diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index 8530ae1a6b6095339d7ca9597f94ba3686699840..3360e35551261b615cdb03deba92c69f88529e7a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -37,26 +37,22 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
for (T sbmlElement : getSbmlElementList(sbmlModel)) {
result.add(parse(sbmlElement, sbmlModel));
}
- if (layout != null) {
- return mergeLayout(result, layout, sbmlModel);
- } else {
- return result;
- }
+ return result;
}
protected abstract ListOf<T> getSbmlElementList(Model sbmlModel);
- protected List<Element> mergeLayout(List<Element> elements, Layout sbmlLayout, Model sbmlModel)
+ protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
Set<Element> used = new HashSet<>();
Map<String, Element> elementById = new HashMap<>();
+ List<Element> result = new ArrayList<>();
for (Element species : elements) {
if (elementById.get(species.getElementId()) != null) {
throw new InvalidInputDataExecption("Duplicated element id: " + species.getElementId());
}
elementById.put(species.getElementId(), species);
}
- List<Element> result = new ArrayList<>();
for (Pair<String, AbstractReferenceGlyph> idGlyphPair : getGlyphs(sbmlLayout)) {
String id = idGlyphPair.getLeft();
@@ -66,18 +62,21 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
}
used.add(source);
AbstractReferenceGlyph glyph = idGlyphPair.getRight();
- Element SpeciesWithLayout = source.copy();
- SpeciesWithLayout.setElementId(glyph.getId());
- SpeciesWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
- SpeciesWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
- SpeciesWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
- SpeciesWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
- result.add(SpeciesWithLayout);
+ Element elementWithLayout = source.copy();
+ elementWithLayout.setElementId(glyph.getId());
+ elementWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
+ elementWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
+ elementWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
+ elementWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
+ minervaModel.addElement(elementWithLayout);
+ result.add(elementWithLayout);
}
- for (Element Species : elements) {
- if (!used.contains(Species)) {
- logger.warn("Layout doesn't contain information about Element: " + Species.getElementId());
- result.add(Species);
+ for (Element element : elements) {
+ if (!used.contains(element)) {
+ logger.warn("Layout doesn't contain information about Element: " + element.getElementId());
+ result.add(element);
+ } else {
+ minervaModel.removeElement(element);
}
}
return result;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index a14a15c80cda8faedc8dc0540c774fb96f6eaa6c..36b25f1bb68a02c6db5faede9e2de8b24349d21d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -51,6 +51,7 @@ public class SbmlParser implements IConverter {
SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout, model);
SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
+ SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
if (annotations.size() > 0) {
@@ -58,6 +59,15 @@ public class SbmlParser implements IConverter {
}
model.addElements(compartmentParser.parseList(sbmlModel));
model.addElements(speciesParser.parseList(sbmlModel));
+ model.addReactions(reactionParser.parseList(sbmlModel));
+
+ if (layout != null) {
+ compartmentParser.mergeLayout(model.getCompartments(), layout, sbmlModel);
+ speciesParser.mergeLayout(model.getSpeciesList(), layout, sbmlModel);
+ reactionParser.mergeLayout(model.getReactions(), layout, sbmlModel);
+ }
+ reactionParser.validateReactions(model.getReactions());
+
if (sbmlModel.getConstraintCount() > 0) {
throw new NotImplementedException("Constraints not implemented for model");
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..627c2db528ef6660e593ee892db66c24ff0ac5f0
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -0,0 +1,162 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.Annotation;
+import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ModifierSpeciesReference;
+import org.sbml.jsbml.SpeciesReference;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.ReactionGlyph;
+import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
+import org.sbml.jsbml.util.NotImplementedException;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+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.ReactionNode;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+public class SbmlReactionParser {
