diff --git a/CHANGELOG b/CHANGELOG
index d9f196003ed28438e2fded7d718afdee0c5e5a17..c0aedb3bea0c6d69da97a1871df71aac404d2dd4 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,6 +1,7 @@
-minerva (11alpha) stable; urgency=medium
+minerva (10.0.1) unstable; urgency=medium
- * Export to image without selecting region
+ * Bug fix: export to image
+ * Bug fix: trigger reaction and physical stimulation reactions are no longer allowed (CellDesigner data model issue)
minerva (10) stable; urgency=medium
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
deleted file mode 100644
index 2de617ad83e0f73dc2ff265aaab059dbaefd884b..0000000000000000000000000000000000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner physical stimulation reaction. It
- * must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("PHYSICAL_STIMULATION_REACTION")
-public class PhysicalStimulationReaction extends Reaction implements SimpleReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public PhysicalStimulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public PhysicalStimulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Physical stimulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public PhysicalStimulationReaction copy() {
- if (this.getClass() == PhysicalStimulationReaction.class) {
- return new PhysicalStimulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
deleted file mode 100644
index f3e2b83952cfe7b8b84d063761c5b9961065eb0d..0000000000000000000000000000000000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner trigger reaction. It must have at
- * least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRIGGER_REACTION")
-public class TriggerReaction extends Reaction implements SimpleReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public TriggerReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public TriggerReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Trigger";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public TriggerReaction copy() {
- if (this.getClass() == TriggerReaction.class) {
- return new TriggerReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index c93c52c6c9fceea90b5b27e4bf488436c440213f..7e8fc6042ca893c833da491c4e85ad14eed6ffc6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -1,300 +1,300 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-public class ReactionComparatorTest {
-
- ReactionComparator comparator = new ReactionComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
- assertEquals(0, comparator.compare(reaction1, reaction2));
- assertEquals(0, comparator.compare(reaction2, reaction1));
- assertEquals(0, comparator.compare(reaction1, reaction1));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent3() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.setNotes("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setIdReaction("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setKineticLaw(true);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setSymbol("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setFormula("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setSubsystem("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setGeneProteinReaction("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setMechanicalConfidenceScore(1);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setLowerBound(1.2);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setUpperBound(4.3);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addSynonym("syn");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addNode(new AndOperator());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent4() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.addNode(new AndOperator());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- Reaction reaction1 = createReaction();
- assertTrue(comparator.compare(reaction1, null) != 0);
- assertTrue(comparator.compare(null, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
-
- assertTrue(comparator.compare(new TransportReaction(), new TriggerReaction()) != 0);
-
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.setReversible(true);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addModifier(new Modifier());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getModifiers().get(0).getAlias().setAliasId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addReactant(new Reactant());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getReactants().get(0).getAlias().setAliasId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addProduct(new Product());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getProducts().get(0).getAlias().setAliasId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getOperators().get(0).getLine().addPoint(new Point2D.Double(2, 2));
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNKNOWN, "c"));
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- private Reaction createReaction() {
- Reaction reaction = new Reaction();
- Protein protein = new Protein();
- protein.setName("ASD");
- SpeciesAlias alias = new SpeciesAlias(protein);
- Reactant reactant = new Reactant(alias, protein);
-
- Protein protein2 = new Protein();
- protein2.setName("ASD2");
- SpeciesAlias alias2 = new SpeciesAlias(protein2);
