custom naming startegy implemented to add _table suffix for all automatically generated table names

model/src/main/java/lcsb/mapviewer/model/Project.java

@@ -19,7 +19,6 @@ import javax.persistence.JoinColumn;
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
 import javax.persistence.OrderBy;
-import javax.persistence.Table;
 
 import org.apache.log4j.Appender;
 import org.apache.log4j.Logger;
@@ -48,7 +47,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
  * 
  */
 @Entity
-@Table(name = "project_table")
 public class Project implements Serializable {
 
   /**

model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java

@@ -16,7 +16,6 @@ import javax.persistence.Table;
  * 
  */
 @Entity
-@Table(name = "cache_type")
 public class CacheType implements Serializable {
 
   /**

model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java

@@ -24,7 +24,6 @@ import javax.persistence.Table;
  *
  */
 @Entity
-@Table(name = "file_entry")
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @DiscriminatorColumn(name = "file_type_db", discriminatorType = DiscriminatorType.STRING)
 public abstract class FileEntry implements Serializable {

model/src/main/java/lcsb/mapviewer/model/map/Comment.java

@@ -10,7 +10,6 @@ import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.ManyToOne;
-import javax.persistence.Table;
 
 import org.hibernate.annotations.Type;
 
@@ -25,7 +24,6 @@ import lcsb.mapviewer.model.user.User;
  * 
  */
 @Entity
-@Table(name = "feedback")
 public class Comment implements Serializable {
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java

@@ -8,7 +8,6 @@ import javax.persistence.Enumerated;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
@@ -23,7 +22,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
  * 
  */
 @Entity
-@Table(name = "miriam_data_table")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
 public class MiriamData implements Comparable<MiriamData>, Serializable {

model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java

@@ -12,7 +12,6 @@ import javax.persistence.Id;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
 import javax.persistence.OrderBy;
-import javax.persistence.Table;
 
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
@@ -31,7 +30,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
  * 
  */
 @Entity
-@Table(name = "overview_image_table")
 public class OverviewImage implements Serializable {
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java

@@ -16,7 +16,6 @@ import javax.persistence.Id;
 import javax.persistence.Inheritance;
 import javax.persistence.InheritanceType;
 import javax.persistence.ManyToOne;
-import javax.persistence.Table;
 
 /**
  * Abstract class representing link that connects {@link OverviewImage parent
@@ -34,7 +33,6 @@ import javax.persistence.Table;
  * 
  */
 @Entity
-@Table(name = "overview_link_table")
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @DiscriminatorColumn(name = "link_type", discriminatorType = DiscriminatorType.STRING)
 @DiscriminatorValue("GENERIC_VIEW")

model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java

@@ -7,7 +7,6 @@ import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.ManyToOne;
-import javax.persistence.Table;
 
 import org.apache.log4j.Logger;
 
@@ -23,7 +22,6 @@ import lcsb.mapviewer.model.map.species.Element;
  * 
  */
 @Entity
-@Table(name = "search_index_table")
 public class SearchIndex implements Serializable {
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java

@@ -15,7 +15,6 @@ import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.OrderColumn;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
@@ -29,7 +28,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
  * 
  */
 @Entity
-@Table(name = "sbml_function")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
 public class SbmlFunction implements Serializable, SbmlArgument {

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java

@@ -16,7 +16,6 @@ import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.JoinTable;
 import javax.persistence.ManyToMany;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
@@ -32,7 +31,6 @@ import lcsb.mapviewer.model.map.species.Element;
  * 
  */
 @Entity
-@Table(name = "sbml_kinetics")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
 public class SbmlKinetics implements Serializable {

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java

@@ -7,7 +7,6 @@ import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.ManyToOne;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
@@ -19,7 +18,6 @@ import org.apache.log4j.Logger;
  * 
  */
 @Entity
-@Table(name = "sbml_parameter")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
 public class SbmlParameter implements Serializable, SbmlArgument {