+ Logger logger = Logger.getLogger(SbmlReactionParser.class);
+
+ Layout layout;
+
+ lcsb.mapviewer.model.map.model.Model minervaModel;
+ ElementUtils eu = new ElementUtils();
+
+ public SbmlReactionParser(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.layout = sbmlLayout;
+ this.minervaModel = minervaModel;
+ }
+
+ public List<Reaction> parseList(Model sbmlModel) throws InvalidInputDataExecption {
+ List<Reaction> result = new ArrayList<>();
+ for (org.sbml.jsbml.Reaction sbmlElement : getSbmlElementList(sbmlModel)) {
+ result.add(parse(sbmlElement, sbmlModel));
+ }
+ return result;
+ }
+
+ protected ListOf<org.sbml.jsbml.Reaction> getSbmlElementList(Model sbmlModel) {
+ return sbmlModel.getListOfReactions();
+ }
+
+ protected void mergeLayout(Collection<Reaction> elements, Layout sbmlLayout, Model sbmlModel)
+ throws InvalidInputDataExecption {
+ Set<Reaction> used = new HashSet<>();
+ Map<String, Reaction> elementById = new HashMap<>();
+ for (Reaction species : elements) {
+ if (elementById.get(species.getIdReaction()) != null) {
+ throw new InvalidInputDataExecption("Duplicated reaction id: " + species.getIdReaction());
+ }
+ elementById.put(species.getIdReaction(), species);
+ }
+
+ for (ReactionGlyph glyph : sbmlLayout.getListOfReactionGlyphs()) {
+ Reaction source = elementById.get(glyph.getReaction());
+ if (source == null) {
+ throw new InvalidInputDataExecption("Layout contains invalid Species id: " + glyph.getReaction());
+ }
+ used.add(source);
+ Reaction reactionWithLayout = source.copy();
+ reactionWithLayout.setIdReaction(glyph.getId());
+ for (SpeciesReferenceGlyph speciesGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
+ ReactionNode minervaNode = null;
+ Element minervaElement = minervaModel.getElementByElementId(speciesGlyph.getSpeciesReference());
+ if (minervaElement == null) {
+ throw new InvalidInputDataExecption("Cannot find source reaction node for layouted reaction: "
+ + speciesGlyph.getSpeciesReference() + ", " + glyph.getId());
+ }
+ for (ReactionNode node : reactionWithLayout.getReactionNodes()) {
+ if (node.getElement().equals(minervaElement)) {
+ minervaNode = node;
+ }
+ }
+ if (minervaNode == null) {
+ throw new InvalidInputDataExecption("Cannot find reaction node for layouted reaction: "
+ + speciesGlyph.getSpeciesReference() + ", " + glyph.getId());
+ }
+ minervaElement = minervaModel.getElementByElementId(speciesGlyph.getId());
+ if (minervaElement == null) {
+ throw new InvalidInputDataExecption("Cannot find layouted reaction node for layouted reaction: "
+ + speciesGlyph.getId() + ", " + glyph.getId());
+ }
+ minervaNode.setElement(minervaElement);
+ }
+ try {
+ minervaModel.addReaction(new StateTransitionReaction(reactionWithLayout));
+ } catch (InvalidArgumentException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+ }
+ for (Reaction reaction : elements) {
+ if (!used.contains(reaction)) {
+ logger.warn("Layout doesn't contain information about Element: " + reaction.getIdReaction());
+ } else {
+ minervaModel.removeReaction(reaction);
+ }
+ }
+ }
+
+ protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction, Model sbmlModel) throws InvalidInputDataExecption {
+ Reaction reaction = new Reaction();
+ reaction.setIdReaction(sbmlReaction.getId());
+ if (sbmlReaction.getKineticLaw() != null) {
+ throw new NotImplementedException("KineticLaw not implemented");
+ }
+ for (SpeciesReference reactant : sbmlReaction.getListOfReactants()) {
+ Species element = minervaModel.getElementByElementId(reactant.getSpecies());
+ reaction.addReactant(new Reactant(element));
+ }
+ for (SpeciesReference product : sbmlReaction.getListOfProducts()) {
+ Species element = minervaModel.getElementByElementId(product.getSpecies());
+ reaction.addProduct(new Product(element));
+ }
+
+ for (ModifierSpeciesReference modifier : sbmlReaction.getListOfModifiers()) {
+ Species element = minervaModel.getElementByElementId(modifier.getSpecies());
+ reaction.addModifier(new Modifier(element));
+ }
+
+ return reaction;
+ }
+
+ protected Set<MiriamData> parseAnnotation(Annotation annotation) {
+ if (annotation.getCVTermCount() > 0) {
+ throw new NotImplementedException();
+ }
+ Set<MiriamData> result = new HashSet<>();
+ return result;
+ }
+
+ public void validateReactions(Set<Reaction> reactions) throws InvalidInputDataExecption {
