data overlay entry name must not be null

model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntry.java

@@ -2,9 +2,25 @@ package lcsb.mapviewer.model.overlay;
 
 import java.awt.Color;
 import java.io.Serializable;
-import java.util.*;
-
-import javax.persistence.*;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
 
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
@@ -30,9 +46,11 @@ public abstract class DataOverlayEntry implements Serializable {
   private int id;
 
   /**
-   * Name of the {@link Element Element}. If null then this field will be skipped.
+   * Name of the {@link Element Element}. If empty then this field will be
+   * skipped.
    */
-  private String name = null;
+  @Column(nullable = false)
+  private String name = "";
 
   /**
    * Name of the {@link Model} to which this schema should be limited. If null
@@ -93,7 +111,8 @@ public abstract class DataOverlayEntry implements Serializable {
   @Cascade({ CascadeType.ALL })
   @ManyToMany()
   @JoinTable(name = "data_overlay_entry_miriam_table", joinColumns = {
-      @JoinColumn(name = "data_overlay_entry_id", referencedColumnName = "id", nullable = false, updatable = false) }, inverseJoinColumns = {
+      @JoinColumn(name = "data_overlay_entry_id", referencedColumnName = "id", nullable = false, updatable = false) },
+      inverseJoinColumns = {
           @JoinColumn(name = "miriam_id", referencedColumnName = "id", nullable = true, updatable = true) })
   private Set<MiriamData> miriamData = new HashSet<>();
 
@@ -117,7 +136,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * @param original
    *          original object used for initialization
    */
-  protected DataOverlayEntry(DataOverlayEntry original) {
+  protected DataOverlayEntry(final DataOverlayEntry original) {
     this.setName(original.getName());
     this.setElementId(original.getElementId());
     this.setReverseReaction(original.getReverseReaction());
@@ -136,7 +155,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * @param types2
    *          list of classes to add
    */
-  public void addTypes(Collection<Class<? extends BioEntity>> types2) {
+  public void addTypes(final Collection<Class<? extends BioEntity>> types2) {
     for (Class<? extends BioEntity> clazz : types2) {
       addType(clazz);
     }
@@ -148,7 +167,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * @param compartments2
    *          elements to add
    */
-  public void addCompartments(String[] compartments2) {
+  public void addCompartments(final String[] compartments2) {
     for (String string : compartments2) {
       compartments.add(string);
     }
@@ -160,7 +179,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * @param compartments2
    *          elements to add
    */
-  public void addCompartments(Collection<String> compartments2) {
+  public void addCompartments(final Collection<String> compartments2) {
     for (String string : compartments2) {
       compartments.add(string);
     }
@@ -211,9 +230,9 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the name to set
    * @see #name
    */
-  public void setName(String name) {
+  public void setName(final String name) {
     if (name == null) {
-      this.name = null;
+      this.name = "";
     } else {
       this.name = name.trim();
     }
@@ -232,7 +251,7 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the compartments to set
    * @see #compartments
    */
-  public void setCompartments(Set<String> compartments) {
+  public void setCompartments(final Set<String> compartments) {
     this.compartments = compartments;
   }
 
@@ -257,7 +276,7 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the value to set
    * @see #value
    */
-  public void setValue(Double value) {
+  public void setValue(final Double value) {
     this.value = value;
   }
 
@@ -274,7 +293,7 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the color to set
    * @see #color
    */
-  public void setColor(Color color) {
+  public void setColor(final Color color) {
     this.color = color;
   }
 
@@ -282,7 +301,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * Adds identifier to {@link #miriamData} set.
    * 
    */
-  public void addMiriamData(MiriamData md) {
+  public void addMiriamData(final MiriamData md) {
     miriamData.add(md);
   }
 
@@ -299,7 +318,7 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the lineWidth to set
    * @see #lineWidth
    */
-  public void setLineWidth(Double lineWidth) {
+  public void setLineWidth(final Double lineWidth) {
     this.lineWidth = lineWidth;
   }
 
@@ -316,7 +335,7 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the reverseReaction to set
    * @see #reverseReaction
    */
-  public void setReverseReaction(Boolean reverseReaction) {
+  public void setReverseReaction(final Boolean reverseReaction) {
     this.reverseReaction = reverseReaction;
   }
 
