issues that were discovered during biohackathon 2019 in Paris

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java

@@ -21,8 +21,7 @@ import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
 import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.compartment.*;
 import lcsb.mapviewer.model.map.layout.graphics.*;
 import lcsb.mapviewer.model.map.model.Model;
@@ -31,7 +30,6 @@ import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.reaction.type.*;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.*;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
 import lcsb.mapviewer.wikipathway.model.*;
 import lcsb.mapviewer.wikipathway.model.biopax.BiopaxFactory;
 
@@ -70,6 +68,9 @@ public class ModelContructor {
     INALID_COMPLEX_SHAPE_CHILDREN.add("Arc");
     INALID_COMPLEX_SHAPE_CHILDREN.add("Triangle");
     INALID_COMPLEX_SHAPE_CHILDREN.add("Hexagon");
+    INALID_COMPLEX_SHAPE_CHILDREN.add("None");
+    INALID_COMPLEX_SHAPE_CHILDREN.add("Pentagon");
+    INALID_COMPLEX_SHAPE_CHILDREN.add("mim-phosphorylated");
   }
 
   /**
@@ -96,11 +97,9 @@ public class ModelContructor {
    *
    * @param dataNode
    *          object from which species is created
-   * @param data
-   *          ...
    * @return {@link Species} created from input {@link DataNode}
    */
-  protected Species createSpecies(DataNode dataNode, Data data) {
+  protected Species createSpecies(DataNode dataNode) {
     Species res = null;
     String type = dataNode.getType();
     if (type == null || type.equals("")) {
@@ -122,7 +121,7 @@ public class ModelContructor {
     } else if (type != null && type.equalsIgnoreCase("None")) {
       res = new Unknown(dataNode.getGraphId());
     } else {
-      logger.warn("[" + dataNode.getGraphId() + "]\tUnknown species type: " + type + ". Using Unknown");
+      logger.warn(dataNode.getLogMarker(), "Unknown species type: " + type + ". Using Unknown");
       res = new Unknown(dataNode.getGraphId());
     }
 
@@ -140,37 +139,42 @@ public class ModelContructor {
    * This function adds {@link Complex} to model from graph. ComplexName is set as
    * groupId from GPML
    *
-   * @param model
-   *          to this model complexes will be added
-   * @param graph
-   *          gpml data model
+   * @param groups
+   *          list of groups
    * @param data
    *          ...
    */
-  protected void addComplex(Model model, Graph graph, Data data) {
-    for (Group group : graph.getGroups()) {
-      Complex complex = new Complex(group.getGraphId());
-      complex.setName(group.getGraphId());
+  protected List<Element> createElementsFromGroup(Collection<Group> groups, Data data) {
+    List<Element> result = new ArrayList<>();
+    for (Group group : groups) {
+      Element element = null;
       if ("Complex".equalsIgnoreCase(group.getStyle())) {
-        complex.setHypothetical(false);
+        element = new Complex(group.getGraphId());
+        ((Complex) element).setHypothetical(false);
+      } else if ("Pathway".equalsIgnoreCase(group.getStyle())) {
+        element = new PathwayCompartment(group.getGraphId());
       } else {
-        complex.setHypothetical(true);
+        element = new Complex(group.getGraphId());
+        ((Complex) element).setHypothetical(true);
       }
 
+      element.setName(group.getGraphId());
+
       Rectangle2D rec = group.getRectangle();
       if (rec == null) {
         rec = new Rectangle2D.Double(0, 0, 0, 0);
       }
-      complex.setX(rec.getX());
-      complex.setY(rec.getY());
-      complex.setWidth((int) rec.getWidth());
-      complex.setHeight((int) rec.getHeight());
-      complex.setZ(group.getzOrder());
-      complex.setFillColor(DEFAULT_COMPLEX_ALIAS_COLOR);
+      element.setX(rec.getX());
+      element.setY(rec.getY());
+      element.setWidth(rec.getWidth());
+      element.setHeight(rec.getHeight());
+      element.setZ(group.getzOrder());
+      element.setFillColor(DEFAULT_COMPLEX_ALIAS_COLOR);
 
-      data.id2alias.put(group.getGraphId(), complex);
-      model.addElement(complex);
+      data.id2alias.put(group.getGraphId(), element);
+      result.add(element);
     }
+    return result;
   }
 