- Reactant reactant2 = new Reactant(alias2, protein2);
-
- SimpleMolecule molecule = new SimpleMolecule();
- molecule.setName("mol");
- SpeciesAlias moelculeAlias = new SpeciesAlias(molecule);
- Product product = new Product(moelculeAlias, molecule);
-
- Unknown unknown = new Unknown();
- unknown.setName("unk");
- SpeciesAlias unknownAlias = new SpeciesAlias(unknown);
- Modifier modifier = new Catalysis(unknownAlias, unknown);
-
- AndOperator operator = new AndOperator();
- operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
- operator.addInput(reactant);
- operator.addInput(reactant2);
-
- reaction.addModifier(modifier);
- reaction.addReactant(reactant);
- reaction.addReactant(reactant2);
- reaction.addProduct(product);
- reaction.addNode(operator);
- return reaction;
- }
-
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
- reaction2.setAbbreviation("ABRR");
-
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+public class ReactionComparatorTest {
+
+ ReactionComparator comparator = new ReactionComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+ assertEquals(0, comparator.compare(reaction1, reaction2));
+ assertEquals(0, comparator.compare(reaction2, reaction1));
+ assertEquals(0, comparator.compare(reaction1, reaction1));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent3() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setNotes("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setIdReaction("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setKineticLaw(true);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setSymbol("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setFormula("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setSubsystem("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setGeneProteinReaction("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setMechanicalConfidenceScore(1);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setLowerBound(1.2);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setUpperBound(4.3);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addSynonym("syn");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addNode(new AndOperator());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent4() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.addNode(new AndOperator());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ Reaction reaction1 = createReaction();
+ assertTrue(comparator.compare(reaction1, null) != 0);
+ assertTrue(comparator.compare(null, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+
+ assertTrue(comparator.compare(new TransportReaction(), new StateTransitionReaction()) != 0);
+
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setReversible(true);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addModifier(new Modifier());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getModifiers().get(0).getAlias().setAliasId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addReactant(new Reactant());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getReactants().get(0).getAlias().setAliasId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addProduct(new Product());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getProducts().get(0).getAlias().setAliasId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getOperators().get(0).getLine().addPoint(new Point2D.Double(2, 2));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNKNOWN, "c"));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ private Reaction createReaction() {
+ Reaction reaction = new Reaction();
+ Protein protein = new Protein();
+ protein.setName("ASD");
+ SpeciesAlias alias = new SpeciesAlias(protein);
+ Reactant reactant = new Reactant(alias, protein);
+
+ Protein protein2 = new Protein();
+ protein2.setName("ASD2");
+ SpeciesAlias alias2 = new SpeciesAlias(protein2);
+ Reactant reactant2 = new Reactant(alias2, protein2);
+
+ SimpleMolecule molecule = new SimpleMolecule();
+ molecule.setName("mol");
+ SpeciesAlias moelculeAlias = new SpeciesAlias(molecule);
+ Product product = new Product(moelculeAlias, molecule);
+
+ Unknown unknown = new Unknown();
+ unknown.setName("unk");
+ SpeciesAlias unknownAlias = new SpeciesAlias(unknown);
+ Modifier modifier = new Catalysis(unknownAlias, unknown);
+
+ AndOperator operator = new AndOperator();
+ operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
+ operator.addInput(reactant);
+ operator.addInput(reactant2);
+
+ reaction.addModifier(modifier);
+ reaction.addReactant(reactant);
+ reaction.addReactant(reactant2);
+ reaction.addProduct(product);
+ reaction.addNode(operator);
+ return reaction;
+ }
+
+ @Test
+ public void testDifferentNewFields() throws Exception {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+ reaction2.setAbbreviation("ABRR");
+
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
index 65378cef4adcdbee7707aa77e73736fd3d27f1b5..814c337da84987b319d81f56d972b0152feb120e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
@@ -1,33 +1,32 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BooleanLogicGateReactionTest.class, //
- DissociationReactionTest.class, //
- HeterodimerAssociationReactionTest.class, //
- KnownTransitionOmittedReactionTest.class, //
