Skip to content
Snippets Groups Projects
Commit 2c9558f0 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch '480-reduced-modulation-edge-transfer-to-minerva' into 'master' 

Resolve "'Reduced modulation' edge transfer to Minerva"

Closes #480

See merge request !380
parents 9bcf2651 af268d0a
No related branches found
No related tags found
1 merge request!380Resolve "'Reduced modulation' edge transfer to Minerva"
Pipeline #
Hide whitespace changes
Inline Side-by-side
Showing
with 511 additions and 474 deletions
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
+ 1
− 1
View file @ 2c9558f0
......@@ -98,7 +98,7 @@ public enum ReactionLineData {
/**
* Information about arrows/lines for {@link ReducedModulationReaction} class.
*/
REDUCED_MODULATION(ReducedModulationReaction.class, "REDUCED_MODULATION", LineType.SOLID, ArrowType.BLANK),
REDUCED_MODULATION(ReducedModulationReaction.class, "REDUCED_MODULATION", LineType.SOLID, ArrowType.DIAMOND),
/**
* Information about arrows/lines for {@link ReducedPhysicalStimulationReaction}
......
model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+ 5
− 3
View file @ 2c9558f0
......@@ -45,6 +45,7 @@ import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
import lcsb.mapviewer.model.map.species.Element;
......@@ -469,9 +470,7 @@ public class Reaction implements BioEntity {
if (firstOperator != null) {
startPoint = firstOperator.getLine().getPoints().get(firstOperator.getLine().getPoints().size() - 2);
}
}
if (this instanceof TwoProductReactionInterface) {
} else if (this instanceof TwoProductReactionInterface) {
NodeOperator firstOperator = null;
......@@ -483,6 +482,9 @@ public class Reaction implements BioEntity {
if (firstOperator != null) {
endPoint = firstOperator.getLine().getPoints().get(firstOperator.getLine().getPoints().size() - 2);
}
} else if (this instanceof ReducedNotation) {
startPoint = reactant.getLine().getEndPoint();
endPoint = product.getLine().getBeginPoint();
}
return new Line2D.Double(startPoint, endPoint);
......
persist/src/main/resources/applicationContext-persist.xml
+ 7
− 0
View file @ 2c9558f0
......@@ -55,9 +55,13 @@
<value>lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.DissociationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.CatalysisReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.InhibitionReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.ModulationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction</value>
......@@ -66,7 +70,10 @@
<value>lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TranslationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TransportReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TriggerReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.TruncationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction</value>
......
persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+ 498
− 470
View file @ 2c9558f0
package lcsb.mapviewer.persist.dao.map;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import java.awt.Color;
import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
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;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ModelDaoTest extends PersistTestFunctions {
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());
ModelComparator comparator = new ModelComparator();
assertEquals(0, comparator.compare(model, new ModelFullIndexed(model2)));
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);
Residue mr = new Residue();
mr.setName("mr");
mr.setPosition(new Point2D.Double(10, 20));
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;
}
}
package lcsb.mapviewer.persist.dao.map;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import java.awt.Color;
import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
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;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ModelDaoTest extends PersistTestFunctions {
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());
ModelComparator comparator = new ModelComparator();
assertEquals(0, comparator.compare(model, new ModelFullIndexed(model2)));
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 testModulationReaction() throws Exception {
try {
Model model = createModel();
Reaction reaction = new ModulationReaction();
reaction.addProduct(new Product(model.getElementByElementId("sa2")));
reaction.addReactant(new Reactant(model.getElementByElementId("sa1117")));
reaction.setIdReaction("re" + identifierCounter++);
model.addReaction(reaction);
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);
Residue mr = new Residue();
mr.setName("mr");
mr.setPosition(new Point2D.Double(10, 20));
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;
}
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment