Bug fix for DnaSample record basis

[cdmlib.git] / cdmlib-model / src / main / java / eu / etaxonomy / cdm / model / molecular / DnaSample.java

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java
index fe11c1b4dd225b06f05b6695d68204173f3f4205..2ef4788c93caa60052d9bbe73bac8db88b751a3c 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java
@@ -17,6 +17,7 @@ import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.OneToMany;
 import javax.persistence.Transient;
 import javax.persistence.FetchType;
 import javax.persistence.OneToMany;
 import javax.persistence.Transient;

+import javax.validation.constraints.NotNull;

 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;


@@ -30,32 +31,40 @@ import org.apache.log4j.Logger;
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
 import org.hibernate.envers.Audited;
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
 import org.hibernate.envers.Audited;

+import org.hibernate.search.annotations.ContainedIn;

 import org.hibernate.search.annotations.Indexed;
 
 import eu.etaxonomy.cdm.model.occurrence.Collection;
 import org.hibernate.search.annotations.Indexed;
 
 import eu.etaxonomy.cdm.model.occurrence.Collection;

-import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
-import eu.etaxonomy.cdm.model.occurrence.Specimen;
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;

 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
 
 /**
 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
 
 /**

+ * A DNA Sample is the extracted DNA of a given tissue sample. It may be stored in
+ * a DNA Bank and should then be handled as a collection unit.
+ * DNA Sample are used to determine their {@link Sequence DNA sequences}
+ * starting with a process called {@link Amplification amplification}.
+ *  

  * @author m.doering
  * @author m.doering

- * @version 1.0
- * @created 08-Nov-2007 13:06:22
+ * @created 08-Nov-2007

  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "DnaSample", propOrder = {
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "DnaSample", propOrder = {

-    "sequences"
+    "sequences",
+    "amplifications"

 })
 @XmlRootElement(name = "DnaSample")
 @Entity
 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
 @Audited
 })
 @XmlRootElement(name = "DnaSample")
 @Entity
 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
 @Audited

-public class DnaSample extends Specimen implements Cloneable {
+public class DnaSample extends DerivedUnit implements Cloneable {

        private static final long serialVersionUID = -2978411330023671805L;
        @SuppressWarnings("unused")
        private static final Logger logger = Logger.getLogger(DnaSample.class);
        
        private static final long serialVersionUID = -2978411330023671805L;
        @SuppressWarnings("unused")
        private static final Logger logger = Logger.getLogger(DnaSample.class);
        

+// ****************** FACTORY METHOD *****************/
+       

        /**
         * Factory method
         * @return
        /**
         * Factory method
         * @return


@@ -64,6 +73,7 @@ public class DnaSample extends Specimen implements Cloneable {
                return new DnaSample();
        }
 
                return new DnaSample();
        }
 

+// ************** ATTRIBUTES ****************************/     

        
 //     @XmlElement(name = "BankNumber")
 //     private String bankNumber;
        
 //     @XmlElement(name = "BankNumber")
 //     private String bankNumber;


@@ -77,29 +87,56 @@ public class DnaSample extends Specimen implements Cloneable {
     private Set<Sequence> sequences = new HashSet<Sequence>();
 
        
     private Set<Sequence> sequences = new HashSet<Sequence>();
 
        

+       @XmlElementWrapper(name = "Amplifications")
+       @XmlElement(name = "Amplification")
+       @OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
+       @Cascade( { CascadeType.SAVE_UPDATE, CascadeType.DELETE})
+    @ContainedIn
+    @NotNull
+       private Set<Amplification> amplifications = new HashSet<Amplification>();
+
+
+// ******************* CONSTRUCTOR *************************/

        
        /**
         * Constructor
         */
        private DnaSample() {
        
        /**
         * Constructor
         */
        private DnaSample() {

-               super();
-               this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Specimen>();
+               super(SpecimenOrObservationType.DnaSample);
+               this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<DerivedUnit>();

        }
        
        }
        

+//************ GETTER / SETTER  **********************************/    
+
+       //sequencings

        public Set<Sequence> getSequences() {
                return sequences;
        }
 
        public Set<Sequence> getSequences() {
                return sequences;
        }
 

-       // FIXME shouldn't this be the singular? i.e. addSequence( . . . )
-       public void addSequences(Sequence sequence) {
+       public void addSequence(Sequence sequence) {

                this.sequences.add(sequence);
        }
 
                this.sequences.add(sequence);
        }
 

-       // FIXME shouldn't this be the singular? i.e. removeSequence( . . . )
-       public void removeSequences(Sequence sequence) {
+       public void removeSequence(Sequence sequence) {

                this.sequences.remove(sequence);
        }
                this.sequences.remove(sequence);
        }

+       
+       //amplifications
+       public Set<Amplification> getAmplifications() {
+               return amplifications;
+       }

 
 

+       public void addAmplification(Amplification amplification) {
+               this.amplifications.add(amplification);
+               amplification.setDnaSample(this);
+       }
+
+       public void removeAmplification(Amplification amplification) {
+               this.amplifications.remove(amplification);
+       }
+
+// ************* Convenience Getter / Setter ************/
+       

        @Transient
        public Collection getStoredAt(){
                return this.getCollection();
        @Transient
        public Collection getStoredAt(){
                return this.getCollection();


@@ -131,19 +168,20 @@ public class DnaSample extends Specimen implements Cloneable {
         * create a new instance that differs only slightly from <i>this</i> dna sample
         * by modifying only some of the attributes.<BR>
         * This method overrides the clone method from {@link Specimen Specimen}.
         * create a new instance that differs only slightly from <i>this</i> dna sample
         * by modifying only some of the attributes.<BR>
         * This method overrides the clone method from {@link Specimen Specimen}.

+        * @throws CloneNotSupportedException 

         * 
         * @see Specimen#clone()
         * 
         * @see Specimen#clone()

-        * @see DerivedUnitBase#clone()
+        * @see DerivedUnit#clone()

         * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
         * @see java.lang.Object#clone()
         */
        @Override
         * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
         * @see java.lang.Object#clone()
         */
        @Override

-       public DnaSample clone(){
+       public DnaSample clone() {

                DnaSample result = (DnaSample)super.clone();
                //sequenceSet
                result.sequences = new HashSet<Sequence>();
                for(Sequence sequence : this.sequences) {
                DnaSample result = (DnaSample)super.clone();
                //sequenceSet
                result.sequences = new HashSet<Sequence>();
                for(Sequence sequence : this.sequences) {

-                       result.addSequences(sequence);
+                       result.addSequence(sequence);

                }
                //no changes to: bankNumber
                return result;
                }
                //no changes to: bankNumber
                return result;