@@ -326,7 +345,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * @param name
    *          compartment name
    */
-  public void addCompartment(String name) {
+  public void addCompartment(final String name) {
     compartments.add(name);
   }
 
@@ -336,7 +355,7 @@ public abstract class DataOverlayEntry implements Serializable {
    * @param clazz
    *          class to add
    */
-  public void addType(Class<? extends BioEntity> clazz) {
+  public void addType(final Class<? extends BioEntity> clazz) {
     this.types.add(clazz);
   }
 
@@ -353,7 +372,7 @@ public abstract class DataOverlayEntry implements Serializable {
    *          the description to set
    * @see #description
    */
-  public void setDescription(String description) {
+  public void setDescription(final String description) {
     this.description = description;
   }
 
@@ -368,7 +387,7 @@ public abstract class DataOverlayEntry implements Serializable {
     return modelName;
   }
 
-  public void setModelName(String modelName) {
+  public void setModelName(final String modelName) {
     this.modelName = modelName;
   }
 
@@ -376,7 +395,7 @@ public abstract class DataOverlayEntry implements Serializable {
     return elementId;
   }
 
-  public void setElementId(String elementId) {
+  public void setElementId(final String elementId) {
     this.elementId = elementId;
   }
 
@@ -388,7 +407,7 @@ public abstract class DataOverlayEntry implements Serializable {
     return id;
   }
 
-  public void setDataOverlay(DataOverlay dataOverlay) {
+  public void setDataOverlay(final DataOverlay dataOverlay) {
     this.dataOverlay = dataOverlay;
   }
 }

persist/src/main/java/lcsb/mapviewer/persist/dao/map/DataOverlayDao.java

@@ -101,10 +101,7 @@ public class DataOverlayDao extends BaseDao<DataOverlay> {
         + " entry left join entry.compartments compartment left join entry.miriamData entry_miriam, "
         + Element.class.getSimpleName() + " element left join element.miriamData element_miriam"
         + " where element.model in :maps and entry.dataOverlay.id = :overlayId "
-        // "not entry.name <>''" is equivalent to
-        // "dataoverla0_.name='' or dataoverla0_.name is null"
-        // but faster
-        + " and (lower(element.name) = lower(entry.name) or not entry.name <>'') "
+        + " and (lower(element.name) = lower(entry.name) or entry.name ='') "
         + " and (lower(element.model.name) = lower(entry.modelName) or entry.modelName='' or entry.modelName is null) "
         + " and (entry_miriam is null or (entry_miriam.dataType = element_miriam.dataType and lower(entry_miriam.resource) = lower(element_miriam.resource)) ) "
         + " and (compartment is null or"
@@ -164,10 +161,7 @@ public class DataOverlayDao extends BaseDao<DataOverlay> {
         + " entry left join entry.compartments compartment left join entry.miriamData entry_miriam, "
         + Reaction.class.getSimpleName() + " reaction left join reaction.miriamData reaction_miriam"
         + " where reaction.model in :maps and entry.dataOverlay.id = :overlayId "
-        // "not entry.name <>''" is equivalent to
-        // "dataoverla0_.name='' or dataoverla0_.name is null"
-        // but faster
-        + " and (lower(reaction.name) = lower(entry.name) or not entry.name <>'') "
+        + " and (lower(reaction.name) = lower(entry.name) or entry.name ='') "
         + " and (lower(reaction.model.name) = lower(entry.modelName) or entry.modelName='' or entry.modelName is null) "
         + " and (entry_miriam is null or (entry_miriam.dataType = reaction_miriam.dataType and lower(entry_miriam.resource) = lower(reaction_miriam.resource)) ) "
         + " and (lower(reaction.idReaction) = lower(entry.elementId) or entry.elementId='' or entry.elementId is null) ";

persist/src/main/resources/db/migration/hsql/16.0.6/V16.0.6.20220105__data_overlay_entry_name_cannot_be_null.sql

+update data_overlay_entry_table set name ='' where name is null;
+alter table data_overlay_entry_table ALTER COLUMN name SET NOT NULL;
\ No newline at end of file

persist/src/main/resources/db/migration/postgres/16.0.6/V16.0.6.20220105__data_overlay_entry_name_cannot_be_null.sql

+update data_overlay_entry_table set name ='' where name is null;
+alter table data_overlay_entry_table ALTER COLUMN name SET NOT NULL;
\ No newline at end of file