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Commit 4a474119 authored by Piotr Gawron's avatar Piotr Gawron
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export of reaction where product has no valid line doesn't crash

parent 6d3f3f23
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
View file @ 4a474119
......@@ -48,6 +48,7 @@ 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.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sbml.jsbml.Reaction> {
/**
......@@ -217,8 +218,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
assignStyleToGlyph(reactantGlyph, style);
}
Point p = reactantGlyph.getCurve().getCurveSegment(0).getStart();
reactantEndPoint = new Point2D.Double(p.getX(), p.getY());
if (reactantGlyph.getCurve().getCurveSegmentCount() > 0) {
Point p = reactantGlyph.getCurve().getCurveSegment(0).getStart();
reactantEndPoint = new Point2D.Double(p.getX(), p.getY());
} else {
reactantEndPoint = new Point2D.Double(reactant.getElement().getCenterX(), reactant.getElement().getCenterY());
}
}
if (reactionGlyph.getCurve().getCurveSegmentCount() > 0) {
Point p = reactionGlyph.getCurve().getCurveSegment(reactionGlyph.getCurve().getCurveSegmentCount() - 1).getEnd();
......@@ -254,8 +259,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
assignStyleToGlyph(productGlyph, style);
}
Point p = productGlyph.getCurve().getCurveSegment(0).getStart();
productStartPoint = new Point2D.Double(p.getX(), p.getY());
if (productGlyph.getCurve().getCurveSegmentCount() > 0) {
Point p = productGlyph.getCurve().getCurveSegment(0).getStart();
productStartPoint = new Point2D.Double(p.getX(), p.getY());
} else {
productStartPoint = new Point2D.Double(product.getElement().getCenterX(), product.getElement().getCenterY());
}
}
if (segmentCount < reactionGlyph.getCurve().getCurveSegmentCount()) {
......@@ -360,6 +369,9 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
curve.addCurveSegment(segment);
}
}
if (curve.getCurveSegmentCount() == 0) {
logger.warn(new ElementUtils().getElementTag(node) + " Problematic line");
}
return curve;
}
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
View file @ 4a474119
......@@ -672,6 +672,21 @@ public class SbmlExporterTest extends SbmlTestFunctions {
ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
assertEquals(0, comparator.compare(lines1, lines2));
}
@Test
public void testExportIronMetabolismReaction() throws Exception {
try {
Model originalModel = new CellDesignerXmlParser()
.createModel(new ConverterParams().filename("testFiles/cell_designer_problems/iron_metabolism_reaction.xml"));
exporter.setProvideDefaults(false);
String xml = exporter.toXml(originalModel);
assertNotNull(xml);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
converter-sbml/testFiles/cell_designer_problems/iron_metabolism_reaction.xml 0 → 100644
View file @ 4a474119
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="Dopamine_Neurotransmitter_Release_Cycle" id="A_comprehensive_Parkinsons_disease_map">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="9000" sizeY="5500"/>
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias id="csa106" species="irme_458">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="2247.5" y="2007.0" w="103.0" h="171.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:backupSize w="0.0" h="0.0"/>
<celldesigner:backupView state="none"/>
<celldesigner:usualView>
<celldesigner:boxSize width="103.0" height="171.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa10326" species="irme_72">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="2378.000000000001" y="2072.166666666668" w="40.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:boxSize width="40.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ff9999ff" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="7906.815893308081" y="5845.130208333333"/>
<celldesigner:boxSize width="40.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ff9999ff" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins/>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00539" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00540" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00541" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00542" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00543" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="5" id="5" name="Mitochondrial_space_ROS_space_Metabolism" size="1" units="volume" outside="default"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="irme_458" id="irme_458" name="labile iron pool" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:hypothetical>true</celldesigner:hypothetical>
<celldesigner:name>labile iron pool</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#irme_458">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:27293957"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="irme_72" id="irme_72" name="Fe2_plus_" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>ION</celldesigner:class>
<celldesigner:name>Fe2_plus_</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re4888" id="re4888" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="irme_458" alias="csa106">
<celldesigner:linkAnchor position="E"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="irme_72" alias="sa10326">
<celldesigner:linkAnchor position="W"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="horizontal"/>
<celldesigner:lineDirection index="1" value="vertical"/>
<celldesigner:lineDirection index="2" value="horizontal"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.8391667847539281,0.009990080770847953 0.8393084880263331,-0.0019129941901638858</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#re4888">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:25231526"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:26106291"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00414" species="irme_458">
<annotation>
<celldesigner:extension>
<celldesigner:alias>csa106</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00415" species="irme_72">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa10326</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
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