From 8be2e0569535a39e678065448a5dc79a0b7ce319 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 6 Feb 2018 17:23:14 +0100
Subject: [PATCH] persistence annotations added
---
.../lcsb/mapviewer/model/map/MiriamData.java | 2 +-
.../model/map/kinetics/SbmlFunction.java | 20 +-
.../model/map/kinetics/SbmlKinetics.java | 24 +-
.../model/map/kinetics/SbmlParameter.java | 4 +
.../model/map/kinetics/SbmlUnit.java | 25 +-
.../map/kinetics/SbmlUnitTypeFactor.java | 18 +
.../mapviewer/model/map/model/ModelData.java | 20 +-
.../model/map/model/ModelFullIndexed.java | 3 +-
.../model/map/reaction/Reaction.java | 4 +-
.../mapviewer/model/map/species/Species.java | 1 +
persist/src/db/12.0.0/fix_db_20180206.sql | 208 +++++
.../resources/applicationContext-persist.xml | 6 +
.../persist/dao/map/ModelDaoTest.java | 808 ++++++++++--------
13 files changed, 769 insertions(+), 374 deletions(-)
create mode 100644 persist/src/db/12.0.0/fix_db_20180206.sql
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
index f6f3ba7142..5e5dffd5a5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
+++ b/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;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
index 03680db73c..c3e23b4573 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
+++ b/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;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
index a4f1ec484c..aa0a577447 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
+++ b/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);
}
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
index cef71ff79a..acd4e885ec 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
+++ b/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;
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
index 004f9c533b..3a0b60ad84 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
+++ b/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;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
index 16f20feb52..1e4c15b550 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
+++ b/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;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index f0644e2241..4090c9f25a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/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
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 93768e9ab6..4d2d833420 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/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
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 43299fd65b..567e40b0cf 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/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;
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index 5f8e2f0b25..9d631041aa 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/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;
/**
diff --git a/persist/src/db/12.0.0/fix_db_20180206.sql b/persist/src/db/12.0.0/fix_db_20180206.sql
new file mode 100644
index 0000000000..ec3c2a8e25
--- /dev/null
+++ b/persist/src/db/12.0.0/fix_db_20180206.sql
@@ -0,0 +1,208 @@
+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
+);
+
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 329bbf4c8b..718f752f95 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/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>
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index 315bc6abbd..a364f4f340 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -19,10 +19,17 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -38,367 +45,444 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ModelDaoTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(ModelDaoTest.class);
- private Project project;
- String projectId = "Some_id";
- int identifierCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void testLoadFromDb() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
-
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- assertNotNull(model2);
- assertFalse(model2 == model);
-
- assertEquals(model.getElements().size(), model2.getElements().size());
- assertEquals(model.getLayers().size(), model2.getLayers().size());
- assertEquals(model.getReactions().size(), model2.getReactions().size());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIndexesReload() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- Model fullModel = new ModelFullIndexed(model2);
- assertNotNull(model2);
-
- assertEquals(model.getElements().size(), model2.getElements().size());
- assertEquals(model.getLayers().size(), model2.getLayers().size());
- assertEquals(model.getReactions().size(), model2.getReactions().size());
-
- // check if we really performed a test
- boolean test = false;
-
- for (Element alias : model.getElements()) {
- assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
- test = true;
- }
- assertTrue(test);
-
- test = false;
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
- test = true;
- }
- }
- assertTrue(test);
-
- model2.setHeight(32);
- modelDao.update(model2.getModel());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionInModelAfterReload() throws Exception {
- try {
- Model model = createModel();
- Reaction reaction = model.getReactions().iterator().next();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- Reaction reaction2 = null;
- for (Reaction r : model2.getReactions()) {
- if (r.getIdReaction().equals(reaction.getIdReaction())) {
- reaction2 = r;
- }
- }
- assertNotNull(reaction2);
- assertFalse(reaction.equals(reaction2));
-
- assertEquals(reaction.getNodes().size(), reaction2.getNodes().size());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLastModelForProjectName() throws Exception {
- try {
- ModelData model3 = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNull(model3);
-
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
-
- ModelData newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNotNull(newModel);
- assertEquals(model.getId(), newModel.getId());
-
- Model model2 = createModel();
- project.addModel(model2);
- modelDao.add(model2);
-
- newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNotNull(newModel);
- assertEquals(model2.getId(), newModel.getId());
-
- modelDao.delete(model2);
- modelDao.delete(model);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db, modification residues disappear from the model...
- *
- * @throws Exception
- */
- @Test
- public void testModificationsInProteins() throws Exception {
- try {
- Model model = createModel();
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
- Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
-
- assertFalse(originalSpecies.equals(fromDbSpecies));
- assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db, miriam annotations disappear...
