diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
index 6c55012a2060f64dd75f88f229f5851b886d291c..638c44995c5a7eb91696bd4fff80c27c9dedfbec 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
@@ -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}
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 0d1ce039b1905b51a62db90dc91fb56f23c39d68..84d23941b6c06e77cd312e4f1ccffe65574456c9 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
@@ -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);
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 104c0fb09f89b0e439566319960bf65309fed9ef..34d97465abee91ce63a5d2ac5e9ed8f589f992f5 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -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>
diff --git a/persist/src/db/12.0.3/fix_db_20180827.sql b/persist/src/main/resources/db/migration/12.0.3/V12.0.3.20180827__empty_file_to_force_directory_to_be_commited_to_git_repo.sql
similarity index 100%
rename from persist/src/db/12.0.3/fix_db_20180827.sql
rename to persist/src/main/resources/db/migration/12.0.3/V12.0.3.20180827__empty_file_to_force_directory_to_be_commited_to_git_repo.sql
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 02bf55c42b3c0adef12ae00f1fb6a1cc8e479e70..b2687c6e02d9f799635d51cc71f27eef207c063c 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
@@ -1,470 +1,498 @@
-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;
+ }
+
+}