prefixing should be done only on unprefixed reactions

CHANGELOG

@@ -4,6 +4,8 @@ minerva (14.0.8) stable; urgency=medium
   * Bug fix: upload of data overlay with two entries having different uniprot
     identifier but pointing to the same gene crashed (#1083)
   * Bug fix: don't allow to remove plugin twice (#1081)
+  * Bug fix: upload of SBML file with very short reaction length could produce
+    a map that couldn't be exported to SBML anymore (#1078)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 23 Jan 2020 12:00:00 +0200
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -633,9 +633,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
   }
 
   protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction) throws InvalidInputDataExecption {
-    Reaction reaction = new Reaction();
+    Reaction reaction = new Reaction(sbmlReaction.getId());
     assignBioEntityData(sbmlReaction, reaction);
-    reaction.setIdReaction(sbmlReaction.getId());
     reaction.setReversible(sbmlReaction.isReversible());
     if (sbmlReaction.getKineticLaw() != null) {
       if (sbmlReaction.getKineticLaw().getMath() == null) {

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

@@ -12,8 +12,7 @@ import org.junit.Test;
 
 import lcsb.mapviewer.commands.CreateHierarchyCommand;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.*;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.*;
@@ -232,4 +231,11 @@ public class SbmlParserTest extends SbmlTestFunctions {
         reactant.getLine().getBeginPoint().distance(120, 40), Configuration.EPSILON);
   }
 
+  @Test
+  public void xxx() throws FileNotFoundException, InvalidInputDataExecption, ConverterException {
+    Model m = parser.createModel(new ConverterParams().filename("testFiles/problematic_layout.xml"));
+    String xml = parser.model2String(m);
+    assertNotNull(xml);
+  }
+
 }

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java

@@ -109,10 +109,6 @@ public abstract class ApplyLayoutModelCommand extends ModelCommand {
     return addReactionPrefixes;
   }
 
-  public void setAddReactionPrefixes(boolean addReactionPrefixes) {
-    this.addReactionPrefixes = addReactionPrefixes;
-  }
-
   protected String getNextId() {
     return (idCounter++) + "";
   }

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java

@@ -5,6 +5,7 @@ import java.util.*;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.hibernate.sql.ordering.antlr.GeneratedOrderByLexer;
 
 import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.common.Configuration;
@@ -23,6 +24,7 @@ import lcsb.mapviewer.model.map.reaction.type.*;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
 
@@ -218,9 +220,13 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     modifyModifiers(reaction, middle);
 
     if (super.isAddReactionPrefixes()) {
-      super.getModel().removeReaction(reaction);
-      reaction.setIdReaction("reaction_glyph_" + getNextId() + "__" + reaction.getIdReaction());
-      super.getModel().addReaction(reaction);
+      if (reaction.getIdReaction().contains("__")) {
+        logger.warn(new ElementUtils().getElementTag(reaction) + "Reaction identifier already prefixed");
+      } else {
+        super.getModel().removeReaction(reaction);
+        reaction.setIdReaction("reaction_glyph_" + getNextId() + "__" + reaction.getIdReaction());
+        super.getModel().addReaction(reaction);
+      }
     }
   }