+ for (Reaction reaction : reactions) {
+ if (reaction.getReactants().size() == 0) {
+ throw new InvalidInputDataExecption(
+ eu.getElementTag(reaction) + "At least one reactant is required for reaction");
+ }
+ if (reaction.getProducts().size() == 0) {
+ throw new InvalidInputDataExecption(
+ eu.getElementTag(reaction) + "At least one product is required for reaction");
+ }
+ }
+
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
index d84c48257f2a101a428596cfdaf5de71cf6cc862..ea3fd6196b7c5ce61c2ec8d426cc55f8b82ab46d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
@@ -60,7 +60,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
@Override
- protected List<Element> mergeLayout(List<Element> elements, Layout sbmlLayout, Model sbmlModel)
+ protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
List<Element> result = super.mergeLayout(elements, sbmlLayout, sbmlModel);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..09c74b274e253e3a351041451ea8e71351248769
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+
+@RunWith(Parameterized.class)
+public class SbmlPareserForInvalidReactionTest {
+
+ static Logger logger = Logger.getLogger(SbmlPareserForInvalidReactionTest.class.getName());
+
+ private Path filePath;
+
+ public SbmlPareserForInvalidReactionTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/invalidReaction")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ IConverter converter = new SbmlParser();
+
+ converter.createModel(new ConverterParams().filename(filePath.toString()));
+ fail("Exception expected when parsing file: " + filePath.toString());
+ } catch (InvalidInputDataExecption e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example.xml b/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f12628c5d0ff0c62e09abf8838441f866610c912
--- /dev/null
+++ b/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
+ xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+ level="3" version="1" layout:required="false">
+ <model id="TestModel_with_modifiers">
+ <listOfReactions>
+ <reaction id="Hexokinase" reversible="false" fast="false">
+ </reaction>
+ </listOfReactions>
+ <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:width="400"
+ layout:height="230" />
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="glyph_Hexokinase"
+ layout:reaction="Hexokinase">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ </model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id.xml b/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2+id.xml
similarity index 100%
rename from converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id.xml
rename to converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2+id.xml
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id_level3.xml b/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2+id_level3.xml
similarity index 100%
rename from converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2+id_level3.xml
rename to converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2+id_level3.xml
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2.xml b/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2.xml
similarity index 100%
rename from converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2.xml
rename to converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2.xml
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2_level3.xml b/converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2_level3.xml
similarity index 100%
rename from converter-sbml/testFiles/layoutExample/ReactionGlyph_Example_level2_level3.xml
rename to converter-sbml/testFiles/invalidReaction/ReactionGlyph_Example_level2_level3.xml
diff --git a/converter-sbml/testFiles/layoutExample/Complete_Example.xml b/converter-sbml/testFiles/layoutExample/Complete_Example.xml
index d7081bf344afa5318c871d6c91fcc7e3a1e6e6ac..679d836a8f5839797e5d98d1aa225a82cca3dd39 100644
--- a/converter-sbml/testFiles/layoutExample/Complete_Example.xml
+++ b/converter-sbml/testFiles/layoutExample/Complete_Example.xml
@@ -1,262 +1,273 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
-xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
-level="3" version="1" layout:required="false" >
-<model id="TestModel_with_modifiers" timeUnits="time">
-<listOfUnitDefinitions>
-<unitDefinition id="volume">
-<listOfUnits>
-<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition id="substance">
-<listOfUnits>
