diff --git a/CHANGELOG b/CHANGELOG
index a6e36d2891c1ec9e873814281574adc94ddd82db..86db56ad63814bb83ac79ddd4fb93b101f209299 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,4 +1,5 @@
minerva (14.0.0~beta.2) unstable; urgency=low
+ * Bug fix: exported SBML passes online validation (#831)
* Bug fix: allow user to remove own comments (#931)
* Bug fix: validation of project name length is provided (#950)
* Bug fix: after reducing privileges on himself interface is refreshed (#948)
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 4bf203532dbe74413bec5d4d06f29d0be383bcfc..d4184cb7b4e211f4b6370c32635b14e4976af7a3 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
@@ -1,16 +1,15 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
-import java.awt.*;
+import java.awt.BasicStroke;
+import java.awt.Stroke;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.util.*;
-import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.*;
import org.sbml.jsbml.ext.layout.*;
-import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.render.*;
import org.w3c.dom.Node;
@@ -237,13 +236,45 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
reactionGlyph.setBoundingBox(new BoundingBox());
}
if (reactionGlyph.getBoundingBox().getPosition() == null) {
- reactionGlyph.getBoundingBox().setPosition(new Point());
+ reactionGlyph.getBoundingBox().setPosition(curveToPoint(reactionGlyph.getCurve()));
+ reactionGlyph.getBoundingBox().setDimensions(curveToDimension(reactionGlyph.getCurve()));
}
reactionGlyph.getBoundingBox().getPosition().setZ(reaction.getZ());
removeColinearPoints(reactionGlyph);
}
+ private Dimensions curveToDimension(Curve curve) {
+ Point p = curveToPoint(curve);
+ double x = Double.MIN_VALUE;
+ double y = Double.MIN_VALUE;
+ for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
+ LineSegment segment = (LineSegment) curve.getCurveSegment(i);
+ x = Math.max(x, segment.getStart().getX());
+ x = Math.max(x, segment.getEnd().getX());
+
+ y = Math.max(y, segment.getStart().getY());
+ y = Math.max(y, segment.getEnd().getY());
+
+ }
+ return new Dimensions(x - p.getX(), y - p.getY(), 0, getSbmlModel().getLevel(), getSbmlModel().getVersion());
+ }
+
+ private Point curveToPoint(Curve curve) {
+ double x = Double.MAX_VALUE;
+ double y = Double.MAX_VALUE;
+ for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
+ LineSegment segment = (LineSegment) curve.getCurveSegment(i);
+ x = Math.min(x, segment.getStart().getX());
+ x = Math.min(x, segment.getEnd().getX());
+
+ y = Math.min(y, segment.getStart().getY());
+ y = Math.min(y, segment.getEnd().getY());
+
+ }
+ return new Point(x, y);
+ }
+
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
int separatorIndex = glyphId.indexOf("__");
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 69a6def9d470176ca912ff0471997393eaf21efd..bfd1a1fb25345e09d433aabbf1e5449b19457457 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
@@ -26,6 +26,7 @@ import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
SbmlExporterFromCellDesignerTest.class,
SbmlPareserForInvalidReactionTest.class,
SbmlParserTest.class,
+ SbmlValidationTests.class,
})
public class AllSbmlConverterTests {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlValidationTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlValidationTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..171cd9c3bfd8048a478c0efc245912079228149c
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlValidationTests.java
@@ -0,0 +1,79 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.*;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.mime.MultipartEntityBuilder;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.util.EntityUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.model.Model;
+
+@RunWith(Parameterized.class)
+public class SbmlValidationTests extends SbmlTestFunctions {
+ Logger logger = LogManager.getLogger();
+
+ String filename;
+
+ public SbmlValidationTests(String filename) {
+ this.filename = filename;
+ }
+
+ @Parameters(name = "{0}")
+ public static Collection<Object[]> data() throws IOException {
+ List<Object[]> result = new ArrayList<>();
+ result.add(new Object[] { "testFiles/small/empty.xml" });
+ result.add(new Object[] { "testFiles/small/reaction/dissociation.xml" });
+ return result;
+ }
+
+ @Test
+ public void testIsValidSbml() throws Exception {
+ SbmlParser parser = new SbmlParser();
+ Model model = parser.createModel(new ConverterParams().filename(filename));
+ String xml = parser.model2String(model);
+
+ CloseableHttpClient httpClient = HttpClients.createDefault();
+ HttpPost uploadFile = new HttpPost("http://sbml.org/validator/");
+ MultipartEntityBuilder builder = MultipartEntityBuilder.create();
+ builder.addTextBody("file", xml, ContentType.TEXT_PLAIN);
+ builder.addBinaryBody(
+ "file",
+ new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)),
+ ContentType.APPLICATION_OCTET_STREAM,
+ filename);
+ builder.addTextBody("output", "xml", ContentType.TEXT_PLAIN);
+ builder.addTextBody("offcheck", "u,r", ContentType.TEXT_PLAIN);
+
+ HttpEntity multipart = builder.build();
+ uploadFile.setEntity(multipart);
+ CloseableHttpResponse response = httpClient.execute(uploadFile);
+ String responseXml = EntityUtils.toString(response.getEntity());
+ Document document = XmlParser.getXmlDocumentFromString(responseXml);
+ List<Node> problems = XmlParser.getAllNotNecessirellyDirectChild("problem", document);
+ if (problems.size() > 0) {
+ logger.debug(responseXml);
+ }
+ assertEquals("SBML is invalid", 0, problems.size());
+ }
+
+}