From 6cccf92891cd9d6975194450c35070a235db6ee3 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 16 Nov 2018 15:52:26 +0100
Subject: [PATCH] toString uses UTF-8 encoding
---
.../converter/model/sbml/SbmlExporter.java | 51 +++++++++++--------
1 file changed, 29 insertions(+), 22 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 3d860fecee..e8129d4803 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.io.UnsupportedEncodingException;
+
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
@@ -14,6 +16,7 @@ import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.render.GlobalRenderInformation;
import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
+import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
@@ -25,30 +28,34 @@ public class SbmlExporter {
public String toXml(lcsb.mapviewer.model.map.model.Model model)
throws SBMLException, XMLStreamException, InconsistentModelException {
- SBMLDocument doc = new SBMLDocument(3, 1);
- Model result = doc.createModel(model.getIdModel());
- result.setName(model.getName());
- Layout layout = createSbmlLayout(model, result);
+ try {
+ SBMLDocument doc = new SBMLDocument(3, 1);
+ Model result = doc.createModel(model.getIdModel());
+ result.setName(model.getName());
+ Layout layout = createSbmlLayout(model, result);
- SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
- SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
- compartmentExporter);
- SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter,
- compartmentExporter);
- SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
- SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
- SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
+ SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
+ SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+ compartmentExporter);
+ SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter,
+ compartmentExporter);
+ SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
+ SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
+ SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
- compartmentExporter.exportElements(result);
- speciesExporter.exportElements(result);
- reactionExporter.exportElements(result);
- unitExporter.exportUnits(result);
- parameterExporter.exportParameter(result);
- functionExporter.exportFunction(result);
+ compartmentExporter.exportElements(result);
+ speciesExporter.exportElements(result);
+ reactionExporter.exportElements(result);
+ unitExporter.exportUnits(result);
+ parameterExporter.exportParameter(result);
+ functionExporter.exportFunction(result);
- ByteArrayOutputStream stream = new ByteArrayOutputStream();
- SBMLWriter.write(doc, stream, "minerva", "1.0");
- return stream.toString();
+ ByteArrayOutputStream stream = new ByteArrayOutputStream();
+ SBMLWriter.write(doc, stream, "minerva", "1.0");
+ return stream.toString("UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ throw new InvalidStateException(e);
+ }
}
public Layout createSbmlLayout(lcsb.mapviewer.model.map.model.Model model, Model result) {
@@ -68,7 +75,7 @@ public class SbmlExporter {
layout.setDimensions(dimensions);
layoutPlugin.add(layout);
result.addExtension("layout", layoutPlugin);
-
+
createSbmlRenderPlugin(layout, result);
return layout;
}
--
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