info about species is added to marker

CHANGELOG

@@ -2,6 +2,8 @@ minerva (16.0.0~alpha.2) stable; urgency=medium
   * Backward incompatibility: debian package cannot be upgraded from version
     prior to 12.1.0 (#1464)
   * Small improvement: homomultimer information is provided in API (#1468)
+  * Small improvement: missing info about species for SBML parsing warning
+    (#1472)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Mar 2021 10:00:00 +0200
 

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

@@ -8,6 +8,8 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.species.*;
 
 public enum SBOTermSpeciesType {
@@ -50,7 +52,7 @@ public enum SBOTermSpeciesType {
     this.hypothetical = hypothetical;
   }
 
-  private static SBOTermSpeciesType getTypeSBOTerm(String sboTerm) {
+  private static SBOTermSpeciesType getTypeSBOTerm(String sboTerm, org.sbml.jsbml.Species species) {
     if (sboTerm == null || sboTerm.isEmpty()) {
       return SIMPLE_MOLECULE;
     }
@@ -63,17 +65,18 @@ public enum SBOTermSpeciesType {
       }
     }
     if (result == null) {
-      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for species");
+      logger.warn(SbmlModelUtils.createMarker(ProjectLogEntryType.PARSING_ISSUE, species),
+          "Don't know how to handle SBOTerm " + sboTerm);
       result = SIMPLE_MOLECULE;
     }
     return result;
   }
 
-  public static Species createElementForSBOTerm(String sboTerm, String elementId) {
+  public static Species createElementForSBOTerm(String sboTerm, org.sbml.jsbml.Species species) {
     try {
-      SBOTermSpeciesType type = getTypeSBOTerm(sboTerm);
+      SBOTermSpeciesType type = getTypeSBOTerm(sboTerm, species);
       Class<? extends Species> clazz = type.clazz;
-      Species result = clazz.getConstructor(String.class).newInstance(elementId);
+      Species result = clazz.getConstructor(String.class).newInstance(species.getId());
       if (type.hypothetical) {
         result.setHypothetical(true);
       }

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

@@ -514,7 +514,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
   @Override
   protected Species parse(org.sbml.jsbml.Species species) throws InvalidInputDataExecption {
     String sboTerm = extractSBOTermFromSpecies(species);
-    Species result = SBOTermSpeciesType.createElementForSBOTerm(sboTerm, species.getId());
+    Species result = SBOTermSpeciesType.createElementForSBOTerm(sboTerm, species);
     if (!Double.isNaN(species.getInitialAmount())) {
       result.setInitialAmount(species.getInitialAmount());
     }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/AllSbmlSpeciesTests.java

@@ -6,10 +6,11 @@ import org.junit.runners.Suite.SuiteClasses;
 
 @RunWith(Suite.class)
 @SuiteClasses({
-  ModificationResidueExporterTest.class,
-  SbmlSpeciesExporterRenderShapeTest.class,
-  SbmlSpeciesExporterTest.class,
-  SbmlSpeciesParserTest.class })
+    ModificationResidueExporterTest.class,
+    SbmlSpeciesExporterRenderShapeTest.class,
+    SbmlSpeciesExporterTest.class,
+    SbmlSpeciesParserTest.class,
+    SBOTermSpeciesTypeTest.class })
 public class AllSbmlSpeciesTests {
 
 }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesTypeTest.java

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.Test;
+import org.sbml.jsbml.Species;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.model.map.species.Element;
+
+public class SBOTermSpeciesTypeTest extends SbmlTestFunctions {
+
+  @Test
+  public void testCreateElementForSBOTerm() {
+    Species species = new Species(3, 2);
+    species.setSBOTerm("SBO:0000000");
+    Element element = SBOTermSpeciesType.createElementForSBOTerm("SBO:0000000", species);
+    assertNotNull(element);
+    assertEquals(1, super.getWarnings().size());
+    assertNotNull(super.getWarnings().get(0).getMarker());
+  }
+
+}