update factory methods for original sources #1549

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / common / mapping / DbImportDescriptionElementCreationMapperBase.java

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportDescriptionElementCreationMapperBase.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportDescriptionElementCreationMapperBase.java
index fb5546358bb47e7ea7896579d98c6af58fea22e4..45d82dffece29073c46c3cc534424b474458d34e 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportDescriptionElementCreationMapperBase.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportDescriptionElementCreationMapperBase.java
@@ -14,11 +14,13 @@ import java.sql.ResultSet;
 import java.sql.SQLException;\r
 import java.util.Set;\r
 \r
+import org.apache.commons.lang.StringUtils;\r
 import org.apache.log4j.Logger;\r
 \r
 import eu.etaxonomy.cdm.common.CdmUtils;\r
 import eu.etaxonomy.cdm.io.common.DbImportStateBase;\r
 import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.OriginalSourceType;\r
 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
 import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
 import eu.etaxonomy.cdm.model.reference.Reference;\r
@@ -55,7 +57,7 @@ public abstract class DbImportDescriptionElementCreationMapperBase<ELEMENT exten
 \r
 //************************************ METHODS *******************************************/\r
 \r
-       public DbImportDescriptionElementCreationMapperBase setSource(String dbCitationAttribute, String sourceNamespace, String dbMicroCitationAttribute){\r
+       public DbImportDescriptionElementCreationMapperBase<ELEMENT,STATE> setSource(String dbCitationAttribute, String sourceNamespace, String dbMicroCitationAttribute){\r
                this.dbCitationAttribute = dbCitationAttribute;\r
                this.sourceNamespace = sourceNamespace;\r
                this.dbMicroCitationAttribute = dbMicroCitationAttribute;\r
@@ -74,7 +76,7 @@ public abstract class DbImportDescriptionElementCreationMapperBase<ELEMENT exten
                        logger.info("Taxon could not be determined. Description element was not add to any description or taxon");\r
                }\r
                //Source\r
-               if (CdmUtils.isNotEmpty(dbCitationAttribute)){\r
+               if (StringUtils.isNotBlank(dbCitationAttribute)){\r
                        addSource(rs, element);\r
                }\r
                return element;\r
@@ -88,8 +90,8 @@ public abstract class DbImportDescriptionElementCreationMapperBase<ELEMENT exten
         */\r
        private void addSource(ResultSet rs, ELEMENT element) throws SQLException {\r
                String microCitation = getStringDbValue(rs, dbMicroCitationAttribute);\r
-               Reference citation = (Reference) getState().getRelatedObject(sourceNamespace, String.valueOf(rs.getObject(dbCitationAttribute)));\r
-               element.addSource(null, null, citation, microCitation);\r
+               Reference<?> citation = (Reference<?>) getState().getRelatedObject(sourceNamespace, String.valueOf(rs.getObject(dbCitationAttribute)));\r
+               element.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, microCitation);\r
        }\r
 \r
        /**\r
@@ -99,7 +101,7 @@ public abstract class DbImportDescriptionElementCreationMapperBase<ELEMENT exten
         */\r
        protected Taxon getAcceptedTaxon(ResultSet rs) throws SQLException {\r
                String taxonFk = getForeignKey(rs, dbTaxonFkAttribute);\r
-               TaxonBase taxonBase = (TaxonBase)getRelatedObject(taxonNamespace, taxonFk);\r
+               TaxonBase<?> taxonBase = (TaxonBase<?>)getRelatedObject(taxonNamespace, taxonFk);\r
                Taxon taxon = null;\r
                if (taxonBase == null){\r
                        logger.warn("TaxonBase not found: " + taxonFk);\r