   /**
@@ -185,7 +189,7 @@ public class ModelContructor {
    */
   protected void addElement(Model model, Graph graph, Data data) {
     for (DataNode dataNode : graph.getDataNodes()) {
-      Species species = createSpecies(dataNode, data);
+      Species species = createSpecies(dataNode);
       species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
 
       Element alias = updateAlias(dataNode, species);
@@ -255,6 +259,11 @@ public class ModelContructor {
         if (mr != null) {
           mr.setIdModificationResidue(state.getGraphId());
           mr.setState(state.getType());
+          if (state.getTypeName() != null) {
+            mr.setName(state.getTypeName());
+          } else {
+            mr.setName("");
+          }
 
           Double x = state.getRelX() * species.getWidth() / 2 + species.getCenterX();
           Double y = state.getRelY() * species.getHeight() / 2 + species.getCenterY();
@@ -485,8 +494,18 @@ public class ModelContructor {
     Rectangle2D rec = gpmlElement.getRectangle();
     element.setX(rec.getX());
     element.setY(rec.getY());
-    element.setWidth((int) rec.getWidth());
-    element.setHeight((int) rec.getHeight());
+    element.setWidth(rec.getWidth());
+    if (element.getWidth() <= 0) {
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
+          "Element width must be positive. Setting to 1.0");
+      element.setWidth(1.0);
+    }
+    element.setHeight(rec.getHeight());
+    if (element.getHeight() <= 0) {
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
+          "Element height must be positive. Setting to 1.0");
+      element.setHeight(1.0);
+    }
     element.setFillColor(gpmlElement.getFillColor());
     if (element instanceof Compartment && !Objects.equals(Color.WHITE, gpmlElement.getFillColor())) {
       element.setBorderColor(gpmlElement.getFillColor());
@@ -547,29 +566,42 @@ public class ModelContructor {
    *          GPML data model
    * @param data
    *          ...
-   * @throws UnknownChildClassException
-   *           thrown when complex contain invalid child
+   * @throws ConverterException
    */
-  protected void putSpeciesIntoComplexes(Graph graph, Data data) throws UnknownChildClassException {
+  protected void putSpeciesIntoComplexes(Graph graph, Data data) throws ConverterException {
     for (Group group : graph.getGroups()) {
-
-      Complex complex = (Complex) data.id2alias.get(group.getGraphId());
+      Complex complex = null;
+      Compartment compartment = null;
+      Element parent = null;
+      if (data.id2alias.get(group.getGraphId()) instanceof Complex) {
+        complex = (Complex) data.id2alias.get(group.getGraphId());
+        parent = complex;
+      } else if (data.id2alias.get(group.getGraphId()) instanceof Compartment) {
+        compartment = (Compartment) data.id2alias.get(group.getGraphId());
+        parent = compartment;
+      }
       for (PathwayElement pe : group.getNodes()) {
         Element element = data.id2alias.get(pe.getGraphId());
         if (element != null) {
-          if (element instanceof Species) {
-            Species species = (Species) element;
-            complex.addSpecies(species);
+          if (complex != null) {
+            if (element instanceof Species) {
+              Species species = (Species) element;
+              complex.addSpecies(species);
+            }
+          } else if (compartment != null) {
+            compartment.addElement(element);
+          } else {
+            throw new ConverterException("Parent doesn't exists: " + group.getGraphId());
           }
           // we have label
         } else if (graph.getLabelByGraphId(pe.getGraphId()) != null) {
           Label label = graph.getLabelByGraphId(pe.getGraphId());
           // if complex has generic name then change it into label
-          if (complex.getName().equals(group.getGraphId())) {
-            complex.setName(label.getTextLabel());
+          if (parent.getName().equals(group.getGraphId())) {
+            parent.setName(label.getTextLabel());
           } else {
             // if there are more labels than one then merge labels
-            complex.setName(complex.getName() + "\n" + label.getTextLabel());
+            parent.setName(parent.getName() + "\n" + label.getTextLabel());
           }
         } else if (graph.getShapeByGraphId(pe.getGraphId()) != null) {
           Shape shape = graph.getShapeByGraphId(pe.getGraphId());
@@ -828,7 +860,7 @@ public class ModelContructor {
       throw new InvalidStateException("This modifier is invalid");
     }
 
