export of old map (uploaded before 14.0.0 ) to SBML produced invalid SBML

CHANGELOG

@@ -16,6 +16,8 @@ minerva (14.0.3) stable; urgency=medium
   * Bug fix: opening map with no available background crashed (#964)
   * Bug fix: uploading SBGN file that does not pass xsd validation provides a 
     warning, but does not fail upload (#937)
+  * Bug fix: export of the map to SBML that was imported with older version 
+    (below 14.0.0) didn't produce valid SBML (#970)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Oct 2019 9:00:00 +0200
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java

@@ -27,7 +27,6 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
 
   protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph speciesGlyph) {
     BoundingBox boundingBox = new BoundingBox();
-
     boundingBox.setPosition(new Point(element.getX(), element.getY(), element.getZ()));
     Dimensions dimensions = new Dimensions();
     dimensions.setWidth(element.getWidth());

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java

 package lcsb.mapviewer.converter.model.sbml.species;
 
-import java.awt.*;
+import java.awt.Color;
 import java.util.*;
-import java.util.List;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ext.layout.*;
-import org.sbml.jsbml.ext.layout.Point;
 import org.sbml.jsbml.ext.multi.*;
 import org.sbml.jsbml.ext.render.*;
-import org.sbml.jsbml.ext.render.Rectangle;
 
 import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
@@ -335,14 +332,21 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
     if (element.getInitialConcentration() != null) {
       result.setInitialConcentration(element.getInitialConcentration());
     }
+    if (element.getInitialAmount() == null && element.getInitialConcentration() == null) {
+      result.setInitialConcentration(0);
+    }
     if (element.hasOnlySubstanceUnits() != null) {
       result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
     }
     if (element.getBoundaryCondition() != null) {
       result.setBoundaryCondition(element.getBoundaryCondition());
+    } else {
+      result.setBoundaryCondition(false);
     }
     if (element.getConstant() != null) {
       result.setConstant(element.getConstant());
+    } else {
+      result.setConstant(false);
     }
     if (isExtensionEnabled(SbmlExtension.MULTI)) {
       assignMultiExtensionData(element, result);

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java

@@ -19,6 +19,7 @@ import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
     ElementPropertiesExport.class,
     ElementPropertiesExportToMultiTest.class,
     ElementPropertiesExportToLayoutTest.class,
+    GeneratedSbmlValidationTests.class,
     MultiParserTest.class,
     ReactionPropertiesExportToMultiTest.class,
     SbmlBioEntityExporterTest.class,

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GeneratedSbmlValidationTests.java

+package lcsb.mapviewer.converter.model.sbml;
+
+import java.io.IOException;
+import java.util.*;
+
+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 lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.ZIndexPopulator;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+@RunWith(Parameterized.class)
+public class GeneratedSbmlValidationTests extends SbmlTestFunctions {
+  Logger logger = LogManager.getLogger();
+
+  Model model ;
+
+  public GeneratedSbmlValidationTests(Model model, String name) {
+    this.model= model;
+  }
+
+  @Parameters(name = "{index}: {1}")
+  public static Collection<Object[]> data() throws Exception {
+    List<Object[]> result = new ArrayList<>();
+    result.add(createRow( createModelWithSingleSpecies() ));
+    return result;
+  }
+
+  private static Object[] createRow(Model model) {
+    new ZIndexPopulator().populateZIndex(model);
+    return new Object[] {model, model.getName()};
+  }
+
+  private static Model createModelWithSingleSpecies() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    model.setName("Single species");
+    Species species = new GenericProtein("id");
+    species.setBoundaryCondition(null);
+    species.setInitialConcentration(null);
+    species.setInitialAmount(null);
+    species.setConstant(null);
+    model.addElement(species);
+    new ApplySimpleLayoutModelCommand(model).execute();
+    return model;
+  }
+  
+  @Test
+  public void testIsValidSbml() throws Exception {
+    SbmlParser parser = new SbmlParser();
+    String xml = parser.model2String(model);
+
+    validateSBML(xml, "xxx");
+  }
+
+}

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java

 package lcsb.mapviewer.converter.model.sbml;
 
-import java.awt.*;
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Desktop;
 import java.awt.geom.Point2D;
 import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.util.List;
 
+import org.apache.http.HttpEntity;
+import org.apache.http.client.ClientProtocolException;
+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.log4j.Logger;
 import org.apache.logging.log4j.core.LogEvent;
 import org.junit.*;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
 
-import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.common.UnitTestFailedWatcher;
+import lcsb.mapviewer.common.*;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.graphics.*;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
@@ -136,4 +150,30 @@ public class SbmlTestFunctions {
     return model2;
   }
 
+  protected void validateSBML(String xmlContent, String filename) throws IOException, ClientProtocolException, InvalidXmlSchemaException {
+    CloseableHttpClient httpClient = HttpClients.createDefault();
+    HttpPost uploadFile = new HttpPost("http://sbml.org/validator/");
+    MultipartEntityBuilder builder = MultipartEntityBuilder.create();
+    builder.addTextBody("file", xmlContent, ContentType.TEXT_PLAIN);
+    builder.addBinaryBody(
+        "file",
+        new ByteArrayInputStream(xmlContent.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());
+  }
+
+
 }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlValidationTests.java

 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;
 
@@ -52,28 +37,7 @@ public class SbmlValidationTests extends SbmlTestFunctions {
     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());
+    validateSBML(xml, filename);
   }
 
 }