- NegativeInfluenceReactionTest.class, //
- PhysicalStimulationReactionTest.class, //
- PositiveInfluenceReactionTest.class, //
- ReactionRectTest.class, //
- ReducedModulationReactionTest.class, //
- ReducedPhysicalStimulationReactionTest.class, //
- ReducedTriggerReactionTest.class, //
- StateTransitionReactionTest.class, //
- TranscriptionReactionTest.class, //
- TranslationReactionTest.class, TransportReactionTest.class, //
- TriggerReactionTest.class, //
- TruncationReactionTest.class, //
- UnknownNegativeInfluenceReactionTest.class, //
- UnknownPositiveInfluenceReactionTest.class, //
- UnknownReducedModulationReactionTest.class, //
- UnknownReducedPhysicalStimulationReactionTest.class, //
- UnknownReducedTriggerReactionTest.class, //
- UnknownTransitionReactionTest.class, //
-})
-public class AllReactionTypeTests {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BooleanLogicGateReactionTest.class, //
+ DissociationReactionTest.class, //
+ HeterodimerAssociationReactionTest.class, //
+ KnownTransitionOmittedReactionTest.class, //
+ NegativeInfluenceReactionTest.class, //
+ PositiveInfluenceReactionTest.class, //
+ ReactionRectTest.class, //
+ ReducedModulationReactionTest.class, //
+ ReducedPhysicalStimulationReactionTest.class, //
+ ReducedTriggerReactionTest.class, //
+ StateTransitionReactionTest.class, //
+ TranscriptionReactionTest.class, //
+ TranslationReactionTest.class, //
+ TransportReactionTest.class, //
+ TruncationReactionTest.class, //
+ UnknownNegativeInfluenceReactionTest.class, //
+ UnknownPositiveInfluenceReactionTest.class, //
+ UnknownReducedModulationReactionTest.class, //
+ UnknownReducedPhysicalStimulationReactionTest.class, //
+ UnknownReducedTriggerReactionTest.class, //
+ UnknownTransitionReactionTest.class, //
+})
+public class AllReactionTypeTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReactionTest.java
deleted file mode 100644
index 9b0b015a796fc5d5e697f236a5847255d13969e1..0000000000000000000000000000000000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReactionTest.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class PhysicalStimulationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new PhysicalStimulationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new PhysicalStimulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new PhysicalStimulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- PhysicalStimulationReaction validReaction = new PhysicalStimulationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- PhysicalStimulationReaction original = new PhysicalStimulationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- PhysicalStimulationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new PhysicalStimulationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- PhysicalStimulationReaction original = new PhysicalStimulationReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TriggerReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TriggerReactionTest.java
deleted file mode 100644
index 87deb1a50e799766676847330d889d58023ad4a2..0000000000000000000000000000000000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TriggerReactionTest.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class TriggerReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TriggerReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new TriggerReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new TriggerReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- TriggerReaction validReaction = new TriggerReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testCopy() {
- try {
- TriggerReaction original = new TriggerReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- TriggerReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new TriggerReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- TriggerReaction original = new TriggerReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
diff --git a/persist/src/db/11/fix_db_20160907.sql b/persist/src/db/10.0.1/fix_db_20160907.sql
similarity index 100%
rename from persist/src/db/11/fix_db_20160907.sql
rename to persist/src/db/10.0.1/fix_db_20160907.sql
diff --git a/persist/src/db/10.0.1/fix_db_20160909.sql b/persist/src/db/10.0.1/fix_db_20160909.sql
new file mode 100644
index 0000000000000000000000000000000000000000..9fb11c2f43a3a690d3f8d8760359531a93d10b00
--- /dev/null
+++ b/persist/src/db/10.0.1/fix_db_20160909.sql
@@ -0,0 +1,4 @@
+-- fix on issue #8
+update reaction_table set reaction_type_db='REDUCED_TRIGGER_REACTION' where reaction_type_db = 'TRIGGER_REACTION';
+update reaction_table set reaction_type_db='REDUCED_PHYSICAL_STIMULATION' where reaction_type_db = 'PHYSICAL_STIMULATION_REACTION';
+
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index d551dccd27377605ab35db17e27a9b3bd768bf7d..868a5f46896a9b02d3f58a1e17b35e7c49a25910 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -76,7 +76,6 @@
<value>lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction</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>
@@ -85,7 +84,6 @@
<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.UnknownNegativeInfluenceReaction</value>
<value>lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction</value>