-    Modifier mod = createModifierByType(modifierType, (Species) data.id2alias.get(id));
+    Modifier mod = createModifierByType(modifierType, data.id2alias.get(id));
 
     ModifierType mt = mtu.getModifierTypeForClazz(mod.getClass());
 
@@ -863,7 +895,7 @@ public class ModelContructor {
    *          {@link Species alias } to which modifier is attached
    * @return new instance of the modifierType
    */
-  private Modifier createModifierByType(Class<? extends ReactionNode> modifierType, Species alias) {
+  private Modifier createModifierByType(Class<? extends ReactionNode> modifierType, Element alias) {
     try {
       Modifier result = (Modifier) modifierType.getConstructor(Element.class).newInstance(alias);
       return result;
@@ -889,7 +921,7 @@ public class ModelContructor {
       model.setWidth(graph.getBoardWidth());
       model.setHeight(graph.getBoardHeight());
 
-      addComplex(model, graph, data);
+      model.addElements(createElementsFromGroup(graph.getGroups(), data));
       addElement(model, graph, data);
       putSpeciesIntoComplexes(graph, data);
 
@@ -900,6 +932,8 @@ public class ModelContructor {
 
       removeEmptyComplexes(model);
 
+      removeSelfLoops(model);
+
       fixCompartmentAliases(model);
 
       StringBuilder tmp = new StringBuilder();
@@ -941,6 +975,18 @@ public class ModelContructor {
     }
   }
 
+  void removeSelfLoops(Model model) {
+    Set<Reaction> toRemove = new HashSet<>();
+    for (Reaction reaction : model.getReactions()) {
+      if (reaction.getReactants().get(0).getElement().equals(reaction.getProducts().get(0).getElement())) {
+        logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
+            "Self loops are not supported. Removing");
+        toRemove.add(reaction);
+      }
+    }
+    model.removeReactions(toRemove);
+  }
+
   private void putMissingZIndexes(Collection<Drawable> bioEntities) {
     int maxZIndex = 0;
     for (Drawable bioEntity : bioEntities) {
@@ -1016,31 +1062,39 @@ public class ModelContructor {
    * @param model
    *          model where operation is performed
    */
-  private void removeEmptyComplexes(Model model) {
+  void removeEmptyComplexes(Model model) {
     Set<Element> aliasesInReaction = new HashSet<>();
     for (Reaction reaction : model.getReactions()) {
       for (ReactionNode node : reaction.getReactionNodes()) {
         aliasesInReaction.add(node.getElement());
       }
     }
-    List<Element> toRemove = new ArrayList<>();
-    ElementUtils eu = new ElementUtils();
+    Set<BioEntity> toRemove = new HashSet<>();
     for (Element element : model.getElements()) {
       if (element instanceof Complex) {
         Complex complex = (Complex) element;
         if (complex.getSize() <= EPSILON && complex.getAllChildren().size() == 0) {
+          toRemove.add(element);
           if (aliasesInReaction.contains(element)) {
             logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
                 "Empty element is invalid, but it's a part of reaction.");
+            for (Reaction reaction : model.getReactions()) {
+              for (ReactionNode node : reaction.getReactionNodes()) {
+                if (node.getElement().equals(element)) {
+                  toRemove.add(reaction);
+                  logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
+                      "Reaction to empty element is invalid.");
+                }
+              }
+            }
           } else {
-            toRemove.add(element);
             logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element), "Empty element is invalid");
           }
         }
       }
     }
-    for (Element alias : toRemove) {
-      model.removeElement(alias);
+    for (BioEntity bioEntitiy : toRemove) {
+      model.removeBioEntity(bioEntitiy);
     }
   }
 
@@ -1164,7 +1218,7 @@ public class ModelContructor {
    *
    * @author Jan Badura
    */
-  private final class Data {
+  final class Data {
     /**
      * Map between graphId and aliases created from gpml elements.
      */
@@ -1183,8 +1237,8 @@ public class ModelContructor {
     /**
      * Default constructor.
      */
-    private Data() {
-      id2alias = new HashMap<String, Element>();
+    Data() {
+      id2alias = new HashMap<>();
       layer = new Layer();
       layer.setVisible(true);
       layer.setLayerId("1");