persistence annotations added

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

@@ -49,7 +49,7 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
 	private int								 id;
 
 	/**
-	 * What is the connection between element and the anntoation.
+	 * What is the connection between element and the annotation.
 	 */
 	private MiriamRelationType relationType			= null;
 

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

@@ -8,16 +8,20 @@ import javax.persistence.CollectionTable;
 import javax.persistence.Column;
 import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.apache.log4j.Logger;
 import org.hibernate.annotations.IndexColumn;
 
+import lcsb.mapviewer.model.map.model.ModelData;
+
 /**
  * Representation of a single SBML function
  * 
@@ -62,6 +66,12 @@ public class SbmlFunction implements Serializable, SbmlArgument {
   @Column(name = "argument_name")
   private List<String> arguments = new ArrayList<>();
 
+  /**
+   * Map model object to which function belongs to.
+   */
+  @ManyToOne(fetch = FetchType.LAZY)
+  private ModelData model;
+
   /**
    * Constructor required by hibernate.
    */
@@ -77,7 +87,7 @@ public class SbmlFunction implements Serializable, SbmlArgument {
     this.functionId = original.getFunctionId();
     this.definition = original.getDefinition();
     this.name = original.getName();
-    for (String argument: original.getArguments()) {
+    for (String argument : original.getArguments()) {
       this.addArgument(argument);
     }
   }
@@ -128,4 +138,12 @@ public class SbmlFunction implements Serializable, SbmlArgument {
     return getFunctionId();
   }
 
+  public ModelData getModel() {
+    return model;
+  }
+
+  public void setModel(ModelData model) {
+    this.model = model;
+  }
+
 }

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

@@ -9,10 +9,15 @@ import java.util.Set;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
-import javax.persistence.OneToMany;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlRootElement;
 
@@ -20,6 +25,7 @@ import org.apache.log4j.Logger;
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
 
+import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 
 /**
@@ -46,13 +52,24 @@ public class SbmlKinetics implements Serializable {
   private static final long serialVersionUID = 1L;
 
   @Cascade({ CascadeType.ALL })
-  @OneToMany(mappedBy = "model", orphanRemoval = true)
+  @ManyToMany(fetch = FetchType.EAGER)
+  @JoinTable(name = "kinetic_law_parameters", joinColumns = {
+      @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+          @JoinColumn(name = "parameter_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
   private Set<SbmlParameter> parameters = new HashSet<>();
 
   @Cascade({ CascadeType.ALL })
-  @OneToMany(mappedBy = "model", orphanRemoval = true)
+  @ManyToMany(fetch = FetchType.EAGER)
+  @JoinTable(name = "kinetic_law_functions", joinColumns = {
+      @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+          @JoinColumn(name = "function_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
   private Set<SbmlFunction> functions = new HashSet<>();
 
+  @Cascade({ CascadeType.ALL })
+  @ManyToMany(fetch = FetchType.EAGER)
+  @JoinTable(name = "kinetic_law_elements", joinColumns = {
+      @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+          @JoinColumn(name = "element_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
   private Set<Element> elements = new HashSet<>();
 
   /**
@@ -163,5 +180,4 @@ public class SbmlKinetics implements Serializable {
   public void removeElement(Element elementToRemove) {
     elements.remove(elementToRemove);
   }
-
 }

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

@@ -4,9 +4,11 @@ import java.io.Serializable;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
 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;
 
@@ -48,6 +50,8 @@ public class SbmlParameter implements Serializable, SbmlArgument {
   private String name;
 
   private Double value;
+  
+  @ManyToOne()
   private SbmlUnit units;
 
   /**

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

@@ -2,18 +2,24 @@ package lcsb.mapviewer.model.map.kinetics;
 
 import java.io.Serializable;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Set;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 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;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.model.ModelData;
 
 /**
  * Representation of a single SBML unit
@@ -49,8 +55,16 @@ public class SbmlUnit implements Serializable {
   private String unitId;
   private String name;
 
+  @Cascade({ CascadeType.ALL })
+  @OneToMany(mappedBy = "unit", orphanRemoval = true)
   private Set<SbmlUnitTypeFactor> unitTypeFactors = new HashSet<>();
 