-<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition id="time">
-<listOfUnits>
-<unit kind="second" exponent="1" scale="0" multiplier="1"/>
-</listOfUnits>
-</unitDefinition>
-</listOfUnitDefinitions>
-<listOfCompartments>
-<compartment id="Yeast" spatialDimensions="3" units="volume" constant="true"/>
-</listOfCompartments>
-<listOfSpecies>
-<species id="Glucose" compartment="Yeast" substanceUnits="substance"
-hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-<species id="G6P" name="Glucose-6-phosphate" compartment="Yeast"
-substanceUnits="substance" hasOnlySubstanceUnits="false"
-boundaryCondition="false" constant="false"/>
-<species id="ATP" compartment="Yeast" substanceUnits="substance"
-hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-<species id="ADP" compartment="Yeast" substanceUnits="substance"
-hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-<species id="Pi" compartment="Yeast" substanceUnits="substance"
-hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
-</listOfSpecies>
-<listOfReactions>
-<reaction id="Hexokinase" reversible="false" fast="false">
-<listOfReactants>
-<speciesReference id="SpeciesReference_Glucose" species="Glucose"
-stoichiometry="1" constant="true"/>
-<speciesReference id="SpeciesReference_ATP" species="ATP"
-stoichiometry="1" constant="true"/>
-</listOfReactants>
-<listOfProducts>
-<speciesReference id="SpeciesReference_G6P" species="G6P"
-stoichiometry="1" constant="true"/>
-<speciesReference id="SpeciesReference_ADP" species="ADP"
-stoichiometry="1" constant="true"/>
-</listOfProducts>
-<listOfModifiers>
-<modifierSpeciesReference id="ModifierSpeciesReference_G6P" species="G6P"/>
-<modifierSpeciesReference id="ModifierSpeciesReference_Pi" species="Pi"/>
-</listOfModifiers>
-</reaction>
-</listOfReactions>
-<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-<layout:layout layout:id="Layout_1">
-<layout:dimensions layout:width="400" layout:height="230"/>
-<layout:listOfCompartmentGlyphs>
-<layout:compartmentGlyph layout:id="CompartmentGlyph_1" layout:compartment="Yeast">
-<layout:boundingBox layout:id="bb1">
-<layout:position layout:x="5" layout:y="5"/>
-<layout:dimensions layout:width="390" layout:height="220"/>
-</layout:boundingBox>
-</layout:compartmentGlyph>
-</layout:listOfCompartmentGlyphs>
-<layout:listOfSpeciesGlyphs>
-<layout:speciesGlyph layout:id="SpeciesGlyph_Glucose" layout:species="Glucose">
-<layout:boundingBox layout:id="bb2">
-<layout:position layout:x="105" layout:y="20"/>
-<layout:dimensions layout:width="130" layout:height="20"/>
-</layout:boundingBox>
-</layout:speciesGlyph>
-<layout:speciesGlyph layout:id="SpeciesGlyph_G6P" layout:species="G6P">
-<layout:boundingBox layout:id="bb5">
-<layout:position layout:x="50" layout:y="190"/>
-<layout:dimensions layout:width="270" layout:height="20"/>
-</layout:boundingBox>
-</layout:speciesGlyph>
-<layout:speciesGlyph layout:id="SpeciesGlyph_ATP" layout:species="ATP">
-<layout:boundingBox layout:id="bb3">
-<layout:position layout:x="270" layout:y="70"/>
-<layout:dimensions layout:width="80" layout:height="20"/>
-</layout:boundingBox>
-</layout:speciesGlyph>
-<layout:speciesGlyph layout:id="glyph_ADP" layout:species="ADP">
-<layout:boundingBox layout:id="bb4">
-<layout:position layout:x="270" layout:y="140"/>
-<layout:dimensions layout:width="80" layout:height="20"/>
-</layout:boundingBox>
-</layout:speciesGlyph>
-<layout:speciesGlyph layout:id="SpeciesGlyph_Pi" layout:species="Pi">
-<layout:boundingBox layout:id="bb6">
-<layout:position layout:x="50" layout:y="100"/>
-<layout:dimensions layout:width="60" layout:height="20"/>
-</layout:boundingBox>
-</layout:speciesGlyph>
-</layout:listOfSpeciesGlyphs>
-<layout:listOfReactionGlyphs>
-<layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="LineSegment">
-<layout:start layout:x="170" layout:y="100"/>
-<layout:end layout:x="170" layout:y="130"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-<layout:listOfSpeciesReferenceGlyphs>
-<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_Glucose"
-layout:speciesReference="SpeciesReference_Glucose"
-layout:speciesGlyph="SpeciesGlyph_Glucose"
-layout:role="substrate">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="LineSegment">
-<layout:start layout:x="170" layout:y="100"/>
-<layout:end layout:x="170" layout:y="50"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-</layout:speciesReferenceGlyph>
-<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ATP"