- *
- * @throws Exception
- */
- @Test
- public void testMiriamInSpecies() throws Exception {
- try {
- Model model = createModel();
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
- Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
-
- assertFalse(originalSpecies.equals(fromDbSpecies));
- assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsInModel() throws Exception {
- try {
- Model model = createModel();
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle("temporary name");
- model.addLayout(layout);
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(1, model2.getLayouts().size());
- assertEquals("tmp", model2.getLayouts().get(0).getDirectory());
- assertEquals("temporary name", model2.getLayouts().get(0).getTitle());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(alias);
-
- ModificationResidue mr = new ModificationResidue();
- mr.setName("mr");
- alias.addModificationResidue(mr);
-
- alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein(aliasId);
- alias.setName("SNCA");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
- alias.setElementId(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- @Test
- public void testModelWithDataMining() throws Exception {
- try {
- Model model = createModel();
- model.addDataMiningSet(new DataMiningSet());
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
-
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- assertEquals(1, model2.getDataMiningSets().size());
-
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ ModelComparator modelComparator = new ModelComparator();
+
+ Logger logger = Logger.getLogger(ModelDaoTest.class);
+ private Project project;
+ String projectId = "Some_id";
+ int identifierCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void testLoadFromDb() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ assertNotNull(model2);
+ assertFalse(model2 == model);
+
+ assertEquals(model.getElements().size(), model2.getElements().size());
+ assertEquals(model.getLayers().size(), model2.getLayers().size());
+ assertEquals(model.getReactions().size(), model2.getReactions().size());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIndexesReload() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ Model fullModel = new ModelFullIndexed(model2);
+ assertNotNull(model2);
+
+ assertEquals(model.getElements().size(), model2.getElements().size());
+ assertEquals(model.getLayers().size(), model2.getLayers().size());
+ assertEquals(model.getReactions().size(), model2.getReactions().size());
+
+ // check if we really performed a test
+ boolean test = false;
+
+ for (Element alias : model.getElements()) {
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
+ test = true;
+ }
+ assertTrue(test);
+
+ test = false;
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Compartment) {
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
+ test = true;
+ }
+ }
+ assertTrue(test);
+
+ model2.setHeight(32);
+ modelDao.update(model2.getModel());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionInModelAfterReload() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ Reaction reaction2 = null;
+ for (Reaction r : model2.getReactions()) {
+ if (r.getIdReaction().equals(reaction.getIdReaction())) {
+ reaction2 = r;
+ }
+ }
+ assertNotNull(reaction2);
+ assertFalse(reaction.equals(reaction2));
+
+ assertEquals(reaction.getNodes().size(), reaction2.getNodes().size());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionInWithKinetics() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addElement(reaction.getReactants().get(0).getElement());
+ kinetics.addFunction(createFunction());
+ model.addFunctions(kinetics.getFunctions());
+ kinetics.addParameter(createParameter());
+ model.addUnit(kinetics.getParameters().iterator().next().getUnits());
+ reaction.setKinetics(kinetics);
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelWithParameters() throws Exception {
+ try {
+ Model model = createModel();
+ model.addParameter(createParameter());
+ model.addUnit(model.getParameters().iterator().next().getUnits());
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private SbmlParameter createParameter() {
+ SbmlParameter parameter = new SbmlParameter("param_id");
+ parameter.setName("X");
+ parameter.setValue(4.7);
+ parameter.setUnits(createUnits());
+ return parameter;
+ }
+
+ private SbmlUnit createUnits() {
+ SbmlUnit unit = new SbmlUnit("unit_id");
+ unit.setName("u name");
+ unit.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 2, 3));
+ return unit;
+ }
+
+ private SbmlFunction createFunction() {
+ SbmlFunction result = new SbmlFunction ("fun_id");
+ result.setDefinition("def(k1)");
+ result.addArgument("k1");
+ result.setName("fun name");
+ return result;
+ }
+
+ @Test
+ public void testGetLastModelForProjectName() throws Exception {
+ try {
+ ModelData model3 = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNull(model3);
+
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+
+ ModelData newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNotNull(newModel);
+ assertEquals(model.getId(), newModel.getId());
+
+ Model model2 = createModel();
+ project.addModel(model2);
+ modelDao.add(model2);
+
+ newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNotNull(newModel);
+ assertEquals(model2.getId(), newModel.getId());
+
+ modelDao.delete(model2);
+ modelDao.delete(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db, modification residues disappear from the model...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testModificationsInProteins() throws Exception {
+ try {
+ Model model = createModel();
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
+
+ assertFalse(originalSpecies.equals(fromDbSpecies));
+ assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db, miriam annotations disappear...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testMiriamInSpecies() throws Exception {
+ try {
+ Model model = createModel();
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
+
+ assertFalse(originalSpecies.equals(fromDbSpecies));
+ assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsInModel() throws Exception {
+ try {
+ Model model = createModel();
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle("temporary name");
+ model.addLayout(layout);
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(1, model2.getLayouts().size());
+ assertEquals("tmp", model2.getLayouts().get(0).getDirectory());
+ assertEquals("temporary name", model2.getLayouts().get(0).getTitle());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpecies(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpecies(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpecies(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpecies(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpecies(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(alias);
+
+ ModificationResidue mr = new ModificationResidue();
+ mr.setName("mr");
+ alias.addModificationResidue(mr);
+
+ alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartment(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private GenericProtein createSpecies(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
+ alias.setName("SNCA");
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ alias.setElementId(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplex(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ @Test
+ public void testModelWithDataMining() throws Exception {
+ try {
+ Model model = createModel();
+ model.addDataMiningSet(new DataMiningSet());
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ assertEquals(1, model2.getDataMiningSets().size());
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
--
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