+  /**
+   * Map model object to which unit belongs to.
+   */
+  @ManyToOne(fetch = FetchType.LAZY)
+  private ModelData model;
+
   /**
    * Constructor required by hibernate.
    */
@@ -80,10 +94,19 @@ public class SbmlUnit implements Serializable {
 
   public void addUnitTypeFactor(SbmlUnitTypeFactor factor) {
     unitTypeFactors.add(factor);
+    factor.setUnit(this);
   }
 
   public Set<SbmlUnitTypeFactor> getUnitTypeFactors() {
     return unitTypeFactors;
   }
 
+  public ModelData getModel() {
+    return model;
+  }
+
+  public void setModel(ModelData model) {
+    this.model = model;
+  }
+
 }

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

@@ -4,14 +4,20 @@ import java.io.Serializable;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
 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;
 
+import lcsb.mapviewer.model.map.model.ModelData;
+
 /**
  * Representation of a single SBML unit factor. For example unit for velocity is
  * m/s. It means that we have two unit types here:
@@ -48,12 +54,16 @@ public class SbmlUnitTypeFactor implements Serializable {
   @Column(name = "idDb", unique = true, nullable = false)
   private int id;
 
+  @Enumerated(EnumType.STRING)
   private SbmlUnitType unitType;
 
   private int exponent = 1;
   private int scale = 0;
   private double multiplier = 1.0;
 
+  @ManyToOne(fetch = FetchType.LAZY)
+  private SbmlUnit unit;
+
   /**
    * Constructor required by hibernate.
    */
@@ -100,4 +110,12 @@ public class SbmlUnitTypeFactor implements Serializable {
     this.multiplier = multiplier;
   }
 
+  public SbmlUnit getUnit() {
+    return unit;
+  }
+
+  public void setUnit(SbmlUnit unit) {
+    this.unit = unit;
+  }
+
 }

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

@@ -14,6 +14,9 @@ import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
 import javax.persistence.OrderBy;
@@ -115,7 +118,10 @@ public class ModelData implements Serializable {
   private Set<SbmlFunction> functions = new HashSet<>();
 
   @Cascade({ CascadeType.ALL })
-  @OneToMany(mappedBy = "model", orphanRemoval = true)
+  @ManyToMany(fetch = FetchType.EAGER)
+  @JoinTable(name = "model_parameters", joinColumns = {
+      @JoinColumn(name = "model_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+          @JoinColumn(name = "parameter_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
   private Set<SbmlParameter> parameters = new HashSet<>();
 
   @Cascade({ CascadeType.ALL })
@@ -763,7 +769,9 @@ public class ModelData implements Serializable {
   }
 
   public void addUnits(Collection<SbmlUnit> units) {
-    this.units.addAll(units);
+    for (SbmlUnit sbmlUnit : units) {
+      addUnit(sbmlUnit);
+    }
   }
 
   public Set<SbmlUnit> getUnits() {
@@ -772,6 +780,7 @@ public class ModelData implements Serializable {
 
   public void addUnit(SbmlUnit unit) {
     this.units.add(unit);
+    unit.setModel(this);
   }
 
   public void addParameters(Collection<SbmlParameter> sbmlParameters) {
@@ -784,5 +793,12 @@ public class ModelData implements Serializable {
 
   public void addFunction(SbmlFunction sbmlFunction) {
     this.functions.add(sbmlFunction);
+    sbmlFunction.setModel(this);
+  }
+
+  public void addFunctions(Collection<SbmlFunction> functions) {
+    for (SbmlFunction sbmlFunction : functions) {
+      addFunction(sbmlFunction);
+    }
   }
 }
\ No newline at end of file

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

@@ -18,7 +18,6 @@ import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
 import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
 import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
 import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -667,7 +666,7 @@ public class ModelFullIndexed implements Model {
 
   @Override
   public void addFunctions(Collection<SbmlFunction> functions) {
-    modelData.getFunctions().addAll(functions);
+    modelData.addFunctions(functions);
   }
 
   @Override

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

@@ -27,6 +27,7 @@ import javax.persistence.JoinTable;
 import javax.persistence.ManyToMany;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
 import javax.persistence.OrderBy;
 import javax.persistence.Table;
 import javax.xml.bind.annotation.XmlTransient;
@@ -36,7 +37,6 @@ import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
 import org.hibernate.annotations.IndexColumn;
 
