sbml file always contain model identifier

CHANGELOG

@@ -11,6 +11,7 @@ minerva (14.0.5) stable; urgency=medium
   * Bug fix: search for NADH drug resulted in drug with empty name (#1018)
   * Bug fix: export to SBML didn't handle properly arrows (#1015)
   * Bug fix: Font colour of text area was preserved in Empty view (#1014)
+  * Bug fix: exported sbml file always contain model identifier (#1013)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 02 Dec 2019 16:00:00 +0200
 

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

@@ -79,6 +79,9 @@ public class SbmlExporter {
     } catch (IllegalArgumentException e) {
       logger.warn("Invalid model identifier: \"" + model.getIdModel() + "\". Ignoring.");
     }
+    if (model.getIdModel() == null || model.getIdModel().isEmpty()) {
+      model.setIdModel("unknown");
+    }
     result.setName(model.getName());
     try {
       result.setNotes(NotesUtility.prepareEscapedXmlNotes(model.getNotes()));

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

@@ -3,8 +3,8 @@ package lcsb.mapviewer.converter.model.sbml;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 
-import java.io.File;
-import java.io.IOException;
+import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.*;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -17,7 +17,8 @@ import org.junit.runner.RunWith;
 import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
-import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.*;
+import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 
@@ -50,26 +51,32 @@ public class GenericSbmlToXmlParserTest extends SbmlTestFunctions {
 
   @Test
   public void toXmlModelTest() throws Exception {
-    String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
-
     SbmlParser converter = new SbmlParser();
-    converter.setProvideDefaults(false);
 
     Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
-    model.setName(null);
+    testSbmlSerialization(model);
+  }
+
+  private void testSbmlSerialization(Model model) throws InconsistentModelException,
+      IOException, ConverterException, InvalidInputDataExecption, FileNotFoundException {
 
-    String pathWithouExtension = dir + "/"
-        + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
-    String xmlFilePath = pathWithouExtension.concat(".xml");
-    converter.model2File(model, xmlFilePath);
+    SbmlParser converter = new SbmlParser();
+    converter.setProvideDefaults(false);
+
+    String xml = converter.model2String(model);
+    InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+    
+    Model model2 = converter.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
 
-    Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
+    model.setName(null);
     model2.setName(null);
 
+    model.setIdModel("unk");
+    model2.setIdModel("unk");
+
     assertNotNull(model2);
     ModelComparator comparator = new ModelComparator(1.0);
     assertEquals(0, comparator.compare(model, model2));
-    FileUtils.deleteDirectory(new File(dir));
   }
 
 }