From 228abca827f4a10536080639f29bc1053aa0360e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Mar 2018 10:07:33 +0100
Subject: [PATCH] when sbo term for reaction didn't exists there was exception
thrown
---
converter-sbml/.gitignore | 2 +
.../sbml/reaction/SbmlReactionExporter.java | 11 +++-
.../model/sbml/AllSbmlConverterTests.java | 6 +-
.../reaction/AllSbmlReactionParserTests.java | 13 ++++
.../reaction/SbmlReactionExporterTest.java | 62 +++++++++++++++++++
5 files changed, 90 insertions(+), 4 deletions(-)
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
diff --git a/converter-sbml/.gitignore b/converter-sbml/.gitignore
index 3ef28bc255..b63db0be70 100644
--- a/converter-sbml/.gitignore
+++ b/converter-sbml/.gitignore
@@ -1,3 +1,5 @@
+.settings/org.eclipse.wst.validation.prefs
+
/bin/
tmp.png
tmp.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index ef9da4db73..59dce0b23a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -10,6 +10,7 @@ import org.apache.log4j.Logger;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.KineticLaw;
import org.sbml.jsbml.LocalParameter;
+import org.sbml.jsbml.Model;
import org.sbml.jsbml.SimpleSpeciesReference;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
@@ -63,7 +64,10 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
result = getSbmlModel().createReaction(reactionId);
result.setReversible(reaction.isReversible());
- result.setSBOTerm(SBOTermReactionType.getTermByType(reaction.getClass()));
+ String sboTerm = SBOTermReactionType.getTermByType(reaction.getClass());
+ if (sboTerm != null) {
+ result.setSBOTerm(sboTerm);
+ }
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
@@ -222,4 +226,9 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
return curve;
}
+ @Override
+ protected void setSbmlModel(Model sbmlModel) {
+ super.setSbmlModel(sbmlModel);
+ }
+
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index 8996139330..30246e7ed2 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -4,16 +4,16 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
-import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParserTest;
+import lcsb.mapviewer.converter.model.sbml.reaction.AllSbmlReactionParserTests;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParserTest;
@RunWith(Suite.class)
-@SuiteClasses({ GenericSbmlParserTest.class, //
+@SuiteClasses({ AllSbmlReactionParserTests.class, //
+ GenericSbmlParserTest.class, //
GenericSbmlToXmlParserTest.class, //
SbmlExporterTest.class, //
SbmlPareserForInvalidReactionTest.class, //
SbmlParserTest.class, //
- SbmlReactionParserTest.class, //
SbmlSpeciesParserTest.class,//
})
public class AllSbmlConverterTests {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
new file mode 100644
index 0000000000..50a0ba00c3
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
@@ -0,0 +1,13 @@
+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SbmlReactionExporterTest.class, //
+ SbmlReactionParserTest.class //
+})
+public class AllSbmlReactionParserTests {
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
new file mode 100644
index 0000000000..dd090c25ea
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
@@ -0,0 +1,62 @@
+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.Test;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SbmlReactionExporterTest {
+
+ @Test
+ public void testTriggerReactionToSbml() throws InconsistentModelException {
+ ModelFullIndexed model = new ModelFullIndexed(null);
+
+ SbmlReactionExporter exporter = createExporter(model);
+ org.sbml.jsbml.Reaction result = exporter.createSbmlElement(new TriggerReaction());
+ assertNotNull(result);
+ }
+
+ private SbmlReactionExporter createExporter(ModelFullIndexed model) {
+ SBMLDocument doc = new SBMLDocument(3, 1);
+ Model result = doc.createModel(model.getIdModel());
+ result.setName(model.getName());
+ LayoutModelPlugin plugin = new LayoutModelPlugin(result);
+
+ Layout layout = new Layout();
+ Dimensions dimensions = new Dimensions();
+ if (model.getHeight() != null) {
+ dimensions.setHeight(model.getHeight());
+ } else {
+ dimensions.setHeight(640);
+ }
+ if (model.getWidth() != null) {
+ dimensions.setWidth(model.getWidth());
+ } else {
+ dimensions.setWidth(480);
+ }
+ layout.setDimensions(dimensions);
+ plugin.add(layout);
+ result.addExtension("layout", plugin);
+
+ SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
+ SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+ compartmentExporter);
+
+ SbmlReactionExporter exporter = new SbmlReactionExporter(layout, model, speciesExporter, compartmentExporter);
+ exporter.setSbmlModel(result);
+ return exporter;
+ }
+
+}
--
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