-import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.model.map.BioEntity;
@@ -209,6 +209,8 @@ public class Reaction implements BioEntity {
   @ManyToOne(fetch = FetchType.LAZY)
   private ModelData model;
 
+  @Cascade({ CascadeType.ALL })
+  @OneToOne
   private SbmlKinetics kinetics;
 
   /**

model/src/main/java/lcsb/mapviewer/model/map/species/Species.java

@@ -127,6 +127,7 @@ public abstract class Species extends Element {
 
   private Boolean constant;
 
+  @Enumerated(EnumType.STRING)
   private SbmlUnitType substanceUnits;
 
   /**

persist/src/db/12.0.0/fix_db_20180206.sql

+alter table element_table drop column if exists boundarycondition;
+alter table element_table add boundarycondition boolean;
+
+alter table element_table drop column if exists constant;
+alter table element_table add constant boolean;
+
+alter table element_table drop column if exists substanceunits;
+alter table element_table add substanceunits varchar(255);
+
+alter table reaction_table drop column if exists kineticlaw;
+
+alter table reaction_table drop column if exists kinetics_iddb;
+alter table reaction_table add kinetics_iddb integer;
+
+drop table if exists kinetic_law_parameters;
+drop table if exists kinetic_law_functions;
+drop table if exists kinetic_law_elements;
+drop table if exists sbml_function_arguments;
+drop table if exists sbml_unit_factor;
+DROP SEQUENCE if exists sbml_unit_factor_iddb_seq;
+drop table if exists sbml_kinetics;
+DROP SEQUENCE if exists sbml_kinetics_iddb_seq;
+drop table if exists sbml_function;
+DROP SEQUENCE if exists sbml_function_iddb_seq;
+drop table if exists model_parameters;
+drop table if exists sbml_parameter;
+DROP SEQUENCE if exists sbml_parameter_iddb_seq;
+drop table if exists sbml_unit;
+DROP SEQUENCE if exists sbml_unit_iddb_seq;
+
+--definition of sbml unit
+
+CREATE SEQUENCE sbml_unit_iddb_seq
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE sbml_unit
+(
+  iddb integer NOT NULL DEFAULT nextval('sbml_unit_iddb_seq'::regclass),
+  unitid  varchar(255),  
+  name  varchar(255),
+  model_iddb integer NOT NULL,
+  
+  CONSTRAINT sbml_unit_pk PRIMARY KEY (iddb),
+  CONSTRAINT sbml_unit_model_fk FOREIGN KEY (model_iddb)
+      REFERENCES public.model_table (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+--definition of sbml parameter
+CREATE SEQUENCE sbml_parameter_iddb_seq
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE sbml_parameter
+(
+  iddb integer NOT NULL DEFAULT nextval('sbml_parameter_iddb_seq'::regclass),
+  parameterid  varchar(255),  
+  name  varchar(255),
+	value  numeric,
+	units_iddb integer,
+  
+  CONSTRAINT sbml_parameter_pk PRIMARY KEY (iddb),
+  CONSTRAINT sbml_parameter_units_fk FOREIGN KEY (units_iddb)
+      REFERENCES public.sbml_unit (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+
+--definition of many to many relation between model and sbml parameter
+CREATE TABLE model_parameters
+(
+  model_id integer NOT NULL,
+  parameter_id integer NOT NULL,  
+  CONSTRAINT model_parameters_unique UNIQUE (model_id, parameter_id),
+  CONSTRAINT model_parameters_model_fk FOREIGN KEY (model_id)
+      REFERENCES public.model_table (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE,
+  CONSTRAINT model_parameters_parameter_fk FOREIGN KEY (parameter_id)
+      REFERENCES public.sbml_parameter (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+--definition of sbml function
+CREATE SEQUENCE sbml_function_iddb_seq
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE sbml_function
+(
+  iddb integer NOT NULL DEFAULT nextval('sbml_function_iddb_seq'::regclass),
+  functionid  varchar(255),  
+  name  varchar(255),
+  definition  text,
+  model_iddb integer NOT NULL,
+  
+  CONSTRAINT sbml_function_pk PRIMARY KEY (iddb),
