when target or source of AF reaction is invalid provide warning instead of exception

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -244,7 +244,9 @@ public class SbgnmlXmlParser {
     for (Arc arc : activityFlowArcs) {
       try {
         Reaction r = createActivityFlowReaction(arc, model);
-        model.addReaction(r);
+        if (r != null) {
+          model.addReaction(r);
+        }
       } catch (Exception e) {
         throw new InvalidInputDataExecption("Unable to parse the reaction: " + arc.getId(), e);
       }
@@ -301,11 +303,19 @@ public class SbgnmlXmlParser {
     }
 
     Glyph source = getSourceGlyph(arc);
+    if (model.getElementByElementId(source.getId()) == null) {
+      logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model), "Cannot find source element. Skipping arc.");
+      return null;
+    }
     Reactant reactant = new Reactant(model.getElementByElementId(source.getId()));
     reactant.setLine(new PolylineData(reactantPoints));
     result.addReactant(reactant);
 
     Glyph target = getTargetGlyph(arc);
+    if (model.getElementByElementId(target.getId()) == null) {
+      logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model), "Cannot find target element. Skipping arc.");
+      return null;
+    }
     Product product = new Product(model.getElementByElementId(target.getId()));
     product.setLine(parseLine(arc, productPoints));
     result.addProduct(product);

converter-SBGNML/testFiles/sbgnmlParserTestFiles/generated/production__and__unspecified_entity.sbgn

+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="process description">
+    <glyph id="n59" class="macromolecule">
+      <label text="C4"/>
+      <bbox x="662.16473" y="277.00546" w="80" h="40"/>
+    </glyph>
+    <glyph id="n61" class="and">
+      <label text="C4a"/>
+      <bbox x="662.16473" y="472.85104" w="80" h="40"/>
+    </glyph>
+    <glyph id="glyph3" orientation="vertical" class="process">
+        <bbox y="448.0" x="478.0" h="24.0" w="24.0"/>
+        <port y="436.0" x="490.0" id="glyph3.1"/>
+        <port y="484.0" x="490.0" id="glyph3.2"/>
+    </glyph>
+    <arc id="e28" class="production" source="n59" target="n61">
+      <start x="702.16473" y="317.50546"/>
+      <end x="702.16473" y="382.92825"/>
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file