issues that were discovered during biohackathon 2019 in Paris

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

@@ -14,7 +14,9 @@ import org.xml.sax.SAXException;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.wikipathway.model.*;
@@ -148,6 +150,7 @@ public class GpmlParser {
         }
         if (style != null &&
             !"Complex".equalsIgnoreCase(style) &&
+            !"Pathway".equalsIgnoreCase(style) &&
             !"Group".equalsIgnoreCase(style)) {
           throw new UnknownAttributeValueException(
               "Unknown value of \"style\" attribute for group node: " + style
@@ -432,6 +435,8 @@ public class GpmlParser {
       }
       addGroups(groups, graph);
 
+      resizeGroupsByIncludedLines(graph.getGroups(), lines);
+
       graph.addDataNodes(dataNodeParser.parseCollection(dataNodes));
       graph.addLabels(labelParser.parseCollection(labels));
       graph.addShapes(shapeParser.parseCollection(shapes));
@@ -466,6 +471,22 @@ public class GpmlParser {
     }
   }
 
+  private void resizeGroupsByIncludedLines(Collection<Group> groups, List<Node> lines) throws UnknownTypeException {
+    for (Node lNode : lines) {
+      String groupId = XmlParser.getNodeAttr("GroupRef", lNode);
+      if (groupId != null) {
+        for (Group group : groups) {
+          if (group.getGroupId().equals(groupId)) {
+            PolylineData polyline = parseLine(lNode);
+            if (polyline != null) {
+              group.addBounds(PolylineDataFactory.getBounds(polyline));
+            }
+          }
+        }
+      }
+    }
+  }
+
   /**
    * This method merge edges that should be merged into single line.
    *
@@ -622,41 +643,49 @@ public class GpmlParser {
    *           thrown when the type of line defined in xml node is unknown
    */
   private Collection<PolylineData> parseLines(List<Node> lines) throws UnknownTypeException {
-    List<PolylineData> result = new ArrayList<PolylineData>();
+    List<PolylineData> result = new ArrayList<>();
     for (Node lNode : lines) {
-      int refs = 0;
-      PolylineData line = new PolylineData();
-      NodeList nodes = lNode.getChildNodes();
-      for (int i = 0; i < nodes.getLength(); i++) {
-        Node node = nodes.item(i);
-        if (node.getNodeType() == Node.ELEMENT_NODE) {
-          if (node.getNodeName().equalsIgnoreCase("Graphics")) {
-            NodeList nodes2 = node.getChildNodes();
-            for (int j = 0; j < nodes2.getLength(); j++) {
-              Node node2 = nodes2.item(j);
-              if (node2.getNodeType() == Node.ELEMENT_NODE) {
-                Element element = (Element) node2;
-                if (node2.getNodeName().equalsIgnoreCase("Point")) {
-                  PointData point = pointParser.parse(element);
-                  if (point.hasGraphRef()) {
-                    refs++;
-                  }
-                  line.addPoint(point.toPoint());
-                } else {
-                  logger.warn("Unknown node in line: " + node2.getNodeName());
+      PolylineData line = parseLine(lNode);
+      if (line != null) {
+        result.add(line);
+      }
+    }
+    return result;
+  }
+
+  private PolylineData parseLine(Node lNode) throws UnknownTypeException {
+    int refs = 0;
+    PolylineData line = new PolylineData();
+    NodeList nodes = lNode.getChildNodes();
+    for (int i = 0; i < nodes.getLength(); i++) {
+      Node node = nodes.item(i);
+      if (node.getNodeType() == Node.ELEMENT_NODE) {
+        if (node.getNodeName().equalsIgnoreCase("Graphics")) {
+          NodeList nodes2 = node.getChildNodes();
+          for (int j = 0; j < nodes2.getLength(); j++) {
+            Node node2 = nodes2.item(j);
+            if (node2.getNodeType() == Node.ELEMENT_NODE) {
+              Element element = (Element) node2;
+              if (node2.getNodeName().equalsIgnoreCase("Point")) {
+                PointData point = pointParser.parse(element);
+                if (point.hasGraphRef()) {
+                  refs++;
                 }
+                line.addPoint(point.toPoint());
+              } else {
+                logger.warn("Unknown node in line: " + node2.getNodeName());
               }
             }
-
-          } else {
-            logger.warn("Unknown node in line: " + node.getNodeName());
           }
+
+        } else {
+          logger.warn("Unknown node in line: " + node.getNodeName());
         }
       }
-      if (refs < 2) {
-        result.add(line);
-      }
     }
-    return result;
+    if (refs >= 2) {
+      line = null;
+    }
+    return line;
   }
 }