-layout:speciesReference="SpeciesReference_ATP"
-layout:speciesGlyph="SpeciesGlyph_ATP"
-layout:role="sidesubstrate">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="CubicBezier">
-<layout:start layout:x="170" layout:y="100"/>
-<layout:end layout:x="260" layout:y="80"/>
-<layout:basePoint1 layout:x="170" layout:y="80"/>
-<layout:basePoint2 layout:x="170" layout:y="80"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-</layout:speciesReferenceGlyph>
-<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_1"
-layout:speciesReference="SpeciesReference_G6P"
-layout:speciesGlyph="SpeciesGlyph_G6P"
-layout:role="product">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="LineSegment">
-<layout:start layout:x="170" layout:y="130"/>
-<layout:end layout:x="170" layout:y="180"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-</layout:speciesReferenceGlyph>
-<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_ADP"
-layout:speciesReference="SpeciesReference_ADP"
-layout:speciesGlyph="glyph_ADP"
-layout:role="sideproduct">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="CubicBezier">
-<layout:start layout:x="170" layout:y="130"/>
-<layout:end layout:x="260" layout:y="150"/>
-<layout:basePoint1 layout:x="170" layout:y="150"/>
-<layout:basePoint2 layout:x="170" layout:y="150"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-</layout:speciesReferenceGlyph>
-<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_G6P_2"
-layout:speciesReference="ModifierSpeciesReference_G6P"
-layout:speciesGlyph="SpeciesGlyph_G6P"
-layout:role="inhibitor">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="CubicBezier">
-<layout:start layout:x="45" layout:y="200"/>
-<layout:end layout:x="165" layout:y="120"/>
-<layout:basePoint1 layout:x="0" layout:y="200"/>
-<layout:basePoint2 layout:x="0" layout:y="120"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-</layout:speciesReferenceGlyph>
-<layout:speciesReferenceGlyph layout:id="SpeciesReferenceGlyph_PI"
-layout:speciesReference="ModifierSpeciesReference_Pi"
-layout:speciesGlyph="SpeciesGlyph_Pi"
-layout:role="activator">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="CubicBezier">
-<layout:start layout:x="115" layout:y="110"/>
-<layout:end layout:x="165" layout:y="110"/>
-<layout:basePoint1 layout:x="140" layout:y="110"/>
-<layout:basePoint2 layout:x="140" layout:y="110"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-</layout:speciesReferenceGlyph>
-</layout:listOfSpeciesReferenceGlyphs>
-</layout:reactionGlyph>
-</layout:listOfReactionGlyphs>
-<layout:listOfTextGlyphs>
-<layout:textGlyph layout:id="TextGlyph_Glucose"
-layout:originOfText="Glucose"
-layout:graphicalObject="SpeciesGlyph_Glucose">
-<layout:boundingBox layout:id="bbA">
-<layout:position layout:x="115" layout:y="20"/>
-<layout:dimensions layout:width="110" layout:height="20"/>
-</layout:boundingBox>
-</layout:textGlyph>
-<layout:textGlyph layout:id="TextGlyph_G6P"
-layout:originOfText="G6P"
-layout:graphicalObject="SpeciesGlyph_G6P">
-<layout:boundingBox layout:id="bbD">
-<layout:position layout:x="60" layout:y="190"/>
-<layout:dimensions layout:width="250" layout:height="20"/>
-</layout:boundingBox>
-</layout:textGlyph>
-<layout:textGlyph layout:id="TextGlyph_ATP"
-layout:originOfText="ATP"
-layout:graphicalObject="SpeciesGlyph_ATP">
-<layout:boundingBox layout:id="bbB">
-<layout:position layout:x="280" layout:y="70"/>
-<layout:dimensions layout:width="60" layout:height="20"/>
-</layout:boundingBox>
-</layout:textGlyph>
-<layout:textGlyph layout:id="TextGlyph_ADP"
-layout:originOfText="ADP"
-layout:graphicalObject="glyph_ADP">
-<layout:boundingBox layout:id="bbC">
-<layout:position layout:x="280" layout:y="140"/>
-<layout:dimensions layout:width="60" layout:height="20"/>
-</layout:boundingBox>
-</layout:textGlyph>
-<layout:textGlyph layout:id="TextGlyph_PI"
-layout:originOfText="Pi"
-layout:graphicalObject="SpeciesGlyph_Pi">
-<layout:boundingBox layout:id="bbE">
-<layout:position layout:x="60" layout:y="100"/>
-<layout:dimensions layout:width="40" layout:height="20"/>
-</layout:boundingBox>
-</layout:textGlyph>
-</layout:listOfTextGlyphs>
-</layout:layout>
-</layout:listOfLayouts>
-</model>
+ xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+ level="3" version="1" layout:required="false">
+ <model id="TestModel_with_modifiers" timeUnits="time">
+ <listOfUnitDefinitions>
+ <unitDefinition id="volume">
+ <listOfUnits>