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java

@@ -11,7 +11,6 @@ import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
@@ -27,7 +26,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
  * 
  */
 @Entity
-@Table(name = "sbml_unit")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
 public class SbmlUnit implements Serializable {

model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java

@@ -10,7 +10,6 @@ import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.ManyToOne;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
@@ -27,7 +26,6 @@ import org.apache.log4j.Logger;
  * 
  */
 @Entity
-@Table(name = "sbml_unit_factor")
 @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
 @XmlRootElement
 public class SbmlUnitTypeFactor implements Serializable {

model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java

@@ -14,7 +14,6 @@ import javax.persistence.Id;
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
 import javax.persistence.OrderBy;
-import javax.persistence.Table;
 
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
@@ -30,7 +29,6 @@ import lcsb.mapviewer.model.map.MiriamData;
  *
  */
 @Entity
-@Table(name = "reference_genome")
 public class ReferenceGenome implements Serializable {
   /**
    * 

model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java

@@ -8,7 +8,6 @@ import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.ManyToOne;
-import javax.persistence.Table;
 
 /**
  * This object defines information about mapping genes to gene. This data is
@@ -21,7 +20,6 @@ import javax.persistence.Table;
  *
  */
 @Entity
-@Table(name = "reference_genome_gene_mapping")
 public class ReferenceGenomeGeneMapping implements Serializable {
   /**
    * 

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java

@@ -15,7 +15,6 @@ import javax.persistence.JoinTable;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
 import javax.persistence.OrderColumn;
-import javax.persistence.Table;
 
 import org.apache.log4j.Logger;
 import org.hibernate.annotations.Cascade;
@@ -33,7 +32,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
  * 
  */
 @Entity
-@Table(name = "layer_table")
 public class Layer implements Serializable {
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java

@@ -20,7 +20,6 @@ import javax.persistence.ManyToMany;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
 import javax.persistence.OrderBy;
-import javax.persistence.Table;
 import javax.persistence.Transient;
 import javax.xml.bind.annotation.XmlTransient;
 
@@ -56,7 +55,6 @@ import lcsb.mapviewer.model.map.species.Element;
  * 
  */
 @Entity
-@Table(name = "model_table")
 public class ModelData implements Serializable {
 
   /**
@@ -117,7 +115,7 @@ public class ModelData implements Serializable {
 
   @Cascade({ CascadeType.ALL })
   @ManyToMany(fetch = FetchType.EAGER)
-  @JoinTable(name = "model_parameters", joinColumns = {
+  @JoinTable(name = "model_parameters_table", joinColumns = {
       @JoinColumn(name = "model_id", referencedColumnName = "id", nullable = false, updatable = false) }, inverseJoinColumns = {
           @JoinColumn(name = "parameter_id", referencedColumnName = "id", nullable = true, updatable = true) })
   private Set<SbmlParameter> parameters = new HashSet<>();

model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java

@@ -27,7 +27,6 @@ import org.apache.log4j.Logger;
  * 
  */
 @Entity
-@Table(name = "submodel_connection_table")
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @DiscriminatorColumn(name = "submodel_connections_type_db", discriminatorType = DiscriminatorType.STRING)
 @DiscriminatorValue("SUBMODEL_CONNECTION")

model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java

@@ -38,10 +38,10 @@ import lcsb.mapviewer.model.graphics.PolylineData;
  * 
  */
 @Entity
-@Table(name = "node_table")
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @DiscriminatorColumn(name = "node_type_db", discriminatorType = DiscriminatorType.STRING)
 @DiscriminatorValue("GENERIC_NODE")
+@Table(name = "reaction_node_table")
 public abstract class AbstractNode implements Serializable {
   /**
    * 

model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java

@@ -30,7 +30,6 @@ import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
 import javax.persistence.OrderBy;
 import javax.persistence.OrderColumn;
-import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlTransient;
 
 import org.apache.log4j.Logger;
@@ -73,7 +72,6 @@ import lcsb.mapviewer.model.map.species.Element;
  * 
  */
 @Entity
-@Table(name = "reaction_table")
 @Inheritance(strategy = InheritanceType.SINGLE_TABLE)
 @DiscriminatorColumn(name = "reaction_type_db", discriminatorType = DiscriminatorType.STRING)
 @DiscriminatorValue("GENERIC_REACTION")