From: Andreas Müller <a.mueller@bgbm.org>
Date: Wed, 28 May 2008 22:17:27 +0000 (+0000)
Subject: (no commit message)
X-Git-Tag: firstMonocotsOnline~572
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/commitdiff_plain/6f7d91bd1e4e95cc9c3f778f2a09ff3193a7f0f6?ds=sidebyside

---

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java
index 0e2f3e388e..32dc45a66c 100644
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java
@@ -22,7 +22,7 @@ import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
 
 import eu.etaxonomy.cdm.model.agent.Person;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+
 
 
 
@@ -247,7 +247,7 @@ public abstract class CdmBase implements Serializable, ICdmBase{
 		return this.getClass().getSimpleName()+"#"+this.getId()+"<"+this.getUuid()+">";
 	}
 	
-	protected void useSetMethod(Method method, Object object){
+	protected void invokeSetMethod(Method method, Object object){
 		try {
 			method.invoke(object, this);
 		} catch (Exception e) {
diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
index 323cbb26fc..9cfa20a92e 100644
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
@@ -606,7 +606,7 @@ public abstract class TaxonNameBase<T extends TaxonNameBase> extends Identifiabl
 	public void addTaxonBase(TaxonBase taxonBase){
 		taxonBases.add(taxonBase);
 		initMethods();
-		useSetMethod(methodTaxonBaseSetName, taxonBase);
+		invokeSetMethod(methodTaxonBaseSetName, taxonBase);
 	}
 
 	private void initMethods(){
diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java
index 708f3344c8..ec30a662e4 100644
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java
@@ -34,9 +34,7 @@ public class Synonym extends TaxonBase implements IRelated<SynonymRelationship>{
 
 
 	public static Synonym NewInstance(TaxonNameBase taxonName, ReferenceBase sec){
-		Synonym result = new Synonym();
-		result.setTaxonName(taxonName);
-		result.setSec(sec);
+		Synonym result = new Synonym(taxonName, sec);
 		return result;
 	}
 	
@@ -44,7 +42,10 @@ public class Synonym extends TaxonBase implements IRelated<SynonymRelationship>{
 	public Synonym(){
 	}
 	
-
+	public Synonym(TaxonNameBase taxonNameBase, ReferenceBase sec){
+		super(taxonNameBase, sec);
+	}
+	
 	@OneToMany(mappedBy="relatedFrom", fetch=FetchType.EAGER)
 	@Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE})
 	public Set<SynonymRelationship> getSynonymRelations() {
diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java
index 3274f36cc2..9cb5813b03 100644
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java
@@ -46,7 +46,7 @@ public class Taxon extends TaxonBase implements Iterable<Taxon>, IRelated<Relati
 	// shortcut to the taxonomicIncluded (parent) taxon. Managed by the taxonRelations setter
 	private Taxon taxonomicParentCache;
 
-	static Method methodDescriptionSetTaxon;
+	private static Method methodDescriptionSetTaxon;
 	
 	
 
@@ -57,16 +57,19 @@ public class Taxon extends TaxonBase implements Iterable<Taxon>, IRelated<Relati
 	 * @return
 	 */
 	public static Taxon NewInstance(TaxonNameBase taxonNameBase, ReferenceBase sec){
-		Taxon result = new Taxon();
-		result.setTaxonName(taxonNameBase);
-		result.setSec(sec);
+		Taxon result = new Taxon(taxonNameBase, sec);
 		return result;
 	}
 	
 	//TODO should be private, but still produces Spring init errors
+	@Deprecated
 	public Taxon(){
 	}
 	
+	public Taxon(TaxonNameBase taxonNameBase, ReferenceBase sec){
+		super(taxonNameBase, sec);
+	}
+	
 
 	@OneToMany(mappedBy="taxon", fetch= FetchType.EAGER)
 	@Cascade({CascadeType.SAVE_UPDATE})
diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java
index 330b1f3e87..b63579e464 100644
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java
@@ -9,7 +9,6 @@
 
 package eu.etaxonomy.cdm.model.taxon;
 
-
 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
@@ -18,11 +17,8 @@ import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
 import org.apache.log4j.Logger;
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
-import org.hibernate.collection.PersistentSet;
-
 
-import java.lang.reflect.Field;
-import java.util.*;
+import java.lang.reflect.Method;
 
 import javax.persistence.*;
 
@@ -36,13 +32,32 @@ import javax.persistence.*;
 public abstract class TaxonBase extends IdentifiableEntity {
 	static Logger logger = Logger.getLogger(TaxonBase.class);
 	
