Merge branch '1475-sbml-conversion-individual-source-sink-objects-for-all-reactions' into 'master'

Resolve "SBML conversion: individual source/sink objects for all reactions"

Closes #1475

See merge request !1295

CHANGELOG

 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: artifitial source and sink is created separately for
+    each uncomplete reaction (#1475)
   * Small improvement: homomultimer information is provided in API (#1468)
   * Small improvement: missing info about species for SBML parsing warning
     (#1472)

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

@@ -26,8 +26,7 @@ import lcsb.mapviewer.model.map.species.field.*;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
-  private static String ARTIFITIAL_SINK_ID = "sbml_artifitial_sink";
-  private static String ARTIFITIAL_SOURCE_ID = "sbml_artifitial_source";
+  private static String ARTIFITIAL_ID = "sbml_artifitial_";
   Logger logger = LogManager.getLogger();
 
   Map<String, String> structuralStateIdMap = new HashMap<>();
@@ -433,8 +432,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
         speciesId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId()).getSpeciesInstance())
             .getId();
       } else {
-        if (!element.getElementId().equals(ARTIFITIAL_SINK_ID)
-            && !element.getElementId().equals(ARTIFITIAL_SOURCE_ID)) {
+        if (!element.getElementId().startsWith(ARTIFITIAL_ID)) {
           compartmentId = getSbmlModel().getSpecies(element.getElementId()).getCompartment();
         }
       }
@@ -547,22 +545,16 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
   }
 
   public Species getArtifitialInput() {
-    Species result = getMinervaModel().getElementByElementId(ARTIFITIAL_SOURCE_ID);
-    if (result == null) {
-      result = new Unknown(ARTIFITIAL_SOURCE_ID);
-      result.setName("Artifitial source");
-      getMinervaModel().addElement(result);
-    }
+    Species result = new Unknown(ARTIFITIAL_ID + getNextId());
+    result.setName("Artifitial source");
+    getMinervaModel().addElement(result);
     return result;
   }
 
   public Species getArtifitialOutput() {
-    Species result = getMinervaModel().getElementByElementId(ARTIFITIAL_SINK_ID);
-    if (result == null) {
-      result = new Degraded(ARTIFITIAL_SINK_ID);
-      result.setName("Artifitial sink");
-      getMinervaModel().addElement(result);
-    }
+    Species result = new Degraded(ARTIFITIAL_ID + getNextId());
+    result.setName("Artifitial sink");
+    getMinervaModel().addElement(result);
     return result;
   }