import of stimulation modifiers crashed minerva

CHANGELOG

 minerva (14.0.8) stable; urgency=medium
-  * Bug fix: API didn't allow to upload pluins with local url (#1084, 
+  * Bug fix: API didn't allow to upload pluins with local url (#1084,
     regression 14.0.7)
   * 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)
-  * Bug fix: import of structural state from SBGN-ML PD that cannot be 
+  * Bug fix: import of structural state from SBGN-ML PD that cannot be
     normalized to residue is changed into structural state without losing
     information (#1062)
+  * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter
+    (#1063)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 23 Jan 2020 12:00:00 +0200
 

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

@@ -4,14 +4,14 @@ import java.awt.Color;
 import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
 import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.sbgn.*;
 import org.sbgn.bindings.*;
 import org.sbgn.bindings.Arc.*;
+import org.sbgn.bindings.Map;
 
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -390,8 +390,9 @@ public class SbgnmlXmlParser {
    *          arc to be parsed
    * @param model
    *          model to be updated
+   * @throws InvalidInputDataExecption
    */
-  private void parseArc(Arc a, Model model) {
+  private void parseArc(Arc a, Model model) throws InvalidInputDataExecption {
     switch (ArcClazz.fromClazz(a.getClazz())) {
     case CONSUMPTION:
       Port arcTargetPort = (Port) a.getTarget();
@@ -422,35 +423,56 @@ public class SbgnmlXmlParser {
     case MODULATION:
     case NECESSARY_STIMULATION:
     case STIMULATION:
-      Glyph targetGlyph = (Glyph) a.getTarget();
-      if (GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)) {
-        if (!(a.getSource() instanceof Glyph)) {
-          logger.warn("Invalid phenotype arc: " + a.getId());
-          break;
-        }
-        try {
-          parsePhenotypeArc(a, model);
-        } catch (Exception e) {
-          logger.warn(e.getMessage(), e);
-        }
-        break;
-      }
-      if (a.getSource() instanceof Glyph) {
-        Glyph sourceGlyph = (Glyph) a.getSource();
-        if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
-            && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
+      if (a.getTarget() instanceof Glyph) {
+        Glyph targetGlyph = (Glyph) a.getTarget();
+        if (GlyphClazz.fromClazz(targetGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)) {
+          if (!(a.getSource() instanceof Glyph)) {
+            logger.warn("Invalid phenotype arc: " + a.getId());
+            break;
+          }
           try {
             parsePhenotypeArc(a, model);
-          } catch (InvalidArgumentException ex) {
-            logger.warn("The arc " + a.getId() + " of class " + a.getClazz() + " is not a valid reduced notation arc.");
+          } catch (Exception e) {
+            logger.warn(e.getMessage(), e);
           }
           break;
         }
-      }
-      for (Process p : processes) {
-        if (p.getCentralPoint().getId().equals(targetGlyph.getId())) {
-          p.addInfluenceArc(a);
-          break;
+        if (a.getSource() instanceof Glyph) {
+          Glyph sourceGlyph = (Glyph) a.getSource();
+          if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
+              && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
+            try {
+              parsePhenotypeArc(a, model);
+            } catch (InvalidArgumentException ex) {
+              logger
+                  .warn("The arc " + a.getId() + " of class " + a.getClazz() + " is not a valid reduced notation arc.");
+            }
+            break;
+          }
+        }
+        for (Process p : processes) {
+          if (p.getCentralPoint().getId().equals(targetGlyph.getId())) {
+            p.addInfluenceArc(a);
+            break;
+          }
+        }
+      } else {
+        Port targetPort = (Port) a.getTarget();
+        boolean found = false;
+        for (Process p : processes) {
+          Set<String> ids = new HashSet<>();
+          ids.add(p.getCentralPoint().getId());
+          for (Port port : p.getCentralPoint().getPort()) {
+            ids.add(port.getId());
+          }
+          if (ids.contains(targetPort.getId())) {
+            p.addInfluenceArc(a);
+            found = true;
+            break;
+          }
+        }
+        if (!found) {
+          throw new InvalidInputDataExecption("Problem with processing arc: " + a.getId());
         }
       }
       break;
@@ -1180,6 +1202,7 @@ public class SbgnmlXmlParser {
       throw new InvalidArgumentException(
           p.getCentralPoint().getId() + ": The process must have at least one outgoing arc.");
     }
+
     p.setProductsPort((Port) p.getProductArcs().get(0).getSource());
     for (Arc productArc : p.getProductArcs()) {
       if (!((Port) productArc.getSource()).equals(p.getProductsPort())) {