+ <unit kind="litre" exponent="1" scale="0" multiplier="1" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="substance">
+ <listOfUnits>
+ <unit kind="mole" exponent="1" scale="0" multiplier="1" />
+ </listOfUnits>
+ </unitDefinition>
+ <unitDefinition id="time">
+ <listOfUnits>
+ <unit kind="second" exponent="1" scale="0" multiplier="1" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="Yeast" spatialDimensions="3" units="volume"
+ constant="true" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="Glucose" compartment="Yeast" substanceUnits="substance"
+ hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+ <species id="G6P" name="Glucose-6-phosphate" compartment="Yeast"
+ substanceUnits="substance" hasOnlySubstanceUnits="false"
+ boundaryCondition="false" constant="false" />
+ <species id="ATP" compartment="Yeast" substanceUnits="substance"
+ hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+ <species id="ADP" compartment="Yeast" substanceUnits="substance"
+ hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+ <species id="Pi" compartment="Yeast" substanceUnits="substance"
+ hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="Hexokinase" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference id="SpeciesReference_Glucose"
+ species="Glucose" stoichiometry="1" constant="true" />
+ <speciesReference id="SpeciesReference_ATP"
+ species="ATP" stoichiometry="1" constant="true" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference id="SpeciesReference_G6P"
+ species="G6P" stoichiometry="1" constant="true" />
+ <speciesReference id="SpeciesReference_ADP"
+ species="ADP" stoichiometry="1" constant="true" />
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference id="ModifierSpeciesReference_G6P"
+ species="G6P" />
+ <modifierSpeciesReference id="ModifierSpeciesReference_Pi"
+ species="Pi" />
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <layout:layout layout:id="Layout_1">
+ <layout:dimensions layout:width="400"
+ layout:height="230" />
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:id="CompartmentGlyph_1"
+ layout:compartment="Yeast">
+ <layout:boundingBox layout:id="bb1">
+ <layout:position layout:x="5" layout:y="5" />
+ <layout:dimensions layout:width="390"
+ layout:height="220" />
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Glucose"
+ layout:species="Glucose">
+ <layout:boundingBox layout:id="bb2">
+ <layout:position layout:x="105" layout:y="20" />
+ <layout:dimensions layout:width="130"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_G6P"
+ layout:species="G6P">
+ <layout:boundingBox layout:id="bb5">
+ <layout:position layout:x="50" layout:y="190" />
+ <layout:dimensions layout:width="270"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_ATP"
+ layout:species="ATP">
+ <layout:boundingBox layout:id="bb3">
+ <layout:position layout:x="270" layout:y="70" />
+ <layout:dimensions layout:width="80"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="glyph_ADP"
+ layout:species="ADP">
+ <layout:boundingBox layout:id="bb4">
+ <layout:position layout:x="270" layout:y="140" />
+ <layout:dimensions layout:width="80"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="SpeciesGlyph_Pi"
+ layout:species="Pi">
+ <layout:boundingBox layout:id="bb6">
+ <layout:position layout:x="50" layout:y="100" />
+ <layout:dimensions layout:width="60"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="glyph_Hexokinase"
+ layout:reaction="Hexokinase">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="130" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph
+ layout:id="SpeciesReferenceGlyph_Glucose"
+ layout:speciesReference="SpeciesReference_Glucose"
+ layout:speciesGlyph="SpeciesGlyph_Glucose" layout:role="substrate">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="170" layout:y="50" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph
+ layout:id="SpeciesReferenceGlyph_ATP" layout:speciesReference="SpeciesReference_ATP"
+ layout:speciesGlyph="SpeciesGlyph_ATP" layout:role="sidesubstrate">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="100" />
+ <layout:end layout:x="260" layout:y="80" />
+ <layout:basePoint1 layout:x="170" layout:y="80" />
+ <layout:basePoint2 layout:x="170" layout:y="80" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph
+ layout:id="SpeciesReferenceGlyph_G6P_1" layout:speciesReference="SpeciesReference_G6P"