-	//TODO make static for performance reasons
-	private static Field taxonBaseField;
+	private static Method methodTaxonNameAddTaxonBase;
+	
+	private static void initMethods()  { 
+		if (methodTaxonNameAddTaxonBase == null){
+			try {
+				methodTaxonNameAddTaxonBase = TaxonNameBase.class.getDeclaredMethod("addTaxonBase", TaxonBase.class);
+				methodTaxonNameAddTaxonBase.setAccessible(true);
+			} catch (Exception e) {
+				e.printStackTrace();
+				//TODO handle exception
+			}
+		}
+	}
 	
 	protected TaxonBase(){
 		super();
 	}
 	
+	protected TaxonBase(TaxonNameBase taxonNameBase, ReferenceBase sec){
+		super();
+		if (taxonNameBase != null){
+			initMethods(); 
+			this.invokeSetMethod(methodTaxonNameAddTaxonBase, taxonNameBase);  
+		}
+		this.setSec(sec);
+	}
 	
 	//The assignment to the Taxon or to the Synonym class is not definitive
 	private boolean isDoubtful;
@@ -77,19 +92,6 @@ public abstract class TaxonBase extends IdentifiableEntity {
 		this.name = newName;
 	}
 	
-	@Transient
-	public TaxonNameBase getTaxonName(){
-		return this.name;
-	}
-	public void setTaxonName(TaxonNameBase newName){
-		if (newName != null){
-			newName.addTaxonBase(this);
-		}else{
-			//FIXME implement
-			//this.name.removeTaxonBase(this);
-		}
-	}
-	
 	@Transient
 	public HomotypicalGroup getHomotypicGroup(){
 		if (this.getName() == null){
diff --git a/cdmlib-model/src/main/resources/terms/NomenclaturalCode.csv b/cdmlib-model/src/main/resources/terms/NomenclaturalCode.csv
index 7e04f426d5..50966c9c18 100644
--- a/cdmlib-model/src/main/resources/terms/NomenclaturalCode.csv
+++ b/cdmlib-model/src/main/resources/terms/NomenclaturalCode.csv
@@ -1,4 +1,4 @@
-"fa032b1a-1ad2-4fb0-a1d9-3016399a80fa",,"NomenclaturalCodeTerm","NomenclaturalCodeTerm",
+"fa032b1a-1ad2-4fb0-a1d9-3016399a80fa",,"NomenclaturalCode","NomenclaturalCode",
 "ff4b0979-7abf-4b40-95c0-8b8b1e8a4d5e",,"Bacteriological","Bacteriological",
 "540fc02a-8a8e-4813-89d2-581dad4dd482",,"ICBN","ICBN",
 "65a432b5-92b1-4c9a-8090-2a185e423d2e",,"ICNCP","ICNCP",
diff --git a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonBaseTest.java b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonBaseTest.java
index 226c0675d4..d7f45524bf 100644
--- a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonBaseTest.java
+++ b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonBaseTest.java
@@ -60,7 +60,7 @@ public class TaxonBaseTest extends EntityTestBase {
 	 */
 	@Before
 	public void setUp() throws Exception {
-		sec=new Book();
+		sec= Book.NewInstance();
 		sec.setTitleCache("Schoenes saftiges Allg�u");
 		name1 = ZoologicalName.NewInstance(Rank.SPECIES(),"Panthera","onca",null,null,null,"p.1467", null);
 		HomotypicalGroup homotypicalGroup = HomotypicalGroup.NewInstance();
@@ -88,19 +88,19 @@ public class TaxonBaseTest extends EntityTestBase {
 		assertEquals(name1.getTitleCache(), taxon1.getName().getTitleCache());
 		assertNull(freeT.getName());
 	}
-
-	/**
-	 * Test method for {@link eu.etaxonomy.cdm.model.taxon.TaxonBase#setName(eu.etaxonomy.cdm.model.name.TaxonNameBase)}.
-	 */
-	@Test
-	public final void testSetName() {
-		assertNull(freeT.getName());
-		freeT.setTaxonName(name2);
-		assertNotNull(freeT.getName());
-		assertSame(freeT.getName(), name2);
-		assertTrue(name1.getTaxa().contains(taxon1));
-		assertTrue(name2.getSynonyms().contains(synonym1));
-	}
+//
+//	/**
+//	 * Test method for {@link eu.etaxonomy.cdm.model.taxon.TaxonBase#setName(eu.etaxonomy.cdm.model.name.TaxonNameBase)}.
+//	 */
+//	@Test
+//	public final void testSetName() {
+//		assertNull(freeT.getName());
+//		freeT.setName(name2);
+//		assertNotNull(freeT.getName());
+//		assertSame(freeT.getName(), name2);
+//		assertTrue(name1.getTaxa().contains(taxon1));
+//		assertTrue(name2.getSynonyms().contains(synonym1));
+//	}
 
 	/**
 	 * Test method for {@link eu.etaxonomy.cdm.model.taxon.TaxonBase#isDoubtful()}.
@@ -150,11 +150,8 @@ public class TaxonBaseTest extends EntityTestBase {
 	public final void testIsSaveable() {
 		assertFalse(freeT.isSaveable());
 		assertTrue(taxon1.isSaveable());
-		freeT.setTaxonName(name1);
 		assertFalse(freeT.isSaveable());
 		freeT.setSec(sec);
-		assertTrue(freeT.isSaveable());
-		freeT.setTaxonName(null);
 		assertFalse(freeT.isSaveable());
 	}