null && synName.isHomotypic(accName)\r
                                                                                        && ( synRelType.equals(SynonymType.SYNONYM_OF()))){\r
                                                                        synRelType = SynonymType.HOMOTYPIC_SYNONYM_OF();\r
@@ -521,7 +521,7 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
 \r
                                                try{\r
                                                        String nameUri = "urn:lsid:ipni.org:names:"+ id;\r
-                                                       TaxonNameBase name = rdfNameImport.handleRdfElementFromStream(nameStream, rdfConfig, (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE), nameUri);\r
+                                                       TaxonName name = rdfNameImport.handleRdfElementFromStream(nameStream, rdfConfig, (MapWrapper<TaxonName>)state.getStore(ICdmIO.TAXONNAME_STORE), nameUri);\r
                                                        if (name != null){\r
                                                                if (name.getTaxa().isEmpty()){\r
 \r
@@ -544,7 +544,7 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
                                }else{\r
                                        String title = elToTaxonConcept.getTextNormalize();\r
                                        //TODO synonym?\r
-                                       TaxonNameBase<?,?> taxonName = NonViralName.NewInstance(null);\r
+                                       TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);\r
                                        taxonName.setTitleCache(title, true);\r
                                        logger.warn("Free text related taxon seems to be bug in TCS");\r
                                        if (isSynonym){\r
@@ -571,10 +571,10 @@ public class TcsXmlTaxonRelationsImport extends TcsXmlImportBase implements ICdm
        }\r
 \r
        private boolean makeHomotypicSynonymRelations(Taxon aboutTaxon){\r
-               TaxonNameBase<?,?> aboutName = aboutTaxon.getName();\r
+               TaxonName aboutName = aboutTaxon.getName();\r
                if (aboutName != null){\r
-                       Set<TaxonNameBase> typifiedNames = aboutName.getHomotypicalGroup().getTypifiedNames();\r
-                       for (TaxonNameBase<?,?> typifiedName : typifiedNames){\r
+                       Set<TaxonName> typifiedNames = aboutName.getHomotypicalGroup().getTypifiedNames();\r
+                       for (TaxonName typifiedName : typifiedNames){\r
                                //TODO check if name is part of this tcs file\r
                                if (typifiedName.equals(aboutName)){\r
                                        continue;\r