+ layout:speciesGlyph="SpeciesGlyph_G6P" layout:role="product">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="LineSegment">
+ <layout:start layout:x="170" layout:y="130" />
+ <layout:end layout:x="170" layout:y="180" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph
+ layout:id="SpeciesReferenceGlyph_ADP" layout:speciesReference="SpeciesReference_ADP"
+ layout:speciesGlyph="glyph_ADP" layout:role="sideproduct">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="CubicBezier">
+ <layout:start layout:x="170" layout:y="130" />
+ <layout:end layout:x="260" layout:y="150" />
+ <layout:basePoint1 layout:x="170" layout:y="150" />
+ <layout:basePoint2 layout:x="170" layout:y="150" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph
+ layout:id="SpeciesReferenceGlyph_G6P_2" layout:speciesReference="ModifierSpeciesReference_G6P"
+ layout:speciesGlyph="SpeciesGlyph_G6P" layout:role="inhibitor">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="CubicBezier">
+ <layout:start layout:x="45" layout:y="200" />
+ <layout:end layout:x="165" layout:y="120" />
+ <layout:basePoint1 layout:x="0" layout:y="200" />
+ <layout:basePoint2 layout:x="0" layout:y="120" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph
+ layout:id="SpeciesReferenceGlyph_PI" layout:speciesReference="ModifierSpeciesReference_Pi"
+ layout:speciesGlyph="SpeciesGlyph_Pi" layout:role="activator">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:type="CubicBezier">
+ <layout:start layout:x="115" layout:y="110" />
+ <layout:end layout:x="165" layout:y="110" />
+ <layout:basePoint1 layout:x="140" layout:y="110" />
+ <layout:basePoint2 layout:x="140" layout:y="110" />
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:id="TextGlyph_Glucose"
+ layout:originOfText="Glucose" layout:graphicalObject="SpeciesGlyph_Glucose">
+ <layout:boundingBox layout:id="bbA">
+ <layout:position layout:x="115" layout:y="20" />
+ <layout:dimensions layout:width="110"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_G6P"
+ layout:originOfText="G6P" layout:graphicalObject="SpeciesGlyph_G6P">
+ <layout:boundingBox layout:id="bbD">
+ <layout:position layout:x="60" layout:y="190" />
+ <layout:dimensions layout:width="250"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_ATP"
+ layout:originOfText="ATP" layout:graphicalObject="SpeciesGlyph_ATP">
+ <layout:boundingBox layout:id="bbB">
+ <layout:position layout:x="280" layout:y="70" />
+ <layout:dimensions layout:width="60"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_ADP"
+ layout:originOfText="ADP" layout:graphicalObject="glyph_ADP">
+ <layout:boundingBox layout:id="bbC">
+ <layout:position layout:x="280" layout:y="140" />
+ <layout:dimensions layout:width="60"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph_PI"
+ layout:originOfText="Pi" layout:graphicalObject="SpeciesGlyph_Pi">
+ <layout:boundingBox layout:id="bbE">
+ <layout:position layout:x="60" layout:y="100" />
+ <layout:dimensions layout:width="40"
+ layout:height="20" />
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ </model>
</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example.xml b/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example.xml
deleted file mode 100644
index 189da3871f8be71bd50ceec690db47fe7725ccb2..0000000000000000000000000000000000000000
--- a/converter-sbml/testFiles/layoutExample/ReactionGlyph_Example.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
-xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
-level="3" version="1" layout:required="false" >
-<model id="TestModel_with_modifiers">
-<listOfReactions>
-<reaction id="Hexokinase" reversible="false" fast="false">
-</reaction>
-</listOfReactions>
-<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-<layout:layout layout:id="Layout_1">
-<layout:dimensions layout:width="400" layout:height="230"/>
-<layout:listOfReactionGlyphs>
-<layout:reactionGlyph layout:id="glyph_Hexokinase" layout:reaction="Hexokinase">
-<layout:curve>
-<layout:listOfCurveSegments>
-<layout:curveSegment
-xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-xsi:type="LineSegment">
-<layout:start layout:x="170" layout:y="100"/>
-<layout:end layout:x="170" layout:y="130"/>
-</layout:curveSegment>
-</layout:listOfCurveSegments>
-</layout:curve>
-<layout:listOfSpeciesReferenceGlyphs>
-</layout:listOfSpeciesReferenceGlyphs>
-</layout:reactionGlyph>
-</layout:listOfReactionGlyphs>
-</layout:layout>
-</layout:listOfLayouts>
-</model>
-</sbml>
\ No newline at end of file