+  CONSTRAINT sbml_function_model_fk FOREIGN KEY (model_iddb)
+      REFERENCES public.model_table (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+--definition of sbml kinetics
+CREATE SEQUENCE sbml_kinetics_iddb_seq
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE sbml_kinetics
+(
+  iddb integer NOT NULL DEFAULT nextval('sbml_function_iddb_seq'::regclass),
+  definition  text,
+  
+  CONSTRAINT sbml_kinetics_pk PRIMARY KEY (iddb)
+);
+
+ALTER TABLE reaction_table ADD FOREIGN KEY (kinetics_iddb) REFERENCES sbml_kinetics(iddb);
+
+
+--definition of sbml kinetics
+CREATE SEQUENCE sbml_unit_factor_iddb_seq
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE sbml_unit_factor
+(
+  iddb integer NOT NULL DEFAULT nextval('sbml_unit_factor_iddb_seq'::regclass),
+  unit_iddb  integer not null,
+  exponent  integer not null default 1,
+  scale  integer not null default 0,
+  multiplier  numeric not null default 1.0,
+  unittype varchar(255), 
+  
+  CONSTRAINT sbml_unit_factor_pk PRIMARY KEY (iddb),
+  CONSTRAINT sbml_unit_factor_unit_fk FOREIGN KEY (unit_iddb)
+      REFERENCES public.sbml_unit (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+  
+);
+
+CREATE TABLE sbml_function_arguments
+(
+  idx integer NOT NULL,
+  sbml_function_iddb integer not null,
+  argument_name varchar(255), 
+  
+  CONSTRAINT sbml_function_arguments_sbml_function_fk FOREIGN KEY (sbml_function_iddb)
+      REFERENCES public.sbml_function (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+  
+);
+
+CREATE TABLE kinetic_law_parameters
+(
+  kinetic_law_id integer NOT NULL,
+  parameter_id integer not null,
+  
+  CONSTRAINT kinetic_law_parameters_unique UNIQUE (kinetic_law_id, parameter_id),
+  CONSTRAINT kinetic_law_parameters_sbml_kinetics_fk FOREIGN KEY (kinetic_law_id)
+      REFERENCES public.sbml_kinetics (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE,
+  CONSTRAINT kinetic_law_parameters_parameter_fk FOREIGN KEY (parameter_id)
+      REFERENCES public.sbml_parameter (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+CREATE TABLE kinetic_law_functions
+(
+  kinetic_law_id integer NOT NULL,
+  function_id integer not null,
+  
+  CONSTRAINT kinetic_law_functions_unique UNIQUE (kinetic_law_id, function_id),
+  CONSTRAINT kinetic_law_functions_sbml_kinetics_fk FOREIGN KEY (kinetic_law_id)
+      REFERENCES public.sbml_kinetics (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE,
+  CONSTRAINT kinetic_law_functions_function_fk FOREIGN KEY (function_id)
+      REFERENCES public.sbml_function (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+
+CREATE TABLE kinetic_law_elements
+(
+  kinetic_law_id integer NOT NULL,
+  element_id integer not null,
+  
+  CONSTRAINT kinetic_law_elements_unique UNIQUE (kinetic_law_id, element_id),
+  CONSTRAINT kinetic_law_elements_sbml_kinetics_fk FOREIGN KEY (kinetic_law_id)
+      REFERENCES public.sbml_kinetics (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE,
+  CONSTRAINT kinetic_law_elements_element_fk FOREIGN KEY (element_id)
+      REFERENCES public.element_table (iddb) MATCH SIMPLE
+      ON UPDATE CASCADE ON DELETE CASCADE
+);
+

persist/src/main/resources/applicationContext-persist.xml

@@ -98,6 +98,12 @@
 				<value>lcsb.mapviewer.model.map.OverviewLink</value>
 				<value>lcsb.mapviewer.model.map.OverviewModelLink</value>
 				<value>lcsb.mapviewer.model.map.OverviewSearchLink</value>
+
+				<value>lcsb.mapviewer.model.map.kinetics.SbmlFunction</value>
+				<value>lcsb.mapviewer.model.map.kinetics.SbmlKinetics</value>
+				<value>lcsb.mapviewer.model.map.kinetics.SbmlParameter</value>
+				<value>lcsb.mapviewer.model.map.kinetics.SbmlUnit</value>
+				<value>lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor</value>
 	
 				<value>lcsb.mapviewer.model.map.layout.Layout</value>